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# What's New in HIPE 5.0

## Core system

### HIPE

#### Startup & Shutdown

• If the running Java platform is not supported, a warning is popped up.

#### Plug-ins

HIPE now supports plug-ins, with are small packages that anyone can easily create and distribute to share code (Java or Jython) and data (LocalStores). Plug-ins can be downloaded and installed with a single-click.

#### View to access Calibration Sources Database

A new view has been added to HIPE for easy access to the Calibration Sources Database (Calsdb).

### Plotting

* Title and label can accept LaTeX commands \textrm \textit \textbf \mathrm \mathit \mathbf. for example, V$_{\textrm{LSR}}$

### Numeric routines

#### Random Numbers

• New random numbers generators from different distribution: Uniform, Gaussian, Poisson, Gamma, Cauchy (Lorentz), Exponential and Jeffreys.

#### Statistics functions

• RMS has been renamed to QRMS
• RMS implements a new functionality (see URM)
• Improved StdDev and Variance algorithms.
• Improved CorrelateMatrix algorithm.

##### 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.

#### Other functions

• SigClip
• Median mode uses Median Absolute Deviation instead of Standard deviation.
• Iterative use is allowed.

### Source extraction

• No significant changes to functionality.

### 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

### Herschel Science Archive

#### Pipeline processing

• Crated a daemon dispatcher mechanism.
• Aliases set tool has been modified for performing the required verifications before a tag is ingested.
• HsaPoolDaemon
• releases memory calling Java garbage collector if it is needed.
• can write compressed files.
• can save a binary representation of a product if the FITS save operation fails.
• HsaStagePool can export products into a LocalStore.
• HSA ingestion procedure can generate an XML ingestion request file even if a previous version does not contain its own XML.
• Improved test-harnesses to include an HAIO simulated server framework.

### Products and datasets

#### Observation context

• Include new metadata "slewTime" returning the scheduled start time of the slew as a FineTime
• Specific accessors, getSlewStartTime() and setSlewStartTime(), where added to the ObservationContext class
• For old observations in the hsa without this value, the method will return a null value indicating that this field was never set before

#### History

A new history dataset viewer is available: When you click on the History dataset in your product then two tables appear above another:

• An overview table which shows all the tasks used to generate the product. For each task, the name, execution time, build number and used calibration files are shown.
• When you click on a row in this overview table then a second table is shown with details for the selected task. This table contains the details of this task: For each parameter its simple value and some product information is shown (when available).

### Product Access Layer

#### Cache

Several bugfixes to improve the effectiveness of caching and the robustness has been introduced. One of these is a check to verify that the default LocalStore directory is not modified at any time during the cache's existence, which is a common source of corruption of the cache.

#### HsaPool

• HsaReadPool/HsaXmlPool can work with compressed data.
• HsaReadPool can retrieve product metadata directly.

### Quality control

• New metadata into the QualityContext product. The field is fixed and the main interest is to include this information into the FITs file associated to the product.

FITS keyword Value
PCAVEATS Please refer to http://herschel.esac.esa.int/DpKnownIssues.shtml for known problems in products

• Perform bulk actions on several qc reports simultaneously
• Flags color codes depending on their importance

### Systematic product generation

• New framework to process/combine data from several observations in the same pipeline
• This will allow, for instances, better results using MADmap algorithm with cross-scan data from two or more observations
• Automatic processing:
• New start-time algorithm based on the DTCP time of the OD being processed instead of fixed timestamps
• New check on TM data based on the gap checker reports. Only those observations with complete tm data will be processed at this point
• Uplink plugin is executed without problems in different conditions, even for manual commanding and no uplink data at all.
• Obsids shown also in decimal format in all the application tables
• Include proper motion data into the ObservationContext
• SPG stand-alone application can now run on MAC O.S. with no versant libraries available.
• On-demand request are now recorded into a report file

### Data input-output

• FitsArchive
• FITS Metadata direct access.
• ESO Hierarch keyword implemented when reading FITS files.
• FITS translation dictionary updated:  Herschel keyword FITS keyword pmRA PMRA pmDEC PMDEC state STATUS action ACTION slewTime SLEWTIME proCaveats PCAVEATS
• FitsArchive allow flag for compression when saving FITS files.
• HeaderWriter exceptions have been modified to include more information.
• JExamples automatic testing support.

### Documentation

To improve the quality of the examples, we have introduced automatic testing of (many of) the source code examples occurring in manuals such as the Data Analysis Guide and the HIPE Owner's Guide. We have also introduced automatic testing of the examples occurring in the User's Reference Manual.

## 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.
Calibration products are now delivered as a directory of FITS files.
This directory with calibration products can be found in the data/pcal sub-directory of your installation directory.
HIPE> fm = getCalTree(verbose=1)
CalTree read from: /Software/Herschel/hcss.dp.pacs-5.0.500/data/pcal
The calibration framework is adapted and will read these FITS files by default.
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.
• a new Pacs Documentation page has been opened on the public wiki.

#### Photometry

• Extended Madmap (using scan and cross scan) for interactive usage
• HIPE -> Menu -> pipeline -> PACS -> L2_scanMap.py
Based on HCSS-9361, a prototype for the extended Madmap pipeline is now available in HIPE for interactive usage. The extended Madmap pipeline is designed to combine scans and cross-scans in order to produce optional map. Unlike DP pipelines (which normally starts with one ObservationContext), this pipeline takes an obsList (an ArrayList) which is a list of ObservationContext. The pipeline will run even there is only one obs in the obsList. Below is an example creating an obsList:
HIPE> obsList=ArrayList()

• 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.
The MapIndexViewer now also displays the signal vectors in the "timeordered" mode.
• PacsSpr:2921: the MapIndexViewer shows mean/median +/- error permanently in the signal plot
• PacsSpr:2807: the Full MapIndex needs less memory than before
• 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 has been checked for NaN
• PacsSpr:2543 : exposure map has been removed in favour of the coverage map
• 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.
• Pointing
• 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

• new AOR mode "unchopped" including improved spatial calibration:
• 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
• new interactive tool SpectrumExplorer:
• improved wavelength calibration:
• PacsScr:2964: new wavelength calibration applied in waveCalc task using the wavePolynomes cal file
• spectrometer trend analysis product for the calibration blocks:
• PacsScr:2777: calibration block trendAnalysis product added to the observation context
• Extra options to specDiffChop (note these are EXPERT options for the analysis of special observations!)
• PacsScr:2717: extra option 'extend' added which allows for other pairwise differencing schemes. These schemes will subtract more datapoints from each other than the standard scheme.
• PacsScr:2427: extra option 'chopNodScheme' which provides different scheme for determining which label is on-source and which is off-source for a given nodding position. Needed for some special test AORs.
• Different bands in a range scan are now stored in their own blocks in the block table. This means that it is now possible to slice SEDs per band (PacsScr:2963).
• Several fixes to specWaveRebin, etc. to reduce the amount of NaNs considerably in the rebinned data.
• SpecProject sets the flux to Jy.

### Calibration

#### 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

#### Spectrometry

• Compatibility of PACS products with HCSS tools improved: One can now properly select data points and use the fitter tool on PACS frames and cubes.

## SPIRE

### 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

### Interactive Analysis and Tools

• Added the new DTMosaic class that allows the user to plot data recorded by many detectors during one observation on a single page to compare data more effectively (mosaic plot). This features is available from HIPE command line or within DetectorTimelineExplorer
• DetectorTimelineExplorer and DetectorTimelineExplorerComponent :
• Added a new features that allows the creation of mosaic plot of the detectors via right-click on the desired array
• Added a new Color&Mask Preferences panel
• Improved the color scale (using the Color&Mask Preferences it's now possible to select the Min/Max value fot the color scale)
• Improved the mask visualization (using the Color&Mask Preferences it's now possible to visualize any specific mask value directly on the array display)
• Made available the Mosaic class which creates a mosaic of plots in the shape of the SLW, SSW or coaligned detectors of the SPIRE FTS. The Mosaic class is intended to provide a means for viewing (at a glance) the spectra or interferograms associated with each detector.
• Changed SpecExplorer's detector display so that it automatically resizes to fit the enclosing frame. Also, SpecExplorer's detectors are now enclosed in a splitter pane. This enables you to maximize or hide the detector display with a single click.

### Other

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Topic revision: r28 - 2010-09-16 - JaimeSaiz