hifiPipeline task

• Bug fix: the auxilliary product was not repopulated when running the hifiPipeline task with aux=True. This is now fixed.
• First steps towards making the HIFI pipeline fully configurable are made with the introduction of doPipelineConfiguration. At present changes to the level 2 pipeline algorithm are not passed to the hifiPipeline task. This feature will be much more robust and user-friendly in HIPE 7.0

Level 1 Pipeline

• Improved error message handling from output of DoDeconvolution

<-- ---++++  Analysis -->

<-- ---++++  Display -->

<-- ---++++ hifiPipeline task -->

<-- ---+++ HiClass export tool -->

<-- ---++++ Photometry -->

Mosaic plotting utility

• SUSSEXtractor no longer fails to find sources close to NaN pixels in the image or in the error map
• SUSSEXtractor produced strange results when then error map had very small values. This was a problem because the naive mapper error is the standard error on the mean of the bolometer samples in the pixel, which can be extremely small if the pixel contains a small number of samples that happen to have very similar values. SUSSEXtractor now estimates its own value for the error when the naive mapper uncertainty is implausibly small.

• Added section on on-demand reprocessing.

Photometer

• Improvement to flux conversion.

Spectrometer

• Improved phase correction module in the pipeline no longer requires a calibration file. The final correction should be better using the new method.
• Rsrfs and beamParam updated to follow the new v6 pipeline scheme and use improved phase correction - should be improvement in shape of final spectra.
• BeamParam file modified to improve information for IA - updated beamAreas and added point source RSRF - this should have no effect on the SPG pipeline.
• OpdLimits added to clean up the pipeline script - should be no effect on data.
• Fix to non-linearity correction.

• Jump detection in signal timelines, allowing better temperature drift correction.

• Addition of getCalTree enables download of new calibration from HSA into a local store
  • task is called as cal = getHifiCal(useHsa=True, overWrite=False, calName="hifi-cal")

• The little-used Hifi Pipeline view is removed from HIPE

• Now only the subbands affected by a major spur are flagged, previously it was all four subbands of the WBS regardless of whether they were all affected or not.

• The WBS metadata produced by the doFreqGrid step of the pipeline has been clarified: the frequencyWidth metadata description is changed from 'The unique (!) channel width for the output grids of all subband' to 'The spacing of the frequency grids after resampling'.
• The items 'forwardEff' and 'beamEff' and are added to the metadata after the completion of the doAntennaTemp or doMainBeamTemp steps of the level 2 pipeline, as applicable.
• MkFreqGrid task is adjusted so that all output spectra have the same length of subbands. This allows all types of output to continue to be handled by HifiSpectrumDataset
• Improvements to messages from doMainBeamTemp, the following messages are now given:
  • When no beam efficiency is passed, or no beam efficiency is present in the calibration product passed to the task: "Product with name beamEfficiency-H not found in context. No information on the beam efficiency has been passed to the task doMainBeamTemp or the calibration data is outdated. Correction in task doMainBeamTemp is not applied."
  • When no input has been found in the calibration product: "No information on the beam efficiency was found in the calibration product. Please provide a value by hand".

• HifiSpectrumDataset is converted such that it contains upConvert_H or upConvert_V metadata when the band is 6 or 7. This allows to read off the value in order to convert to sky frequency,

• Bug fix: tasks under hifi_dp_tools did not load into HIPE
• Improved error messages from ConvertK2Jy

• New 'sds_index' option allowing the processing of specific datasets in ObservationContexts.

• New options wingChannels and minChannels to improve automated line masking (domask=2).

• DoDeconvolution now accepts an array of obsids, enabling a combination of data for which deconvolution can be performed.
• DoDeconvolution now keeps a log of problems encountered with its inputs, outputs, and difficulties. The log is accessible with an ASCII reader.

• Major updates to doGridding GUI: improved variable entry, tooltips and design. Task GUI now opens on the expert view.

• Updates to the following sections of the HIFI User Manual: Data Primer, Running the HIFI Pipeline, Quality Flags, HIFI Standing Wave Removal Tool, HIFI Baseline Removal, Exporting HIFI Data to CLASS
• Addition of two sections to the HIFI User Manual: Reference Frames in HIFI Data, Making Publication Quality Plots
• Many outdated references to JIDE removed from URM

• New 'automask' option that allows automated line masking to be switched off.
• New 'sds_index' option allowing the processing of specific datasets in ObservationContexts.

• New options wingChannels and minChannels to improve automated line masking (domask=2).

Quick start guide

• Added level 2.5 to the list of data processing levels.

HIPE Owner's Guide

• Improved section on properties and preferences.
• Improved section on customising views and perspectives.

Data Analysis Guide

• Added section on getObservation and saveObservation.
• Added warning on storing sensitive data in property files.
• Added section on subplots.
• Updated section on viewing spectra and cubes.
• Added section on running image analysis tasks.
• Removed duplicated content from image arithmetics section, added links to User's Reference Manual.
• Added tip on drawing filled shapes on an image display.

Scripting and Data Mining

• Revised section on array filtering.
• Added instructions on converting PACS data cubes.
• Added section on a couple of common problems with local pools.
• Added information on comparing products held in pools.

Products Definitions Document

• More updates to SPIRE product tables.
• Added level 2.5 to the list of data processing levels.

• Fully functional slicing framework.
  • Used for spectrometer processing, only partly used for photometer processing.

• New structure of Menu -> Pipeline -> PACS.
• A number of instrument-mode-specific user-provided IA scripts are available now.

• Implemented proposal for a two-stage photometer pipeline with masked highpass filtering.
• MMT Deglitching may mask a glitch, although the signal would be unmodified.
• Improvements on data filtering (usage of BBID in removeCalBlocks, usage of scan legs etc.).
• Significant improvements in the SSO astrometry (correctRaDec4Sso).
• Fully functional MadMap processing implementation inclusive of cross scans.

• Linearity correction removed from pipeline scripts.
• Usage of elements of the Spectrum Explorer.

• New wavelength calibration applied by using the cal file wavePolynomes.
• The NominalResponse cal file is active, including the 1.3 and 1.1 ILT to flight conversion factors.
  • This means that if you process data you shall not apply these correction factors manually.

• • If you want to start the update manually, go to the Tools > pacs-cal menu and select run Updater.

• • This should solve many problems when you just want to download and save an observation from the HSA on your local machine, as the data will not be saved twice (once in the cache and once in the local store pool) anymore.

• Updated the PACS Data Reduction Guide to follow the new spectroscopy pipeline scripts (Chapter 3), and added a chapter on MadMap. Minor updates to the other chapters to reflect other changes in the system.

• Added PCAL calibration products for the spectrometer.

• Added processing of PCAL flashes executed in spectrometer observations.

• You are informed about variables that could not be saved. Note that saving variables on exit is optional; it can be set in preferences.

• Enhanced mechanism for file identification; it supports XML file descriptors of observations.

• Fixed some memory issues. The display does no longer keep a lot of memory in use.
• It is possible to hide or show the panel with the panner and the zoom.

• Improved documentation.

• Simplified localStoreWriter task.

• QCR Browser allows you to perform bulk actions on several quality control reports simultaneously.

• Show metadata proCaveats in the browser.
• Operator can assign different colors to the quality flags.

• SPG GUI can now launch OD preprocessing (Missing TM , Events Log , HK products).
• Connect to database only when needed, releasing this resource otherwise.

• • Re-process feature for SYSTEMATIC and ON_DEMAND when the original data is obsolete.

• • Limit the number of observations being processed.
  • Memory management in operation's environment for subordinate jobs.
• On-demand pipelines must be able to process any observation with the latest auxiliary and calibration data.

• Operator can now re-execute individual jobs.
• Ability to launch one of two parallel mode obsids.

• Completely redesigned Welcome page.
• Advanced search functionality.
• Added information about currently viewed document and current version of HIPE.
• New functionality to jump to the index page of the currently open manual.

• A Spectrum Integrator is available as prototype. Currently only the basic functionality is available from the commandline and it allows to integrate part of a (background subtracted) spectrum. The data is expected to be in the form of a SpectralSegment (seg in the examples below).
  • Integration: The return value is a double.
    • i = Integrator.doIntegration(seg)
  • Integration over ranges: The return value is an array of n doubles. The windows are formatted as [start, stop, start, stop, ...]. So for one window from a to b: [a, b], and for n windows: [a1, b1, a2, b2, ..., an, bn]
    • i = Integrator.doIntegration(seg, [windows])
  • Integration over ranges with 1st order background removal: The background is removed by fitting a 1st order poly in the [masks] areas. The format of [masks] is similar to the [windows] format.
    • i = Integrator.doIntegration(seg, [windows], [masks])
  • Integration over ranges with nth order background removal:
    • from herschel.ia.toolbox.spectrum.integrator import Integrator
    • i = Integrator.doIntegration(seg, [windows], [masks], n)

How to get a SpectralSegment (HIFI example)

To get a SpectralSegment from the HIFI observation context 'obs', e.g. the first dataset of the level-2 HRS_L_LSB:

d = obs.refs["level2"].product.refs["HRS-H-LSB"].product.refs["1"].product["dataset"]

This is a HrsSpectrumDataset (which is a SpectrumContainer). Visualising this in the SpectrumExplorer shows that is contains one spectrum with 8 subbands. Each of the subbands is a SpectralSegment. Get any as:

seg = d.getPointSpectrum(0).getSegment('any')

The variable 'seg' can now be used in the Integrator.

• Added PCAL calibration products for the spectrometer

• Added processing of PCAL flashes executed in spectrometer observations

• Added flag to include or exclude turnaround data inscan map observations.

Plug-ins

A number of different small issues related to plug-ins have been resolved, including

• issues with the installation,
• path names containing spaces (important for Windows XP),
• proper clean-up in case of failed installation,
• reducing the number of required restarts.

• Updated the PACS Data Reduction Guide to follow the new spectroscopy pipeline scripts (chp3), and added a chapter on MadMap (this only got in a bit later in 6Track, however). Minor updates to the other chapters to reflect other changes in the system.

Help & Support

• Help > About shows the HIPE release number as well as the build number.
• Data reduction guides for the different instruments are available directly from the Help menu.
• HSC Helpdesk can be accessed from the Help menu.
• Crash reports can be sent for analysis to the HSC upon user confirmation.
• Tip of the Day additions.
• Enhanced help for jylaunch tool in the terminal.

Startup & Shutdown

• The user is informed about variables that couldn't be saved. Note that saving variables on exit is optional; it can be set in preferences.
• If HIPE is closed while having opened a script from the installation, and a different HIPE version is started afterwards, a warning is shown informing that the opened script belongs to other version.
• LOCK files from previous connections to the HSA not properly closed are asked to be removed at HIPE startup.
• Panel for Startup & Shutdown preferences has been improved.

Editors & Views

Outline

When a task is selected, a summary information of it is shown.

Console

The awkward horizontal scroll bar has been removed.

History

Copying an entire exception trace can be done with the history entry collapsed.

Variables

Delete (selection) and Delete all buttons distinguished.

Navigator

• Compressed FITS files are recognized and opened as such.
• Enhanced mechanism for file identification; it supports XML file descriptors of observations -see MyHSA-.

Jython editor

• Autoindent and unident improved. Note that the corresponding preference must be marked to make use of this functionality.
• The line continuation character \ is highlighted at the end of a line.

Task dialogue

Checkboxes for boolean parameters accept variables holding an integer with value 0 (false) or 1 (true).

Menus

• All dialogs and windows opened from HIPE, including plots, can be accessed through Window > Select Window.
• Available views have been categorized under Window > Show View.
• Entries of the File > New... menu have been simplified.

Preferences

• Configuration properties can be edited directly from the preferences dialogue, by means of the new Advanced... button.
• Saving preferences (with OK or Apply) is now faster and robust against failures.
• Panel for Startup & Shutdown preferences has been improved.

Jobs control

• Running jobs can be consulted and cancelled individually with the new Running Jobs button at the left side of the progress bar.
• If more than one job is running, clicking on the Stop button will show a similar dialogue to choose the job(s) to stop.

Miscellanea

• The criterion for determining the valid FITS extensions has been unified among different views and dialogues of HIPE.
• The error dialogue that includes an exception trace has it collapsed by default.

• • Screen Shot Calibration Framework:
    

• Full functional slicing framework
  • used for spectrometer processing, only partly used for photometer processing
• Significant cleanup and re organisation of interactive processing scripts.
• New structure of Menu -> Pipeline -> PACS
• A number of instrument mode specific user provided IA scripts are available now

• Proposal for a two-stage photometer pipeline with masked highpass filtering implemented
• MMT Deglitching may mask a glitch, although the signal would be unmodified
• Improvements on data filtering (usage of BBID in removeCalBlocks, usage of scan legs etc.)
• Significant improvements in the SSO astrometry (correctRaDec4Sso)
• Full functional MadMap processing implementation inclusive of cross scans

• Linearity correction removed from pipeline scripts
• Usage of elements of the Spectrum Explorer
• The fitter tool can now be used for all PACS products.

• New wavelength calibration applied by using the cal file wavePolynomes
• The NominalResponse cal file is active, including the 1.3 and 1.1 ILT to flight conversion factors.
  • This means, if you process data you shall not apply these correction factors manually.
• Also the pixel-pixel flatfield improvement described in PICC-KL-TN-045 (available in the central file) is implemented in this NominalResponse calfile

• Calibration framework : As of build 6.0.1452 the calibration framework will read the calibration products no longer from the distribution, but from a directory on your local machine.
  • You will be presented with a popup dialog asking to install the calibration. The dialog looks like this.
    • *Please go through the process of installing the calibration products on your local machine.
  • During the HIPE startup process, the calibration framework will check for new updates in the background and notify you of any updates.
  • If you want to start the update manually, go to the Tools>pacs-cal menu and select Run Updater...
  • You can read more about the PACS Calibration Framework in the comprehensive document available in the public part of the Wiki.

• Data Access : A new keyword is introduced to getObservation which allows the user to disable the Cache when using the HSA.
  • obs = getObservation(123456789, useHsa=True, useCache=False)
  • This should solve many problems when the user just wants to download and save an observation from the HSA on his/her local machine, as the data will not be saved twice (once in the cache and once in the local store pool) anymore.

• QCR Browser allow to perform bulk actions on several qc reports simultaneously

1. The spectral averaging step is now only apply to Sparse, Point-source observations.
2. The error column in the output data product is now populated with the standard error of the mean (Standard Deviation / SQRT(Number of Samples)) of the input spectral samples.

1. filterChannels. A task that allows one to remove a selection of channels from any type of SPRIE FTS data product.
2. removeOutOfBand A utility task that allows one to remove a from a SPIRE FTS Spectral data product spectral samples outside a specified band.
3. makeSameOpds A utility task that allows one to remove a from a SPIRE FTS Interferogram data product samples outside a specified OPD range.
4. mergeFtsBuildingBlocks A utility task that merges Level-1 SPIRE FTS Interferogram and Nominal Housekeeping products.
5. specMergeHighLowSds A utility task that is used for HR=+=LR SPIRE FTS observations. This task appends the LR portion of the interferograms from the HR buildling block to the interferograms from the LR building block at each Point and Jiggle position of the observation.
6. observationLayout A utility task that inspects the Level-0.5 context of a SPIRE FTS observation and returns a table linking the Building Block ID numbers with Point numbers, Jiggle numbers, and the commanded resolution.

Level 0 to Level 0.5

• See Engineering Conversion

Level 0.5 to Level 1

Processing Steps

Phase Correction

• A new algorithm has been implemented that corrects for asymmetries using the low-resolution portion of the measured interferograms.

Data Products

• Level-1 spectral products now contain all measured extended flux-calibrated spectra rather than the average spectra per detector.

Level 1 to Level 2

Processing Steps

Spectral Averaging

• The spectral averaging step is now only apply to Sparse, Point-source observations.
• The error column in the output data product is now populated with the standard error of the mean (Standard Deviation / SQRT(Number of Samples)) of the input spectral samples.

Spectral Maps

• NaiveProjectionTask replaces NearestNeighbourProjectionTask for spectral cube creation

• All measured spectra per detector per Point and Jiggle position are now supplied as input to the Spectral mapping step.
• The execution speed of NaiveProjectionTask has been greatly improved - a set of high resolution spectra is now processed in approximately 10 seconds.

Data Products

• Level-1 spectral products now contain all measured extended flux-calibrated spectra rather than the average spectra per detector.

New Utitlities

filterChannels

removeOutOfBand

makeSameOpds

mergeFtsBuildingBlocks

specMergeHighLowSds

observationLayout

Mosaic plotting utility

• QCR Browser should allow to perform bulk actions on several qc reports simultaneously
  • This includes: Generate QC Summary directly as a menu option
• Show metadata proCaveats in the browser
• Operator can assign different colors to the quality flags

• SPG GUI can now launch OD preprocessing ( Missing TM , Events Log , HK products )
• Connect to database only when needed, releasing this resource otherwise
• Extended process:
  • Re-process feature for SYSTEMATIC and ON_DEMAND when the original data is obsolete
  • Cancel the OC ingestion if the process throws an Error or Exception.
  • Limit the number of obs. being processed
  • Memory management in operation's environment for subordinate jobs
• On-demand pipelines must be able to process any observation with the latest auxiliary and calibration data

Bulk specific tool:

• Operator can now re-execute individual jobs
• Ability to launch one of 2 parallel mode obsids

Help viewer

• Added descriptions to tasks. All tasks can provide a high level description (shown in tooltips in Task View).

NaiveProjectionTask replaces NearestNeighbourProjectionTask for spectral cube creation

Browse product image for observations

• Simplified localStoreWriter task

• Improved documentation
• Added descriptions to tasks. All tasks should provide a high level description (shown in tooltips in Task View).

• A small subplot can be put inside a bigger plot.

New Module: spire_ia_pipeline_spec_util

This module contains helper classes used in the SPIRE spectrometer pipelines.

FilterChannelsTask

This task removes or retains a list of channels from an SDT, SDI, or SDS.

RemoveOutOfBandTask

This task removes out-of-band spectral components from an input SDS. The input SDS will be modified and returned as output.

ObservationLayoutTask

This task determines the characteristics of an observation, namely point numbers, jiggle numbers, resolution, and building blocks IDs, and places them into a SpecObsContents dataset.

MakeSameOpdsTask

This task makes all interferograms in an SDI have an OPD range consistent with the commanded resolution, truncating the data if necessary.

MergeFtsBuildingBlocksTask

This task merges multiple SDIs and NHKTs into a single SDI and NHKT.

Documentation

Spectroscopy

Spectroscopy

Spectroscopy

Spectroscopy

HIFI Software Configuration and Properties

HIFI Calibration

HIFI Pipeline

hifiPipeline task

Level 0 Pipeline

WBS Pipeline

HRS Pipeline

Level 1 Pipeline

Level 2 Pipeline

HIFI Products

HIFI Spectrum Toolbox

Spectrum Explorer (HIFI specifics)

Spectrum tasks (HIFI specifics)

HIFI Data Processing Tools

Standing Wave Removal

Baseline Removal

Deconvolution

Spectral Cube creation

HIFI Documentation

<-- 

 Set ALLOWTOPICCHANGE = RegisteredUsersGroup, TWikiAdminGroup
 
-->

• Major speedup when zooming in on images. Less memory is used when zooming in.
• Fixed some memory issues. The display does not longer keep a lot of memory in use.
• It is possible to hide or show the panel with the panner and the zoom

What's New in HIPE 6

Core system

HIPE

Plotting

TablePlotter

OverPlotter

Dataset viewer

Astronomical utilities

Numeric routines

Data fitting

Data interpolation

Random numbers

Statistics

Trend analysis

Mapping

Other functions

Source extraction

Images

Display

Analysis

Spectra

Display

Analysis

Data cubes

Display

Analysis

Herschel Science Archive

Calibration sources

Products and datasets

Observation context

Product Access Layer

Tasks

Quality control

Systematic product generation

Data input-output

Virtual Observatory

Installer

Documentation

HIFI

hifiPipelineTask

HRS Pipeline

WBS Pipeline

Level 1 Pipeline

Level 2 Pipeline

Products

DoDeconvolution

DoGridding

FitHifiFringe

HiClass export tool

Flags

SpectrumExplorer (HIFI specifics)

HIFI DP scripts (User tool scripts)

Documentation

Other

PACS

Pipeline

Photometry

Spectrometry

Calibration

Photometry

Spectrometry

Analysis tools

Photometry

Spectrometry

Product changes

Photometry

Spectrometry

Documentation

Other

SPIRE

Calibration Products

Calibration Framework

Preprocessing

Engineering Conversion

Common Pipeline

Photometer Pipeline

Spectrometer Pipeline

Interactive Analysis and Tools

Documentation

Other