Changes between Version 62 and Version 63 of UvmatHelp


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Timestamp:
Jun 11, 2013, 2:32:02 PM (7 years ago)
Author:
sommeria
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  • UvmatHelp

    v62 v63  
    22[[TracNav]]
    33
    4 == 1 Generalities ==
     4== 1 - Generalities ==
    55=== 1.1 Aim ===
    66The package uvmat can be used to visualise, scan and analyse a wide variety of input data: all image and movie formats recognised by Matlab (see [#a3.1Inputdataformats section 3.1]),  NetCDF binary files(see [#a7.1TheNetCDFformat section 7]). It is however particularly designed for laboratory data obtained  from imaging systems: it includes a Particle Image Velocimetry  software, as well as tools for geometric calibration, masks, grid generation and image pre-processing (e.g. background removal), and editing documentation files in the format xml. Stereoscopic PIV, PIV-LIF and 3D PIV in a volume (still under development) are handled.
     
    4040UVMAT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See theGNU General Public License (file {COPYING.txt}) for more details.
    4141
    42 ----
    43 == 2 Overview of the GUI uvmat.fig ==
     42-------
     43== 2 - Overview of the GUI uvmat.fig ==
    4444=== 2.1 Opening the GUI ===
    4545Type '>>uvmat' in the Matlab prompt to display the GUI. If the function is unknown by Matlab, add the appropriate path (see the Matlab command '>>help path'). When the GUI is opening, the date of last modfication is displayed in the central window. During opening, the program checks the Matlab path to all the functions of the package (using the function ''check_functions.m''). If a function is missing, or if it is overridden by a function with the same name at another path location, a message is  displayed in the central window at the opening of the  GUI '''uvmat.fig'''. Finally, if the svn server is accessible by line-command, the latest version number of the uvmat package is indicated.
     
    105105
    106106--------------------
    107 == 3 Input files and navigation with uvmat ==
     107== 3 - Input files and navigation with uvmat ==
    108108=== 3.1  Input data formats ===
    109109uvmat 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.
     
    215215'''Mirror data trees''' can be created to process a source data set in read only mode, to preserve the safety of the data source, and to allow several users to work in parallel without interference. This is done by opening the source Campaign with the menu bar option Open/browse campaign from uvmat. Select the source campaign directory with the browser. Then the GUI 'browse_data' appears. Then press 'create_mirror' and select the directory which must contain the mirror Campaign. A set of directory is then created for each experiment, in which are created symbolic  links to the !DataSeries directories. Data processing then results in real !DataSeries directories created in the Experiment directory.  An xml mirror.xml is created inside the directory mirror to mark its role; This xml file contains  the path and name of the source directory under the label <!SourceDir>. The mirror directory can be regularly updated by pressing the button 'update_mirror'.
    216216----------------------------
    217 == 4 Scalar and vector display ==
     217== 4 - Scalar and vector display ==
    218218The uvmat interface primarily reads and visualises two-dimensional fields, which can be images or scalars, or vector fields.
    219219
     
    299299-'''Plotting:''' plot the results of projection, using the function ''plot_field.m''.
    300300----------------------------
    301 == 5- Field structures ==
     301== 5 - Field structures ==
    302302=== 5.1 Griding of data ===
    303303Physical fields can be defined either on regular grids, either scattered on an unstructured set of positions. Some measurements techniques, like PIV or particle tracking, provided unstructured data, while most methods of analysis require data  on a regular grid. This can be done by interpolation, defining a projection on a plane (with !ProjMode='interp...', see  [#ProjObject next section]).  The three possibilities of griding are defined as follows:
     
    413413 * 'nb_subdomain' denotes the dimension for the subdomain index for tps coefficients
    414414----------------------------
    415 == 6- Projection objects == #ProjObject
     415== 6 - Projection objects == #ProjObject
    416416=== 6.1 Definition and editing with the uvmat interface ===
    417417These are geometrical objects used to define cuts along lines or planes, to interpolate fields on a regular grid, to restrict the analysis or visualisation to field subregions. When a 2D or 3D field is opened by uvmat, a default projection plane object is created. New objects are created by the menu bar command  '''[Projection object]''' in '''uvmat.fig'''.  The creation of a new object ('''points''', '''line'''....) can be initiated by selecting the corresponding item in the menu. Alternatively, an existing xml object file can be opened by selecting the menu option '''[browse...]'''.
     
    502502 * 'plane': plane with associated cartesian coordinates
    503503 * 'volume': volume with associated cartesian coordinates
    504 
    505 == 7- Netcdf files and the GUI get_field ==
     504-----------------
     505== 7 - Netcdf files and the GUI get_field ==
    506506=== 7.1 The NetCDF format ===
    507507NetCDF (network Common Data Form) is a machine-independent format for representing scientific data, suitable for large arrays (http://www.unidata.ucar.edu/software/netcdf/). Each piece of data can be directly accessed by its tag name without reading the whole file. New records can be added to the file without perturbing the remaining information. The next release of NetCDF is now connected to the more recent hdf format.
     
    544544In the case of a 3D input field, the fig is set to uvmat. A middle plane of cut is automatically selected. This can be moved then with the slider on the interface set_object (see section 5). The default cuts are made at constant z coordiante, but any of the three initial coordiantes can be used as z coordinate, using the menu coord_z.
    545545----------------------------
    546 == 8- Geometric calibration ==
     546== 8 - Geometric calibration ==
    547547=== 8.1 Generalities ===
    548548Transforming image to physical coordinates is a key problem for measuring techniques based on imaging.   The ''image coordinates'' represent the two cartesian axis X,Y of the image, with origin at the lower left corner. The coordinate of the first lower left pixel centre is therefore (1/2,1/2). Note that the Y axis is directed upward, while the corresponding image index j increases downward. Therefore, denoting npy the number of pixels along Y, the (X,Y) coordinates of a pixel indexed (i,j) are [[BR]] X=i-1/2, Y=npy-j+1/2.
     
    626626 * <SliceDPhi> step angle for angular scan.
    627627
    628 == 9- Masks and grids ==
     628== 9 - Masks and grids ==
    629629=== 9.1 Masks ===
    630630Mask files are used to restrict the domain of CIV processing, to take into account fluid boundaries or invalid image zones. They must be stored as .png images with 8 bits, as described in [section 3.6->#sec3.6_mask].  Mas files are automatically recognised by '''uvmat.fig''' and '''civ.fig''' if they are named [filebase '_xxmask_' 'filenumber' '.png'], where xx is the number of masks (nbslices) used when the series of fields corresponds physically to a set of nbslices positions. The mask filenumber used is the image field number modulo nbslices. Use xx=1 in the default case of a fixed position and a single mask. Masks can be made by pressing the menu bar Tools/make mask on the GUI uvmat. The mask is created interactively with the mouse on the current image.
     
    835835
    836836---------------
    837 == 12 Tridimensional features:(to update **) ==
     837== 12 - Tridimensional features:(to update **) ==
    838838=== 12-1 Multilevel image scanning ===
    839839or multiplane scanning it also describes the set of laser planes. Then the current plane index is indicated by the text box z_index and the total number of planes by the text box nb_slice.
     
    843843This is performed by the GUI '''civ_3D.fig'''. The program requires input volume images .vol. These are images in the  png format, where  npz slices are concatenated along the y direction, forming a composite image of dimension (npy x npz, npx) from the images (npy x npx). These volume images can be created by the function {ima2vol.m} in {/series}.
    844844----------------------------
    845 == 13 Editing xml files with the GUI editxml ==
     845== 13 - Editing xml files with the GUI editxml ==
    846846  This GUI '''editxml.fig''' visualises and edits xml files. It is automatically called by the browser of '''uvmat.fig''' when a file with extension .xml is opened.
    847847
     
    852852  Manual editing of element value is possible. Select the element and use the lower edit box. This edit box transforms in a menu when a preselected list of allowed input values has been set by the schema.
    853853----------------------------
    854 == 14-Appendix: overview of the package functions ==
     854== 14 - Appendix: overview of the package functions ==
    855855=== Master GUI ===
    856856 * 'uvmat';...% master function for file scanning and visualisation of 2D fields