Difference: HipeKnownIssues (1 vs. 189)

Revision 1892016-04-12 - MiguelSanchez

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STR switch-overs and SVV resets are not properly handled by the auxiliary processor creating the pointing product

Changed:
<
<
Affected versions: Fixed from HIPE 14.0.
>
>
Affected versions: HIPE versions prior to 14.1.
  Description: In HCSS 13.0, the auxiliary processor that creates the pointing product was updated to automatically check for STR switch-overs and SVV rests and applies the corrections whenever appropriate. However, this was only implemented for the "simple-corrected" attitude (column simpleCorrFilterQuat) and not for the "gyro-propagated" one (column filterQuat).
Line: 113 to 113
  However, in case of doubt of if you have observations in one of the ODs referred below and processed with SPG < 13.0, please contact the HSC Helpdesk for more information and support. Please refer to the HSC Helpdesk web link
Changed:
<
<
The problem has been fully solved in HCSS 14.0. Hence, future HSA products will be free of anomalies.
>
>
The problem was initially fixed in HIPE 14.0. However, it was found that the STR misalignment was not properly handled in early ODs (<= 113) and has been fixed in HIPE 14.1. (see SPR HCSS-20990). Nevertheless, some issues still exist for a small set of SPIRE parallel observations in OD 111 (investigation on-going).
  A more comprehensive description and a full list of affected periods and observations is given here.

Revision 1882016-04-08 - AlvarGarcia

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You cannot import your saved session state and variables from HIPE 14

Changed:
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<
Ticket number: HCSS-21177
>
>
Ticket number: HCSS-21177 (Third party; Jython breaking change)
  Versions affected: HIPE 15 (opening) any previous version (saved session state)
Line: 73 to 72
 

Known issues in HIPE 14

WCS information of HIFI spectral cubes for Solar System Objects (SSO) should not be changed within HIPE

Changed:
<
<
Ticket numbers: HCSS-20497 / HIFI-6196
>
>
Ticket numbers: HCSS-20497 / HIFI-6196 (Won't fix; by design)
  Versions affected: All.
Line: 105 to 103
 

STR switch-overs and SVV resets are not properly handled by the auxiliary processor creating the pointing product

Added:
>
>
Affected versions: Fixed from HIPE 14.0.
 Description: In HCSS 13.0, the auxiliary processor that creates the pointing product was updated to automatically check for STR switch-overs and SVV rests and applies the corrections whenever appropriate. However, this was only implemented for the "simple-corrected" attitude (column simpleCorrFilterQuat) and not for the "gyro-propagated" one (column filterQuat).

Hence, the astrometry of the SPG 13.0 products retrieved from the archive (processed with the gyro-propagated attitude) are still affected by these anomalies.

Line: 117 to 117
  A more comprehensive description and a full list of affected periods and observations is given here.
Deleted:
<
<

Known issues in HIPE 12

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Ticket number: HCSS-15583 (Won't fix)

Versions affected: All versions of HIPE since 8.0

Description: If any of the tasks is applied to a spectrum that contains a column of errors instead of weights, the task converts the errors to weights, propagates the weights and repopulates the error column by converting the propagated weights back to errors. This gives an error column that has not been propagated correctly for the operation applied.

Workaround: Take into account that the output error column should be disregarded in the case of source data that lack a proper error column.

HIPE FITS Writer format could be incorrectly read by other software

Ticket number: HCSS-19248

Versions affected: HIPE 12.x

Description: HIPE makes use of OGIP, a non-standard convention to include long values in FITS fields. The OGIP convention writes an & at the end of a line (for example, describing a column name) that would be considered valid for all FITS compliant readers (it contains less than 68 characters) followed by the special keyword CONTINUE '' / & and completing the long value with a COMMENT Rest of value line. For example:

TTYPE1  = 'designation&'
CONTINUE  '' / &
COMMENT Original element type: char, Empty values appear as null

Many FITS readers ignore this convention, so the special character & is read and included as the final character of the value. Others (IDL) do the same but, additionally, consider & an invalid character and it is replaced by an underscore _.

Workaround: None at this time.

Old syntax using HIFI class PolarPair gives wrong results

Ticket number: none (API change)

Versions affected: HIPE 12.0

Description: PolarPair (the class) use is now discouraged for users and polarPair (the task, note capitalisation) has been modified in order to allow it to be used as a part of the interactive HIFI pipeline and to bring its syntax in-line with other tasks in the Spectral Toolbox. If the old syntax is used, e.g.,

pp = PolarPair(wbs_h, wbs_v)
av = pp.avg()

incorrect results are obtained.

This problem did not affect previous HIPE versions. A warning will be written to the console in HIPE 13 if the old syntax is used.

Workaround: Use the new syntax running the task:

av=polarPair(ds1=wbs_h, ds2=wbs_v)

Limitations of the task for updating scripts that use the old syntax to access return parameters

Ticket number: HCSS-19080 (Won't fix)

Versions affected: HIPE 12.

  • Task calls spanning multiple lines (with \ separation) are not detected. Some SPIRE scripts use multiple line task call scripts.
  • The dialog box should show all lines which are going to be changed, but only the first line is shown there.
  • Some non-standard task calls, like using two = signs to put the result into two variables at once, are not detected.

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on OS X

Ticket number: HCSS-18891 (Third party; Won't fix)

Versions affected: HIPE 12.

Error message:

$ ./hcss.dp.pacs-12.0.1553/bin/hipe
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x000000010794f647, pid=49119, tid=6403
#
# JRE version: Java(TM) SE Runtime Environment (7.0_45-b18) (build 1.7.0_45-b18)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.45-b08 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# C  [libjvmlinkage.dylib+0x3647]  JVM_GetClassCPEntriesCount+0x17
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/USER/hcss/hcss.dp.pacs-12.0.2340/bin/hs_err_pid49119.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

Root cause: The cause is that the shared library path has references to the old Java 6 installation.

$ env | grep DYLD_LIBRARY_PATH
DYLD_LIBRARY_PATH=:/Applications/MATLAB/MATLAB_Compiler_Runtime/v716/runtime/maci64:
/Applications/MATLAB/MATLAB_Compiler_Runtime/v716/sys/os/maci64:
/Applications/MATLAB/MATLAB_Compiler_Runtime/v716/bin/maci64:
/System/Library/Frameworks/JavaVM.framework/JavaVM:
/System/Library/Frameworks/JavaVM.framework/Libraries

Workaround: The current workaround is to remove the entries that contain JavaVM from this environment variable. To do that, modify or create the .bash_profile configuration file of the terminal and add the environment variable in an export statement without the corresponding entries. That should persist the changes.

 

Older HIPE versions

Known issues for older HIPE versions are listed in a separate page.

Revision 1872016-04-05 - AlvarGarcia

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Line: 39 to 39
 

For other issues affecting the installer, check this page.

Known issues in HIPE 15

Added:
>
>

Product browser does not refresh for MyHSA data in the current session

Ticket number: HCSS-18240 (by design; won't fix)

Versions affected: All HIPE versions

Description: If you retrieve observations from the Herschel Science Archive using getObservation, these are not available from the Product Browser perspective until you restart HIPE.

Root cause: For this to happen, you have Save data on demand enabled in Preferences > MyHSA > Advanced. This happens because the Product Browser only searches in the direct retrieval sessions for MyHSA where the connection status is OFF and, in this use case, the observation has been downloaded into one which is ON-CACHED so it isn't checked when you launch the query from the product browser in the current session. When you close HIPE and re-open it, it locks this direct retrieval session so it is OFF and that is why it then works and resolves the ProductRef locally in a new session.

Workaround: Restart HIPE. NOTE: Disabling the Save data on demand option will not work because then the observation will not be saved locally so the Product Browser will still not find it.

 

You cannot import your saved session state and variables from HIPE 14

Ticket number: HCSS-21177

Line: 46 to 59
 Versions affected: HIPE 15 (opening) any previous version (saved session state)

Description: While trying to restore the saved session state and variables, you receive the following exception:

Added:
>
>
 
herschel.ia.task.TaskException: failed: The file <yourSerFile.ser> could not be loaded
Changed:
<
<
Because org.python.core.PyObject; local class incompatible: stream classdesc serialVersionUID = -5518487409570819225, local class serialVersionUID = -2690220732157457541
>
>
Because org.python.core.PyObject; local class incompatible: stream classdesc serialVersionUID = -5518487409570819225, local class serialVersionUID = -2690220732157457541
  Where yourSerFile.ser is the saved session state and variables generated with HIPE 14 and earlier.
Line: 631 to 644
 

What are all the tmp_product_sink_* pools in my local store directory?

Changed:
<
<
You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.
>
>
You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.</verbatim>
 
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 Permissions security feature" date="1389952811" name="Screen_Shot_2014-01-16_at_16.28.23.png" path="Screen_Shot_2014-01-16_at_16.28.23.png" size="49454" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Error message when sending data to VOSpec" date="1358258421" name="vospec.png" path="vospec.png" size="12133" user="Main.DavideRizzo" version="1"

Revision 1862016-03-10 - AlvarGarcia

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META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 38 to 38
 

For other issues affecting the installer, check this page.

Added:
>
>

Known issues in HIPE 15

You cannot import your saved session state and variables from HIPE 14

Ticket number: HCSS-21177

Versions affected: HIPE 15 (opening) any previous version (saved session state)

Description: While trying to restore the saved session state and variables, you receive the following exception:

herschel.ia.task.TaskException: failed: The file <yourSerFile.ser> could not be loaded
 Because org.python.core.PyObject; local class incompatible: stream classdesc serialVersionUID = -5518487409570819225, local class serialVersionUID = -2690220732157457541

Where yourSerFile.ser is the saved session state and variables generated with HIPE 14 and earlier.

Root cause: A change in how the serialisation is handled in the new version of Jython (2.7) used in HIPE 15.

Workaround: None at the moment.

 

Known issues in HIPE 14

WCS information of HIFI spectral cubes for Solar System Objects (SSO) should not be changed within HIPE

Line: 612 to 631
 

What are all the tmp_product_sink_* pools in my local store directory?

Changed:
<
<
You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.
>
>
You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.
 
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 Permissions security feature" date="1389952811" name="Screen_Shot_2014-01-16_at_16.28.23.png" path="Screen_Shot_2014-01-16_at_16.28.23.png" size="49454" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Error message when sending data to VOSpec" date="1358258421" name="vospec.png" path="vospec.png" size="12133" user="Main.DavideRizzo" version="1"

Revision 1852015-12-10 - PedroGarciaLario

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Changed:
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HIPE known issues

>
>

HIPE Known Issues

 
Changed:
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Help Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to installation/uninstallation, startup, help, Science Archive and other issues common to different HIPE versions.
>
>
Help Welcome to the HIPE Known Issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to installation/uninstallation, startup, help, Science Archive and other issues common to different HIPE versions.
 
ALERT! This page is for known issues in the HIPE software. For known issues in data products see this page.
Changed:
<
<
ALERT! These known issues happen in the latest versions of HIPE and its dependent software (for example, Java 6/7). Any issue that is resolved with an update to the operational version of HIPE or Java, is listed on this page.
>
>
ALERT! These known issues are applicable to the latest versions of HIPE and its dependent software (for example, Java 6/7). Any issue that is resolved with an update to the operational version of HIPE or Java, is listed on this page.
 

Please note that some issues detected in previous versions may still be present in HIPE 11. Scroll down and check earlier versions if you do not see your particular issue listed for HIPE 11.

Revision 1842015-12-02 - AlvarGarcia

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META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 38 to 38
 

For other issues affecting the installer, check this page.

Added:
>
>

Known issues in HIPE 14

WCS information of HIFI spectral cubes for Solar System Objects (SSO) should not be changed within HIPE

Ticket numbers: HCSS-20497 / HIFI-6196

Versions affected: All.

Description: HIFI FITS keywords are now also correct for SSO as well as standard maps. The HIPE software allows now the WCS projection type of OFLN-GLS and OFLT-GLS.

Root cause: HIFI maps are read correctly by the HIPE software, but the actual projection types of OFLN-GLS and OFLT-GLS are NOT implemented in HIPE, just the keywords are accepted.

Workaround: None, the manipulation of WCS coordinates for SSO should not be done within HIPE.

 

Known issues in HIPE 13

HSA ping from HIPE does not work (but connection is OK), affecting SPIRE calibration updating

Line: 60 to 72
 

STR switch-overs and SVV resets are not properly handled by the auxiliary processor creating the pointing product

Changed:
<
<
Description: In HCSS 13.0, the auxiliary processor that creates the pointing product was updated to automatically check for STR switch-overs and SVV rests and applies the corrections whenever appropriate. However, this was only implemented for the "simple-corrected" attitude (column simpleCorrFilterQuat) and not for the "gyro-propagated" one (column filterQuat).
>
>
Description: In HCSS 13.0, the auxiliary processor that creates the pointing product was updated to automatically check for STR switch-overs and SVV rests and applies the corrections whenever appropriate. However, this was only implemented for the "simple-corrected" attitude (column simpleCorrFilterQuat) and not for the "gyro-propagated" one (column filterQuat).
  Hence, the astrometry of the SPG 13.0 products retrieved from the archive (processed with the gyro-propagated attitude) are still affected by these anomalies.
Changed:
<
<
Workaround: it is required to reprocess the data. Since the simpleCorrFilterQuat is properly corrected for the anomalies, it is possible to overwrite the column filterQuat of the pointing product with the simpleCorrFilterQuat and then launch the pipeline processing ensuring that you use the new pointing product.
>
>
Workaround: it is required to reprocess the data. Since the simpleCorrFilterQuat is properly corrected for the anomalies, it is possible to overwrite the column filterQuat of the pointing product with the simpleCorrFilterQuat and then launch the pipeline processing ensuring that you use the new pointing product.
 
Changed:
<
<
However, in case of doubt of if you have observations in one of the ODs referred below and processed with SPG < 13.0, please contact the HSC Helpdesk for more information and support. Please refer to the HSC Helpdesk web link
>
>
However, in case of doubt of if you have observations in one of the ODs referred below and processed with SPG < 13.0, please contact the HSC Helpdesk for more information and support. Please refer to the HSC Helpdesk web link
  The problem has been fully solved in HCSS 14.0. Hence, future HSA products will be free of anomalies.
Line: 247 to 262
 

Trying to use the Versant object database with Java 8 will not work

Changed:
<
<
Versions affected: All developer builds installed using Java 8.
>
>
Versions affected: HIPE 14.0.
  Description: If you use developer builds installed using Java 8, you can experience errors related to Versant. HIPE versions 12 and 13 use Java 7 because of these Versant incompatibilities. The user installer will set up a private JRE with version 7 isolated from the system Java installation, so you will not be affected by this issue.

Revision 1832015-11-26 - MiguelSanchez

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 37 to 40
 

Known issues in HIPE 13

HSA ping from HIPE does not work (but connection is OK), affecting SPIRE calibration updating

Added:
>
>
 The testing of the HSA connection from HIPE is reporting that HIPE is unable to connect to the HSA. This is, in fact, not true and data can be retrieved from the HSA with no problems. It is a problem with the ping itself. As a consequence the spire-cal Updater is not working. A workaround exists that it is to retrieve the latest calibration tree (the appropriate one to work with HIPE 13.0) directly from the HSA by running this command from the command line:
Added:
>
>
 
Changed:
<
<
cal=spireCal(calTree="spire_cal_13_1", saveTree=True)
>
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cal=spireCal(calTree="spire_cal_13_1", saveTree=True)
 

It is not possible to use getObservation with obsid and tag parameters

Added:
>
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 Ticket number: HCSS-20262 (Won't fix; by design)

Versions affected: All versions of HIPE since 11.0.

Line: 52 to 57
 Root cause: The task will first look in MyHSA pool (which does not store tags, being a cache for the archive), when no poolname is supplied as an argument, and won't find any tagged observation there.

Workaround: Always use the poolname where the tagged observation is stored. MyHSA does not support tags.

Added:
>
>

STR switch-overs and SVV resets are not properly handled by the auxiliary processor creating the pointing product

Description: In HCSS 13.0, the auxiliary processor that creates the pointing product was updated to automatically check for STR switch-overs and SVV rests and applies the corrections whenever appropriate. However, this was only implemented for the "simple-corrected" attitude (column simpleCorrFilterQuat) and not for the "gyro-propagated" one (column filterQuat).

Hence, the astrometry of the SPG 13.0 products retrieved from the archive (processed with the gyro-propagated attitude) are still affected by these anomalies.

Workaround: it is required to reprocess the data. Since the simpleCorrFilterQuat is properly corrected for the anomalies, it is possible to overwrite the column filterQuat of the pointing product with the simpleCorrFilterQuat and then launch the pipeline processing ensuring that you use the new pointing product.

However, in case of doubt of if you have observations in one of the ODs referred below and processed with SPG < 13.0, please contact the HSC Helpdesk for more information and support. Please refer to the HSC Helpdesk web link

The problem has been fully solved in HCSS 14.0. Hence, future HSA products will be free of anomalies.

A more comprehensive description and a full list of affected periods and observations is given here.

 

Known issues in HIPE 12

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Line: 73 to 95
 
TTYPE1  = 'designation&'
CONTINUE  '' / &
Changed:
<
<
COMMENT Original element type: char, Empty values appear as null
>
>
COMMENT Original element type: char, Empty values appear as null
 Many FITS readers ignore this convention, so the special character & is read and included as the final character of the value. Others (IDL) do the same but, additionally, consider & an invalid character and it is replaced by an underscore _.

Workaround: None at this time.

Line: 84 to 107
 Versions affected: HIPE 12.0

Description: PolarPair (the class) use is now discouraged for users and polarPair (the task, note capitalisation) has been modified in order to allow it to be used as a part of the interactive HIFI pipeline and to bring its syntax in-line with other tasks in the Spectral Toolbox. If the old syntax is used, e.g.,

Deleted:
<
<
 
pp = PolarPair(wbs_h, wbs_v)
Changed:
<
<
av = pp.avg()
>
>
av = pp.avg()
  incorrect results are obtained.
Line: 95 to 116
 This problem did not affect previous HIPE versions. A warning will be written to the console in HIPE 13 if the old syntax is used.

Workaround: Use the new syntax running the task:

Deleted:
<
<
 
Changed:
<
<
av=polarPair(ds1=wbs_h, ds2=wbs_v)
>
>
av=polarPair(ds1=wbs_h, ds2=wbs_v)
 

Limitations of the task for updating scripts that use the old syntax to access return parameters

Line: 138 to 158
 # http://bugreport.sun.com/bugreport/crash.jsp # The crash happened outside the Java Virtual Machine in native code. # See problematic frame for where to report the bug.
Changed:
<
<
#
>
>
#
  Root cause: The cause is that the shared library path has references to the old Java 6 installation.
Added:
>
>
 
$ env | grep DYLD_LIBRARY_PATH
DYLD_LIBRARY_PATH=:/Applications/MATLAB/MATLAB_Compiler_Runtime/v716/runtime/maci64:
Line: 148 to 168
 /Applications/MATLAB/MATLAB_Compiler_Runtime/v716/sys/os/maci64: /Applications/MATLAB/MATLAB_Compiler_Runtime/v716/bin/maci64: /System/Library/Frameworks/JavaVM.framework/JavaVM:
Changed:
<
<
/System/Library/Frameworks/JavaVM.framework/Libraries Workaround: The current workaround is to remove the entries that contain JavaVM from this environment variable. To do that, modify or create the .bash_profile configuration file of the terminal and add the environment variable in an export statement without the corresponding entries. That should persist the changes.
>
>
/System/Library/Frameworks/JavaVM.framework/Libraries
 
Added:
>
>
Workaround: The current workaround is to remove the entries that contain JavaVM from this environment variable. To do that, modify or create the .bash_profile configuration file of the terminal and add the environment variable in an export statement without the corresponding entries. That should persist the changes.
 

Older HIPE versions

Line: 178 to 196
 
Error occurred during initialization of VM
Could not reserve enough space for object heap
Changed:
<
<
Could not create the Java virtual machine.
>
>
Could not create the Java virtual machine.
  To fix this error you have to modify two properties in the installed.properties file within your HIPE installation directory. There is no need to reinstall HIPE.
Line: 184 to 201
 To fix this error you have to modify two properties in the installed.properties file within your HIPE installation directory. There is no need to reinstall HIPE.

The properties you need to modify are the following. You have to lower the amount of allocated memory:

Deleted:
<
<
 
java.vm.memory.max
Changed:
<
<
java.vm.options=-XX:PermSize
>
>
java.vm.options=-XX:PermSize
  Possible values are the following:
Deleted:
<
<
 
java.vm.memory.max=1024m
Changed:
<
<
java.vm.options=-XX:PermSize=128m
>
>
java.vm.options=-XX:PermSize=128m
  Try running HIPE after modifying the values until it successfully starts.
Line: 224 to 237
 

I get startup messages about missing HIFI/PACS/SPIRE modules. Is that serious?

You are probably referring to messages such as the following (for HIFI; messages for PACS and SPIRE are the same):

Deleted:
<
<
 
Import "from herschel.hifi.all import *" returns:
Changed:
<
<
Import Error -> No module named hifi
>
>
Import Error -> No module named hifi
  Such messages are harmless and just reflect the fact that you have not installed the software related to the specified instruments.
Line: 249 to 260
 Description: When executing HIPE in the context of a user that has redirected shell folders, environment variables in the Desktop path in the Registry or doesn't have a roaming profile for the domain, the Java VM cannot determine the working directory for the user or, as it is called in Windows parlance, "home path". Instead, it uses the "user profile" directory, which can be shared between several users, be read-only or even can be unresolvable for Java because it contains environment variables. In those cases, writing to this home directory (in Java terms "user.home") can fail with an error message like the one shown below.

Error message: HIPE writes a WARNING message when Java is unable to resolve the correct home directory for the user. Other error messages can be displayed and they are related to HIPE-managed pools like MyHSA, preferences, automatic backup files or anything that it is written automatically to the .hcss directory inside the home dir.

Changed:
<
<
18-Mar-14 11:41:16.968 WARNING LogView : Could not log to file:

>
>
18-Mar-14 11:41:16.968 WARNING LogView : Could not log to file:

 java.io.IOException: Couldn't get lock for C:\Users\wrongdir\.hcss\apps\hipe\logs\hipe_user_20140318_114116.log at java.util.logging.FileHandler.openFiles(Unknown Source)
Changed:
<
<
at java.util.logging.FileHandler.(Unknown Source) at herschel.ia.jconsole.views.LogView.(LogView.java:119)
>
>
at java.util.logging.FileHandler.(Unknown Source) at herschel.ia.jconsole.views.LogView.(LogView.java:119)
  at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
Line: 304 to 316
  Workaround: The simple workaround is to:
Changed:
<
<
  1. Completely remove java 7 from the system following the instructions in http://www.java.com/en/download/help/mac_uninstall_java.xml and http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-jdk.html
  2. Then reinstall the Java Developer Kit 7 (JDK) and Java Runtime Environment 7 from a Firefox browser following the instructions at http://www.java.com/en/download/help/mac_install.xml
>
>
  1. Completely remove java 7 from the system following the instructions in http://www.java.com/en/download/help/mac_uninstall_java.xml and http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-jdk.html
  2. Then reinstall the Java Developer Kit 7 (JDK) and Java Runtime Environment 7 from a Firefox browser following the instructions at http://www.java.com/en/download/help/mac_install.xml
 

Java dialogue pops up after closing an external application launched from HIPE using Java Web Start on Mac OS X

Line: 331 to 342
 
WARNING WindowsPreferences <init>: Could not open/create
prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKey
Changed:
<
<
Ex(...) returned error code 5.
>
>
Ex(...) returned error code 5.
  Root cause: In a Windows installation with Java 7 version 21 or later, the Windows Preferences classes in Oracle's JVM try to read from the Windows Registry key: HKEY_LOCAL_MACHINE\Software\JavaSoft\Prefs . Since the key has not been created by the Java installer (as was the case in previous versions of Java), these classes try to create them and fail due to insufficient privileges. This is displayed on the Java console as seen above in the warning message.
Line: 359 to 368
 
    • Delete the temporary directory created by the help system in /private/var/folders/[1]/[2]/T/yahajs_[username]_[HIPE version]/jetty/instance_[instance number]/webapp (the first ellipsis [1] is a pair of alphanumeric characters and the second [2] is a string of 30 alphanumeric characters). For Linux, the path will be something like /tmp/yahajs_[username]_[HIPE version]/jetty/instance_[instance number]/webapp depending on the distribution.
    • If the previous solution does not work, please try rebooting the computer.
  • Older browser versions may not display documentation correctly. For example, links from HIPE to the Help System, like the Help in URM menu entries for tasks, work in Firefox 3.6.x but not in Firefox 3.0.x. Other legacy browsers may have similar problems.
Changed:
<
<
  • If you are using Linux and get an error message like Firefox can not contact the server www.%u.com, change your default browser from firefox %u to firefox %s (same if mozilla is your default browser). See the documentation of your Linux distribution for how to change default web browser. Alternatively, in HIPE choose Edit --> Preferences, go to Help & Documentation and enter the path to Firefox, or to another browser on your system, in the Browser field. Click Test to check if it works.
>
>
  • If you are using Linux and get an error message like Firefox can not contact the server www.%u.com, change your default browser from firefox %u to firefox %s (same if mozilla is your default browser). See the documentation of your Linux distribution for how to change default web browser. Alternatively, in HIPE choose Edit --> Preferences, go to Help & Documentation and enter the path to Firefox, or to another browser on your system, in the Browser field. Click Test to check if it works.
 
  • In general, when you encounter a problem with the Help System you should follow these steps:
    • See if the help works with another browser. If possible, upgrade your browser to the latest version.
    • Clear the browser cache
Line: 426 to 437
 (Invalid syntax in filename, directory name or volume name.) at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager.java:706) at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager.java:661)
Changed:
<
<
at herschel.ia.pal.pool.hsa.myhsa.cache.HsaCachedReadPool.getXmlRootFor(HsaCachedReadPool.java:189)
>
>
at herschel.ia.pal.pool.hsa.myhsa.cache.HsaCachedReadPool.getXmlRootFor(HsaCachedReadPool.java:189)
  Root cause: The Java cache directory (where Java stores JAR files downloaded from the Internet) is corrupted.
Changed:
<
<
Workaround: Do not try to clear the cache using Java Control Panel -> General -> Settings -> Delete files (select all checkboxes), as Java won't be able to clear it because of the corruption. Delete the storage directory (C:\Users\username\AppData\LocalLow\Sun\Java\Deployment\cache on Windows Vista, 7 and 8.1; C:\Documents and Settings\username\Local Settings\Application Data\Sun\Java\Deployment\cache on Windows XP) and Java will re-create the cache successfully. For more information about the paths, check this link on application data directories on different versions of Windows or the official description of the Java cache on Java's website.
>
>
Workaround: Do not try to clear the cache using Java Control Panel -> General -> Settings -> Delete files (select all checkboxes), as Java won't be able to clear it because of the corruption. Delete the storage directory (C:\Users\username\AppData\LocalLow\Sun\Java\Deployment\cache on Windows Vista, 7 and 8.1; C:\Documents and Settings\username\Local Settings\Application Data\Sun\Java\Deployment\cache on Windows XP) and Java will re-create the cache successfully. For more information about the paths, check this link on application data directories on different versions of Windows or the official description of the Java cache on Java's website.
 

If you change the default path for the MyHSA directory, be sure to use / as directory separator

Added:
>
>
 Ticket: HCSS-19940
Changed:
<
<
Description: When changing the default path for the MyHSA directory ( Edit > Preferences > MyHSA ) on Windows, use forward slashes for the path. This text box takes the content as a Java String, considering the Windows directory separator (\) as an escape character. Example D:\data\myhsa should be entered as D:/data/myhsa.
>
>
Description: When changing the default path for the MyHSA directory ( Edit > Preferences > MyHSA ) on Windows, use forward slashes for the path. This text box takes the content as a Java String, considering the Windows directory separator (\) as an escape character. Example D:\data\myhsa should be entered as D:/data/myhsa.
 
Changed:
<
<

How to log in with new credentials after changing the password for HSA I have changed/reset the password of the account I use to access Herschel Science Archive, but HIPE still tells me I am logged in (with the old password), even after restarting HIPE. How do I log in with the new password?

>
>

How to log in with new credentials after changing the password for HSA I have changed/reset the password of the account I use to access Herschel Science Archive, but HIPE still tells me I am logged in (with the old password), even after restarting HIPE. How do I log in with the new password?

  Description: HIPE stores your HSA password for you if you log in and check the "Remember Me" checkbox. If you restart you can access the HSA without having to enter your info again.
Line: 493 to 504
  If you export a FITS file from HIPE and modify it with an external program, HIPE may not be able to import it anymore. If this happens, follow these steps:

Changed:
<
<
  1. Open the FITS file with a FITS editing program such as fv.
  2. Delete the HCSS____ keyword from the header of all extensions.
  3. Save the file.
>
>
  1. Open the FITS file with a FITS editing program such as fv.
  2. Delete the HCSS____ keyword from the header of all extensions.
  3. Save the file.
  HIPE should now be able to read the file.
Line: 509 to 520
  To allow a WebStart application that is blocked, change the Allow applications downloaded from option in Gatekeeper from Mac App Store to one of the two less restrictive options. If the application has a valid certificate, the Mac App Store and identified developers option will suffice. Otherwise you will need to select the Anywhere option.
Changed:
<
<
Warning, important The Gatekeeper feature only handled Java applications for the Apple-specific version in older Mac OS X (before Mac OS 10.7.2). The Java version from Oracle has a mechanism for validating publisher certificates completely independent from the operating system (see the related archived known issue for the HSA UI).
>
>
Warning, important The Gatekeeper feature only handled Java applications for the Apple-specific version in older Mac OS X (before Mac OS 10.7.2). The Java version from Oracle has a mechanism for validating publisher certificates completely independent from the operating system (see the related archived known issue for the HSA UI).
 

"Invalid context" errors on Mac OS X Lion

Line: 514 to 525
 

"Invalid context" errors on Mac OS X Lion

When you start HIPE form a Terminal window on Mac OS X Lion, you may see errors such as these:

Deleted:
<
<
 
Changed:
<
<
java[40745] : CGContextGetCTM: invalid context
>
>
java[40745] : CGContextGetCTM: invalid context
  These errors are harmless and can be safely ignored.
Line: 530 to 538
 
  • In any case involving large observations or the use of the bg command (you may get an org.apache.lucene.store.LockObtainFailedException).

Both problems are solved by setting the following property:

Added:
>
>
 
Changed:
<
<
hcss.ia.pal.pool.lstore.lock = simple
>
>
hcss.ia.pal.pool.lstore.lock = simple
 See the HIPE Owner's Guide for information on how to set properties.

If this solution does not work, please try removing the lock files (write.lock) present in the local store directory. This bash one-liner script can speed up the process on UNIX-based systems (including OS X):

Line: 536 to 545
 See the HIPE Owner's Guide for information on how to set properties.

If this solution does not work, please try removing the lock files (write.lock) present in the local store directory. This bash one-liner script can speed up the process on UNIX-based systems (including OS X):

Deleted:
<
<
 
Changed:
<
<
find -name 'write.lock' -exec rm {} \;
>
>
find -name 'write.lock' -exec rm {} \;
 

Why do I get a ClassCastException when trying to save an observation with the saveObservation command?

Line: 547 to 554
  To solve this problem follow these steps:
Changed:
<
<
  1. Reinstall HIPE, including the software of the desired instrument.
  2. Delete the following directories (home being your home directory):
>
>
  1. Reinstall HIPE, including the software of the desired instrument.
  2. Delete the following directories (home being your home directory):
 
    • home/.hcss/lstore/hsa_cache
    • home/.hcss/pal_cache/hsa
Changed:
<
<
  1. Retrieve the observation again.
>
>
  1. Retrieve the observation again.
 

I get an OutOfMemoryError related to PermGen space. What can I do?

Line: 556 to 563
 

I get an OutOfMemoryError related to PermGen space. What can I do?

Add or edit the following property in your hipe.props property file:

Deleted:
<
<
 
Changed:
<
<
java.vm.options = -XX:MaxPermSize=256m
>
>
java.vm.options = -XX:MaxPermSize=256m
  Note that this parameter is specific to the Sun/Oracle Java implementation, which is the only one officially supported by HIPE.

Revision 1822015-09-15 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 36 to 36
 

For other issues affecting the installer, check this page.

Known issues in HIPE 13

Added:
>
>

HSA ping from HIPE does not work (but connection is OK), affecting SPIRE calibration updating

The testing of the HSA connection from HIPE is reporting that HIPE is unable to connect to the HSA. This is, in fact, not true and data can be retrieved from the HSA with no problems. It is a problem with the ping itself. As a consequence the spire-cal Updater is not working. A workaround exists that it is to retrieve the latest calibration tree (the appropriate one to work with HIPE 13.0) directly from the HSA by running this command from the command line:
cal=spireCal(calTree="spire_cal_13_1", saveTree=True) 
 

It is not possible to use getObservation with obsid and tag parameters

Ticket number: HCSS-20262 (Won't fix; by design)

Revision 1812015-09-01 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 516 to 516
 These errors are harmless and can be safely ignored.
Changed:
<
<

Problems saving observations to NFS-mounted disks and FAT32 disks

>
>

Problems saving observations

  When saving observation to your computer, you may experience problems in the following cases:
  • When saving data to NFS-mounted disks (you may get an IllegalMonitorStateException).
  • When saving data to a FAT32 filesystem from a Mac (you may get an OverlappingFileLockException).
Added:
>
>
  • In any case involving large observations or the use of the bg command (you may get an org.apache.lucene.store.LockObtainFailedException).
 Both problems are solved by setting the following property:
hcss.ia.pal.pool.lstore.lock = simple
Changed:
<
<
See the HIPE Owner's Guide for information on how to set properties.
>
>
See the HIPE Owner's Guide for information on how to set properties.

If this solution does not work, please try removing the lock files (write.lock) present in the local store directory. This bash one-liner script can speed up the process on UNIX-based systems (including OS X):

find <pool> -name 'write.lock' -exec rm {} \;
 

Why do I get a ClassCastException when trying to save an observation with the saveObservation command?

Revision 1802015-05-18 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 37 to 37
 

Known issues in HIPE 13

It is not possible to use getObservation with obsid and tag parameters

Changed:
<
<
Ticket number: HCSS-20262
>
>
Ticket number: HCSS-20262 (Won't fix; by design)
  Versions affected: All versions of HIPE since 11.0.

Description: When using both obsid and tag as parameters for getObservation (GetObsTask), the task is unable to retrieve tagged observations from local pools.

Changed:
<
<
Workaround: If you take care of making your tags unique, you can supply only tag as parameter for the task and it will retrieve the observation correctly.
>
>
Root cause: The task will first look in MyHSA pool (which does not store tags, being a cache for the archive), when no poolname is supplied as an argument, and won't find any tagged observation there.

Workaround: Always use the poolname where the tagged observation is stored. MyHSA does not support tags.

 

Known issues in HIPE 12

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Revision 1792015-04-13 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 35 to 35
 

For other issues affecting the installer, check this page.

Added:
>
>

Known issues in HIPE 13

It is not possible to use getObservation with obsid and tag parameters

Ticket number: HCSS-20262

Versions affected: All versions of HIPE since 11.0.

Description: When using both obsid and tag as parameters for getObservation (GetObsTask), the task is unable to retrieve tagged observations from local pools.

Workaround: If you take care of making your tags unique, you can supply only tag as parameter for the task and it will retrieve the observation correctly.

 

Known issues in HIPE 12

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Revision 1782015-04-09 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 215 to 215
  Such messages are harmless and just reflect the fact that you have not installed the software related to the specified instruments.
Added:
>
>

Java 8 issues

Trying to use the Versant object database with Java 8 will not work

Versions affected: All developer builds installed using Java 8.

Description: If you use developer builds installed using Java 8, you can experience errors related to Versant. HIPE versions 12 and 13 use Java 7 because of these Versant incompatibilities. The user installer will set up a private JRE with version 7 isolated from the system Java installation, so you will not be affected by this issue.

Root cause: The Versant version included in HCSS software is completely incompatible with Java 8.

 

Java 7 issues

In a Windows domain-joined computer (or with special folder redirection for user profiles) Java can be unable to write to the user home directory

Revision 1772015-04-08 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 35 to 35
 

For other issues affecting the installer, check this page.

Deleted:
<
<

Known issues in HIPE 13

 

Known issues in HIPE 12

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Revision 1762015-04-07 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 17 to 17
 

Installation and de-installation issues

Added:
>
>

The installer for HIPE 13 crashes on OS X Lion (10.7)

Ticket number: INFR-1600 (Third party; Won't Fix)

Versions affected: User release for HIPE 13 (13.0.0)

Description: The installer for HIPE 13.0 crashes on OS X Lion (10.7) even if HIPE itself is currently supported on that platform.

Root cause: The installer software provider (Flexera) has dropped support for Mac OS Lion 10.7 when using authentication (special write access for protected directories).

 

The installer for Mac complains about write permissions. Why?

You need write permissions for the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.

The installer for Windows does not start and issues the error message Not a valid Win32 application. Why?

Line: 28 to 37
 

Known issues in HIPE 13

Deleted:
<
<

SUSSEXtractor returns many more sources for SPIRE maps from version 12.66 onwards

Ticket number: HCSS-18988

Versions affected: All versions of HIPE from build 12.0.66 to 13.0.4919 (both included).

Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.0.66 to 13.0.4919 returns 3-4 times the number of sources it returned previously with the same parameters (except the PRF grid size, which has increased internally from 5x5 to 13x13 pixels). The fluxes of the detected sources are also different and generally higher by around 5 percent.

Workaround: You can force SUSSEXtractor to produce the original results by imposing a 5x5 PRF grid size, as tests have concluded that the photometry of the results of this task for the versions affected is worse than before. SUSSEXtractor has reverted to the original 5x5 PRF from HIPE builds later than 13.0.4919.

Example script:

myImage = SimpleImage("your SPIRE map")
myPrf = PrfGaussian([myImage.getWidth(),myImage.getHeight()],5.0)
sourceList = sourceExtractorSussextractor( \
    image = myImage,        # Image name \
    ...
    prf = myPrf,            # 5x5 PRF \
    ... 
    )
 

Known issues in HIPE 12

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Changed:
<
<
Ticket number: HCSS-15583
>
>
Ticket number: HCSS-15583 (Won't fix)
  Versions affected: All versions of HIPE since 8.0
Line: 77 to 64
  Workaround: None at this time.

Old syntax using HIFI class PolarPair gives wrong results

Changed:
<
<
Ticket number: none
>
>
Ticket number: none (API change)
  Versions affected: HIPE 12.0
Line: 100 to 87
 

Limitations of the task for updating scripts that use the old syntax to access return parameters

Changed:
<
<
Ticket number: HCSS-19080
>
>
Ticket number: HCSS-19080 (Won't fix)
  Versions affected: HIPE 12.
Line: 110 to 97
 

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on OS X

Changed:
<
<
Ticket number: HCSS-18891
>
>
Ticket number: HCSS-18891 (Third party; Won't fix)
  Versions affected: HIPE 12.
Line: 150 to 137
  Workaround: The current workaround is to remove the entries that contain JavaVM from this environment variable. To do that, modify or create the .bash_profile configuration file of the terminal and add the environment variable in an export statement without the corresponding entries. That should persist the changes.
Deleted:
<
<

Known issues in HIPE 11

Reading observations stored as tarball archives that contain new data types does not work in HIPE 11

Ticket number: HCSS-19572

Versions affected: Potentially all versions older than HIPE 12.

Error message: While loading an observation from a tarball archive (.TAR file), HIPE returns the following error:

WARNING: Could not open /home/user/1342219630-herschel.ia.obs.ObservationContext-580157.xml: 
herschel.ia.task.TaskException: Error processing getObservation task: 
Class definition not found for urn urn:hsa:herschel.spire.ia.dataset.PhotApertureEfficiency:0: herschel.spire.ia.dataset.PhotApertureEfficiency

Root cause: The root cause is that the class herschel.spire.ia.dataset.PhotApertureEfficiency (among others) is new for data processed with HCSS 12 and doesn't exist in previous versions of HIPE. Previous versions cannot open tarballs containing these types of data.

Workaround: The recommended workaround is updating HIPE to version 12.1.

If you cannot upgrade HIPE, please contact the Helpdesk.

Migrating pools across incompatible versions of HIPE

HIPE 10 developer versions (builds between 2069 and 2674) and HIPE 11 (all builds) pools are incompatible with any other version of HIPE (including all public releases of HIPE 10).

In order to use these existing pools with an incompatible version, you should rebuild the index of the pool. Given that it is not guaranteed that newer data should work with older versions of the software, this guide will focus only on making the pools workable in the following cases:

  • Case 1: Using pools created/modified in a HIPE 10 version prior to 2069 with a HIPE 10 version between 2069 and 2674.
  • Case 2: Using pools created/modified in a HIPE 10 version between 2069 and 2674 with a HIPE 10 version between after 2674.
  • Case 3: Using pools created/modified in a HIPE 10 version other than the 2069-2674 range with HIPE 11.
  • Case 4: Using pools with an index rebuilt for a HIPE 10 version other than the 2069-2674 range with HIPE 11.

Prerequisite:

A pool created with a HIPE 10 version prior to 2069.

Case 1:

Pool you want to open: A pool like the one detailed in the prerequisite.

Error message: There is no error displayed and the pool is completely usable in HIPE 10 versions 2069-2674.

Case 2:

Pool you want to open: A pool that is like the prerequisite or has been processed in a scenario like CASE 1.

Error message: Querying the pool using the Product Browser returns nothing (no error message). Opening the observation from the Console using getObservation returns the following error message:

herschel.ia.task.TaskException: Error processing getObservation task: Index Version not compatible. Expected : 4 Existing: 6. 
Pool <pool_name> requires upgrading before you can use it with this software. In order to do so, you need to run pool_name.rebuildIndex() to upgrade. 
Depending on the size of the pool this process can take a long time, please be patient! 
More information can be found in the Data Analysis Guide, section 1.2.2.1 (Update of index format for local stores).

Notes about the error message:

  • pool_name is the name of the pool you are trying to load.
  • pool_name.rebuildIndex() is not the proper command to rebuild the pool. See below for the appropriate commands.
  • The section of the Data Analysis Guide referenced is not correct. When ready, a copy of this procedure will be available in the section 1.11 (Migrating pools across incompatible versions of HIPE)

Workaround: Any of the following commands will rebuild the index of the pool:

  • This ensures we are rebuilding the specified pool using a static method from the class LocalStoreFactory:
LocalStoreFactory.getStore(pool_name).rebuildIndex()
store.writablePool.rebuildIndex()

Case 3:

Pool you want to open: A pool that is like the prerequisite.

Error message: There is no error displayed and the pool is completely usable in HIPE 11.

Case 4:

Pool you want to open: A pool which index was rebuilt following CASE 2 instructions.

Error message: There is no error displayed and the pool is completely usable in HIPE 11.

That's it! You should now be able to use your pool in any of the above cases. If you find you cannot, contact the Helpdesk.

Tip, idea Note that the index files will not be backed up while you run rebuildIndex(), unless you invoke Configuration.setProperty("hcss.ia.pal.pool.lstore.index.backup", "true") first. For more information execute the following command: help('dag:sec-lstore-index-compatibility'). See the HIPE Owner's Guide: Section 4.
 

Older HIPE versions

Revision 1752015-02-16 - ChrisPearson

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 34 to 34
  Versions affected: All versions of HIPE from build 12.0.66 to 13.0.4919 (both included).
Changed:
<
<
Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.0.66 to 13.0.4919 returns 3-4 times the number of sources it returned previously with the same parameters (excepting the PRF grid size, which has increased internally). The fluxes of the detected sources are also different and generally higher.
>
>
Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.0.66 to 13.0.4919 returns 3-4 times the number of sources it returned previously with the same parameters (except the PRF grid size, which has increased internally from 5x5 to 13x13 pixels). The fluxes of the detected sources are also different and generally higher by around 5 percent.
 
Changed:
<
<
Workaround: You can force the old results by imposing a 5x5 PRF grid size, as tests have concluded that the photometry of the results of this task for the versions affected is worse than before. Example script:
>
>
Workaround: You can force SUSSEXtractor to produce the original results by imposing a 5x5 PRF grid size, as tests have concluded that the photometry of the results of this task for the versions affected is worse than before. SUSSEXtractor has reverted to the original 5x5 PRF from HIPE builds later than 13.0.4919.

Example script:

 
myImage = SimpleImage("your SPIRE map")
myPrf = PrfGaussian([myImage.getWidth(),myImage.getHeight()],5.0)

Revision 1742015-02-16 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 28 to 28
 

Known issues in HIPE 13

Deleted:
<
<

Known issues in HIPE 12

 

SUSSEXtractor returns many more sources for SPIRE maps from version 12.66 onwards

Ticket number: HCSS-18988

Changed:
<
<
Versions affected: All versions of HIPE 12 from build 66 (included)
>
>
Versions affected: All versions of HIPE from build 12.0.66 to 13.0.4919 (both included).
 
Changed:
<
<
Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.66 onwards returns 3-4 times the number of sources it returned previously with the same parameters (excepting the PRF grid size, which has increased internally). The fluxes of the detected sources are also different and generally higher.
>
>
Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.0.66 to 13.0.4919 returns 3-4 times the number of sources it returned previously with the same parameters (excepting the PRF grid size, which has increased internally). The fluxes of the detected sources are also different and generally higher.
 
Changed:
<
<
Workaround: You can force the old results by imposing a 5x5 PRF grid size, but tests are ongoing to decide whether the current settings produce more reliable photometry. Example script:
>
>
Workaround: You can force the old results by imposing a 5x5 PRF grid size, as tests have concluded that the photometry of the results of this task for the versions affected is worse than before. Example script:
 
myImage = SimpleImage("your SPIRE map")
myPrf = PrfGaussian([myImage.getWidth(),myImage.getHeight()],5.0)
Line: 51 to 48
  )
Added:
>
>

Known issues in HIPE 12

 

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Ticket number: HCSS-15583

Revision 1732015-02-12 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 28 to 28
 

Known issues in HIPE 13

Deleted:
<
<

Cut levels in Display don't work properly for very small values in images

Ticket number: HCSS-19897

Versions affected: HIPE 13.0

Description: You cannot modify the cut levels of an image, loaded with the help of the Display class, that contains very small values (close to zero). For example, the image aa created by this script:

aa = Double2d(257,257)

width = 20.0
for i in range(257):
   for j in range(257):
      aa[i,j] = EXP(-(((j-128.)**2)+((i-128.)**2))/(2*width**2))

bb = aa + 0.001

On the other hand, the cut levels of image bb would be handled properly.

Workaround: Use an older version of HIPE to adjust cut levels in images.

 

Known issues in HIPE 12

Revision 1722015-02-04 - AlvarGarcia

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  Side effects: The attempt to read this Registry key does not affect the behaviour of HIPE, since HIPE stores the user preferences in the CURRENT_USER hive of the Windows Registry.
Deleted:
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Crash when a HIPE session is left unattended for a long time with Java 7 on Mac OS X, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

Ticket: HCSS-18424

Configuration prone to cause the error

  • Operating system: Any version of Mac OS X.
  • Java version: any Java 7 version.

Usage prone to cause the error

  • Leave HIPE running unattended for several hours.
  • Return to work with HIPE and:
    • Switch applications.
    • Wake the computer/monitor from sleep.
    • Change the display resolution.
    • Send an application to another monitor in a multimonitor setup.

Error message

The crash displays a long error trace that begins with:

Thread 0 Crashed:: AppKit Thread  Dispatch queue: com.apple.main-thread
0   com.apple.CoreFoundation         0x00007fff8d7e2a1b CFRelease + 27
1   liblwawt.dylib                   0x000000011b557647 __Java_sun_lwawt_macosx_CWrapper_00024NSObject_release_block_invoke_1 + 91
2   JavaNativeFoundation             0x000000011a8ea5f5 +[JNFRunLoop _performCopiedBlock:] + 20
3   com.apple.CoreFoundation         0x00007fff8d8a7d9d +[NSObject performSelector:withObject:] + 61
4   com.apple.Foundation             0x00007fff85d9dd70 __NSThreadPerformPerform + 214
5   com.apple.CoreFoundation         0x00007fff8d7ec4f1 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
6   com.apple.CoreFoundation         0x00007fff8d7ebd5d __CFRunLoopDoSources0 + 253
7   com.apple.CoreFoundation         0x00007fff8d812b49 __CFRunLoopRun + 905
8   com.apple.CoreFoundation         0x00007fff8d812486 CFRunLoopRunSpecific + 230
9   com.apple.HIToolbox              0x00007fff8acda2bf RunCurrentEventLoopInMode + 277

General information

If you are affected by this problem, it is useful to know that:

  • This is a Mac OS X problem, it does not affect any other operating system.
  • This is a Java 7 bug, being worked on by Oracle and set to be fixed in Java 8. More information can be found at http://bugs.java.com/view_bug.do?bug_id=8009012

Workarounds

From the information above, the only identified workarounds for those of you that run long sessions of HIPE are:

 

General Help System issues

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Installation and de-installation issues

Deleted:
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<

Installer or start-up hang on Mac OSX and Java 1.6.0_51

Ticket number: HCSS-18288

    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
    • How to fix: Users need to manually download and install the Java update.
    • Apple support notes that "This update corrects an issue with Java applications failing to draw or respond to user input."
 

The installer for Mac complains about write permissions. Why?

You need write permissions for the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.

The installer for Windows does not start and issues the error message Not a valid Win32 application. Why?

This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.

Why does the uninstaller leave some icons and files/directories behind?

This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
Deleted:
<
<

Sometimes when you run HIPE on your laptop for the first time you may get following error message:

% ./runhipe Error occurred during initialization of VM

Could not reserve enough space for object heap

Could not create the Java virtual machine.

 
Deleted:
<
<
This error typically happens because you have either set or have as default a too large memory for the Java Virtual Machine and hence it cannot start. Edit the file called "installed.properties" under your hipe_v11_RC2 (or alternative directory, as appropriate) installation directory and edit the line

java.vm.memory.max=2872m

to have a smaller value than 1500m and smaller than the RAM memory of your machine.

 

For other issues affecting the installer, check this page.

Known issues in HIPE 13

Line: 141 to 118
 av=polarPair(ds1=wbs_h, ds2=wbs_v)
Deleted:
<
<

Problem with doGridding in rotated maps with HIFI

Ticket number: HIFI-5716

Versions affected: HIPE 12.0

Description: for maps taken with a non-zero orientation on the sky, the HIFI pipeline will generate two cubes: one non-rotated cube projected onto the Equatorial frame (cubesContext) and one rotated by the scanning orientation angle (cubesContextRotated). In HIPE 12.0 a bug was introduced that generates both cubes in the rotated frame.

Workaround: In order to generate non-rotated cubes you can apply the doGridding task on the level 2 products with the option flyAngle=1e-5 (for example - it is just a matter of using a very small, non-strictly zero, angle). The problem will be solved in 12.1.

computeVelocityTask plots absorption profiles as emission

Ticket number: HCSS-19133

Versions affected: HIPE 12.

Description: The computeVelocityTask in the Cube Analysis Toolbox returns and plots a fittedLineCube. This plot displays absorption profiles as emission, even if isEmission=False. The data returned is correct, but this plot must be disregarded.

Workaround: Simply disregard the plot generated by the task and trust the data stored in the fittedLineCube.

 

Limitations of the task for updating scripts that use the old syntax to access return parameters

Ticket number: HCSS-19080

Line: 480 to 437
 

Crash when a HIPE session is left unattended for a long time with Java 7 on Mac OS X, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

Added:
>
>
Ticket: HCSS-18424
 Configuration prone to cause the error
  • Operating system: Any version of Mac OS X.
  • Java version: any Java 7 version.
Line: 524 to 483
 
  • Use another operating system if you believe that your HIPE usage will match the pattern that triggers the crash.
Deleted:
<
<

Cursor position in the editor view is inaccurate in high-DPI (Retina) displays using Java 7 version

Ticket number: HCSS-18698
Versions affected: HIPE 12 or older
Description: The cursor position appears inside characters instead of between them.

Workaround

From Java 7 Update 55, Oracle has fixed the issue. As the bundled JRE for HIPE 12 or older is Java 7 Update 45, to be able to benefit from the patch you must change the script that launches HIPE and point it to the Java 7 Update 55 or later installed at system level. To do that, edit the file HIPE_DIR/bin/_launch.sh and edit or delete the line(s) that export the PATH variable:

PATH=/Applications/hipe_v12.0.0/jre/Contents/Home/jre/bin:$PATH
export PATH

NOTE: You should only delete the lines if you are completely sure that the default version of the system is Update 55 or later. In order to check if that is the case, you can execute java -version or /usr/libexec/java_home -V on the Terminal and then, after confirming the default version, use that path to update the _launch.sh file.

 

General Help System issues

When Google Chrome is the default browser for Mac OS X, the navigation arrows at the top of the help pages are not rendered

Line: 760 to 699
  For more information about property files, see the HIPE Owner's Guide.
Changed:
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There are PACS files I cannot delete! Why?

>
>

There are PACS files I cannot delete on Windows! Why?

  It might not be possible to delete the following files on Windows because their full path exceeds the 260 characters limit. This is caused by a limitation in Windows Explorer and the Command Prompt to maintain backwards compatibility (even if the operating system supports longer file paths).

Revision 1702015-01-30 - JaimeSaiz

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  Description: When trying to open the HSA UI from HIPE, you receive an exception trace similar to this one:
Changed:
<
<
INFO: HAIO request: http://archives.esac.esa.int/hsa/aio/jsp/product.jsp?urn=urn :hsa:herschel.ia.obs.BrowseImageProduct:283481&protocol=HTTP Jan 15, 2015 4:38:58 PM herschel.ia.pal.pool.hsa.myhsa.cache.AbstractDownloadJob warn WARNING: java.io.IOException: Error writting file 'D:\data\MyHSA\session\1421311 115192\products\1342220914-herschel.ia.obs.ObservationContext-601367.xml': java.io.FileNotFoundException: file:\D:\data\MyHSA\session\1421311115192\product s\1342220914-herschel.ia.obs.ObservationContext-601367.xml (Invalid syntax in filename, directory name or volume name.) at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager .java:706) at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager .java:661) at herschel.ia.pal.pool.hsa.myhsa.cache.HsaCachedReadPool.getXmlRootFor( HsaCachedReadPool.java:189
>
>
INFO: HAIO request: http://archives.esac.esa.int/hsa/aio/jsp/product.jsp?urn=urn:hsa:herschel.ia.obs.BrowseImageProduct:283481&protocol=HTTP Jan 15, 2015 4:38:58 PM herschel.ia.pal.pool.hsa.myhsa.cache.AbstractDownloadJob warn WARNING: java.io.IOException: Error writting file 'D:\data\MyHSA\session\1421311115192\products\1342220914-herschel.ia.obs.ObservationContext-601367.xml': java.io.FileNotFoundException: file:\D:\data\MyHSA\session\1421311115192\products\1342220914-herschel.ia.obs.ObservationContext-601367.xml (Invalid syntax in filename, directory name or volume name.) at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager.java:706) at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager.java:661) at herschel.ia.pal.pool.hsa.myhsa.cache.HsaCachedReadPool.getXmlRootFor(HsaCachedReadPool.java:189)
 

Root cause: The Java cache directory (where Java stores JAR files downloaded from the Internet) is corrupted.

Revision 1692015-01-30 - AlvarGarcia

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Herschel Science Archive issues

Added:
>
>

Herschel Science Archive (HSA) UI cannot start if the Java cache is corrupted

Ticket: HCSS-19940

Description: When trying to open the HSA UI from HIPE, you receive an exception trace similar to this one:

INFO: HAIO request: http://archives.esac.esa.int/hsa/aio/jsp/product.jsp?urn=urn
:hsa:herschel.ia.obs.BrowseImageProduct:283481&protocol=HTTP
Jan 15, 2015 4:38:58 PM herschel.ia.pal.pool.hsa.myhsa.cache.AbstractDownloadJob
warn
WARNING: java.io.IOException: Error writting file 'D:\data\MyHSA\session\1421311
115192\products\1342220914-herschel.ia.obs.ObservationContext-601367.xml':
java.io.FileNotFoundException: file:\D:\data\MyHSA\session\1421311115192\product
s\1342220914-herschel.ia.obs.ObservationContext-601367.xml (Invalid syntax in filename, directory name or volume name.)
at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager
.java:706)
at herschel.ia.pal.pool.hsa.xml.HsaXmlManager.writeXmlFile(HsaXmlManager
.java:661)
at herschel.ia.pal.pool.hsa.myhsa.cache.HsaCachedReadPool.getXmlRootFor(
HsaCachedReadPool.java:189

Root cause: The Java cache directory (where Java stores JAR files downloaded from the Internet) is corrupted.

Workaround: Do not try to clear the cache using Java Control Panel -> General -> Settings -> Delete files (select all checkboxes), as Java won't be able to clear it because of the corruption. Delete the storage directory (C:\Users\username\AppData\LocalLow\Sun\Java\Deployment\cache on Windows Vista, 7 and 8.1; C:\Documents and Settings\username\Local Settings\Application Data\Sun\Java\Deployment\cache on Windows XP) and Java will re-create the cache successfully. For more information about the paths, check this link on application data directories on different versions of Windows or the official description of the Java cache on Java's website.

If you change the default path for the MyHSA directory, be sure to use / as directory separator

Ticket: HCSS-19940

Description: When changing the default path for the MyHSA directory ( Edit > Preferences > MyHSA ) on Windows, use forward slashes for the path. This text box takes the content as a Java String, considering the Windows directory separator (\) as an escape character. Example D:\data\myhsa should be entered as D:/data/myhsa.

 

How to log in with new credentials after changing the password for HSA I have changed/reset the password of the account I use to access Herschel Science Archive, but HIPE still tells me I am logged in (with the old password), even after restarting HIPE. How do I log in with the new password?

Description: HIPE stores your HSA password for you if you log in and check the "Remember Me" checkbox. If you restart you can access the HSA without having to enter your info again.

Revision 1682014-12-12 - AlvarGarcia

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 to have a smaller value than 1500m and smaller than the RAM memory of your machine.

For other issues affecting the installer, check this page.

Added:
>
>

Known issues in HIPE 13

Cut levels in Display don't work properly for very small values in images

Ticket number: HCSS-19897

Versions affected: HIPE 13.0

Description: You cannot modify the cut levels of an image, loaded with the help of the Display class, that contains very small values (close to zero). For example, the image aa created by this script:

aa = Double2d(257,257)

width = 20.0
for i in range(257):
   for j in range(257):
      aa[i,j] = EXP(-(((j-128.)**2)+((i-128.)**2))/(2*width**2))

bb = aa + 0.001

On the other hand, the cut levels of image bb would be handled properly.

Workaround: Use an older version of HIPE to adjust cut levels in images.

 

Known issues in HIPE 12

SUSSEXtractor returns many more sources for SPIRE maps from version 12.66 onwards

Revision 1672014-11-13 - AlvarGarcia

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  If you are affected by this problem, it is useful to know that:
  • This is a Mac OS X problem, it does not affect any other operating system.
Changed:
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>
>
  Workarounds

Revision 1662014-10-31 - AlvarGarcia

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Other issues

Added:
>
>

HCSS applications do not run shutdown hooks when terminating the launcher

Ticket number: INFR-1425

Description: Shutdown hooks added to the running instance of the Java Runtime may not be executed when terminating a HCSS application started with the common launcher launcher.jar.

Root cause: This happens because the hooks are added to the child process created by the launcher and terminating the launcher process does not guarantee that the hooks will run. For more information see this bug in Oracle's database.

Workaround: Kill the child process directly in the manner appropriate to each platform. Shutdown hooks added to the child process will execute.

 

HIPE crashed/froze! What do I do?

If you cannot find a solution in this document, you may have found a bug in HIPE. Please report it by opening a Helpdesk ticket. If the system produced a dump file when the crash happened, make sure to include it in your ticket. For more information about dump files and where to look for them, see the HIPE Owner's Guide.

Revision 1652014-10-21 - AlvarGarcia

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 Workaround: You can force the old results by imposing a 5x5 PRF grid size, but tests are ongoing to decide whether the current settings produce more reliable photometry. Example script:
myImage = SimpleImage("your SPIRE map")
Changed:
<
<
myPrf = PrfGaussian([image.getWidth(),image.getHeight()],5.0)
>
>
myPrf = PrfGaussian([myImage.getWidth(),myImage.getHeight()],5.0)
 sourceList = sourceExtractorSussextractor( image = myImage, # Image name ...

Revision 1642014-10-20 - AlvarGarcia

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  Root cause: The root cause is that the class herschel.spire.ia.dataset.PhotApertureEfficiency (among others) is new for data processed with HCSS 12 and doesn't exist in previous versions of HIPE. Previous versions cannot open tarballs containing these types of data.
Changed:
<
<
Workaround: The recommended workaround is updating HIPE to version 12.1. Another option is to retrieve the same observation but processed with HCSS 11 from the Herschel Science Archive (HSA) by running the getObservation task in HIPE. For example:
myObs = getObservation(obsid=1342219630, useHsa=True, save=True, spgVersion="11.1.0")
Note that it is not possible to download tarball archives of a specific SPG version using the HSA UI.
>
>
Workaround: The recommended workaround is updating HIPE to version 12.1.
 
Changed:
<
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If none of the workarounds are suitable for you, please contact the Helpdesk.
>
>
If you cannot upgrade HIPE, please contact the Helpdesk.
 

Migrating pools across incompatible versions of HIPE

Revision 1632014-10-20 - AlvarGarcia

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 Class definition not found for urn urn:hsa:herschel.spire.ia.dataset.PhotApertureEfficiency:0: herschel.spire.ia.dataset.PhotApertureEfficiency
Changed:
<
<
Root cause: The root cause is that the class herschel.spire.ia.dataset.PhotApertureEfficiency (and others) is new for data processed with HCSS 12 and doesn't exist in previous versions of HIPE. Previous versions cannot open tarballs containing these types of data.
>
>
Root cause: The root cause is that the class herschel.spire.ia.dataset.PhotApertureEfficiency (among others) is new for data processed with HCSS 12 and doesn't exist in previous versions of HIPE. Previous versions cannot open tarballs containing these types of data.
 
Changed:
<
<
Workaround: The recommended workaround is updating HIPE to version 12.1. If for any reason you do not want to upgrade to this latest HIPE version please contact the Helpdesk.
>
>
Workaround: The recommended workaround is updating HIPE to version 12.1. Another option is to retrieve the same observation but processed with HCSS 11 from the Herschel Science Archive (HSA) by running the getObservation task in HIPE. For example:
myObs = getObservation(obsid=1342219630, useHsa=True, save=True, spgVersion="11.1.0")
Note that it is not possible to download tarball archives of a specific SPG version using the HSA UI.

If none of the workarounds are suitable for you, please contact the Helpdesk.

 

Migrating pools across incompatible versions of HIPE

Revision 1622014-10-20 - BrunoMerin

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  Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.66 onwards returns 3-4 times the number of sources it returned previously with the same parameters (excepting the PRF grid size, which has increased internally). The fluxes of the detected sources are also different and generally higher.
Changed:
<
<
Workaround: You can force the old results by imposing a 5x5 PRF grid size, but test are ongoing to decide if the current results are better for photometry. Example script:
>
>
Workaround: You can force the old results by imposing a 5x5 PRF grid size, but tests are ongoing to decide whether the current settings produce more reliable photometry. Example script:
 
myImage = SimpleImage("your SPIRE map")
myPrf = PrfGaussian([image.getWidth(),image.getHeight()],5.0)

Revision 1612014-10-20 - AlvarGarcia

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Known issues in HIPE 12

Added:
>
>

SUSSEXtractor returns many more sources for SPIRE maps from version 12.66 onwards

Ticket number: HCSS-18988

Versions affected: All versions of HIPE 12 from build 66 (included)

Description: Running the SUSSEXtractor task on the same SPIRE maps using versions of HIPE from version 12.66 onwards returns 3-4 times the number of sources it returned previously with the same parameters (excepting the PRF grid size, which has increased internally). The fluxes of the detected sources are also different and generally higher.

Workaround: You can force the old results by imposing a 5x5 PRF grid size, but test are ongoing to decide if the current results are better for photometry. Example script:

myImage = SimpleImage("your SPIRE map")
myPrf = PrfGaussian([image.getWidth(),image.getHeight()],5.0)
sourceList = sourceExtractorSussextractor( \
    image = myImage,        # Image name \
    ...
    prf = myPrf,            # 5x5 PRF \
    ... 
    )
 

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Added:
>
>
 Ticket number: HCSS-15583

Versions affected: All versions of HIPE since 8.0

Revision 1602014-10-06 - AlvarGarcia

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  Root cause: The root cause is that the class herschel.spire.ia.dataset.PhotApertureEfficiency (and others) is new for data processed with HCSS 12 and doesn't exist in previous versions of HIPE. Previous versions cannot open tarballs containing these types of data.
Changed:
<
<
Workaround: The recommended workaround is updating HIPE to version 12.1. Another workaround is not using tarball archives but employing getObservation from HIPE. This second method seems to work but is undergoing additional testing. See below for an example (that saves the complete observation to disk).
obs = getObservation(1342243284, useHsa=True, save=True)

1342243284 is an observation containing another new data type (herschel.pacs.cal.spectrometer.TelBackCorB2B) for SPG version 12 and would also fail when opened as a tarball archive.

>
>
Workaround: The recommended workaround is updating HIPE to version 12.1. If for any reason you do not want to upgrade to this latest HIPE version please contact the Helpdesk.
 

Migrating pools across incompatible versions of HIPE

Revision 1592014-10-06 - AlvarGarcia

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  Root cause: The root cause is that the class herschel.spire.ia.dataset.PhotApertureEfficiency (and others) is new for data processed with HCSS 12 and doesn't exist in previous versions of HIPE. Previous versions cannot open tarballs containing these types of data.
Changed:
<
<
Workaround: The recommended workaround is updating HIPE to version 12.1. Another workaround is not using tarball archives but employing getObservation from HIPE. That will retrieve from the Herschel Science Archive the appropriate SPG version of the observation for the current HIPE version.
>
>
Workaround: The recommended workaround is updating HIPE to version 12.1. Another workaround is not using tarball archives but employing getObservation from HIPE. This second method seems to work but is undergoing additional testing. See below for an example (that saves the complete observation to disk).
 
Changed:
<
<
obs = getObservation(1342243284,useHsa=True)
>
>
obs = getObservation(1342243284, useHsa=True, save=True)
 

1342243284 is an observation containing another new data type (herschel.pacs.cal.spectrometer.TelBackCorB2B) for SPG version 12 and would also fail when opened as a tarball archive.

Revision 1582014-10-06 - AlvarGarcia

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Known issues in HIPE 11

Added:
>
>

Reading observations stored as tarball archives that contain new data types does not work in HIPE 11

Ticket number: HCSS-19572

Versions affected: Potentially all versions older than HIPE 12.

Error message: While loading an observation from a tarball archive (.TAR file), HIPE returns the following error:

WARNING: Could not open /home/user/1342219630-herschel.ia.obs.ObservationContext-580157.xml: 
herschel.ia.task.TaskException: Error processing getObservation task: 
Class definition not found for urn urn:hsa:herschel.spire.ia.dataset.PhotApertureEfficiency:0: herschel.spire.ia.dataset.PhotApertureEfficiency

Root cause: The root cause is that the class herschel.spire.ia.dataset.PhotApertureEfficiency (and others) is new for data processed with HCSS 12 and doesn't exist in previous versions of HIPE. Previous versions cannot open tarballs containing these types of data.

Workaround: The recommended workaround is updating HIPE to version 12.1. Another workaround is not using tarball archives but employing getObservation from HIPE. That will retrieve from the Herschel Science Archive the appropriate SPG version of the observation for the current HIPE version.

obs = getObservation(1342243284,useHsa=True)

1342243284 is an observation containing another new data type (herschel.pacs.cal.spectrometer.TelBackCorB2B) for SPG version 12 and would also fail when opened as a tarball archive.

 

Migrating pools across incompatible versions of HIPE

HIPE 10 developer versions (builds between 2069 and 2674) and HIPE 11 (all builds) pools are incompatible with any other version of HIPE (including all public releases of HIPE 10).

Revision 1572014-07-31 - AlvarGarcia

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Known issues in HIPE 12

Added:
>
>

SmoothSpectrumTask and ResampleSpectrumTask do not propagate weights correctly

Ticket number: HCSS-15583

Versions affected: All versions of HIPE since 8.0

Description: If any of the tasks is applied to a spectrum that contains a column of errors instead of weights, the task converts the errors to weights, propagates the weights and repopulates the error column by converting the propagated weights back to errors. This gives an error column that has not been propagated correctly for the operation applied.

Workaround: Take into account that the output error column should be disregarded in the case of source data that lack a proper error column.

 

HIPE FITS Writer format could be incorrectly read by other software

Ticket number: HCSS-19248

Revision 1562014-05-29 - JorgoBakker

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  • Use another operating system if you believe that your HIPE usage will match the pattern that triggers the crash.
Changed:
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<

Cursor position in the editor view is inaccurate in high-DPI (Retina) displays when using latest Java 7 version (45)

>
>

Cursor position in the editor view is inaccurate in high-DPI (Retina) displays using Java 7 version

 
Changed:
<
<
Ticket number: HCSS-18698

Versions affected: HIPE 12 or older

Description: The cursor position appears inside characters instead of between them.

java7u45-font-issue.png

>
>
Ticket number: HCSS-18698
Versions affected: HIPE 12 or older
Description: The cursor position appears inside characters instead of between them.

  Workaround

Revision 1552014-05-23 - AlvarGarcia

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  Ticket number: HCSS-18698
Changed:
<
<
The cursor position appears inside characters instead of between them.
>
>
Versions affected: HIPE 12 or older

Description: The cursor position appears inside characters instead of between them.

  java7u45-font-issue.png

Workaround

Changed:
<
<
The only workaround right now is to roll back to a previous version of Java 7 (which is not aware of Retina displays, so the UI looks fuzzy).
>
>
From Java 7 Update 55, Oracle has fixed the issue. As the bundled JRE for HIPE 12 or older is Java 7 Update 45, to be able to benefit from the patch you must change the script that launches HIPE and point it to the Java 7 Update 55 or later installed at system level. To do that, edit the file HIPE_DIR/bin/_launch.sh and edit or delete the line(s) that export the PATH variable:
PATH=/Applications/hipe_v12.0.0/jre/Contents/Home/jre/bin:$PATH
export PATH

NOTE: You should only delete the lines if you are completely sure that the default version of the system is Update 55 or later. In order to check if that is the case, you can execute java -version or /usr/libexec/java_home -V on the Terminal and then, after confirming the default version, use that path to update the _launch.sh file.

 

General Help System issues

Revision 1542014-05-22 - AlvarGarcia

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Known issues in HIPE 12

Added:
>
>

HIPE FITS Writer format could be incorrectly read by other software

Ticket number: HCSS-19248

Versions affected: HIPE 12.x

Description: HIPE makes use of OGIP, a non-standard convention to include long values in FITS fields. The OGIP convention writes an & at the end of a line (for example, describing a column name) that would be considered valid for all FITS compliant readers (it contains less than 68 characters) followed by the special keyword CONTINUE '' / & and completing the long value with a COMMENT Rest of value line. For example:

TTYPE1  = 'designation&'
CONTINUE  '' / &
COMMENT Original element type: char, Empty values appear as null
Many FITS readers ignore this convention, so the special character & is read and included as the final character of the value. Others (IDL) do the same but, additionally, consider & an invalid character and it is replaced by an underscore _.

Workaround: None at this time.

 

Old syntax using HIFI class PolarPair gives wrong results

Ticket number: none

Revision 1532014-04-02 - AlvarGarcia

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Known issues in HIPE 12

Added:
>
>

Old syntax using HIFI class PolarPair gives wrong results

Ticket number: none

Versions affected: HIPE 12.0

Description: PolarPair (the class) use is now discouraged for users and polarPair (the task, note capitalisation) has been modified in order to allow it to be used as a part of the interactive HIFI pipeline and to bring its syntax in-line with other tasks in the Spectral Toolbox. If the old syntax is used, e.g.,

pp = PolarPair(wbs_h, wbs_v)
av = pp.avg()

incorrect results are obtained.

This problem did not affect previous HIPE versions. A warning will be written to the console in HIPE 13 if the old syntax is used.

Workaround: Use the new syntax running the task:

av=polarPair(ds1=wbs_h, ds2=wbs_v)
 

Problem with doGridding in rotated maps with HIFI

Ticket number: HIFI-5716

Revision 1522014-03-27 - AlvarGarcia

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Known issues in HIPE 12

Added:
>
>

Problem with doGridding in rotated maps with HIFI

Ticket number: HIFI-5716

Versions affected: HIPE 12.0

Description: for maps taken with a non-zero orientation on the sky, the HIFI pipeline will generate two cubes: one non-rotated cube projected onto the Equatorial frame (cubesContext) and one rotated by the scanning orientation angle (cubesContextRotated). In HIPE 12.0 a bug was introduced that generates both cubes in the rotated frame.

Workaround: In order to generate non-rotated cubes you can apply the doGridding task on the level 2 products with the option flyAngle=1e-5 (for example - it is just a matter of using a very small, non-strictly zero, angle). The problem will be solved in 12.1.

 

computeVelocityTask plots absorption profiles as emission

Ticket number: HCSS-19133

Revision 1512014-03-24 - AlvarGarcia

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 If not, you have probably encountered a bug. The following are known issues that can prevent you from viewing the documentation, resulting either in a blank page or an error message:

  • A caching bug in Safari 4.0 can be solved by clearing the browser cache. Alternatively, open the help page with another web browser: copy and paste the address (something like http://127.0.0.1:8082/index.jsp?mark=null) to the address bar of the other browser.
Changed:
<
<
  • A problem with Mac OS X can result in error messages when viewing the documentation of any installed HIPE version. In particular, you may get an HTTP ERROR: 404 NOT FOUND message in your browser, and a message about index.jsp not found in the command line terminal. There are two options to solve the problem:
    • Delete the temporary directory created by the help system in /private/var/folders/[1]/[2]/T/yahajs_[username]_[HIPE version]/jetty/instance_[instance number]/webapp (the first ellipsis [1] is a pair of alphanumeric characters and the second [2] is a string of 30 alphanumeric characters).
>
>
  • A problem with Jetty's file management (Jetty is part of the help system) can result in error messages when viewing the documentation of any installed HIPE version. In particular, you may get an HTTP ERROR: 404 NOT FOUND message in your browser, and a message about index.jsp not found in the command line terminal. There are two options to solve the problem:
    • Delete the temporary directory created by the help system in /private/var/folders/[1]/[2]/T/yahajs_[username]_[HIPE version]/jetty/instance_[instance number]/webapp (the first ellipsis [1] is a pair of alphanumeric characters and the second [2] is a string of 30 alphanumeric characters). For Linux, the path will be something like /tmp/yahajs_[username]_[HIPE version]/jetty/instance_[instance number]/webapp depending on the distribution.
 
    • If the previous solution does not work, please try rebooting the computer.
  • Older browser versions may not display documentation correctly. For example, links from HIPE to the Help System, like the Help in URM menu entries for tasks, work in Firefox 3.6.x but not in Firefox 3.0.x. Other legacy browsers may have similar problems.
  • If you are using Linux and get an error message like Firefox can not contact the server www.%u.com, change your default browser from firefox %u to firefox %s (same if mozilla is your default browser). See the documentation of your Linux distribution for how to change default web browser. Alternatively, in HIPE choose Edit --> Preferences, go to Help & Documentation and enter the path to Firefox, or to another browser on your system, in the Browser field. Click Test to check if it works.

Revision 1502014-03-18 - AlvarGarcia

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  • The dialog box should show all lines which are going to be changed, but only the first line is shown there.
  • Some non-standard task calls, like using two = signs to put the result into two variables at once, are not detected.
Changed:
<
<

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on Mac OS

>
>

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on OS X

  Ticket number: HCSS-18891
Line: 177 to 177
 Error message: There is no error displayed and the pool is completely usable in HIPE 11.
Changed:
<
<
That's it! You should now be able to use your pool in any of the above cases. If you find you cannot, contact the Helpdesk.
>
>
That's it! You should now be able to use your pool in any of the above cases. If you find you cannot, contact the Helpdesk.
 
Tip, idea Note that the index files will not be backed up while you run rebuildIndex(), unless you invoke Configuration.setProperty("hcss.ia.pal.pool.lstore.index.backup", "true") first. For more information execute the following command: help('dag:sec-lstore-index-compatibility'). See the HIPE Owner's Guide: Section 4.
Line: 309 to 309
  The Web Start applications downloaded from the sites you add in this way will not be subject to security checks.
Changed:
<
<

Cannot find Java Runtime Environment (JRE) when launching external Web Start applications from HIPE on Mac OS

>
>

Cannot find Java Runtime Environment (JRE) when launching external Web Start applications from HIPE on Mac OS X

  Description: In certain combinations of Mac OS X 10.7 and Java 7, you might get an error message when trying to open the HSA user interface from HIPE. In that case, an error appears (see Error Message below) that states that there is no Java Runtime Environment installed. Even installing again, the HSA does not execute correctly.
Line: 326 to 326
 
  1. Completely remove java 7 from the system following the instructions in http://www.java.com/en/download/help/mac_uninstall_java.xml and http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-jdk.html
  2. Then reinstall the Java Developer Kit 7 (JDK) and Java Runtime Environment 7 from a Firefox browser following the instructions at http://www.java.com/en/download/help/mac_install.xml
Changed:
<
<

Java dialogue pops up after closing an external application launched from HIPE using Java Web Start on Mac OS

>
>

Java dialogue pops up after closing an external application launched from HIPE using Java Web Start on Mac OS X

  Description: When you close an external application opened from HIPE (like the Herschel Science Archive, VOSpec, Aladin, etc.), the dialogue in section "Error message" below pops up.
Line: 334 to 334
  Screen_Shot_2014-01-27_at_10.23.53.png
Changed:
<
<
Root cause: This is a known bug (although is not available at Oracle's bug database at the moment, it is in OpenJDK bug database) of Java on Mac OS that will be fixed in Java 7 Update 60. The error is apparently caused by the presence of an alternative JavaLaunchHelper implementation in a dynamic library (.dylib extension) provided by a third party and registered as a Safari browser plug-in.
>
>
Root cause: This is a known bug (although is not available at Oracle's bug database at the moment, it is in OpenJDK bug database) of Java on Mac OS X that will be fixed in Java 7 Update 60. The error is apparently caused by the presence of an alternative JavaLaunchHelper implementation in a dynamic library (.dylib extension) provided by a third party and registered as a Safari browser plug-in.
  Workaround: There is no workaround at the moment (see below in "Side effects") except waiting for the new update from Oracle.
Line: 359 to 359
  Side effects: The attempt to read this Registry key does not affect the behaviour of HIPE, since HIPE stores the user preferences in the CURRENT_USER hive of the Windows Registry.
Changed:
<
<

Crash when a HIPE session is left unattended for a long time with Java 7 on Mac OS, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

>
>

Crash when a HIPE session is left unattended for a long time with Java 7 on Mac OS X, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

  Configuration prone to cause the error
  • Operating system: Any version of Mac OS X.
Line: 394 to 394
 General information

If you are affected by this problem, it is useful to know that:

Changed:
<
<
  • This is a Mac OS problem, it does not affect any other operating system.
>
>
  • This is a Mac OS X problem, it does not affect any other operating system.
 

Workarounds

Line: 419 to 419
 

General Help System issues

Changed:
<
<

When Google Chrome is the default browser for Mac OS, the navigation arrows at the top of the help pages are not rendered

>
>

When Google Chrome is the default browser for Mac OS X, the navigation arrows at the top of the help pages are not rendered

  After repeated uses of the help pages for HIPE with Chrome, the images for the navigation arrow icons located in the header of the pages are (supposedly) retrieved from the browser cache but not rendered at all.
Line: 441 to 441
 
    • Clear the browser cache
    • Delete the browser cookies
    • Reboot the computer
Changed:
<
<
If none of the above works, please raise a ticket with the Helpdesk.
>
>
If none of the above works, please raise a ticket with the Helpdesk.
 

Is there a way to open the HIPE Help System without starting HIPE?

Line: 480 to 480
  Alternatively, you can click the envelope icon on the top toolbar of any help page. This opens a new message in your email client, where you can add your feedback.
Changed:
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<
If you want your issue to be officially tracked and supported, please raise a ticket with the Helpdesk of the Herschel Science Centre.
>
>
If you want your issue to be officially tracked and supported, please raise a ticket with the Helpdesk of the Herschel Science Centre.
 

Other help issues

Line: 541 to 541
  HIPE should now be able to read the file.
Changed:
<
<

Cannot run WebStart applications on Mac OS Lion or Mountain Lion because of security settings

>
>

Cannot run WebStart applications on Mac OS X Lion or Mountain Lion because of security settings

  WebStart applications that can be opened from within HIPE include the HSA User Interface, Aladin, VOSpec and so on. When trying to open one of such applications, a window like the following may appear:

topcat.png

Changed:
<
<
This is caused by the security settings of the Gatekeeper feature of Mac OS. For more information about Gatekeeper, see the Apple support website.
>
>
This is caused by the security settings of the Gatekeeper feature of Mac OS X. For more information about Gatekeeper, see the Apple support website.
  To allow a WebStart application that is blocked, change the Allow applications downloaded from option in Gatekeeper from Mac App Store to one of the two less restrictive options. If the application has a valid certificate, the Mac App Store and identified developers option will suffice. Otherwise you will need to select the Anywhere option.
Changed:
<
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Warning, important The Gatekeeper feature only handled Java applications for the Apple-specific version in older Mac OS (before Mac OS 10.7.2). The Java version from Oracle has a mechanism for validating publisher certificates completely independent from the operating system (see the related archived known issue for the HSA UI).
>
>
Warning, important The Gatekeeper feature only handled Java applications for the Apple-specific version in older Mac OS X (before Mac OS 10.7.2). The Java version from Oracle has a mechanism for validating publisher certificates completely independent from the operating system (see the related archived known issue for the HSA UI).
 

"Invalid context" errors on Mac OS X Lion

Revision 1492014-03-18 - AlvarGarcia

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Known issues in HIPE 12

Added:
>
>

computeVelocityTask plots absorption profiles as emission

Ticket number: HCSS-19133

Versions affected: HIPE 12.

Description: The computeVelocityTask in the Cube Analysis Toolbox returns and plots a fittedLineCube. This plot displays absorption profiles as emission, even if isEmission=False. The data returned is correct, but this plot must be disregarded.

Workaround: Simply disregard the plot generated by the task and trust the data stored in the fittedLineCube.

 

Limitations of the task for updating scripts that use the old syntax to access return parameters

Added:
>
>
Ticket number: HCSS-19080

Versions affected: HIPE 12.

 
  • Task calls spanning multiple lines (with \ separation) are not detected. Some SPIRE scripts use multiple line task call scripts.
  • The dialog box should show all lines which are going to be changed, but only the first line is shown there.
  • Some non-standard task calls, like using two = signs to put the result into two variables at once, are not detected.

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on Mac OS

Added:
>
>
Ticket number: HCSS-18891
 Versions affected: HIPE 12.
Changed:
<
<
Error:
>
>
Error message:
 
$ ./hcss.dp.pacs-12.0.1553/bin/hipe
#

Revision 1482014-03-18 - AlvarGarcia

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Java 7 issues

Added:
>
>

In a Windows domain-joined computer (or with special folder redirection for user profiles) Java can be unable to write to the user home directory

Description: When executing HIPE in the context of a user that has redirected shell folders, environment variables in the Desktop path in the Registry or doesn't have a roaming profile for the domain, the Java VM cannot determine the working directory for the user or, as it is called in Windows parlance, "home path". Instead, it uses the "user profile" directory, which can be shared between several users, be read-only or even can be unresolvable for Java because it contains environment variables. In those cases, writing to this home directory (in Java terms "user.home") can fail with an error message like the one shown below.

Error message: HIPE writes a WARNING message when Java is unable to resolve the correct home directory for the user. Other error messages can be displayed and they are related to HIPE-managed pools like MyHSA, preferences, automatic backup files or anything that it is written automatically to the .hcss directory inside the home dir.

18-Mar-14 11:41:16.968 WARNING LogView : Could not log to file:
java.io.IOException: Couldn't get lock for C:\Users\wrongdir\.hcss\apps\hipe\logs\hipe_user_20140318_114116.log
       at java.util.logging.FileHandler.openFiles(Unknown Source)
       at java.util.logging.FileHandler.(Unknown Source)
       at herschel.ia.jconsole.views.LogView.(LogView.java:119)
       at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
       at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
       at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
       at java.lang.reflect.Constructor.newInstance(Unknown Source)
       at java.lang.Class.newInstance(Unknown Source)
       at herschel.share.util.ObjectUtil.newInstance(ObjectUtil.java:153)
wrongdir is the directory that Java has retrieved using the faulty algorithm described below. user is the Windows username of the current user. In a "normal" set-up, these two strings should match.

Root cause: Due to a bug in Java, probably present since the first version, the Virtual Machine uses a non-supported method for determining the user home directory (which is retrieving a well known path from the Registry: the Desktop path, and considering the base directory as home directory). This usually works for single user, or multiple user computers which are not joined to a Windows domain, but causes errors if the computer is domain-joined, has special configuration for the redirection (symbolic links) of user directories or any other non-standard configuration related to user profiles.

Workaround: If the special folder redirection is not applied using group policies but it is a persistent change of configuration (perhaps added to the system image used to install Windows), you can change the path of the value Desktop to a user-writable directory. This value is inside the following Registry key:

HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders

NOTE: Please take care editing the Windows Registry and be sure to follow the Microsoft recommended procedure.

 

Application blocked by security settings when trying to launch external Web Start applications that lack the proper publisher certificate (e.g. Aladin)

Description: As part of the security overhaul for the latest versions of Java 7, Oracle has also introduced a mechanism in which Web Start applications that are not signed with the proper publisher certificate or are self-signed are blocked. See the screenshot below in Error message.

Revision 1472014-03-17 - JeroenDeJong

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Limitations of the task for updating scripts that use the old syntax to access return parameters

Added:
>
>
  • Task calls spanning multiple lines (with \ separation) are not detected. Some SPIRE scripts use multiple line task call scripts.
  • The dialog box should show all lines which are going to be changed, but only the first line is shown there.
  • Some non-standard task calls, like using two = signs to put the result into two variables at once, are not detected.
 

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on Mac OS

Versions affected: HIPE 12.

Revision 1462014-03-14 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
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<-- Google Analytics script END -->
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Known issues in HIPE 12

Added:
>
>

Limitations of the task for updating scripts that use the old syntax to access return parameters

 

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on Mac OS

Versions affected: HIPE 12.

Revision 1452014-02-26 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
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<-- Google Analytics script END -->
Line: 381 to 381
 If not, you have probably encountered a bug. The following are known issues that can prevent you from viewing the documentation, resulting either in a blank page or an error message:

  • A caching bug in Safari 4.0 can be solved by clearing the browser cache. Alternatively, open the help page with another web browser: copy and paste the address (something like http://127.0.0.1:8082/index.jsp?mark=null) to the address bar of the other browser.
Changed:
<
<
  • A problem with Mac OS X can result in error messages when viewing the documentation of any installed HIPE version. In particular, you may get an HTTP ERROR: 404 NOT FOUND message in your browser, and a message about index.jsp not found in the command line terminal. Rebooting the computer solves the issue.
>
>
  • A problem with Mac OS X can result in error messages when viewing the documentation of any installed HIPE version. In particular, you may get an HTTP ERROR: 404 NOT FOUND message in your browser, and a message about index.jsp not found in the command line terminal. There are two options to solve the problem:
    • Delete the temporary directory created by the help system in /private/var/folders/[1]/[2]/T/yahajs_[username]_[HIPE version]/jetty/instance_[instance number]/webapp (the first ellipsis [1] is a pair of alphanumeric characters and the second [2] is a string of 30 alphanumeric characters).
    • If the previous solution does not work, please try rebooting the computer.
 
  • Older browser versions may not display documentation correctly. For example, links from HIPE to the Help System, like the Help in URM menu entries for tasks, work in Firefox 3.6.x but not in Firefox 3.0.x. Other legacy browsers may have similar problems.
  • If you are using Linux and get an error message like Firefox can not contact the server www.%u.com, change your default browser from firefox %u to firefox %s (same if mozilla is your default browser). See the documentation of your Linux distribution for how to change default web browser. Alternatively, in HIPE choose Edit --> Preferences, go to Help & Documentation and enter the path to Firefox, or to another browser on your system, in the Browser field. Click Test to check if it works.
  • In general, when you encounter a problem with the Help System you should follow these steps:

Revision 1442014-02-14 - AlvarGarcia

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META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
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Java 7 issues

Added:
>
>

Application blocked by security settings when trying to launch external Web Start applications that lack the proper publisher certificate (e.g. Aladin)

Description: As part of the security overhaul for the latest versions of Java 7, Oracle has also introduced a mechanism in which Web Start applications that are not signed with the proper publisher certificate or are self-signed are blocked. See the screenshot below in Error message.

Error message: When sending images to Aladin (which currently is self-signed), the following modal dialogue appears:

Screen_Shot_2014-01-22_at_11.09.14_AM.png

Workaround: General instructions on how to override the security mechanisms set in place by Oracle in the latest versions of the JRE are described here. Our recommendation is that you add the site from which the .jnlp file of Aladin is downloaded to the Java Exception Site List. These are the steps:

  • Open the Java Control Panel (inside Control Panel in Windows, inside System Preferences in OS X, depends on the distribution in Linux).
  • Click on the Security tab.
  • Inside the Exception Site List panel, click on the Edit Site List... button.
  • Click Add in the dialogue that opens.
  • Enter the root URI for the Aladin site (http://aladin.u-strasbg.fr).
  • An alert is displayed telling you that trusting HTTP sites is a security risk. Please click Continue to acknowledge the alert and complete the addition.

The Web Start applications downloaded from the sites you add in this way will not be subject to security checks.

 

Cannot find Java Runtime Environment (JRE) when launching external Web Start applications from HIPE on Mac OS

Description: In certain combinations of Mac OS X 10.7 and Java 7, you might get an error message when trying to open the HSA user interface from HIPE. In that case, an error appears (see Error Message below) that states that there is no Java Runtime Environment installed. Even installing again, the HSA does not execute correctly.

Line: 569 to 587
 
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 WebStart message" date="1390828055" name="Screen_Shot_2014-01-27_at_10.23.53.png" path="Screen_Shot_2014-01-27_at_10.23.53.png" size="33867" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 update 45 font issue" date="1385024831" name="java7u45-font-issue.png" path="java7u45-font-issue.png" size="11541" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 self-signed WS applications" date="1392367563" name="Screen_Shot_2014-01-22_at_11.09.14_AM.png" path="Screen_Shot_2014-01-22_at_11.09.14_AM.png" size="29650" user="Main.AlvarGarcia" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"

Revision 1432014-02-05 - AlvarGarcia

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<-- Google Analytics script END -->
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hcss.ia.pal.pool.lstore.lock = simple
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See the HIPE Owner's Guide for information on how to set properties.
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See the HIPE Owner's Guide for information on how to set properties.
 

Why do I get a ClassCastException when trying to save an observation with the saveObservation command?

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There are PACS files I cannot delete! Why?

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It might not be possible to delete the following files on Windows because their full path exceeds the 260 characters limit.
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It might not be possible to delete the following files on Windows because their full path exceeds the 260 characters limit. This is caused by a limitation in Windows Explorer and the Command Prompt to maintain backwards compatibility (even if the operating system supports longer file paths).
 
  • PCalSpectrometer_RelCalSourceFlux_FM_v1.fits_2009...80Z.fits
  • PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...55Z.fits
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  You can avoid this problem by installing HIPE with a short initial path, such as C:\hipe, so that full paths remain below the limit.
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If you already have several files with long paths that you wish to delete, you can delete them from the Command Prompt (CMD.EXE) prepending the path with \\?\. For example for deleting C:\too\long\path\fitsfilename.fits you should write:
C:\>del \\?\C:\too\long\path\fitsfilename.fits
and press Enter.
 

HIPE does not accept keyboard input anymore! What's wrong?

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If you are running Linux, this could be due to a compatibility problem between Java and SCIM (Smart Common Input Method). A workaround is to stop SCIM or uninstall it. Please refer to the documentation of your distribution for how to do so.
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If you are running Linux, this could be due to a compatibility problem between Java and the input method in use, like IBus or SCIM (Smart Common Input Method). A workaround is to stop the service of the input method or uninstall it. Please refer to the documentation of your distribution for how to do so.
  The problem is described in more detail on these pages:

Revision 1422014-02-04 - AlvarGarcia

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 These errors are harmless and can be safely ignored.
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"Can't connect to X11" error when using the jylaunch command

Executing a script outside HIPE with the jylaunch command may fail with a java.lang.InternalError: Can't connect to X11 window server error. This may happen even if the script does not open any graphical window, since it may indirectly call components that require an X11 server. The workaround is to run the script with the command jylaunch -Djava.awt.headless=true instead of just jylaunch.

 

Problems saving observations to NFS-mounted disks and FAT32 disks

When saving observation to your computer, you may experience problems in the following cases:

Revision 1412014-02-04 - AlvarGarcia

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  To allow a WebStart application that is blocked, change the Allow applications downloaded from option in Gatekeeper from Mac App Store to one of the two less restrictive options. If the application has a valid certificate, the Mac App Store and identified developers option will suffice. Otherwise you will need to select the Anywhere option.
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Warning, important The Gatekeeper feature only handled Java applications for the Apple-specific version in older Mac OS (before Mac OS 10.7.2). The Java version from Oracle has a mechanism for validating publisher certificates completely independent from the operating system (see the related archived known issue for the HSA UI).
 

"Invalid context" errors on Mac OS X Lion

When you start HIPE form a Terminal window on Mac OS X Lion, you may see errors such as these:

Line: 491 to 493
  These errors are harmless and can be safely ignored.
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Jython bug when comparing NaN values with numbers

Jython behaves differently from Python when comparing NaN values with numbers.

In Python 2.4 or 2.5:

nan = float("nan")
print 0 < nan
# False
print 0 > nan
# False

In Jython 2.5.2:

nan = float("nan")
print 0 < nan
# False
print 0 > nan
# True
 
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An issue has been opened on the Jython bug tracker.
 

"Can't connect to X11" error when using the jylaunch command

Revision 1402014-02-04 - AlvarGarcia

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How to log in with new credentials after changing the password for HSA I have changed/reset the password of the account I use to access Herschel Science Archive, but HIPE still tells me I am logged in (with the old password), even after restarting HIPE. How do I log in with the new password?

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HIPE stores your HSA password for you if you log in and check the "Remember Me" checkbox. If you restart you can access the HSA without having to enter your info again.
>
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Description: HIPE stores your HSA password for you if you log in and check the "Remember Me" checkbox. If you restart you can access the HSA without having to enter your info again.
  However, if you reset your password using the Automated user Password Fixer, and restart HIPE, then HIPE will still report you as being logged in, even though you can't be, because you haven't told HIPE your new password yet.
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To work around the situation, double-click on your username in the HIPE status bar at the bottom of the window to log out explicitly. (If you are not logged in, the status bar will show a label "HSA Log-in" and you don't need to do anything).
>
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Versions affected: HIPE 11 or earlier.

Ticket number: HCSS-17907

Workaround: To work around the situation, double-click on your username in the HIPE status bar at the bottom of the window to log out explicitly. (If you are not logged in, the status bar will show a label "HSA Log-in" and you don't need to do anything).

  After this, you can double-click again to log in again, using the correct password, or you can wait until HIPE prompts you to log in.
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  If you are using Windows, the problem might be that you instructed your browser to auto-detect proxy settings. In Windows this is a system-wide setting which affects any application connecting to the Internet, including HIPE.
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You can change proxy settings for HIPE by following the instructions in the HIPE Owner's Guide.
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You can change proxy settings for HIPE by following the instructions in the HIPE Owner's Guide.
 

When I click Send to external Application in the HSA interface, nothing seems to happen. What is going on?

Revision 1392014-02-04 - AlvarGarcia

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ALERT! This page is for known issues in the HIPE software. For known issues in data products see this page.
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ALERT! These known issues happen in the latest versions of HIPE and its dependent software (for example, Java 6/7). Any issue that is resolved with an update to the operational version of HIPE or Java, is listed on this page
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ALERT! These known issues happen in the latest versions of HIPE and its dependent software (for example, Java 6/7). Any issue that is resolved with an update to the operational version of HIPE or Java, is listed on this page.
 
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Installation and de-installation issues

Installer or start-up hang on Mac OSX and Java 1.6.0_51

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Ticket number: HCSS-18288
 
    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
    • How to fix: Users need to manually download and install the Java update.
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HIPE cannot start: SAXNotRecognizedException

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Ticket number: HCSS-7112
 The terminal/command window from which you invoke HIPE shows a SAXNotRecognizedException.

To solve this issue, add the following line to the installed.properties file in your HIPE installation directory:

Line: 215 to 220
 

HIPE cannot start: exception access violation.

Added:
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Ticket number: HCSS-7139
 The terminal/command window from which you invoke HIPE shows an EXCEPTION_ACCESS_VIOLATION error related to a class in org.apache.xerces.

Restart HIPE to resolve the issue.

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Warning appears in the console when running HIPE with a user that is not administrator in Windows 8 and later

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Ticket number: HCSS-18807
 Error message: This appears in a Command Prompt when starting HIPE.
WARNING WindowsPreferences <init>: Could not open/create
Line: 282 to 291
  Side effects: The attempt to read this Registry key does not affect the behaviour of HIPE, since HIPE stores the user preferences in the CURRENT_USER hive of the Windows Registry.
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Crash when a HIPE session is left unattended for a long time in Mac OS with Java 7, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

>
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Crash when a HIPE session is left unattended for a long time with Java 7 on Mac OS, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

  Configuration prone to cause the error
  • Operating system: Any version of Mac OS X.
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Cursor position in the editor view is inaccurate in high-DPI (Retina) displays when using latest Java 7 version (45)

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Ticket number: HCSS-18698
 The cursor position appears inside characters instead of between them.

java7u45-font-issue.png

Revision 1382014-02-04 - AlvarGarcia

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ALERT! This page is for known issues in the HIPE software. For known issues in data products see this page.
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ALERT! These known issues happen in the latest versions of HIPE and its dependent software (for example, Java 6/7). Any issue that is resolved with an update to the operational version of HIPE or Java, is listed on this page
 

Please note that some issues detected in previous versions may still be present in HIPE 11. Scroll down and check earlier versions if you do not see your particular issue listed for HIPE 11.

Revision 1372014-02-03 - AlvarGarcia

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  Side effect: This message does not actually indicate an error, as the external application was correctly launched, used and closed. The modal dialogue is displayed because HIPE gathers any console (error) output when the external application is executing and displays it in a modal dialogue when it is closed.
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New security requirement in Java 7 causes the Herschel Science Archive application to fail at launch

 
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Description: If you have a recently patched Java 7 installation (update 40 or later), a new security requirement in Java 7 that requires the JAR file to have a Permissions attribute, is no longer reported only (note the information message with a yellow background) as it was in previous versions:

Screen_Shot_2014-01-16_at_16.28.23.png

Now the Java runtime blocks the JAR file execution when you click the Run button.

Error message: The following error dialogs are displayed when trying to run the HSA application and clicking the Details button: Screen_Shot_2014-01-16_at_16.29.26.png

Workaround: Please follow the instructions provided by Oracle to run applications that lack the currently enforced security features.

 

Warning appears in the console when running HIPE with a user that is not administrator in Windows 8 and later

Revision 1362014-02-03 - AlvarGarcia

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Installation and de-installation issues

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Installer or start-up hang on Mac OSX and Java 1.6.0_51

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    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
>
>
    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
 
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
    • How to fix: Users need to manually download and install the Java update.
    • Apple support notes that "This update corrects an issue with Java applications failing to draw or respond to user input."
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Cannot install on Mac OS X 10.8 "Mountain Lion"

HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
  • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
  • In Mac OS X, from System Preferences --> Security & Privacy --> General --> Allow applications downloads from select ANYWHERE.
 

The installer for Mac complains about write permissions. Why?

You need write permissions fo r the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.

The installer for Windows does not start and issues the error message Not a valid Win32 application. Why?

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  Could not create the Java virtual machine.
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This error typically happens because you have either set or have as default a too large memory for the Java Virtual Machine and hence it cannot start. Edit the file called "installed.properties" under your hipe_v11_RC2 i(or alternative directory, as appropriate) installation directory and edit the line
>
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This error typically happens because you have either set or have as default a too large memory for the Java Virtual Machine and hence it cannot start. Edit the file called "installed.properties" under your hipe_v11_RC2 (or alternative directory, as appropriate) installation directory and edit the line
  java.vm.memory.max=2872m
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Known issues in HIPE 12

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Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash

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Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash on Mac OS

  Versions affected: HIPE 12.
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General HIPE startup issues

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When Google Chrome is the default browser for Mac OS, the navigation arrows at the top of the help pages are not rendered

After repeated uses of the help pages for HIPE with Chrome, the images for the navigation arrow icons located in the header of the pages are (supposedly) retrieved from the browser cache but not rendered at all.

Workaround: The current workaround for this behaviour is to clear Google Chrome's cache, following these instructions.

 

HIPE does not start at all, without giving error messages. What's wrong?

This can happen for different reasons, that are explored in the next entries. When you start HIPE by clicking on its icon and a problem occurs, you may only see a terminal/command window appear for a fraction of a second, leaving you without information on the error.

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General Help System issues

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When Google Chrome is the default browser for Mac OS, the navigation arrows at the top of the help pages are not rendered

After repeated uses of the help pages for HIPE with Chrome, the images for the navigation arrow icons located in the header of the pages are (supposedly) retrieved from the browser cache but not rendered at all.

Workaround: The current workaround for this behaviour is to clear Google Chrome's cache, following these instructions.

 

The help does not work anymore! What's wrong?

First, check if your issue is that described below, in Why is the HIPE Help System suddenly unable to connect to any help page?

Revision 1352014-02-03 - AlvarGarcia

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<-- ANALYTICS CODE - DO NOT EDIT -->
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  Description: In certain combinations of Mac OS X 10.7 and Java 7, you might get an error message when trying to open the HSA user interface from HIPE. In that case, an error appears (see Error Message below) that states that there is no Java Runtime Environment installed. Even installing again, the HSA does not execute correctly.
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Ticket number: HCSS-18932
 Error message: The error displayed is similar to this screenshot:

Screen_Shot_2014-01-15_at_12.19.51_PM.png

Revision 1342014-01-31 - AlvarGarcia

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Installation and de-installation issues

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There is a known problem with the InstallAnywhere installer when the bash \u special character is present in some environment variables

Versions affected: HIPE 9, 10, 11.
 
Deleted:
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Error message: Installation fails with any of the following errors:

"Configuring the installer for this system's environment...

strings: '/lib/libc.so.6': No such file"
Or
An internal LaunchAnywhere application error has occured and this application cannot proceed. (LAX)

Stack Trace:
java.lang.IllegalArgumentException: Malformed \uxxxx encoding.
at java.util.Properties.loadConvert(Unknown Source)
at java.util.Properties.load0(Unknown Source)
at java.util.Properties.load(Unknown Source)
at com.zerog.common.java.util.PropertiesUtil.loadProperties(Unknown Source)
at com.zerog.lax.LAX.<init>(Unknown Source)
at com.zerog.lax.LAX.main(Unknown Source)

Solution: Un-setting or substituting the /u bash special character (using instead $USER or $LOGNAME) in the PS1 environment variable solves the problem. To do that, you should edit the .bashrc file located at the home directory of the current user. In there, any occurrence of the \u special character should be replaced by $USER or $LOGNAME. Example:

PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
should be replaced by
PS1='${debian_chroot:+($debian_chroot)}$USER@\h:\w\$ '

Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941

 

Installer or start-up hang on Mac OSX and Java 1.6.0_51

Revision 1332014-01-31 - AlvarGarcia

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Please note that some issues detected in previous versions may still be present in HIPE 10. Scroll down and check earlier versions if you do not see your particular issue listed for HIPE 10.
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Please note that some issues detected in previous versions may still be present in HIPE 11. Scroll down and check earlier versions if you do not see your particular issue listed for HIPE 11.
 

Installation and de-installation issues

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When installing only HIFI or PACS modules in HIPE you cannot transfer products from HSA to HIPE

    • Versions affected: HIPE 11.
    • Solution: The current workaround is to install all modules even if you are not going to use them.
 

There is a known problem with the InstallAnywhere installer when the bash \u special character is present in some environment variables

Versions affected: HIPE 9, 10, 11.
Line: 200 to 196
 
Tip, idea Note that the index files will not be backed up while you run rebuildIndex(), unless you invoke Configuration.setProperty("hcss.ia.pal.pool.lstore.index.backup", "true") first. For more information execute the following command: help('dag:sec-lstore-index-compatibility'). See the HIPE Owner's Guide: Section 4.
Deleted:
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Known issues in HIPE 10.3

Problems seeing PACS error maps

This problem, reported in 10.3, but previously present too, is caused by the history dataset which is "hiding" the error. To resolve it, after running photCoverage2Noise task, give these commands:

history = image["History"]

image.remove("History")

image["History"] = history

Where the "image" is the product that you have been working on. This will append the history dataset at the end of the product and "solve" the problem. There will be a fix in place for this issue in HIPE 11.

Known issues in HIPE 10.2

None known in addition to those listed for HIPE 10.1.

Known issues in HIPE 10.1

Problems with the aberration correction for Solar System Objects in HIFI

There is a previously existing issue that has become important in some cases when processing Solar System Object observations in HIPE that affects all Level 2.5 HIFI map products. Ephemeris positions are calculated (and stored in the ra_centre/dec_centre columns) with a spurious correction for stellar aberration. This is being fixed but, until patched, the recommended doOffset approach to translate Level 2 coordinates to a co-moving frame (see the corresponding known issue below on this issue in HIPE 10.0) will lead to coordinate offsets that are off by ~10" on average (depending on the relative velocity between target and Herschel at observation time).

This is being fixed in HIPE 12 and it is expected that a patch will be made for HIPE 11 and, possibly, also patched in later releases of HIPE 10.

Known issues in HIPE 10.0

Can't open plug-ins panel under KDE or Gnome 3

The Plug-ins panel cannot be opened (from the Tools menu) if you're working under Linux and you don't have the Gnome 2 library installed. Gnome 2 is a desktop environment, and typically if you use a different desktop environment (Gnome 3, KDE, Unity, etc), then you will not have this library.

In both cases, the problem can be solved by installing the Gnome 2 library. For example on Ubuntu (or Kubuntu), the command is:

sudo apt-get install libgnome2-0

A patch is planned for this issue in HIPE 10.2.

Clicking on the 'plug-in' button to add the cassis plugin, nothing happens and you see multiple java exceptions

The "Desktop API", which is used to access the browser when you click "Find more.." button in the HIPE plugin dialogue, is not supported on KDE. It "was designed to work on Windows and Gnome". However, you can also open it directly by pointing your browser directly to http://herschel.esac.esa.int/twiki/bin/view/Public/DpHipePlugins, and copying the URL to the respective .jar files for the particular plugin you are interested in and pasting it in the HIPE plugins dialog to install it.

If you would like to have the "Find more.." button working, all you need is to have the Gnome libraries installed.

Some instructions: - To install Gnome 3 libraries on Ubuntu (http://www.filiwiese.com/installing-gnome-on-ubuntu-12-04-precise-pangolin/). Note that if you're using version 11.10 or later, you probably don't need the first command (sudo apt-add-repository ...). I would just skip it and if the last command does not complain about "package not found" or something similar, then all is well. - To install Gnome 2 libraries on Ubuntu: http://askubuntu.com/questions/123690/how-to-install-gnome2-on-ubuntu-11-10

A patch is planned for this issue in HIPE 10.2.

Pools unreadable with Unknown format version: -11 error

If you installed a developer build of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools you will find those pools are no longer readable in any other HIPE version; when trying to load a pool with getObservation you will get the following error message:

herschel.ia.task.TaskException: Error processing getObservation task: Unknown format version: -11

See the Data Analysis Guide for a recovery procedure. You can download from this page the first and second script mentioned in the procedure. Change the extension from .py.txt to .py after downloading.

The WCS explorer for cubes does not work with PACS and SPIRE cubes

The WCS explorer does not work on cubes for which ImageIndex is used to specify the wavescale axis. This is true for SPIRE and PACS cubes. If crpix3, crval3 and cdelt3 are used instead, the WCS explorer works. To be fixed in HIPE 11.

Issues with reading text files from SExtractor or Topcat

While reading files from SExtractor or Topcat you may encounter the following issues:

  • Some SExtractor headers are not read successfully, due to an issue with the column position of units in the file header. Workaround: read the file with the tableType parameter set to SPACES. You can then fill any missing information by hand.
  • Some Topcat files are not read successfully, due to an issue with quoted cells with spaces. Workaround: export the data from Topcat in FITS format, then read the FITS file back into HIPE. For information about reading FITS files into HIPE, see the Data Analysis Guide.

Format change for exported variables

The file format of variables exported with File --> Session --> Export has changed in HIPE 10. This means that HIPE 10 will not be able to read session variables exported with HIPE 9, and vice-versa.
If you exported variables with HIPE 9 or a previous version, follow this workaround to read them in HIPE 10:

  1. Open HIPE 9 and import the exported variables with File --> Session --> Import.
  2. Set Save variables on exit in the Preferences dialogue window, under General --> Startup & Shutdown.
  3. Exit HIPE 9.
  4. Open HIPE 10. The variables shall be restored in the Variables view.
  5. Export the variables with the new format of HIPE 10, with File --> Session --> Export.

HIPE cannot send data to an external application via SAMP

When you try to send data to an external application via the SAMP Virtual Observatory protocol, the following window may appear:

vospec.png

The reason is that HIPE tries to send data before the external application has initialised properly. This issue seems to occur more frequently with VOSpec.

The solution is to send the data again without closing the external application.

Separate, undocked instances Cube Toolbox talk to each other

If you have two or more separate Spectrum Explorer GUIs open and at least one is undocked, when using its Cube Toolbox the separate SE instances talk to each other--spectra or new cubes you create in one instance will also appear in the other one.

New PACS calibration version 45 should not be used with HIPE 10

In HIPE 10 a new spectroscopy telescope background calibration was introduced. This update is not compatible with the code in HIPE 9.

You can alway check the calibration version that you are using with the following command:

print getCalTree().version

If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.

Generating a co-moving frame for HIFI mapping observations of solar system objects

There is a task in HIPE that allows you to transform level-2 coordinates into a coordinate system co-moving with the target ephemeris. That task is called doOffset,

http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#hifi_um:hdrg_offsetposn_use

A typical code snippet would be:

comet = getObservation(1342227173, useHsa=True)

htp=comet.refs["level2"].product.refs["WBS-H-USB"].product # extract USB, pol H

htp2=doOffset(htp=htp, overwrite=0, relative=1) # make coordinates relative to ephemeris

HiClassTask()(product=htp2, fileName='cometHUSB_relativeCoords.fits') # export in CLASS-readable format

However, the target ephemeris inside HIPE doesn't get updated. I.e., doOffset uses the ephemeris current as of observation uplink to the spacecraft. Work is in progress to automatically update target ephemerids. If your target ephemeris was very uncertain at observation time (and if it has improved since), then you may be better off using a manual approach of downloading the Horizons ephemeris for each target.

Printing a HIPE script to a file in Snowleopard sends the job to a printer instead

 
Deleted:
<
<
When a user tries to print a script to a file on disk, HIPE sends it to the printer instead. A patch will be issued for this problem in HIPE 11 and a definitive fix included in HIPE 12.
 

Older HIPE versions

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Java 7 issues

Changed:
<
<

Java plug-in installation is ambiguous and Web Start applications (such as the Herschel Science Archive) cannot run on Mac OS

>
>

Cannot find Java Runtime Environment (JRE) when launching external Web Start applications from HIPE on Mac OS

  Description: In certain combinations of Mac OS X 10.7 and Java 7, you might get an error message when trying to open the HSA user interface from HIPE. In that case, an error appears (see Error Message below) that states that there is no Java Runtime Environment installed. Even installing again, the HSA does not execute correctly.

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Java 7 issues

Changed:
<
<

Java dialogue pops up after closing an external application launched from HIPE using Java WebStart on Mac OS

>
>

Java plug-in installation is ambiguous and Web Start applications (such as the Herschel Science Archive) cannot run on Mac OS

Description: In certain combinations of Mac OS X 10.7 and Java 7, you might get an error message when trying to open the HSA user interface from HIPE. In that case, an error appears (see Error Message below) that states that there is no Java Runtime Environment installed. Even installing again, the HSA does not execute correctly.

Error message: The error displayed is similar to this screenshot:

Screen_Shot_2014-01-15_at_12.19.51_PM.png

Root cause: This error is due to a change in the repository directory for the Java Runtime Environment and the Java Developer Kit distributions from previous versions. References to older versions of the plug-in are kept in the system and conflict when launching Java Web Start applications. This issue is related to the one below.

Workaround: The simple workaround is to:

  1. Completely remove java 7 from the system following the instructions in http://www.java.com/en/download/help/mac_uninstall_java.xml and http://docs.oracle.com/javase/7/docs/webnotes/install/mac/mac-jdk.html
  2. Then reinstall the Java Developer Kit 7 (JDK) and Java Runtime Environment 7 from a Firefox browser following the instructions at http://www.java.com/en/download/help/mac_install.xml

Java dialogue pops up after closing an external application launched from HIPE using Java Web Start on Mac OS

  Description: When you close an external application opened from HIPE (like the Herschel Science Archive, VOSpec, Aladin, etc.), the dialogue in section "Error message" below pops up.
Line: 740 to 755
 
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 Permissions error dialog" date="1389953004" name="Screen_Shot_2014-01-16_at_16.29.26.png" path="Screen_Shot_2014-01-16_at_16.29.26.png" size="91428" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 corrupted installation" date="1391078835" name="Screen_Shot_2014-01-15_at_12.19.51_PM.png" path="Screen_Shot_2014-01-15_at_12.19.51_PM.png" size="289109" user="Main.AlvarGarcia" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 WebStart message" date="1390828055" name="Screen_Shot_2014-01-27_at_10.23.53.png" path="Screen_Shot_2014-01-27_at_10.23.53.png" size="33867" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 update 45 font issue" date="1385024831" name="java7u45-font-issue.png" path="java7u45-font-issue.png" size="11541" user="Main.AlvarGarcia" version="1"

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Java 7 issues

Added:
>
>

Java dialogue pops up after closing an external application launched from HIPE using Java WebStart on Mac OS

Description: When you close an external application opened from HIPE (like the Herschel Science Archive, VOSpec, Aladin, etc.), the dialogue in section "Error message" below pops up.

Error message: The following modal dialogue is displayed after closing the external application:

Screen_Shot_2014-01-27_at_10.23.53.png

Root cause: This is a known bug (although is not available at Oracle's bug database at the moment, it is in OpenJDK bug database) of Java on Mac OS that will be fixed in Java 7 Update 60. The error is apparently caused by the presence of an alternative JavaLaunchHelper implementation in a dynamic library (.dylib extension) provided by a third party and registered as a Safari browser plug-in.

Workaround: There is no workaround at the moment (see below in "Side effects") except waiting for the new update from Oracle.

Side effect: This message does not actually indicate an error, as the external application was correctly launched, used and closed. The modal dialogue is displayed because HIPE gathers any console (error) output when the external application is executing and displays it in a modal dialogue when it is closed.

 

New security requirement in Java 7 causes the Herschel Science Archive application to fail at launch

Description: If you have a recently patched Java 7 installation (update 40 or later), a new security requirement in Java 7 that requires the JAR file to have a Permissions attribute, is no longer reported only (note the information message with a yellow background) as it was in previous versions:

Line: 727 to 741
 
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 Permissions error dialog" date="1389953004" name="Screen_Shot_2014-01-16_at_16.29.26.png" path="Screen_Shot_2014-01-16_at_16.29.26.png" size="91428" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" user="Main.DavideRizzo" version="1"
Added:
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META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 WebStart message" date="1390828055" name="Screen_Shot_2014-01-27_at_10.23.53.png" path="Screen_Shot_2014-01-27_at_10.23.53.png" size="33867" user="Main.AlvarGarcia" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 update 45 font issue" date="1385024831" name="java7u45-font-issue.png" path="java7u45-font-issue.png" size="11541" user="Main.AlvarGarcia" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"

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Java 7 issues

Added:
>
>

New security requirement in Java 7 causes the Herschel Science Archive application to fail at launch

Description: If you have a recently patched Java 7 installation (update 40 or later), a new security requirement in Java 7 that requires the JAR file to have a Permissions attribute, is no longer reported only (note the information message with a yellow background) as it was in previous versions:

Screen_Shot_2014-01-16_at_16.28.23.png

Now the Java runtime blocks the JAR file execution when you click the Run button.

Error message: The following error dialogs are displayed when trying to run the HSA application and clicking the Details button: Screen_Shot_2014-01-16_at_16.29.26.png

Workaround: Please follow the instructions provided by Oracle to run applications that lack the currently enforced security features.

 

Warning appears in the console when running HIPE with a user that is not administrator in Windows 8 and later

Error message: This appears in a Command Prompt when starting HIPE.

Line: 708 to 721
 You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 Permissions security feature" date="1389952811" name="Screen_Shot_2014-01-16_at_16.28.23.png" path="Screen_Shot_2014-01-16_at_16.28.23.png" size="49454" user="Main.AlvarGarcia" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Error message when sending data to VOSpec" date="1358258421" name="vospec.png" path="vospec.png" size="12133" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
Added:
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META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 Permissions error dialog" date="1389953004" name="Screen_Shot_2014-01-16_at_16.29.26.png" path="Screen_Shot_2014-01-16_at_16.29.26.png" size="91428" user="Main.AlvarGarcia" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 update 45 font issue" date="1385024831" name="java7u45-font-issue.png" path="java7u45-font-issue.png" size="11541" user="Main.AlvarGarcia" version="1"

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Java 7 issues

Added:
>
>

Warning appears in the console when running HIPE with a user that is not administrator in Windows 8 and later

Error message: This appears in a Command Prompt when starting HIPE.

WARNING WindowsPreferences <init>: Could not open/create
prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKey
Ex(...) returned error code 5.

Root cause: In a Windows installation with Java 7 version 21 or later, the Windows Preferences classes in Oracle's JVM try to read from the Windows Registry key: HKEY_LOCAL_MACHINE\Software\JavaSoft\Prefs . Since the key has not been created by the Java installer (as was the case in previous versions of Java), these classes try to create them and fail due to insufficient privileges. This is displayed on the Java console as seen above in the warning message.

Workaround: This warning message can be safely ignored. But if you want to remove it completely the easiest workaround is starting HIPE at least once as administrator.

Side effects: The attempt to read this Registry key does not affect the behaviour of HIPE, since HIPE stores the user preferences in the CURRENT_USER hive of the Windows Registry.

 

Crash when a HIPE session is left unattended for a long time in Mac OS with Java 7, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

Configuration prone to cause the error

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 to have a smaller value than 1500m and smaller than the RAM memory of your machine.

For other issues affecting the installer, check this page.

Added:
>
>

Known issues in HIPE 12

Old Java 6 entries in the dynamic library environment variable cause HIPE 12 to crash

Versions affected: HIPE 12.

Error:

$ ./hcss.dp.pacs-12.0.1553/bin/hipe
#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x000000010794f647, pid=49119, tid=6403
#
# JRE version: Java(TM) SE Runtime Environment (7.0_45-b18) (build 1.7.0_45-b18)
# Java VM: Java HotSpot(TM) 64-Bit Server VM (24.45-b08 mixed mode bsd-amd64 compressed oops)
# Problematic frame:
# C  [libjvmlinkage.dylib+0x3647]  JVM_GetClassCPEntriesCount+0x17
#
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
#
# An error report file with more information is saved as:
# /Users/USER/hcss/hcss.dp.pacs-12.0.2340/bin/hs_err_pid49119.log
#
# If you would like to submit a bug report, please visit:
#   http://bugreport.sun.com/bugreport/crash.jsp
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.
#

Root cause: The cause is that the shared library path has references to the old Java 6 installation.

$ env | grep DYLD_LIBRARY_PATH
DYLD_LIBRARY_PATH=:/Applications/MATLAB/MATLAB_Compiler_Runtime/v716/runtime/maci64:
/Applications/MATLAB/MATLAB_Compiler_Runtime/v716/sys/os/maci64:
/Applications/MATLAB/MATLAB_Compiler_Runtime/v716/bin/maci64:
/System/Library/Frameworks/JavaVM.framework/JavaVM:
/System/Library/Frameworks/JavaVM.framework/Libraries
Workaround: The current workaround is to remove the entries that contain JavaVM from this environment variable. To do that, modify or create the .bash_profile configuration file of the terminal and add the environment variable in an export statement without the corresponding entries. That should persist the changes.
 

Known issues in HIPE 11

Migrating pools across incompatible versions of HIPE

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  • Use another operating system if you believe that your HIPE usage will match the pattern that triggers the crash.
Added:
>
>

Cursor position in the editor view is inaccurate in high-DPI (Retina) displays when using latest Java 7 version (45)

The cursor position appears inside characters instead of between them.

java7u45-font-issue.png

Workaround

The only workaround right now is to roll back to a previous version of Java 7 (which is not aware of Retina displays, so the UI looks fuzzy).

 

General Help System issues

Line: 646 to 655
 
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="" autoattached="1" comment="Java 7 update 45 font issue" date="1385024831" name="java7u45-font-issue.png" path="java7u45-font-issue.png" size="11541" user="Main.AlvarGarcia" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"

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General HIPE startup issues

Added:
>
>

When Google Chrome is the default browser for Mac OS, the navigation arrows at the top of the help pages are not rendered

After repeated uses of the help pages for HIPE with Chrome, the images for the navigation arrow icons located in the header of the pages are (supposedly) retrieved from the browser cache but not rendered at all.

Workaround: The current workaround for this behaviour is to clear Google Chrome's cache, following these instructions.

 

HIPE does not start at all, without giving error messages. What's wrong?

This can happen for different reasons, that are explored in the next entries. When you start HIPE by clicking on its icon and a problem occurs, you may only see a terminal/command window appear for a fraction of a second, leaving you without information on the error.

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    • Solution: The current workaround is to install all modules even if you are not going to use them.

There is a known problem with the InstallAnywhere installer when the bash \u special character is present in some environment variables

Changed:
<
<
    • Versions affected: HIPE 9, 10, 11.
    • Error message: Installation fails with any of the following errors:
>
>
Versions affected: HIPE 9, 10, 11.

Error message: Installation fails with any of the following errors:

 
"Configuring the installer for this system's environment...
Line: 41 to 42
 at com.zerog.lax.LAX.(Unknown Source) at com.zerog.lax.LAX.main(Unknown Source)
Deleted:
<
<
 
Changed:
<
<
>
>
Solution: Un-setting or substituting the /u bash special character (using instead $USER or $LOGNAME) in the PS1 environment variable solves the problem. To do that, you should edit the .bashrc file located at the home directory of the current user. In there, any occurrence of the \u special character should be replaced by $USER or $LOGNAME. Example:
PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
should be replaced by
PS1='${debian_chroot:+($debian_chroot)}$USER@\h:\w\$ '

Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941

 

Installer or start-up hang on Mac OSX and Java 1.6.0_51

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    • Versions affected: HIPE 11.
    • Solution: The current workaround is to install all modules even if you are not going to use them.
Changed:
<
<

There is a known problem with the InstallAnywhere installer observed on a Linux 64 bits, Debian wheezy/sid, java 1.6.0_24 computer.

    • Versions affected: HIPE 9, 10.
Installation fails with the following error:
>
>

There is a known problem with the InstallAnywhere installer when the bash \u special character is present in some environment variables

    • Versions affected: HIPE 9, 10, 11.
    • Error message: Installation fails with any of the following errors:
 "Configuring the installer for this system's environment...

strings: '/lib/libc.so.6': No such file"

Added:
>
>
Or
An internal LaunchAnywhere application error has occured and this application cannot proceed. (LAX)

Stack Trace:
java.lang.IllegalArgumentException: Malformed \uxxxx encoding.
at java.util.Properties.loadConvert(Unknown Source)
at java.util.Properties.load0(Unknown Source)
at java.util.Properties.load(Unknown Source)
at com.zerog.common.java.util.PropertiesUtil.loadProperties(Unknown Source)
at com.zerog.lax.LAX.<init>(Unknown Source)
at com.zerog.lax.LAX.main(Unknown Source)
 
Changed:
<
<
Un-setting the PS1 envar solves the problem. Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941
>
>
 
Deleted:
<
<
This issue is still present in HIPE 10.0.
 

Installer or start-up hang on Mac OSX and Java 1.6.0_51

    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:

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Installation and de-installation issues

Changed:
<
<
  • When installing only HIFI or PACS modules in HIPE you cannot transfer products from HSA to HIPE
>
>

When installing only HIFI or PACS modules in HIPE you cannot transfer products from HSA to HIPE

 
    • Versions affected: HIPE 11.
    • Solution: The current workaround is to install all modules even if you are not going to use them.
Changed:
<
<
  • There is a known problem with the InstallAnywhere installer observed on a Linux 64 bits, Debian wheezy/sid, java 1.6.0_24 computer.
>
>

There is a known problem with the InstallAnywhere installer observed on a Linux 64 bits, Debian wheezy/sid, java 1.6.0_24 computer.

 
    • Versions affected: HIPE 9, 10.
Installation fails with the following error:
Line: 31 to 31
  This issue is still present in HIPE 10.0.
Changed:
<
<
  • Installer or start-up hang on Mac OSX and Java 1.6.0_51
>
>

Installer or start-up hang on Mac OSX and Java 1.6.0_51

 
    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
    • How to fix: Users need to manually download and install the Java update.
Line: 39 to 39
 
    • Apple support notes that "This update corrects an issue with Java applications failing to draw or respond to user input."
Changed:
<
<
  • Cannot install on Mac OS X 10.8 "Mountain Lion". HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
>
>

Cannot install on Mac OS X 10.8 "Mountain Lion"

HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
 
    • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
    • In Mac OS X, from System Preferences --> Security & Privacy --> General --> Allow applications downloads from select ANYWHERE.
Changed:
<
<
  • The installer for Mac complains about write permissions. Why? You need write permissions fo r the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.
  • The installer for Windows does not start and issues the error message Not a valid Win32 application. Why? This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.
  • Why does the uninstaller leave some icons and files/directories behind? This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
  • Sometimes when you run HIPE on your laptop for the first time you may get following error message:
>
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The installer for Mac complains about write permissions. Why?

You need write permissions fo r the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.

The installer for Windows does not start and issues the error message Not a valid Win32 application. Why?

This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.

Why does the uninstaller leave some icons and files/directories behind?

This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.

Sometimes when you run HIPE on your laptop for the first time you may get following error message:

 
% ./runhipe Error occurred during initialization of VM
Line: 58 to 62
 java.vm.memory.max=2872m

to have a smaller value than 1500m and smaller than the RAM memory of your machine.

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  • For other issues affecting the installer, check this page.
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For other issues affecting the installer, check this page.

 

Known issues in HIPE 11

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Migrating pools across incompatible versions of HIPE

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Migrating pools across incompatible versions of HIPE

  HIPE 10 developer versions (builds between 2069 and 2674) and HIPE 11 (all builds) pools are incompatible with any other version of HIPE (including all public releases of HIPE 10).
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Known issues in HIPE 10.3

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Problems seeing PACS error maps

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Problems seeing PACS error maps

  This problem, reported in 10.3, but previously present too, is caused by the history dataset which is "hiding" the error. To resolve it, after running photCoverage2Noise task, give these commands:
Line: 151 to 155
 

Known issues in HIPE 10.1

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Problems with the aberration correction for Solar System Objects in HIFI

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Problems with the aberration correction for Solar System Objects in HIFI

  There is a previously existing issue that has become important in some cases when processing Solar System Object observations in HIPE that affects all Level 2.5 HIFI map products. Ephemeris positions are calculated (and stored in the ra_centre/dec_centre columns) with a spurious correction for stellar aberration. This is being fixed but, until patched, the recommended doOffset approach to translate Level 2 coordinates to a co-moving frame (see the corresponding known issue below on this issue in HIPE 10.0) will lead to coordinate offsets that are off by ~10" on average (depending on the relative velocity between target and Herschel at observation time).
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Known issues in HIPE 10.0

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Can't open plug-ins panel under KDE or Gnome 3

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Can't open plug-ins panel under KDE or Gnome 3

  The Plug-ins panel cannot be opened (from the Tools menu) if you're working under Linux and you don't have the Gnome 2 library installed. Gnome 2 is a desktop environment, and typically if you use a different desktop environment (Gnome 3, KDE, Unity, etc), then you will not have this library.
Line: 170 to 174
  A patch is planned for this issue in HIPE 10.2.
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Clicking on the 'plug-in' button to add the cassis plugin, nothing happens and you see multiple java exceptions

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Clicking on the 'plug-in' button to add the cassis plugin, nothing happens and you see multiple java exceptions

  The "Desktop API", which is used to access the browser when you click "Find more.." button in the HIPE plugin dialogue, is not supported on KDE. It "was designed to work on Windows and Gnome". However, you can also open it directly by pointing your browser directly to http://herschel.esac.esa.int/twiki/bin/view/Public/DpHipePlugins, and copying the URL to the respective .jar files for the particular plugin you are interested in and pasting it in the HIPE plugins dialog to install it.
Line: 182 to 186
  A patch is planned for this issue in HIPE 10.2.
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Pools unreadable with Unknown format version: -11 error

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Pools unreadable with Unknown format version: -11 error

  If you installed a developer build of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools you will find those pools are no longer readable in any other HIPE version; when trying to load a pool with getObservation you will get the following error message:
Line: 192 to 196
  See the Data Analysis Guide for a recovery procedure. You can download from this page the first and second script mentioned in the procedure. Change the extension from .py.txt to .py after downloading.
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The WCS explorer for cubes does not work with PACS and SPIRE cubes

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The WCS explorer for cubes does not work with PACS and SPIRE cubes

  The WCS explorer does not work on cubes for which ImageIndex is used to specify the wavescale axis. This is true for SPIRE and PACS cubes. If crpix3, crval3 and cdelt3 are used instead, the WCS explorer works. To be fixed in HIPE 11.
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Issues with reading text files from SExtractor or Topcat

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Issues with reading text files from SExtractor or Topcat

  While reading files from SExtractor or Topcat you may encounter the following issues:

  • Some SExtractor headers are not read successfully, due to an issue with the column position of units in the file header. Workaround: read the file with the tableType parameter set to SPACES. You can then fill any missing information by hand.
  • Some Topcat files are not read successfully, due to an issue with quoted cells with spaces. Workaround: export the data from Topcat in FITS format, then read the FITS file back into HIPE. For information about reading FITS files into HIPE, see the Data Analysis Guide.
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Format change for exported variables

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Format change for exported variables

  The file format of variables exported with File --> Session --> Export has changed in HIPE 10. This means that HIPE 10 will not be able to read session variables exported with HIPE 9, and vice-versa.
If you exported variables with HIPE 9 or a previous version, follow this workaround to read them in HIPE 10:
Line: 213 to 217
 
  1. Open HIPE 10. The variables shall be restored in the Variables view.
  2. Export the variables with the new format of HIPE 10, with File --> Session --> Export.
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HIPE cannot send data to an external application via SAMP

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HIPE cannot send data to an external application via SAMP

  When you try to send data to an external application via the SAMP Virtual Observatory protocol, the following window may appear:
Line: 223 to 227
  The solution is to send the data again without closing the external application.
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Separate, undocked instances Cube Toolbox talk to each other

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Separate, undocked instances Cube Toolbox talk to each other

  If you have two or more separate Spectrum Explorer GUIs open and at least one is undocked, when using its Cube Toolbox the separate SE instances talk to each other--spectra or new cubes you create in one instance will also appear in the other one.
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New PACS calibration version 45 should not be used with HIPE 10

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New PACS calibration version 45 should not be used with HIPE 10

  In HIPE 10 a new spectroscopy telescope background calibration was introduced. This update is not compatible with the code in HIPE 9.
Line: 237 to 241
  If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.
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Generating a co-moving frame for HIFI mapping observations of solar system objects

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Generating a co-moving frame for HIFI mapping observations of solar system objects

  There is a task in HIPE that allows you to transform level-2 coordinates into a coordinate system co-moving with the target ephemeris. That task is called doOffset,
Line: 255 to 259
  However, the target ephemeris inside HIPE doesn't get updated. I.e., doOffset uses the ephemeris current as of observation uplink to the spacecraft. Work is in progress to automatically update target ephemerids. If your target ephemeris was very uncertain at observation time (and if it has improved since), then you may be better off using a manual approach of downloading the Horizons ephemeris for each target.
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Printing a HIPE script to a file in Snowleopard sends the job to a printer instead

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Printing a HIPE script to a file in Snowleopard sends the job to a printer instead

  When a user tries to print a script to a file on disk, HIPE sends it to the printer instead. A patch will be issued for this problem in HIPE 11 and a definitive fix included in HIPE 12.
Line: 266 to 270
 

General HIPE startup issues

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HIPE does not start at all, without giving error messages. What's wrong?

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HIPE does not start at all, without giving error messages. What's wrong?

  This can happen for different reasons, that are explored in the next entries. When you start HIPE by clicking on its icon and a problem occurs, you may only see a terminal/command window appear for a fraction of a second, leaving you without information on the error.
Line: 274 to 278
  The next entries list some common problems that prevent HIPE from starting.
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HIPE cannot start: the JVM cannot reserve enough memory

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HIPE cannot start: the JVM cannot reserve enough memory

  This only applies if you installed HIPE using the installer, and not downloading a developer build from the Continuous Integration System.
Line: 308 to 312
 
ALERT! You may have the same properties defined in a hipe.props or user.props file, located in the .hcss directory within your home directory. In this case, any values set in hipe.props override those in user.props, which override those in installed.properties. Make sure to edit the properties in the file with highest proprity for your changes to take effect. See this page for more information on property files and their precedence order.
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HIPE cannot start: SAXNotRecognizedException

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HIPE cannot start: SAXNotRecognizedException

  The terminal/command window from which you invoke HIPE shows a SAXNotRecognizedException.
Line: 316 to 320
  java.vm.options = -Djavax.xml.parsers.SAXParserFactory=com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl
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HIPE cannot start: exception access violation.

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HIPE cannot start: exception access violation.

  The terminal/command window from which you invoke HIPE shows an EXCEPTION_ACCESS_VIOLATION error related to a class in org.apache.xerces.
Line: 324 to 328
  This error is probably due to a bug in the Java Virtual Machine, and has so far been found only on Windows XP 32 bit.
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I get startup messages about missing HIFI/PACS/SPIRE modules. Is that serious?

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I get startup messages about missing HIFI/PACS/SPIRE modules. Is that serious?

  You are probably referring to messages such as the following (for HIFI; messages for PACS and SPIRE are the same):
Line: 337 to 341
 

Java 7 issues

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When a HIPE session is left unattended for a long time in Mac OS with Java 7, any display change like: setting resolution, configuring additional monitors or even switching applications can crash HIPE

>
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Crash when a HIPE session is left unattended for a long time in Mac OS with Java 7, after any display change like: setting resolution, configuring additional monitors or even switching applications after resuming work

  Configuration prone to cause the error
  • Operating system: Any version of Mac OS X.
Line: 386 to 390
 

General Help System issues

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The help does not work anymore! What's wrong?

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The help does not work anymore! What's wrong?

  First, check if your issue is that described below, in Why is the HIPE Help System suddenly unable to connect to any help page? If not, you have probably encountered a bug. The following are known issues that can prevent you from viewing the documentation, resulting either in a blank page or an error message:
Line: 402 to 406
 
    • Reboot the computer
If none of the above works, please raise a ticket with the Helpdesk.
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Is there a way to open the HIPE Help System without starting HIPE?

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Is there a way to open the HIPE Help System without starting HIPE?

  Yes, via the hipe_help command, which resides in the apps folder in your HIPE installation. The hipe_help command will start a standalone Help System in a window called Yet Another JAva Help System. Press the Display button to open the Help initial page in your default browser.
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The Help System opens in my web browser. Does it mean I need to be connected to the Internet?

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The Help System opens in my web browser. Does it mean I need to be connected to the Internet?

  No, the Help System resides on your computer and does not need Internet connection, except of course for links to online resources, such as YouTube videos and pages hosted on the Herschel Wiki website, including the What's New and Known Issues documents.
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Why does searching the documentation take such a long time?

>
>

Why does searching the documentation take such a long time?

  When you execute the first search with a new HIPE version, HIPE has to index the contents of the documentation. This can take up to several minutes, depending on the performance of your system. Indexing of the documentation is only done for the first search. Subsequent searches will be much faster.

We are investigating ways to include pre-built indexes in the documentation shipped with HIPE, so you will not have to wait for the results of your first search.

Changed:
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Why is the HIPE Help System suddenly unable to connect to any help page?

>
>

Why is the HIPE Help System suddenly unable to connect to any help page?

  The Help System relies on a local web server to display help pages. If you close the application that started the web server, the server will shut down as well:
Line: 425 to 429
  Note that when the Help System stops, any browser window or tab showing help pages will remain open, but links on them will not work anymore.
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Why are several important packages missing from the Javadoc?

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Why are several important packages missing from the Javadoc?

  You are probably looking at the static Javadoc located in the doc/api/ folder of your HIPE installation. The complete Javadoc can now be accessed from the HIPE Help System by clicking on HCSS Developer's Reference Manual (API) in the Developer Reference section. The plan is to remove the static version of the Javadoc completely.
Changed:
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Is it possible to have the traditional, frame-based Javadoc layout?

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Is it possible to have the traditional, frame-based Javadoc layout?

  Javadoc pages appear within the HIPE Help System frame structure. If you click on the FRAME link on any Javadoc page, you will obtain the traditional Javadoc layout. To go back to the HIPE Help System layout you will have to use the Back button of your browser (clicking on the NO FRAMES link will not work). To avoid losing the HIPE Help System layout, you may want to right-click on the FRAMES link to open the traditional Javadoc layout into a new tab of your web browser.
Changed:
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How can I provide feedback/requests regarding HIPE documentation?

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How can I provide feedback/requests regarding HIPE documentation?

  You can leave a comment using the box at the bottom of any documentation page in the HIPE Help System. You must be connected to the Internet to view and submit comments.
Line: 441 to 445
  If you want your issue to be officially tracked and supported, please raise a ticket with the Helpdesk of the Herschel Science Centre.
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Other help issues

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>

Other help issues

 
  • URM categories: Some entries in the three instruments User's Reference Manuals have wrong or missing categories.
  • URM examples: Some examples in the User's Reference Manuals may not work as expected. Please use the feedback icon in the HIPE Help System to let us know about broken examples.
Line: 449 to 453
 

Herschel Science Archive issues

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I have changed/reset the password of the account I use to access Herschel Science Archive, but HIPE still tells me I am logged in (with the old password), even after restarting HIPE. How do I log in with the new password?

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How to log in with new credentials after changing the password for HSA I have changed/reset the password of the account I use to access Herschel Science Archive, but HIPE still tells me I am logged in (with the old password), even after restarting HIPE. How do I log in with the new password?

  HIPE stores your HSA password for you if you log in and check the "Remember Me" checkbox. If you restart you can access the HSA without having to enter your info again.
Line: 459 to 463
  After this, you can double-click again to log in again, using the correct password, or you can wait until HIPE prompts you to log in.
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I have downloaded FITS files in a tar archive from the HSA, but they are corrupted. How can I fix them?

>
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I have downloaded FITS files in a tar archive from the HSA, but they are corrupted. How can I fix them?

  You may have used WinZip under Windows. WinZip has an option called TAR file smart CR/LF conversion, in the Miscellaneous tab of the Configuration dialogue window (at least up to version 15.0), that is enabled by default and causes the corruption. Disable the option to solve this problem. You can also use other software such as 7-Zip.
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In the HSA user interface I can query and select observations, but I do not get the option in the HSA to pass the data to HIPE, or in HIPE to load the selected products. Why?

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In the HSA user interface I can query and select observations, but I do not get the option in the HSA to pass the data to HIPE, or in HIPE to load the selected products. Why?

  If you are using Windows, the problem might be that you instructed your browser to auto-detect proxy settings. In Windows this is a system-wide setting which affects any application connecting to the Internet, including HIPE.

You can change proxy settings for HIPE by following the instructions in the HIPE Owner's Guide.

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When I click Send to external Application in the HSA interface, nothing seems to happen. What is going on?

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When I click Send to external Application in the HSA interface, nothing seems to happen. What is going on?

  The data is being transferred in the background. Clicking Send to external Application should bring to the front the main HIPE window, which will tell you that data is indeed being received. In some cases however the HIPE window does not appear. Bring it to the front manually to follow the progress of your action.
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When I try to retrieve data from the HSA I get an error message in the console about an invalid magic number for FITS file. What is going on?

>
>

When I try to retrieve data from the HSA I get an error message in the console about an invalid magic number for FITS file. What is going on?

  The reason is that the "data" being downloaded is in reality a small file containing an error message. Two issues have been shown to cause this problem:
Line: 482 to 486
 

Other issues

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HIPE crashed/froze! What do I do?

>
>

HIPE crashed/froze! What do I do?

  If you cannot find a solution in this document, you may have found a bug in HIPE. Please report it by opening a Helpdesk ticket. If the system produced a dump file when the crash happened, make sure to include it in your ticket. For more information about dump files and where to look for them, see the HIPE Owner's Guide.
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Cannot open a FITS file created by HIPE

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Cannot open a FITS file created by HIPE

  If you export a FITS file from HIPE and modify it with an external program, HIPE may not be able to import it anymore. If this happens, follow these steps:

Line: 496 to 500
  HIPE should now be able to read the file.
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Cannot run WebStart applications on Mac OS Lion or Mountain Lion because of security settings

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Cannot run WebStart applications on Mac OS Lion or Mountain Lion because of security settings

  WebStart applications that can be opened from within HIPE include the HSA User Interface, Aladin, VOSpec and so on. When trying to open one of such applications, a window like the following may appear:
Line: 506 to 510
  To allow a WebStart application that is blocked, change the Allow applications downloaded from option in Gatekeeper from Mac App Store to one of the two less restrictive options. If the application has a valid certificate, the Mac App Store and identified developers option will suffice. Otherwise you will need to select the Anywhere option.
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"Invalid context" errors on Mac OS X Lion

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"Invalid context" errors on Mac OS X Lion

  When you start HIPE form a Terminal window on Mac OS X Lion, you may see errors such as these:
Line: 516 to 520
  These errors are harmless and can be safely ignored.
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Jython bug when comparing NaN values with numbers

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Jython bug when comparing NaN values with numbers

  Jython behaves differently from Python when comparing NaN values with numbers.
Line: 542 to 546
  An issue has been opened on the Jython bug tracker.
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"Can't connect to X11" error when using the jylaunch command

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>

"Can't connect to X11" error when using the jylaunch command

  Executing a script outside HIPE with the jylaunch command may fail with a java.lang.InternalError: Can't connect to X11 window server error. This may happen even if the script does not open any graphical window, since it may indirectly call components that require an X11 server. The workaround is to run the script with the command jylaunch -Djava.awt.headless=true instead of just jylaunch.
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Problems saving observations to NFS-mounted disks and FAT32 disks

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Problems saving observations to NFS-mounted disks and FAT32 disks

  When saving observation to your computer, you may experience problems in the following cases:
  • When saving data to NFS-mounted disks (you may get an IllegalMonitorStateException).
Line: 557 to 561
  See the HIPE Owner's Guide for information on how to set properties.
Changed:
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Why do I get a ClassCastException when trying to save an observation with the saveObservation command?

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Why do I get a ClassCastException when trying to save an observation with the saveObservation command?

  You probably retrieved the observation without having the corresponding instrument software installed (for instance, you retrieved a PACS observation without having the PACS modules in HIPE).
Line: 569 to 573
 
    • home/.hcss/pal_cache/hsa
  1. Retrieve the observation again.
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I get an OutOfMemoryError related to PermGen space. What can I do?

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I get an OutOfMemoryError related to PermGen space. What can I do?

  Add or edit the following property in your hipe.props property file:
Line: 581 to 585
  For more information about property files, see the HIPE Owner's Guide.
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There are PACS files I cannot delete! Why?

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There are PACS files I cannot delete! Why?

  It might not be possible to delete the following files on Windows because their full path exceeds the 260 characters limit.
Line: 593 to 597
  You can avoid this problem by installing HIPE with a short initial path, such as C:\hipe, so that full paths remain below the limit.
Changed:
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HIPE does not accept keyboard input anymore! What's wrong?

>
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HIPE does not accept keyboard input anymore! What's wrong?

  If you are running Linux, this could be due to a compatibility problem between Java and SCIM (Smart Common Input Method). A workaround is to stop SCIM or uninstall it. Please refer to the documentation of your distribution for how to do so.
Line: 602 to 606
 
Changed:
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What are all the tmp_product_sink_* pools in my local store directory?

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What are all the tmp_product_sink_* pools in my local store directory?

  You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.

Revision 1212013-08-08 - AlvarGarcia

Line: 1 to 1
 
META TOPICPARENT name="WebHome"
<-- ANALYTICS CODE - DO NOT EDIT -->
<-- Google Analytics script BEGIN -->
<-- Google Analytics script END -->
Line: 261 to 260
 When a user tries to print a script to a file on disk, HIPE sends it to the printer instead. A patch will be issued for this problem in HIPE 11 and a definitive fix included in HIPE 12.
Deleted:
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Known issues in HIPE 9.2

New PACS calibration version 45 should not be used with HIPE 9

In HIPE 10 a new spectroscopy telescope background calibration was introduced. This update is not compatible with the code in HIPE 9.

If you use the background normalisation ipipe script for chopped spectroscopy in HIPE 9, you should not update the PACS calibration tree to version 45. You should keep using the calibration set 41 and cancel the update when the automatic calibration updater in HIPE asks to install set 45.

If you have updated to set 45 and want to use the background normalisation in HIPE 9, you can switch back to version 41 in two ways:

  • With the command getCalTree(version=41).
  • By removing the file PCalBase_TimeDependency_FM_v45.fits from the directory ~/.hcss/data/pcal-community.

You can alway check the calibration version that you are using with the following command:

print getCalTree().version

If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.

Issues with computePVMap task

The computePVMap task has the following issues:

  • There are remaining aesthetic issues regarding the pvMap aspect ratio modification in the task.
  • There is a known error when extracting a pvMap with row < col (velocity dimension < spatial dimension). Workaround: set the correctAspectRatio parameter to False (in the graphical interface, untick the corresponding checkbox).

Known issues in HIPE 9.1

None known in addition to those listed for HIPE 9.0.

Known issues in HIPE 9.0

Performance issues of convolution task with NaN values

The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem. Fixed in HIPE 9.1.

Performance issues with very large images

Images larger than about 100 MB in FITS format can still take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.

Problem with PACS background normalization script

The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:

target = obs.meta["object"].value.replace(" ","_")

PACS task specFlatFieldLine problem with NaN values

The specFlatFieldLine task cannot handle NaNs in the fluxes of PacsCube products. This affected one observation as far as we tested. If you encounter this problem then you can mask the NaNs by running the function shown below. Copy and paste the function code in a new Jython script window in the Editor view of HIPE, then click the green double arrow icon in the HIPE toolbar to run the script. After that you can call the function from the Console view, passing the variable contaning your cube as argument: addInvalidMask(myCube).

def addInvalidMask(slicedCube):
    for i in range(0,slicedCube.numberOfSlices):
       cube = slicedCube.get(i)
       invalid = IS_NAN(cube.flux)
       if not cube.containsMask("INVALID"):
          cube.addMask("INVALID","Invalid signal values")
       cube.setMask("INVALID",invalid)
       slicedCube.replace(i,cube)

HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions

This button is enabled only when you change the state of one or more masks. Fixed in HIPE 9.1.

<-- PACS-4626 -->

Image analysis tasks start only from Applicable section

Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks. To be fixed in HIPE 10. The problem affects the following tasks:

  • annularSkyAperturePhotometry
  • circleHistogram
  • crop
  • ellipseHistogram
  • fixedSkyAperturePhotometry
  • polygonHistogram
  • profile
  • rectangleHistogram
  • rectangularSkyAperturePhotometry
  • sourceFitting

PV diagrams created with computePVMap on HIFI cubes cannot be easily viewed

HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: open the variable created from the variables pane and use the full Display/Image Viewer.

<-- use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in Appendix C of the Data Analysis Guide. For position-velocity diagrams, see subsection C.6.8.1.-->

HIPE crash linked to JAMA (Java Matrix) library

HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:

  1. Go to the .hcss directory in your open directory. Open the hipe.props file, or create it if it does not exist.
  2. Add the following line to the file:
    java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>
  3. Restart HIPE.

Problem with transpose task

In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur. To be fixed in HIPE 10.

Velocity map creation in Legacy Cube Spectrum Analysis Toobox (CSAT) fails

The creation of velocity maps with the Legacy CSAT fails; the task will hang without an error message. CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead. See 6.8.3 in the Herschel Data Analysis Guide for information about using the new cube toolbox.

Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task

This is a display issue only, the flags set by flagTool are, in fact, used.

PACS specific: convertL1ToScanam fails

convertL1ToScanam fails because of a missing import for the calibration tree, when assignRaDec is set to True. The work around solution is :

calTree = getCalTree(time=frames.startDate)
frames=photAssignRaDec(frames,calTree=calTree)
convertL1ToScanam(frames,assignRaDec=False)

Fixed in HIPE 9.2.

 

Older HIPE versions

Known issues for older HIPE versions are listed in a separate page.

Line: 451 to 335
  Such messages are harmless and just reflect the fact that you have not installed the software related to the specified instruments.
Added:
>
>

Java 7 issues

When a HIPE session is left unattended for a long time in Mac OS with Java 7, any display change like: setting resolution, configuring additional monitors or even switching applications can crash HIPE

Configuration prone to cause the error

  • Operating system: Any version of Mac OS X.
  • Java version: any Java 7 version.

Usage prone to cause the error

  • Leave HIPE running unattended for several hours.
  • Return to work with HIPE and:
    • Switch applications.
    • Wake the computer/monitor from sleep.
    • Change the display resolution.
    • Send an application to another monitor in a multimonitor setup.

Error message

The crash displays a long error trace that begins with:

Thread 0 Crashed:: AppKit Thread  Dispatch queue: com.apple.main-thread
0   com.apple.CoreFoundation         0x00007fff8d7e2a1b CFRelease + 27
1   liblwawt.dylib                   0x000000011b557647 __Java_sun_lwawt_macosx_CWrapper_00024NSObject_release_block_invoke_1 + 91
2   JavaNativeFoundation             0x000000011a8ea5f5 +[JNFRunLoop _performCopiedBlock:] + 20
3   com.apple.CoreFoundation         0x00007fff8d8a7d9d +[NSObject performSelector:withObject:] + 61
4   com.apple.Foundation             0x00007fff85d9dd70 __NSThreadPerformPerform + 214
5   com.apple.CoreFoundation         0x00007fff8d7ec4f1 __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__ + 17
6   com.apple.CoreFoundation         0x00007fff8d7ebd5d __CFRunLoopDoSources0 + 253
7   com.apple.CoreFoundation         0x00007fff8d812b49 __CFRunLoopRun + 905
8   com.apple.CoreFoundation         0x00007fff8d812486 CFRunLoopRunSpecific + 230
9   com.apple.HIToolbox              0x00007fff8acda2bf RunCurrentEventLoopInMode + 277

General information

If you are affected by this problem, it is useful to know that:

Workarounds

From the information above, the only identified workarounds for those of you that run long sessions of HIPE are:

 

General Help System issues

The help does not work anymore! What's wrong?

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Herschel Science Archive issues

Added:
>
>

I have changed/reset the password of the account I use to access Herschel Science Archive, but HIPE still tells me I am logged in (with the old password), even after restarting HIPE. How do I log in with the new password?

 
Added:
>
>
HIPE stores your HSA password for you if you log in and check the "Remember Me" checkbox. If you restart you can access the HSA without having to enter your info again.

However, if you reset your password using the Automated user Password Fixer, and restart HIPE, then HIPE will still report you as being logged in, even though you can't be, because you haven't told HIPE your new password yet.

To work around the situation, double-click on your username in the HIPE status bar at the bottom of the window to log out explicitly. (If you are not logged in, the status bar will show a label "HSA Log-in" and you don't need to do anything).

After this, you can double-click again to log in again, using the correct password, or you can wait until HIPE prompts you to log in.

 

I have downloaded FITS files in a tar archive from the HSA, but they are corrupted. How can I fix them?

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Known issues in HIPE 11

Changed:
<
<

Compatibility workaround for using HIPE 11 pools in earlier versions

>
>

Migrating pools across incompatible versions of HIPE

 
Changed:
<
<
New pool index version (6): HIPE 10 developer versions (builds between 2069 and 2674) and HIPE 11 (all builds) Old pool index version (4): Every other HIPE version.
>
>
HIPE 10 developer versions (builds between 2069 and 2674) and HIPE 11 (all builds) pools are incompatible with any other version of HIPE (including all public releases of HIPE 10).
 
Changed:
<
<
If you installed any of the developer versions of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools, or have created a pool with HIPE 11 that you wish to read back later with HIPE 10, you will find those pools are no longer readable in the previous HIPE version. When trying to load a pool with getObservation you will get the following error message:
herschel.ia.pal.pool.lstore.lucene.IndexVersionIncompatibleException: Index Version not compatible. Expected : 4 Existing: 6.Pool <pool_name> requires upgrading before you can use it with this software.
>
>
In order to use these existing pools with an incompatible version, you should rebuild the index of the pool. Given that it is not guaranteed that newer data should work with older versions of the software, this guide will focus only on making the pools workable in the following cases:
  • Case 1: Using pools created/modified in a HIPE 10 version prior to 2069 with a HIPE 10 version between 2069 and 2674.
  • Case 2: Using pools created/modified in a HIPE 10 version between 2069 and 2674 with a HIPE 10 version between after 2674.
  • Case 3: Using pools created/modified in a HIPE 10 version other than the 2069-2674 range with HIPE 11.
  • Case 4: Using pools with an index rebuilt for a HIPE 10 version other than the 2069-2674 range with HIPE 11.
 
Changed:
<
<
The cause of this is a Lucene update to version 4.1, originally intended to be included in HIPE 10, which has a major upgrade in the search functionality in the HIPE documentation. However, Lucene 4.1 has serious backwards compatibility issues that Lucene say will have been resolved in future releases. These have caused problems with the indexing of pools stored on local disk. You can fix the pools you modified with versions of HIPE between 10.0.2069 and 10.0.2674 (at which point the Lucene version was rolled back as a temporary solution), or in HIPE 11 where the upgrade has been made definitive, so that they can be read in the previous version of HIPE, in two steps, as described below.
  • With a HIPE version between 10.0.2069 and 10.0.2674, or for HIPE 11, run the following script for each pool that you need to correct. The script should be run with the run all button (the double arrows) and you should modify the first line to indicate the name of the pool (replace ) you want to correct. To do this, you should run these commands:
    
lstore = LocalStoreFactory.getStore(<pool_name>)
lstore.rebuildIndex()
>
>

Prerequisite:

A pool created with a HIPE 10 version prior to 2069.

Case 1:

Pool you want to open: A pool like the one detailed in the prerequisite.

Error message: There is no error displayed and the pool is completely usable in HIPE 10 versions 2069-2674.

Case 2:

Pool you want to open: A pool that is like the prerequisite or has been processed in a scenario like CASE 1.

Error message: Querying the pool using the Product Browser returns nothing (no error message). Opening the observation from the Console using getObservation returns the following error message:

 
Changed:
<
<
That's it! You should now be able to read your pool. If you find you cannot, contact the Helpdesk.
>
>
herschel.ia.task.TaskException: Error processing getObservation task: Index Version not compatible. Expected : 4 Existing: 6. 
Pool <pool_name> requires upgrading before you can use it with this software. In order to do so, you need to run pool_name.rebuildIndex() to upgrade. 
Depending on the size of the pool this process can take a long time, please be patient! 
More information can be found in the Data Analysis Guide, section 1.2.2.1 (Update of index format for local stores).

Notes about the error message:

  • pool_name is the name of the pool you are trying to load.
  • pool_name.rebuildIndex() is not the proper command to rebuild the pool. See below for the appropriate commands.
  • The section of the Data Analysis Guide referenced is not correct. When ready, a copy of this procedure will be available in the section 1.11 (Migrating pools across incompatible versions of HIPE)

Workaround: Any of the following commands will rebuild the index of the pool:

  • This ensures we are rebuilding the specified pool using a static method from the class LocalStoreFactory:
LocalStoreFactory.getStore(pool_name).rebuildIndex()
store.writablePool.rebuildIndex()

Case 3:

Pool you want to open: A pool that is like the prerequisite.

Error message: There is no error displayed and the pool is completely usable in HIPE 11.

Case 4:

Pool you want to open: A pool which index was rebuilt following CASE 2 instructions.

Error message: There is no error displayed and the pool is completely usable in HIPE 11.

That's it! You should now be able to use your pool in any of the above cases. If you find you cannot, contact the Helpdesk.

 
Tip, idea Note that the index files will not be backed up while you run rebuildIndex(), unless you invoke Configuration.setProperty("hcss.ia.pal.pool.lstore.index.backup", "true") first. For more information execute the following command: help('dag:sec-lstore-index-compatibility'). See the HIPE Owner's Guide: Section 4.

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 to have a smaller value than 1500m and smaller than the RAM memory of your machine.
  • For other issues affecting the installer, check this page.
Added:
>
>

Known issues in HIPE 11

Compatibility workaround for using HIPE 11 pools in earlier versions

New pool index version (6): HIPE 10 developer versions (builds between 2069 and 2674) and HIPE 11 (all builds) Old pool index version (4): Every other HIPE version.

If you installed any of the developer versions of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools, or have created a pool with HIPE 11 that you wish to read back later with HIPE 10, you will find those pools are no longer readable in the previous HIPE version. When trying to load a pool with getObservation you will get the following error message:

herschel.ia.pal.pool.lstore.lucene.IndexVersionIncompatibleException: Index Version not compatible. Expected : 4 Existing: 6.Pool <pool_name> requires upgrading before you can use it with this software.

The cause of this is a Lucene update to version 4.1, originally intended to be included in HIPE 10, which has a major upgrade in the search functionality in the HIPE documentation. However, Lucene 4.1 has serious backwards compatibility issues that Lucene say will have been resolved in future releases. These have caused problems with the indexing of pools stored on local disk. You can fix the pools you modified with versions of HIPE between 10.0.2069 and 10.0.2674 (at which point the Lucene version was rolled back as a temporary solution), or in HIPE 11 where the upgrade has been made definitive, so that they can be read in the previous version of HIPE, in two steps, as described below.

  • With a HIPE version between 10.0.2069 and 10.0.2674, or for HIPE 11, run the following script for each pool that you need to correct. The script should be run with the run all button (the double arrows) and you should modify the first line to indicate the name of the pool (replace ) you want to correct. To do this, you should run these commands:
    
lstore = LocalStoreFactory.getStore(<pool_name>)
lstore.rebuildIndex()

That's it! You should now be able to read your pool. If you find you cannot, contact the Helpdesk.

Tip, idea Note that the index files will not be backed up while you run rebuildIndex(), unless you invoke Configuration.setProperty("hcss.ia.pal.pool.lstore.index.backup", "true") first. For more information execute the following command: help('dag:sec-lstore-index-compatibility'). See the HIPE Owner's Guide: Section 4.
 

Known issues in HIPE 10.3

Problems seeing PACS error maps

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 When a user tries to print a script to a file on disk, HIPE sends it to the printer instead. A patch will be issued for this problem in HIPE 11 and a definitive fix included in HIPE 12.
Deleted:
<
<

When a Product is saved to an incompatible pool (created with a different version of Lucene), then an exception is thrown but the Product is saved anyway.

Affected builds, 10 track only:

The problem occurs only when you create a pool with build between 2069 and 2674 and then save a product to that pool with a build earlier that 2069 or later than 2674.

 

Known issues in HIPE 9.2

New PACS calibration version 45 should not be used with HIPE 9

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    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
    • How to fix: Users need to manually download and install the Java update.
Changed:
<
<
    • <http://support.apple.com/kb/DL1572> (10.7, 10.8+)
    • <http://support.apple.com/kb/DL1573> (10.6-only)
>
>
 
    • Apple support notes that "This update corrects an issue with Java applications failing to draw or respond to user input."

  • Cannot install on Mac OS X 10.8 "Mountain Lion". HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:

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Installation and de-installation issues

Added:
>
>
  • When installing only HIFI or PACS modules in HIPE you cannot transfer products from HSA to HIPE
    • Versions affected: HIPE 11.
    • Solution: The current workaround is to install all modules even if you are not going to use them.

  • There is a known problem with the InstallAnywhere installer observed on a Linux 64 bits, Debian wheezy/sid, java 1.6.0_24 computer.
    • Versions affected: HIPE 9, 10.
Installation fails with the following error:

"Configuring the installer for this system's environment...

strings: '/lib/libc.so.6': No such file"

Un-setting the PS1 envar solves the problem. Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941

This issue is still present in HIPE 10.0.

 
  • Installer or start-up hang on Mac OSX and Java 1.6.0_51
    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
Line: 29 to 45
 
  • The installer for Mac complains about write permissions. Why? You need write permissions fo r the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.
  • The installer for Windows does not start and issues the error message Not a valid Win32 application. Why? This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.
  • Why does the uninstaller leave some icons and files/directories behind? This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
Changed:
<
<
  • * Sometimes when you run HIPE on your laptop for the first time you may get following error message:
>
>
  • Sometimes when you run HIPE on your laptop for the first time you may get following error message:
 
Changed:
<
<
% ./runhipe Error occurred during initialization of VM
>
>
% ./runhipe Error occurred during initialization of VM
  Could not reserve enough space for object heap
Line: 41 to 57
  java.vm.memory.max=2872m
Changed:
<
<
to have a smaller value than 1500m and smaller than the RAM memory of your machine.
  • For other issues affecting the installer, check this page.
>
>
to have a smaller value than 1500m and smaller than the RAM memory of your machine.
  • For other issues affecting the installer, check this page.
 

Known issues in HIPE 10.3

Line: 214 to 230
 

Known issues in HIPE 9.0

Deleted:
<
<

Installation and de-installation issues

There is a known problem with the InstallAnywhere installer observed on a Linux 64 bits, Debian wheezy/sid, java 1.6.0_24 computer. Installation fails with the following error:

"Configuring the installer for this system's environment...

strings: '/lib/libc.so.6': No such file"

Un-setting the PS1 envar solves the problem. Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941

This issue is still present in HIPE 10.0.

 

Performance issues of convolution task with NaN values

The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem. Fixed in HIPE 9.1.

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Known issues in HIPE 10.3

Changed:
<
<
None known in addition to those listed for HIPE 10.1.
>
>

Problems seeing PACS error maps

This problem, reported in 10.3, but previously present too, is caused by the history dataset which is "hiding" the error. To resolve it, after running photCoverage2Noise task, give these commands:

history = image["History"]

image.remove("History")

image["History"] = history

Where the "image" is the product that you have been working on. This will append the history dataset at the end of the product and "solve" the problem. There will be a fix in place for this issue in HIPE 11.

 

Known issues in HIPE 10.2

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 to have a smaller value than 1500m and smaller than the RAM memory of your machine.
  • For other issues affecting the installer, check this page.
Added:
>
>

Known issues in HIPE 10.3

None known in addition to those listed for HIPE 10.1.

Known issues in HIPE 10.2

None known in addition to those listed for HIPE 10.1.

 

Known issues in HIPE 10.1

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Installation and de-installation issues

Added:
>
>
  • Installer or start-up hang on Mac OSX and Java 1.6.0_51
    • Some users have found that the InstallAnywhere GUI hangs leaving all buttons frozen; this may happen either when installing, or when starting HIPE after an apparently successful installation. This appears to be due to a failed Apple java update and can, in principle, occur with any HIPE version. You can check for this issue following these steps:
    • How to detect a failed update. Run: /usr/libexec/java_home -v 1.6 -exec java -version in a terminal. If the output includes "M4508" you have the bad update.
    • How to fix: Users need to manually download and install the Java update.
    • <http://support.apple.com/kb/DL1572> (10.7, 10.8+)
    • <http://support.apple.com/kb/DL1573> (10.6-only)
    • Apple support notes that "This update corrects an issue with Java applications failing to draw or respond to user input."
 
  • Cannot install on Mac OS X 10.8 "Mountain Lion". HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
    • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
    • In Mac OS X, from System Preferences --> Security & Privacy --> General --> Allow applications downloads from select ANYWHERE.

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  When a user tries to print a script to a file on disk, HIPE sends it to the printer instead. A patch will be issued for this problem in HIPE 11 and a definitive fix included in HIPE 12.
Added:
>
>

When a Product is saved to an incompatible pool (created with a different version of Lucene), then an exception is thrown but the Product is saved anyway.

Affected builds, 10 track only:

The problem occurs only when you create a pool with build between 2069 and 2674 and then save a product to that pool with a build earlier that 2069 or later than 2674.

 

Known issues in HIPE 9.2

New PACS calibration version 45 should not be used with HIPE 9

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  • The installer for Mac complains about write permissions. Why? You need write permissions for the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.
  • The installer for Windows does not start and issues the error message Not a valid Win32 application. Why? This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.
  • Why does the uninstaller leave some icons and files/directories behind? This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
Added:
>
>
  • * Sometimes when you run HIPE on your laptop for the first time you may get following error message:

% ./runhipe Error occurred during initialization of VM

Could not reserve enough space for object heap

Could not create the Java virtual machine.

This error typically happens because you have either set or have as default a too large memory for the Java Virtual Machine and hence it cannot start. Edit the file called "installed.properties" under your hipe_v11_RC2 i(or alternative directory, as appropriate) installation directory and edit the line

java.vm.memory.max=2872m

to have a smaller value than 1500m and smaller than the RAM memory of your machine.

 
  • For other issues affecting the installer, check this page.

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  You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.
Deleted:
<
<

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blog comments powered by Disqus
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META FILEATTACHMENT attr="h" autoattached="1" comment="Error message when sending data to VOSpec" date="1358258421" name="vospec.png" path="vospec.png" size="12133" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"

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Known issues in HIPE 10.1

Changed:
<
<
There are no changes with respect to the 10.0 issues detailed below.
>
>

Problems with the aberration correction for Solar System Objects in HIFI

There is a previously existing issue that has become important in some cases when processing Solar System Object observations in HIPE that affects all Level 2.5 HIFI map products. Ephemeris positions are calculated (and stored in the ra_centre/dec_centre columns) with a spurious correction for stellar aberration. This is being fixed but, until patched, the recommended doOffset approach to translate Level 2 coordinates to a co-moving frame (see the corresponding known issue below on this issue in HIPE 10.0) will lead to coordinate offsets that are off by ~10" on average (depending on the relative velocity between target and Herschel at observation time).

This is being fixed in HIPE 12 and it is expected that a patch will be made for HIPE 11 and, possibly, also patched in later releases of HIPE 10.

 

Known issues in HIPE 10.0

Revision 1072013-05-16 - LucaConversi

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Revision 1062013-05-16 - MarkRKidger

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Printing a HIPE script to a file in Snowleopard sends the job to a printer instead

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When a user tries to print a script to a file on disk, HIPE sends it to the printer instead.

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When a user tries to print a script to a file on disk, HIPE sends it to the printer instead. A patch will be issued for this problem in HIPE 11 and a definitive fix included in HIPE 12.
 

Known issues in HIPE 9.2

Revision 1052013-05-14 - MarkRKidger

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  • Why does the uninstaller leave some icons and files/directories behind? This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
  • For other issues affecting the installer, check this page.
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Known issues in HIPE 10.1

There are no changes with respect to the 10.0 issues detailed below.

 

Known issues in HIPE 10.0

Can't open plug-ins panel under KDE or Gnome 3

Revision 1042013-05-06 - MarkRKidger

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  However, the target ephemeris inside HIPE doesn't get updated. I.e., doOffset uses the ephemeris current as of observation uplink to the spacecraft. Work is in progress to automatically update target ephemerids. If your target ephemeris was very uncertain at observation time (and if it has improved since), then you may be better off using a manual approach of downloading the Horizons ephemeris for each target.
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Printing a HIPE script to a file in Snowleopard sends the job to a printer instead

When a user tries to print a script to a file on disk, HIPE sends it to the printer instead.

 

Known issues in HIPE 9.2

Revision 1032013-04-23 - MarkRKidger

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  If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.
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Generating a co-moving frame for HIFI mapping observations of solar system objects

There is a task in HIPE that allows you to transform level-2 coordinates into a coordinate system co-moving with the target ephemeris. That task is called doOffset,

http://herschel.esac.esa.int/hcss-doc-10.0/index.jsp#hifi_um:hdrg_offsetposn_use

A typical code snippet would be:

comet = getObservation(1342227173, useHsa=True)

htp=comet.refs["level2"].product.refs["WBS-H-USB"].product # extract USB, pol H

htp2=doOffset(htp=htp, overwrite=0, relative=1) # make coordinates relative to ephemeris

HiClassTask()(product=htp2, fileName='cometHUSB_relativeCoords.fits') # export in CLASS-readable format

However, the target ephemeris inside HIPE doesn't get updated. I.e., doOffset uses the ephemeris current as of observation uplink to the spacecraft. Work is in progress to automatically update target ephemerids. If your target ephemeris was very uncertain at observation time (and if it has improved since), then you may be better off using a manual approach of downloading the Horizons ephemeris for each target.

 

Known issues in HIPE 9.2

Revision 1022013-04-19 - MarkRKidger

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  A patch is planned for this issue in HIPE 10.2.
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Clicking on the 'plug-in' button to add the cassis plugin, nothing happens and you see multiple java exceptions

The "Desktop API", which is used to access the browser when you click "Find more.." button in the HIPE plugin dialogue, is not supported on KDE. It "was designed to work on Windows and Gnome". However, you can also open it directly by pointing your browser directly to http://herschel.esac.esa.int/twiki/bin/view/Public/DpHipePlugins, and copying the URL to the respective .jar files for the particular plugin you are interested in and pasting it in the HIPE plugins dialog to install it.

If you would like to have the "Find more.." button working, all you need is to have the Gnome libraries installed.

Some instructions: - To install Gnome 3 libraries on Ubuntu (http://www.filiwiese.com/installing-gnome-on-ubuntu-12-04-precise-pangolin/). Note that if you're using version 11.10 or later, you probably don't need the first command (sudo apt-add-repository ...). I would just skip it and if the last command does not complain about "package not found" or something similar, then all is well. - To install Gnome 2 libraries on Ubuntu: http://askubuntu.com/questions/123690/how-to-install-gnome2-on-ubuntu-11-10

A patch is planned for this issue in HIPE 10.2.

 

Pools unreadable with Unknown format version: -11 error

If you installed a developer build of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools you will find those pools are no longer readable in any other HIPE version; when trying to load a pool with getObservation you will get the following error message:

Revision 1012013-04-18 - MarkRKidger

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Installation and uninstallation issues

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Please note that some issues detected in previous versions may still be present in HIPE 10. Scroll down and check earlier versions if you do not see your particular issue listed for HIPE 10.

Installation and de-installation issues

 
  • Cannot install on Mac OS X 10.8 "Mountain Lion". HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
    • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
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Known issues in HIPE 9.0

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Installation and de-installation issues

There is a known problem with the InstallAnywhere installer observed on a Linux 64 bits, Debian wheezy/sid, java 1.6.0_24 computer. Installation fails with the following error:

"Configuring the installer for this system's environment...

strings: '/lib/libc.so.6': No such file"

Un-setting the PS1 envar solves the problem. Further details of the InstallAnywhere issue can be found here: http://kb.flexerasoftware.com/selfservice/viewContent.do?externalID=Q112941

This issue is still present in HIPE 10.0.

 

Performance issues of convolution task with NaN values

The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem. Fixed in HIPE 9.1.

Revision 1002013-04-17 - MarkRKidger

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Known issues in HIPE 10.0

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Can't open plug-ins panel under KDE or Gnome 3

The Plug-ins panel cannot be opened (from the Tools menu) if you're working under Linux and you don't have the Gnome 2 library installed. Gnome 2 is a desktop environment, and typically if you use a different desktop environment (Gnome 3, KDE, Unity, etc), then you will not have this library.

In both cases, the problem can be solved by installing the Gnome 2 library. For example on Ubuntu (or Kubuntu), the command is:

sudo apt-get install libgnome2-0

A patch is planned for this issue in HIPE 10.2.

 

Pools unreadable with Unknown format version: -11 error

If you installed a developer build of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools you will find those pools are no longer readable in any other HIPE version; when trying to load a pool with getObservation you will get the following error message:

Revision 992013-02-27 - BrunoMerin

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  If you have two or more separate Spectrum Explorer GUIs open and at least one is undocked, when using its Cube Toolbox the separate SE instances talk to each other--spectra or new cubes you create in one instance will also appear in the other one.
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New PACS calibration version 45 should not be used with HIPE 10

In HIPE 10 a new spectroscopy telescope background calibration was introduced. This update is not compatible with the code in HIPE 9.

You can alway check the calibration version that you are using with the following command:

print getCalTree().version

If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.

 

Known issues in HIPE 9.2

New PACS calibration version 45 should not be used with HIPE 9

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META FILEATTACHMENT attr="h" autoattached="1" comment="Error message when sending data to VOSpec" date="1358258421" name="vospec.png" path="vospec.png" size="12133" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"

Revision 982013-02-11 - DavideRizzo

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  • The installer for Mac complains about write permissions. Why? You need write permissions for the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.
  • The installer for Windows does not start and issues the error message Not a valid Win32 application. Why? This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.
  • Why does the uninstaller leave some icons and files/directories behind? This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
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  • For other issues affecting the installer, check this page.
 

Known issues in HIPE 10.0

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META FILEATTACHMENT attr="h" autoattached="1" comment="Error message when sending data to VOSpec" date="1358258421" name="vospec.png" path="vospec.png" size="12133" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
 
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Revision 972013-02-01 - DavideRizzo

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What are all the tmp_product_sink_* pools in my local store directory?

You may find these pools in your local store directory (by default .hcss/lstore in your home directory) after reducing data with HIPE. These are temporary pools that are not deleted upon quitting HIPE due to a known bug. You can safely delete them by hand after quitting HIPE.

 
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Revision 962013-01-25 - KatrinaExter

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  The solution is to send the data again without closing the external application.
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Separate, undocked instances Cube Toolbox talk to each other

If you have two or more separate Spectrum Explorer GUIs open and at least one is undocked, when using its Cube Toolbox the separate SE instances talk to each other--spectra or new cubes you create in one instance will also appear in the other one.

 

Known issues in HIPE 9.2

New PACS calibration version 45 should not be used with HIPE 9

Revision 952013-01-24 - DavideRizzo

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Known issues in HIPE 9.2

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New PACS calibration version 45 should not be used with HIPE 9

In HIPE 10 a new spectroscopy telescope background calibration was introduced. This update is not compatible with the code in HIPE 9.

If you use the background normalisation ipipe script for chopped spectroscopy in HIPE 9, you should not update the PACS calibration tree to version 45. You should keep using the calibration set 41 and cancel the update when the automatic calibration updater in HIPE asks to install set 45.

If you have updated to set 45 and want to use the background normalisation in HIPE 9, you can switch back to version 41 in two ways:

  • With the command getCalTree(version=41).
  • By removing the file PCalBase_TimeDependency_FM_v45.fits from the directory ~/.hcss/data/pcal-community.

You can alway check the calibration version that you are using with the following command:

print getCalTree().version

If you use HIPE 10, you should update to version 45 of the calibration tree to make use of several new calibration files.

 

Issues with computePVMap task

The computePVMap task has the following issues:

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META FILEATTACHMENT attr="h" autoattached="1" comment="Error message when sending data to VOSpec" date="1358258421" name="vospec.png" path="vospec.png" size="12133" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
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Revision 942013-01-15 - DavideRizzo

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  1. Open HIPE 10. The variables shall be restored in the Variables view.
  2. Export the variables with the new format of HIPE 10, with File --> Session --> Export.
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HIPE cannot send data to an external application via SAMP

When you try to send data to an external application via the SAMP Virtual Observatory protocol, the following window may appear:

vospec.png

The reason is that HIPE tries to send data before the external application has initialised properly. This issue seems to occur more frequently with VOSpec.

The solution is to send the data again without closing the external application.

 

Known issues in HIPE 9.2

Issues with computePVMap task

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META FILEATTACHMENT attr="h" autoattached="1" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attachment="vospec.png" attr="h" comment="Error message when sending data to VOSpec" date="1358258420" name="vospec.png" path="vospec.png" size="12133" stream="vospec.png" user="Main.DavideRizzo" version="1"

Revision 932013-01-11 - DavideRizzo

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  HIPE should now be able to read the file.
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Mac OS 10.8 Mountain Lion requires Java 7 to open WebStart applications

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Cannot run WebStart applications on Mac OS Lion or Mountain Lion because of security settings

 
Changed:
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Mac OS 10.8 "Mountain Lion" requires Java Runtime Environment (JRE) 7 to open WebStart applications. WebStart applications that can be opened from within HIPE include the HSA User Interface, Aladin, VOSpec and so on. When a WebStart application is started and version 7 of the JRE is not installed, a warning with instructions is shown. Follow the instructions provided and try again.
>
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WebStart applications that can be opened from within HIPE include the HSA User Interface, Aladin, VOSpec and so on. When trying to open one of such applications, a window like the following may appear:

topcat.png

This is caused by the security settings of the Gatekeeper feature of Mac OS. For more information about Gatekeeper, see the Apple support website.

To allow a WebStart application that is blocked, change the Allow applications downloaded from option in Gatekeeper from Mac App Store to one of the two less restrictive options. If the application has a valid certificate, the Mac App Store and identified developers option will suffice. Otherwise you will need to select the Anywhere option.

 

"Invalid context" errors on Mac OS X Lion

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META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
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META FILEATTACHMENT attachment="topcat.png" attr="h" comment="Mac OS security warning for WebStart applications" date="1357901311" name="topcat.png" path="topcat.png" size="27534" stream="topcat.png" user="Main.DavideRizzo" version="1"

Revision 922013-01-11 - DavideRizzo

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Known issues in HIPE 10.0

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Pools unreadable with Unknown format version: -11 error

If you installed a developer build of HIPE 10 between 10.0.2069 and 10.0.2674 and modified any of your pools you will find those pools are no longer readable in any other HIPE version; when trying to load a pool with getObservation you will get the following error message:

herschel.ia.task.TaskException: Error processing getObservation task: Unknown format version: -11

See the Data Analysis Guide for a recovery procedure. You can download from this page the first and second script mentioned in the procedure. Change the extension from .py.txt to .py after downloading.

 

The WCS explorer for cubes does not work with PACS and SPIRE cubes

The WCS explorer does not work on cubes for which ImageIndex is used to specify the wavescale axis. This is true for SPIRE and PACS cubes. If crpix3, crval3 and cdelt3 are used instead, the WCS explorer works. To be fixed in HIPE 11.

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META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="First script to recover unreadable pools" date="1357897204" name="firstScript.py.txt" path="firstScript.py.txt" size="832" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attachment="secondScript.py.txt" attr="h" comment="Second script to recover unreadable pools" date="1357897236" name="secondScript.py.txt" path="secondScript.py.txt" size="1820" stream="secondScript.py.txt" user="Main.DavideRizzo" version="1"

Revision 912013-01-08 - DavideRizzo

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Known issues in HIPE 10.0

Added:
>
>

The WCS explorer for cubes does not work with PACS and SPIRE cubes

The WCS explorer does not work on cubes for which ImageIndex is used to specify the wavescale axis. This is true for SPIRE and PACS cubes. If crpix3, crval3 and cdelt3 are used instead, the WCS explorer works. To be fixed in HIPE 11.

 

Issues with reading text files from SExtractor or Topcat

While reading files from SExtractor or Topcat you may encounter the following issues:

Revision 902013-01-03 - DavideRizzo

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  Fixed in HIPE 9.2.
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Known issues in HIPE 8.3

None known in addition to those listed for HIPE 8.2.

Known issues in HIPE 8.2

  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.

  • PACS photometer scan map processing : Due to the new scheme of filtering turnaround manoeuvres between scan legs with the task filterOnScanSpeed task (masking frames in the 'ScanSpeedMask' mask, instead of removing the frames), photProject will project maps including the slew to target, hence exploding the memory in Hipe and leading to huge map sizes, because the photProject WCS doesn't take into account this new mask. A workaround solution is to run the filterSlew task previously, at the expense of possibly loosing a few frames on the first scan leg or alternatively run photProject in the following way:
ScanSpeedMask = frames.getMask('ScanSpeedMask')[0,0,:] 
indexSpeed    = ScanSpeedMask.where(ScanSpeedMask==False)
map          = photProject(frames.select(indexSpeed), calTree=calTree,calibration=True)
This bug shall be corrected in the next Hipe versions.

Known issues in HIPE 8.1

None known in addition to those listed for HIPE 8.0.

Known issues in HIPE 8.0

  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur.

  • Problem with NaN values with imageConvolution task. Starting from HIPE 7, the imageConvolution task works with images containing NaNs too. However, the results when NaNs are present (either in the map or around the coverage area) are not reliable. A fixed version of the task is scheduled for HIPE 9.

  • Problem with correction of MADmap point-source artifacts. The PACS task photCorrMadmapArtifacts, used to correct point-source artifacts in MADmap produced Level 2.5 products, only works when the initial time-ordered data product (TOD) is created with scale factor of 1. All other values of scale factor may produce incorrect results. A fix, possibly distributed as a plug-in, will be available later.

  • Problem with units in the Cube Spectrum Analysis Toolbox. This tool returns the wrong units of measurement with extraction plots and integrated maps. This issue has been detected with PACS data and is under investigation. Previous HIPE versions are not affected.

  • User pool names (pool ID) restrictions: Old pools that do not follow the restrictions on the allowed names cannot be read in HIPE (eg a dot "." in the name is such a case). The user can safely rename the folder (found in the local store) following the rules: allowed characters in name: alphanumeric, dash ("-") and underscore ("_"), the name cannot start with a dash ("-") and cannot have "urn" as name. The pool ID is case-sensitive and must be with less than 255 characters.

  • High memory usage with Mac OS 10.6 Snow Leopard. There are reports of HIPE 8.0.1 using all available memory and freezing while reprocessing observations under Mac OS 10.6 Snow Leopard. This problem does not seem to appear on other platforms, including other Mac OS versions. The problem is being investigated.

  • Velocity Maps in the Cube Spectrum Analysis Toolbox. Fitting of faint lines (less than 2 sigma) or non-gaussian lines can result in incorrect velocities in the velocity map. It is advised to fit the velocity in a few positions manually in the spectrum explorer and verify the consistency with the calculated velocities at these positions in the velocity map in the cube explorer.

  • Upgrade to Jython 2.5. Starting from version 8.0, HIPE will include a new version of Jython. You may have to adapt your scripts for them to work with the new version. See this page for the details.

  • Links in the User's Reference Manual. Some hyperlinks in entries of the User's Reference Manual do not work, pointing instead to the top of the same page.

  • Opening the HSA User Interface under Windows XP: If you open the HSA User Interface from HIPE while being logged in, the following error appears: JNLParseException[ Could not parse launch file. Error at line 0.]. The workaround is to log out in HIPE and start the HSA User Interface. If necessary, log in in the HSA User Interface and log back in in HIPE.

  • Sending data from HIPE to DS9 under Mac OS: Using DS9 version 6.2, due to a problem with the DS9 application, HIPE fails to start DS9 automatically. Either use DS9 version 6.1 or start DS9 manually and re-send your image from HIPE. The DS9 team states that they plan on fixing this in the next release.

  • Sending data from DS9 to HIPE under Windows. The following issues were reported when trying to send images via SAMP from DS9 to HIPE under Windows:
    • Windows 7: The option to send an image is sometimes disabled in DS9.
    • Windows XP: A SAMP message appears to be sent, but the image is not received by HIPE.
    • All Windows versions: At DS9 shutdown, the following Cygwin warning appears, even when data transfer works correctly, like in Windows Vista.

cygwinpopup.png

  • Solved known issue with step by step execution. The known issue found in HIPE 7.0 with step by step execution has been solved. You can revert to the old behaviour by choosing Edit --> Preferences, going to Editors & Viewers --> Jython Editor and unticking the Use improved step by step execution checkbox.

  • HIPE drops Versant database connection under Windows XP: A problem can occur if HIPE is run under Windows XP connected via WiFi to a Versant database server. If the connection is interrupted briefly, the HIPE session may fail with a "Network layer read error". Linux does not have this problem because it keeps retrying for several minutes.

  • Garbled text after horizontal scrolling in Ubuntu 11.10. A problem on systems with NVidia cards and running Ubuntu 11.10 can cause text to appear garbled when scrolling horizontally, as shown by the figure below. To solve the problem, add the following property to the user.props file, located in the .hcss directory within your home directory. If there is no user.props file, create it.

java.vm.options = -Dsun.java2d.opengl=true

garbledtext.png

 

Older HIPE versions

Known issues for older HIPE versions are listed in a separate page.

Line: 379 to 316
  HIPE should now be able to read the file.
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Mac OS 10.8 Mountain Lion requires Java 7 to open WebStart applications

Mac OS 10.8 "Mountain Lion" requires Java Runtime Environment (JRE) 7 to open WebStart applications. WebStart applications that can be opened from within HIPE include the HSA User Interface, Aladin, VOSpec and so on. When a WebStart application is started and version 7 of the JRE is not installed, a warning with instructions is shown. Follow the instructions provided and try again.

 

"Invalid context" errors on Mac OS X Lion

When you start HIPE form a Terminal window on Mac OS X Lion, you may see errors such as these:

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META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
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META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"

Revision 892012-11-23 - DavideRizzo

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 convertL1ToScanam(frames,assignRaDec=False)
Added:
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Fixed in HIPE 9.2.
 

Known issues in HIPE 8.3

None known in addition to those listed for HIPE 8.2.

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META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
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Revision 882012-11-23 - DavideRizzo

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  1. Open HIPE 10. The variables shall be restored in the Variables view.
  2. Export the variables with the new format of HIPE 10, with File --> Session --> Export.
Added:
>
>

Known issues in HIPE 9.2

Issues with computePVMap task

The computePVMap task has the following issues:

  • There are remaining aesthetic issues regarding the pvMap aspect ratio modification in the task.
  • There is a known error when extracting a pvMap with row < col (velocity dimension < spatial dimension). Workaround: set the correctAspectRatio parameter to False (in the graphical interface, untick the corresponding checkbox).
 

Known issues in HIPE 9.1

None known in addition to those listed for HIPE 9.0.

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META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
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META FILEATTACHMENT attr="h" autoattached="1" comment="Script for Google Analytics" date="1351239505" name="GoogleAnalytics.txt" path="GoogleAnalytics.txt" size="549" user="Main.DavideRizzo" version="1"

Revision 872012-11-21 - DavideRizzo

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Known issues in HIPE 10.0

Changed:
<
<
  • Format change for exported variables. The file format of variables exported with File --> Session --> Export has changed in HIPE 10. This means that HIPE 10 will not be able to read session variables exported with HIPE 9, and vice-versa.
    If you exported variables with HIPE 9 or a previous version, follow this workaround to read them in HIPE 10:
>
>

Issues with reading text files from SExtractor or Topcat

While reading files from SExtractor or Topcat you may encounter the following issues:

  • Some SExtractor headers are not read successfully, due to an issue with the column position of units in the file header. Workaround: read the file with the tableType parameter set to SPACES. You can then fill any missing information by hand.
  • Some Topcat files are not read successfully, due to an issue with quoted cells with spaces. Workaround: export the data from Topcat in FITS format, then read the FITS file back into HIPE. For information about reading FITS files into HIPE, see the Data Analysis Guide.

Format change for exported variables

The file format of variables exported with File --> Session --> Export has changed in HIPE 10. This means that HIPE 10 will not be able to read session variables exported with HIPE 9, and vice-versa.
If you exported variables with HIPE 9 or a previous version, follow this workaround to read them in HIPE 10:

 
  1. Open HIPE 9 and import the exported variables with File --> Session --> Import.
  2. Set Save variables on exit in the Preferences dialogue window, under General --> Startup & Shutdown.
Line: 36 to 45
 

Known issues in HIPE 9.0

Changed:
<
<
  • Performance issues of convolution task with NaN values. The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem. Fixed in HIPE 9.1.
>
>

Performance issues of convolution task with NaN values

The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem. Fixed in HIPE 9.1.

 
Changed:
<
<
  • Performance issues with very large images. Images larger than about 100 MB in FITS format can still take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.
>
>

Performance issues with very large images

 
Changed:
<
<
  • Problem with PACS background normalization script. The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:
>
>
Images larger than about 100 MB in FITS format can still take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.

Problem with PACS background normalization script

The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:

 
target = obs.meta["object"].value.replace(" ","_")
Changed:
<
<
  • PACS task specFlatFieldLine problem with NaN values. The specFlatFieldLine task cannot handle NaNs in the fluxes of PacsCube products. This affected one observation as far as we tested. If you encounter this problem then you can mask the NaNs by running the function shown below. Copy and paste the function code in a new Jython script window in the Editor view of HIPE, then click the green double arrow icon in the HIPE toolbar to run the script. After that you can call the function from the Console view, passing the variable contaning your cube as argument: addInvalidMask(myCube).
>
>

PACS task specFlatFieldLine problem with NaN values

The specFlatFieldLine task cannot handle NaNs in the fluxes of PacsCube products. This affected one observation as far as we tested. If you encounter this problem then you can mask the NaNs by running the function shown below. Copy and paste the function code in a new Jython script window in the Editor view of HIPE, then click the green double arrow icon in the HIPE toolbar to run the script. After that you can call the function from the Console view, passing the variable contaning your cube as argument: addInvalidMask(myCube).

 
def addInvalidMask(slicedCube):
    for i in range(0,slicedCube.numberOfSlices):
Line: 57 to 74
  slicedCube.replace(i,cube)
Changed:
<
<
  • HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions. This button is enabled only when you change the state of one or more masks. Fixed in HIPE 9.1.
    <-- PACS-4626 -->
>
>

HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions

This button is enabled only when you change the state of one or more masks. Fixed in HIPE 9.1.

<-- PACS-4626 -->
 
Changed:
<
<
  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks. To be fixed in HIPE 10. The problem affects the following tasks:
>
>

Image analysis tasks start only from Applicable section

Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks. To be fixed in HIPE 10. The problem affects the following tasks:

 
    • annularSkyAperturePhotometry
    • circleHistogram
    • crop
Line: 71 to 92
 
    • rectangularSkyAperturePhotometry
    • sourceFitting
Changed:
<
<
  • PV diagrams created with computePVMap on HIFI cubes cannot be easily viewed. HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: open the variable created from the variables pane and use the full Display/Image Viewer.
>
>

PV diagrams created with computePVMap on HIFI cubes cannot be easily viewed

HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: open the variable created from the variables pane and use the full Display/Image Viewer.

 
<-- use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in Appendix C of the Data Analysis Guide. For position-velocity diagrams, see subsection C.6.8.1.-->
Changed:
<
<
  • HIPE crash linked to JAMA (Java Matrix) library. HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
>
>

HIPE crash linked to JAMA (Java Matrix) library

HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:

 
    1. Go to the .hcss directory in your open directory. Open the hipe.props file, or create it if it does not exist.
    2. Add the following line to the file:
      java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>
    3. Restart HIPE.
Changed:
<
<
  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur. To be fixed in HIPE 10.
>
>

Problem with transpose task

In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur. To be fixed in HIPE 10.

Velocity map creation in Legacy Cube Spectrum Analysis Toobox (CSAT) fails

The creation of velocity maps with the Legacy CSAT fails; the task will hang without an error message. CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead. See 6.8.3 in the Herschel Data Analysis Guide for information about using the new cube toolbox.

Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task

This is a display issue only, the flags set by flagTool are, in fact, used.

 
Changed:
<
<
  • Velocity map creation in Legacy Cube Spectrum Analysis Toobox (CSAT) fails. The creation of velocity maps with the Legacy CSAT fails; the task will hang without an error message. CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead. See 6.8.3 in the Herschel Data Analysis Guide for information about using the new cube toolbox.
>
>

PACS specific: convertL1ToScanam fails

 
Changed:
<
<
  • Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task. This is a display issue only, the flags set by flagTool are, in fact, used.
>
>
convertL1ToScanam fails because of a missing import for the calibration tree, when assignRaDec is set to True. The work around solution is :
 
Deleted:
<
<
  • PACS specific:
    • convertL1ToScanam fails because of a missing import for the calibration tree, when assignRaDec is set to True. The work around solution is :
 
      calTree = getCalTree(time=frames.startDate)
      frames=photAssignRaDec(frames,calTree=calTree)

Revision 862012-11-19 - DavideRizzo

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  HIPE should now be able to read the file.
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"Invalid context" errors on Mac OS X Lion

When you start HIPE form a Terminal window on Mac OS X Lion, you may see errors such as these:

java[40745] <Error>: CGContextGetCTM: invalid context

These errors are harmless and can be safely ignored.

 

Jython bug when comparing NaN values with numbers

Jython behaves differently from Python when comparing NaN values with numbers.

Revision 852012-10-31 - DavideRizzo

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HIPE known issues

Changed:
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Help Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to installation, startup, help and other issues common to different HIPE versions.
>
>
Help Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to installation/uninstallation, startup, help, Science Archive and other issues common to different HIPE versions.
 
ALERT! This page is for known issues in the HIPE software. For known issues in data products see this page.

Changed:
<
<

Installation issues

>
>

Installation and uninstallation issues

 
  • Cannot install on Mac OS X 10.8 "Mountain Lion". HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
    • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
    • In Mac OS X, from System Preferences --> Security & Privacy --> General --> Allow applications downloads from select ANYWHERE.
Added:
>
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  • The installer for Mac complains about write permissions. Why? You need write permissions for the directory where you want to install HIPE. For example, you need Administrator privileges to install in /Applications. If you have installed HIPE successfully in the past, and are now experiencing write permission problems, it may be that some other application changed the permissions in the meantime. There have been cases of scientific applications such as SciSoft doing this. Once you revert write permissions to their correct values, HIPE installation should succeed.
  • The installer for Windows does not start and issues the error message Not a valid Win32 application. Why? This problem has been encountered under Windows Vista because the installer had not been downloaded correctly, resulting in an empty file. The exact cause is not yet known. As a workaround, try downloading the installer in a different way (for instance, via command line FTP rather than a web browser) or from another computer.
  • Why does the uninstaller leave some icons and files/directories behind? This incomplete uninstallation is a known issue and may be caused by a corrupted InstallAnywhere global registry. As a workaround, try renaming the InstallAnywhere registry file. See point 7 in the InstallAnywhere issues page for detailed information. If you add files (such as Jython scripts) into HIPE directories after installation, these will not be removed by the uninstaller.
 

Known issues in HIPE 10.0

Line: 217 to 220
  This error is probably due to a bug in the Java Virtual Machine, and has so far been found only on Windows XP 32 bit.
Added:
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I get startup messages about missing HIFI/PACS/SPIRE modules. Is that serious?

You are probably referring to messages such as the following (for HIFI; messages for PACS and SPIRE are the same):

Import "from herschel.hifi.all import *" returns:
          Import Error -> No module named hifi

Such messages are harmless and just reflect the fact that you have not installed the software related to the specified instruments.

 

General Help System issues

The help does not work anymore! What's wrong?

Line: 239 to 253
  Yes, via the hipe_help command, which resides in the apps folder in your HIPE installation. The hipe_help command will start a standalone Help System in a window called Yet Another JAva Help System. Press the Display button to open the Help initial page in your default browser.
Added:
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The Help System opens in my web browser. Does it mean I need to be connected to the Internet?

No, the Help System resides on your computer and does not need Internet connection, except of course for links to online resources, such as YouTube videos and pages hosted on the Herschel Wiki website, including the What's New and Known Issues documents.

 

Why does searching the documentation take such a long time?

When you execute the first search with a new HIPE version, HIPE has to index the contents of the documentation. This can take up to several minutes, depending on the performance of your system. Indexing of the documentation is only done for the first search. Subsequent searches will be much faster.

We are investigating ways to include pre-built indexes in the documentation shipped with HIPE, so you will not have to wait for the results of your first search.

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The Help System opens in my web browser. Does it mean I need to be connected to the Internet?

No, the Help System resides on your computer and does not need Internet connection, except for the What's New document, which is hosted on the Herschel Wiki website.

 

Why is the HIPE Help System suddenly unable to connect to any help page?

The Help System relies on a local web server to display help pages. If you close the application that started the web server, the server will shut down as well:

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  • URM examples: Some examples in the User's Reference Manuals may not work as expected. Please use the feedback icon in the HIPE Help System to let us know about broken examples.
  • JIDE vs HIPE: The documentation shipped with HIPE may still mention JIDE in some places. JIDE was the data reduction application that came before HIPE and is no longer supported. All references to JIDE can be applied to HIPE.
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Herschel Science Archive issues

I have downloaded FITS files in a tar archive from the HSA, but they are corrupted. How can I fix them?

You may have used WinZip under Windows. WinZip has an option called TAR file smart CR/LF conversion, in the Miscellaneous tab of the Configuration dialogue window (at least up to version 15.0), that is enabled by default and causes the corruption. Disable the option to solve this problem. You can also use other software such as 7-Zip.

In the HSA user interface I can query and select observations, but I do not get the option in the HSA to pass the data to HIPE, or in HIPE to load the selected products. Why?

If you are using Windows, the problem might be that you instructed your browser to auto-detect proxy settings. In Windows this is a system-wide setting which affects any application connecting to the Internet, including HIPE.

You can change proxy settings for HIPE by following the instructions in the HIPE Owner's Guide.

When I click Send to external Application in the HSA interface, nothing seems to happen. What is going on?

The data is being transferred in the background. Clicking Send to external Application should bring to the front the main HIPE window, which will tell you that data is indeed being received. In some cases however the HIPE window does not appear. Bring it to the front manually to follow the progress of your action.

When I try to retrieve data from the HSA I get an error message in the console about an invalid magic number for FITS file. What is going on?

The reason is that the "data" being downloaded is in reality a small file containing an error message. Two issues have been shown to cause this problem:

  • Your HSA password has non-alphanumeric characters in it. Change it to a password containing only letters and numbers.
  • Your HSA username has uppercase characters. Write it using only lowercase letters.
 

Other issues

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HIPE crashed/froze! What do I do?

If you cannot find a solution in this document, you may have found a bug in HIPE. Please report it by opening a Helpdesk ticket. If the system produced a dump file when the crash happened, make sure to include it in your ticket. For more information about dump files and where to look for them, see the HIPE Owner's Guide.

 

Cannot open a FITS file created by HIPE

If you export a FITS file from HIPE and modify it with an external program, HIPE may not be able to import it anymore. If this happens, follow these steps:

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hcss.ia.pal.pool.lstore.lock = simple
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See the HIPE Owner's Guide for information on how to set properties.
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See the HIPE Owner's Guide for information on how to set properties.
 

Why do I get a ClassCastException when trying to save an observation with the saveObservation command?

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    • home/.hcss/pal_cache/hsa
  1. Retrieve the observation again.
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I get an OutOfMemoryError related to PermGen space. What can I do?

Add or edit the following property in your hipe.props property file:

java.vm.options = -XX:MaxPermSize=256m

Note that this parameter is specific to the Sun/Oracle Java implementation, which is the only one officially supported by HIPE.

For more information about property files, see the HIPE Owner's Guide.

There are PACS files I cannot delete! Why?

It might not be possible to delete the following files on Windows because their full path exceeds the 260 characters limit.

  • PCalSpectrometer_RelCalSourceFlux_FM_v1.fits_2009...80Z.fits
  • PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...55Z.fits
  • PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...14Z.fits
  • PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...21Z.fits
  • PCalSpectrometer_RelCalSourceFlux_FM_v2.fits_2009...58Z.fits

You can avoid this problem by installing HIPE with a short initial path, such as C:\hipe, so that full paths remain below the limit.

HIPE does not accept keyboard input anymore! What's wrong?

If you are running Linux, this could be due to a compatibility problem between Java and SCIM (Smart Common Input Method). A workaround is to stop SCIM or uninstall it. Please refer to the documentation of your distribution for how to do so.

The problem is described in more detail on these pages:

 
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Revision 842012-10-29 - DavideRizzo

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  1. Open HIPE 10. The variables shall be restored in the Variables view.
  2. Export the variables with the new format of HIPE 10, with File --> Session --> Export.
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Known issues in HIPE 9.1

None known in addition to those listed for HIPE 9.0.

 

Known issues in HIPE 9.0

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  • Performance issues of convolution task with NaN values. The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem.
>
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  • Performance issues of convolution task with NaN values. The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem. Fixed in HIPE 9.1.
 
  • Performance issues with very large images. Images larger than about 100 MB in FITS format can still take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.
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  slicedCube.replace(i,cube)
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  • HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions. This button is enabled only when you change the state of one or more masks.
    <-- PACS-4626 -->
>
>
  • HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions. This button is enabled only when you change the state of one or more masks. Fixed in HIPE 9.1.
    <-- PACS-4626 -->
 
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  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks. The problem affects the following tasks:
>
>
  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks. To be fixed in HIPE 10. The problem affects the following tasks:
 
    • annularSkyAperturePhotometry
    • circleHistogram
    • crop
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    1. Add the following line to the file:
      java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>
    2. Restart HIPE.
Changed:
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<
  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur.
>
>
  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur. To be fixed in HIPE 10.
 
  • Velocity map creation in Legacy Cube Spectrum Analysis Toobox (CSAT) fails. The creation of velocity maps with the Legacy CSAT fails; the task will hang without an error message. CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead. See 6.8.3 in the Herschel Data Analysis Guide for information about using the new cube toolbox.
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Revision 832012-10-26 - DavideRizzo

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HIPE known issues

Help Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to installation, startup, help and other issues common to different HIPE versions.
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  • HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions. This button is enabled only when you change the state of one or more masks.
    <-- PACS-4626 -->
Changed:
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<
  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks.
>
>
  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks. The problem affects the following tasks:
    • annularSkyAperturePhotometry
    • circleHistogram
    • crop
    • ellipseHistogram
    • fixedSkyAperturePhotometry
    • polygonHistogram
    • profile
    • rectangleHistogram
    • rectangularSkyAperturePhotometry
    • sourceFitting
 
  • PV diagrams created with computePVMap on HIFI cubes cannot be easily viewed. HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: open the variable created from the variables pane and use the full Display/Image Viewer.
<-- use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in Appendix C of the Data Analysis Guide. For position-velocity diagrams, see subsection C.6.8.1.-->
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Revision 822012-10-18 - DavideRizzo

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HIPE known issues

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    • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
    • In Mac OS X, from System Preferences --> Security & Privacy --> General --> Allow applications downloads from select ANYWHERE.
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Known issues in HIPE 10.0

  • Format change for exported variables. The file format of variables exported with File --> Session --> Export has changed in HIPE 10. This means that HIPE 10 will not be able to read session variables exported with HIPE 9, and vice-versa.
    If you exported variables with HIPE 9 or a previous version, follow this workaround to read them in HIPE 10:

  1. Open HIPE 9 and import the exported variables with File --> Session --> Import.
  2. Set Save variables on exit in the Preferences dialogue window, under General --> Startup & Shutdown.
  3. Exit HIPE 9.
  4. Open HIPE 10. The variables shall be restored in the Variables view.
  5. Export the variables with the new format of HIPE 10, with File --> Session --> Export.
 

Known issues in HIPE 9.0

  • Performance issues of convolution task with NaN values. The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem.

Revision 812012-10-15 - DavideRizzo

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HIPE known issues

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Other issues

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Cannot open a FITS file created by HIPE

If you export a FITS file from HIPE and modify it with an external program, HIPE may not be able to import it anymore. If this happens, follow these steps:

  1. Open the FITS file with a FITS editing program such as fv.
  2. Delete the HCSS____ keyword from the header of all extensions.
  3. Save the file.

HIPE should now be able to read the file.

 

Jython bug when comparing NaN values with numbers

Jython behaves differently from Python when comparing NaN values with numbers.

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Revision 802012-09-19 - DavideRizzo

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HIPE known issues

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ALERT! This page is for known issues in the HIPE software. For known issues in data products see this page.
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ALERT! See this page for documentation errata and last-minute updates.
 

Installation issues

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How can I provide feedback/requests regarding HIPE documentation?

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For informal feedback, click on the envelope icon on the top toolbar of any help page. This opens a new message in your email client, where you can add your feedback. If you want your issue to be officially tracked and supported, please raise a ticket with the Helpdesk of the Herschel Science Centre.
>
>
You can leave a comment using the box at the bottom of any documentation page in the HIPE Help System. You must be connected to the Internet to view and submit comments.

Alternatively, you can click the envelope icon on the top toolbar of any help page. This opens a new message in your email client, where you can add your feedback.

If you want your issue to be officially tracked and supported, please raise a ticket with the Helpdesk of the Herschel Science Centre.

Other help issues

  • URM categories: Some entries in the three instruments User's Reference Manuals have wrong or missing categories.
  • URM examples: Some examples in the User's Reference Manuals may not work as expected. Please use the feedback icon in the HIPE Help System to let us know about broken examples.
  • JIDE vs HIPE: The documentation shipped with HIPE may still mention JIDE in some places. JIDE was the data reduction application that came before HIPE and is no longer supported. All references to JIDE can be applied to HIPE.
 

Other issues

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Revision 792012-09-12 - DavideRizzo

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Help Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to startup, help and other issues common to different HIPE versions.
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Help Welcome to the known issues page. Please take a look at the table of contents below. You can find known issues for each HIPE version, in addition to installation, startup, help and other issues common to different HIPE versions.
 
ALERT! This page is for known issues in the HIPE software. For known issues in data products see this page.
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Installation issues

  • Cannot install on Mac OS X 10.8 "Mountain Lion". HIPE user installers do not work on Mac OS X 10.8 due to additional security checks implemented by this operating system. Note that HIPE is not yet officially supported on Mac OS X 10.8. There are two workarounds:
    • In a terminal window, use the chmod u+x command to change the permissions of the file HIPE_9_1_0_INSTALLER.app/Contents/MacOS/HIPE_9_1_0_INSTALLER. Change the file name according to the HIPE version you are installing.
    • In Mac OS X, from System Preferences --> Security & Privacy --> General --> Allow applications downloads from select ANYWHERE.
 

Known issues in HIPE 9.0

  • Performance issues of convolution task with NaN values. The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem.

Revision 782012-08-10 - CarolynMcCoey

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HIPE known issues

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  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur.
Changed:
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  • Velocity map creation in Legacy Cube Spectrum Analysis Toobox (CSAT) fails. The creation of velocity maps with the Legacy CSAT fails; the task will hang without an error message. CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead. See 6.8.3 in the Herschel Daat Analysis Guide for information about using the new cube toolbox.
>
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  • Velocity map creation in Legacy Cube Spectrum Analysis Toobox (CSAT) fails. The creation of velocity maps with the Legacy CSAT fails; the task will hang without an error message. CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead. See 6.8.3 in the Herschel Data Analysis Guide for information about using the new cube toolbox.
 
  • Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task. This is a display issue only, the flags set by flagTool are, in fact, used.

Revision 772012-08-03 - DavideRizzo

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HIPE known issues

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Known issues in HIPE 9.0

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  • Performance issues of convolution task with NaN values. The performance of the imageConvolution task is severely degraded when NaN values are found in input data. HIPE 8.3 is not affected by this problem.
 
  • Performance issues with very large images. Images larger than about 100 MB in FITS format can still take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.

  • Problem with PACS background normalization script. The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:
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Revision 762012-07-25 - BrunoMerin

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Known issues in HIPE 9.0

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  • Performance issues with large images. Images larger than about 100 MB in FITS format can take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.
>
>
  • Performance issues with very large images. Images larger than about 100 MB in FITS format can still take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.
 
  • Problem with PACS background normalization script. The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:
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META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"

Revision 752012-07-25 - BrunoMerin

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Changed:
<
<
  • Performance degradation with large images. Images larger than about 100 MB in FITS format can take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.
>
>
  • Performance issues with large images. Images larger than about 100 MB in FITS format can take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.
 
  • Problem with PACS background normalization script. The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:

Revision 742012-07-25 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Added:
>
>
  • Performance degradation with large images. Images larger than about 100 MB in FITS format can take over a minute to load. During such time HIPE is unresponsive. Image analysis operations, such as cropping and adding contours, also take a long time on large images.
 
  • Problem with PACS background normalization script. The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:
target = obs.meta["object"].value.replace(" ","_")

Revision 732012-07-20 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Added:
>
>
  • Problem with PACS background normalization script. The ChopNodBackgroundNormalizationRange interactive pipeline script (Pipelines --> PACS --> Spectrometer --> Chopper large range scan SED --> Background Normalization) is missing a definition of the variable target. After loading the observation, assuming it is stored in a variable called obs, you can define the missing target variable as follows:
target = obs.meta["object"].value.replace(" ","_")

  • PACS task specFlatFieldLine problem with NaN values. The specFlatFieldLine task cannot handle NaNs in the fluxes of PacsCube products. This affected one observation as far as we tested. If you encounter this problem then you can mask the NaNs by running the function shown below. Copy and paste the function code in a new Jython script window in the Editor view of HIPE, then click the green double arrow icon in the HIPE toolbar to run the script. After that you can call the function from the Console view, passing the variable contaning your cube as argument: addInvalidMask(myCube).
def addInvalidMask(slicedCube):
    for i in range(0,slicedCube.numberOfSlices):
       cube = slicedCube.get(i)
       invalid = IS_NAN(cube.flux)
       if not cube.containsMask("INVALID"):
          cube.addMask("INVALID","Invalid signal values")
       cube.setMask("INVALID",invalid)
       slicedCube.replace(i,cube)
 
  • HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions. This button is enabled only when you change the state of one or more masks.
    <-- PACS-4626 -->

  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks.
Line: 290 to 307
 
<-- END OF COMMENT BOX CODE -->

Deleted:
<
<
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"

Revision 722012-07-19 - BrunoAltieri

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 32 to 32
 
  • PACS specific:
    • convertL1ToScanam fails because of a missing import for the calibration tree, when assignRaDec is set to True. The work around solution is :
Changed:
<
<
    1.  calTree = getCalTree(time=frames.startDate)
    2.  frames=photAssignRaDec(frames,calTree=calTree)
    3.  convertL1ToScanam(frames,assignRaDec=False)
>
>
      calTree = getCalTree(time=frames.startDate)
      frames=photAssignRaDec(frames,calTree=calTree)
      convertL1ToScanam(frames,assignRaDec=False)
      
 

Known issues in HIPE 8.3

Line: 45 to 47
 
  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.

  • PACS photometer scan map processing : Due to the new scheme of filtering turnaround manoeuvres between scan legs with the task filterOnScanSpeed task (masking frames in the 'ScanSpeedMask' mask, instead of removing the frames), photProject will project maps including the slew to target, hence exploding the memory in Hipe and leading to huge map sizes, because the photProject WCS doesn't take into account this new mask. A workaround solution is to run the filterSlew task previously, at the expense of possibly loosing a few frames on the first scan leg or alternatively run photProject in the following way:
Changed:
<
<
==
>
>
 ScanSpeedMask = frames.getMask('ScanSpeedMask')[0,0,:] indexSpeed = ScanSpeedMask.where(ScanSpeedMask==False) map = photProject(frames.select(indexSpeed), calTree=calTree,calibration=True)
Changed:
<
<
==
>
>
 This bug shall be corrected in the next Hipe versions.

Known issues in HIPE 8.1

Revision 712012-07-19 - BrunoAltieri

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 31 to 31
 
  • Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task. This is a display issue only, the flags set by flagTool are, in fact, used.

  • PACS specific:
Changed:
<
<
    • convertL1ToScanam fails because of a missing import for the calibration tree. The following line should be added:
from herschel.pacs.cal.all import getCalTree
>
>
    • convertL1ToScanam fails because of a missing import for the calibration tree, when assignRaDec is set to True. The work around solution is :
    1.  calTree = getCalTree(time=frames.startDate)
    2.  frames=photAssignRaDec(frames,calTree=calTree)
    3.  convertL1ToScanam(frames,assignRaDec=False)
 

Known issues in HIPE 8.3

Line: 45 to 45
 
  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.

  • PACS photometer scan map processing : Due to the new scheme of filtering turnaround manoeuvres between scan legs with the task filterOnScanSpeed task (masking frames in the 'ScanSpeedMask' mask, instead of removing the frames), photProject will project maps including the slew to target, hence exploding the memory in Hipe and leading to huge map sizes, because the photProject WCS doesn't take into account this new mask. A workaround solution is to run the filterSlew task previously, at the expense of possibly loosing a few frames on the first scan leg or alternatively run photProject in the following way:
Changed:
<
<
>
>
==
 ScanSpeedMask = frames.getMask('ScanSpeedMask')[0,0,:] indexSpeed = ScanSpeedMask.where(ScanSpeedMask==False) map = photProject(frames.select(indexSpeed), calTree=calTree,calibration=True)
Changed:
<
<
>
>
==
 This bug shall be corrected in the next Hipe versions.

Known issues in HIPE 8.1

Revision 702012-07-19 - BrunoAltieri

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 30 to 30
 
  • Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task. This is a display issue only, the flags set by flagTool are, in fact, used.
Added:
>
>
  • PACS specific:
    • convertL1ToScanam fails because of a missing import for the calibration tree. The following line should be added:
from herschel.pacs.cal.all import getCalTree
 

Known issues in HIPE 8.3

None known in addition to those listed for HIPE 8.2.

Revision 692012-07-19 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Added:
>
>
  • HIPE hangs when pressing the activate/deactivate button in the mask panel of the Spectrum Explorer PACS extensions. This button is enabled only when you change the state of one or more masks.
    <-- PACS-4626 -->
 
  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks.

  • PV diagrams created with computePVMap on HIFI cubes cannot be easily viewed. HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: open the variable created from the variables pane and use the full Display/Image Viewer.
Line: 280 to 282
 
<-- END OF COMMENT BOX CODE -->

Deleted:
<
<
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"
Added:
>
>
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"

Revision 682012-07-18 - CarolynMcCoey

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 14 to 14
 
  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks.
Changed:
<
<
  • PV diagrams created with computePVMap on HIFI cubes cannot be viewed. HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in Appendix C of the Data Analysis Guide. For position-velocity diagrams, see subsection C.6.8.1.
>
>
  • PV diagrams created with computePVMap on HIFI cubes cannot be easily viewed. HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: open the variable created from the variables pane and use the full Display/Image Viewer.
<-- use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in Appendix C of the Data Analysis Guide. For position-velocity diagrams, see subsection C.6.8.1.-->
 
  • HIPE crash linked to JAMA (Java Matrix) library. HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
    1. Go to the .hcss directory in your open directory. Open the hipe.props file, or create it if it does not exist.
Line: 279 to 280
 
<-- END OF COMMENT BOX CODE -->

Deleted:
<
<
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
Added:
>
>
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"

Revision 672012-07-12 - CarolynMcCoey

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 23 to 23
 
  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur.
Added:
>
>
  • Velocity map creation in Legacy Cube Spectrum Analysis Toobox (CSAT) fails. The creation of velocity maps with the Legacy CSAT fails; the task will hang without an error message. CSAT is no longer supported and the new cube toolbox, which uses an improved algorithm for velocity map making, should be used instead. See 6.8.3 in the Herschel Daat Analysis Guide for information about using the new cube toolbox.

  • Flag set in HIFI's flagTool task do not appear to be used by the fitBaseline task. This is a display issue only, the flags set by flagTool are, in fact, used.
 

Known issues in HIPE 8.3

None known in addition to those listed for HIPE 8.2.

Revision 662012-07-04 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Added:
>
>
  • Image analysis tasks start only from Applicable section. Image analysis tasks will open only from the Applicable folder of the Tasks view. These tasks will not open when selected from the All or By Category folders. Note that you must select an image variable in the Variables view for the Applicable folder to be filled with the available tasks.
 
  • PV diagrams created with computePVMap on HIFI cubes cannot be viewed. HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in Appendix C of the Data Analysis Guide. For position-velocity diagrams, see subsection C.6.8.1.

  • HIPE crash linked to JAMA (Java Matrix) library. HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
Line: 273 to 275
 
<-- END OF COMMENT BOX CODE -->

Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
Deleted:
<
<
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"

Revision 652012-07-03 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 21 to 21
 
  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur.
Added:
>
>

Known issues in HIPE 8.3

None known in addition to those listed for HIPE 8.2.

 

Known issues in HIPE 8.2

  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.
Line: 269 to 273
 
<-- END OF COMMENT BOX CODE -->

Deleted:
<
<
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"

Revision 642012-06-27 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Added:
>
>
  • PV diagrams created with computePVMap on HIFI cubes cannot be viewed. HIFI cubes have in general a small number of rows and columns, while the spectral dimension is rather large (thousands of channels). The PV map is very narrow in the x direction and really wide in the y-direction, so that it does not fit in the Spectrum panel. When displaying the y-axis values, at its smaller zoom, only a small number of channels can be seen. Workaround: use the old Cube Spectrum Analysis Toolbox, still available in HIPE 9. Legacy documentation is available in Appendix C of the Data Analysis Guide. For position-velocity diagrams, see subsection C.6.8.1.
 
  • HIPE crash linked to JAMA (Java Matrix) library. HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
    1. Go to the .hcss directory in your open directory. Open the hipe.props file, or create it if it does not exist.
    2. Add the following line to the file:
      java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>
Line: 267 to 269
 
<-- END OF COMMENT BOX CODE -->

Added:
>
>
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"
 
META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"
Deleted:
<
<
META FILEATTACHMENT attr="" autoattached="1" comment="Garbled text after horizontal scrolling, in Ubuntu 11.10 with NVidia card" date="1327331942" name="garbledtext.png" path="garbledtext.png" size="18498" user="Main.DavideRizzo" version="1"

Revision 632012-06-11 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 17 to 17
 
    1. Add the following line to the file:
      java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>
    2. Restart HIPE.
Added:
>
>
  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur.
 

Known issues in HIPE 8.2

  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.

Revision 622012-06-06 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Deleted:
<
<
  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.
 
  • HIPE crash linked to JAMA (Java Matrix) library. HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
    1. Go to the .hcss directory in your open directory. Open the hipe.props file, or create it if it does not exist.
    2. Add the following line to the file:
      java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>

Revision 612012-06-05 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 12 to 12
 

Known issues in HIPE 9.0

Added:
>
>
  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.
 
  • HIPE crash linked to JAMA (Java Matrix) library. HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
    1. Go to the .hcss directory in your open directory. Open the hipe.props file, or create it if it does not exist.
    2. Add the following line to the file:
      java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>
Line: 19 to 21
 

Known issues in HIPE 8.2

Added:
>
>
  • Task createRgbImage puts wrong WCS in the output. Instead of using the WCS provided by the Wcs input parameter, this task uses the WCS of one of the input images.
 
  • PACS photometer scan map processing : Due to the new scheme of filtering turnaround manoeuvres between scan legs with the task filterOnScanSpeed task (masking frames in the 'ScanSpeedMask' mask, instead of removing the frames), photProject will project maps including the slew to target, hence exploding the memory in Hipe and leading to huge map sizes, because the photProject WCS doesn't take into account this new mask. A workaround solution is to run the filterSlew task previously, at the expense of possibly loosing a few frames on the first scan leg or alternatively run photProject in the following way:
ScanSpeedMask = frames.getMask('ScanSpeedMask')[0,0,:] 

Revision 602012-05-29 - DavideRizzo

Line: 1 to 1
 
META TOPICPARENT name="WebHome"

HIPE known issues

Line: 33 to 33
 

Known issues in HIPE 8.0

Added:
>
>
  • Problem with transpose task. In some cases the transpose task does not convert correctly the WCS of the input image. This problem occurs only when the WCS of the image defines the rotation angle (CROTA2). When the transformation matrix (PCx_y or CDx_y) is used, the problem does not occur.
 
  • Problem with NaN values with imageConvolution task. Starting from HIPE 7, the imageConvolution task works with images containing NaNs too. However, the results when NaNs are present (either in the map or around the coverage area) are not reliable. A fixed version of the task is scheduled for HIPE 9.

  • Problem with correction of MADmap point-source artifacts. The PACS task photCorrMadmapArtifacts, used to correct point-source artifacts in MADmap produced Level 2.5 products, only works when the initial time-ordered data product (TOD) is created with scale factor of 1. All other values of scale factor may produce incorrect results. A fix, possibly distributed as a plug-in, will be available later.

Revision 592012-05-23 - DavideRizzo

Line: 1 to 1
 
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HIPE known issues

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Known issues in HIPE 9.0

  • HIPE crash linked to JAMA (Java Matrix) library. HIPE may crash without warning when executing parts of the bundled JAMA library. If you experience a sudden crash when running a script, this may be the cause, even if there are no obvious references to matrices in the script. Take the following steps to prevent the crash from happening:
    1. Go to the .hcss directory in your open directory. Open the hipe.props file, or create it if it does not exist.
    2. Add the following line to the file:
      java.vm.options = -XX:CompileCommand=exclude,Jama/LUDecomposition,<init>
    3. Restart HIPE.
 

Known issues in HIPE 8.2

  • PACS photometer scan map processing : Due to the new scheme of filtering turnaround manoeuvres between scan legs with the task filterOnScanSpeed task (masking frames in the 'ScanSpeedMask' mask, instead of removing the frames), photProject will project maps including the slew to target, hence exploding the memory in Hipe and leading to huge map sizes, because the photProject WCS doesn't take into account this new mask. A workaround solution is to run the filterSlew task previously, at the expense of possibly loosing a few frames on the first scan leg or alternatively run photProject in the following way:

Revision 582012-05-14 - DavideRizzo

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HIPE known issues

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    • home/.hcss/pal_cache/hsa
  1. Retrieve the observation again.
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<-- COMMENT BOX CODE - DO NOT EDIT -->
blog comments powered by Disqus
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META FILEATTACHMENT attr="h" autoattached="1" comment="Cygwin warning when closing DS9." date="1320242088" name="cygwinpopup.png" path="cygwinpopup.png" size="28796" user="Main.DavideRizzo" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="Screenshot for: PAL Storage Manager: Can't add pools to storages" date="1279552092" name="HIPE_addPools.png" path="HIPE_addPools.png" size="40134" user="Main.PaulBalm" version="1"

Revision 572012-04-17 - DavideRizzo

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  • A caching bug in Safari 4.0 can be solved by clearing the browser cache. Alternatively, open the help page with another web browser: copy and paste the address (something like http://127.0.0.1:8082/index.jsp?mark=null) to the address bar of the other browser.
  • A problem with Mac OS X can result in error messages when viewing the documentation of any installed HIPE version. In particular, you may get an HTTP ERROR: 404 NOT FOUND message in your browser, and a message about index.jsp not found in the command line terminal. Rebooting the computer solves the issue.
  • Older browser versions may not display documentation correctly. For example, links from HIPE to the Help System, like the Help in URM menu entries for tasks, work in Firefox 3.6.x but not in Firefox 3.0.x. Other legacy browsers may have similar problems.
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  • If you are using Linux and get an error message like Firefox can not contact the server www.%u.com, change your default browser from firefox %u to firefox %s (same if mozilla is your default browser). See the documentation of your Linux distribution for how to change default web browser. Alternatively, in HIPE choose Edit --> Preferences, go to Help & Documentation and enter the path to Firefox, or to another browser on your system, in the Browser field. Click Test to check if it works.
 
  • In general, when you encounter a problem with the Help System you should follow these steps:
    • See if the help works with another browser. If possible, upgrade your browser to the latest version.
    • Clear the browser cache
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  Note that when the Help System stops, any browser window or tab showing help pages will remain open, but links on them will not work anymore.
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Why are some code examples slightly different in the PDF and HTML versions of the documentation?

Code examples and commands in the PDF versions of the manuals sometimes have extra dashes added (for instance, -XX:MaxPermSize=256m becomes --XX:MaxPermSize=256m). If an example or a command does not work as expected, try checking the HTML version of the documentation, which is not affected by this bug.

 

Why are several important packages missing from the Javadoc?

You are probably looking at the static Javadoc located in the doc/api/ folder of your HIPE installation. The complete Javadoc can now be accessed from the HIPE Help System by clicking on HCSS Developer's Reference Manual (API) in the Developer Reference section. The plan is to remove the static version of the Javadoc completely.

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Known issues in HIPE 8.2

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  • PACS photometer scan map processing : Due to the new scheme of filtering turnaround manoeuvres between scan legs with the task filterOnScanSpeed task (masking frames in the 'ScanSpeedMask' mask, instead of removing the frames), photProject will project maps including the slew to target, hence exploding the memory in Hipe and leading to huge map sizes, because the photProject WCS doesn't take into account this new mask. A workaround solution is to run the filterSlew task previously, at the expense of possibly loosing a few frames on the first scan leg or alternatively run photProject in the following way:
ScanSpeedMask = frames.getMask('ScanSpeedMask')[0,0,:] 
indexSpeed    = ScanSpeedMask.where(ScanSpeedMask==False)
map          = photProject(frames.select(indexSpeed), calTree=calTree,calibration=True)
This bug shall be corrected in the next Hipe versions.
 

Known issues in HIPE 8.1

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Known issues in HIPE 8.2

None known in addition to those listed for HIPE 8.0.

 

Known issues in HIPE 8.1

None known in addition to those listed for HIPE 8.0.

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Known issues in HIPE 7.3

None known in addition to those listed for HIPE 7.0.

Known issues in HIPE 7.2

None known in addition to those listed for HIPE 7.0.

Known issues in HIPE 7.1

None known in addition to those listed for HIPE 7.0.

Known issues in HIPE 7.0

  • Cannot download data from the Herschel Archive due to corrupted cache.

Error messages about product cache corruption may vary. One example is the following:

herschel.share.util.ConfigurationException: Failed to locate product in cache

To solve the problem, try one or more of the following:

  • Choose Edit --> Preferences and go to Data Access --> Storages & Pools. Select a pool in the Pools pane and click the Clear cache button. Note that this button will not be available if there are no pools listed in the Pools pane.
  • If the above does not work, clear the HSA cache manually by deleting the home/.hcss/pal_cache/hsa directory, where home is your home directory.
  • If the above does not work, clear all caches manually by deleting the home/.hcss/pal_cache directory.

  • High disk activity with many local pools

If you have a high number of local pools on your disk (of the order of hundreds or more) you may experience noticeably high disk activity at HIPE startup.

  • Step by step execution sometimes runs two statements at once

This happens when executing a compound statement, such as a for loop. The first command after the compound statement will be executed in the same step as the compound statement. Consider for example the following script:

for i in range(3):
  print i
print "Finished"

The line by line execution will run the for loop and the print "Finished' statement in the same step. A workaround for this behaviour is to add a pass command after the end of the compound statement. The pass command will be executed in the same step as the for loop, but without any effect:

for i in range(3):
  print i
pass
print "Finished"
 

Older HIPE versions

Known issues for older HIPE versions are listed in a separate page.

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Other issues

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Jython bug when comparing NaN values with numbers

Jython behaves differently from Python when comparing NaN values with numbers.

In Python 2.4 or 2.5:

nan = float("nan")
print 0 < nan
# False
print 0 > nan
# False

In Jython 2.5.2:

nan = float("nan")
print 0 < nan
# False
print 0 > nan
# True

An issue has been opened on the Jython bug tracker.

 

"Can't connect to X11" error when using the jylaunch command

Executing a script outside HIPE with the jylaunch command may fail with a java.lang.InternalError: Can't connect to X11 window server error. This may happen even if the script does not open any graphical window, since it may indirectly call components that require an X11 server. The workaround is to run the script with the command jylaunch -Djava.awt.headless=true instead of just jylaunch.

Revision 532012-02-15 - DavideRizzo

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