1 | %'civ_series': PIV function activated by the general GUI series |
---|
2 | % --- call the sub-functions: |
---|
3 | % civ: PIV function itself |
---|
4 | % fix: removes false vectors after detection by various criteria |
---|
5 | % filter_tps: make interpolation-smoothing |
---|
6 | %------------------------------------------------------------------------ |
---|
7 | % function [Data,errormsg,result_conv]= civ_series(Param) |
---|
8 | % |
---|
9 | %OUTPUT |
---|
10 | % Data=structure containing the PIV results and information on the processing parameters |
---|
11 | % errormsg=error message char string, default='' |
---|
12 | % resul_conv: image inter-correlation function for the last grid point (used for tests) |
---|
13 | % |
---|
14 | %INPUT: |
---|
15 | % Param: Matlab structure of input parameters |
---|
16 | % Param contains info of the GUI series using the fct read_GUI. |
---|
17 | % Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation |
---|
18 | % Param.InputTable: sets the input file(s) |
---|
19 | % if absent, the fct looks for input data in Param.ActionInput (test mode) |
---|
20 | % Param.OutputSubDir: sets the folder name of output file(s, |
---|
21 | % if absent no file is produced, result in the output structure Data (test mode) |
---|
22 | % Param.ActionInput: substructure with the parameters provided by the GUI civ_input |
---|
23 | % .Civ1: parameters for civ1 |
---|
24 | % .Fix1: parameters for fix1 |
---|
25 | % .Patch1: |
---|
26 | % .Civ2: for civ2 |
---|
27 | % .Fix2: |
---|
28 | % .Patch2: |
---|
29 | |
---|
30 | %======================================================================= |
---|
31 | % Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
---|
32 | % http://www.legi.grenoble-inp.fr |
---|
33 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
---|
34 | % |
---|
35 | % This file is part of the toolbox UVMAT. |
---|
36 | % |
---|
37 | % UVMAT is free software; you can redistribute it and/or modify |
---|
38 | % it under the terms of the GNU General Public License as published |
---|
39 | % by the Free Software Foundation; either version 2 of the license, |
---|
40 | % or (at your option) any later version. |
---|
41 | % |
---|
42 | % UVMAT is distributed in the hope that it will be useful, |
---|
43 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
---|
44 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
---|
45 | % GNU General Public License (see LICENSE.txt) for more details. |
---|
46 | %======================================================================= |
---|
47 | |
---|
48 | function [Data,errormsg,result_conv]= civ_series(Param) |
---|
49 | errormsg=''; |
---|
50 | |
---|
51 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed |
---|
52 | if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN |
---|
53 | path_series=fileparts(which('series')); |
---|
54 | addpath(fullfile(path_series,'series')) |
---|
55 | Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input |
---|
56 | if isempty(Data) |
---|
57 | Data=Param;% if civ_input has been cancelled, keep previous parameters |
---|
58 | end |
---|
59 | Data.Program=mfilename;%gives the name of the current function |
---|
60 | Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
---|
61 | Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
---|
62 | if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices')&& strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') |
---|
63 | Data.Desable_j_index='on';% hide the j index in series (set by the pair choice in civ_input) |
---|
64 | end |
---|
65 | Data.NbSlice='off'; %nbre of slices ('off' by default) |
---|
66 | Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
---|
67 | Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
---|
68 | Data.FieldTransform = 'off';%can use a transform function |
---|
69 | Data.ProjObject='off';%can use projection object(option 'off'/'on', |
---|
70 | Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
---|
71 | Data.OutputDirExt='.civ';%set the output dir extension |
---|
72 | Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default) |
---|
73 | Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) |
---|
74 | Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
---|
75 | return |
---|
76 | end |
---|
77 | |
---|
78 | %% read input parameters from an xml file if input is a file name (batch mode) |
---|
79 | checkrun=1; |
---|
80 | if ischar(Param) |
---|
81 | Param=xml2struct(Param);% read Param as input file (batch case) |
---|
82 | checkrun=0; |
---|
83 | end |
---|
84 | |
---|
85 | %% test input |
---|
86 | if ~isfield(Param,'ActionInput') |
---|
87 | disp_uvmat('ERROR','no parameter set for PIV',checkrun) |
---|
88 | return |
---|
89 | end |
---|
90 | iview_A=0;%default values |
---|
91 | NbField=1; |
---|
92 | RUNHandle=[]; |
---|
93 | CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) |
---|
94 | CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) |
---|
95 | |
---|
96 | %% input files and indexing (skipped in Test mode) |
---|
97 | if CheckInputFile |
---|
98 | hseries=findobj(allchild(0),'Tag','series'); |
---|
99 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
---|
100 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
---|
101 | MaxIndex_i=Param.IndexRange.MaxIndex_i; |
---|
102 | MinIndex_i=Param.IndexRange.MinIndex_i; |
---|
103 | MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); |
---|
104 | if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') |
---|
105 | MaxIndex_j=Param.IndexRange.MaxIndex_j; |
---|
106 | MinIndex_j=Param.IndexRange.MinIndex_j; |
---|
107 | end |
---|
108 | if isfield(Param,'InputTable') |
---|
109 | [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
---|
110 | iview_A=0;% series index (iview) for the first image series |
---|
111 | iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) |
---|
112 | if Param.ActionInput.CheckCiv1 |
---|
113 | iview_A=1;% usual PIV, the image series is on the first line of the table |
---|
114 | elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line |
---|
115 | iview_A=2;% the second line is used for the input images of Civ2 |
---|
116 | end |
---|
117 | if strcmp(Param.ActionInput.ListCompareMode,'shift') |
---|
118 | iview_B=iview_A+1; % the second image series is on the next line of the input table |
---|
119 | end |
---|
120 | if iview_A~=0 |
---|
121 | RootPath_A=Param.InputTable{iview_A,1}; |
---|
122 | RootFile_A=Param.InputTable{iview_A,3}; |
---|
123 | SubDir_A=Param.InputTable{iview_A,2}; |
---|
124 | NomType_A=Param.InputTable{iview_A,4}; |
---|
125 | FileExt_A=Param.InputTable{iview_A,5}; |
---|
126 | if iview_B==0 |
---|
127 | iview_B=iview_A;% the second image series is the same as the first |
---|
128 | end |
---|
129 | RootPath_B=Param.InputTable{iview_B,1}; |
---|
130 | RootFile_B=Param.InputTable{iview_B,3}; |
---|
131 | SubDir_B=Param.InputTable{iview_B,2}; |
---|
132 | NomType_B=Param.InputTable{iview_B,4}; |
---|
133 | FileExt_B=Param.InputTable{iview_B,5}; |
---|
134 | end |
---|
135 | |
---|
136 | PairCiv2=''; |
---|
137 | switch Param.ActionInput.ListCompareMode |
---|
138 | case 'PIV' |
---|
139 | PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; |
---|
140 | if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') |
---|
141 | PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair |
---|
142 | end |
---|
143 | if iview_A==1% if Civ1 is performed |
---|
144 | [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... |
---|
145 | find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); |
---|
146 | if ~isempty(PairCiv2) |
---|
147 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... |
---|
148 | find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); |
---|
149 | check_bounds=check_bounds | check_bounds_Civ2; |
---|
150 | end |
---|
151 | else% we start from an existing Civ1 file |
---|
152 | i1_series_Civ1=i1_series{1}; |
---|
153 | i2_series_Civ1=i2_series{1}; |
---|
154 | j1_series_Civ1=j1_series{1}; |
---|
155 | j2_series_Civ1=j2_series{1}; |
---|
156 | NomTypeNc=Param.InputTable{1,4}; |
---|
157 | if ~isempty(PairCiv2) |
---|
158 | [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... |
---|
159 | find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); |
---|
160 | end |
---|
161 | end |
---|
162 | case 'displacement' |
---|
163 | i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); |
---|
164 | i2_series_Civ1=i1_series{1};i2_series_Civ2=i1_series{1}; |
---|
165 | j1_series_Civ1=ones(size(i1_series{1}));% first j index is 1 |
---|
166 | if isempty(j1_series_Civ1) |
---|
167 | j2_series_Civ1=ones(size(i1_series{1})); |
---|
168 | else |
---|
169 | j2_series_Civ1=j1_series_Civ1; |
---|
170 | end |
---|
171 | i1_series_Civ2=i1_series_Civ1; |
---|
172 | j1_series_Civ2=j1_series_Civ1; |
---|
173 | j2_series_Civ2=j2_series_Civ1; |
---|
174 | NomTypeNc=Param.InputTable{1,4}; |
---|
175 | case 'PIV volume' |
---|
176 | % TODO, TODO |
---|
177 | end |
---|
178 | if isempty(j1_series_Civ1) |
---|
179 | FrameIndex_A_Civ1=i1_series_Civ1; |
---|
180 | FrameIndex_B_Civ1=i2_series_Civ1; |
---|
181 | j1_series_Civ1=ones(size(i1_series_Civ1)); |
---|
182 | j2_series_Civ1=ones(size(i1_series_Civ1)); |
---|
183 | else |
---|
184 | FrameIndex_A_Civ1=j1_series_Civ1; |
---|
185 | FrameIndex_B_Civ1=j2_series_Civ1; |
---|
186 | end |
---|
187 | if isempty(PairCiv2) |
---|
188 | FrameIndex_A_Civ2=FrameIndex_A_Civ1; |
---|
189 | FrameIndex_B_Civ2=FrameIndex_B_Civ1; |
---|
190 | else |
---|
191 | if isempty(j1_series_Civ2) |
---|
192 | FrameIndex_A_Civ2=i1_series_Civ2; |
---|
193 | FrameIndex_B_Civ2=i2_series_Civ2; |
---|
194 | j1_series_Civ2=ones(size(i1_series_Civ2)); |
---|
195 | j2_series_Civ2=ones(size(i1_series_Civ2)); |
---|
196 | else |
---|
197 | FrameIndex_A_Civ2=j1_series_Civ2; |
---|
198 | FrameIndex_B_Civ2=j2_series_Civ2; |
---|
199 | end |
---|
200 | end |
---|
201 | if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) |
---|
202 | disp_uvmat('ERROR','no image pair fo civ in the input file index range',checkrun) |
---|
203 | return |
---|
204 | end |
---|
205 | end |
---|
206 | |
---|
207 | %% check the first image pair |
---|
208 | try |
---|
209 | if Param.ActionInput.CheckCiv1% Civ1 is performed |
---|
210 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1),[],j1_series_Civ1(1)); |
---|
211 | if ~exist(ImageName_A,'file') |
---|
212 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
---|
213 | return |
---|
214 | end |
---|
215 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
---|
216 | FileType_A=FileInfo_A.FileType; |
---|
217 | if strcmp(FileInfo_A.FileType,'netcdf') |
---|
218 | FieldName_A=Param.InputFields.FieldName; |
---|
219 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
---|
220 | par_civ1.ImageA=DataIn.(FieldName_A); |
---|
221 | else |
---|
222 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(1)); |
---|
223 | end |
---|
224 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1),[],j2_series_Civ1(1)); |
---|
225 | if ~exist(ImageName_B,'file') |
---|
226 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
---|
227 | return |
---|
228 | end |
---|
229 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
---|
230 | FileType_B=FileInfo_B.FileType; |
---|
231 | if strcmp(FileInfo_B.FileType,'netcdf') |
---|
232 | FieldName_B=Param.InputFields.FieldName; |
---|
233 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
---|
234 | par_civ1.ImageB=DataIn.(FieldName_B); |
---|
235 | else |
---|
236 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(1)); |
---|
237 | end |
---|
238 | NbField=numel(i1_series_Civ1); |
---|
239 | elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 |
---|
240 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ2(1),[],j1_series_Civ2(1)); |
---|
241 | if ~exist(ImageName_A,'file') |
---|
242 | disp_uvmat('ERROR',['first input image ' ImageName_A ' does not exist'],checkrun) |
---|
243 | return |
---|
244 | end |
---|
245 | [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); |
---|
246 | FileType_A=FileInfo_A.FileType; |
---|
247 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileInfo_A.FileType,VideoObject_A,FrameIndex_A_Civ2(1)); |
---|
248 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ2(1),[],j2_series_Civ2(1)); |
---|
249 | if ~exist(ImageName_B,'file') |
---|
250 | disp_uvmat('ERROR',['first input image ' ImageName_B ' does not exist'],checkrun) |
---|
251 | return |
---|
252 | end |
---|
253 | [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); |
---|
254 | FileType_B=FileInfo_B.FileType; |
---|
255 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1)); |
---|
256 | NbField=numel(i1_series_Civ2); |
---|
257 | else |
---|
258 | NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK |
---|
259 | end |
---|
260 | catch ME |
---|
261 | if ~isempty(ME.message) |
---|
262 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
263 | return |
---|
264 | end |
---|
265 | end |
---|
266 | |
---|
267 | |
---|
268 | %% Output directory |
---|
269 | OutputDir=''; |
---|
270 | if CheckOutputFile |
---|
271 | OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
---|
272 | end |
---|
273 | end |
---|
274 | |
---|
275 | %% prepare output Data |
---|
276 | ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
277 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
278 | Data.Program='civ_series'; |
---|
279 | Data.CivStage=0;%default |
---|
280 | check_civx=0;%default |
---|
281 | |
---|
282 | %% get timing from the ImaDoc file or input video |
---|
283 | if iview_A~=0 |
---|
284 | XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A); |
---|
285 | Time=[]; |
---|
286 | if ~isempty(XmlFileName) |
---|
287 | XmlData=imadoc2struct(XmlFileName); |
---|
288 | if isfield(XmlData,'Time') |
---|
289 | Time=XmlData.Time; |
---|
290 | TimeSource='xml'; |
---|
291 | end |
---|
292 | if isfield(XmlData,'Camera') |
---|
293 | if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) |
---|
294 | NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform |
---|
295 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
---|
296 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
---|
297 | end |
---|
298 | end |
---|
299 | if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) |
---|
300 | TimeUnit=XmlData.Camera.TimeUnit; |
---|
301 | end |
---|
302 | end |
---|
303 | end |
---|
304 | if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input |
---|
305 | Time=zeros(FileInfo_A.NumberOfFrames+1,2); |
---|
306 | Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; |
---|
307 | TimeSource='video'; |
---|
308 | ColorType='truecolor'; |
---|
309 | end |
---|
310 | if isempty(Time)% Time = index i +0.001 index j by default |
---|
311 | %MinIndex_i=min(i1_series_Civ1); |
---|
312 | MaxIndex_i=max(i2_series_Civ1); |
---|
313 | %MinIndex_j=min(j1_series_Civ1); |
---|
314 | MaxIndex_j=max(j2_series_Civ1); |
---|
315 | Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); |
---|
316 | Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); |
---|
317 | Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros |
---|
318 | Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros |
---|
319 | end |
---|
320 | |
---|
321 | if length(FileInfo_A) >1 %case of image with multiple frames |
---|
322 | nbfield=length(FileInfo_A); |
---|
323 | nbfield_j=1; |
---|
324 | end |
---|
325 | end |
---|
326 | |
---|
327 | %%%%% MAIN LOOP %%%%%% |
---|
328 | maskname='';% initiate the mask name |
---|
329 | tic; |
---|
330 | CheckOverwrite=1;%default |
---|
331 | if isfield(Param,'CheckOverwrite') |
---|
332 | CheckOverwrite=Param.CheckOverwrite; |
---|
333 | end |
---|
334 | for ifield=1:NbField |
---|
335 | if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series (checkrun=1) |
---|
336 | update_waitbar(WaitbarHandle,ifield/NbField) |
---|
337 | if checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
---|
338 | disp('program stopped by user') |
---|
339 | break |
---|
340 | end |
---|
341 | end |
---|
342 | if CheckInputFile |
---|
343 | if iview_A==0 % no nc file has been entered |
---|
344 | ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... |
---|
345 | NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
346 | else% an existing nc file has been entered |
---|
347 | if iview_A==1% if Civ1 is performed |
---|
348 | Civ1Dir=OutputDir; |
---|
349 | else |
---|
350 | Civ1Dir=Param.InputTable{1,2}; |
---|
351 | end |
---|
352 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
353 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... |
---|
354 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
355 | else |
---|
356 | ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... |
---|
357 | j1_series_Civ1(ifield),j2_series_Civ1(ifield)); |
---|
358 | end |
---|
359 | end |
---|
360 | ncfile_out=ncfile;% by default |
---|
361 | if isfield (Param.ActionInput,'Civ2') |
---|
362 | i1_civ2=i1_series_Civ2(ifield); |
---|
363 | i2_civ2=i1_civ2; |
---|
364 | if ~isempty(i2_series_Civ2) |
---|
365 | i2_civ2=i2_series_Civ2(ifield); |
---|
366 | end |
---|
367 | j1_civ2=1; |
---|
368 | if ~isempty(j1_series_Civ2) |
---|
369 | j1_civ2=j1_series_Civ2(ifield); |
---|
370 | end |
---|
371 | j2_civ2=i1_civ2; |
---|
372 | if ~isempty(j2_series_Civ2) |
---|
373 | j2_civ2=j2_series_Civ2(ifield); |
---|
374 | end |
---|
375 | if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
376 | ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); |
---|
377 | else % displacement |
---|
378 | ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); |
---|
379 | end |
---|
380 | end |
---|
381 | if ~CheckOverwrite && exist(ncfile_out,'file') |
---|
382 | disp(['existing output file ' ncfile_out ' already exists, skip to next field']) |
---|
383 | continue% skip iteration if the mode overwrite is desactivated and the result file already exists |
---|
384 | end |
---|
385 | end |
---|
386 | %% Civ1 |
---|
387 | % if Civ1 computation is requested |
---|
388 | if isfield (Param.ActionInput,'Civ1') |
---|
389 | if CheckInputFile |
---|
390 | disp('civ1 started') |
---|
391 | end |
---|
392 | par_civ1=Param.ActionInput.Civ1; |
---|
393 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
394 | try |
---|
395 | ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); |
---|
396 | if strcmp(FileInfo_A.FileType,'netcdf')% case of input images in format netcdf |
---|
397 | FieldName_A=Param.InputFields.FieldName; |
---|
398 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); |
---|
399 | par_civ1.ImageA=DataIn.(FieldName_A); |
---|
400 | else % usual image formats for image A |
---|
401 | [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); |
---|
402 | end |
---|
403 | ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); |
---|
404 | if strcmp(FileInfo_B.FileType,'netcdf') % case of input images in format netcdf |
---|
405 | FieldName_B=Param.InputFields.FieldName; |
---|
406 | [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); |
---|
407 | par_civ1.ImageB=DataIn.(FieldName_B); |
---|
408 | else % usual image formats for image B |
---|
409 | [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); |
---|
410 | end |
---|
411 | catch ME % display errors in reading input images |
---|
412 | if ~isempty(ME.message) |
---|
413 | disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) |
---|
414 | return |
---|
415 | end |
---|
416 | end |
---|
417 | par_civ1.ImageWidth=size(par_civ1.ImageA,2);%FileInfo_A.Width; |
---|
418 | par_civ1.ImageHeight=size(par_civ1.ImageA,1);%FileInfo_A.Height; |
---|
419 | list_param=(fieldnames(Param.ActionInput.Civ1))'; |
---|
420 | list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list |
---|
421 | Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param |
---|
422 | Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images |
---|
423 | %indicate the values of all the global attributes in the output data |
---|
424 | Data.Civ1_ImageA=ImageName_A; |
---|
425 | Data.Civ1_ImageB=ImageName_B; |
---|
426 | i1=i1_series_Civ1(ifield); |
---|
427 | i2=i1; |
---|
428 | if ~isempty(i2_series_Civ1) |
---|
429 | i2=i2_series_Civ1(ifield); |
---|
430 | end |
---|
431 | j1=1; |
---|
432 | if ~isempty(j1_series_Civ1) |
---|
433 | j1=j1_series_Civ1(ifield); |
---|
434 | end |
---|
435 | j2=j1; |
---|
436 | if ~isempty(j2_series_Civ1) |
---|
437 | j2=j2_series_Civ1(ifield); |
---|
438 | end |
---|
439 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
440 | Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image |
---|
441 | Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading |
---|
442 | else |
---|
443 | Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair |
---|
444 | Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); |
---|
445 | end |
---|
446 | for ilist=1:length(list_param) |
---|
447 | Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); |
---|
448 | end |
---|
449 | Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; |
---|
450 | Data.CivStage=1; |
---|
451 | end |
---|
452 | % set the list of variables |
---|
453 | Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record |
---|
454 | Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; |
---|
455 | Data.VarAttribute{1}.Role='coord_x'; |
---|
456 | Data.VarAttribute{2}.Role='coord_y'; |
---|
457 | Data.VarAttribute{3}.Role='vector_x'; |
---|
458 | Data.VarAttribute{4}.Role='vector_y'; |
---|
459 | Data.VarAttribute{5}.Role='warnflag'; |
---|
460 | if par_civ1.CheckMask&&~isempty(par_civ1.Mask) |
---|
461 | if strcmp(maskname,par_civ1.Mask)% mask exist, not already read in civ1 |
---|
462 | par_civ1.Mask=mask; %use mask already opened |
---|
463 | else |
---|
464 | try |
---|
465 | par_civ1.Mask=imread(par_civ1.Mask);%update the mask, an store it for future use |
---|
466 | catch ME |
---|
467 | if ~isempty(ME.message) |
---|
468 | errormsg=['error reading input image: ' ME.message]; |
---|
469 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
470 | return |
---|
471 | end |
---|
472 | end |
---|
473 | mask=par_civ1.Mask; |
---|
474 | maskname=par_civ1.Mask; |
---|
475 | end |
---|
476 | end |
---|
477 | if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume') |
---|
478 | Data.ListVarName=[Data.ListVarName 'Civ1_Z']; |
---|
479 | Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; |
---|
480 | Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; |
---|
481 | for ivol=1:NbSlice |
---|
482 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
483 | [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); |
---|
484 | if ~isempty(errormsg) |
---|
485 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
486 | return |
---|
487 | end |
---|
488 | Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; |
---|
489 | Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; |
---|
490 | Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates |
---|
491 | Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; |
---|
492 | Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; |
---|
493 | Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; |
---|
494 | Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; |
---|
495 | end |
---|
496 | else %usual PIV |
---|
497 | % caluclate velocity data (y and v in indices, reverse to y component) |
---|
498 | [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); |
---|
499 | if ~isempty(errormsg) |
---|
500 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
501 | return |
---|
502 | end |
---|
503 | Data.Civ1_X=reshape(xtable,[],1); |
---|
504 | Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); |
---|
505 | Data.Civ1_U=reshape(utable,[],1); |
---|
506 | Data.Civ1_V=reshape(-vtable,[],1); |
---|
507 | Data.Civ1_C=reshape(ctable,[],1); |
---|
508 | Data.Civ1_F=reshape(F,[],1); |
---|
509 | end |
---|
510 | else% we use existing Civ1 data |
---|
511 | if exist('ncfile','var') |
---|
512 | CivFile=ncfile; |
---|
513 | [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format |
---|
514 | if ~isempty(errormsg) |
---|
515 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
516 | return |
---|
517 | end |
---|
518 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
519 | elseif isfield(Param,'Civ1_X') |
---|
520 | Data.ListGlobalAttribute={}; |
---|
521 | Data.ListVarName={}; |
---|
522 | Data.VarDimName={}; |
---|
523 | Data.Civ1_X=Param.Civ1_X; |
---|
524 | Data.Civ1_Y=Param.Civ1_Y; |
---|
525 | Data.Civ1_U=Param.Civ1_U; |
---|
526 | Data.Civ1_V=Param.Civ1_V; |
---|
527 | Data.Civ1_FF=Param.Civ1_FF; |
---|
528 | end |
---|
529 | end |
---|
530 | |
---|
531 | %% Fix1 |
---|
532 | if isfield (Param.ActionInput,'Fix1') |
---|
533 | disp('fix1 started') |
---|
534 | if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 |
---|
535 | Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); |
---|
536 | Data.ListGlobalAttribute(Fix1_attr)=[]; |
---|
537 | for ilist=1:numel(Fix1_attr) |
---|
538 | Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); |
---|
539 | end |
---|
540 | end |
---|
541 | list_param=fieldnames(Param.ActionInput.Fix1)'; |
---|
542 | Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
543 | %indicate the values of all the global attributes in the output data |
---|
544 | for ilist=1:length(list_param) |
---|
545 | Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist}); |
---|
546 | end |
---|
547 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param]; |
---|
548 | Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; |
---|
549 | Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; |
---|
550 | nbvar=length(Data.ListVarName); |
---|
551 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
552 | Data.Civ1_FF=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V)); |
---|
553 | Data.CivStage=2; |
---|
554 | end |
---|
555 | %% Patch1 |
---|
556 | if isfield (Param.ActionInput,'Patch1') |
---|
557 | disp('patch1 started') |
---|
558 | if check_civx |
---|
559 | errormsg='Civ Matlab input needed for patch'; |
---|
560 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
561 | return |
---|
562 | end |
---|
563 | |
---|
564 | % record the processing parameters of Patch1 as global attributes in the result nc file |
---|
565 | list_param=fieldnames(Param.ActionInput.Patch1)'; |
---|
566 | list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters |
---|
567 | Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before each parameter name |
---|
568 | for ilist=1:length(list_param) |
---|
569 | Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist}); |
---|
570 | end |
---|
571 | Data.CivStage=3;% record the new state of processing |
---|
572 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param]; |
---|
573 | |
---|
574 | % list the variables to record |
---|
575 | nbvar=length(Data.ListVarName); |
---|
576 | Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; |
---|
577 | Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... |
---|
578 | {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; |
---|
579 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
580 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
581 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
582 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
583 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
584 | Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X)); |
---|
585 | Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X)); |
---|
586 | if isfield(Data,'Civ1_FF') |
---|
587 | ind_good=find(Data.Civ1_FF==0); |
---|
588 | else |
---|
589 | ind_good=1:numel(Data.Civ1_X); |
---|
590 | end |
---|
591 | |
---|
592 | % perform Patch calculation using the UVMAT fct 'filter_tps' |
---|
593 | [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... |
---|
594 | filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomainSize,Data.Patch1_FieldSmooth,Data.Patch1_MaxDiff); |
---|
595 | Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other |
---|
596 | Data.Civ1_V_smooth(ind_good)=Vres; |
---|
597 | Data.Civ1_FF(ind_good)=int8(FFres); |
---|
598 | disp('patch1 performed') |
---|
599 | end |
---|
600 | |
---|
601 | %% Civ2 |
---|
602 | if isfield (Param.ActionInput,'Civ2') |
---|
603 | disp('civ2 started') |
---|
604 | par_civ2=Param.ActionInput.Civ2; |
---|
605 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
606 | par_civ2.ImageA=[]; |
---|
607 | par_civ2.ImageB=[]; |
---|
608 | % i1_civ2=i1_series_Civ2(ifield); |
---|
609 | % i2_civ2=i1_civ2; |
---|
610 | % if ~isempty(i2_series_Civ2) |
---|
611 | % i2_civ2=i2_series_Civ2(ifield); |
---|
612 | % end |
---|
613 | % j1_civ2=1; |
---|
614 | % if ~isempty(j1_series_Civ2) |
---|
615 | % j1_civ2=j1_series_Civ2(ifield); |
---|
616 | % end |
---|
617 | % j2_civ2=i1_civ2; |
---|
618 | % if ~isempty(j2_series_Civ2) |
---|
619 | % j2_civ2=j2_series_Civ2(ifield); |
---|
620 | % end |
---|
621 | ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); |
---|
622 | |
---|
623 | if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) |
---|
624 | par_civ2.ImageA=par_civ1.ImageA; |
---|
625 | else |
---|
626 | [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); |
---|
627 | end |
---|
628 | ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); |
---|
629 | if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) |
---|
630 | par_civ2.ImageB=par_civ1.ImageB; |
---|
631 | else |
---|
632 | [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); |
---|
633 | end |
---|
634 | % if strcmp(Param.ActionInput.ListCompareMode,'PIV') |
---|
635 | % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1,i2,j1,j2); |
---|
636 | % else % displacement |
---|
637 | % ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2,[],j2); |
---|
638 | % end |
---|
639 | par_civ2.ImageWidth=FileInfo_A.Width; |
---|
640 | par_civ2.ImageHeight=FileInfo_A.Height; |
---|
641 | if isfield(par_civ2,'Grid')% grid points set as input file |
---|
642 | if ischar(par_civ2.Grid)%read the grid file if the input is a file name |
---|
643 | par_civ2.Grid=dlmread(par_civ2.Grid); |
---|
644 | par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
645 | end |
---|
646 | else% automatic grid |
---|
647 | minix=floor(par_civ2.Dx/2)-0.5; |
---|
648 | maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); |
---|
649 | miniy=floor(par_civ2.Dy/2)-0.5; |
---|
650 | maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); |
---|
651 | [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); |
---|
652 | par_civ2.Grid(:,1)=reshape(GridX,[],1); |
---|
653 | par_civ2.Grid(:,2)=reshape(GridY,[],1); |
---|
654 | end |
---|
655 | end |
---|
656 | |
---|
657 | % get the guess from patch1 or patch2 (case 'CheckCiv3') |
---|
658 | if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) |
---|
659 | if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 |
---|
660 | SubRange= Data.Civ2_SubRange; |
---|
661 | NbCentres=Data.Civ2_NbCentres; |
---|
662 | Coord_tps=Data.Civ2_Coord_tps; |
---|
663 | U_tps=Data.Civ2_U_tps; |
---|
664 | V_tps=Data.Civ2_V_tps; |
---|
665 | CivStage=Data.CivStage;%store the current CivStage |
---|
666 | Civ1_Dt=Data.Civ2_Dt; |
---|
667 | Data=[];%reinitialise the result structure Data |
---|
668 | Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; |
---|
669 | Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes |
---|
670 | Data.Program='civ_series'; |
---|
671 | Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data |
---|
672 | Data.ListVarName={}; |
---|
673 | Data.VarDimName={}; |
---|
674 | else % get the guess from patch1 |
---|
675 | SubRange= Data.Civ1_SubRange; |
---|
676 | NbCentres=Data.Civ1_NbCentres; |
---|
677 | Coord_tps=Data.Civ1_Coord_tps; |
---|
678 | U_tps=Data.Civ1_U_tps; |
---|
679 | V_tps=Data.Civ1_V_tps; |
---|
680 | Civ1_Dt=Data.Civ1_Dt; |
---|
681 | Data.CivStage=4; |
---|
682 | end |
---|
683 | else |
---|
684 | SubRange= par_civ2.Civ1_SubRange; |
---|
685 | NbCentres=par_civ2.Civ1_NbCentres; |
---|
686 | Coord_tps=par_civ2.Civ1_Coord_tps; |
---|
687 | U_tps=par_civ2.Civ1_U_tps; |
---|
688 | V_tps=par_civ2.Civ1_V_tps; |
---|
689 | Civ1_Dt=par_civ2.Civ1_Dt; |
---|
690 | Civ2_Dt=par_civ2.Civ1_Dt; |
---|
691 | Data.ListVarName={}; |
---|
692 | Data.VarDimName={}; |
---|
693 | end |
---|
694 | Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data |
---|
695 | Shifty=zeros(size(par_civ2.Grid,1),1); |
---|
696 | nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains) |
---|
697 | if par_civ2.CheckDeformation |
---|
698 | DUDX=zeros(size(par_civ2.Grid,1),1); |
---|
699 | DUDY=zeros(size(par_civ2.Grid,1),1); |
---|
700 | DVDX=zeros(size(par_civ2.Grid,1),1); |
---|
701 | DVDY=zeros(size(par_civ2.Grid,1),1); |
---|
702 | end |
---|
703 | NbSubDomain=size(SubRange,3); |
---|
704 | for isub=1:NbSubDomain% for each sub-domain of Patch1 |
---|
705 | nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain |
---|
706 | ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &... |
---|
707 | par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain |
---|
708 | if ~isempty(ind_sel) |
---|
709 | epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids) |
---|
710 | ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs |
---|
711 | nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap) |
---|
712 | EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient |
---|
713 | Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1 |
---|
714 | Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub); |
---|
715 | if par_civ2.CheckDeformation |
---|
716 | [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs |
---|
717 | DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub); |
---|
718 | DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub); |
---|
719 | DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub); |
---|
720 | DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub); |
---|
721 | end |
---|
722 | end |
---|
723 | end |
---|
724 | if par_civ2.CheckMask&&~isempty(par_civ2.Mask) |
---|
725 | if strcmp(maskname,par_civ2.Mask)% mask exist, not already read in civ1 |
---|
726 | par_civ2.Mask=mask; %use mask already opened |
---|
727 | else |
---|
728 | par_civ2.Mask=imread(par_civ2.Mask);%update the mask, and store it for future use |
---|
729 | mask=par_civ2.Mask; |
---|
730 | maskname=par_civ2.Mask; |
---|
731 | end |
---|
732 | end |
---|
733 | if CheckInputFile % else Dt given by par_civ2 |
---|
734 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
735 | Civ1_Dt=1; |
---|
736 | Civ2_Dt=1; |
---|
737 | else |
---|
738 | Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); |
---|
739 | end |
---|
740 | end |
---|
741 | par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; |
---|
742 | % shift the grid points by half the expected shift to provide the correlation box position in image A |
---|
743 | par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2]; |
---|
744 | if par_civ2.CheckDeformation |
---|
745 | par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); |
---|
746 | par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); |
---|
747 | par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); |
---|
748 | par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); |
---|
749 | end |
---|
750 | |
---|
751 | % calculate velocity data (y and v in image indices, reverse to y component) |
---|
752 | [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2); |
---|
753 | |
---|
754 | list_param=(fieldnames(Param.ActionInput.Civ2))'; |
---|
755 | list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list |
---|
756 | Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param |
---|
757 | Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images |
---|
758 | %indicate the values of all the global attributes in the output data |
---|
759 | if exist('ImageName_A','var') |
---|
760 | Data.Civ2_ImageA=ImageName_A; |
---|
761 | Data.Civ2_ImageB=ImageName_B; |
---|
762 | if strcmp(Param.ActionInput.ListCompareMode,'displacement') |
---|
763 | Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image |
---|
764 | Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading |
---|
765 | else |
---|
766 | Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2; |
---|
767 | Data.Civ2_Dt=Civ2_Dt; |
---|
768 | end |
---|
769 | end |
---|
770 | for ilist=1:length(list_param) |
---|
771 | Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); |
---|
772 | end |
---|
773 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; |
---|
774 | |
---|
775 | nbvar=numel(Data.ListVarName); |
---|
776 | % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) |
---|
777 | if isempty(find(strcmp('Civ2_X',Data.ListVarName),1)) |
---|
778 | Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];% cell array containing the names of the fields to record |
---|
779 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; |
---|
780 | Data.VarAttribute{nbvar+1}.Role='coord_x'; |
---|
781 | Data.VarAttribute{nbvar+2}.Role='coord_y'; |
---|
782 | Data.VarAttribute{nbvar+3}.Role='vector_x'; |
---|
783 | Data.VarAttribute{nbvar+4}.Role='vector_y'; |
---|
784 | Data.VarAttribute{nbvar+5}.Role='warnflag'; |
---|
785 | end |
---|
786 | Data.Civ2_X=reshape(xtable,[],1); |
---|
787 | Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); |
---|
788 | Data.Civ2_U=reshape(utable,[],1); |
---|
789 | Data.Civ2_V=reshape(-vtable,[],1); |
---|
790 | Data.Civ2_C=reshape(ctable,[],1); |
---|
791 | Data.Civ2_F=reshape(F,[],1); |
---|
792 | disp('civ2 performed') |
---|
793 | elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data |
---|
794 | if exist('ncfile','var') |
---|
795 | CivFile=ncfile; |
---|
796 | [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file |
---|
797 | if ~isempty(errormsg) |
---|
798 | disp_uvmat('ERROR',errormsg,checkrun) |
---|
799 | return |
---|
800 | end |
---|
801 | elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode) |
---|
802 | Data.ListGlobalAttribute={}; |
---|
803 | Data.ListVarName={}; |
---|
804 | Data.VarDimName={}; |
---|
805 | Data.Civ2_X=Param.Civ2_X; |
---|
806 | Data.Civ2_Y=Param.Civ2_Y; |
---|
807 | Data.Civ2_U=Param.Civ2_U; |
---|
808 | Data.Civ2_V=Param.Civ2_V; |
---|
809 | Data.Civ2_FF=Param.Civ2_FF; |
---|
810 | end |
---|
811 | end |
---|
812 | |
---|
813 | %% Fix2 |
---|
814 | if isfield (Param.ActionInput,'Fix2') |
---|
815 | disp('fix2 started') |
---|
816 | list_param=fieldnames(Param.ActionInput.Fix2)'; |
---|
817 | Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
818 | %indicate the values of all the global attributes in the output data |
---|
819 | for ilist=1:length(list_param) |
---|
820 | Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist}); |
---|
821 | end |
---|
822 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param]; |
---|
823 | % |
---|
824 | % ListFixParam=fieldnames(Param.ActionInput.Fix2); |
---|
825 | % for ilist=1:length(ListFixParam) |
---|
826 | % ParamName=ListFixParam{ilist}; |
---|
827 | % ListName=['Fix2_' ParamName]; |
---|
828 | % eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) |
---|
829 | % eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';']) |
---|
830 | % end |
---|
831 | if check_civx |
---|
832 | if ~isfield(Data,'fix2') |
---|
833 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; |
---|
834 | Data.fix2=1; |
---|
835 | Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; |
---|
836 | Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; |
---|
837 | end |
---|
838 | Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); |
---|
839 | else |
---|
840 | Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; |
---|
841 | Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; |
---|
842 | nbvar=length(Data.ListVarName); |
---|
843 | Data.VarAttribute{nbvar}.Role='errorflag'; |
---|
844 | Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); |
---|
845 | Data.CivStage=Data.CivStage+1; |
---|
846 | end |
---|
847 | end |
---|
848 | |
---|
849 | %% Patch2 |
---|
850 | if isfield (Param.ActionInput,'Patch2') |
---|
851 | disp('patch2 started') |
---|
852 | list_param=fieldnames(Param.ActionInput.Patch2)'; |
---|
853 | list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list |
---|
854 | Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before each string in ListFixParam |
---|
855 | %indicate the values of all the global attributes in the output data |
---|
856 | for ilist=1:length(list_param) |
---|
857 | Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist}); |
---|
858 | end |
---|
859 | Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param]; |
---|
860 | |
---|
861 | nbvar=length(Data.ListVarName); |
---|
862 | Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; |
---|
863 | Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... |
---|
864 | {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; |
---|
865 | |
---|
866 | Data.VarAttribute{nbvar+1}.Role='vector_x'; |
---|
867 | Data.VarAttribute{nbvar+2}.Role='vector_y'; |
---|
868 | Data.VarAttribute{nbvar+5}.Role='coord_tps'; |
---|
869 | Data.VarAttribute{nbvar+6}.Role='vector_x'; |
---|
870 | Data.VarAttribute{nbvar+7}.Role='vector_y'; |
---|
871 | Data.Civ2_U_smooth=Data.Civ2_U; |
---|
872 | Data.Civ2_V_smooth=Data.Civ2_V; |
---|
873 | if isfield(Data,'Civ2_FF') |
---|
874 | ind_good=find(Data.Civ2_FF==0); |
---|
875 | else |
---|
876 | ind_good=1:numel(Data.Civ2_X); |
---|
877 | end |
---|
878 | [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=... |
---|
879 | filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff); |
---|
880 | Data.Civ2_U_smooth(ind_good)=Ures; |
---|
881 | Data.Civ2_V_smooth(ind_good)=Vres; |
---|
882 | Data.Civ2_FF(ind_good)=FFres; |
---|
883 | Data.CivStage=Data.CivStage+1; |
---|
884 | disp('patch2 performed') |
---|
885 | end |
---|
886 | |
---|
887 | %% write result in a netcdf file if requested |
---|
888 | if CheckOutputFile |
---|
889 | errormsg=struct2nc(ncfile_out,Data); |
---|
890 | if isempty(errormsg) |
---|
891 | disp([ncfile_out ' written']) |
---|
892 | %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc |
---|
893 | else |
---|
894 | disp(errormsg) |
---|
895 | end |
---|
896 | disp(['ellapsed time ' num2str(toc/60,2) ' minutes']) |
---|
897 | end |
---|
898 | end |
---|
899 | |
---|
900 | |
---|
901 | % 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ |
---|
902 | %-------------------------------------------------------------------------- |
---|
903 | % function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) |
---|
904 | % |
---|
905 | % OUTPUT: |
---|
906 | % xtable: set of x coordinates |
---|
907 | % ytable: set of y coordiantes |
---|
908 | % utable: set of u displacements (along x) |
---|
909 | % vtable: set of v displacements (along y) |
---|
910 | % ctable: max image correlation for each vector |
---|
911 | % typevector: set of flags, =1 for good, =0 for NaN vectors |
---|
912 | % |
---|
913 | %INPUT: |
---|
914 | % par_civ: structure of input parameters, with fields: |
---|
915 | % .ImageA: first image for correlation (matrix) |
---|
916 | % .ImageB: second image for correlation(matrix) |
---|
917 | % .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y |
---|
918 | % .SearchBoxSize: 1,2 vector giving the size of the search box in x and y |
---|
919 | % .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y |
---|
920 | % .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max |
---|
921 | % .ImageWidth: nb of pixels of the image in x |
---|
922 | % .Dx, Dy: mesh for the PIV calculation |
---|
923 | % .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A |
---|
924 | % .Mask: name of a mask file or mask image matrix itself |
---|
925 | % .MinIma: thresholds for image luminosity |
---|
926 | % .MaxIma |
---|
927 | % .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform) |
---|
928 | % .DUDX: matrix of deformation obtained from patch at each grid point |
---|
929 | % .DUDY |
---|
930 | % .DVDX: |
---|
931 | % .DVDY |
---|
932 | |
---|
933 | function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ) |
---|
934 | |
---|
935 | %% prepare measurement grid |
---|
936 | if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A |
---|
937 | if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates) |
---|
938 | par_civ.Grid=dlmread(par_civ.Grid); |
---|
939 | par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) |
---|
940 | end |
---|
941 | % else par_civ.Grid is already an array, no action here |
---|
942 | else% automatic grid in x, y image coordinates |
---|
943 | minix=floor(par_civ.Dx/2)-0.5; |
---|
944 | maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); |
---|
945 | miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy |
---|
946 | maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); |
---|
947 | [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); |
---|
948 | par_civ.Grid(:,1)=reshape(GridX,[],1); |
---|
949 | par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index |
---|
950 | end |
---|
951 | nbvec=size(par_civ.Grid,1); |
---|
952 | |
---|
953 | %% prepare correlation and search boxes |
---|
954 | ibx2=floor(par_civ.CorrBoxSize(1)/2); |
---|
955 | iby2=floor(par_civ.CorrBoxSize(2)/2); |
---|
956 | isx2=floor(par_civ.SearchBoxSize(1)/2); |
---|
957 | isy2=floor(par_civ.SearchBoxSize(2)/2); |
---|
958 | shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value |
---|
959 | shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases |
---|
960 | if numel(shiftx)==1% case of a unique shift for the whole field( civ1) |
---|
961 | shiftx=shiftx*ones(nbvec,1); |
---|
962 | shifty=shifty*ones(nbvec,1); |
---|
963 | end |
---|
964 | |
---|
965 | %% Array initialisation and default output if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation) |
---|
966 | xtable=round(par_civ.Grid(:,1)+0.5)-0.5; |
---|
967 | ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes |
---|
968 | utable=shiftx;%zeros(nbvec,1); |
---|
969 | vtable=shifty;%zeros(nbvec,1); |
---|
970 | ctable=zeros(nbvec,1); |
---|
971 | F=zeros(nbvec,1); |
---|
972 | result_conv=[]; |
---|
973 | errormsg=''; |
---|
974 | |
---|
975 | %% prepare mask |
---|
976 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
977 | if strcmp(par_civ.Mask,'all') |
---|
978 | return % get the grid only, no civ calculation |
---|
979 | elseif ischar(par_civ.Mask) |
---|
980 | par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done |
---|
981 | end |
---|
982 | end |
---|
983 | check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold |
---|
984 | check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); |
---|
985 | |
---|
986 | par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images |
---|
987 | par_civ.ImageB=sum(double(par_civ.ImageB),3); |
---|
988 | [npy_ima npx_ima]=size(par_civ.ImageA); |
---|
989 | if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) |
---|
990 | errormsg='image pair with unequal size'; |
---|
991 | return |
---|
992 | end |
---|
993 | |
---|
994 | %% Apply mask |
---|
995 | % Convention for mask IDEAS TO IMPLEMENT ? |
---|
996 | % mask >200 : velocity calculated |
---|
997 | % 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) |
---|
998 | % 150>=mask >100: velocity not calculated, nor interpolated |
---|
999 | % 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) |
---|
1000 | % 20>=mask: velocity=0 |
---|
1001 | checkmask=0; |
---|
1002 | MinA=min(min(par_civ.ImageA)); |
---|
1003 | %MinB=min(min(par_civ.ImageB)); |
---|
1004 | %check_undefined=false(size(par_civ.ImageA)); |
---|
1005 | if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) |
---|
1006 | checkmask=1; |
---|
1007 | if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) |
---|
1008 | errormsg='mask must be an image with the same size as the images'; |
---|
1009 | return |
---|
1010 | end |
---|
1011 | check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); |
---|
1012 | % par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined area |
---|
1013 | % par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined area |
---|
1014 | end |
---|
1015 | |
---|
1016 | %% compute image correlations: MAINLOOP on velocity vectors |
---|
1017 | corrmax=0; |
---|
1018 | sum_square=1;% default |
---|
1019 | mesh=1;% default |
---|
1020 | CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; |
---|
1021 | if CheckDeformation |
---|
1022 | mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction) |
---|
1023 | par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) |
---|
1024 | end |
---|
1025 | |
---|
1026 | if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) |
---|
1027 | for ivec=1:nbvec |
---|
1028 | iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box |
---|
1029 | jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% j index for the middle of the correlation box in the image A |
---|
1030 | F(ivec)=0; |
---|
1031 | subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage |
---|
1032 | subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage |
---|
1033 | subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage |
---|
1034 | subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage |
---|
1035 | image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A |
---|
1036 | image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A |
---|
1037 | check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 |
---|
1038 | check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; |
---|
1039 | check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 |
---|
1040 | check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; |
---|
1041 | image1_crop(check1_y,check1_x)=par_civ.ImageA(subrange1_y(check1_y),subrange1_x(check1_x));%extract a subimage (correlation box) from image A |
---|
1042 | image2_crop(check2_y,check2_x)=par_civ.ImageB(subrange2_y(check2_y),subrange2_x(check2_x));%extract a larger subimage (search box) from image B |
---|
1043 | if checkmask |
---|
1044 | mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask |
---|
1045 | mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask |
---|
1046 | mask1_crop(check1_y,check1_x)=check_undefined(subrange1_y(check1_y),subrange1_x(check1_x));%extract a mask subimage (correlation box) from image A |
---|
1047 | mask2_crop(check2_y,check2_x)=check_undefined(subrange2_y(check2_y),subrange2_x(check2_x));%extract a mask subimage (search box) from image B |
---|
1048 | sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image |
---|
1049 | if sizemask > 1/2% eliminate point if more than half of the correlation box is masked |
---|
1050 | F(ivec)=3; % |
---|
1051 | utable(ivec)=0; |
---|
1052 | vtable(ivec)=0; |
---|
1053 | else |
---|
1054 | image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) |
---|
1055 | image2_crop=image2_crop.*~mask2_crop; |
---|
1056 | image1_mean=mean(mean(image1_crop))/(1-sizemask); |
---|
1057 | image2_mean=mean(mean(image2_crop))/(1-sizemask); |
---|
1058 | end |
---|
1059 | else |
---|
1060 | image1_mean=mean(mean(image1_crop)); |
---|
1061 | image2_mean=mean(mean(image2_crop)); |
---|
1062 | end |
---|
1063 | %threshold on image minimum |
---|
1064 | if F(ivec)~=3 |
---|
1065 | if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) |
---|
1066 | F(ivec)=3; |
---|
1067 | %threshold on image maximum |
---|
1068 | elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) |
---|
1069 | F(ivec)=3; |
---|
1070 | end |
---|
1071 | if F(ivec)==3 |
---|
1072 | utable(ivec)=0; |
---|
1073 | vtable(ivec)=0; |
---|
1074 | else |
---|
1075 | %mask |
---|
1076 | if checkmask |
---|
1077 | image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts |
---|
1078 | image2_crop=(image2_crop-image2_mean).*~mask2_crop; |
---|
1079 | else |
---|
1080 | image1_crop=(image1_crop-image1_mean); |
---|
1081 | image2_crop=(image2_crop-image2_mean); |
---|
1082 | end |
---|
1083 | %deformation |
---|
1084 | if CheckDeformation |
---|
1085 | xi=(1:mesh:size(image1_crop,2)); |
---|
1086 | yi=(1:mesh:size(image1_crop,1))'; |
---|
1087 | [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); |
---|
1088 | XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); |
---|
1089 | YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); |
---|
1090 | image1_crop=interp2(image1_crop,XIant,YIant); |
---|
1091 | image1_crop(isnan(image1_crop))=0; |
---|
1092 | xi=(1:mesh:size(image2_crop,2)); |
---|
1093 | yi=(1:mesh:size(image2_crop,1))'; |
---|
1094 | image2_crop=interp2(image2_crop,xi,yi,'*spline'); |
---|
1095 | image2_crop(isnan(image2_crop))=0; |
---|
1096 | end |
---|
1097 | sum_square=sum(sum(image1_crop.*image1_crop)); |
---|
1098 | %reference: Oliver Pust, PIV: Direct Cross-Correlation |
---|
1099 | result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); |
---|
1100 | corrmax= max(max(result_conv)); |
---|
1101 | result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 |
---|
1102 | %Find the correlation max, at 255 |
---|
1103 | [y,x] = find(result_conv==255,1); |
---|
1104 | subimage2_crop=image2_crop(y:y+2*iby2/mesh,x:x+2*ibx2/mesh);%subimage of image 2 corresponding to the optimum displacement of first image |
---|
1105 | sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2 |
---|
1106 | sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation |
---|
1107 | if ~isempty(y) && ~isempty(x) |
---|
1108 | try |
---|
1109 | if par_civ.CorrSmooth==1 |
---|
1110 | [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); |
---|
1111 | elseif par_civ.CorrSmooth==2 |
---|
1112 | [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); |
---|
1113 | else |
---|
1114 | [vector,F(ivec)] = quadr_fit(result_conv,x,y); |
---|
1115 | end |
---|
1116 | utable(ivec)=vector(1)*mesh+shiftx(ivec); |
---|
1117 | vtable(ivec)=vector(2)*mesh+shifty(ivec); |
---|
1118 | xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) |
---|
1119 | ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) |
---|
1120 | iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector |
---|
1121 | jref=round(ytable(ivec)+0.5); |
---|
1122 | % eliminate vectors located in the mask |
---|
1123 | if checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100)) |
---|
1124 | utable(ivec)=0; |
---|
1125 | vtable(ivec)=0; |
---|
1126 | F(ivec)=3; |
---|
1127 | end |
---|
1128 | ctable(ivec)=corrmax/sum_square;% correlation value |
---|
1129 | catch ME |
---|
1130 | F(ivec)=3; |
---|
1131 | disp(ME.message) |
---|
1132 | end |
---|
1133 | else |
---|
1134 | F(ivec)=3; |
---|
1135 | end |
---|
1136 | end |
---|
1137 | end |
---|
1138 | end |
---|
1139 | end |
---|
1140 | result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output |
---|
1141 | |
---|
1142 | %------------------------------------------------------------------------ |
---|
1143 | % --- Find the maximum of the correlation function after interpolation |
---|
1144 | % OUPUT: |
---|
1145 | % vector = optimum displacement vector with subpixel correction |
---|
1146 | % F =flag: =0 OK |
---|
1147 | % =-2 , warning: max too close to the edge of the search box (1 pixel margin) |
---|
1148 | % INPUT: |
---|
1149 | % x,y: position of the maximum correlation at integer values |
---|
1150 | |
---|
1151 | function [vector,F] = SUBPIXGAUSS (result_conv,x,y) |
---|
1152 | %------------------------------------------------------------------------ |
---|
1153 | % vector=[0 0]; %default |
---|
1154 | F=0; |
---|
1155 | [npy,npx]=size(result_conv); |
---|
1156 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (=0 by discretisation, to avoid divergence in the log) |
---|
1157 | %the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ᅵ Israel Institute of Technology |
---|
1158 | %http://urapiv.wordpress.com |
---|
1159 | peaky = y; |
---|
1160 | if y < npy && y > 1 |
---|
1161 | f0 = log(result_conv(y,x)); |
---|
1162 | f1 = log(result_conv(y-1,x)); |
---|
1163 | f2 = log(result_conv(y+1,x)); |
---|
1164 | peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
1165 | else |
---|
1166 | F=-2; % warning flag for vector truncated by the limited search box |
---|
1167 | end |
---|
1168 | peakx=x; |
---|
1169 | if x < npx-1 && x > 1 |
---|
1170 | f0 = log(result_conv(y,x)); |
---|
1171 | f1 = log(result_conv(y,x-1)); |
---|
1172 | f2 = log(result_conv(y,x+1)); |
---|
1173 | peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); |
---|
1174 | else |
---|
1175 | F=-2; % warning flag for vector truncated by the limited search box |
---|
1176 | end |
---|
1177 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
1178 | |
---|
1179 | %------------------------------------------------------------------------ |
---|
1180 | % --- Find the maximum of the correlation function after interpolation |
---|
1181 | function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) |
---|
1182 | %------------------------------------------------------------------------ |
---|
1183 | % vector=[0 0]; %default |
---|
1184 | F=-2; |
---|
1185 | peaky=y; |
---|
1186 | peakx=x; |
---|
1187 | result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) |
---|
1188 | [npy,npx]=size(result_conv); |
---|
1189 | if (x < npx) && (y < npy) && (x > 1) && (y > 1) |
---|
1190 | F=0; |
---|
1191 | for i=-1:1 |
---|
1192 | for j=-1:1 |
---|
1193 | %following 15 lines based on |
---|
1194 | %H. Nobach ᅵ M. Honkanen (2005) |
---|
1195 | %Two-dimensional Gaussian regression for sub-pixel displacement |
---|
1196 | %estimation in particle image velocimetry or particle position |
---|
1197 | %estimation in particle tracking velocimetry |
---|
1198 | %Experiments in Fluids (2005) 38: 511ᅵ515 |
---|
1199 | c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); |
---|
1200 | c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); |
---|
1201 | c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); |
---|
1202 | c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); |
---|
1203 | c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); |
---|
1204 | end |
---|
1205 | end |
---|
1206 | c10=(1/6)*sum(sum(c10)); |
---|
1207 | c01=(1/6)*sum(sum(c01)); |
---|
1208 | c11=(1/4)*sum(sum(c11)); |
---|
1209 | c20=(1/6)*sum(sum(c20)); |
---|
1210 | c02=(1/6)*sum(sum(c02)); |
---|
1211 | deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); |
---|
1212 | deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); |
---|
1213 | if abs(deltax)<1 |
---|
1214 | peakx=x+deltax; |
---|
1215 | end |
---|
1216 | if abs(deltay)<1 |
---|
1217 | peaky=y+deltay; |
---|
1218 | end |
---|
1219 | end |
---|
1220 | vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; |
---|
1221 | |
---|
1222 | %------------------------------------------------------------------------ |
---|
1223 | % --- Find the maximum of the correlation function after quadratic interpolation |
---|
1224 | function [vector,F] = quadr_fit(result_conv,x,y) |
---|
1225 | [npy,npx]=size(result_conv); |
---|
1226 | if x<4 || y<4 || npx-x<4 ||npy-y <4 |
---|
1227 | F=-2; |
---|
1228 | vector=[x y]; |
---|
1229 | else |
---|
1230 | F=0; |
---|
1231 | x_ind=x-4:x+4; |
---|
1232 | y_ind=y-4:y+4; |
---|
1233 | x_vec=0.25*(x_ind-x); |
---|
1234 | y_vec=0.25*(y_ind-y); |
---|
1235 | [X,Y]=meshgrid(x_vec,y_vec); |
---|
1236 | coord=[reshape(X,[],1) reshape(Y,[],1)]; |
---|
1237 | result_conv=reshape(result_conv(y_ind,x_ind),[],1); |
---|
1238 | |
---|
1239 | |
---|
1240 | % n=numel(X); |
---|
1241 | % x=[X Y]; |
---|
1242 | % X=X-0.5; |
---|
1243 | % Y=Y+0.5; |
---|
1244 | % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1); |
---|
1245 | p = polyfitn(coord,result_conv,2); |
---|
1246 | A(1,1)=2*p.Coefficients(1); |
---|
1247 | A(1,2)=p.Coefficients(2); |
---|
1248 | A(2,1)=p.Coefficients(2); |
---|
1249 | A(2,2)=2*p.Coefficients(4); |
---|
1250 | vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]'; |
---|
1251 | vector=vector'-[floor(npx/2) floor(npy/2)]-1 ; |
---|
1252 | % zg = polyvaln(p,coord); |
---|
1253 | % figure |
---|
1254 | % surf(x_vec,y_vec,reshape(zg,9,9)) |
---|
1255 | % hold on |
---|
1256 | % plot3(X,Y,reshape(result_conv,9,9),'o') |
---|
1257 | % hold off |
---|
1258 | end |
---|
1259 | |
---|
1260 | %'RUN_FIX': function for fixing velocity fields: |
---|
1261 | %----------------------------------------------- |
---|
1262 | % RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) |
---|
1263 | % |
---|
1264 | %filename: name of the netcdf file (used as input and output) |
---|
1265 | %field: structure specifying the names of the fields to fix (depending on civ1 or civ2) |
---|
1266 | %.vel_type='civ1' or 'civ2'; |
---|
1267 | %.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); |
---|
1268 | %.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) |
---|
1269 | %flagindex: flag specifying which values of vec_f are removed: |
---|
1270 | % if flagindex(1)=1: vec_f=-2 vectors are removed |
---|
1271 | % if flagindex(2)=1: vec_f=3 vectors are removed |
---|
1272 | % if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) |
---|
1273 | %iter=1 for civ1 fields and iter=2 for civ2 fields |
---|
1274 | %thresh_vecC: threshold in the image correlation vec_C |
---|
1275 | %flag_mask: =1 mask used to remove vectors (0 else) |
---|
1276 | %maskname: name of the mask image file for fix |
---|
1277 | %thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists |
---|
1278 | %inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold |
---|
1279 | %fileref: .nc file name for a reference velocity (='': refrence 0 used) |
---|
1280 | %fieldref: 'civ1','filter1'...feld used in fileref |
---|
1281 | |
---|
1282 | function FF=fix(Param,F,C,U,V,X,Y) |
---|
1283 | FF=zeros(size(F));%default |
---|
1284 | |
---|
1285 | %criterium on warn flags |
---|
1286 | FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; |
---|
1287 | FlagVal=[-2 2 3 4]; |
---|
1288 | for iflag=1:numel(FlagName) |
---|
1289 | if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) |
---|
1290 | FF=(FF==1| F==FlagVal(iflag)); |
---|
1291 | end |
---|
1292 | end |
---|
1293 | %criterium on correlation values |
---|
1294 | if isfield (Param,'MinCorr') |
---|
1295 | FF=FF==1 | C<Param.MinCorr; |
---|
1296 | end |
---|
1297 | if (isfield(Param,'MinVel')&&~isempty(Param.MinVel))||(isfield (Param,'MaxVel')&&~isempty(Param.MaxVel)) |
---|
1298 | Umod= U.*U+V.*V; |
---|
1299 | if isfield (Param,'MinVel')&&~isempty(Param.MinVel) |
---|
1300 | FF=FF==1 | Umod<(Param.MinVel*Param.MinVel); |
---|
1301 | end |
---|
1302 | if isfield (Param,'MaxVel')&&~isempty(Param.MaxVel) |
---|
1303 | FF=FF==1 | Umod>(Param.MaxVel*Param.MaxVel); |
---|
1304 | end |
---|
1305 | end |
---|
1306 | |
---|
1307 | |
---|
1308 | %------------------------------------------------------------------------ |
---|
1309 | % --- determine the list of index pairs of processing file |
---|
1310 | function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... |
---|
1311 | find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) |
---|
1312 | %------------------------------------------------------------------------ |
---|
1313 | i1_series=i_series;% set of first image indexes |
---|
1314 | i2_series=i_series; |
---|
1315 | j1_series=j_series;%ones(size(i_series));% set of first image numbers |
---|
1316 | j2_series=j_series;%ones(size(i_series)); |
---|
1317 | r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); |
---|
1318 | if ~isempty(r) |
---|
1319 | mode=['D' r.ind]; |
---|
1320 | ind1=str2num(r.num1); |
---|
1321 | ind2=str2num(r.num2); |
---|
1322 | else |
---|
1323 | mode='j1-j2'; |
---|
1324 | r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); |
---|
1325 | if ~isempty(r) |
---|
1326 | NomTypeNc='_1ab'; |
---|
1327 | else |
---|
1328 | r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); |
---|
1329 | if ~isempty(r) |
---|
1330 | NomTypeNc='_1AB'; |
---|
1331 | else |
---|
1332 | r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); |
---|
1333 | if ~isempty(r) |
---|
1334 | NomTypeNc='_1_1-2'; |
---|
1335 | end |
---|
1336 | end |
---|
1337 | end |
---|
1338 | if isempty(r) |
---|
1339 | display('wrong pair mode input option') |
---|
1340 | else |
---|
1341 | ind1=stra2num(r.num1); |
---|
1342 | ind2=stra2num(r.num2); |
---|
1343 | end |
---|
1344 | end |
---|
1345 | switch mode |
---|
1346 | case 'Di' |
---|
1347 | i1_series=i_series-ind1;% set of first image numbers |
---|
1348 | i2_series=i_series+ind2; |
---|
1349 | check_bounds=i1_series<MinIndex_i | i2_series>MaxIndex_i; |
---|
1350 | if isempty(j_series) |
---|
1351 | NomTypeNc='_1-2'; |
---|
1352 | else |
---|
1353 | j1_series=j_series; |
---|
1354 | j2_series=j_series; |
---|
1355 | NomTypeNc='_1-2_1'; |
---|
1356 | end |
---|
1357 | case 'Dj' |
---|
1358 | j1_series=j_series-ind1; |
---|
1359 | j2_series=j_series+ind2; |
---|
1360 | check_bounds=j1_series<MinIndex_j | j2_series>MaxIndex_j; |
---|
1361 | NomTypeNc='_1_1-2'; |
---|
1362 | otherwise %bursts |
---|
1363 | i1_series=i_series(1,:);% do not sweep the j index |
---|
1364 | i2_series=i_series(1,:); |
---|
1365 | j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice |
---|
1366 | j2_series=ind2*ones(1,size(i_series,2)); |
---|
1367 | check_bounds=zeros(size(i1_series));% no limitations due to min-max indices |
---|
1368 | end |
---|
1369 | |
---|
1370 | |
---|
1371 | |
---|
1372 | |
---|