1 | function GUI_input=merge_proj(num_i1,num_i2,num_j1,num_j2,Series); |
---|
2 | |
---|
3 | %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) |
---|
4 | if ~exist('num_i1','var') |
---|
5 | GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') |
---|
6 | 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) |
---|
7 | 'RootFile';'on';... %root input file name ('on' by default) |
---|
8 | 'FileExt';'on';... %input file extension ('on' by default) |
---|
9 | 'NomType';'on';...%type of file indexing ('on' by default) |
---|
10 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
---|
11 | 'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) |
---|
12 | 'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
---|
13 | 'CoordType';'on';...%can use a transform function 'off' by default |
---|
14 | 'GetObject';'on';...%can use projection object ,'off' by default |
---|
15 | %'GetMask';'on'...%can use mask option ,'off' by default |
---|
16 | %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter |
---|
17 | ''}; |
---|
18 | return %exit the function |
---|
19 | end |
---|
20 | |
---|
21 | %------------------------------------------------- |
---|
22 | hseries=guidata(Series.hseries);%handles of the GUI series |
---|
23 | WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame |
---|
24 | %------------------------------------------------- |
---|
25 | |
---|
26 | %projection object |
---|
27 | test_object=get(hseries.GetObject,'Value'); |
---|
28 | if test_object |
---|
29 | hset_object=findobj(allchild(0),'Name','set_object'); |
---|
30 | ProjObject=read_set_object(guidata(hset_object)); |
---|
31 | if ~isfield(ProjObject,'Style') |
---|
32 | msgbox_uvmat('ERROR','Undefined projection object style') |
---|
33 | return |
---|
34 | end |
---|
35 | if ~isequal(ProjObject.Style,'plane') |
---|
36 | msgbox_uvmat('ERROR','The projection object must be a plane') |
---|
37 | return |
---|
38 | end |
---|
39 | %answeryes=questdlg({['field series projected on ' Series.ProjObject.Style]}); |
---|
40 | answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Style]); |
---|
41 | if ~isequal(answeryes,'Yes') |
---|
42 | return |
---|
43 | end |
---|
44 | end |
---|
45 | |
---|
46 | %numbers of view fields (nbre of inputs in RootPath) |
---|
47 | testcell=iscell(Series.RootFile); |
---|
48 | if ~testcell |
---|
49 | Series.RootPath={Series.RootPath}; |
---|
50 | Series.RootFile={Series.RootFile}; |
---|
51 | Series.SubDir={Series.SubDir}; |
---|
52 | Series.FileExt={Series.FileExt}; |
---|
53 | Series.NomType={Series.NomType}; |
---|
54 | num_i1={num_i1}; |
---|
55 | num_i2={num_i2}; |
---|
56 | num_j1={num_j1}; |
---|
57 | num_j2={num_j2}; |
---|
58 | end |
---|
59 | nbview=length(Series.RootFile);%number of views (file series to merge) |
---|
60 | nbfield=size(num_i1{1},1)*size(num_i1{1},2);%number of fields in the time series |
---|
61 | transform=Series.CoordType; % field transform function |
---|
62 | hhh=which('mmreader'); |
---|
63 | for iview=1:nbview |
---|
64 | test_movie(iview)=0; |
---|
65 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported() |
---|
66 | if isequal(lower(FileExt{iview}),'.avi') |
---|
67 | MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); |
---|
68 | test_movie(iview)=1; |
---|
69 | end |
---|
70 | end |
---|
71 | end |
---|
72 | |
---|
73 | %Calibration data and timing: read the ImaDoc files |
---|
74 | mode=''; %default |
---|
75 | timecell={}; |
---|
76 | itime=0; |
---|
77 | NbSlice_calib={}; %test for z index |
---|
78 | for iview=1:nbview%Loop on views |
---|
79 | XmlData{iview}=[];%default |
---|
80 | filebase{iview}=fullfile(Series.RootPath{iview},Series.RootFile{iview}); |
---|
81 | if exist([filebase{iview} '.xml'],'file') |
---|
82 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
---|
83 | if isfield(XmlData{iview},'Time') |
---|
84 | itime=itime+1; |
---|
85 | timecell{itime}=XmlData{iview}.Time; |
---|
86 | end |
---|
87 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
---|
88 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1); |
---|
89 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
---|
90 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
---|
91 | end |
---|
92 | end |
---|
93 | elseif exist([filebase{iview} '.civ'],'file') |
---|
94 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
---|
95 | itime=itime+1; |
---|
96 | timecell{itime}=time; |
---|
97 | XmlData{iview}.Time=time; |
---|
98 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
---|
99 | GeometryCalib.Tx=0; |
---|
100 | GeometryCalib.Ty=0; |
---|
101 | GeometryCalib.Tz=1; |
---|
102 | GeometryCalib.dpx=1; |
---|
103 | GeometryCalib.dpy=1; |
---|
104 | GeometryCalib.sx=1; |
---|
105 | GeometryCalib.Cx=0; |
---|
106 | GeometryCalib.Cy=0; |
---|
107 | GeometryCalib.f=1; |
---|
108 | GeometryCalib.kappa1=0; |
---|
109 | GeometryCalib.CoordUnit='cm'; |
---|
110 | XmlData{iview}.GeometryCalib=GeometryCalib; |
---|
111 | if error==1 |
---|
112 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
---|
113 | end |
---|
114 | end |
---|
115 | end |
---|
116 | |
---|
117 | %check coincidence in time |
---|
118 | multitime=0; |
---|
119 | if length(timecell)==0 |
---|
120 | time=[]; |
---|
121 | elseif length(timecell)==1 |
---|
122 | time=timecell{1}; |
---|
123 | elseif length(timecell)>1 |
---|
124 | multitime=1; |
---|
125 | for icell=1:length(timecell) |
---|
126 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
---|
127 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
---|
128 | time=timecell{1}; |
---|
129 | multitime=0; |
---|
130 | break |
---|
131 | end |
---|
132 | end |
---|
133 | end |
---|
134 | if multitime |
---|
135 | for icell=1:length(timecell) |
---|
136 | time(icell,:,:)=timecell{icell}; |
---|
137 | end |
---|
138 | diff_time=max(max(diff(time))); |
---|
139 | if diff_time>0 |
---|
140 | msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) |
---|
141 | end |
---|
142 | end |
---|
143 | if size(time,2) < num_i2{1}(end) || size(time,3) < num_j2{1}(end)% ime array absent or too short in ImaDoc xml file' |
---|
144 | time=[]; |
---|
145 | end |
---|
146 | |
---|
147 | % coordinate transform or other user defined transform |
---|
148 | transform_fct=[];%default |
---|
149 | if isfield(Series,'transform_fct') |
---|
150 | transform_fct=Series.transform_fct; |
---|
151 | end |
---|
152 | |
---|
153 | % Field and velocity type (the same for all views) |
---|
154 | Field_str=get(hseries.FieldMenu,'String'); |
---|
155 | val=get(hseries.FieldMenu,'Value'); |
---|
156 | FieldName=Field_str(val);%the same set of fields for all views |
---|
157 | VelType_str=get(hseries.VelTypeMenu,'String'); |
---|
158 | VelType_val=get(hseries.VelTypeMenu,'Value'); |
---|
159 | VelType=VelType_str{VelType_val}; %the same for all views |
---|
160 | if isequal(FieldName,'get_field...') |
---|
161 | hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI |
---|
162 | % hhget_field=guidata(hget_field);%handles of GUI elements in get_field |
---|
163 | SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI |
---|
164 | % if isequal(get(hhget_field.menu_coord,'Visible'),'on') |
---|
165 | % list_transform=get(hhget_field.menu_coord,'String'); |
---|
166 | % val_list=get(hhget_field.menu_coord,'Value'); |
---|
167 | % transform=list_transform{val_list}; |
---|
168 | % end |
---|
169 | end |
---|
170 | %detect whether all the files are 'images' or 'netcdf' |
---|
171 | testima=0; |
---|
172 | testvol=0; |
---|
173 | testcivx=0; |
---|
174 | testnc=0; |
---|
175 | FileExt=get(hseries.FileExt,'String'); |
---|
176 | for iview=1:nbview |
---|
177 | ext=FileExt{iview}; |
---|
178 | form=imformats(ext([2:end])); |
---|
179 | if isequal(lower(ext),'.vol') |
---|
180 | testvol=testvol+1; |
---|
181 | elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab |
---|
182 | testima=testima+1; |
---|
183 | elseif isequal(ext,'.nc') |
---|
184 | testnc=testnc+1; |
---|
185 | end |
---|
186 | end |
---|
187 | if testvol |
---|
188 | msgbox_uvmat('ERROR','volume images not implemented yet') |
---|
189 | return |
---|
190 | end |
---|
191 | if testnc~=nbview && testima~=nbview && testvol~=nbview |
---|
192 | msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input') |
---|
193 | return |
---|
194 | end |
---|
195 | if ~isequal(FieldName,'get_field...') |
---|
196 | testcivx=testnc; |
---|
197 | end |
---|
198 | |
---|
199 | %name of output files and directory: |
---|
200 | % res_subdir=fullfile(Series.RootPath{1},[Series.SubDir{1} '_STAT']); |
---|
201 | ProjectDir=fileparts(fileparts(Series.RootPath{1}));% preoject directory (GERK) |
---|
202 | prompt={['result directory (in' ProjectDir ')']}; |
---|
203 | RootPath=get(hseries.RootPath,'String'); |
---|
204 | SubDir=get(hseries.SubDir,'String'); |
---|
205 | if isequal(length(RootPath),1) |
---|
206 | fulldir=RootPath{1}; |
---|
207 | subdir='merge_proj'; |
---|
208 | res_subdir=fullfile(fulldir,subdir); |
---|
209 | else |
---|
210 | def={fullfile(ProjectDir,'0_RESULTS')}; |
---|
211 | dlgTitle='result directory'; |
---|
212 | lineNo=1; |
---|
213 | answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def); |
---|
214 | fulldir=answer{1}; |
---|
215 | subdir=[]; |
---|
216 | dirlist=sort(Series.RootFile); |
---|
217 | for iview=1:nbview |
---|
218 | if ~isempty(subdir) |
---|
219 | subdir=[subdir '-']; |
---|
220 | end |
---|
221 | subdir=[subdir dirlist{iview}]; |
---|
222 | end |
---|
223 | res_subdir=fullfile(fulldir,subdir); |
---|
224 | end |
---|
225 | ext=FileExt{1}; |
---|
226 | if ~exist(fulldir,'dir') |
---|
227 | msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created']) |
---|
228 | return |
---|
229 | end |
---|
230 | if ~exist(res_subdir,'dir') |
---|
231 | dircur=pwd; |
---|
232 | cd(fulldir) |
---|
233 | error=mkdir(subdir); |
---|
234 | cd(dircur) |
---|
235 | end |
---|
236 | filebasesub=fullfile(res_subdir,Series.RootFile{1}); |
---|
237 | filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files |
---|
238 | |
---|
239 | %MAIN LOOP |
---|
240 | for ifile=1:nbfield |
---|
241 | stopstate=get(hseries.RUN,'BusyAction'); |
---|
242 | if isequal(stopstate,'queue')% enable STOP command from the 'series' interface |
---|
243 | update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) |
---|
244 | Amerge=0; |
---|
245 | |
---|
246 | %----------LOOP ON VIEWS---------------------- |
---|
247 | nbtime=0; |
---|
248 | for iview=1:nbview |
---|
249 | %name of the current file |
---|
250 | filename=name_generator(filebase{iview},num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile),SubDir{iview}); |
---|
251 | if ~exist(filename,'file') |
---|
252 | msgbox_uvmat('ERROR',['missing input file' filename]) |
---|
253 | break |
---|
254 | end |
---|
255 | |
---|
256 | %reading the current file |
---|
257 | if testima |
---|
258 | if test_movie(iview) |
---|
259 | Field{iview}.A=read(MovieObject{iview},num_i1{iview}(ifile)); |
---|
260 | else |
---|
261 | Field{iview}.A=read_image(filename,Series.NomType{iview},num_i1{iview}(ifile)); |
---|
262 | end % TODO: introduce ListVarName |
---|
263 | npxy=size(Field{iview}.A); |
---|
264 | Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
---|
265 | Field{iview}.AY=[npxy(1)-0.5 0.5]; |
---|
266 | Field{iview}.CoordType='px'; |
---|
267 | Field{iview}.AName='image'; |
---|
268 | else |
---|
269 | if testcivx |
---|
270 | [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); |
---|
271 | else |
---|
272 | [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
---|
273 | Field{iview}.VarAttribute=SubField.VarAttribute; |
---|
274 | end |
---|
275 | if isfield(Field{iview},'Time') |
---|
276 | timeread(iview)=Field{iview}.Time; |
---|
277 | nbtime=nbtime+1; |
---|
278 | end |
---|
279 | end |
---|
280 | % coord transform |
---|
281 | % z index |
---|
282 | if ~isempty(NbSlice_calib) |
---|
283 | Field{iview}.ZIndex=mod(num_i1{iview}(ifile)-1,NbSlice_calib{1})+1; |
---|
284 | end |
---|
285 | if ~isempty(transform_fct) |
---|
286 | Field{iview}=transform_fct(Field{iview},XmlData{iview});%transform to phys if requested |
---|
287 | end |
---|
288 | if testcivx |
---|
289 | Field{iview}=calc_field(FieldName,Field{iview}); |
---|
290 | end |
---|
291 | |
---|
292 | %projection on object (gridded plane) |
---|
293 | if test_object |
---|
294 | Field{iview}=proj_field(Field{iview},ProjObject); |
---|
295 | end |
---|
296 | end |
---|
297 | |
---|
298 | %----------END LOOP ON VIEWS---------------------- |
---|
299 | |
---|
300 | %merge the nbview fields |
---|
301 | MergeData=merge_field(Field); |
---|
302 | if isfield(MergeData,'Txt') |
---|
303 | msgbox_uvmat('ERROR',MergeData.Txt) |
---|
304 | return |
---|
305 | end |
---|
306 | |
---|
307 | % generating the name of the merged field |
---|
308 | mergename=name_generator(filebase_merge,num_i1{iview}(ifile),num_j1{iview}(ifile),Series.FileExt{iview},Series.NomType{iview},1,num_i2{iview}(ifile),num_j2{iview}(ifile)); |
---|
309 | |
---|
310 | % time: |
---|
311 | time_i=0;%default |
---|
312 | if isempty(time)% time from ImaDoc prevails |
---|
313 | time_i=sum(timeread)/nbtime; |
---|
314 | else |
---|
315 | time_i=(time(iview,num_i1{iview}(ifile),num_j1{iview}(ifile))+time(iview,num_i2{iview}(ifile),num_j2{iview}(ifile)))/2; |
---|
316 | end |
---|
317 | |
---|
318 | % recording the merged field |
---|
319 | if testima %in case of input images an image is produced |
---|
320 | if isa(MergeData.A,'uint8') |
---|
321 | bitdepth=8; |
---|
322 | elseif isa(MergeData.A,'uint16') |
---|
323 | bitdepth=16; |
---|
324 | end |
---|
325 | imwrite(MergeData.A,mergename,'BitDepth',bitdepth); |
---|
326 | %write xml calibration file |
---|
327 | siz=size(MergeData.A); |
---|
328 | npy=siz(1); |
---|
329 | npx=siz(2); |
---|
330 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
---|
331 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
---|
332 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
---|
333 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
---|
334 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
---|
335 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
---|
336 | else |
---|
337 | Rangx=[0.5 npx-0.5]; |
---|
338 | Rangy=[npy-0.5 0.5];%default |
---|
339 | end |
---|
340 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
---|
341 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
---|
342 | T_x=-pxcmx*Rangx(1)+0.5; |
---|
343 | T_y=-pxcmy*Rangy(2)+0.5; |
---|
344 | GeometryCal.focal=1; |
---|
345 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
---|
346 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
---|
347 | ImaDoc.GeometryCalib=GeometryCal; |
---|
348 | t=struct2xml(ImaDoc); |
---|
349 | t=set(t,1,'name','ImaDoc'); |
---|
350 | save(t,[filebase_merge '.xml']) |
---|
351 | display([filebase_merge '.xml saved']) |
---|
352 | else |
---|
353 | MergeData.ListGlobalAttribute={'Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
---|
354 | MergeData.nb_coord=2; |
---|
355 | MergeData.nb_dim=2; |
---|
356 | MergeData.dt=1; |
---|
357 | MergeData.Time=time_i; |
---|
358 | error=struct2nc(mergename,MergeData); %save result file |
---|
359 | if isempty(error) |
---|
360 | display(['output file ' mergename ' written']) |
---|
361 | else |
---|
362 | display(error) |
---|
363 | end |
---|
364 | end |
---|
365 | end |
---|
366 | end |
---|
367 | |
---|
368 | %-------------------------------------------------------------------------- |
---|
369 | function MergeData=merge_field(Data) |
---|
370 | % initiate Matlab structure for physical field |
---|
371 | if isempty(Data)||~iscell(Data) |
---|
372 | MergeData=[]; |
---|
373 | return |
---|
374 | end |
---|
375 | MergeData=Data{1};%default |
---|
376 | error=0; |
---|
377 | nbview=length(Data); |
---|
378 | if nbview==1 |
---|
379 | return |
---|
380 | end |
---|
381 | for iview=1:nbview |
---|
382 | if ~isequal(MergeData.ListDimName,Data{iview}.ListDimName) |
---|
383 | error=1; |
---|
384 | end |
---|
385 | if ~isequal(MergeData.ListVarName,Data{iview}.ListVarName) |
---|
386 | error=1; |
---|
387 | end |
---|
388 | % if ~isequal(MergeData.VarDimIndex,Data{iview}.VarDimIndex) |
---|
389 | % error=1; |
---|
390 | % end |
---|
391 | end |
---|
392 | if error |
---|
393 | MergeData.Txt='ERROR: attempt at merging fields of incompatible type'; |
---|
394 | return |
---|
395 | end |
---|