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Changes between Version 73 and Version 74 of UvmatHelp

Timestamp:: Jun 27, 2013, 10:44:43 AM (11 years ago)
Author:: sommeria
Comment:: --

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UvmatHelp

-                      v73
+                      v74
 UVMAT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See theGNU General Public License (file {COPYING.txt}) for more details.
 -------
+----
 == 2 - Overview of the GUI uvmat.fig ==
 === 2.1 Opening the GUI ===
 …
  * '''[Help] ''': displays this help file using the Matlab browser.
-<doc58|center>
 === 2.3 Displaying the input file name ===
 After selection by the browser, the path and file names are determined. The path is split into the two first edit boxes '''[!RootPath]''' and '''[!SubDir],''' while the file name is split into a root name '''[!RootFile]''', file index string '''[!FileIndex]''', and file extension '''[!FileExt]'''. The input file name can be directly entered and modified in these edit boxes, without the browser.
 …
  * '''Extracting data''' as Matlab arrays. Information stored in the GUI uvmat  (as ''!UserData'' in the figure) can be extracted in the Matlab work space by the menu bar command  '''[Export/field in workspace]''' (or by pressing the right mouse button on the GUI). Type '>>Data_uvmat.Field' to get the current input field as a Matlab structure. An image or scalar matrix is for instance obtained as Data_uvmat.Field.A.
+--------------------
+[[Image(help_coordiantes_titres.jpg)]]
+----
 == 3 - Input files and navigation with uvmat ==
 === 3.1  Input data formats ===
 …
 '''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'.
+----------------------------
+----
 == 4 - Scalar and vector display ==
 The uvmat interface primarily reads and visualises two-dimensional fields, which can be images or scalars, or vector fields.
 …
 True color images are described by a matrix A(npy,npx,3) of integers between 0 and 255, the last index labeling the color component red, green or blue. They are displayed directly as color images.
+<doc64|center>
+[[Image(help_scalar_titres.jpg)]]
 The greyscale images are described by a matrix A(npy,npx) of integers, whose range depends on the camera dynamics (0 to 255 for 8 bit images, 0 to 65535 for 16 bit images). They are represented with gray levels, according to the colorbar displayed on the right. The luminosity and contrast can be adjusted using the edit boxes '''[num_MinA]''' and '''[num_MaxA]''' on the right of the interface: the luminosity level set by '''[num_MinA]''' (and levels below) is represented as black, and the luminosity level set by '''[num_MaxA]''' (or levels above) as white. When the check box '''[!CheckFixScalar]''' is not selected, these bounds are set automatically to the image minimum and maximum respectively. Then the image may appear dark if a single point is very bright, in that case a lower value must be set by '''[num_MaxA]'''. Greyscale images can be displayed with false colors, from blue to red, by unselecting the check box '''[CheckBW]'''.
 …
 Each 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.
+<doc63|center>
+[[Image(help_vectors_titres.jpg)]]
 -'''Warning flags''': they indicate a vector resulting from a dubious  image correlation process, but not removed from the data set. Their display in black can be desactivated by selecting the check box '''[!CheckHideWarning]'''.
 …
 -'''Plotting:''' plot the results of projection, using the function ''plot_field.m''.
+----------------------------
+----
 == 5 - Field structures ==
 === 5.1 Griding of data ===
 …
 In summary, the ''field structure'' is specified by the following elements:
  * (optional) '''ListGlobalAttribute:''' list (cell array of character strings) of the names of global attributes  Att_1, Att_2...
  * (mandatory) '''ListVarName:''' list of the variable names Var_1, Var_2....(cell array of character strings).
  * (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.
  * (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]).
+ * (optional) '''!ListGlobalAttribute:''' list (cell array of character strings) of the names of global attributes  Att_1, Att_2...
+ * (mandatory) '''!ListVarName:''' list of the variable names Var_1, Var_2....(cell array of character strings).
+ * (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.
+ * (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]).
  * .Att_1, Att_2... : values of the listed global attributes.
  * .Var_1, .Var_2...: variables arrays whose names are listed in !ListVarName.
 …
 In some cases, it is useful to define the field object independently from its data content. Then the variables .Var1... are replaced by the lists of dimension names and values.
  * '''ListDimName:''' list of dimension names (cell array of character strings)
  * '''DimValue:''' array of dimension values corresponding to !LisDimName.
+ * '''!ListDimName:''' list of dimension names (cell array of character strings)
+ * '''!DimValue:''' array of dimension values corresponding to !LisDimName.
 The following temporary information is added to manage projection and field substraction oerations, which must be done in general after projection:
 …
  * 'nb_tps': dimension of the index for the tps centres
  * 'nb_subdomain' denotes the dimension for the subdomain index for tps coefficients
+----------------------------
+----
 == 6 - Projection objects == #ProjObject
 === 6.1 Definition and editing with the uvmat interface ===
 These are geometrical objects used to define cuts along lines or planes, to interpolate fields on a regular grid, to restrict the analysis or visualisation to field subregions. The projection of fields on objects is performed by the function ''proj_field.m'', which can be used as well in data processing outside the GUI '''uvmat''', using for instance [#a10-Processingfieldseries series.fig]).
+These are geometrical objects used to define cuts along lines or planes, to interpolate fields on a regular grid, to restrict the analysis or visualisation to field subregions. The projection of fields on objects is performed by the function ''proj_field.m'', which can be used as well in data processing outside the GUI '''uvmat''', using for instance [#a10-Processingfieldseries series.fig]).
 When 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'''.
 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]'''.
 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.ProjObject''.
+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]'''.
+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]''.
 === 6.2 Object properties ===
 …
 === 6.4 Object representation ===
  * 'points' are represented by dots surrounded by a dashed circle showing the range of projection.
  * 'line' , 'polyline' are plotted as lines, surrounded by two dashed lines showing the range of projection, when applicable (i.e. not in the case !ProjMode='interp...').
 …
 Object can be interactively drawn with the mouse on the GUI '''uvmat.fig ''' . First activate the creation mode by selecting the appropriate item in the menu bar Tools, and possibly adjust parameters on the GUI '''set_object.fig'''. Then mark the set of point coordinates by pressing (then release) the left mouse button. Those appear in the table '''[Coord]''' of '''set_object.fig'''. For 'polyline' or 'polygon', press the right hand mouse button to end the line. 'Plane' and 'volume' cannot be created or modified with the mouse.
 In edit mode, the position of each defining point can be adjusted with the mouse: press the left button and maintain it to drag the point. The object can be similarly translated by selecting a defining line.
 -----------------
+In edit mode, the position of each defining point can be adjusted with the mouse: press the left button and maintain it to drag the point. The object can be similarly translated by selecting a defining line.
+----
 == 7 - Netcdf files and the GUI get_field ==
 === 7.1 The NetCDF format ===
 …
 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.
+----------------------------
+----
 == 8 - Geometric calibration ==
 === 8.1 Generalities ===
 …
 -''' Plotting calibration points: ''' press the menu bar command button '''[Plot] ''' to visualise the list of calibration points. The physical or image coordinates will be used in the list '''[!ListCoord]''', depending on the option 'phys' or 'px' in the menu '''[transform_fct]''' of ''' uvmat.fig''' .
 -''' Appending  calibration points with the mouse: ''' Calibration points can be manually picked out by the mouse (left button click) after a calibration image has been opened by '''uvmat.fig''' (with the option 'blank' in the popup menu '''[transform_fct]'''), and the option '''[mouse_active]''' (at the very bottom) has been selected. 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). The coordinates in pixel of the selected points get listed in the box '''[!ListCoord]''' of '''geometry_calib.fig'''. A calibration point can be later adjusted by selecting it with the mouse and moving it while pressing the left mouse button. Points can be accumulated from several images (use the key board short cuts 'p' and 'm' to move in the image series without monopolising the mouse).''
+-''' Appending  calibration points with the mouse: ''' Calibration points can be manually picked out by the mouse (left button click) after a calibration image has been opened by '''uvmat.fig''' (with the option 'blank' in the popup menu '''[transform_fct]'''), and the option '''[mouse_active]''' (at the very bottom) has been selected. 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). The coordinates in pixel of the selected points get listed in the box '''[!ListCoord]''' of '''geometry_calib.fig'''. A calibration point can be later adjusted by selecting it with the mouse and moving it while pressing the left mouse button. Points can be accumulated from several images (use the key board short cuts 'p' and 'm' to move in the image series without monopolising the mouse).''''
 -''' Editing the  coordinates: '''
 …
 The grid will be limited to an  image , or to the common region of two images, depending whether one or two image names are indicated in the edit boxes image_1 and image_2. Press save to save the corresponding grid file (s). A dialog box appears to edit the name of the output grid file, and a second one in case of two images.
+----------------------------
+----
 == 10 - Processing field series ==
 === 10.1 The GUI series.fig ===
 …
 By selecting the press button 'peaklocking' on the 'plotgraph' interface, you smooth the current velocity histograms while preserving its integral over each unity (in pixels). This appears in red. Then an estimate of the peaklocking error is obtained by comparing the initial histogram to the smooth one.
+----------------------------
+----
 == 11 - PIV: Particle Imaging Velocimetry ==
 === 11.1 Overview ===
 PIV can be performed by selecting the Matlab function ''civ_series'' as '''[!ActionName]''' in the GUI '''series.fig''': then the '''GUI civ_input''' appears to enter the processing parameters. An image file series must have been entered as input of '''series.fig''', or alternatively a Netcdf file resulting form a previous PIV processing (with conventions 'civdata').
+An alternative possibility is to use the older Fortran program ''CivX'' from the GUI '''civ.fig'''. This can be called directly on the Matlab prompt, by typing  ''>>civ'', or from uvmat by the menu bar command '''[RUN/PIV (old civ)]'''.
+'''-Modes of frame pair indexing'''
+A first menu '''[ListCompareMode]''' selects one among four modes of operation:
+An alternative possibility is to use the older Fortran program ''CivX'' from the GUI '''civ.fig'''. This can be called directly on the Matlab prompt, by typing  ''>>civ'', or from uvmat by the menu bar command '''[RUN/PIV (old civ)]'''.    '''-Modes of frame pair indexing''' A first menu '''[ListCompareMode]''' selects one among four modes of operation:
  * '''PIV''': makes image comparisons on sliding index pairs, as usual for measuring velocities by particle displacements. A second menu '''[ListPairMode]''' in the panel '''[PairIndices]''' then selects one among three possibilities (not always available depending on the file indexing):
    * ''pair j1-j2:'' selects a given j index pair (sometimes denoted by letter index) for the whole time series. This is the most common case for PIV. Pair selection is performed in the menu '''[ListPairCiv1]''' and '''[ListPairCiv2]''' for the second iteration Civ2, see below. If timing from an xml file [#a3.5Imagedocumentationfiles.xml ImaDoc] has been detected, this is indicated in the edit box '''[ImaDoc]''' and the corresponding time intervals are indicated (in ms). For some applications, this time interval may evolve in time, so that reference indices ref_i and ref_j are chosen for the display.
+   * ''pair j1-j2:'' selects a given j index pair (sometimes denoted by letter index) for the whole time series. This is the most common case for PIV. Pair selection is performed in the menu '''[ListPairCiv1]''' and '''[ListPairCiv2]''' for the second iteration Civ2, see below. If timing from an xml file [#a3.5Imagedocumentationfiles.xml ImaDoc] has been detected, this is indicated in the edit box '''[ImaDoc]''' and the corresponding time intervals are indicated (in ms). For some applications, this time interval may evolve in time, so that reference indices ref_i and ref_j are chosen for the display.
    * series (Di): selects a given  index interval for the i index, around a set of reference i indices. The intervals are denoted Di=0|1, -1|1, -1|2, -2|2 ... , corresponding to the index pairs i|i+1, i-1|i+1, i-1|i+2, i-2|i+2 ...around each reference index i. Pair selection is then performed in the menu '''[ListPairCiv1]''' and '''[ListPairCiv2]''' like for 'pair j1-j2'.
    * series (Dj): same as series (Di) but with the j index.
+   * series (Dj): same as series (Di) but with the j index.
  * '''displacement''': compare the current image to a fixed reference frame, as needed to measure the displacement with respect to this reference. The reference index (i index) is set by an edit box '''[num_OriginIndex]'''.
  * '''shift''': compares the corresponding images in two separate series, as need for stereographic views. The opening of a second file series is proposed by a browser when this option is selected.
 …
 -''' Succession of operations: '''
+The CIV process involves a succession of iterative operations:
+ * civ1: the initial image correlation process.
+ * fix1: detection of 'false' velocity vectors according to different criteria.
+ * patch1: interpolation and filtering on a regular grid, providing access to spatial derivatives of the velocity (diverrgence, curl, strain).
+ * civ2: advanced image correlation algorithm using the result of civ1 as a first approximation.
+ * fix2 and patch2: similar as fix1 and patch1, but applied to the civ2 results.
+The CIV process involves a succession of iterative operations:
+ * civ1: the initial image correlation process.
+ * fix1: detection of 'false' velocity vectors according to different criteria.
+ * patch1: interpolation and filtering on a regular grid, providing access to spatial derivatives of the velocity (diverrgence, curl, strain).
+ * civ2: advanced image correlation algorithm using the result of civ1 as a first approximation.
+ * fix2 and patch2: similar as fix1 and patch1, but applied to the civ2 results.
 This series of operations is chosen by selecting the corresponding  check boxes on the left of the GUI '''civ_series''', which give access to the corresponding parameter input panels. Note that the result of each of these operations is stored in the output netcdf file, so the process can be split in several runs. When an existing netcdf velocity file has been initially opened, the GUI '''civ.fig''' is automaticaly configured to perform the next operation (fix1, patch1, civ2...) needed in the process.
 …
 The time interval of the image pair (selected by '''[ListPairCiv1]''', see above) must be chosen sufficiently small to provide a good image correlation, and sufficiently large to provide good measurement precision: a displacement of 5-10 pixels is generally optimum.
  Examples of xml files are provides in /XML_SCHEMAS/ImaDoc_templates.
+  Examples of xml files are provides in /XML_SCHEMAS/ImaDoc_templates.
 ('''[num_CorrBoxSize_1,_2,_3], [iby])''' set the size (in pixels) of the 'correlation box', the sliding window used to get image correlations. '''[num_SearchBoxSize_1,_2,_3]''' set the size of the 'search box' in which image correlation is calculated, see figure.  This search box can be shifted with respect to the correlation box by parameters  ([num_SearchBoxShift_1,_2,_3]). This is useful in the presence of a known mean flow. The default value SearchBoxSize=(25,25) is generally good, use a larger size for images with few particles, use an elongated box , e.g. (11,41), to optimise the resolution in one direction (for instance in a boundary layer).
 …
 Conventions 'uvmat/civdata'.
+||  '''tag''' ||  '''        content'''  ||
+||     Civ1_X|| x coordinates||
+|| Civ1_Y || y coordinates||
+||  Civ1_Z || z coordinates (for PIV in volume)||
+||  Civ1_U || x velocity component||
+|| Civ1_V || y velocity component ||
+||  Civ1_W|| z velocity component (if relevant)||
+||   Civ1_F|| warning flag||
+|| Civ1_C|| image correlation||
+||              Civ1_FF|| error flag||
+||                Civ1_U_smooth|| smoothed x velocity component||
+||               Civ1_V_smooth || smoothed y velocity component||
+||             Civ1_W_smooth || smoothed z velocity component ||
+||          Civ1_SubRange || sub range bounds||
+||          Civ1_NbSites || nbre of tps sites in each sub-range||
+||               Civ1_Coord_tps || tps coordinates ||
+||              Civ1_U_tps || tps weights for x vel component ||
+||              Civ1_V_tps || tps weights for y vel component ||
+||             Civ1_W_tps|| tps weights for z vel component||
+-'''List of constants, old CIVx conventions):'''
+ * nb_coord: =2 for PIV in a plane, =3 for PIV in a volume.
+ * nb_dim: =2 for the usual 2 component PIV, =3 for 3 component PIV (stereoscopic or volume).
+ * constant_pixcm: =1 for a simple linear calibration provided by the scaling factors pixcmx and pixcmy, =0 otherwise.
+ * pixcmx: scale pixel/space unit (cm by default) along the x direction (only if constant_pixcm=1).
+ * pixcmy: scale pixel/space unit (cm by default) along the y direction (only if constant_pixcm=1)
+ * absolut_time_T0: time elapsed since the time origin of the series (the mean time for the two images of the pair is taken).
+ * dt: time interval between the two images of the pair.
+ * absolut_time_T0_2: same as absolute_time_T0 for the fields obtained by the second iteration (civ2), using a possibly different image pair.
+ * dt2: same as dt for the fields obtained by the second iteration (civ2).
+ * hart: =1 if the Hart option has been used for processing (see ref.???), =0 otherwise.
+ * civ: =1 if a civ1 operation has been performed (=0 if the field is not obtained from an image pair)
+ * fix: =1 if a fix1 operation has been performed,
+ * patch: =1 if a patch1 operation has been performed.
+ * civ2: =1 if a civ2 operation has been performed.
+ * fix2:=1 if a fix2 operation has been performed.
+ * patch2: =1 if a Patch2 operation has been performed.
+ * patch_nx: number of grid points in the x direction for the patch field
+ * patch_ny: number of grid points in the y direction for the patch field
+ * ro_patch: smoothing coefficient rho used for patch
+ * patch2_nx: number of grid points in the x direction for the patch2 field
+ * patch2_ny: number of grid points in the y direction for the patch2 field
+||'''tag'''||'''        content'''||
+||Civ1_X||x coordinates||
+||Civ1_Y||y coordinates||
+||Civ1_Z||z coordinates (for PIV in volume)||
+||Civ1_U||x velocity component||
+||Civ1_V||y velocity component||
+||Civ1_W||z velocity component (if relevant)||
+||Civ1_F||warning flag||
+||Civ1_C||image correlation||
+||Civ1_FF||error flag||
+||Civ1_U_smooth||smoothed x velocity component||
+||Civ1_V_smooth||smoothed y velocity component||
+||Civ1_W_smooth||smoothed z velocity component||
+||Civ1_SubRange||sub range bounds||
+||Civ1_NbSites||nbre of tps sites in each sub-range||
+||Civ1_Coord_tps||tps coordinates||
+||Civ1_U_tps||tps weights for x vel component||
+||Civ1_V_tps||tps weights for y vel component||
+||Civ1_W_tps||tps weights for z vel component||
+-'''List of constants, old CIVx conventions):'''
+ * nb_coord: =2 for PIV in a plane, =3 for PIV in a volume.
+ * nb_dim: =2 for the usual 2 component PIV, =3 for 3 component PIV (stereoscopic or volume).
+ * constant_pixcm: =1 for a simple linear calibration provided by the scaling factors pixcmx and pixcmy, =0 otherwise.
+ * pixcmx: scale pixel/space unit (cm by default) along the x direction (only if constant_pixcm=1).
+ * pixcmy: scale pixel/space unit (cm by default) along the y direction (only if constant_pixcm=1)
+ * absolut_time_T0: time elapsed since the time origin of the series (the mean time for the two images of the pair is taken).
+ * dt: time interval between the two images of the pair.
+ * absolut_time_T0_2: same as absolute_time_T0 for the fields obtained by the second iteration (civ2), using a possibly different image pair.
+ * dt2: same as dt for the fields obtained by the second iteration (civ2).
+ * hart: =1 if the Hart option has been used for processing (see ref.???), =0 otherwise.
+ * civ: =1 if a civ1 operation has been performed (=0 if the field is not obtained from an image pair)
+ * fix: =1 if a fix1 operation has been performed,
+ * patch: =1 if a patch1 operation has been performed.
+ * civ2: =1 if a civ2 operation has been performed.
+ * fix2:=1 if a fix2 operation has been performed.
+ * patch2: =1 if a Patch2 operation has been performed.
+ * patch_nx: number of grid points in the x direction for the patch field
+ * patch_ny: number of grid points in the y direction for the patch field
+ * ro_patch: smoothing coefficient rho used for patch
+ * patch2_nx: number of grid points in the x direction for the patch2 field
+ * patch2_ny: number of grid points in the y direction for the patch2 field
  * ro2_patch: smoothing coefficient rho used for patch2
 …
 -*Names of field variables for civ1 and patch1
 ||  '''   ||     civ1'''          || '''interp1'''  ||        '''filter1 '''
 || dim.  ||        nb_vectors  ||        nb_vec_patch  ||        nb_vec_patch
 ||x   ||vec_X          ||vec_patch_X  ||        vec_patch_X ||
 || y          ||         vec_Y  ||        vec_patch_Y ||         vec_patch_Y ||
 ||z          ||        vec_Z ||         vec_patch_Z  ||        vec_patch_Z ||
 ||u                  ||vec_U ||         vec_patch0_U  ||        vec_patch_U ||
 ||v                   ||vec_V          ||vec_patch0_V  ||        vec_patch_V ||
 ||w           ||       vec_W          || vec_patch0_W||          vec_patch_W ||
 ||correlation  ||        vec_C  ||          ||          ||
 ||warning flag  ||        vec_F ||          ||          ||
 ||false flag  ||        vec_FixFlag ||          ||    ||
 ||du/dx  ||         ||vec_patch0_DUDX          ||vec_patch_DUDX          ||
 ||du/dy  ||         ||vec_patch0_DUDY          ||vec_patch_DUDY          ||
 ||dv/dx  ||         ||vec_patch0_DVDX          ||vec_patch_DVDX          ||
 ||dv/dy  ||         ||vec_patch0_DVDY          ||vec_patch_DVDY          ||
+||'''   '''||civ1||'''interp1'''||'''filter1 '''||
+||dim.||nb_vectors||nb_vec_patch||nb_vec_patch||
+||x||vec_X||vec_patch_X||vec_patch_X||
+||y||vec_Y||vec_patch_Y||vec_patch_Y||
+||z||vec_Z||vec_patch_Z||vec_patch_Z||
+||u||vec_U||vec_patch0_U||vec_patch_U||
+||v||vec_V||vec_patch0_V||vec_patch_V||
+||w||vec_W||vec_patch0_W||vec_patch_W||
+||correlation||vec_C||||||
+||warning flag||vec_F||||||
+||false flag||vec_FixFlag||||||
+||du/dx||||vec_patch0_DUDX||vec_patch_DUDX||
+||du/dy||||vec_patch0_DUDY||vec_patch_DUDY||
+||dv/dx||||vec_patch0_DVDX||vec_patch_DVDX||
+||dv/dy||||vec_patch0_DVDY||vec_patch_DVDY||
 -*Names of field variables for civ2 and patch2
 …
 same as previous, replacing 'vec' by 'vec2'.
 ---------------
+----
 == 12 - Tridimensional features:(to update **) ==
 === 12-1 Multilevel image scanning ===
 …
 === 12-3 3D3C PIV ** ===
 This is performed by the GUI '''civ_3D.fig'''. The program requires input volume images .vol. These are images in the  png format, where  npz slices are concatenated along the y direction, forming a composite image of dimension (npy x npz, npx) from the images (npy x npx). These volume images can be created by the function {ima2vol.m} in {/series}.
+----------------------------
+----
 == 13 - Editing xml files with the GUI editxml ==
   This GUI '''editxml.fig''' visualises and edits xml files. It is automatically called by the browser of '''uvmat.fig''' when a file with extension .xml is opened.
 …
   Manual editing of element value is possible. Select the element and use the lower edit box. This edit box transforms in a menu when a preselected list of allowed input values has been set by the schema.
+----------------------------
+----
 == 14 - Appendix: overview of the package functions ==
 === Master GUI ===