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Changes between Version 111 and Version 112 of UvmatHelp

Timestamp:: Dec 6, 2014, 2:59:54 PM (9 years ago)
Author:: sommeria
Comment:: --

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UvmatHelp

-                      v111
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 = --- Help for UVMAT --- =
 == 1 - Generalities ==
 === 1.1 Aim ===
 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.
 …
 === 1.4 Copyright and licence ===
 Copyright (C) Joel Sommeria, 2008-2014, LEGI UMR 5519 / CNRS UJF Grenoble-INP / Grenoble, France - joel.sommeria(at)legi.grenoble-inp.fr.
 …
    * Intensity>200  the vector will be computed  The mask corresponding to an image or velocity field can be displayed in '''uvmat.fig''' by selecting the check box '''[view_mask]([CheckMask])''' on the upper left. Images with appropriate name can be automatically recognised by '''uvmat.fig''' and civ functions, see [#a9-Masksandgrids section 9.1]. Otherwise file selection by a browser is proposed when '''[view_mask]''' is selected.
+ * ''' Grid:''' List of numbers (in ASCII text) specifying the set of points where the PIV processing is performed.
+ It specifies the number of points n and a corresponding list of x and y coordinates expressed in image pixels, as follows
+ {{{
+ * ''' Grid:''' List of numbers (in ASCII text) specifying the set of points where the PIV processing is performed. It specifies the number of points n and a corresponding list of x and y coordinates expressed in image pixels, as follows
+{{{
 n X1 Y1 X2 Y2  ......  Xn Yn
 }}}
 …
  * ''''.civ' ''' (obsolete)  ASCII text file containing the list of image times and the scaling in pixels/cm. This is an obsolete version of the XML image documentation file. It is stored in the same directory as the corresponding series of images, with name ''root .civ''. It is automatically sought by '''uvmat.fig''' and '''series.fig''', in the absence of an XML file <!ImaDoc>. (it is read by the function ''read_imatext.m''). The following example is from an experience with 19 bursts of 4 images, named aa001a,aa001b,aa001c,aa001d,aa002a,aa002b,...,aa019c,aa019d, with an extension .png. The corresponding .civ file is named aa.civ. Comments (not included in the file) are indicated with %...
  {{{
+{{{
                               % number of bursts
 1024                       % image size npx npy
 …
  * `<Tx_Ty_Tz>`: translation, (Tz=1 for the options calib_lin and calib_rescale)
  * `<R>`: rotation matrix (in 3 lines). For the option <[https://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/search?q=wiki%3ACalibrationType CalibrationType]>= 'rescale', [[BR]] R (i=1)= [pxcmx 0 0] R (i=2)= [0 pxcmy 0] R (i=3)= [0 0 1], [[BR]]where pxcmx and pxcmy are the scaling factors along ''x'' and ''y''.
+ * `<R>`: rotation matrix (in 3 lines). For the option <[https://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/search?q=wiki%3ACalibrationType !CalibrationType]>= 'rescale', [[BR]] R (i=1)= [pxcmx 0 0] R (i=2)= [0 pxcmy 0] R (i=3)= [0 0 1], [[BR]]where pxcmx and pxcmy are the scaling factors along ''x'' and ''y''.
  * <omc> 3 components of the rotation vector (this is for diagnostic use, it is redondant with the matrix R used for actual coordinate transforms).  The physical coordinate axis are transformed to the image coordinate axis by a composition of the translation T and the rotation)
 …
 === 10.8 Other functions Action... ===
 With the option '''more...' ''in !ActionName, a browsers pops up to choose an Action function. Some examples of  functions are in the subdirectory ''{/series}'' of the folder containing '''''umat'''''.'''''
+With the option ''more...'' in !ActionName, a browsers pops up to choose an Action function. Some examples of  functions are in the subdirectory ''{/series}'' of the folder containing '''''umat'''''. A few more examples (less reliable) are in the subfolder ''{/series/usr_fct }'', a good place to put your own functions.
  * ''sub_background.m'': used to removed a mean background to the images. This is useful before CIV processing when some fiked features are visible in the background (when the laser sheet is close to the bottom).
  * ''ima_levels.m'': provides images with modified grey scale intensity to avoid blinking effects on particles.'''''''
+ * ''ima_levels.m'': provides images with modified grey scale intensity to avoid blinking effects on particles.''''''''''
  * ''ima2vol.m'' produce volume images for 3D3C PIV.
  * ''turb_stat.m'': produces turbulent statistics (Reynolds stress tensor)
 These can be used as template to create other functions. The general input of these functions in Matlab structure 'Param' which contains all the input parameters as given by the GUI series (see comments in the function for details). For batch operations, as needed for the cluster, this input is replaced by the name of an XML file which contains these parameters (this is the file produced in the floder '''/0_XML''' under the result directrory Output Subdir ). The first part of the function must give some options for the requested input information and may interactively introduce specific parameters needed for the function. The second part of the function, where the processing itself takes place, is then free from any input (so the operation can be easily dispatched to a remote computer).
+The first part of the function is activated when the function is selected in the menu !ActionName of the GUI '''series''', which yields the input !Param.Action.RUN=0. It is aimed at setting the GUI configuration appropriate for the specific function, and to provide all the needed input parameters. The second part is activated by the action RUN and should not contain any interactive input to allow for batch mode outside the current Matlab session.
+The settings of the GUI ''' series''' are controlled by the following parameters:
+-Data.AllowInputSort='off'/'on' ('off' by default) provides an automatic alphabetic sorting of the list of input files SubDir.
+-Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
+-Data.NbSlice='off'; %nbre of slices ('off' by default)
+-Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
+-Data.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
+-Data.FieldTransform = 'off'/'on' (default 'off') controls the visibility of the menu 'transform function'.
+-Data.ProjObject='off';%can use projection object(option 'off'/'on',
+-Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
+-Data.OutputDirExt='.stereo';%set the output dir extension
+-Data.OutputSubDirMode='all'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default)
+-Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
 To update (**): LIF_series: do LIF analysis, Stereo_PIV: combine two velicity series to yield the 3 components, part_stat: count particles and provides their density and luminosity histogramm, Peaklocking errors: estimate errors in PIV . By selecting the press button 'peaklocking' on the 'plotgraph' interface, you smooth the current velocity histograms while preserving its integral over each unity (in pixels). This appears in red. Then an estimate of the peaklocking error is obtained by comparing the initial histogram to the smooth one.