wiki:Installation

Version 21 (modified by sommeria, 2 years ago) (diff)

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WikiStart / Installation

Download the .zip archive uvmat_toolbox.v... available at http://servforge.legi.grenoble-inp.fr/pub/soft-uvmat and unzip at the appropriate location on your computer. The current version number is indicated in the archive name, after '.v'.

Add the path to the folder 'UVMAT' containing the software in the list of Matlab paths (command 'addpath') so that the functions of the package are recognised (save this path to keep it when Matlab is next opened). Then it should be ready for operations: the command 'uvmat' should open the main GUI, see [UvmatHelp] or Tutorial/ImageDisplay for an introduction. Beware of multiple occurrence of function names: Matlab searches function names firstly in its current working folder, then following the order of its path list. When the GUI 'uvmat' is opened, it checks the current selected path of each function of the package and lists possible path conflicts.

Instead of the zip archive, the latest version under development can be obtained from the SVN server http://servforge.legi.grenoble-inp.fr/svn/soft-uvmat/trunk/src/. On Linux, go to a folder where you want to install uvmat and type the command line:

svn checkout http://servforge.legi.grenoble-inp.fr/svn/soft-uvmat/trunk/src UVMAT

This will create the folder 'UVMAT' containing the whole toollbox (including the master function uvmat.m). Then set the path to the folder UVMAT in the Matlab paths as before.

Updates can be further obtained by opening a terminal in the folder UVMAT and typing the command

svn update

To use the SVN server under Windows, you can install for instance slik subversion, http://www.sliksvn.com/en/download, open a Dos terminal, and type the same command lines as for Linux. You can also use Tortoise SVN with graphic interface. However the command line version is needed to allows uvmat to automatically check the consistency of the current package with the svn server.

Specific toobox and proprietary image formats

Note that the package contains the toolbox xmltree (http://www.artefact.tk/software/matlab/xml), used for reading and editing xml files. This contains .ddl and mex files which may need to be updated from their source web site depending on the system and Matlab version. A set of xml schemas, updated by SVN, is also provided as templates for editing xml files within uvmat.

The package is able to read movies using Matlab tools, and proprietary image formats which may require updates of reading functions.

  • fast cameras Phantom (.cine images): functions read_cine_phantom.m and readCineHeader.m.
  • system DaVis? of the company Lavision (.imx images): mex files readimix.meca64 and readimix.mexw64 (limited to Matlab versions of 2013 or older).
  • company Rdvision: function read_rdvision.m

It is possible to add your own specific reading functions by first adding a specific format in the function get_file_info.m (recognised by means of file name extension for instance), and then modified the functions read_field.m and read_image.m.

User parameters

The five last input file names and specific functions used are stored for convenience in a file (uvmat_perso.mat) automatically created in the user preference directory of Matlab (indicated by the Matlab command '>>prefdir'. A corruption of this file uvmat_perso.mat may lead to problems for opening UVMAT. To revert to the initial configuration, delete this file by typing '>>reinit' on the Matlab prompt.

Installation on a cluster

The package contains a GUI called 'series' to launch computations in parallel on a computer cluster. This requires to define parameters in a file series.xml associated with a Matlab function (whose name is given in series.xml) which produces the system command needed to launch computations. The file series.xml.default and the associated function cluster_command.m, used at LEGI, are given as templates. Other examples are provided, for instance cluster_command_psmn.m used at ENSLyon.

For using UVMAT on the cluster at LEGI, please see Installation/LegiCluster.

Launching compiled functions

On a cluster each job requires a Matlab license, which may be a restriction to the number of jobs run in parallel. If the compiler toolbox of Matlab is installed, you can compile the functions and launch them on cluster nodes as .sh executable files without additional Matlab license.

CivX installation (obsolete)

Binary files compiled from the Fortran programs CivX are available in the archive bin_civx.zip at http://servforge.legi.grenoble-inp.fr/pub/soft-uvmat. This is however not advised as it is replaced by Matlab functions within uvmat, with improved capabilities. These binaries depend on the operating system, unlike the Matlab toolboxes, so that archives are provided for different systems:

  • linux32: for linux 32 bits
  • linux64: for linux 64 bits
  • osx_x86_64: for Macintosh
  • win32: for Windows 32 bits

put the appropriate one in the sub-folder /bin of uvmat, and update the file PARAM.xml which indicates the paths to the binaries. A template file PARAM.xml.default is provided from the package.

To recompile these programs (for advanced users), see Installation/CivxDevelloper: