Changes between Version 38 and Version 39 of UvmatHelp


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Jun 3, 2013, 12:43:48 AM (7 years ago)
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sommeria
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  • UvmatHelp

    v38 v39  
    573573== 10- Processing field series: ==
    574574=== 10.1 The GUI series.fig: ===
    575   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').
    576 
    577   Several input file series can be introduced simultaneously by the menu bar command''' [Open_insert]'''. By contrast, the current input series are refreshed by the browser from the menu bar command''' [Open]'''.
    578 
    579   The velocity type and field is automatioally chosen by default, but it can be specified by VelType and Field. For that purpose use the menus VelTypeMenu and fieldsinput. In case of multiple input file series, these menus act only on the first line.
    580 
    581   The processing function is chosen in the menu '''[ACTION]'''.  All actions operate on the same series of input files, whose list can be obtained with the option 'check_files'. The option 'aver_stat' calculates  a global average on the successive fields, while 'time_series' provides a time series. The option 'merge_proj' is used to project a whole series on a given grid, or to create a file series by concatenation of different fields .  Finally any additional function can be called and included in the menu by selecting the option 'more...' .
    582 
    583   The series of file indices is set in the frame '''[RANGE]'''. Any action is performed from field index '''[first_i] ''' to '''[last_i] '''  with increment '''[incr_i]''' . In case of double indexing, action is similarly performed from field index''' [first_j]''' to '''[last_j]''' with increment '''[incr_j]'''. Succesive file names are ordered as a matrix {j,i} with the index j varying the fastest. The parameter nb_slice can be introduced to scan the i index modulo nb_slice.
    584 
    585   For pair indexing, the selected pair must be chosen in the menu list_pair-civ in the frame PAIRS (browse again an input field if this menu does not appear). Then the first_i and last_i refer to the 'reference indices'. With the option '*-*' in '''[list_pair_civ]''', available pairs are automatically chosen (this is appropriate if several image pairs are used in a time series, to account for a changing mean velocity).
    586 
    587   A projection object can be introduced by selecting the check box '''[PROJECTION OBJECT]'''. If a projection object has been already created the  opened interface '''set_object.fig''' will be used. Otherwise a browser apperas to open an object file (xml).
     575Operations 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 operates. The root path, subdirectory, root file name and extension are introduced in the same way as with the uvmat interface, in the different columns of the table '''InputTable'''. The nomenclature for file indexing is represented in the column '''[NomType]'''.
     576
     577Several input file series can be introduced simultaneously by the menu bar command''' [Open_append]''', filling the successive lines of '''InputTable'''. By contrast, the current input series is refreshed by the browser displayed by the menu bar command''' [Open]'''. The cells in the table can be also edited manually.
     578
     579The velocity type and field is automatioally chosen by default, but it can be specified by VelType and Field. For that purpose use the menus VelTypeMenu and fieldsinput. In case of multiple input file series, these menus act only on the first line.
     580
     581The processing function is chosen in the menu '''[ActionName]'''.  All actions operate on the same series of input files, whose list can be obtained with the first option 'check_data_files'. The option 'aver_stat' calculates  a global average on the successive fields, while 'time_series' provides a time series. The option 'merge_proj' is used to project a whole series on a given grid, or to create a file series by concatenation of different fields. The option civ_series gives acees to the PIV processsing, see section [wiki:#a11-PIV:ParticleImagingVelocimetry: section 11]. Finally any additional function can be called and included in the menu by selecting the option 'more...' . The corresponding path is displayed in '''ActionPath'''.
     582
     583Each function in series can be run in local mode, i;e. on the current Matlab session, or as background, by selecting the corresponding option in '''!RunMode'''. In background mode, calculation is done a new Matlab session (without graphics) so that the current Matlab session is free for new operations. If a cluster system has been detected, a third option 'cluster' appears in the menu, allowing to dispatch parallel computations on a computer cluster. For the latter option, a compiled version of the Action function is useful, to avoid installing Matlab on each node of the cluster. This is achieved by selecting the option .sh in the menu '''ActionExt'''. If the compiled version is not yet available, or outdated, the GUI proposes a new compilation of the selected function.
     584
     585The series of file indices is set in the frame '''[!IndexRange]'''. Any action is performed from field index '''[num_first_i] ''' to '''[num_last_i] '''  with increment '''[num_incr_i]''' . In case of double indexing, action is similarly performed from field index''' [num_first_j]''' to '''[num_last_j]''' with increment '''[num_incr_j]'''. Succesive file names are ordered as a matrix {j,i} with the index j varying the fastest. The box '''num_NbSlice''' can be introduced to scan the i index modulo NbSlice.
     586
     587For pair indexing, the selected pair must be chosen in the menu list_pair-civ in the frame PAIRS (browse again an input field if this menu does not appear). Then the first_i and last_i refer to the 'reference indices'. With the option '*-*' in '''[list_pair_civ]''', available pairs are automatically chosen (this is appropriate if several image pairs are used in a time series, to account for a changing mean velocity).
     588
     589A transform function can be introduced. A projection object can be introduced by selecting the check box '''[CheckObject]'''. If a projection object has been already created the  opened interface '''set_object.fig''' will be used. Otherwise a browser appears to open an object file (xml). Similarly the check box '''[CheckMask]''' can be used to select a mask option.
     590
     591
    588592
    589593=== 10.2 check_files: ===
     
    621625
    622626== 11- PIV: Particle Imaging Velocimetry ==
    623 {===11.1 Overview:===}
     627=== 11.1 Overview: ===
    624628
    625629The GUI '''civ.fig''' is used to run the programs [CIVx->3]  (Correlation Imaging Velocimetry). It is a free advanced Imaging Velocimetry implementation that relies on direct cross-correlation of pattern boxes between image pairs. The binary executable files suitable for the computer operating system need to be properly installed (see {uvmat_doc/README_INSTALL.txt }).
     
    635639The CIV process involves a succession of iterative operations:  -*civ1: the initial image correlation process. -*fix1: detection of 'false' velocity vectors according to different criteria. -*patch1: interpolation and filtering on a regular grid, providing access to spatial derivatives of the velocity (diverrgence, curl, strain). -* civ2: advanced image correlation algorithm using the result of civ1 as a first approximation. -* fix2 and patch2: similar as fix1 and patch1, but applied to the civ2 results. This series of operations is chosen by selecting the corresponding  check boxes on the left, which give access to the corresponding parameter input panels. Note that the result of each of these operations is stored in the output netcdf file, so the process can be split in several runs. When an existing netcdf velocity file is opened, the GUI '''civ.fig''' is automaticaly configured to perform the next operation (fix1, patch1, civ2...) needed in the process.
    636640
    637 {===11.2 CIV1:===} The image pair is selected in the menu '''[list_pair_civ1]''', see sub-section 10.1. The time interval of the image pair must be chosen sufficiently small to provide a good correlation, and sufficiently large to provide good measurment precision: a displacement of 5-10 pixels is generally optimum.
     641=== 11.2 CIV1: ===
     642 The image pair is selected in the menu '''[list_pair_civ1]''', see sub-section 10.1. The time interval of the image pair must be chosen sufficiently small to provide a good correlation, and sufficiently large to provide good measurment precision: a displacement of 5-10 pixels is generally optimum.
    638643
    639644The time interval for each image pair is indicated in '''[list_pair_civ1]''' iif the information is made available, either from a movie file, or from a detected xml file (with the name RootName.xml). The source of the timing information is indicated in the edit box '''[ImaDoc]'''. Examples of xml files are provides in /XML_SCHEMAS/ImaDoc_templates. In the absence of information, the file index is taken for the time.  The time interval for a given index pair may change with time, so the time interval display is taken for given reference indices, given by '''[i_ref]''' and ''' [j_ref].'''.
     
    649654<doc72|center>
    650655
    651   The grid determines the positions of measured velocity vectors: it sets the central positions of the correlation boxes (in pixels) for the first image. A default regular grid can be set by the meshes '''[dx] ''' and '''[dy]''' (in pixels). Alternatively a custom [grid->#sec3.6_grid] can be stored in a text file and selected by the check box '''[GET_GRID]'''. This is convenient to limitate the processing to a subregion or to fine tune the resolution.
     656The grid determines the positions of measured velocity vectors: it sets the central positions of the correlation boxes (in pixels) for the first image. A default regular grid can be set by the meshes '''[dx] ''' and '''[dy]''' (in pixels). Alternatively a custom [grid->#sec3.6_grid] can be stored in a text file and selected by the check box '''[GET_GRID]'''. This is convenient to limitate the processing to a subregion or to fine tune the resolution.
    652657
    653658A subregion can be alternatively  selected by a mask image, selecting the edit box '''[MASK]'''. If a mask image with an appropriate name is found in the image directory, it wil be detected, and the indication 'xxmask' appears in the edit box. (xx is the number of slices, equal to 1 for a single mask). Otherwise a browser appears to select a (single) mask file.
     
    655660Finally thresholds on image intensity can be introduced to suppress underexposed or overexposed parts of the image: select the check box '''[THRESH],''' and edit the boxes '''[MinIma] ''' and '''[MaxIma] ''' which then appear.
    656661
    657   The velocity results are stored in the subdirectory set by the edit box '''[subdir_civ1].''' Use the browser''' [list_subdir_civ1]''' to check the existing subdirectories.
     662The velocity results are stored in the subdirectory set by the edit box '''[subdir_civ1].''' Use the browser''' [list_subdir_civ1]''' to check the existing subdirectories.
    658663
    659664-''' {RUN and BATCH:} '''
    660665
    661   The PIV calculation is started by the press button [RUN], or [BATCH] if this option has been installed. BATCH sends the same computations as background computing tasks in a network.
    662 
    663   In both cases, the status of the computations can be checked by opening {.cmx } and {.log} files, using the uvmat browser or any text editor. These files are writtent in the same subdirectory as the NetCDF result files. Each {.cmx} file contains the set of parameters used for a civ computation. It is written by the civ interface just before ordering the computations. By contrast , the {.log} file is produced after completion of the computations, and it contains some information on the process, including possible error messages.
     666The PIV calculation is started by the press button [RUN], or [BATCH] if this option has been installed. BATCH sends the same computations as background computing tasks in a network.
     667
     668In both cases, the status of the computations can be checked by opening {.cmx } and {.log} files, using the uvmat browser or any text editor. These files are writtent in the same subdirectory as the NetCDF result files. Each {.cmx} file contains the set of parameters used for a civ computation. It is written by the civ interface just before ordering the computations. By contrast , the {.log} file is produced after completion of the computations, and it contains some information on the process, including possible error messages.
    664669
    665670[sec11.3<-] {===11.3 FIX===}
     
    669674-''' {Code for FixFlag:} ''' -*FixFlag(i)=0 :default, everything is fine -*FixFlag(i)=1. : value 1 for the second digit: vector removed by criteria on vec_F or/and low correlation value -*FixFlag(i)=1..: value 1 for the third digit: vector selected by a criterium of difference with another field, for instance filter, or a field with differnt time interval. -*FixFlag(i)=...1, 2, 3  different criteria for elimination set by the program Fix of CIVx (not yet documented).
    670675
    671 {===11.4 PATCH===}
     676=== 11.4 PATCH ===
    672677
    673678-'''PATCH1: ''' interpolates the velocity values on a regular grid with a smoothing parameter rho. This also provides the spatial derivatives (vorticity, divergence) needed for the refined processing civ2. The numbers of grid points in x and y are set by nx and ny. The vectors which are too far from the smoothed field (erratic vectors) can be eliminated, using a threshold expressed in pixel displacement. The thin plate spline method must be done by subdomains for computational saving, use the default value 300.
    674679
    675 {===11.5 CIV2===}
     680=== 11.5 CIV2 ===
    676681
    677682-'''CIV2:''' provides a refined calculation of the velocity field, using the civ1 result as previous estimate. The search range is determined by the civ1 field so there is no parameter. Use the option decimal shift to reduce peaklocking effects (advised). The option deformation is useful in the presence of strong shear or vorticity. Then image deformation and rotation is introduced before calculating the correlations. The other parameters (rho, ibx,iby, grid, mask) are used like for civ1 (take the same by default). The image pair for civ2 can be different than the one used in civ1 to get the first estimate. It is generally advised to use a moderate time interval for civ1, to avoid false vectors, and to take a larger intervel for civ2, in order to optimize precision. As civ2 already knows where to look and takes into account image strain and rotation (with the option deformation) it allows for higher time intervals.