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.

HIPE known issues

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

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

• 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.

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?

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. Reinstall HIPE, including the software of the desired instrument.
2. Delete the following directories (home being your home directory):

1. Retrieve the observation again.

Problems saving observations to NFS-mounted disks and FAT32 disks

Known issues in HIPE 13

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 11

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

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()

• This rebuilds the pool using a ProductStorage instance named store:

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.

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 12

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.

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:

• Use Java 6 instead of Java 7 for running HIPE. To do this, you should:
  • Remove Java 7 manually from your installation. Detailed instructions for this procedure can be found at http://stikine.wordpress.com/2012/03/02/howto-remove-java/
  • Install Java 6 from Apple (which provided Java 6 versions). Choose carefully the appropriate download from https://developer.apple.com/search/index.php?q=java
• Use another operating system if you believe that your HIPE usage will match the pattern that triggers the crash.

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.
    • 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."

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.

java.vm.memory.max=2872m

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

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.

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.

There are PACS files I cannot delete! Why?

• 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.sun.com/bugdatabase/view_bug.do?bug_id=8009012

myObs = getObservation(obsid=1342219630, useHsa=True, save=True, spgVersion="11.1.0")

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.

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

Versions affected: HIPE 12 or older

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

• 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).

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

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

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

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

• This is a Mac OS problem, it does not affect any other operating system.

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

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

• 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.

"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.

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

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

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

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:

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

• • 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:

Cannot install on Mac OS X 10.8 "Mountain Lion"

• 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.

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

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.

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

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

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

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\$ '

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

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.

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:

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

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

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