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---+ What's New in HIPE 6

| *PDF Version* | [[%SCRIPTURLPATH%/genpdf%SCRIPTSUFFIX%/%WEB%/%TOPIC%?pdforientation=portrait&pdftoclevels=2][Click here]] |

%TOC%

---++ Core system

The Java Virtual Machine included in Windows and Linux downloads has been updated to version 1.6.0_22. 

---+++ HIPE

---++++ 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
   * You are informed about variables that could not 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

<blockquote>
---+++++ 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.

---+++++ 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).
</blockquote>

---++++ 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.

---++++ 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.

---+++ Plotting
   * A small subplot can be put inside a bigger plot.
---++++  !TablePlotter
---++++  !OverPlotter
---++++  Dataset viewer

---+++ Astronomical utilities

---+++ Numeric routines
---++++  Data fitting
---++++  Data interpolation
---++++ Random numbers
---++++ Statistics
---++++  Trend analysis
---++++  Mapping
---++++ Other functions

---+++ Source extraction

---+++ Images
---++++  Display
   * Major speedup when zooming in on images. Less memory is used when zooming in.
   * 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.

---++++  Analysis

---+++ Spectra
---++++  Display
---++++  Analysis
   * A Spectrum Integrator is available as prototype.  Currently only the basic functionality is available from the command line 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.


---+++ Data cubes
---++++  Display
---++++  Analysis

---+++ Herschel Science Archive

---+++ Calibration sources

---+++ Products and datasets
---++++  Observation context

---+++ Product Access Layer 

---+++ Tasks
   * Improved documentation.
   * Added descriptions to tasks. All tasks can provide a high level description (shown in tooltips in Task View).
   * Simplified localStoreWriter task.

---+++ Quality control

   * QCR Browser allows you to perform bulk actions on several quality control 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.

---+++ Systematic product generation

   * 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 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.

Bulk specific tool:

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

---+++ Data input-output

---+++ Virtual Observatory

---+++ Installer

---+++ Documentation

---+++ Help viewer
   * 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.

---++ HIFI

---+++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

---+++ !HiClass export tool

---+++ Documentation

---++ PACS

---+++ Pipeline
   * Fully 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.

---++++ Photometry
   * 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.

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

---+++ Calibration
---++++ Photometry
---++++ Spectroscopy
   * 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.
   * Also the pixel-pixel flatfield improvement described in PICC-KL-TN-045 (available in the central file) is implemented 
      in this !NominalResponse calfile.

---+++ Analysis tools
   * 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.
      * Screen Shot Calibration Framework: <br />
     <img src="%ATTACHURLPATH%/Screen_shot_2010-12-14_at_10.34.04.png" alt="Screen_shot_2010-12-14_at_10.34.04.png" width='692' height='324' />
      * 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 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. 

---++++ Photometry
---++++ Spectroscopy

---+++ Product changes
---++++ Photometry
---++++ Spectroscopy

---+++ Documentation
   * 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.

---++ SPIRE

---+++ Calibration Products
   * Added PCAL calibration products for the spectrometer.
---+++ Calibration Framework

---+++ Preprocessing
   * Added processing of PCAL flashes executed in spectrometer observations.

---+++ Engineering Conversion

---+++ Common Pipeline

---+++ Photometer Pipeline
   * Added flag to include or exclude turnaround data inscan map observations.

---+++ Spectrometer Pipeline

---++++ Level 0 to Level 0.5
See [[http://herschel.be/twiki/bin/view/Public/HipeWhatsNew6x#Engineering_Conversion][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
   1. The spectral averaging step is now only apply to Sparse, Point-source observations.  
   1. 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
Level2 spectral cubes are now created by averaging flux values within each pixel in the output map.  In addition, the execution speed of Spectral Mapping processing step 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
A new set of utility functions and tasks have been implemented for HIPE version 6.

   1. ==filterChannels==.  A task that allows one to remove a selection of channels from any type of SPRIE FTS data product.
   1. ==removeOutOfBand== A utility task that allows one to remove a from a SPIRE FTS Spectral data product spectral samples outside a specified band.
   1. ==makeSameOpds== A utility task that allows one to remove a from a SPIRE FTS Interferogram data product samples outside a specified OPD range.
   1. ==mergeFtsBuildingBlocks== A utility task that merges Level-1 SPIRE FTS Interferogram and Nominal Housekeeping products.
   1. ==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.
   1.  ==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.


---+++ Interactive Analysis and Tools

---+++++ ==Mosaic== plotting utility
A new plotting utility, ==Mosaic==, has been developed to allow one to plot the contents of a SPIRE FTS Interferogram or Spectral Data Product in a grid that corresponds to the physical layout of the SPIRE SLW and SSW detector arrays.


---+++ Documentation

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I	Attachment	History	Action	Size	Date	Who	Comment
png	Screen_shot_2010-12-14_at_10.34.04.png	r1	manage	53.5 K	2011-01-17 - 14:29	EkkehardWieprecht	Screen Shot Calibration Framework
Topic revision: r28 - 2011-02-18 - DavideRizzo
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