| 158 | | Image series in uvmat are documented by a file providing image timing, geometric calibration, camera type and illumination. This file is in the format ''xml'', a hierarchically organised text file. The content is labelled by tags, represented by brackets <.>, whose names and organisation are specified by a schema file (.xsd). A general introduction to the xml language and schemas is provided for instance in http://www.w3schools.com/xml. The schema used for image documentation is ''!ImaDoc.xsd'', available in the uvmat package in a sub-directory ''/Schemas''. Simple templates of xml files are also provided there. |
| 159 | | |
| 160 | | When a new file series is opened in uvmat, the xml documentation file is automatically sought in the folder containing the data series folder: the documentation of the file series !RootPath/SubDir/RootFile_1,... is in the file !RootPath/RootFile.xml. As a second choice (corresponding to an earlier convention), the xml file will be sought inside the data series folder, as !RootPath/SubDir/RootFile.xml (if this file does not exist, a text file with the same root name but extension .civ is sought as an obsolete option). The detection of the image documentation 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. In uvmat, it is read by the function ''imadoc2struct.m''. |
| | 158 | Image series in uvmat are documented by a file providing image timing, geometric calibration, camera type and illumination. This file is in the format ''xml'', a hierarchically organised text file. The content is labelled by tags, represented by brackets <.>, whose names and organisation are specified by a schema file (.xsd). A general introduction to the xml language and schemas is provided for instance in http://www.w3schools.com/xml. The schema used for image documentation is ''!ImaDoc.xsd'', available in the uvmat package in a sub-directory ''/Schemas''. Simple templates of xml files are also provided there. |
| | 159 | |
| | 160 | When a new file series is opened in uvmat, the xml documentation file is automatically sought in the folder containing the data series folder: the documentation of the file series !RootPath/SubDir/RootFile_1,... is in the file !RootPath/RootFile.xml. As a second choice (corresponding to an earlier convention), the xml file will be sought inside the data series folder, as !RootPath/SubDir/RootFile.xml (if this file does not exist, a text file with the same root name but extension .civ is sought as an obsolete option). The detection of the image documentation 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. In uvmat, it is read by the function ''imadoc2struct.m''. |
| 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 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. |
| 220 | | |
| 221 | | Once created, this mirror campaign folder can be opened instead of the source. |
| 222 | | It can be regularly updated from the source folder by pressing the button 'update_mirror' in '''browse_data.fig'''. |
| | 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 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. |
| | 220 | |
| | 221 | Once created, this mirror campaign folder can be opened instead of the source. It can be regularly updated from the source folder by pressing the button 'update_mirror' in '''browse_data.fig'''. |
| 245 | | Scalars (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]'''. |
| 246 | | |
| 247 | | === 4.2 Vectors === |
| | 244 | === 4.2 Contour plots === |
| | 245 | Scalars (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. |
| | 246 | |
| | 247 | 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. '''''' |
| | 248 | |
| | 249 | === 4.3 Vectors === |
| 266 | | -'''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). |
| 268 | | * second line: the vector components |
| | 269 | -'''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 |
| | 270 | |
| | 271 | * fist line: the position coordinates ''x'', ''y'', ''z'' for 3D cases). |
| | 272 | * second line: the vector components |
| 349 | | * (optional) '''!! |
| 350 | | * (mandatory) '''!! |
| 351 | | * (mandatory) '''!! |
| 352 | | * (optional) '''!! |
| | 353 | * (optional) '''!!!ListGlobalAttribute:''' list (cell array of character strings) of the names of global attributes Att_1, Att_2... |
| | 354 | * (mandatory) '''!!!ListVarName:''' list of the variable names Var_1, Var_2....(cell array of character strings). |
| | 355 | * (mandatory) '''!!!VarDimName:''' list of the dimensions associated with each variable: this is a cell array whose number of element is equal to that of '''ListVarName'''. Each element is the dimension name for a unidimensional variable, or a cell array specifying the list of dimension names for a multidimensional variable. |
| | 356 | * (optional) '''!!!VarAttribute:''' cell array of structures of the form !VarAttribute{ivar}.key=value, defining an attribute tag name and value for the variable #ivar (variable number in the list !ListVarName]). |
| 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 . For calibration performed inside water, the option of introducing the ''z'' position of water upper surface is provided. |
| | 598 | -'''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 . For calibration performed inside water, the option of introducing the ''z'' position of water upper surface is provided. |
| 599 | | -'''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 ''z''=0, 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 multiplane scan). The chosen option can be doucumented in the file <ImaDoc> by the menu bar command '''[Tools/set planes]''' of '''geometry_calib.fig'''. A dialog box appears for entering the set of section plane positions ''z'', as lower value, upper value and increment. Similarly an angular scan be be introduced. After introduction of the multi-plane information, the z-index is displayed in the frame '''[FileIndices]''' of '''uvmat.fig'''. The local z position of the mouse pointer, assuemed to lay on the current section plane, is then displayed in '''[text_display]'''. |
| | 602 | -'''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 ''z''=0, 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 multiplane scan). The chosen option can be doucumented in the file <ImaDoc> by the menu bar command '''[Tools/set planes]''' of '''geometry_calib.fig'''. A dialog box appears for entering the set of section plane positions ''z'', as lower value, upper value and increment. Similarly an angular scan be be introduced. After introduction of the multi-plane information, the z-index is displayed in the frame '''[FileIndices]''' of '''uvmat.fig'''. The local z position of the mouse pointer, assuemed to lay on the current section plane, is then displayed in '''[text_display]'''. |
| 614 | | * {{{<Tx_Ty_Tz>}}}: translation, (Tz=1 for the options calib_lin and calib_rescale) |
| 615 | | |
| 616 | | * {{{<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''. |
| | 617 | * `<Tx_Ty_Tz>`: translation, (Tz=1 for the options calib_lin and calib_rescale) |
| | 618 | |
| | 619 | * `<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''. |
