Euro3D Visualization Tool

The Euro3D Research Training Network (RTN) was put forward with the intention to promote integral field spectroscopy (IFS), or ``3D'' spectroscopy, and to help making it a common user technique. In order to accomplish this, one of the major tasks was identified as the need of providing standard software tools for the visualization and analysis of datacubes. These tools should be general enough to be entirely independent of the origin of data, i.e.\ 3D instrument. Previously, a heterogenous collection of instrument-specific data formats and software tools (e.g.\ XOASIS), proprietary software packages and a lack of any standard have hampered a break-through of this powerful observing method, leaving it merely as an expert technique with comparatively limited scientific impact. Recognizing the importance of this problem, a work plan was devised to start creating a package of tools for the analysis and visualization of IFS data. Entitled 3D Visualization, Task~2.2 of this work plan foresees the development of a programme, which should be capable of reading, writing, and visualizing reduced data from 3D spectrographs of any kind. We have named this tool E3D. We describe here the progress on the coding of E3D. The last stable version is distributed in the Euro3D webpage.

You can download the last compiled version here:
E3D, 1.3a, source code
E3D, 1.3a, Linux binaries

Expecifications : AIP January mini-meeting

  • 31st January, 2005 E3D is distributed freely to the general public.
  • 6th Augost, 2004 New bugs solved. E3D includes new standalone programs, like "interpol" a program for interpolate non regular grid slices. Version change to 1.3.
  • May, 2004 E3D distributed within the GEMINI and ESO astronomers. Lots of bugs detected (as expected!).
  • 30th April, 2004 New tutorial to work with E3D, based in the Euro3D software tutorial meeting (Potsdam, 28-30 April 2004).
  • 20 of February, 2004 A major bug when reloading new images or plotting new spectra have been solved. The new version is uploaded.
  • 28 of January, 2004 Some minor cosmetic changes introduced. New version upload.
  • 06 of January, 2004 A lot of changes have been introduced in E3D, during the last month. A new version (1.2) is available to download. There are three main lines of modifications:
    • Memory bug solved. This implies that now E3D can handle large IFU data without a large cost of memory, and that it does not collapse when performing consecutive file loads. We have tested E3D with MUSE like data sets (90000 spectra, 712Mb on the disk), in a 512Mb Pentium IV. It takes 2m to read the data, and although the plotting is slow, it actually works. We have also tested with with consecutive PMAS file loadings, until a limit of 10000 uploads. The memory use increases from 21Mb to 41Mb, in total. With the previous version this increase in the memory use was found in the 5th upload, collapsing the computer at the 30th upload.
    • Different bugs solved. They were mainly related to the call of pointers still not allocated, which causes crashes of the program. There is still some of them, although they are identified. I will fix them ASAP.
    • New features included: (1) Import/Export different data formats, including datacubes and Row Staked Spectra, and 2D images or 2D spectra (ie., slit spectra); (2) Different spectra representation, not only the default pseudo-slit plus average, now the user can define the best representation for his/her spectra; (3) Different spaxels selection. To the spaxel-to-spaxel selection, already implemented, we have added two new selection methods (a) a circular area selection, with a radius defined by the user, and (b) a pseudo-slit spaxel selection; (4) Spaxel flux statistics. Basic statistic on the flux of the selected spaxels has been implemented; (5) Slice intensity 2D profiles. It is possible to plot the slice intensity profile of the selected spaxels, and determine the FWHM and peak intensity, by a simple fitting; (6) Single emission line fitting. We have implemented a simple and fast single emission line fitting. The emission line is fitted to a gaussian+continuum. The initial guess is automatically determined. Although not very precise, it gives the user a guess of the FWHM, line Flux, EW and continuum (See the snap shot fitting); (7) Automatic Kinematic Analysis. Based on the single line fitting, we have implemented a simple and automatic Kinematic Analysis tool. Once a spectral region is selected, and running this procedure, the program derived the Intensity map, velocity map, velocity dispersion map and continuum flux map of a single line. It gives a first guess of the kinematic structure of the data. We have compared the results from this technique with external tools, and the results are surprisingly precise (considering the simplicity of the method). (8) Changes in the overall GUI apparency and small details, like the asking of files prompts, etc...
    • Documentation. Although the documentation ( included in the doc directory was started in the very beggining, it has been stacked for a while. I have updated and modified sustantially this documentation. It is still not complete, although it contains some valuable information. If you intent to use E3D, please read the documentation!!!
    Finally, I want to remind the E3D users that I am on touch for any question regarding the program. Ie, if you cannot install it in a not tested arquitecture (or in a tested one!), please report me. Our intention is to distribute a static, compiled version of the program for different arquitectures, but this will take a while.
  • 20 of October, 2003 A bug on the DAR correction has been found. It is related with the former change from the NCARG interpolation to own coded interpolation routines. A new version has been uploaded (same name). It is recommended to use the PEAK DAR correction, when possible, and the Theoretical does not work.
  • 12-15 of October, 2003 E3D presented to the general public in the XIII ADASS conference, with a poster and a demo. The demo is a collection of examples of the E3D scripts. One of these scripts is now included in the distribution of E3D, under the directory script (plot_map.tcl, an utility for plotting maps).
  • 20 of August, 2003 Some bugs corrected, new options included.
  • 28 of July, 2003 A major change has been introduced on V3D. It will not need anymore the NCARG libraries. I have included new interpolation routines. Using the button "MAP" it is possible to select different interpolation options. The default one is the Cubic Spline, that is fast enough. This change affects sustantially to V3D, so I have upgrade the version to 1.0d.
  • 15 of July, 2003 After the visit of Sebastien Foucaud to the AIP, we have made some progress on V3D. We have added another system to comunicate with external routines (like IDL, PYTHON, IRAF...), sending commands to the visualization tool and getting data from it. We have tested it under PYTHON (S.Foucaud) and IDL, and it seems to be stable. Further tests may be required. A new system to write commands to the visualization has been added, and the documentation has been substatially updated.
    We have also tested V3D with VIMOS mosaic data (7150 spectra). We have identify some minor problem for large files, that force some changes in the visualization tool. However, even in actual status the visualization tool handle these data pretty well. Here you can see two examples (VIMOS 1,VIMOS 2).
    I have upload a new version (1.0c) of V3D in the internal webpage.
  • 3 of June, 2003 Bug with the colormap solved. New version uploaded (16:34)
  • 27 of May, 2003 I discovered a Bug in the SAVE SLICE option. Please download the last version from the Euro3D internal page!
  • 26 of May, 2003 The Beta version of the visualization tool is available for downloading. It is distributed under the restrictions of the Euro3D network. Actual Version On the Euro3D internal webpage
    It is really very poorly documented. The major change is the inclusion of a minor version of the NCARG mathematical libraries within the scripts directory. Instructions of how to install them are included at the end of the "configure" script. If you do not have a complete installation of NCARG, this short version would be enough for compiling V3D.
    (Its use should explicitally acknowlodge to Euro3D network: V3D is a product of the Euro3D Research Training Network, under contract of the European Comunitty, and include the reference: S.F.Sanchez, 2003, proceedings of the Euro3D Science Workshop, Cambridge, 21th-23th May, 2003, Astronomische Nachrichten)
  • 22 of April, 2003 The last version of the Lyon library has been released, including a nice documentation of how to produce your own project, and create a distribution. I have created a 1st version of the documentation here. It includes an example of how to install the actual "distribution" of the visualization tool. Some problems have been solved, and now it is possible to save fits file from the created map.
  • 6 of March, 2003 Still working on a proper documentation. A basic draf can be found here. Including new abilities (Map creating, interpolation, basic arithmetic). VT tested on a Suse Linux, a RedHat linux and a Solaris Ultra 5. No major problems. New library included NCARG (proper interpolation/fitting rutines). For a copy of the V3D (Euro3D visualization Tool), please send me an email:
  • 17 of February, 2003 New abilities added to the VT: Spectral range selection, Spaxels/Spectra inspectors, Spaxels selection for Spectra plotting, "Objects" definition and spectra plot, Postscript out-put. Tests of the scripting abilities using TCL code plus the new added commands (100% scriptable system). Snapshoots & PS output:
    • Snap 1: VT main window. Staked Spectra inspector. TIGER data of NGC1358, the groups info was still not included in the file (note the circular shape of the spaxels, instead of the tiger square shape: circles are default)
    • Snap 1: VT spaxels inspector. Cut over an spectral range.
    • Snap 2: VT spectra inspector. Spectra of the central region, selected using the spaxels inspector.
    • PS output:Postscript output of Snap 1,generated using the VT.
    • PS output:Postscript output of Snap 2,generated using the VT.
    10 of February, 2003 Final SHM server created. Set of C functions to interact with the server, load a new image, ask for a usual data, E3D information, etc... Tcl/Tk integration of the server. Creationg of a PGPLOT/TK interpreter, new commands added to 'mirror' the basic C functions. New Tcl/Tk+SHM server prototype: Load a file, plot the staked spectra, change of color map, max-min, intensity reader.
  • 1st of February, 2003 Tests of another approach. Instead of saving all the data on the SHM, we only save the descriptors, and any peace of data needed by the client will be asked to the server (a always running program) that 'server' the information to the client. Problem that solves: The memory limitation on SHM, Problem that generates: An always running program is mandaroty.
    Tests on the candecy has to be performed.
  • End of January, 2003 Shared Memory tests. SHM standard C library used (System V SHM). Physical limitation found to the total amount of memory to share (No use of the SWAP memory). Aditional limitation to the total amount of memory to share, depending on each computer (standard Suse instalation 32M, only root can change, and a reboot of the computer is needed).
    How to comunicate? Put all the data on a row on the SHM or use a semaphores based program that works as a server of the SHM. Tests: If no further comunication with other external programs where needed it will prefered the 2nd system. However, every new development out of the standard SHM serving will requires a new additional change into the server-program. 1st solution more flexible. Problem: it will require a large memory computer to handle with VIMOS-like data (not even thought about MUSE!).
    Prototype remade, splitting the load of the file into the SHM and the plotting routines. It works faster. All functionality reproduced.
  • 27/28 January, 2003 Presentation of the Prototype. Proposition of the visualization tool requeriments: scripting ability, scalability, comunication with different scripting languages, modularity, comunication with further analysis tool.
    PGPLOT still considered the best option for the Graphics handle. Further studies has to be made of how to comunicate between different processes: Shared Memory?
    PGPLOT TK-driver decided to use for the graphic presentation. Waiting for the minutes
  • January, 2003 First Visualization Tool prototype. Based on the Lyon I/O library and PGPLOT. Monolitic, only one C-file based. It reads a Euro3D format file, plot a staked spectra image, a monochromatic spaxels image (taking in account both the spaxels structure and the groups), plot an spectrum over a selected region on the staked image.
  • Dec 4/5, 2002 Mini-Meeting in Lyon. Discussion about the situation of the I/O Library. First Beta version provided. Maybe further changes due to the changes in the physical way the data are stored on a disk (Euro3D format).
  • Before Dec, 2002 Studies of the viability of different Graphics libraries: GTK+, PGPLOT, PLPLOT. Tests with PGPLOT, considering its driver for TK and its portability has made it the best candidate.
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