Data Analysis Guide

Version 11.1, Document Number: HERSCHEL-HSC-DOC-1199
10 April 2017

Table of Contents

Preface
1. Conventions used in this manual
1. Data input/output
1.1. Components of an observation
1.2. Typical workflow
1.3. How data are stored on your disk
1.3.1. Managing storages and pools
1.4. Getting observations from the Herschel Science Archive
1.4.1. Logging into the HSA
1.4.2. Finding observations in the HSA
1.4.3. Inspecting the query results of an observation
1.4.4. Finding observation IDs outside the HUI
1.4.5. Downloading one entire observation
1.4.6. Using HIPE to inspect an observation in the HSA with known OBSID
1.4.7. Downloading multiple observations
1.5. Loading observations downloaded from the HSA into HIPE
1.6. Managing your HSA downloads
1.6.1. Advanced configuration
1.7. Retrieving an observation from disk
1.8. Customising the Product Browser results
1.9. How to use the Quick Analysis perspective
1.10. Saving data (products and observations) to disk
1.11. Migrating pools across incompatible versions of HIPE
1.12. Exporting an observation to a colleague
1.13. Retrieving products from disk
1.14. Removing data from disk
1.15. On-demand reprocessing of observations
1.16. Exchanging data with FITS files
1.16.1. Saving a product to a FITS file
1.16.2. Retrieving a Herschel product from a FITS file
1.16.3. Translation of Herschel metadata to FITS keywords
1.16.4. Structure of Herschel products when saved as FITS
1.16.5. Troubleshooting FITS import/export
1.16.6. Importing a non-Herschel FITS file into HIPE
1.16.7. Importing a Herschel FITS file into external applications
1.17. Working with the VO (External Tools)
1.17.1. Sending products from HIPE to external tools
1.17.2. Sending products from external tools to HIPE
1.17.3. Opening VO Tables from HIPE
1.17.4. Writing tables to files in VO-table XML format
2. Saving data as text files
2.1. Considerations and concepts for working with text files
2.2. Worked example: Saving a Spectrum product as a text file
2.3. Worked example: Saving a SourceListProduct as a text file
2.4. Worked example: Reading a Spitzer spectrum into a table dataset
2.5. Worked example: Reading a VizieR catalogue into a table dataset
2.6. Reading a comma-separated-value (CSV) file into a table dataset
2.7. Reading a space-separated file into a table dataset
2.8. Reading an IPAC, SExtractor or Topcat file into a table dataset
2.9. Reading a generic ASCII table file into a table dataset
2.10. Writing a table dataset to a comma-separated-values (CSV) file
2.11. Writing a table dataset into a space-separated-value file
2.12. Writing a spectrum to an ASCII table file
2.13. Writing a table dataset to a generic ASCII table file
2.14. Reading column names from a file
2.15. Defining which lines to ignore when reading a file
2.16. Specifying the data types when reading a file
2.17. Specifying how data values are separated when reading a file
2.18. Saving and loading a configuration for reading from file
2.19. Adding a header to an ASCII table file
2.20. Adding table dataset metadata to an ASCII table file
2.21. Defining a custom prefix for commented lines
2.22. Choosing how to separate data values
2.23. Saving and loading options for writing to file
2.24. Parsers, formatters and templates
2.25. Creating and configuring table templates
2.26. Creating and configuring parsers for reading in data
2.27. Creating and configuring formatters for writing data
2.28. Regular expressions
3. Plotting
3.1. Getting started
3.2. Creating a plot
3.3. Customising title and subtitle
3.4. Managing layers
3.5. Showing and customising a legend
3.6. Customising plot properties
3.6.1. Command line equivalents
3.7. Setting margins
3.8. Saving and printing
3.9. Setting line and symbol styles
3.10. Customising axes
3.11. Drawing grid lines
3.12. Managing annotations
3.13. Drawing filled areas
3.13.1. Drawing filled areas between curves
3.14. Drawing a straight line
3.14.1. Drawing an arbitrarily-positioned straight line
3.15. Customising auxiliary axes
3.16. Changing the thickness of axes
3.17. Adding error bars
3.18. Switching to histogram mode
3.19. Adding subplots
3.20. Embedding monochromatic images in plots
3.21. Embedding RGB images in plots
3.22. Inserting math and special symbols
3.23. Creating a plot in batch mode
3.24. Drawing multiple plots per window
3.25. Colours in plots
3.26. Methods for colours, fonts and visibility
3.27. Invisible plots
3.28. Getting mouse coordinates on plots
3.29. More on plot methods
3.30. Worked example: Plot with an image
3.31. Worked example: Initial plot of this chapter
3.32. Worked example: Multi-panel plot
3.33. Worked example: Error bars
3.34. Worked example: Auxiliary axes
3.35. Worked example: Histograms
3.36. Worked example: Styles
3.37. Worked example: Two plots in one
3.38. Worked example: Coloured band
3.39. Worked example: Plot with PACS and SPIRE spectra
3.40. The TablePlotter
3.40.1. Invoking TablePlotter
3.40.2. Layout of the TablePlotter
3.40.3. Controls and functions
3.41. The Over Plotter
3.41.1. Invoke Over Plotter
3.41.2. Layout of Over Plotter
3.41.3. Controls and Functions
3.42. The Power Spectrum Generator
4. Working with images
4.1. Summary
4.2. Running image manipulation and analysis tasks
4.3. Importing and exporting images
4.3.1. Importing
4.3.2. Exporting
4.4. Viewing an image
4.5. Measuring angular distances
4.6. Creating masks
4.7. Viewing metadata and array data associated to an image
4.8. Saving an image
4.9. SimpleImage editing
4.10. Manipulating the axes (cropping, rotating, scaling...)
4.11. Manipulating fluxes
4.11.1. Image arithmetics
4.11.2. Smoothing images
4.11.3. Converting image units
4.11.4. Convolving images
4.12. Flagging saturated pixels
4.13. Getting cut levels
4.14. Combining images (stitching, RGB)
4.14.1. Stitching
4.14.2. Creating RGB images
4.15. Defining and using the World Coordinates System (WCS)
4.16. Creating intensity profiles
4.17. Creating contour plots
4.18. Creating histograms
4.18.1. Histograms via the command line
4.19. Finding and extracting sources
4.20. Fitting sources
4.21. Aperture photometry
4.21.1. Centroiding
4.21.2. Units and aperture photometry
4.21.3. Point sources
4.22. Comparing PSFs to point source profiles
4.22.1. Setting up and getting the data
4.22.2. Rotate the PSF and match it to the astronomical source
4.22.3. EEF Curves
4.22.4. Measuring the sky background scatter on PACS and SPIRE maps
4.22.5. Fitting the PACS PSF (for SPIRE it will be similar)
5. Spectral analysis
5.1. Summary
5.2. Spectra in HIPE
5.3. How to display spectra
5.3.1. Showing and Hiding spectra
5.3.2. Overplotting spectra
5.3.3. Viewing multiple plots
5.3.4. Zooming and Panning
5.3.5. Changing Display Axes
5.3.6. Changing Plot Properties
5.3.7. Viewing large datasets
5.3.8. Filtering and sorting what is viewed
5.3.9. Viewing Flags/masks and plot information
5.3.10. Viewing SpectralLineLists
5.3.11. Printing and saving
5.3.12. Plotting from the command line
5.4. Working on Spectra
5.4.1. Using the Spectrum Toolbox
5.4.2. Spectral Selection: extraction, and flagging
5.4.3. Spectrum Arithmetics
5.4.4. Spectral Averaging and Statistics
5.4.5. Spectral Manipulation: resampling, smoothing, replacing, gridding, stitching, and folding
5.4.6. Spectral Unit Conversion
5.4.7. Finding the integral under a line
5.4.8. Weight/error and flag/mask propagation
5.5. Dealing with baseline issues
5.5.1. General Standing Wave Removal Tool
5.5.2. Baseline Smoothing and Line Masking Tool
6. Spectral analysis for cubes
6.1. Summary
6.2. Cubes and the Spectrum Explorer
6.3. A message about cube coordinates and the WCS
6.4. A message about errors, weights, flags
6.5. A quick cube viewer: the Standard Cube Viewer
6.6. Using the Spectrum Explorer to look at cubes
6.6.1. Opening the Spectrum Explorer on a cube
6.6.2. Showing and hiding cube spectra; clearing stubborn spectra
6.6.3. Zooming and panning
6.6.4. Real-time spectrum display: preview panel
6.6.5. (Over)plotting spectra from multiple cubes
6.6.6. Linking the display of spectra from multiple cubes
6.6.7. A grid layout of the spectra in a cube
6.6.8. Viewing in subplots (multiple spectrum plots)
6.6.9. Standalone plot panel
6.6.10. Changing display axes
6.6.11. Changing plot properties and behaviour
6.6.12. A table of the plot—mouse interactions
6.6.13. Changing your Spectrum Explorer preferences
6.6.14. Viewing plot information
6.6.15. Viewing datapoint flags
6.6.16. Printing and saving
6.6.17. Creating a new variable from a plotted spectrum
6.6.18. A meta data list: and how to relate spaxel coordinates to index coordinates
6.6.19. Filtering what is viewed: not useful for cubes
6.6.20. Plotting from the command line
6.7. Working on cubes: the Spectrum and Cube Toolboxes
6.7.1. How to open the Toolboxes; getting extra help
6.7.2. Defining the input, looking at the output
6.7.3. Spectrum extraction and cube cropping
6.7.4. Spectrum arithmetics
6.7.5. Spectrum averaging/summing and statistics
6.7.6. Spectrum manipulation: resampling, smoothing, replacing, gridding, stitching, and folding
6.7.7. Spectrum flagging
6.7.8. Spectrum wave unit conversion
6.7.9. Weight/error and flag propagation
6.7.10. Making 2d flux maps from cubes
6.7.11. Velocity maps
6.7.12. Position-velocity maps
6.7.13. Removing the continuum from cubes
6.7.14. Dealing with baseline issues
6.7.15. Exporting to ASCII or FITS
6.7.16. Converting units for Cube Toolbox flux maps
6.8. Combining the PACS and SPIRE full SED for point sources
7. Spectral Fitting
7.1. Spectrum fitting
7.1.1. Using the Spectrum Fitter GUI: an overview
7.1.2. Using the Spectrum Fitter (command-line fitting): an overview
7.1.3. Fitting tips
7.2. Worked Example: Fitting a polynomial to the baseline/continuum
7.2.1. Worked Example: Fitting a polynomial to the baseline/continuum in the command line
7.3. Worked Example: Fitting a polynomial to a spectral cube (or any multi-spectrum dataset)
7.3.1. Worked Example: Fitting a polynomial to a spectral cube (or any multi-spectrum dataset) in the command line
7.4. Worked Example: Fitting Gaussians and a polynomial to a spectrum
7.4.1. Worked Example: Fitting Gaussians and a polynomial to a spectrum in the command line
7.5. Worked Example: Fitting multiple lines (Gaussians) and a Polynomial baseline to a cube and making maps of the results
7.5.1. With the GUI
7.5.2. On the command line
7.5.3. Making 2d maps from the fit results
7.6. Adding and Initialising Models
7.7. Configuring the Spectrum Fitter GUI to automatically apply a fit upon opening
7.8. Setting weights
7.9. Setting limits to model parameters
7.10. Fixing model parameters
7.11. Modifying Models
7.12. Applying a fit
7.13. Inspecting fit parameter results
7.14. Deleting models and excluding models from a fit
7.15. Resetting and restarting fitting
7.16. Saving a script
7.17. Saving the residual and models
7.18. Saving a SpectralLineList
7.19. Obtaining a line integral
7.20. Using Saved models
7.21. Automatic fitting of multiple datasets
7.22. Continuing work on the residual outside of the Spectrum Fitter GUI
7.23. Using the Combo Model
7.24. Models available to the fitter
7.25. How to add your own model
7.26. Selecting the best fitter engine
7.27. NaNs and the Spectrum Fitter
7.28. Making images from fitting results to cubes: the ParameterCube
7.28.1. After fitting with the MultiFitter tab of the Spectrum Fitter GUI
7.28.2. After fitting with the MultiFitter on the command line
7.28.3. Manipulating the images taken from the ParameterCube.
7.29. Calculating uncertainty and error after fitting
7.29.1. Introduction to errors or fitting and confidence
7.29.2. Practical information for getting the fitting errors in HIPE
7.29.3. Advanced practical information
7.30. Troubleshooting and limitations of the fitter
8. Unit Conversion
8.1. Units in HIPE
8.2. Built-in units and how to define new ones
8.2.1. Defining new units
8.3. How to convert data products units
8.3.1. Worked Example: Converting the units of an instance of a subclass of Spectrum1d
8.3.2. Worked Example: Converting the units of an instance of a subclass of Spectrum2d
8.3.3. Worked Example: Converting the units of an instance of a subclass of SimpleCube
8.3.4. Worked Example: Converting the units of an instance of SimpleImage
Index

List of Figures

1.1. Typical workflow for downloading, reprocessing and saving an observation.
1.2. Pools and storages
1.3. Preferences for data access
1.4. Workflows for retrieving observation data from the Herschel Science Archive
1.5. Logging in to the Herschel Science Archive
1.6. Accessing the Herschel Science Archive
1.7. The HSA view
1.8. The Web Herschel Science Archive UI main interface.
1.9. WHUI results screen.
1.10. WHUI detailed results screen.
1.11. Share dialogue.
1.12. Information summary for an observation returned as a query result.
1.13. QCR summary missing for this observation.
1.14. The Observing Log webpage.
1.15. Downloading an observation from the Herschel Science Archive.
1.16. Selecting which part of an observation to inspect.
1.17. Product loaded into HIPE from the HSA.
1.18. Download multiple observations.
1.19. A Herschel observation ready to be loaded into HIPE.
1.20. The My HSA preferences dialogue window.
1.21. A detail of the Indexed Datasets table showing the Requires and Is required by columns.
1.22. The Advanced tab of the My HSA preferences dialogue window.
1.23. The Product Browser.
1.24. Main window of Quick Analysis.
1.25. Quick Analysis - Browse.
1.26. Quick Analysis - Observation.
1.27. The Save Products tool.
1.28. Product export from HIPE into standard Herschel directory structure.
1.29. FITS save task dialogue window.
1.30. FITS read task dialogue window.
1.31. Structure of a FITS file produced from a SimpleImage.
1.32. Structure of a FITS file produced from a SpectralSimpleCube from a PACS observation. The two columns of the ImageIndex binary table extension are shown.
1.33. Structure of a FITS file produced from a SpectralSimpleCube from a SPIRE observation. The two columns of the ImageIndex binary table extension are shown.
1.34. Structure of a FITS file produced from a SpectralSimpleCube from a HIFI observation.
1.35. Structure of a FITS file produced from a PacsRebinnedCube. The two columns of the ImageIndex binary table extension are shown.
1.36. Structure of a FITS file produced from a HifiTimelineProduct. This product cannot be saved directly as a FITS file, but the summary table and each DatasetWrapper can. The dashed gray lines show the contents of each FITS file.
1.37. Structure of a FITS file produced from a SpectrometerPointSourceSpectrum. The five table columns are shown for the SSWD4 extension. They are the same for the SLWC3 extension.
1.38. Structure of the History extension of a FITS file created from a Herschel product. Column names for each of the three binary table extensions are shown.
1.39. The SAMP Hub Monitor window.
2.1. Excerpt from the output of exportSpectrumToAscii
2.2. The TableDataset resulting from running the example script
2.3. The initial SourceListProduct generated by sourceExtractorSussextractor.
2.4. Excerpt from the text file written from the SourceListProduct.
2.5. The reconstituted SourceListProduct with data read in from the text file.
2.6. Excerpt from the a Spitzer spectrum product.
2.7. The table dataset resulting from running the example script.
2.8. Excerpt from the Planck Early Cold Cores Catalogue.
2.9. Excerpt from ReadMe file for Planck Early Cold Cores Catalogue.
2.10. The table dataset resulting from running the example script.
2.11. A table dataset imported from a CSV file.
2.12. A table dataset imported from a space-separated-value file.
2.13. A simple table dataset.
2.14. A simple table dataset.
2.15. Input spectrum for the exportSpectrumToAscii task.
3.1. Some of the features of HIPE plots. If you are reading the HTML version of this manual, click on any of the blue labels to jump straight to the relevant section.
3.2. The Property Panel window.
3.3. Available filling closure types.
3.4. The filling patterns produced by the three LineHatchPaint objects shown in the previous example.
3.5. The filled area between the sinc(x) curves.
3.6. Plot with a customised auxiliary axis.
3.7. The same data set plotted as LINECHART (default) and HISTOGRAM.
3.8. Plot with embedded subplot.
3.9. RGB image in a plot.
3.10. Using special characters for labels.
3.11. Classes involved in plot operations.
3.12. The result of the commented plot example presented in this section.
3.13. The result of the plot example created with the simplified version of the script.
3.14. A plot with four panels.
3.15. A plot with horizontal and vertical error bars.
3.16. A plot with three layers and customised auxiliary axes.
3.17. A plot with three panels, each containing superimposed histograms.
3.18. A plot using several styles and colours for lines and plot symbols.
3.19. A plot made of two independent plots.
3.20. A plot with different symbol styles, error bars and a coloured horizontal band.
3.21. The result of the commented plot example presented in this section.
3.22. Viewers available for a table dataset in the product viewer, among them TablePlotter and OverPlotter.
3.23. Layout of the TablePlotter GUI.
3.24. The plot with selected (blue) and hidden (red crosses) data points.
3.25. Extract Selected Data from Multi Columns to a New DataSet.
3.26. Simple overlay plots of different columns plotted against the same X-axis are created by marking the Overlay field.
3.27. Preferences: Complex data can be displayed in four different ways as shown in this properties menu.
3.28. The main panel of Over Plotter is very similar to that of the Table Plotter. New features include the Layer Controls panel and the synchronization buttons. This Over Plotter is in All Layers mode.
3.29. This Over Plotter is in "Single Layer" mode. The primary layer is displayed in its selected colour and the secondary layer is displayed in green. All other layers are displayed in grey colour.
3.30. This Over Plotter is in "Single Layer" mode. The primary layer is displayed in its selected colour and the secondary layer is displayed in green. All other layers are displayed in grey colour. These are the same layers as in the previous figure, but after selecting Layer 1 to become prime.
3.31. A complex example for illustration. The Over Potter is in "Single Layer" mode. The primary layer is displayed in blue with large symbols and connected by a line. The Y-axis is set to logarithmic mode. The secondary layer is displayed in green with large filled diamonds. The third layer is displayed in grey colour.
3.32. A signal timeline displayed in Table Plotter that the Power Spectrum generator can be applied to.
3.33. Main view of the Power Spectrum Generator.
3.34. Displaying the newly created power spectra in the Table Plotter.
4.1. Finding variable types in the Variables view.
4.2. Viewing an image in HIPE.
4.3. Measuring angular distances on an image.
4.4. Opening the Dataset Viewer from the Outline view.
4.5. Colour map window.
4.6. Cut level selection window.
4.7. The annotation toolbox.
4.8. Adding annotations to a Display.
4.9. Jython code appearing in the annotation toolbox.
4.10. Example image transformation dialogue window. Rotating an image using the "rotate" task. Several interpolation options are available.
4.11. Example image arithmetic dialogue window.
4.12. The createRgbImage task dialogue window.
4.13. The intensity profile below the image.
4.14. Dialogue window for automaticContour .
4.15. Circle histogram area selection and parameter selection.
4.16. Display of the histogram task results, held in the histogram output dataset.
4.17. List of parameters for the two source extraction tasks.
4.18. The list of sources shown in the Product Viewer, with the internal dataset highlighted.
4.19. Opening the SkyMask toolbox.
4.20. Drawing a region of interest on the image.
4.21. Aperture photometry with an annular sky aperture as displayed in HIPE.
4.22. Aperture photometry results plot and tables. Note that n.a. stands for "not applicable" and typically occurs when units are not assigned to the image.
5.1. The Spectrum Explorer for a single spectrum.
5.2. The new layout properties panel.
5.3. Filters on attributes.
5.4. fitFringe task UI.
5.5. Plot with standing waves.
5.6. Overplot of fitFringe results.
6.1. HIFI cube: data arrays
6.2. The Standard Cube viewer: zoom to fit is indicated
6.3. The Spectrum Explorer with a cube loaded
6.4. The cube comparison buttons
6.5. Mosaic/raster view
6.6. The Subplot menu.
6.7. changing layer properties
6.8. The arrays in a cube.
6.9. Tab arrangement in the Cube Explorer.
6.10. Combination of PACS and SPIRE spectra.
7.1. Selecting one spectrum to fit with the Spectrum Fitter GUI. Here a pixel near the centre of the cube (highlighted with a green box) is displayed in the top left Spectrum Explorer and the second subband of a HIFI WBS spectrum is displayed in the bottom right Spectrum Explorer.
7.2. The SFG accessed via the Spectrum Explorer, and showing a Polynomial fitted to one pixel from a SPIRE cube. The labelled Spectrum Explorer and Fitter GUI panes are described in the text below.
7.3. The working area of the SFG.
7.4. The MultiFit_Parms output.
7.5. Plot one spectrum (a spaxel/pixel) and open the Spectrum Fitter GUI.
7.6. Add a Polynomial model using addModel and press Accept to fit.
7.7. Reset the Spectrum Fitter GU to start work on the original spectrum again.addModel and press Accept to fit.
7.8. Set weights by opening the Weights tab and drawing a range on the spectrum.
7.9. After setting weights go back to the Models tab and re-initialise the fit.
7.10. Setting the weights to zero at the line edges still did not produce a satisfactory fit.
7.11. Set weights to one either side of the line in the Weights tab before reinitialising the Polynomial fit in the Models tab.
7.12. A script, the models and the residual can be saved in the Export tab.
7.13. The contents of MultiFit_Parms
7.14. Plot one spectrum (a spaxel/pixel) and open the Spectrum Fitter GUI.
7.15. The cross-hair indicating the layer the cube is displayed at may be obtrusive, you can move it to the edge of the spectrum in the Spectrum Explorer Data Selection Panel.
7.16. Add a Polynomial model using addModel in the Models tab.
7.17. Add a Gaussian model using addModel and set the position and amplitude of the peak by clicking on the spectrum.
7.18. Use addModel to add another Gaussian.
7.19. Add another Gaussian for the absorption, you will need to zoom out in order to set the amplitude of the line below zero. Press Accept to fit.
7.20. The total model and Polynomial fit are plotted over the original spectrum, while the Gaussian models appear below with the residual.
7.21. A script and the model parameters (and also the residual) can be saved from the Export tab.
7.22. Plot one spectrum (a spaxel/pixel) and open the Spectrum Fitter GUI.
7.23. Set weights by opening the Weights tab and drawing a range on the spectrum.
7.24. Add a Polynomial model using addModel and press Accept to fit.
7.25. Add a Gaussian model using addModel and set the position and amplitude of the peak by clicking on the parameter boxes ("Amplitude" or "X-Position") to the right and then on the spectrum.
7.26. To fit an entire cube, use the MultiFit tab
7.27. The contents of MultiFit_Parms
7.28. Load models.
7.29. The MultiFit_Parms output
7.30. Linear model fitting.
7.31. Non-linear model fitting.
7.32. Non-linear model fitting.
7.33. Non-linear model fitting.
7.34. Mixed sine model fitting.
7.35. Combined model fitting.
7.36. Combined model fitting.

List of Tables

2.1. Regular expressions.
3.1. Plot line styles
3.2. Symbol codes and images.
7.1. SpectrumFitter models
7.2. Spectrum fit model types and their use.
8.1. Built-in units.

List of Examples

1. Printing "hello" to the console.
2. How to retrieve an observation given an observation ID.
3. Setting a title plot.
4. Setting properties using Jython syntax.
1.1. Getting an observation from the HSA and saving it locally.
1.2. Creating a variable from an observation previously saved to disk.
1.3. How to save a product to a local pool, in the background.
1.4. Getting an observation from the HSA given the observation ID.
1.5. Saving an observation to disk from the HSA given the observation ID.
1.6. Getting an observation from the HSA given an observation ID.
1.7. Setting on the connected status of the MyHSA pool.
1.8. Setting off the connected status of the MyHSA pool.
1.9. Retrieving an observation from the HSA given the observation ID.
1.10. Browse all the versions of an observation (part 1).
1.11. Browse all the versions of an observation (part 2a).
1.12. Browse all the versions of an observation (part 2b).
1.13. Browse all the versions of an observation (part 3).
1.14. Downloading multiple observations from an array of obs ids.
1.15. Retrieving several observations from the HSA as tar.gz and opening them in HIPE.
1.16. Retrieve an observation from the HSA given the observation ID.
1.17. Load an observation from disk into a new variable.
1.18. Retrieving an observation from the HSA as a tar.gz and opening it in HIPE.
1.19. Load an observation from disk, specifying both path and observation ID.
1.20. Perform a query on a local store using the result of another query.
1.21. Retrieve an observation given the observation ID.
1.22. Load an observation from disk specifying both the observation ID and the pool directory.
1.23. Load an observation from disk specifying the observation ID, the local pool name and the pool location.
1.24. Several examples using the getObservation task.
1.25. Save an observation to disk specifying the pool name and a tag.
1.26. How to rebuild the index of a local pool.
1.27. Second option for rebuilding the index of a local pool.
1.28. How to get the current workind directory for the Jython interpreter.
1.29. Creating a new empty data product and writing it to disk as a FITS file.
1.30. Creating a SimpleImage with random data and saving it to disk as a FITS file, reading it back afterwards.
1.31. Using a dataset as a wrapper to store an array in a FITS file.
1.32. Load a product from a FITS file.
1.33. Setting a metadata property to a StringParameter value.
1.34. Create FITS file from random data and read it back.
1.35. Printing a FineTime formatted string to the console.
1.36. Importing a non-Herschel FITS file with the simpleFitsReader task.
1.37. Importing non-Herschel FITS files using specific image import tasks.
1.38. Importing non-Herschel FITS files using specific spectral import tasks.
1.39. Complete example to convert a Spectrum1d class to a CLASS FITS file.
1.40. Converting a VO table in XML format to TableDataset.
1.41. Writing a TableDataset from an observation to an XML-based VO file.
1.42. Writing a synthetic TableDataset to an XML-based VO file.
2.1. Creating a TableDataset with a Column made up of array data.
2.2. Read a numeric array from a file and loop over its values.
2.3. Read a numeric array from a file and tokenise its values in a loop.
2.4. Script to export a SpectralSimpleCube to ASCII, and read back into a TableDataset
2.5. Script to generate a SourceListProduct, write it to a text file, and read it back into HIPE
2.6. Worked example for reading in a Spitzer spectrum in "IPAC table" format
2.7. Complete script for reading in the Planck Early Cold Cores Catalogue.
2.8. A standard comma-separated-value (CSV) file with a four-line header.
2.9. A standard comma-separated-value (CSV) file with only column titles specified.
2.10. Reading a table from a file, specifying its tabular format as CSV.
2.11. A space-separated-value file of the type that can be imported into HIPE with default options.
2.12. A space-separated-value file with only column titles specified.
2.13. Read a table from an ASCII file, specifying that its values are space-separated.
2.14. Read a table from an ASCII file, specifying the input format as IPAC.
2.15. Reading a table from an ASCII file, without specifying any input format.
2.16. Write a table to an ASCII file.
2.17. Creating a formatter that separates values using a single space character.
2.18. Creating a space-separated formatter and using it to write a table as an ASCII file.
2.19. Writing spectrum data to an ASCII file.
2.20. Writing spectrum data to an ASCII file without including metadata.
2.21. Writing spectrum data to an ASCII file, including flags.
2.22. Writing spectrum data to an ASCII file, including weights.
2.23. Writing spectrum data to an ASCII file, concatenating the spectral segments.
2.24. Writing spectrum data to an ASCII file, specifying a selection of spectral indices.
2.25. Writing spectrum data to an ASCII file, with a literal array of spectral indices.
2.26. Writing spectrum data to an ASCII file, specifying a selection of spectral segments.
2.27. Writing spectrum data to an ASCII file, specifying a literal array of spectral segments.
2.28. Creating a space-delimited formatter.
2.29. Writing spectrum data to an ASCII file, specifying a space-delimited formatter.
2.30. Writing a table to disk.
2.31. Reading a table from a file, specifying the ADVANCED type of table for parsing.
2.32. Reading a table from a file, specifying the ADVANCED table type for parsing and skipping header lines.
2.33. Reading a table from an ASCII file, with ADVANCED type and character ignore options for the parser.
2.34. Reading a table from an ASCII file, with ADVANCED type and an ignore pattern that trims spaces at the beginning.
2.35. Reading a table from an ASCII file, with ADVANCED type and guessing all value types.
2.36. Reading a table from an ASCII file, with ADVANCED type and parsing all values as doubles.
2.37. Reading a table from an ASCII file, with ADVANCED type and a custom table template.
2.38. Reading a table from an ASCII file, with ADVANCED type and assuming 18 character-wide columns and space separators.
2.39. Reading a table from an ASCII file, with ADVANCED type and providing a fully customised parser.
2.40. Reading a table from an ASCII file while writing the parsing configuration to a file for reuse.
2.41. Reading a table from an ASCII file, specifying a parsing configuration file.
2.42. Writing a table to an ASCII file without a header.
2.43. Writing a table to an ASCII file including metadata.
2.44. Writing a table to an ASCII file including metadata with a custom prefix.
2.45. Writing a table to an ASCII file with a custom formatter.
2.46. Writing a table to an ASCII file saving the writing configuration to another file.
2.47. Writing a table to an ASCII file, specifying a previously-saved writing configuration file.
2.48. Creating a TableTemplate with 3 columns.
2.49. Customising a TableTemplate with column names, types, units and descriptions.
2.50. Setting column descriptions for a partial set of columns.
2.51. Creating a unit variable and checking if it is built in the system.s
2.52. Creating and customising a TableTemplate in one step.
2.53. Creating a comma-separated CSV parser.
2.54. Creating a CSV parser with a dollar sign for quoting values.
2.55. Creating a parser that specifies the widths of the columns.
2.56. Creating a parser based on a regular expression.
2.57. Creating a CSV parser that ignores line starting with a specific string.
2.58. Creating a fixed width parser that skips a number of header lines.
2.59. Create a parser based on a regular expression that trims the lines of the file.
2.60. Creating a CSV formatter that specifies a space character as a delimiter.
2.61. Creating a CSV formatter with the default options.
2.62. Creating a CSV formatter that uses a tab as a delimiter.
2.63. Creating a fixed width formatter.
2.64. Creating a CSV formatter that includes a header.
2.65. Creating a fixed width formatter with commented metadata.
2.66. Creating a CSV formatter with a custom comment prefix.
2.67. Creating a CSV formatter that includes a header, delimited with spaces and with comments with a custom prefix.
2.68. Creating a fixed width formatter.
3.1. Creating a double array and populating with a range of values.
3.2. Creating a plot and adding layers to it in two steps.
3.3. Creating a plot and adding a layer to it in one step.
3.4. Setting the dimensions of the plot.
3.5. Creating a plot with initial dimensions.
3.6. Creating a plot with initial dimensions and auto-adjust.
3.7. Setting title and subtitle text in a plot.
3.8. Setting the visibility for a plot's title and subtitle.
3.9. Sets the text to be displayed.
3.10. Sets the horizontal alignment. Possible values are LEFT, CENTER and RIGHT.
3.11. Sets the vertical alignment. Possible values are MIDDLE, TOP and BOTTOM.
3.12. Sets the position of the title. Possible values are BOTTOMCENTER, BOTTOMLEFT, BOTTOMRIGHT, TOPCENTER, TOPLEFT, TOPRIGHT and CUSTOMIZED. If set to CUSTOMIZED, the title position is controlled by the setLocation method.
3.13. Sets the x and y location of the title, automatically switching the position to CUSTOMIZED.
3.14. Sets the x position of the title.
3.15. Sets the x and y position of the title. Equivalent to setLocation .
3.16. How to create an additional layer in a plot.
3.17. Changes the name (and thus the legend) of the layer.
3.18. Sets the line style of the layer. Possible values are NONE, SOLID, MARKED, DASHED and MARK_DASHED. You can also use the numbers 0, 1, 2, 3 and 4.
3.19. Sets the size of the layer symbols, in points.
3.20. Sets the shape of the symbol. See Table 3.2 for the names and numbers of available symbols.
3.21. Sets the line thickness, in points. Only for line plots.
3.22. Sets the style of the layer. The input parameter is an instance of the Style class. For more information on creating styles see Section 3.9 .
3.23. Adds a point to the layer.
3.24. Adds a set of points to the layer.
3.25. Waits for mouse click and returns the coordinates of the pointer. Returns a double[] .
3.26. Like the previous method, but this one does the job for n successive clicks. Returns a double[][] , that is, an array of double arrays. Each array holds the coordinates of a mouse click.
3.27. The difference with respect to the previous two methods is that this time the coordinates of the layer point closer to the mouse pointer are returned. Returns a double[] .
3.28. Like the previous method, but this one does the job for n successive clicks. Returns a double[][] , that is, an array of double arrays. Each array holds the coordinates of the data point closest to each mouse click.
3.29. Returns an int representing the index of the current layer inside the PlotXY .
3.30. Sets whether the layer is shown in the legend. Getter method isInLegend available.
3.31. Customising the appearance of the different plot symbols.
3.32. Adding a customised range and title to a plot axis.
3.33. If flag is true, adjusts the range of the specified axis so that all data points will be shown.
3.34. Sets the range of the axis. The lower and upper limit are passed as separate double parameters. Note that there is no "Jython style" example because lists and tuples in Jython use the same syntax. See the row just below for the example.
3.35. Set the range of the specified axis to values between lower and upper. Note that instead of two arguments for the lower and upper limits, there is one array argument containing both values.
3.36. Show grid lines for the specified axis if flag is true, hide the grid lines otherwise.
3.37. Sets the axis type. Available types are LINEAR , LOG , DATE , RIGHT_ASCENSION and DECLINATION .
3.38. Gets the axis orientation, either HORIZONTAL or VERTICAL . Setter method not available.
3.39. Sets the axis to a linear scale. Equivalent to setType(Axis.LINEAR) .
3.40. Sets the axis to a logarithmic scale. Equivalent to setType(Axis.LOG) .
3.41. Sets whether values on the axis are displayed in inverted order (for instance, right to left for the abscissa).
3.42. Sets the position of the axis with respect to the plot. Possible values are TOP or BOTTOM for abscissa axis and LEFT or RIGHT for ordinate axis. Get method available.
3.43. Sets the text to be displayed.
3.44. Sets the physical height of the major ticks.
3.45. Sets the interval between major ticks, in axis units.
3.46. Sets the side of the axis on which the ticks are drawn. Possible values are INWARD , OUTWARD and BOTH .
3.47. Sets the number of minor ticks displayed between two major ticks.
3.48. Sets whether the number of ticks on the axis is adjusted automatically to avoid overlapping labels. Getter method isAutoAdjustNumber available.
3.49. Sets whether grid lines are displayed for major ticks. Getter method isGridLines available.
3.50. Sets the colour of labels.
3.51. Sets the font of labels.
3.52. Sets the physical size of labels.
3.53. Sets the interval (in ticks) between successive labels. For example, a value of two displays a label on every other tick.
3.54. Sets the orientation of the labels (0 for horizontal, 1 for vertical).
3.55. Replaces the current labels with the values in an array of String objects.
3.56. Sets the side of the axis on which the labels are drawn. Possible values are INWARD and OUTWARD .
3.57. Sets the x axis to the specified Axis instance. The x axis will be reinstantiated with its default settings plus whatever is indicated in the Axis instance. So any prior manipulations of the axis are lost.
3.58. Sets the range of the x axis.
3.59. Sets the title of the x axis.
3.60. Sets the type of the x axis. Available types are LINEAR and LOG.
3.61. Sets the x and y values, passed as elements of an "array of arrays" of size two. Get method available. Note that there is no setYx method!
3.62. Sets the x and y values, passed as two separate arrays. Note that there is no setYx method!
3.63. Sets the ordinate values. Get method available. Note there is a getX method but not a setX method.
3.64. Removes the x axis and uses the given axis as a shared x axis.
3.65. Creates an empty annotation.
3.66. Creates an annotation with the given text.
3.67. Creates an annotation with the given position and text.
3.68. Sets the position angle, in degrees, counterclockwise.
3.69. Sets the horizontal alignment.
3.70. Sets the vertical alignment.
3.71. Sets the x position.
3.72. Sets the x and y position.
3.73. Sets the text of the annotation.
3.74. Gets the unique id of the annotation. No setter available.
3.75. Adds an Annotation object to the layer.
3.76. Adds several Annotation objects to the layer. The input Annotations are passed as an array.
3.77. Sets an annotation to a given id, replacing what was there before.
3.78. Replaces all the annotations with the ones provided in the array.
3.79. Retrieves one annotation from the layer.
3.80. Retrieves all the annotations from the layer. The annotations are returned as an array.
3.81. Removes the annotation with the specified id.
3.82. Removes all the annotations.
3.83. Filling the areas between the curves.
3.84. Drawing an arbitrarily-positioned straight line using LayerXY.
3.85. Appends a low and high error value of x.
3.86. Appends a set of low and high error values of x.
3.87. Sets low and high error values of x.
3.88. Sets the low and high error values of x.
3.89. Returns an array of Ordered1dData with length equal to 2.
3.90. How to add and customise a subplot inside a main plot.
3.91. How to manually combine three bands to create an RGB image, respecting WCS information.
3.92. Batching several plots to improve speed.
3.93. Distributing layers inside a main plot.
3.94. Sets whether the component is visible.
3.95. Sets the foreground colour of the component.
3.96. Sets the font of the component. You can specify a font by giving a name, style and point size. Available font styles are PLAIN , BOLD and ITALIC . You can also use the numbers 0, 1 and 2, respectively.
3.97. Sets the name of the font of the component.
3.98. Sets the size of the font of the component.
3.99. Sets the style of the font of the component. Possible values are PLAIN , BOLD and ITALIC . You can also use the numbers 0, 1 and 2, respectively.
3.100. Creating a plot that is not drawn on the screen.
3.101. Complete example that demonstrates the use of the PlotXY class.
3.102. Version of the example above using the Display class.
3.103. Plotting the figure that appears at the beginning of this chapter.
3.104. Distributing multiple plots using panels.
3.105. Plotting horizontal and vertical error bars.
3.106. Adding multiple layers and customised auxiliary axes to a plot.
3.107. Using several panels with histograms.
3.108. Plotting with customised line and plot styles.
3.109. Plotting two independent subplots.
3.110. How to add error bars and customised horizontal bars to a plot.
3.111. Complete example using PACS and SPIRE data of AFGL 2688.
4.1. Printing the type of a variable.
4.2. Setting the image value of a SimpleImage object.
4.3. Set the wavelength value of an image.
4.4. Set the wavelength value of an image, including units.
4.5. Setting the units of an image directly.
4.6. Setting the exposure of an image.
4.7. Setting the error and coverage datsets of an image.
4.8. Constructing a Display object from an image.
4.9. Saving the current view of a Display object.
4.10. Saving an image to disk without blocking the GUI.
4.11. Adding annotations and setting formatting options in a Display object.
4.12. Filling shapes with oversized lines in a Display.
4.13. Opening the annotation toolbox programmatically.
4.14. Opening the colour and cut level dialogues programmatically.
4.15. Clamping an image with explicit limits.
4.16. Cropping an image specifying the rectangle dimensions.
4.17. Regridding an image and getting the flux change factor.
4.18. Rotating an image without specifying an interpolation method.
4.19. Rotating an image with a specific interpolation method.
4.20. Scaling an image both with and without custom interpolation.
4.21. Translating an image using two different sets of coordinates.
4.22. Transpose an image with a horizontal flip.
4.23. Adding images and also scalars to images.
4.24. Subtracting images and also scalars from images.
4.25. Multiplying images and also images by scalars.
4.26. Changing the pixel size of an image while ensuring flux conservation.
4.27. Dividing images and also images by scalars.
4.28. Integer division of images and image by scalar.
4.29. Applying the absolute value to the intensity values of an image.
4.30. Rounding the intensity values of an image.
4.31. Rounding the intensity values of an image to the largest previous integer.
4.32. Rouding the intensity values of an image to the smallest following integer.
4.33. Raising the intensity values of an image to the n-th power.
4.34. Squaring the intensity values with an specific task.
4.35. Taking the square root of the intensity values of an image.
4.36. How to obtain the natural logarithm of the intensity values of an image.
4.37. How to obtain the base 10 logarithm of the intensity values of an image.
4.38. How to obtain the base N logarithm of all intensity values of an image.
4.39. How to obtain the exponential of the intensity values of an image.
4.40. Raising 10 to the intensity value for all image intensity values.
4.41. Raising N to the intensity value for all image intensity values.
4.42. Smoothing an image using four different algorithms.
4.43. Converting image units with a specific task.
4.44. Convolving an image with a specific kernel.
4.45. Flagging pixels whose value exceeds the limit provided.
4.46. Getting the minimum and maximum values for a certain cut-off percentage.
4.47. Mosaicking images with the help of an intermediate array.
4.48. Creating an RGB image with specific weights for each channel.
4.49. Creating an RGB image with cut levels for each channel.
4.50. Creating an RGB image with weights, overall cut level and new WCS information.
4.51. Printing the WCS information of an image.
4.52. Creating WCS coordinate data.
4.53. Creating WCS coordinate data with parameters.
4.54. Creating a profile plot of an image.
4.55. Retrieving the pixel coordinates of the beginning of the line.
4.56. Retrieving the sky coordinates of the beginning of the line.
4.57. Converting the profile plot to a Double1d.
4.58. Getting the unit of the profile plot.
4.59. Creating the pixel profile plot of a synthetic image.
4.60. Creating an automatic line contour specifying distribution and plotting details.
4.61. Creating a manual line contour providing contour level values.
4.62. Creating a contour containing one single contour level.
4.63. Plotting automatically-generated contours on top of an image.
4.64. Creating a histogram from an image.
4.65. Getting the number of bins from the histogram.
4.66. Getting the lower cut level of the histogram.
4.67. Converting the histogram to a table dataset.
4.68. Getting the values of the bins as a Double1d array.
4.69. Getting the count for each histogram bin as a Double1d.
4.70. Get the unit of the histogram values.
4.71. Getting the centre pixel coordinates of the circle histogram.
4.72. Getting the centre sky coordinates of the circle histogram.
4.73. Getting the radius of the circle histogram in pixels.
4.74. Getting the radius of the circle histogram in arcseconds.
4.75. Getting the centre pixel coordinates for the ellipse histogram.
4.76. Getting the centre sky coordinates for the ellipse histogram.
4.77. Getting the width of the ellipse histogram in pixels.
4.78. Getting the width of the ellipse histogram in arcseconds.
4.79. Getting the upper left corner pixel coordinates of a rectangle histogram.
4.80. Getting the upper left corner sky coordinates of a rectangle histogram.
4.81. Getting the width in pixels of a rectangle histogram.
4.82. Getting the width in arcseconds of a rectangle histogram.
4.83. Getting the edges of a polygon histogram.
4.84. Getting the vertices of a polygon histogram as a table dataset.
4.85. Getting the vertices of a polygon histogram as a Double2D array.
4.86. Getting the edges of a polygon histogram in sky coordinates.
4.87. Creating a residual image subtracting the sources for the original image.
4.88. Creating an image containing only the sources of the original image.
4.89. Extracting the results of the task from the output array.
4.90. Removing a row from a sources list.
4.91. Plotting the source list along with the image with the help of the Display class.
4.92. Customising the size of the position circles when plotting sources with Display.
4.93. Making the position circles of plotted sources proportional to the flux intensity.
4.94. Plotting fully customised position circles by passing Color and Float1d objects.
4.95. Plotting position circles that take the sizes as sky coordinates by passing a Wcs object.
4.96. Creating a rectangular region of interest (SkyMask) using sky coordinates in decimal degrees.
4.97. Creating a circular region of interest (SkyMask) using sky coordinates in decimal degrees.
4.98. Creating a region of interest from a bidimensional array of booleans.
4.99. Applying the boolean OR operation between SkyMasks.
4.100. Inverting a region of interest.
4.101. Joining the areas of three different SkyMasks.
4.102. Masking an image with a complex, boolean SkyMask.
4.103. Retrieving the source list dataset from the results output list of a source extraction task.
4.104. Creating a SourceListProduct from a source list table dataset.
4.105. Creating a SourceListProduct from a source list dataset.
4.106. Fitting sources in an image.
4.107. Performing annular sky aperture photometry on a PACS map.
4.108. Performing annular sky aperture photometry on a SPIRE map.
4.109. Getting the centre pixel coordinates for the target.
4.110. Getting the centre sky coordinates for the target.
4.111. Getting the target radius in pixels.
4.112. Getting the target radius in arcseconds.
4.113. Getting the outer target radius in pixels.
4.114. Getting the inner radius of the sky estimation annulus in arcseconds.
4.115. Getting the name of the algorithm used by the aperture photometry task.
4.116. Checking if the aperture photometry task considers fractional or entire pixels.
4.117. Getting the results of the aperture photometry task as a table dataset.
4.118. Getting the results of the aperture photometry task as a Double2d table.
4.119. Getting the total flux (target+sky).
4.120. Getting the total number of pixels (target+sky).
4.121. Getting the flux intensity averaged by the total pixels (target+sky).
4.122. Getting the curve of growth for the results of aperture photometry task.
4.123. Getting the growth radius for the results of the aperture photometry task.
4.124. Getting the growth flux column of the results of the aperture photometry task.
4.125. Getting the intensity plot as a table dataset.
4.126. Getting the sky intensity radius of the intensity plot.
4.127. Getting the sky intensity values from the intensity plot as a Double1d.
4.128. Performing rectangular sky aperture photometry.
4.129. Getting the width in pixels of the rectangular aperture.
4.130. Getting the width in arcseconds of the rectangular aperture.
4.131. Getting the upper left corner of the rectangular aperture in pixel coordinates.
4.132. Getting the upper left corner of the rectangular aperture in sky coordinates.
4.133. Performing fixed sky aperture photometry.
4.134. Running the aperture photometry correction task for point sources.
4.135. Importing the required classes for the PSF-point source comparison example.
4.136. Reading the data from a PACS calibration observation (PSF-point source comparison).
4.137. Retrieving the beam profile from the latest SPIRE calibration (PSF-point source comparison).
4.138. Retrieving the necessary properties for PACS and SPIRE (PSF-point source comparison).
4.139. Creating auxiliary variables with the obsid and band (PSF-point source comparison).
4.140. Rotating the PSF and matching to the source (PSF-point source comparison).
4.141. Updating the Wcs information (PSF-point source comparison).
4.142. Matching the WCS of the beam and the source (PSF-point source comparison).
4.143. Retrieving the RA and declination in decimal degrees (PSF-point source comparison).
4.144. Retrieving the X, Y coordinates in pixels (PSF-point source comparison).
4.145. Setting the coordinates to the centre of the map (PSF-point source comparison).
4.146. Finding the exact centre of the PSF (PSF-point source comparison).
4.147. Find the exact centre of the point source (PSF-point source comparison).
4.148. Matching the WCS of the PSF to the coordinates of the source (PSF-point source comparison).
4.149. Defining the coordinates for building the EEF curve.
4.150. Creating an array of apertures.
4.151. Removing the first aperture from the array.
4.152. Creating a variable for storing two arrays of fluxes.
4.153. Performing the point source aperture photometry for every aperture in the array.
4.154. Performing the PSF aperture photometry for every aperture in the array.
4.155. Scaling the fluxes of the PSF and point source to peak (min aperture).
4.156. Defining apertures for the beam model.
4.157. Scaling the fluxes of the PSF and point source to median.
4.158. Plotting the results of this comparative aperture photometry.
4.159. Measuring the FWHM of the point source using a cubic spline interpolator.
4.160. Measuring the FWHM of the PSF using a cubic spline interpolator.
4.161. Comparing both values for FWHM.
4.162. Measuring the sky background scatter of beam and astro source.
4.163. Defining recommended values for circular photometry.
4.164. Performing the aperture photometry for all the small spot apertures.
4.165. Removing outliers from the sample.
4.166. Performing PSF comparison for PACS point sources.
4.167. Performing PSF comparison for SPIRE point sources.
4.168. Setting the camera and aperture variables.
4.169. Defining scaling factors for the data.
4.170. Setting up recommended aperture photometry values for all observation ids.
4.171. Scaling and subtracting the PSF.
4.172. Performing the aperture photometry of the residual image, computing the EEF and printing every result.
5.1. Opening the Spectrum Explorer from a script.
5.2. Opening the Spectrum Explorer forcing all spectra to be plotted
5.3. Adding a new spectrum to a plot.
5.4. Usage of SpectrumPlot variables (overplotting spectra).
5.5. Adding spectra using the overloaded method add()
5.6. Selecting point spectra and segments.
5.7. Selecting point spectra and segments (second variation).
5.8. Importing the Integrator class
5.9. Integrating over a set of ranges
5.10. Integration over a set of ranges with masking.
5.11. Integration over a set of ranges with masking and removing up to n levels of background
5.12. Fitting the fringes.
5.13. Smoothing the background baseline.
6.1. Creating an SpectralSimpleCube object.
6.2. Printing a cube dimensions
6.3. Printing all the spaxel coordinates that make up this cube.
6.4. Getting different coordinates from the WCS information of a cube
6.5. Opening the Spectrum Explorer and plotting a cube.
6.6. Opening the Spectrum Explorer and plotting all spectra from a cube.
6.7. Opening the Spectrum Explorer and plotting all spectra from a cube
6.8. Adding cube data to a Spectrum Explorer instance
6.9. Creating a plotting variable for later use with splot
6.10. Creating an array for selecting a particular spectrum from a cube
6.11. Creating a selection array with spaxel coordinates.
6.12. Creating a spectrum selection array.
6.13. Creating a deep copy of a cube.
6.14. Creating a wavelength/frequency grid for resampling data.
6.15. Using resampling tasks with cubes.
6.16. Declaring a Short3d array as flags for a cube.
6.17. Creating a mask using list slicing.
6.18. Creating start and end point array for integration.
6.19. Getting a layer from the images dataset of a cube.
6.20. Inspecting the contents of the images dataset of a cube.
6.21. Defining some Double1d arrays for range selection.
6.22. Converting the units of the flux maps generated by the Cube Toolbox
6.23. Converting the units of a map represented as a SimpleImage.
7.1. Creating a new instance of the Spectrum Fitter with and without a plot window.
7.2. Creating a Spectrum Fitter specifying the particular spectra by segment number(s).
7.3. Creating a Spectrum Fitter specifying the spectra by cube coordinates.
7.4. Creating a new instance of the Spectrum Fitter specifying both segment number and the display of the plot window.
7.5. Retrieving an observation whose data will be used for a Polynomial interpolation.
7.6. Extracting a product from the observation that will be used for Polynomial interpolation.
7.7. Script automatically (some manual changes added for the sake of clarity) generated by Spectrum Fitter (example 1).
7.8. Script automatically generated by Spectrum Fitter (example 1), and modified for this example.
7.9. Multifitting a cube using exported models.
7.10. Retrieving an observation from the HSA to use its data for multimodel fitting.
7.11. Script automatically generated by the Spectrum Fitter (example 3), slightly modified for this example.
7.12. Retrieving an observation from the HSA to use it in a multimodel fitting through the GUI.
7.13. Extracting a product to use the data for multimodel fitting through the GUI.
7.14. Example script fitting a spectrum with multiple models as exported by HIPE.
7.15. Multifitting a cube with a set of exported models.
7.16. Extracting the parameters from the results of the multifitting.
7.17. Manually setting the unit of the velocity and intensity maps
7.18. Worked example of a manual conversion of all data in a cube from Jy·u to W/m while creating flux maps.
7.19. Worked example of a manual conversion of all data in a cube from W/(m2 Hz Sr) to W/m while creating flux maps.
7.20. Adding a new model to an instance of the Spectrum Fitter
7.21. Setting weighted regions for the fitting using the setMask method.
7.22. Setting "binary" weights to effectively mask out ranges of the spectrum from the fit.
7.23. Setting a mask array that weights every point in the x-axis.
7.24. Setting limits for MultiFitting.
7.25. Setting limits for a particular model parameter in the MultiFitter.
7.26. Setting limits for all the parameters of a model in the MultiFitter (generic).
7.27. Setting limits for all the parameters of a model in the MultiFitter (with values).
7.28. Fixing the value of a model parameter during fitting.
7.29. Printing the model information, including expected parameters.
7.30. Running the fit after setting parameters and (optional) limits and masks.
7.31. Printing the fitted parameters of a model.
7.32. Creating a table of fitted parameters.
7.33. Removing one or all models from an instance of the Spectrum Fitter.
7.34. Mostly complete example on iterative fitting (using the residual for the next step).
7.35. Exporting a fitting script with the same actions performed in the GUI
7.36. Saving a residual data as an ASCII file.
7.37. Retrieving the residual in the same format as the input was.
7.38. Exporting the (total) model details as an ASCII file.
7.39. Exporting model details as an ASCII file.
7.40. Getting the model or total model in the same format as the input data.
7.41. Saving the fit parameters to an ASCII file.
7.42. Saving the model fit parameters as an XML file.
7.43. Getting the model parameters as a TableDataset.
7.44. Saving the model fit parameters as a SpectralLineList for use with other spectra.
7.45. Getting the integral of the model line.
7.46. Computing the integrated flux after MultiFitting a spectral cube.
7.47. Printing several data in MultiFit_Parms.
7.48. MultiFitting a SpectrumContainer with a set of previously exported models.
7.49. Using ComboModels with a specific relationship between fit parameters.
7.50. Setting the parameters of the added model.
7.51. Setting the parameters of a multi model fitting or a MultiFitting.
7.52. Creating a non-linear model for use with the Spectrum Fitter.
7.53. Adding a custom model, previously exported as a Jython file.
7.54. Selecting the fitting algorithm to use.
7.55. Extracting images from the ParameterCube after MultiFitting a cube
7.56. Retrieving the ParameterCube from the MultiFitter results.
7.57. Getting the peak flux image from the ParameterCube.
7.58. Converting the peak flux image of the ParameterCube into an image of the integrated flux, for a PACS cube.
7.59. Manual conversion of map units from Jy·u to W/m
7.60. Manual conversion of map units from W/(m2 Hz Sr) to W/m
7.61. Getting the cube of the total fitted model, and parameters and errors datasets.
7.62. Getting the Chi-squared on the command line
7.63. Simple polynomial fitting with error calculation using MonteCarloError.
7.64. Arctan fit with evidence estimation using a prior.
7.65. Fitting with PadeModel and evidence estimation using a prior range.
7.66. Fitting data with a non-linear SineModel, using a Hessian matrix as confidence; then fitting with a mixed SineModel and estimating error with MonteCarloError.
7.67. Fitting data with a combined model of Gaussian, Polynomial and Sine models.
7.68. Fitting data with a combined model of Gaussian, Polynomial and Sine models.
8.1. Getting the product stored in the results of a MultiFitting.
8.2. Creating an empty matrix that can hold the frequency values of the fitted products.
8.3. Filling the matrix with the fitting results data.
8.4. Defining constants required for the conversion.
8.5. Converting the whole matrix values taking advantage of the capabilities of HIPE arrays.
8.6. Creating a new image object to hold the velocity values.
8.7. Manually setting the units of the output velocity map.
8.8. How to convert an instance of SpireSpectrum1d.
8.9. How to convert an instance of HrsSpectrumDataset.
8.10. How to convert an instance of SpectralSimpleCube.
8.11. How to convert an instance of SimpleImage.

List of Procedures

3.1. Useful methods of the PlotTitle class. See Section 3.29 for the conventions used in this table.
3.2. Miscellaneous setters of the LayerXY class. See Section 3.29 for the conventions used in this table.
3.3. Other methods of the LayerXY class. See Section 3.29 for the conventions used in this table.
3.4. Useful methods of the Axis class. See Section 3.29 for the conventions used in this table.
3.5. Useful methods of the AxisTitle class. See Section 3.29 for the conventions used in this table.
3.6. Some methods of the AxisTick class. See Section 3.29 for the conventions used in this table.
3.7. Some methods of the AxisTickLabel class. See Section 3.29 for the conventions used in this table.
3.8. Axis-related methods of the LayerXY class. See Section 3.29 for the conventions used in this table.
3.9. Methods of the Annotation class. See Section 3.29 for the conventions used in this table.
3.10. Methods of the PlotXY class for handling annotations. See Section 3.29 for the conventions used in this table.
3.11. Methods for handling error bars in layers. See Section 3.29 for the conventions used in this table.
3.12. Common methods to customise colours, fonts and visibility. See Section 3.29 for the conventions used in this table.
4.1. Available methods for profilePixel and profileSky .
4.2. Available methods for the output of histogram tasks.
4.3. Available methods for the output of the circleHistogram task.
4.4. Available methods for the output of the ellipseHistogram task.
4.5. Available methods for the output of the rectangleHistogram tasks.
4.6. Available methods for the output of the polygonHistogram task.
4.7. Available methods for the output of the annularSkyAperturePhotometry task.
4.8. Available methods for the output of the rectangularSkyAperturePhotometry task.