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---+ What's New in HIPE 5.0

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---++ Core system

---+++ HIPE

---+++ Plotting
 * Title and label can accept LaTeX commands \textrm \textit \textbf \mathrm \mathit \mathbf. for example, V$_{\textrm{LSR}}$
---++++  !TablePlotter
---++++  !OverPlotter
---++++  Dataset viewer

---+++ Astronomical utilities

---+++ Numeric routines
---++++  Data fitting
   * A complete new GUI for the SpectrumFitter is added. Start it from the SpectrumExplorer right mouse menu, select SpectrumFitterGUI. Besides the functionality that was available in the SpectrumFitterTool, the -GUI has an export TAB that enables the user to export the residual, total model, and individual models as an object with the type of the input object and as ASCII.
   * The SpectrumFitter (commandline version) accepts Container with PointSpectrum and SpectralSegment index.
   * The SpectrumFitter (commandline version) has methods to export the data as the input type and as ASCII.
   * The SpectrumFitter (commandline version) has method that returns a jython script
---++++  Data interpolation
---++++  Statistics functions
---+++++ New functions
   * GeoMean which calculates the geometric mean of a array of numeric data types with 1 to 5 dimensions. 
   * Mode which returns the mode(s), or the most common element(s), of an array of numeric data with 1 to 5 dimensions.
   * Covariance which yields the covariance between two random variables/vectors x and y with finite second moments.  If one vector is longer than the other, only the values up to the length of the shorter vector will be taken into account.
   * CovarianceMatrix which returns the covariance matrix of the input M x N matrix. The result is a N x N matrix with each i, j value equal to the covariance of the ith and jth columns of the original matrix.


---++++  Trend analysis
---++++  Mapping

---+++ Source extraction

---+++ Images
---++++  Display
   * Images can be opened as RgbImage directly from the Navigator in HIPE.
   * Regular image files (jpg, gif, png, ...) are shown as preview in the outline when being clicked on in the navigator view of hipe.
   * 2 images can be compared by setting the opacity of the image. This can be done using the setOpacity(float) method or using a slider in the Image Display.
---++++  Analysis
   * Added the methods containsNorthCelestialPole and containsSouthCelestialPole on the Wcs.
   * Regridding an image on the grid of another image using RegridTask
   * Speed improvement of createRgbImageTask
   * Update of URM documentation
   * Cropping an image by drawing a rectangle on it
   * Correction of the calculation of the dimensions of a mosaic
---+++ 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
   * PACS "New Style Sliced" pipeline implementation is now activated  
      * PacsSpr:2647 : phot and spec ipipe script names are changed to be more logic and intuitive 
      * Pipeline Script access
         * HIPE -> Menu -> pipeline -> PACS 
   * Calibration framework
   Calibration products are no longer delivered with the build in a local store. <br>
   Calibration products are now delivered as a directory of FITS files. <br>
   This directory with calibration products can be found in the data/pcal sub-directory of your installation directory.
   <blockquote>
   HIPE> fm = getCalTree(verbose=1)<br>
   !CalTree read from: /Software/Herschel/hcss.dp.pacs-5.0.500/data/pcal
   </blockquote>
   The calibration framework is adapted and will read these FITS files by default. <br>
   The getCalTree() command and all access to calibration data has not changed, under the hood, the local store has been replaced by the directory of FITS files.
   Other small changes:
      * getCalTree(), getCalProduct() now understand the 'verbose=True' keyword and will print information on the location of the calibration products.
      * getCalProduct() the third argument, 'version',  is no longer mandatory, if not given, the last version of the calibration product will be returned.
 

---++++ Photometry
   * MadMap 
      * Extended Madmap (using scan and cross scan) for interactive usage 
         * HIPE -> Menu -> pipeline -> PACS  -> L2_scanMap.py
   * New script for scan Map pipeline
      * PacsSpr:2801  Proposal for a two-stage photometer pipeline with masked highpass filtering
         * Now THE standard processing script for scan maps
   * Photometer Mapping
      * PacsSpr:2853: Photometer mapping accepts a variable input pixelsize (parameter pixfrac in the !PhotProjectTask and the !MapIndexTask). 
      * PacsSpr:2789: The !MapIndexViewer has a Sigclip gui to display the effect of different Sigclip parameters on the second level deglitching. Now it is not necessary any 
                             more to guess Sigclip parameters, run the deglitching and check the quality afterwards. The new option allows to find the best parameter quickly 
                             BEFORE deglitching has been applied. <br>
                            The !MapIndexViewer now also displays the signal vectors in the "timeordered" mode.
      * PacsSpr:2859: Wcs4mapTask got a crota option to manually set the requested rotation angle of a map.
      * PacsSpr:2925: CorrectRaDec4SsoTask is now also accepting the new Horizons class definition. An example how to use it can be found in the attached 
      * PacsSpr:2751 : photProject error map not useable
      * PacsSpr:2543 : Clarify mapping exposure vs coverage 
      * PacsSpr:2751 : photProject error map not useable 
   * Noise treatmement
      * PacsSpr:2752: A new modul !herschel.pacs.spg.phot.PhotAddNoisePerPixelTask provides 4 ways to calculate the initial photometer noise.
      *Noise propagation is also implemented in the !HighpassFilter, Mean- and !MedianFilters. <br>
   * Pointing 
      * New Horizons Product used in PACS pipeline (SSO observations)
      * PacsSpr:2391 : Residual spatial offset PACS photometer blue/green vs red
      * PacsSpr:2787 : Corners shall follow changes in PhotAssignRaDec
      * PacsSpr:2617 : Separate blue and green in ArrayInstrument calfile and the code using it 
      * PacsSpr:2809 : Astrometric offset between two scan maps in parallel mode on the same field. 
   * Others 
      * PacsSpr:2761 PACS EDP: phot pipeline adaptation to cope with variable scan velocity 
      * A new module photMaskFrames offer masking :
      * framesOut = photMaskFrames(framesIn [,beforeFirstScanLeg] [,noScanData] [,afterCalblock=0] )
         * beforeFirstScanLeg : Mask data befor the first scan leg
         * noScanData : mask data where the ScanBBID is not set (includes turn arounds)
         * afterCalblock : Mask n data after calibration block
      * HcssSpr:6681: Sigclip can be applied n-times in one go. 

---++++ Spectrometry
   * First draft of the unchopped mode pipeline added to the build
      * PacsScr:2779: a "newstyle" unchopped mode pipeline is in place which can be run automatically or interactively
   * PacsScr:1048 New task specSubtractOffPosition implemented for unchopped pipeline 
   * PACS Product interface to SpectrumExplorer ( e.g. PacsSpr:2843 )

---+++ Calibration


---++++ Photometry
   * PacsSpr:2391 : Residual spatial offset PACS photometer blue/green vs red --> PCalPhotometer_ArrayInstrument_FM_v6.fits
---++++ Spectrometry
   * PacsSpr:2488 : New Wavelength Calibration Product
   * PacsSpr:2855 v8 of the Pacs Spectrometer Array to Intrument  and v4 of the Module2Array cal file is inserted in the system. This generates correct values also for center chopper positions (unchopped and waveswitch mode).
   * PacsSpr:2715 : updated spectrometer spatial cal file --> PCalSpectrometer_ArrayInstrument_FM_v6.fits
   * PacsSpr:2607 The RSRF calibration tables contain "NaN" which are then introduced into the signal by rsrfCal 

---+++ Analysis tools
---++++ Photometry
---++++ Spectrometry

---+++ Product changes
---++++ Photometry
---++++ Spectrometry

---+++ Documentation

---+++ Other 

---++ SPIRE

---+++ Calibration Products

---+++ Calibration Framework

---+++ Preprocessing

---+++ Engineering Conversion

---+++ Common Pipeline
   * Only minor changes in logs and documentation.

---+++ Photometer Pipeline
   * Pipeline scripts:
      * Added time correlation task in scan map pipelines
      * Comment out optical and electrical crosstalk corrections
      * Removed plotting blocks
   * Pipeline tasks:

---+++ Spectrometer Pipeline
 
---+++ Interactive Analysis and Tools

---+++ Documentation

---+++ Other


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Topic revision: r10 - 2010-09-13 - EkkehardWieprecht
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