Changes between Version 84 and Version 85 of UvmatHelp


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Timestamp:
Jul 5, 2013, 9:58:04 AM (7 years ago)
Author:
sommeria
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  • UvmatHelp

    v84 v85  
    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 displayedin the table '''[ListCoord]'''. The three first columns indicate the physical coordinates and the two last ones the corresponding image coordinates. 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''' .
    576576
    577 -Simple scaling: a simple scaling, in pixels/cm.
     577-'''Simple scaling''': a simple scaling, in pixels/cm, can be introduced by the menubar command '''[Tools/Set scale]''', which displays a set of four reference points in the table '''[!ListCoord]'''. The tool 'ruler', from the menu bar command '''[Tools/ruler]''' of '''uvmat.fig''', can be useful to get the scaling. The default origin of the physical coordinates  is set by default to the lower left image corner. Use the tool 'translate points', described below, to change the origin.
    578578
    579579-''' Appending  calibration points with the mouse: ''' Calibration points can be manually picked out by the mouse on the current image displayed by '''uvmat''' (left button click). This requires the activation of the check box '''[enable mouse]'''. The image coordinates (in pixels) are picked by the mouse (the option 'blank' in the popup menu '''[transform_fct]''' is automatically selected when the mouse button is pressed). Zoom can be used to improve the precision, but must be desactivated for mouse selection (then move across the image by the key board directional arrows). Points can be accumulated from several images, using the key board short cuts 'p' and 'm' to move in the image series without the mouse.  A calibration point can be adjusted by selecting it with the mouse and moving it while pressing the left mouse button. The coordinates in pixel of the selected points get listed in the table '''[!ListCoord]''' of '''geometry_calib.fig'''.
    580580
    581 -''' Editing the coordinate table: '''
    582  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]'''.
    583 
    584 -'''Introducing a simple scaling:'''
    585 
    586 -''' Editing the  coordinates: '''
    587 
    588 For editing the physical coordinates of a calibration point, select it in the list '''[ListCoord]''', and use the edit boxes '''[XObject]''', '''[YObject]''', '''[ZObject] ''' (for 3D calibration). The image coordinates can be also edited by '''[XImage]''', '''[YImage]''', although they are preferably set directly by the mouse. Type 'return carriage' to validate the edition. The reference point can be suppressed by typing the 'backward' arrow on the key-board, or by filling the five boxes with blank values.
    589 
    590 -''' Creating a physical grid: ''' This tool '''[Tools/Create grid]''' in the  menu bar command provides the whole set of physical coordinates of a cartesian grid, after all their image coordinates have been picked out by the mouse. In the  GUI '''Create_grid.fig''' which appears, set the first and last x and y values and the meshes for the physical grid corresponding to the points already selected by the mouse. The physical coordinates of all the grid points then appears on '''[ListCoord]'''.
    591 
    592 -''' 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.
    593 
    594 -''' Translation and rotation of calibration points: '''
    595 
    596 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]'''.
    597 
    598 -''' Recording calibration parameters: '''
    599 
    600 Once the list of calibration points has been completed, press '''[APPLY]''', after selecting the appropriate option in '''[calib_type]'''. (see the previous sub-section 7.1). Note that the more advanced Tsai options  require a sufficient number of calibration points (typically > 10) spread over the image. 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]'''.
     581-''' 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]'''.
     582
     583-''' Creating a physical grid: ''' This tool '''[!Tools/Create grid]''' in the  menu bar command provides the whole set of physical coordinates of a cartesian grid, after all their image coordinates have been picked out by the mouse. In the  GUI '''Create_grid.fig''' which appears, set the first and last x and y values and the meshes for the physical grid corresponding to the points already selected by the mouse. The physical coordinates of all the grid points then appears on '''[!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]'''.
     588
     589-''' 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]'''.
    601590
    602591To 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.
    603592
    604 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 '''dataview.fig'''.
     593Alternatively 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 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, then apply calibration with the option 3D_linear or 3D_quadr (if non-linear distortion is significant). Store the points each time, which fills the list [ListCoordFiles] of file names.
    605596
    606597=== 8.3 Structure of the xml file ===