Changes between Version 138 and Version 139 of UvmatHelp
 Timestamp:
 Jan 14, 2015, 2:11:22 PM (9 years ago)
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UvmatHelp
v138 v139 417 417 418 418 * '''Dimension variables:''' these are unique unidimensional variable arrays corresponding to a given dimension, leading to a cell with a single variable, dimension 1. This is interpreted as the set of coordinate values associated with this dimension. An alternative possibility, suitable for a coordiante with a constant grid mesh, is a variable array with two values with the same name as a dimension: it then specifies the lower and upper bounds of the coordinate. 419 * '''Field cell with structured coordinates:''' this is a cell of several variable(s) sharing the same set of dimensions associated with variables. (add ditional dimension may indicate for instance a vector component, not associated with a coordinate).419 * '''Field cell with structured coordinates:''' this is a cell of several variable(s) sharing the same set of dimensions associated with variables. (additional dimension may indicate for instance a vector component, not associated with a coordinate). 420 420 * '''Field cell with unstructured coordinates:''' this is a cell of variables sharing the same set of unstructured coordinates, indicated by the attribute Role=coord_x, coord_y, coord_z. 421 421 * '''Thin plate shell (tps) field cell:''' represents an (unstructured) set of coordinates and tps weights in a way suitable for tps interpolation. … … 426 426 * 'nb_coord': denotes the space dimension for vector components. 427 427 * 'nb_coord_j', 'nb_coord_i': denotes the space dimensions for the two tensor components. 428 * 'rgb' : denotes the di emension of the color component in a true color image.428 * 'rgb' : denotes the dimension of the color component in a true color image. 429 429 * 'nb_point' or 'nb_vec' (for vectors) denotes the set of positions with unstructured coordinates. 430 430 * 'nb_tps': dimension of the index for the tps centres. … … 492 492 * 'plane': linear interpolation on a regular grid with meshes DX, DY and ortigin at (X,Y)=(0,0). This grid is bounded by the two values of RangeX and RangeY along X and Y respectively. 493 493 494 * ''' !ProjMode = 'interp_tps': ''' this behaves with different objects line 'interp_lin', but using the more precise thin spline shell method. This is particularly usefull to calculate sp âtial field derivatives. Furthermore this method provides data exrtrapolation outside the initial convex hull (although it is not reliable at large distances). This mode does require a previous calculation of tps weights, see [#a5.1Gridingofdata section 5.1], so it does not act on the initial field cells with scattered coordinates. This is done by UVMAT if tps projection is requested. Gridded data are linearly interpolated (to clarify...).495 496 * ''' !ProjMode = 'inside' and 'ouside '''': defined only for closed lines: rectangle, polygon, ellipse. For each field U, its probability distribution function Uhist inside, or respectively outside, the line is calculated, as well as the mean Umean (after exclusion of data marked as false) .other statistics...494 * ''' !ProjMode = 'interp_tps': ''' this behaves with different objects line 'interp_lin', but using the more precise thin spline shell method. This is particularly usefull to calculate spatial field derivatives. Furthermore this method provides data extrapolation outside the initial convex hull (although it is not reliable at large distances). This mode does require a previous calculation of tps weights, see [#a5.1Gridingofdata section 5.1], so it does not act on the initial field cells with scattered coordinates. This is done by UVMAT if tps projection is requested. Gridded data are linearly interpolated (to clarify...). 495 496 * ''' !ProjMode = 'inside' and 'ouside '''': defined only for closed lines: rectangle, polygon, ellipse. For each field U, its probability distribution function Uhist inside, or respectively outside, the line is calculated, as well as the mean Umean (after exclusion of data marked as false), other statistics... 497 497 498 498 * ''' !ProjMode = 'none', 'mask_inside', 'mask_outside': ''' no projection operation. The object is used solely for plotting purpose, to show a boundary or to prepare a mask, inside or outside a closed line, see [#a9Masksandgrids section 9]). … … 628 628 * `<R>`: rotation matrix (in 3 lines). For the option <[https://servforge.legi.grenobleinp.fr/projects/softuvmat/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''. 629 629 630 * <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. 631 631 632 632 * <!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''). … … 822 822 823 823 === 11.3 FIX === 824 The FIX operation is used after civ to remove false vectors, using different criteria: ''' {warning flags:} ''' these are flags (vec_F) indicating problems with the image correlation process: *vec_F(i)=0 or 1 : default , the processing is fine *vec_F(i)=2: the maximum of the correlation function is close to the border of the search box (at a distance of two pixels or less), so that its maximum cannot be reliably obtained: the search domain is too small *vec_F(i)=2: (only in civ1) we keep the less accurate Hart result (resulting from combining correlation functions from neighborhing points) and vec_C(i)=1 is chosen by convention. Reference: Hart D. P. (2000) 'PIV error correction',{ Exp. Fluids} '''29''', 1322. *vec_F(i)=3: the optimisation of the correlation function is unstable or local Intensity rms of the image =0 *vec_F(i)=4:only in civ2: the difference between the estimator and the result is more than 1 pixel. The two criteria, vec_F(i)=2, and 3, should be selected (default options). The criterium vec_F=2 (Hart) should not be selected, while vec_F=4 (for civ2) could be selected only for excellent data (otherwise it may be too strict). ''' {Threshold on the image correlation} ''' (vec_C) can be introduced by the edit box [thresh_vecC] (value between 0 and 1). It removes vectors with poor correlation. ''' {Threshold on the velocity modulus } ''' (expressed in pixels): it can remove either too small values (menu '''[inf_sup1]''' set to '<'), or excessive values (menu '''[inf_sup1]''' set to '>'). Erratic zero velocity vectors, produced by a fixed image background, can be eliminated by this criterium. These criteria can be as well applied to the difference with a reference field, defined by a file series (edit box '''[ref_fix1]''') and a field inside the file (menu '''[field_ref1]'''). ''' {Mask fix:} ''' It has the same effect as the one used in civ1, but the removed vectors are kept in memory, labelled as false. ''' {Manual fix:} ''' Interactive fixing with the mouse is also possible, see [section 4.2>#4.2]. 824 The FIX operation is used after civ to remove false vectors, using different criteria: ''' {warning flags:} ''' these are flags (vec_F) indicating problems with the image correlation process: *vec_F(i)=0 or 1 : default , the processing is fine 825 *vec_F(i)=2: the maximum of the correlation function is close to the border of the search box (at a distance of two pixels or less), so that its maximum cannot be reliably obtained: the search domain is too small 826 *vec_F(i)=2: (only in civ1) we keep the less accurate Hart result (resulting from combining correlation functions from neighborhing points) and vec_C(i)=1 is chosen by convention. Reference: Hart D. P. (2000) 'PIV error correction',{ Exp. Fluids} '''29''', 1322. 827 *vec_F(i)=3: the optimisation of the correlation function is unstable or local Intensity rms of the image =0 828 *vec_F(i)=4:only in civ2: the difference between the estimator and the result is more than 1 pixel. The two criteria, vec_F(i)=2, and 3, should be selected (default options). The criterium vec_F=2 (Hart) should not be selected, while vec_F=4 (for civ2) could be selected only for excellent data (otherwise it may be too strict). ''' {Threshold on the image correlation} ''' (vec_C) can be introduced by the edit box [thresh_vecC] (value between 0 and 1). It removes vectors with poor correlation. ''' {Threshold on the velocity modulus } ''' (expressed in pixels): it can remove either too small values (menu '''[inf_sup1]''' set to '<'), or excessive values (menu '''[inf_sup1]''' set to '>'). Erratic zero velocity vectors, produced by a fixed image background, can be eliminated by this criterium. These criteria can be as well applied to the difference with a reference field, defined by a file series (edit box '''[ref_fix1]''') and a field inside the file (menu '''[field_ref1]'''). ''' {Mask fix:} ''' It has the same effect as the one used in civ1, but the removed vectors are kept in memory, labelled as false. ''' {Manual fix:} ''' Interactive fixing with the mouse is also possible, see [section 4.2>#4.2]. 825 829 826 830 ''' {Code for FixFlag:} ''' *FixFlag(i)=0 :default, everything is fine *FixFlag(i)=1. : value 1 for the second digit: vector removed by criteria on vec_F or/and low correlation value *FixFlag(i)=1..: value 1 for the third digit: vector selected by a criterium of difference with another field, for instance filter, or a field with differnt time interval. *FixFlag(i)=...1, 2, 3 different criteria for elimination set by the program Fix of CIVx (not yet documented). … … 916 920 Civ1_W_tpstps weights for z vel component 917 921 918 '''List of constants, old CIVx conventions ):'''922 '''List of constants, old CIVx conventions:''' 919 923 920 924 * nb_coord: =2 for PIV in a plane, =3 for PIV in a volume. … … 970 974 == 12  Tridimensional features:(to update **) == 971 975 === 121 Multilevel image scanning === 972 or multiplane scanning it also describes the set of laser planes. Then the current plane index is indicated by the text box z_index and the total number of planes by the text box nb_slice.976 or multiplane scanning, it also describes the set of laser planes. Then the current plane index is indicated by the text box z_index and the total number of planes by the text box nb_slice. 973 977 974 978 === 122 Volume image scanning === … … 1020 1024 * 'RUN_STLIN';...% combine 2 displacement fields for stereo PIV * 'sub_field';...% combine the two input fields, 1021 1025 1022 === convert and I/O functions ===1026 === Convert and I/O functions === 1023 1027 * 'cell2tab';... % transform a Matlab cell in a character array suitable for display in a table. 1024 1028 * 'fill_GUI';... % fill a GUI with handles 'handles' from input data Param. … … 1036 1040 * 'xml2struct'...% read an XML file as a Matlab structure, converts numeric character strings into numbers. 1037 1041 1038 === ancillary functions ===1042 === Ancillary functions === 1039 1043 * 'activate';...% emulate the mouse selection of a GUI element, for demo. 1040 1044 * 'calc_field_interp': defines fields (velocity, vort, div...) from civ data and calculate them for projection with linear interpolation. … … 1081 1085 * 'update_waitbar';... update the waitbar display, used for ACTION functions in the GUI 'series'. 1082 1086 1083 === series functions ===1087 === Series functions === 1084 1088 * 'aver_stat': calculate field average over a time series. 1085 1089 * 'avi2png': copy an avi movie to a series of B/W .png images (take the average of green and blue color components) … … 1092 1096 * 'time_series': extract a time series after projection on an object (points , line..). 1093 1097 1094 === transform functions ===1098 === Transform functions === 1095 1099 * 'ima_filter': lowpass filter of an image (builtin filtering parameter). 1096 1100 * 'ima_remove_background': removes backgound from an image (using the local minimum).