Changes between Version 62 and Version 63 of UvmatHelp
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- Jun 11, 2013, 2:32:02 PM (11 years ago)
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UvmatHelp
v62 v63 2 2 [[TracNav]] 3 3 4 == 1 Generalities ==4 == 1 - Generalities == 5 5 === 1.1 Aim === 6 6 The 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. … … 40 40 UVMAT 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. 41 41 42 ---- 43 == 2 Overview of the GUI uvmat.fig ==42 ------- 43 == 2 - Overview of the GUI uvmat.fig == 44 44 === 2.1 Opening the GUI === 45 45 Type '>>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. … … 105 105 106 106 -------------------- 107 == 3 Input files and navigation with uvmat ==107 == 3 - Input files and navigation with uvmat == 108 108 === 3.1 Input data formats === 109 109 uvmat 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. … … 215 215 '''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'. 216 216 ---------------------------- 217 == 4 Scalar and vector display ==217 == 4 - Scalar and vector display == 218 218 The uvmat interface primarily reads and visualises two-dimensional fields, which can be images or scalars, or vector fields. 219 219 … … 299 299 -'''Plotting:''' plot the results of projection, using the function ''plot_field.m''. 300 300 ---------------------------- 301 == 5 - Field structures ==301 == 5 - Field structures == 302 302 === 5.1 Griding of data === 303 303 Physical 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: … … 413 413 * 'nb_subdomain' denotes the dimension for the subdomain index for tps coefficients 414 414 ---------------------------- 415 == 6 - Projection objects == #ProjObject415 == 6 - Projection objects == #ProjObject 416 416 === 6.1 Definition and editing with the uvmat interface === 417 417 These 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...]'''. … … 502 502 * 'plane': plane with associated cartesian coordinates 503 503 * '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 == 506 506 === 7.1 The NetCDF format === 507 507 NetCDF (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. … … 544 544 In 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. 545 545 ---------------------------- 546 == 8 - Geometric calibration ==546 == 8 - Geometric calibration == 547 547 === 8.1 Generalities === 548 548 Transforming 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. … … 626 626 * <SliceDPhi> step angle for angular scan. 627 627 628 == 9 - Masks and grids ==628 == 9 - Masks and grids == 629 629 === 9.1 Masks === 630 630 Mask 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. … … 835 835 836 836 --------------- 837 == 12 Tridimensional features:(to update **) ==837 == 12 - Tridimensional features:(to update **) == 838 838 === 12-1 Multilevel image scanning === 839 839 or 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. … … 843 843 This 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}. 844 844 ---------------------------- 845 == 13 Editing xml files with the GUI editxml ==845 == 13 - Editing xml files with the GUI editxml == 846 846 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. 847 847 … … 852 852 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. 853 853 ---------------------------- 854 == 14 -Appendix: overview of the package functions ==854 == 14 - Appendix: overview of the package functions == 855 855 === Master GUI === 856 856 * 'uvmat';...% master function for file scanning and visualisation of 2D fields
