Changes between Version 59 and Version 60 of UvmatHelp


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Timestamp:
Jun 11, 2013, 9:06:31 AM (7 years ago)
Author:
sommeria
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  • UvmatHelp

    v59 v60  
    114114
    115115=== 3.2 Selecting fields from CIV ===
     116To update...
    116117The package uvmat recognizes the NetCDF fields obtained from the CIVx software.  This includes the velocity fields and their spatial derivatives, as well as information about the CIV processing (image correlation values and flags). The vorticity, divergence, or strain are read in the same NetCDF files, but are available only after a PATCH operation has been run in the CIVx software,  see [#a11-PIV:ParticleImagingVelocimetrys section 11].
    117118
     
    153154
    154155=== 3.5  Image documentation files (.xml) ===
    155 Information on image series is provided by a documentation file in the format xml. This file can include sections about image timing, geometric calibration, camera type and illumination. An xml file is a text file in which each element of information, or group of elements, is labelled by a tag. The list of tags and their hierarchical organisation is specified by a schema file (.xsd). The schema used for image documentation is ''ImaDoc.xsd'', available in the uvmat package at the path indicated in {PARAM.xml}). For a general introduction to the xml language, see http://www.w3schools.com/xml.
     156Information on image series is provided by a documentation file in the format xml. This file can include sections about image timing, geometric calibration, camera type and illumination. An xml file is a text file in which each element of information, or group of elements, is labelled by a tag. The list of tags and their hierarchical organisation is specified by a schema file (.xsd). The schema used for image documentation is ''!ImaDoc.xsd'', available in the uvmat package in a sub-directory ''/Schemas''. A general introduction to the xml language and schemas is provided for instance in http://www.w3schools.com/xml.
    156157
    157158When a new file series is opened in uvmat, a documentation file is automatically sought, whose path and name are displayed by ''!RootPath'' and  ''!RootFile'' respectively, with extension {.xml} (''!RootPath'' and ''!RootFile'' are the contents of the edit boxes '''[!RootPath]''' and ''' [!RootFile]''').  The detection of this file is indicated by the visibility of the pushbutton '''[view_xml]''' on the upper right of the GUI '''uvmat.fig'''. Press this button to see the content through an xml editor '''editxml.fig''' (described in [#a10-Processingfieldseries section 10]). The xml file can be also opened directly by the uvmat browser, or by any text editor.
     
    159160The xml file <!ImaDoc> can contain the following sections:
    160161
    161  * <Heading>: contains elements <Campaign>, <Experiment>, <!DataSeries>, which recall the position of the file in the tree structure of data files. This allows the user  to check that the document file has not been displaced.
    162  * <Camera> contains information on the camera settings, as well as the timing of all the images in a subsection <!BurstTiming>. <!TranslationMotor> and <Oscillator> contains information on the mechanical devices used to produce the laser sheet and scan volumes.
    163  * <!GeometryCalib> contains the parameters of the geometric calibration relating the pixel position to the real space coordinates (see [#a8-Geometriccalibration section 8]]). In the case of volume scanning, it also describes the set of laser plane positions and angles.
    164  * <Illumination> describes the illumination system used, including the position of the laser source.
    165  * <Tracor> describes the properties of the flow tracor (particle, dye...)
     162 * '''<Heading>''' contains elements <Campaign>, <Experiment>, <!DataSeries>, which recall the position of the file in the tree structure of data files. This allows the user  to check that the document file has not been displaced.
     163 * '''<Camera>''' contains information on the camera settings, as well as the timing of all the images in a subsection <!BurstTiming>. <!TranslationMotor> and <Oscillator> contains information on the mechanical devices used to produce the laser sheet and scan volumes.
     164 * '''<!GeometryCalib>''' contains the parameters of the geometric calibration relating the pixel position to the real space coordinates (see [#a8-Geometriccalibration section 8]]). In the case of volume scanning, it also describes the set of laser plane positions and angles.
     165 * '''<Illumination>''' describes the illumination system used, including the position of the laser source.
     166 * '''<Tracor>''' describes the properties of the flow tracor (particle, dye...)
    166167
    167168The detailed commented structure is provided  in the schema file ''ImaDoc.xsd''. The xml documentation file is read by the function ''imadoc2struct.m''. If this file does not exist, a file with the same root name but extension .civ is sought (obsolete format).
     
    182183 * '''.fig''' Matlab figures represent plots but also Graphic User Interfaces (GUI). In that case Matlab functions (callbacks) are attached to the graphic objects in the figure and can be activated by the mouse. Matlab figures can be directly opened by the browser of '''uvmat.fig'''.
    183184
    184  * ''''.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'' (instead of {root.xml}). It is automatically sought by '''uvmat.fig''' and '''civ.fig''', in the absence of an xml file ImaDoc. (it is read by the function ''read_imatext.m'').
    185    * Example : %... gives comments (not included in the file). This 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 correspopnding .civ file is named aa.civ.
     185 * ''''.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'' (instead of {root.xml}). It is automatically sought by '''uvmat.fig''' and '''civ.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 %...
    186186
    187187{{{
     
    207207The package is designed to foster a good data organisation. The raw data from a project should be organised as:[[BR]]   '''!Project/Campaign/Experiment/DataSeries/data files'''.
    208208
    209  * 'Project': contains all information from a project.
    210  * 'Campaign' corresponds to a series of experiments obtained by varying a given set of physical parameters. A set of  parameter names (with units) is expected to be associated to a campaign. A project may involve several campaigns corresponding to different configurations, hence different relevant parameters. For a single configuration, 'Campaign' can be at the top of the data tree, without an additional 'Project' level. The uvmat package does not manage levels above 'Campaign'.
    211  * 'Experiment' is a directory containing all the data for a particular experiment, defined by a choice of values for the physical parameters.
    212  * '!DataSeries' contains an image series or movie from a camera, or more generally a data series from a device. Its name must correspond to the device and remain the same for all the experiments using this device. The results from data processing, as provided by 'civ' or 'series', are stored at the same level in a !DataSeries directory, named from the source one with a extension specific to the processing program, for instance .civ for the PIV data.
     209 * '''Project''' contains all information from a project.
     210 * '''Campaign''' corresponds to a series of experiments obtained by varying a given set of physical parameters. A set of  parameter names (with units) is expected to be associated to a campaign. A project may involve several campaigns corresponding to different configurations, hence different relevant parameters. For a single configuration, 'Campaign' can be at the top of the data tree, without an additional 'Project' level. The uvmat package does not manage levels above 'Campaign'.
     211 * '''Experiment''' is a directory containing all the data for a particular experiment, defined by a choice of values for the physical parameters.
     212 * '''!DataSeries''' contains an image series or movie from a camera, or more generally a data series from a device. Its name must correspond to the device and remain the same for all the experiments using this device. The results from data processing, as provided by 'civ' or 'series', are stored at the same level in a !DataSeries directory, named from the source one with a extension specific to the processing program, for instance .civ for the PIV data.
    213213
    214214'''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'.
     
    286286-'''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). 
    287287
    288 -'''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.
    289  
     288-'''Transform:''' by default the 'phys' option transforms each of the input fields from pixel to physical coordinates. This operation can also combine two input field structures into a single field structure.
     289
    290290-'''Histogram:''' This is obtained from the input field in transformed coordinates, or if applicable from the fields resulting from the two input fields. 
    291291
    292 -'''Projection:''' on  the projection object selected in the menu '''[ListObject_1]''', see [#ProjObject section 6]. A second projection, on the object selected by '''[ListObject]''', can be plotted in the ancillary figure '''view_field.fig'''. Projection is performed by the function {proj_field.m}.
     292-'''Projection:''' on  the projection object selected in the menu '''[!ListObject_1]''', see [#ProjObject section 6]. A second projection, on the object selected by '''[!ListObject]''', can be plotted in the ancillary figure '''view_field.fig'''. Projection is performed by the function ''proj_field.m''.
    293293
    294294-'''Field calculation:''' a scalar can be calculated after projection, as selected by the menu '''[Fields]'''.
    295295
    296 -'''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.   
    297 
    298 -'''Plotting:''' plot the results of projection. The function {plot_field.m} is used.
     296-'''Field comparison''': when two fields of the same nature are introduced, the difference is taken. This is skipped if the transform function has already led to a single field.   
     297
     298-'''Plotting:''' plot the results of projection, using the function ''plot_field.m''.
    299299
    300300== 5- Field structures ==
     
    452452
    453453=== 6.3 Projection modes ===
    454 Each field variable yields a corresponding variable with the same name in the projected field. in addition integral quantities (circulation, flux...) can be calculated. The result of projection depends on the object type, the nature of the coordinates, the Role of field variables and on the projection mode !ProjMode:
     454Each field variable yields a corresponding variable with the same name in the projected field. in addition integral quantities (circulation, flux...) can be calculated. The result of projection depends on the object type, the nature of the coordinates, the ''Role'' of field variables and on the projection mode !ProjMode:
    455455
    456456 * ''' !ProjMode = 'projection':  '''  this is a normal projection  of the field data in a range of action around the object, as defined by the parameters 'RangeX', 'RangeY', "RangeZ'. The projection of an input variable defined on unstructured coordinates therefore remains unstructured. By contrast, an input variable defined on a regular grid always yields a projected variable on a regular grid (for instance on a line or plane). Error flags ?
     
    461461   *  no action on 'polyline', 'rectangle', 'polygon', 'ellipse'.
    462462
    463  * ''' !ProjMode 'interp_lin': '''   Linear interpolation of the fields on a grid of regularly spaced points defined on the projection object, with meshes DX, DY, DZ. The grid array along x starts at RangeX(1) and ends at the closest value smaller than RangeX(2). Similar convention is used for y and z in case of planes and volumes.
    464 
    465  * ''' !ProjMode  'interp_tps':  '''  interpolation with thin spline shell.
     463 * ''' !ProjMode 'interp_lin': '''  Linear interpolation of scalar and vector field variables, after exclusion of false data (marqued by error flag). Ancillary data and warning flags are not projected in this mode. Gridded data are interpolated by ..., while fields with scattered coordinates are projected with the Matlab function .... Note that this function provides interpolation only within the convex hull of the initial data set, attributing 'NaN' (undefined) field values out of this domain. To avoid problems with further data processing, uvmat transforms NaN values into zeros, but mark them with an error flag FF=1.
     464   * 'points': linear interpolation on each point of the object.
     465   * 'line','polyline', 'rectangle', 'polygon', 'ellipse': linear interpolation on points regularly spaced on the line, with mesh DX. The X coordinate is the distance following the line, with an origin at the starting point(the first point in 'line','polyline','polygon',the lower left corner for rectangle, the point along the main axis for an ellipse).
     466   * 'plane': linear interpolation on a regular grid with meshes DX, DY and ortigin at (X,Y)=(0,0). This grid is bounded by the two values of RangeX and RangeY along X and Y respectively.
     467 
     468 * ''' !ProjMode  'interp_tps':  '''  This behaves with different objects line 'interp_lin', but using the more precise thin spline shell method. This is particularly usefull to calculate spâtial field derivatives. Furthermore this method provides data exrtrapolation outside the initial convex hull (although it is not reliable at large distances). This mode does require a previous calculation of tps weights, see [#a5.1Gridingofdata section 5.1], so it does not act on the initial field cells with scattered coordinates. This is done by uvmat if tps projection is requested. Gridded data are linearly interpolated (to clarify...).
    466469
    467470 * ''' !ProjMode 'inside' and 'ouside '''': defined only for closed lines: rectangle, polygon, ellipse. For each field U, its probability distribution function Uhist  inside, or respectively outside,  the line is calculated, as well as the mean Umean.
    468471
    469472 * ''' !ProjMode 'none', 'mask_inside', 'mask_outside': ''' no projection operation. The object is used solely for plotting purpose, to show a boundary or to prepare a mask, inside or outside a closed line, see [#a9-Masksandgrids section 9]).
     473
     474Operations, for instance 'vort', 'div' are performed after interpolation. Similarly for field difference, which requires interpolation to compare fields defined at different positions. Field variables to be substracted are initially marqued by an attribute 'CheckSub'. 
    470475
    471476=== 6.4 Projected fields ===