Image Processing for Space & Earth ObservationsMultisource & Multispectral Image Processing via Bayesian Inference
Development of a visualization tool enabling large IFU data cubes upload, navigation and interpretation
Title : CubeVisualization
Keywords : Visualization, massive data sets, hyperspectral data, IFU
Funding : ANR Dahlia
Start date : 2009-01-01
End date : 2013-01-31
SummaryVisualizing multi-dimensional observation data sets is a common challenge for observational sciences and crucial for Integral Field Spectroscopy (IFS) in astronomy. For the specific case of IFS data cubes, like MUSE, the size of the observation requires ad-hoc tools to be able to upload, visualize and navigate inside the 2D+lambda cube. This work package aims at :
Key objectivesThis project aims at providing a visualization tool for IFU (Integral Field Unit) data cubes and their associated parameters (variance, psf,...), either by re-using existing viewers or by designing and developping a specific application. The huge amount of data in an hyperspectral image (up to 2.4Go for MUSE data cubes) requires the development of new tools for visualizing and browsing the cube. Indeed, most of the current 2D/3D viewers are not suitable because the visualization of large hyperspectral data (up to 4000 bands) requires specific design requirements and processings:
QuickVizQuickViz is a Java prototype for such a datacube viewer. It has been designed as a plug-in application of the Aladin VO application which already provides multi-view, multiband images handling catalog overlap and interoperability with other VO applications. QuickViz is currently developed and maintained by the PASEO team by Matthieu Petremand and Mireille Louys with the help of Pierre Fernique at the CDS (for the interaction with Aladin). It is dedicated to the visualization of hyperspectral cubes such as IFU to be obtained with the MUSE instrument (ANR Dahlia) where the variance information is available for each sensor location. Nevertheless, any kind of hyperspectral images may be supported. QuickViz may also run as a standalone application (without Aladin). In addition, QuickViz provides processing algorithms, specific representation modes for variance or uncertainties and a useful interaction with Aladin (catalogs overlap, calibration functions, header management, 2D display...) giving access to a set of scientific features in use in the astronomical community. Indeed, the design strategy of QuickViz has been thought in order to maximize the extensibility of the plug-in. Users can then add:
The following sections introduce the main features of QuickViz.
Spectral extractionIf you click on the image plane in the Aladin frame, the spectrum corresponding to the mouse location in the image is extracted from the data cube, added to the spectrum stack of QuickViz, displayed on the spectrum panel and a position tag is shown on the Aladin's image plane too. If your cube does not provide a FITS standard compliant spectral calibration, QuickViz will ask you, only once, to fill in missing calibration values. In the same way, an astrometrical calibration can be defined from the Image menu of Aladin (Astrometrical calibration entry). Spectra cannot be extracted from Aladin if your data don't provide an astrometrical calibration.
Each newly extracted spectrum replaces the previous one in the spectrum stack to simplify its management. If you want to permanently store a spectrum, press the key K (for Keep) while selecting the spectrum, set it a name and validate. This single-spectrum extraction mode can be disabled in the Extraction menu (Single extraction entry).
As the spectrum stack grows, kept spectra can be simultaneously displayed (shift + left-click on spectra you want to add (resp. remove) to (resp. from) the selection) even if they haven't been extracted from the same cube: the spectral scale is updated according to the current spectrum selection whereas spectra having incompatible units are not selectable. In addition, right-clicking on a spectrum in the stack displays a popup menu allowing you to:
At last, when you let your mouse pointer linger over a spectrum in the stack, a tooltip appears and provides relevant spectrum information.
Extraction and superposition of spectra
Panel interactions: zoom, spectral navigation, selection and panOnce you have extracted spectra of interest, four panel interactions, available in the shortcut toolbar, can be enabled by left-clicking and dragging the mouse on the spectrum panel:
Zoom and spectral selection
An interactive zoom is also available from the shortcut toolbar (accelerator key: R) and might be enabled together with other interactions. Once activated, moving the mouse over the panel displays its zoomed version into a circle or square (if rounded windows are not supported on your operating system) shaped window. The zoom factor is controlled by the mouse wheel. This feature is useful to focus on a specific area while keeping an eye on the whole panel.
Spectrum propertiesAt the bottom of the application frame, a toolbar displays parameter values that are related to the current visualized spectra like minimum and maximum values, mean, standard deviation, name, coordinates of the cursor position... By right-clicking on this toolbar, you can customize the displayed information and copy them into clipboard.
Customizing the toolbar
Managing the spectral calibrationWhenever you right-click on a spectrum in the stack, a popup menu appears that allows you to manage its spectral calibration ("Edit calibration" or "View calibration" menu entries). If your spectrum has been loaded from Aladin, you will only be able to view the calibration. But, if it comes from the output of an algorithm (see below), you can update its spectral calibration (unit, reference, delta...).
Managing the spectral calibration
Multithread loadingAs QuickViz is intented to deal with large hyperspectral data cubes, the spectrum extraction may be time-consuming! That's why QuickViz implements a multithread loading scheme that allows to still use the application while spectra are loading. Moreover, QuickViz keeps you aware of the progression of the extraction process by displaying a progress bar in the spectrum list.
Visualization modesSpectra can show very packed line patterns and therefore can't be simply drawn with simple lines, crosses or points as any other functions, especially when you superimpose spectra. QuickViz allows to customize the way spectra are displayed by introducing various visualization modes. These drawing modes are accessible via the upper shortcut toolbar.
Two different modes of visualization: bars and lines
Variance extraction and visualizationWhen you handle a hyperspectral cube, you may have access to its variance values in the form of another hyperspectral cube. QuickViz provides a way for the joint extraction of spectra and associated variance values. This extraction mode is enabled by selecting the Spectrum + Variances entry in the Extraction menu. Thus, for the next spectrum extraction, QuickViz tries to automatically detect the variance cube associated to your data (based on extension names within the same FITS file, i.e. DATA for data cubes and STAT for variance cubes). If it failed, QuickViz asks you to manually select the variance cube to be associated to your data. Once both cubes have been linked, variance values are extracted for each spectrum and displayed, along the spectral axis, with a dedicated visualization mode named error covering. Another mode (error bars) is also available through the shortcut toolbar.
Visualization of variance values along the spectral axis: error bars and error covering
QuickViz also allows you to visualize your data together with variance values across the field of view (see link for details) in the form of a video. This beta feature can be tested from the View menu by clicking on the 2D variance entry. Once the variance visualization window is opened, you can select a cube's frame, for which you want to visualize the variance movie, by exploring a cube thanks to the cursor in QuickViz. A left-click on the Play button (in the shortcut toolbar of the movie window) starts the video and the next cursor move in QuickViz automatically stops it and selects a new frame (unless the Lock button is checked). At any time, while the video is playing, you can:
Visualization of variance values across the field of view: main frame and duplicated panels
AlgorithmsQuickViz allows to run many algorithms on a set of spectra, all along the spectral axis or on a restricted set of spectral selections over this set. Algorithms are sorted into two groups:
A specific visualization mode, using 3 selections for a color composition average image
MultiviewYou can easily add (resp. remove) spectrum panels to (resp. from) QuickViz thanks to the Panels submenu located in the View menu. This feature allows you to compare spectra without having to superimpose them. In multiview mode, all processings related to panels (like algorithm execution, spectrum extraction, unit change...) will be applied on the selected one. A panel is selected whenever you interact with it and then becomes surrounded by a light blue border. Keep in mind that spectra can be shared between panels.
Shape extraction (still in beta version)Aladin provides a way for the drawing of shapes on cube's frames. QuickViz uses this feature by providing a shape extraction that consists in computing the averaged spectrum (without taking variances into account for now even if they are available) over the shape. For the time being, QuickViz can only deal with circular areas.
To define a circular selection, just left-click on the tag button in Aladin's toolbar and draw a circle over a frame by left-clicking and dragging the mouse. When you release the mouse button, the averaged spectrum will be computed and displayed in QuickViz. Moreover, you can resize and move the circular shape over the frame, leading to the extraction of a new averaged spectrum whenever you have finished to modify the size or the location of the circle. At last, for now, the averaged spectrum is not yet updated while resizing or moving the shape and a new averaged spectrum is systematically created.
Current Release - QuickViz v1.50 (10/01/2012)
Current LimitationsFor the time being, QuickViz is still under development. Several features are not completely available and require additional developments to be fully finalized. The current proposed version of QuickViz has the following limitations:
Download & Installation
QuestionnairePlease, fill in our questionnaire and help us to improve QuickViz: link
Uncertainty representationUncertainties are a significant and valuable output of the fusion algorithm and are available at each location in the reconstructed cube. In addition, variances induced by the acquisition process are also provided for each observation session. The visualization of the behavior of uncertainties along spatial and spectral axes is essential as it may guide further investigations towards image areas or pixels having low uncertainties (e.g. for astrometry and photometry computations). Both coarse and fine views are interesting: a general overview allows to quickly localize high varying regions whereas pixel by pixel representation offers high resolution interpretation. The joint visualization variance/intensity data has been investigated along the spectral axis thanks to visualization modes available in QuickViz but the simultaneous spatial representation remains unsolved and problematic. Indeed, straightforward static visualizations such as colored or transparent compositions fail and instead tend to entangle both information. We have then selected two approaches based on a dynamical viewing process which is the most striking to the human eye.
The first strategy consists in using the third dimension z so that pixels (represented by 3D objects like spheres or cubes) oscillate more or less quickly around the (x,y) plane according to their variance: the highest the variance, the quickest the oscillation. The number of video frames to end a cycle is thus inversely proportional to the variance value. Such a 3D movie is relevant to instantaneously visualize high variance areas in spectral bands but requires the choice of an appropriate projection angle for an efficient perspective view. In addition, when the image size increases, it becomes more difficult to clearly distinguish swinging pixels. Thus, this representation should be preferred for limited regions or for the visualization of covariance values around a neighborhood. Two video examples obtained on simulated data (for testing purpose only) are available:
In the second visualization, a map is created where the intensity of the pixel varies with the corresponding variance measurement. Thus, high variance positions will change their intensity quicker than low variance ones. Contrary to the first strategy, oscillation amplitudes are not spatially constant but are taken in the interval [Yp - x*sigmap;Yp + x*sigmap] where Yp is a pixel intensity with its associated standard deviation sigmap and x is a real positive number. Compared to the 3D method, this one is particularly well-suited for large images because an intensity variation is less confusing than a height one and more attractive to the human eye, i.e. one can easily identify general trends in the image as illustrated in the following movie where variances of the top left corner of the image have been set to high values (link).
The evaluation and validation of both methods with the help of the astronomical community is still in progress.
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