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Changes between Version 48 and Version 49 of UvmatHelp

Timestamp:: Jun 6, 2013, 10:59:50 PM (11 years ago)
Author:: sommeria
Comment:: --

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UvmatHelp

-                      v48
+                      v49
 == 10 - Processing field series ==
 === 10.1 The GUI series.fig ===
 Operations on field series are controled by the GUI '''series.fig''', which allows the user to set the root name(s) and file indices over which a processing function operates. The root path, subdirectory, root file name and extension are introduced in the different columns of the table '''!InputTable'''. The nomenclature for file indexing is represented in the column '''[!NomType]'''.
+Operations on field series are controled by the GUI '''series.fig''', which allows the user to set the root name(s) and file indices over which a processing function operates. The root path, subdirectory, root file name and extension are introduced in the different columns of the table '''[!InputTable]'''. The nomenclature for file indexing is represented in the column '''[!NomType]''', the index extension for the first file in the series.
 Several input file series can be introduced simultaneously by the menu bar command''' [Open_append]''', filling the successive lines of '''!InputTable'''. By contrast, the table of input files is fully refreshed by the browser of the menu bar command '''[Open]'''. The cells in the table can be also edited manually. Then press the button '''[REFRESH]''' to validate the input.
+The velocity type and field are automatioally chosen by default, but can be specified by the menus '''[VelType]''' and '''[Field]'''. For that purpose use the menus VelTypeMenu and fieldsinput. In case of multiple input file series, these menus act only on the first line.
+The processing function is chosen in the menu '''[!ActionName]'''.  All actions operate on the same series of input files, whose list can be obtained with the first option 'check_data_files'. The option 'aver_stat' calculates  a global average on the successive fields, while 'time_series' provides a time series. The option 'merge_proj' is used to project a whole series on a given grid, or to create a file series by concatenation of different fields. The option civ_series gives acees to the PIV processsing, see section [#a11-PIV:ParticleImagingVelocimetry section 11]. Finally any additional function can be called and included in the menu by selecting the option 'more...' . The corresponding path is displayed in '''!ActionPath'''.
+Each function in series can be run in local mode, i;e. on the current Matlab session, or as background, by selecting the corresponding option in '''!RunMode'''. In background mode, calculation is done a new Matlab session (without graphics) so that the current Matlab session is free for new operations. If a cluster system has been detected, a third option 'cluster' appears in the menu, allowing to dispatch parallel computations on a computer cluster. For the latter option, a compiled version of the Action function is useful, to avoid installing Matlab on each node of the cluster. This is achieved by selecting the option .sh in the menu '''ActionExt'''. If the compiled version is not yet available, or outdated, the GUI proposes a new compilation of the selected function.
+The series of file indices is set in the frame '''[!IndexRange]'''. Any action is performed from field index '''[num_first_i] ''' to '''[num_last_i] '''  with increment '''[num_incr_i]''' . In case of double indexing, action is similarly performed from field index''' [num_first_j]''' to '''[num_last_j]''' with increment '''[num_incr_j]'''. Succesive file names are ordered as a matrix {j,i} with the index j varying the fastest. The box '''num_NbSlice''' can be introduced to scan the i index modulo NbSlice.
+For pair indexing, the selected pair must be chosen in the menu list_pair-civ in the frame PAIRS (browse again an input field if this menu does not appear). Then the first_i and last_i refer to the 'reference indices'. With the option '*-*' in '''[list_pair_civ]''', available pairs are automatically chosen (this is appropriate if several image pairs are used in a time series, to account for a changing mean velocity).
+A transform function can be introduced. A projection object can be introduced by selecting the check box '''[CheckObject]'''. If a projection object has been already created the  opened interface '''set_object.fig''' will be used. Otherwise a browser appears to open an object file (xml). Similarly the check box '''[CheckMask]''' can be used to select a mask option.
+=== 10.2 check_files ===
+The processing function is chosen in the menu '''[!ActionName]'''. The first option ''check_data_files'' lists the selected input file series and checks their existence. This is a good first test before starting a processing operation since all actions operate on the same input file series. The option ''aver_stat'' calculates  a global average on the successive fields, while ''time_series'' provides a time series. The option ''merge_proj'' is used to project a whole series on a given grid, or to create a file series by concatenation of different fields. These processing functions are described with more details in next sub-sections. The option ''civ_series'' gives access to the PIV processsing, see section [#a11PIV:ParticleImagingVelocimetry section 11].  Finally any additional function can be called and included in the menu by selecting the option ''more...'' . The corresponding path is displayed in '''!ActionPath'''.
+The action function is first activated when it is selected in the menu '''[ActionName]'''. This first activation checks input data and sets the visibility of input GUI uicontrols.
+The actual start of the processing is triggered by pressing the button '''[RUN]'''. It can be run in local mode, i.e. on the current Matlab session, or as ''background'', by selecting this option in '''!RunMode'''. In mode ''background'', calculation is performed in a new Matlab session (without graphics) so that the current Matlab session is free for new operations. If a cluster system has been detected, a third option ''cluster'' appears in the menu, allowing to dispatch parallel computations on a computer cluster. For the latter option, a compiled version of the action function is useful, to avoid installing Matlab on each node of the cluster. This is achieved by selecting the option ''.sh'' in the menu '''!ActionExt'''. If the compiled version is not yet available, or outdated, the GUI proposes a new compilation of the selected function (launching the function ''compile.m'').
+The series of file indices is set in the frame '''[!IndexRange]'''. Any action is performed from field index '''[num_first_i]''' to '''[num_last_i] ''' with increment '''[num_incr_i]''' . If this increment is empty (or not an integer number), operation is performed on all available files between ''first_i'' and ''last_i''. In case of double indexing, action is similarly performed from field index''' [num_first_j]''' to '''[num_last_j]''' with increment '''[num_incr_j]'''. Succesive file names are ordered as a matrix {j,i} with the index j varying the fastest. The box '''num_NbSlice''' can be introduced to scan the ''i'' index modulo !NbSlice.
+When input files are indexed by pairs i1-i2 or j1-j2, as resulting from PIV, the pair indexing is chosen by the panel '''[Set Pairs]'''. The popup menu [mode] provides the choice between 'bursts', 'Di','Dj'. In mode 'bursts' a single j index pair is selected in the menu '''[ListPairs]'''. In mode 'Di' and 'Dj' it selects a given index interval in i or j respectively. Then the first_i and last_i refer to the ''reference indices''. With the option '*-*' in '''[!ListPairs]''', available pairs are automatically chosen. In case of multiple input lines, the selection from '''[Set pairs]''' refers to the line number displayed in [ListView]. It is  transfered to the corresponding line in the table '''[PairString]'''.
+The velocity type and field are automatioally chosen by default, but can be specified by the menus '''[VelType]''' and '''[FieldName]'''. In case of multiple input file series, these menus only refer to the first line. Then the menus '''[VelType_1]''' and '''[FieldName_1]''' refer to the second line, consistently with the input for the GUI '''uvmat'''.
+A transform function can be introduced by the menu '''[!TransformName]'''. A projection object can be introduced by selecting the check box '''[!CheckObject]'''. If a projection object has been already created the  opened interface '''set_object.fig''' will be used. Otherwise a browser appears to open an object file (xml). Similarly the check box '''[!CheckMask]''' can be used to select a mask option. These different menus only appear if they are needed as input of the currently selected action function.
+=== 10.2 check_data_files ===
 Gives the series of files selected for processing and checks their existence. The oldest modified file is indicated, which is useful to detect whether any file in a civ processing is missing (then the oldest file is not updated).
 …
 === 10.3 aver_stat: ===
 This option provides any average over the processed files. If nb_slice is not equal to 1, the average is performed slice by slice, providing nb_slice results.   If a projection object is selected (check box GetObject), the field is projected before averaging.
 For unstructured coordinates varying for successive fields, the data is linearly interpolated on the coordinates of the first field in the series. It is then advised to project the fields on a regular grid, creating a projection object of type 'plane' with projection mode 'interp'.
 With a projection object with title PATCH, the global histogram of field variables on the selected region will be obtained.
 In the case of two input files series, the field difference will be perfomed like with the interface uvmat.fig. It is not possible to use more than two input series for this funtion.
+This option provides any average over the processed files. If nb_slice is not equal to 1, the average is performed slice by slice, providing nb_slice results.   If a projection object is selected (check box '''[CheckObject]'''), the field is projected before averaging.
+For unstructured coordinates varying for successive fields, the data is linearly interpolated on the coordinates of the first field in the series. It is then advised to project the fields on a regular grid, creating a projection object of type 'plane' with projection mode 'interp_lin' or 'interp_tps'.
+With a projection mode 'inside' or 'outside', the global histogram of field variables on the selected region will be obtained.
+In the case of two input files series, the field difference will be perfomed like with the interface '''uvmat.fig'''. It is not possible to use more than two input series for this funtion.
 === 10.4 time_series ===
 This action provides a time series of the input field. It is advised to use a POINTS projection object, so the series is limited to the selected points.
 In the case of two input files series, the field difference will be perfomed like with the interface uvmat.fig. It is not possible to use more than two input series for this funtion.
+In the case of two input files series, the field difference will be perfomed like with the interface '''uvmat.fig'''. It is not possible to use more than two input series for this funtion.
 === 10.5 merge_proj ===
 This option allows to merge several field series  in a single one. This is useful to merge fields obtained with different cameras. Select the different series, activating the check box add. In this case, it is generally useful to first interpolate the fields on a single grid. For that purpose select the check box GetObject, creating a projection object of type 'plane' with projection mode 'interp'.
+This option allows to merge several field series in a single one. This is useful to merge fields obtained with different cameras. Select the different series, activating the check box add. In this case, it is generally useful to first interpolate the fields on a single grid. For that purpose select the check box GetObject, creating a projection object of type 'plane' with projection mode 'interp'.
 Since the different views have their own calibration, it is important to use the option 'phys' (menu menu_coord), and to create the grid in phys coordinates.
 …
 This action calls any user defined function by its name, acting on the series of fields defiend for ACTION. Some examples of usr_defined functions are in the subdirectory {/series}.
+-List of available functions: -*{sub_background.m}: used to removed a mean background to the images. This is useful before CIV processing when some fiked features are visible in the background (when the laser sheet is close to the bottom). -*{ima2vol.m:} produce volume images for 3D3C PIV.
+-List of available functions:
+ * ''sub_background.m'': used to removed a mean background to the images. This is useful before CIV processing when some fiked features are visible in the background (when the laser sheet is close to the bottom).
+ * ''ima_levels.m''
+ * ''ima2vol.m'' produce volume images for 3D3C PIV.
 To update (**): -uvprofile: calculate the mean velocity profile and Reynolds stress u'v' along a band, averaged over the series of fields. -view_ima3D: provides a perspective view of a 3D image defined by a series of slice 2D images. The isosurfaces of the scalar field are represented. -part_stat: count particles and provides their density and luminosity histogramm Peaklocking errors:(to update **)
 …
 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 - PIV: Particle Imaging Velocimetry ==
 === 11.1 Overview ===
 …
 Make a careful geometric calibration, by taking the images of a grid positioned in the plane of the laser sheet used for particle illumination. Introduce a Tsai calibration with the calibration tool associated with the  image acquisition software Acquix. Calibration can be adjusted with the uvmat interface (see calibration).
   This calibration model is valid in air or with an interface air-water perpendicular to the line of sight for each camera. Otherwise, the calibration problem is more complex.
+This calibration model is valid in air or with an interface air-water perpendicular to the line of sight for each camera. Otherwise, the calibration problem is more complex.
 Perform usual PIV for each image series:
   The images from each camera (camA and camB) must be in the same directory and the PIV results in a single subdirectory. It is advised to do the successive operations including civ2 and fix2. This double series of PIV processing can be done in two steps (keeping the same CIV subdirectory) or simulatenously, using the compare ('-') option.  Then the check boxed test_stereo1 and test_stereo2 in the PATCH1 and PATCH2 frames must be unselected.
   For PIV near a staigth wall, it is advised to create a grid for each image series, corresponding to a common array of physical positions. This can be done by the pusch button grid in uvmat (bottom right).
+The images from each camera (camA and camB) must be in the same directory and the PIV results in a single subdirectory. It is advised to do the successive operations including civ2 and fix2. This double series of PIV processing can be done in two steps (keeping the same CIV subdirectory) or simulatenously, using the compare ('-') option.  Then the check boxed test_stereo1 and test_stereo2 in the PATCH1 and PATCH2 frames must be unselected.
+For PIV near a staigth wall, it is advised to create a grid for each image series, corresponding to a common array of physical positions. This can be done by the pusch button grid in uvmat (bottom right).
 Combine PIV fields:  this is done by selecting PATCH1 and  test_stereo1 (at level civ1), or PATCH2 and  test_stereo2 (at level civ2) in the stereo mode (check box compare selected). The resulting fields camA-camB are in physical coordinates. They are final results which cannot be processed for further Civ operations: one must go back to the two image series for that purpose. Note that this stereo combination is only  possible in the RUN mode for the moment (no BATCH)**.