Known issues in HIPE 10.1

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

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.

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.

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.

Installation and de-installation issues

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.

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.

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.

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

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.

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 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.

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.

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

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.

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.

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.

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).

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:

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

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:

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).

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:

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.

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:

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

"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.

Installation and uninstallation issues

• 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.

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.

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.

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.

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.

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:

• http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6506617
• http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6299259

Known issues in HIPE 9.1

None known in addition to those listed for 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.

• 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:

• 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.

<-- ANALYTICS CODE - DO NOT EDIT -->

<-- Google Analytics script BEGIN -->

<-- Google Analytics script END -->

<-- END OF ANALYTICS CODE -->

• 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

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.

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.

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.

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.

• 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.

• 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.

• 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 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(" ","_")

• 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)

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

• • 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)

• 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

• 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 -->

• 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.-->

• 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.

• 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.

Known issues in HIPE 8.3

None known in addition to those listed for HIPE 8.2.

• 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.

• 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.

• 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.

• 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.

• 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 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.

<-- COMMENT BOX CODE - DO NOT EDIT -->

<-- END OF COMMENT BOX CODE -->

• 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.

• 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)

Known issues in HIPE 8.2

None known in addition to those listed for HIPE 8.0.

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.

Known issues in HIPE 8.1

None known in addition to those listed for HIPE 8.0.

• 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 correction of MADmap point-source artifacts. The PACS module 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.

• 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.

• 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

• 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.

• High memory usage with Mac OS 10.5 Snow Leopard. There are reports of HIPE 8.0.1 using all available memory and freezing while reprocessing observations under Mac OS 10.5 Snow Leopard. This problem does not seem to appear on other platforms, including other Mac OS versions. The problem is being investigated.

• 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.

• 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.

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.

• Sending data from HIPE to DS9 under Mac OS: Using DS9 version 6.2, due to an error in the DS9 start-up script (disclaimer: or so we believe), HIPE fails to start DS9 automatically. Either use DS9 version 6.1 or start DS9 manually and re-send your image from HIPE. The problem has been reported to the DS9 team.

• 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:

• 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.

• 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.

• Velocity Maps in the CubeSpectrumAnalysisToolbox. 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.

• 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.

• Opening the HSA User Interface under Windows XP: If one opens the HSA User Interface from HIPE while being logged in, an error appear: "JNLParseException[ Could not parse launch file. Error at line 0.]". The work-around 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. (See HcssSpr:14151.)

• • Windows 7: The option to send an image is sometimes disabled in DS9.

• 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.

• Step by step execution sometimes runs two statements at once

• 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.

• Issues with 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 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.

• 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.

• Line by line 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 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.

• 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.