Changes between Version 79 and Version 80 of UvmatHelp


Ignore:
Timestamp:
Jul 4, 2013, 8:46:09 AM (7 years ago)
Author:
sommeria
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • UvmatHelp

    v79 v80  
    110110uvmat can read any image format recognised by the Matlab image reading function ''imread.m''. Images can be in true color or B&W, with 8 bit or 16 bit grey levels. Image files containing multiple frames are handled. Movie files can be also opened, using the Matlab function ''!VideoReader.m'', or ''mmreader.m'' for older versions of Matlab.
    111111
    112 ''Uvmat'' can also read various kinds of data in the format Netcdf. Velocity fields obtained by PIV and results of data processing are stored in this format, see [#a7Netcdffilesandget_field.fig section 7] for details. Derived quantities (vorticity, divergence...) can be directly obtained. The input file type is recognized by the function ''get_file_type.m'' of uvmat and the file is opened by the function ''read_field.m'' according to this file type. it is possible to include new input file types by a modification of these two functions.
    113 
    114 The PIV software CIVx requires B&W images in the format png (portable network graphics). It is a binary format for images with lossless (reversible) compression, recommended by w3c (http://www.w3.org/Graphics/PNG). It is an open source patent-free replacement of GIF and can also replace many common uses of TIFF. It can be read directly by all standard programs of image visualisation and processing.  Compressing a raw binary image to its png form typically saves disk storage by a factor of 3.
     112''Uvmat'' can also read various kinds of data in the binary format Netcdf, as described in [#a7Netcdffilesandget_field.fig section 7]. Velocity fields obtained by PIV and results of data processing are stored in this format. Derived quantities (vorticity, divergence...) can be directly obtained. The input file type is recognized by the function ''get_file_type.m'' of uvmat and the file is opened by the function ''read_field.m'' according to this file type. It is possible to include new input file types by a modification of these two functions.
     113
     114The PIV software provided in uvmat can deal with any image or movie format recognised by Matlab, while the older fortran version CIVx requires B&W images in the format png (portable network graphics). It is a binary format for images with lossless (reversible) compression, recommended by w3c (http://www.w3.org/Graphics/PNG). It is an open source patent-free replacement of GIF and can also replace many common uses of TIFF. It can be read directly by all standard programs of image visualisation and processing.  Compressing a raw binary image to its png form typically saves disk storage by a factor of 3.
    115115
    116116For 3D PIV**, 'volume' images, with file extension .vol are used. These are images in the  png format, where the npz slices are concatenated along the y direction, forming a composite image of dimension (npy x npz, npx) from the images (npy x npx).
     
    156156
    157157=== 3.5  Image documentation files (.xml) ===
    158 Information on image series is provided by a documentation file in the format xml. This file can include sections about image timing, geometric calibration, camera type and illumination. An xml file is a text file in which each element of information, or group of elements, is labelled by a tag. The list of tags and their hierarchical organisation is specified by a schema file (.xsd). The schema used for image documentation is ''!ImaDoc.xsd'', available in the uvmat package in a sub-directory ''/Schemas''. Simple templates of xml files are also provided there. A general introduction to the xml language and schemas is provided for instance in http://www.w3schools.com/xml.
    159 
    160 When a new file series is opened in uvmat, a documentation file is automatically sought, whose path and name are displayed by ''!RootPath'' and  ''!RootFile'' respectively, with extension {.xml} (''!RootPath'' and ''!RootFile'' are the contents of the edit boxes '''[!RootPath]''' and ''' [!RootFile]''').  The detection of this file is indicated by the visibility of the pushbutton '''[view_xml]''' on the upper right of the GUI '''uvmat.fig'''. Press this button to see the content through an xml editor '''editxml.fig''' (described in [#a10-Processingfieldseries section 10]). The xml file can be also opened directly by the uvmat browser, or by any text editor.
     158Image series in uvmat are documented by an acillary file providing image timing, geometric calibration, camera type and illumination. This file is in the format ''xml'', a hierarchically organised text file. The content is labelled by tags, represented by brackets <.>, whose names and organisation are specified by a schema file (.xsd). A general introduction to the xml language and schemas is provided for instance in http://www.w3schools.com/xml. The schema used for image documentation is ''!ImaDoc.xsd'', available in the uvmat package in a sub-directory ''/Schemas''. Simple templates of xml files are also provided there.
     159
     160When a new file series is opened in uvmat, the xml documentation file is automatically sought in the folder containing the data series folder: the documentation of the file series RootPath/SubDir/RootFile_1,... is in the file RootPath/RootFile.xml. As a second choice (corresponding to an earlier convention), the xml file will be sought inside the data series folder, as RootPath/SubDir/RootFile.xml. The detection of the image documentation file is indicated by the visibility of the pushbutton '''[view_xml]''' on the upper right of the GUI '''uvmat.fig'''. Press this button to see the content through an xml editor '''editxml.fig''' (described in [#a10-Processingfieldseries section 10]). The xml file can be also opened directly by the uvmat browser, or by any text editor.
    161161
    162162The xml file <!ImaDoc> can contain the following sections: