Changes between Version 132 and Version 133 of UvmatHelp


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Timestamp:
Jan 13, 2015, 8:20:25 PM (6 years ago)
Author:
sommeria
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  • UvmatHelp

    v132 v133  
    244244Scalars (or image intensity) can be also represented with contour plots, by switching the popup menu '''[Contours] ''' from the setting 'image' to the setting 'contours'. Contours for positive scalar values are in sold line while contours for negative values are dashed. The interval between contours can be set by the edit box '''[num_IncrA]'''. The interval is automatically determined if the box content is blank.
    245245
    246 By default, the  contours are further marked by jumps of color levels. This can be set to grey levels by selecting the check box '''[CheckBW]. '''To suppress these images, set '''[Opacity]''' to 0. 
     246By default, the  contours are further marked by jumps of color levels. This can be set to grey levels by selecting the check box '''[CheckBW]. '''To suppress these images, set '''[Opacity]''' to 0.
    247247
    248248=== 4.3 Vectors ===
    249 The vector fields are represented by arrows. The length of the arrows is automatically set by default, or can be adjusted by the edit box '''[num_VecScale]''' when the check box''' [!CheckFixVectors]''' is selected.  For clarity of visualisation, the number of displayed vectors can be divided by 4 or 16  by selecting the check box '''[!CheckDecimate4]''', or '''[!CheckDecimate16]''' respectively.
     249The vector fields are represented by arrows. The length of the arrows is automatically set by default, or can be adjusted by the edit box '''[num_VecScale]''' when the check box''' [!CheckFixVectors]''' is selected.  For clarity of visualisation, the number of displayed vectors can be divided by 4 or 16  by selecting the check box '''[!CheckDecimate4]''', or '''[!CheckDecimate16]''' respectively.
    250250
    251251Each vector has a color, ranging from blue to red, which can represent an associated  scalar value. In addition, black and magenta colors represent warning and error flags respectively. This color system is primarily designed for PIV data but can be used in other contexts as well.
     
    438438When a 2D or 3D field is opened by '''uvmat;fig''', a default projection object called 'plane' is created, so that all field plots (in 2D and 3D) are considered as the result of a projection. New objects are created by the menu bar command  '''[Projection object]''' in '''uvmat.fig'''.  The creation of a new object ('''points''', '''line'''....) can be initiated by selecting the corresponding item in the menu. Alternatively, an existing XML object file can be opened by selecting the menu option '''[browse...]'''. In each case an auxiliary GUI '''set_object.fig''' describing the object properties appears, see next [#a6.2Objectproperties sub-section] for their definitions. This GUI can be directly edited and object coordinates can be set by mouse drawing on the plot, see [#a6.4Objectrepresentation section 6.4]. To validate edition on the GUI '''set_object.fig''', refresh the plots by pressing '''[REFRESH]'''. Objects can be saved as xml files with the (upper right) button '''[SAVE]''' of '''set_object.fig'''.
    439439
    440 The names of the created objects are listed in the menu '''[!ListObject]'''. The properties of the object selected in this menu can be viewed by activating the check box '''[!CheckViewObject]'''. Check '''[!CheckEditObject]''' to allow object editing with '''set_object.fig'''.  The selected object is plotted in magenta, while the inactive ones are in blue. The field plot resulting from projection can be viewed in the GUI view_field.fig by activating '''[!CheckViewField]'''. This option is automatically selected when a new object is created. Then the projection object used for the main plotting window in UVMAT can be selected by the menu '''[!ListObject_1]''' which reproduces the list of available objects. The active objects are plotted in magenta, while the inactive ones are in blue.The object can be deleted by pressing '''[DeleteObject]'''.
    441 
    442 The properties of the projection objects can be extracted as a Matlab structure using the menu bar command '''[Export/field in workspace]''' of '''uvmat.fig'''. Those are contained in the cell of structures ''Data_uvmat.[wiki:ProjObject]''.
     440The names of the created objects are listed in the menu '''[!ListObject]'''. The properties of the object selected in this menu can be viewed by activating the check box '''[!CheckViewObject]'''. Check '''[!CheckEditObject]''' to allow object editing with '''set_object.fig'''.  The selected object is plotted in magenta, while the inactive ones are in blue. The field plot resulting from projection can be viewed in the GUI view_field.fig by activating '''[!CheckViewField]'''. This option is automatically selected when a new object is created. Then the projection object used for the main plotting window in UVMAT can be selected by the menu '''[!ListObject_1]''' which reproduces the list of available objects. The active objects are plotted in magenta, while the inactive ones are in blue.The object can be deleted by pressing '''[[wiki:DeleteObject !DeleteObject]]'''.
     441
     442The properties of the projection objects can be extracted as a Matlab structure using the menu bar command '''[Export/field in workspace]''' of '''uvmat.fig'''. Those are contained in the cell of structures ''Data_uvmat.[wiki:ProjObject !ProjObject]''.
    443443
    444444=== 6.2 Object properties ===
     
    456456   * 'volume': volume with associated cartesian coordinates.
    457457
    458  * ''' !ProjMode: ''': specifies the method of projection of coordinates and field, as described in [#a6.3Projectionmodes next sub-section].
    459 
    460  * ''' Angle: ''': three component rotation vector which defines the orientation of the object coordinate axis, for 'plane' and 'volume'. In 2D, this rotation vector has only one component along z, defining a rotation angle in the plane (expressed in degrees). This applies also to the main axis of 'ellipse' and 'rectangle'. In 3D, line objects ('line', 'polyline','rectangle','polygon','ellipse') are assumed contained in a plane, and 'Angle' defines the orientation of this plane.
     458 * ''' !ProjMode: '''specifies the method of projection of coordinates and field, as described in [#a6.3Projectionmodes next sub-section].
     459
     460 * ''' Angle: '''three component rotation vector which defines the orientation of the object coordinate axis, for 'plane' and 'volume'. In 2D, this rotation vector has only one component along z, defining a rotation angle in the plane (expressed in degrees). This applies also to the main axis of 'ellipse' and 'rectangle'. In 3D, line objects ('line', 'polyline','rectangle','polygon','ellipse') are assumed contained in a plane, and 'Angle' defines the orientation of this plane.
    461461
    462462 * ''' RangeX: ''', ''' RangeY: ''', ''' RangeZ: ''':bounds defining a range of projection along each coordinate with respect to the object. These ranges have one or two values depending on the object type.
     
    466466   * 'rectangle','ellipse': RangeX and RangeY (one value) define the half length and half width respectively. In 3D, RangeZ may set a range of projection transverse to the plane containing the object.
    467467   * 'plane': RangeX and RangeY (two values each) may restrict a region in the coordinates of the plane. In 3D, RangeZ may set a range of projection transverse to the plane.
    468    * 'volume': RangeX, RangeY, rangeZ (two values each) define a selected volume in the data set.
    469 
    470  * ''' DX: ''', ''' DY: ''', ''' DZ: ''':mesh  along each coordinate defining a grid for interpolation.
    471 
    472  * ''' Coord: ''': matrix with two (for 2D fields) or three columns defining the object position.
     468   * 'volume': RangeX, RangeY, RangeZ (two values each) define a selected volume in the data set.
     469
     470 * ''' DX: ''', ''' DY: ''', ''' DZ: '''mesh  along each coordinate defining a grid for interpolation.
     471
     472 * ''' Coord: ''' matrix with two (for 2D fields) or three columns defining the object position.
    473473   * for  'points', 'line', 'polyline', 'polygon': matrix with n lines [xi yi zi], corresponding to each of the n defining points. Note that in 3D case, polygons must be included in a plane, which imposes restrictions on these coordinates.
    474474   * for 'rectangle', 'ellipse': coordinates of the center.
     
    545545-'''1D plot:''' to plot a simple graph, ordinate versus abscissa. Select by the menu '''[ordinate]''' the variable(s) to plot as ordinate (use the key '''Ctrl''' for multiple selection). Then select the corresponding abscissa in the column '''[abscissa]'''.  If the variable is indexed with more than one dimension, each component is plotted versus the first index (like with the plot Matlab function ''plot.m''). If the option '''[matrix index]'''('''[!CheckDimensionX]''') is selected, the ordinate variable is plotted versus its index.
    546546
    547 -'''scalar:''' to plot scalar fields as images. The variable representing the scalar is selected in the first column '''[scalar]''', with coordinates respectively selected in '''[Coord_x] ''' and '''[Coord_y]'''. Alternatively, matrix index can be used as coordinate if the options '''[matrix index]'''('''[!CheckDimensionX]''' and '''[!CheckDimensionY]''') are selected.
    548 
    549 -'''vectors:''' to plot vector fields. The x and y vector components are selected in the first (...) and second columns, while the coordiantes are selected in '''[coord_x_vector] ''' and '''[coord_y_vector]'''. If no variable is selected in '''[coord_x_scalar] '''  or '''[coord_y_scalar] ''' ( blank selected at first line), the index is used as coordinate. A scalar, set in ..., can be represented as vector color.
    550 
    551 The attribute or variable considered as 'time' can be also chosen in the Panel '''[Time]'''. From the menu '''[!SwitchVarIndexTime]''', the time can be considered as the ''file index'', a global ''attribute'', a dimension ''variable'', or a ''dimension index''. Selection of ''attribute'' gives way to a list of global attribute tags in the menu '''[!TimeName]'''. Selection of variable gives way to a list of vartiables, while selection of ''dimension'' gives a list of dimension names.
    552 
    553 In the case of a 3D input field, the fig is set to uvmat. A middle plane of cut is automatically selected. This can be moved then with the slider on the interface set_object (see section 5). The default cuts are made at constant z coordiante, but any of the three initial coordiantes can be used as z coordinate, using the menu coord_z.
     547-'''scalar:''' to plot scalar fields as images. The variable representing the scalar is selected in the first column '''[scalar]''', with coordinates respectively selected in '''[Coord_x] ''' and '''[Coord_y]'''. Alternatively, matrix index can be used as coordinate if the options '''[matrix index]'''('''[CheckDimensionX]''' and '''[CheckDimensionY]''') are selected.
     548
     549-'''vectors:''' to plot vector fields. The x and y vector components are selected in the first (...) and second columns, while the coordinates are selected in '''[coord_x_vector] ''' and '''[coord_y_vector]'''. If no variable is selected in '''[coord_x_scalar] '''  or '''[coord_y_scalar] ''' ( blank selected at first line), the index is used as coordinate. A scalar, set in ..., can be represented as vector color.
     550
     551The attribute or variable considered as 'time' can be also chosen in the Panel '''[Time]'''. From the menu '''[!SwitchVarIndexTime]''', the time can be considered as the ''file index'', a global ''attribute'', a dimension ''variable'', or a ''dimension index''. Selection of ''attribute'' gives way to a list of global attribute tags in the menu '''[!TimeName]'''. Selection of variable gives way to a list of variables, while selection of ''dimension'' gives a list of dimension names.
     552
     553In the case of a 3D input field, the fig is set to uvmat. A middle plane of cut is automatically selected. This can be moved then with the slider on the interface set_object (see section 5). The default cuts are made at constant z coordiante, but any of the three initial coordinates can be used as z coordinate, using the menu coord_z.
    554554
    555555----
     
    572572-'''3D_extrinsic:''' this is like 3D_quadr, but uses intrinsic parameters of the camera, as explained below.
    573573
    574 The 3D options involve a full 3D calibration relying on the [attachment:3D_view.pdf pinhole camera  model]. The method was first proposed by R.Y. Tsai, 'An Efficient and Accurate Camera Calibration Technique for 3D Machine Vision'. Proceedings of IEEE Conference on Computer Vision and Pattern Recognition, Miami Beach, FL, pp. 364-374, 1986). We use a more recent version, with the toolbox [->http://www.vision.caltech.edu/bouguetj/calib_doc/] . 3D calibrations are done in two steps. The camera'' intrinsic parameters'', which are the focal length and the quadratic deformation coefficient, are first determined by different views of the same grid observed at different angles. Then the ''extrinsic parameters'', which represent the rotation angles and translation of the physical coordinates with respect to the camera, are obtained with a single image of the grid positioned in a known plane $z=cte$. The option 3D_extrinsic allows the user to do only the second step from known intrinsic parameters. Those depend only on the camera with its objective lens and focus adjustement. Note that these 3D options require a calibration grid, with a sufficient number of calibration points covering the whole image.
     574The 3D options involve a full 3D calibration relying on the [attachment:3D_view.pdf pinhole camera  model]. The method was first proposed by R.Y. Tsai, 'An Efficient and Accurate Camera Calibration Technique for 3D Machine Vision'. Proceedings of IEEE Conference on Computer Vision and Pattern Recognition, Miami Beach, FL, pp. 364-374 (1986). We use a more recent version, with the toolbox [->http://www.vision.caltech.edu/bouguetj/calib_doc/] . 3D calibrations are done in two steps. The camera'' intrinsic parameters'', which are the focal length and the quadratic deformation coefficient, are first determined by different views of the same grid observed at different angles. Then the ''extrinsic parameters'', which represent the rotation angles and translation of the physical coordinates with respect to the camera, are obtained with a single image of the grid positioned in a known plane $z=cte$. The option 3D_extrinsic allows the user to do only the second step from known intrinsic parameters. Those depend only on the camera with its objective lens and focus adjustement. Note that these 3D options require a calibration grid, with a sufficient number of calibration points covering the whole image.
    575575
    576576The transform coefficients for each image series are stored in the corresponding XML documentation file <!ImaDoc>, described in [#ImaDoc section 3.5],  under the tag <!GeometryCalib>. Calibration creates an xml file, or updates an existing xml file <!ImaDoc>, with the name of the !DataSeries folder containing the images currently opened by uvmat, followed by the file extension .xml. If a new data series is produced in a folder named with an extension, for instance !DataSeries.civ for PIV, the xml file !DataSeries.xml is still used, except if a new xml file !DataSeries.civ.xml also exists.
     
    583583-''' 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''' .
    584584
    585 -'''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.
     585-'''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 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.
    586586
    587587-''' 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'''.
     
    593593-''' 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.
    594594
    595 -''' 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]'''.
    596 
    597 -''' 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]'''.
     595-''' 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]'''.
     596
     597-''' 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]'''.
    598598
    599599To reproduce the same calibrationn for image series, open one of the image in the series, and apply again the calibration with the same points, keeping the GUI geometry_calib opened.
    600600
    601 To calibrate at once a set of experiments, a better alternative is the command '''[REPLICATE]'''. Open a folder  '''Campaign''', parent of the folders '''Experiment''' to treat. The GUI '''data_browser.fig''', also described in [#a3.7Dataorganisationinaproject section 3.7], then pops up. A two-column display appears, with the list of '''Experiments''' on the left and the list of corresponding '''DataSeries''' on the right. Select the list of experiments to calibrate, and a single camera name in '''DataSeries''', then validate by pressing '''OK'''.
    602 
    603 -'''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. A non-zero ''z'' position of this grid can be introduced by a z translation performed with '''Tools/Translate points'''.
    604 
    605 -'''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.
    606 
    607 -'''Section planes:''' deducing the physical coordinates from image coordinates requires information on the section plane. The default assumption is that the objects in the image are in the plane used for calibration, but uvmat can handle volume scanning by a laser plane. A set of section planes can be defined by their origin positions and rotation angle vectors. Theses planes are labelled by a ''z index'', assumed to be the frame index j (case of volume scan), or the index i modulo the number of slices !NbSlice (case of 'multilevel' scan). These settings are stored in the xml file <!ImaDoc> as part of the section <!GeometryCalib> and can be edited from '''uvmat.fig''' with the menu bar command '''[Tools/set slice]'''. A dialog box '''set_slices''' appears for entering the first and last section plane positions ''z'', as well as the number of slices and the option 'volume_scan' ('multilevel' otherwise). In the absence of 3D scan put twice the same value for first and last z.  Finally a tilt angle of the laser sheet, around the ''x'' and ''y'' axis, can be introduced, with a possible angular scanning from first to last section planes. After introduction of the plane position information, the z-index is displayed in the frame '''[FileIndices]''' of '''uvmat.fig'''. The local ''z'' position of the mouse pointer, assumed to lay on the current section plane, is then displayed in '''[text_display]'''.
     601To calibrate at once a set of experiments, a better alternative is the command '''[REPLICATE]'''. Open a folder  '''Campaign''', parent of the folders '''Experiment''' to treat. The GUI '''data_browser.fig''', also described in [#a3.7Dataorganisationinaproject section 3.7], then pops up. A two-column display appears, with the list of '''Experiments''' on the left and the list of corresponding '''[wiki:DataSeries !DataSeries]''' on the right. Select the list of experiments to calibrate, and a single camera name in '''[wiki:DataSeries !DataSeries]''', then validate by pressing '''OK'''.
     602
     603-'''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. A non-zero ''z'' position of this grid can be introduced by a z translation performed with '''!Tools/Translate points'''.
     604
     605-'''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.
     606
     607-'''Section planes:''' deducing the physical coordinates from image coordinates requires information on the section plane. The default assumption is that the objects in the image are in the plane used for calibration, but uvmat can handle volume scanning by a laser plane. A set of section planes can be defined by their origin positions and rotation angle vectors. Theses planes are labelled by a ''z index'', assumed to be the frame index j (case of volume scan), or the index i modulo the number of slices !NbSlice (case of 'multilevel' scan). These settings are stored in the xml file <!ImaDoc> as part of the section <!GeometryCalib> and can be edited from '''uvmat.fig''' with the menu bar command '''[Tools/set slice]'''. A dialog box '''set_slices''' appears for entering the first and last section plane positions ''z'', as well as the number of slices and the option 'volume_scan' ('multilevel' otherwise). In the absence of 3D scan put twice the same value for first and last z.  Finally a tilt angle of the laser sheet, around the ''x'' and ''y'' axis, can be introduced, with a possible angular scanning from first to last section planes. After introduction of the plane position information, the z-index is displayed in the frame '''[[wiki:FileIndices !FileIndices]]''' of '''uvmat.fig'''. The local ''z'' position of the mouse pointer, assumed to lay on the current section plane, is then displayed in '''[text_display]'''.
    608608
    609609-'''Refraction effect:''' refraction effect can be accounted for if calibration was done in air by selecting the check box refraction, and introducing the water height (assumed at ''z''=cte) and refraction index. The apparent distance reduction for objects below the water height will be then taken into account.
     
    628628 * `<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''.
    629629
    630  * <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).
     630 * <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).
    631631
    632632 * <!ErrorRms>: rms difference (in X and Y direction) between the image coordinates measured for the calibration points and the coordinates transformed from their physical coordinates (using the function ''px_XYZ.m in UVMAT'').
    633633
    634  * <!ErrorMax> : maximum difference (in X and Y direction) between the image coordinates measured for the calibration points and the coordinates transformed from their physical coordinates. (using the function ''px_XYZ.m'' in UVMAT).
    635 
    636  * <!SourceCalib> set of the point coordinates used for calibration.
    637 
    638  * <!PointCoord> [x y z X Y] , where x,y,z are the physical coordinates of each point, X Y its image coordinates.
    639 
    640  * <!NbSlice_i> nbre of slices for the first field  index i (multilevel case), =1 by default.
    641 
    642  * <!NbSlice_j> nbre of slices for the second index j (volume scan), =1 by default.
    643 
    644  * <!SliceCoord> [x y z] positions (nb lines) of the nb planes, where nb=NbSlice_i (multilevel case) or nb=NbSlice_j of j indices (volume scan), for parallel volume scan, x=y=0, z= slice height, for angular scan, [x,y,z]=[origin].
    645 
    646  * <SliceDZ>   step distance between planes.
    647 
    648  * <SliceDPhi> step angle for angular scan.
     634 * <!ErrorMax>: maximum difference (in X and Y direction) between the image coordinates measured for the calibration points and the coordinates transformed from their physical coordinates (using the function ''px_XYZ.m'' in UVMAT).
     635
     636 * <!SourceCalib>: set of the point coordinates used for calibration.
     637
     638 * <!PointCoord>: [x y z X Y] , where x,y,z are the physical coordinates of each point, X Y its image coordinates.
     639
     640 * <!NbSlice_i>: nbre of slices for the first field  index i (multilevel case), =1 by default.
     641
     642 * <!NbSlice_j>: nbre of slices for the second index j (volume scan), =1 by default.
     643
     644 * <!SliceCoord>: [x y z] positions (nb lines) of the nb planes, where nb=[wiki:NbSlice !NbSlice]_i (multilevel case) or nb=[wiki:NbSlice !NbSlice]_j of j indices (volume scan), for parallel volume scan, x=y=0, z= slice height, for angular scan, [x,y,z]=[origin].
     645
     646 * <SliceDZ>:   step distance between planes.
     647
     648 * <SliceDPhi>: step angle for angular scan.
    649649
    650650== 9 - Masks and grids ==
    651651=== 9.1 Masks ===
    652 Mask files are used to restrict the domain of CIV processing, to take into account fluid boundaries or invalid image zones. They must be stored as .png images with 8 bits, as described in [section 3.6->#sec3.6_mask].  Mas files are automatically recognised by '''uvmat.fig''' and '''civ.fig''' if they are named [filebase '_xxmask_' 'filenumber' '.png'], where xx is the number of masks (nbslices) used when the series of fields corresponds physically to a set of nbslices positions. The mask filenumber used is the image field number modulo nbslices. Use xx=1 in the default case of a fixed position and a single mask. Masks can be made by pressing the menu bar Tools/make mask on the GUI UVMAT. The mask is created interactively with the mouse on the current image.
    653 
    654 First open an input image file name with the browser, or the edit box and carriadge return. From the image name, a corresponding mask name is proposed in the lower edit box. It should be edited if a series of masks is made, in case of mutipositions (number nbslices) of the laser sheet in a series. The names must be [filebase '_xxmask' 'filenumber' '.png'], where xx is the number of masks (nbslices). The mask filenumber used is the image field number modulo nbslices. The filenumber can be incremented by the NEXT press button.
     652Mask files are used to restrict the domain of CIV processing, to take into account fluid boundaries or invalid image zones. They must be stored as .png images with 8 bits, as described in [section 3.6->#sec3.6_mask].  Mask files are automatically recognised by '''uvmat.fig''' and '''civ.fig''' if they are named [filebase '_xxmask_' 'filenumber' '.png'], where xx is the number of masks (nbslices) used when the series of fields corresponds physically to a set of nbslices positions. The mask filenumber used is the image field number modulo nbslices. Use xx=1 in the default case of a fixed position and a single mask. Masks can be made by pressing the menu bar Tools/make mask on the GUI UVMAT. The mask is created interactively with the mouse on the current image.
     653
     654First open an input image file name with the browser, or the edit box and carriage return. From the image name, a corresponding mask name is proposed in the lower edit box. It should be edited if a series of masks is made, in case of mutipositions (number nbslices) of the laser sheet in a series. The names must be [filebase '_xxmask' 'filenumber' '.png'], where xx is the number of masks (nbslices). The mask filenumber used is the image field number modulo nbslices. The filenumber can be incremented by the NEXT press button.
    655655
    656656Holes can be made by the press button mask_hole which allows to draw a polygon on the image (the matlab image processing toolbox is needed). The inside of this polygone is masked.
    657657
    658658Press the red push button  save_mask which appeared on the lower right. The saved mask is then displayed. A new image can be then entered.
    659 
    660 [sec9.2<-]
    661659
    662660=== 9.2 Grids ===
     
    10661064 * 'peaklock';...%
    10671065 * 'phys_XYZ';...% transform coordinates from pixels to phys.
    1068  * 'px_XYZ';...% transform coordiantes from phys to pixels.
     1066 * 'px_XYZ';...% transform coordinates from phys to pixels.
    10691067 * 'read_civxdata';...reads CIVx data from NetCDF files.
    10701068 * 'read_civdata';... reads new civ data from NetCDF files.