Changes between Version 11 and Version 12 of UvmatHelp


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Timestamp:
Jun 1, 2013, 4:04:11 PM (7 years ago)
Author:
sommeria
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  • UvmatHelp

    v11 v12  
    3333
    3434== 2 Overview of the GUI uvmat.fig ==
    35 
    3635=== 2.1 Opening the GUI ===
    3736  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 availlable,  the latest version number of the uvmat package is indicated (if  line-command version of svn is available).
     
    8988
    9089== 3 Input files and navigation with uvmat ==
    91 
    9290=== 3.1  Input data formats ===
    9391uvmat 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.
     
    192190Scalars (or image intensity) can be also represented with contour plots, by switching the popup menu '''[Contours] ''' from the setting 'mage' to the setting 'contours'. Contours for positive scalar values are in sold line while contours for negative values are dashed. The interval between contours can be set by the edit box '''[IncrA]'''.
    193191
    194 
    195192=== 4.2 Vectors: ===
    196193  The vector fields are represented by arrows. The length of the arrows is automatically set when the check box'''[CheckFixVectors]''' is not selected, or it can be adjusted by the edit box '''[num_VecScale]'''.  For clarity of visualisation, the number of displayed vectors can be divided by 2 in each direction by selecting the check box '''[CheckDecimate4]'''.
     
    234231The following succession of operations is performed by '''uvmat.fig''': -'''File Reading:''' the input field is first read from the input file by the Matlab functions {imread.m}, {mmreader.m}, or {aviread.m} for images,  or the uvmat functions {nc2struct.m} or {read_civxdata.m} for netcdf files. -'''Second file reading:'''  The second input field is similarly read if selected. Note that it is kept in memory, so it is not read again if the file is unchanged (this is useful in the case of substraction of a fixed background for instance).  -'''Transform:''' by default the 'phys' option transforms each of the input fields from pixel to physical coordinates. This operation can also combine two input fields. -'''Histogram:''' This is obtained from the input field in transformed coordinates, or if applicable from the fields resulting from the two input fields. -'''Projection:''' on  the projection object selected in the menu '''[list_object_1]''', see [section 7->#get_field]. A second projection, on the object selected by '''[list_object_1]''', can be plotted in the anciillary figure '''view_field.fig'''. Function used: {proj_field.m}. -'''Field calculation:''' a scalar can be calculated from each of the input fields, as selected by the menu '''[Fields]'''. This is performed by the function {calc_field.m}. -'''Field comparison''': when two fields of the same nature are introduced, the difference is taken by the function {sub_field.m.}. This is skipped if the transform function has already led to a single field.  -'''Plotting:''' plot the results of projection. Function used: {plot_field.m}
    235232
    236 
    237233== 5- Field objects: ==
    238 
    239234[sec5.1<-]
    240235
     
    304299
    305300== 6- Projection objects: ==
    306 
    307301=== 6.1 Definition and editing with the uvmat interface: ===
    308302  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 of fields to subregions. 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 the option 'browse...'.
     
    379373
    380374== 7- Netcdf files and get_field.fig: ==
    381 
    382375=== 7.1 The NetCDF format: ===
    383376NetCDF (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 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 intended to be compatible with the newly developed and more general hdf format.
     
    423416
    424417== 8- Geometric calibration: ==
    425 
    426418=== 8.1 Generalities: ===
    427419  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 y direction is directed upward, while the corresponding image index j increases downward.  The physical coordinates are defined from the experimental set-up. The correspondance is obtained by locating on the image a set of calibration points whose positions are known in the physical coordinate system. A cartesian calibration grid covering the whole image is the best option, but any set of calibration points can be used. We handle three kinds of transforms:
     
    476468[<doc115|right>->#top]
    477469
    478 
    479 == 9- Masks and grids: ==
    480 
     470== 9- Masks and grids: ==
    481471=== 9.1 Masks: ===
    482472  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].
     
    497487The grid will be limited to an  image , or to the common region of two images, depending whether one or two image names are indicated in the edit boxes image_1 and image_2. Press save to save the corresponding grid file (s). A dialog box appears to edit the name of the output grid file, and a second one in case of two images.
    498488
    499 
    500489== 10- Processing field series: ==
    501 
    502490=== 10.1 The GUI series.fig: ===
    503491  Operations on field series are controled by the GUI '''series.fig''', which allows the user to set the root name(s) and file indices over which a processing function  must operate. The root path, subdirectory, root file name and extension are introduced in the same way as with the uvmat interface, in the edit windows '''[RootPath], [SubDir], [RootFile],''' and '''[FileExt],''' respectively. The nomenclature for file indexing is represented in '''[NomType]''' ('Indices').
     
    549537
    550538== 11- PIV: Particle Imaging Velocimetry ==
    551 
    552539{===11.1 Overview:===}
    553540
     
    639626
    640627  Conventions 'uvmat/civdata'.
    641 
    642 |  '''tag''' |  '''        content'''  | | Conventions| sets the conventions| |                Program|name of the processing program| |              CivStage| stage in the sequence civ1,fix1...| |         Civ1_TestCiv1| 0| |    Civ1_CorrBoxSize|size x,y of the correlation box| |  Civ1_SearchBoxSize| size x,y of the search box| |Civ1_SearchBoxShift| (optional) shift of the search box| |        Civ1_CorrSmooth| smooth parameter for the image corr| |                Civ1_Dx |grid mesh along x| |                Civ1_Dy| grid mesh along y| |         Civ1_CheckGrid| =1 if a grid file is used, default=0| |        Civ1_CheckMask| =1 if a mask file is used, default=0| |    Civ1_CheckThreshold| =0/1 image luminosity  threshold used | |         Civ1_FileTypeA| type of input file A, 'image', 'movie'...| |            Civ1_ImageA| path and name of input image A| |        Civ1_FileTypeB| type of input file A, 'image', 'movie'...| |            Civ1_ImageB|path and name of input  image B| |                Civ1_Dt| time interval for image pair| |              Civ1_Time| mean time for the image pair| |     Civ1_ImageBitDepth| nbre of grey level bits| |        Civ1_ImageWidth| nbre of pixels along x| |       Civ1_ImageHeight|  nbre of pixels along y| |       Civ1_FrameIndexA| frame index of image A in the series| |       Civ1_FrameIndexB|  frame index of image B in the series| |             Patch1_Rho| 10| |       Patch1_Threshold| threshold for the elimination of aberrant vectors| |       Patch1_SubDomain| estimated nbre of vectors in a subdomain|
     628 
     629
     630||  '''tag''' ||  '''        content'''  ||
     631
     632|| Conventions|| sets the conventions||
     633
     634||                Program||name of the processing program||
     635
     636|              CivStage| stage in the sequence civ1,fix1...| |         Civ1_TestCiv1| 0| |    Civ1_CorrBoxSize|size x,y of the correlation box| |  Civ1_SearchBoxSize| size x,y of the search box| |Civ1_SearchBoxShift| (optional) shift of the search box| |        Civ1_CorrSmooth| smooth parameter for the image corr| |                Civ1_Dx |grid mesh along x| |                Civ1_Dy| grid mesh along y| |         Civ1_CheckGrid| =1 if a grid file is used, default=0| |        Civ1_CheckMask| =1 if a mask file is used, default=0| |    Civ1_CheckThreshold| =0/1 image luminosity  threshold used | |         Civ1_FileTypeA| type of input file A, 'image', 'movie'...| |            Civ1_ImageA| path and name of input image A| |        Civ1_FileTypeB| type of input file A, 'image', 'movie'...| |            Civ1_ImageB|path and name of input  image B| |                Civ1_Dt| time interval for image pair| |              Civ1_Time| mean time for the image pair| |     Civ1_ImageBitDepth| nbre of grey level bits| |        Civ1_ImageWidth| nbre of pixels along x| |       Civ1_ImageHeight|  nbre of pixels along y| |       Civ1_FrameIndexA| frame index of image A in the series| |       Civ1_FrameIndexB|  frame index of image B in the series| |             Patch1_Rho| 10| |       Patch1_Threshold| threshold for the elimination of aberrant vectors| |       Patch1_SubDomain| estimated nbre of vectors in a subdomain|
    643637
    644638-'''List of variables:'''