Changes between Version 86 and Version 87 of UvmatHelp


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Timestamp:
Jul 5, 2013, 3:23:52 PM (7 years ago)
Author:
sommeria
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  • UvmatHelp

    v86 v87  
    211211 * '''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'.
    212212 * '''Experiment''' is a directory containing all the data for a particular experiment, defined by a choice of values for the physical parameters.
    213  * '''!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.
     213 * '''!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.
    214214
    215215'''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.
    216216
    217 The data organisation can be controlled and managed by the GUI '''browse_data.fig'''. This is called by the menu bar option '''[Open/browse campaign]''' in uvmat: with this browser select the path of the folder considered as 'Campaign' (instead of the data file itself). Then the GUI '''browse_data.fig''' appears with a list of 'Experiments' and a list of '!DataSeries'. Select your choice to open the corresponding file series in '''uvmat.fig'''. The selected campaign path is then recorded for future opening under '''[Open/browse campaign]'' in the menu bar of uvmat.
    218 
    219 Instead of directly opening a file series with '''browse_data.fig''', you can create a 'mirror data tree' by pressing 'create_mirror', then selecting the path chosen for the new mirror folder 'Campaign'.  Inside this mirror folder, a set of folders is then created for each experiment. Furthermore, an xml file 'mirror.xml' is created to indicate the source directory (under the label <!SourceDir>). Inside each mirror folder 'Experiment', the source is reproduced as symbolic  links. Data processing in the mirror campaign then produces 'real' !DataSeries folders.
     217The data organisation can be controlled and managed by the GUI '''browse_data.fig'''. This is called by the menu bar option '''[Open/browse campaign]''' in uvmat: with this browser select the path of the folder considered as 'Campaign' (instead of the data file itself). Then the GUI '''browse_data.fig''' appears with a list of 'Experiments' and a list of '!DataSeries'. Select your choice to open the corresponding file series in '''uvmat.fig'''. The selected campaign path is then recorded for future opening under '''[Open/browse campaign]''' in the menu bar of '''uvmat.fig'''.
     218
     219Instead of directly opening a file series with '''browse_data.fig''', you can create a 'mirror data tree' by pressing 'create_mirror', then selecting the path chosen for the new mirror folder 'Campaign'.  Inside this mirror folder, a set of folders is then created for each experiment. Furthermore, an xml file 'mirror.xml' is created to recall the source directory (under the label <!SourceDir>). Inside each mirror folder 'Experiment', the source is reproduced as symbolic  links. Data processing in the mirror campaign then produces 'real' !DataSeries folders.
    220220
    221221Once created, this mirror campaign folder can be opened instead of the source.
     
    265265
    266266-'''Mouse display''': when the mouse is moved over a vector, it is marked by a circle, and its features appear in the display text boxes on the upper right. These are 
    267  * fist line: the position coordinates x, y, (z for 3D cases). 
     267 * fist line: the position coordinates ''x'', ''y'', ''z'' for 3D cases). 
    268268 * second line: the vector components
    269269 * third line: the vector index in the file, the values of the scalar (C), the warning flag (F) and the error flag (FF). The meaning of the flag values is given in [#a11.3FIX section 11.3].
     
    571571
    572572=== 8.2 The GUI geometry_calib.fig ===
    573 -''' Opening the GUI: ''' it is made visible  from the GUI '''uvmat.fig''' by  the menu bar command '''[!Tools/Geometric calibration] '''.  If calibration data already exist in the current file <!ImaDoc>, the corresponding parameters and the list of reference points are displayed in the table '''[!ListCoord]'''. The three first columns indicate the physical coordinates and the two last ones the corresponding image coordinates (in pixels). The physical unit is imposed as centimeter by the menu '''[CoordUnit]''' to avoid mistakes. Calibration points can be alternatively introduced by opening any  xml file <!ImaDoc> with the menu bar command '''[Import]''' of '''geometry_calib.fig'''. It is possible to import the whole information, option 'All', the calibration point coordiantes only, or the calibration parameters only.
     573-''' Opening the GUI: ''' it is made visible  from the GUI '''uvmat.fig''' by  the menu bar command '''[!Tools/Geometric calibration] '''.  If calibration data already exist in the current file <!ImaDoc>, the corresponding parameters and the list of reference points are displayed in the table '''[!ListCoord]'''. The three first columns indicate the physical coordinates and the two last ones the corresponding image coordinates (in pixels). The physical unit is imposed as centimeter by the menu '''[!CoordUnit]''' to avoid mistakes. Calibration points can be alternatively introduced by opening any  xml file <!ImaDoc> with the menu bar command '''[Import]''' of '''geometry_calib.fig'''. It is possible to import the whole information, option 'All', the calibration point coordiantes only, or the calibration parameters only.
    574574
    575575-''' Plotting calibration points: ''' press the button '''[PLOT PTS] ''' to visualise the current list of calibration points. The physical or image coordinates will be used in the list '''[!ListCoord]''', depending on the option blank or 'phys' in the menu '''[transform_fct]''' of ''' uvmat.fig''' .
     
    581581-''' Editing the coordinate table: ''' After mouse selection, the physical coordinates  must be introduced by editing the table. To make this task easier it is possible to export the table content on the Matlab command window by pressing '''[COPY PTS]''', and copy-paste a column on the table '''[!ListCoord]''' (the column below the introduction cell is filled). A single point can be removed by the 'backward' or 'suppr' keyboard command after selecting its line on the table. The whole set of points can be removed by pressing '''[CLEAR PT]'''. They can be also removed by pressing '''[STORE PT]''', then stored in a xml file (whose path and name is listed in '''[!ListCoordFiles]'''). Stored points can be retrieved by the menu bar command '''[Import/calibration points]'''.
    582582
    583 -''' Creating a physical grid: ''' This tool '''[!Tools/Create grid]''' in the  menu bar command provides the set of physical coordinates of a cartesian grid, ranked line by line from the bottom. First pick the set of image coordinates with the mouse. Then launch  '''[!Tools/Create grid]''' and fill the first and last x and y values, as well as the meshes, in physical coordinates. These coordanates then fill '''[!ListCoord]'''.
    584 
    585 -''' Detecting a physical grid: ''' This tool '''[!Tools/Detect grid]''' provides the same result as '''[!Tools/Create grid]''', but it automatically recognises the grid points on the image, provided the four corners of the grid have been previously selected by the mouse. The calibration points are detected either as image maxima (option 'white markers'), or as black crosses (option 'black markers'). Their position can be adjusted by selection with the mouse.
    586 
    587 -''' Translation and rotation of calibration points: ''' A translation or rotation (in physical space) can be introduced by the menu bar commands '''[!Tools/Translate points]''' and '''[!Tools/Rotate points]'''.  In the case of rotation, the origin of the rotation, as well as the angle (in degree) must be introduced. The resulting coordinates appear in the list '''[!ListCoord]'''.
     583-''' Creating a physical grid: ''' This tool '''[!Tools/Create grid]''' in the  menu bar command provides the set of physical coordinates of a cartesian grid, ranked line by line from the bottom. First pick the set of image coordinates with the mouse. Then launch  '''[!Tools/Create grid]''' and fill the first and last ''x'' and ''y'' values, as well as the meshes, in physical coordinates. These coordinates then fill the table '''[!ListCoord]'''.
     584
     585-''' Detecting a physical grid: ''' This tool '''[!Tools/Detect grid]''' provides the same result as '''[!Tools/Create grid]''', but it automatically recognises the grid points on the image, provided the four corners of the grid have been previously selected by the mouse. The calibration points are detected either as image maxima (option 'white markers'), or as black crosses (option 'black markers'). Their position can be further adjusted by selection with the mouse.
     586
     587-''' Translation and rotation of calibration points: '''In general A translation or rotation (in physical space) can be introduced by the menu bar commands '''[!Tools/Translate points]''' and '''[!Tools/Rotate points]'''.  In the case of rotation, the origin of the rotation, as well as the angle (in degree) must be introduced. The resulting coordinates appear in the list '''[!ListCoord]'''.
    588588
    589589-''' Recording calibration parameters: ''' Once the list of calibration points has been completed, press '''[APPLY]''', after selecting the appropriate option in '''[calib_type]'''. (see the previous [#a8.1Generalities sub-section 8.1]). Note that the 3D options  require a sufficient number of calibration points (typically > 10) spread over the image with different values of z, or a tilted grid, see below. Calibration coefficients are recorded in the xml file <!ImaDoc> associated with the image currently opened by uvmat. If previous calibration data already exist, the previous xml file is updated, but  the original one is preserved with the extension .xml~.  If no xml file already exists, it is created. The image transformation to phys coordinates can be directly seen on the '''uvmat.fig''' interface after completion of the command '''[APPLY]'''.
     
    591591To reproduce the same calibrationn for image series, open one of the image in the series, and apply again the calibration with the same points, or copy-paste the section GeometryCalib of the xml documentation file with a text editor.
    592592
    593 Alternatively the command '''[REPLICATE]''' can be used to calibrate a whole set of experiments, using an overview of the data set provided by the GUI '''data_browser.fig'''.
    594 
    595 -'''3D calibration''': take a set of (typically 5-10) calibrations images using a plane grid with different tilting angles (for precision the grid must cover a large area of the view field). On each image, get calibration points with the tool '''[!Tools/Detect grid]''', introducing the appropriate grid mesh. Do not fill info on ''z'' coordinates. Store the points each time (without applying calibration at this stage), which fills the list [ListCoordFiles] of file names. Then introduce a last grid image which will be considered as defining the orientation of the ''z'' axis, perpendicular to the grid. Detect points on this last image, but instead of storing them, apply the calibration with the option 3D_linear or 3D_quadr (if non-linear distortion is significant). The ''z'' position chosen for this reference calibration plane can be indicated at this stage.
     593Alternatively the command '''[REPLICATE]''' can be used to calibrate a whole set of experiments in a 'Campaign', using an overview of the data set provided by the GUI '''data_browser.fig''', described in [#a3.7Dataorganisationinaproject section 3.7].
     594
     595-'''3D calibration''': 3D projection is handled by the options in '''[calib_type]''' '3D_lin' or '3D_quad' ((if non-linear distortion is significant). By default, the set of calibration points is assumed to be contained in a single plane ''z''=0. For a correct determination of the 3D features, the normal to this plane must be tilted with respect to the line of view. Otherwise this problem of indetermination can be resolved by using a set of (typically 5-10) calibrations images using a plane grid with different tilting angles (for precision the grid must cover a large area of the view field). On each image, get calibration points with the tool '''[!Tools/Detect grid]''', introducing the appropriate grid mesh. Do not fill info on ''z'' coordinates. Store the points each time (without applying calibration at this stage), which fills the list [ListCoordFiles] of file names. Then introduce a last grid image which will be considered as defining the orientation of the ''z'' axis, perpendicular to the grid. Detect points on this last image, but instead of storing them, apply the calibration with the option 3D_linear or 3D_quadr . The ''z'' position chosen for this reference calibration plane can be indicated at this stage.
    596596
    597597-'''Intrinsic parameters''': the previous procedure first determines the extrinsic parameters which characterize the camera optics (focal lengths and nonlinear deformation parameter). Then the extrinsic parameters, translation and rotation of the camera with respect to the reference grid, are determined on the last grid image. if the same optics is used in a new experiment, it is possible to skip the multiplane detection, importing the intrinsic parameters from a previous <!ImaDoc> file by the menu bar tool '''[!Import/Intrinsic]''' parameters, then applying the calibration with the option '3D_extrinsic' with the reference grid image only.