1 | %'aver_stat': calculate field average, used with series.fig |
---|
2 | %------------------------------------------------------------------------ |
---|
3 | % function GUI_input=aver_stat(Param) |
---|
4 | % |
---|
5 | %OUTPUT |
---|
6 | % GUI_input=list of options in the GUI series.fig needed for the function |
---|
7 | % |
---|
8 | %INPUT: |
---|
9 | % Param: structure containing all the parameters read on the GUI series |
---|
10 | % or name of the xml file containing these parameters (BATCH case) |
---|
11 | % |
---|
12 | function GUI_input=aver_stat(Param) |
---|
13 | %---------------------------------------------------------------------- |
---|
14 | % --- make average on a series of files |
---|
15 | %---------------------------------------------------------------------- |
---|
16 | %INPUT: |
---|
17 | %i1_series: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
---|
18 | %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
---|
19 | %j1_series: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) |
---|
20 | %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) |
---|
21 | %OTHER INPUTS given by the structure Series |
---|
22 | % Series.Time: |
---|
23 | % Series.GeometryCalib:%requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) |
---|
24 | if ~exist('Param','var') |
---|
25 | GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') |
---|
26 | 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) |
---|
27 | 'RootFile';'on';... %root input file name ('on' by default) |
---|
28 | 'FileExt';'on';... %input file extension ('on' by default) |
---|
29 | 'NomType';'on';...%type of file indexing ('on' by default) |
---|
30 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
---|
31 | 'VelTypeMenu';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
---|
32 | 'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
---|
33 | 'CoordType'; 'on';...%can use a transform function |
---|
34 | 'GetObject';'on';...%can use projection object(option 'off'/'one'/'two', |
---|
35 | %'GetMask';'on'...%can use mask option |
---|
36 | %'PARAMETER'; %options: name of the user defined parameter',repeat a line for each parameter |
---|
37 | ''}; |
---|
38 | return |
---|
39 | end |
---|
40 | |
---|
41 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
42 | |
---|
43 | %% input parameters |
---|
44 | % read the xml file for batch case |
---|
45 | if ischar(Param) && ~isempty(find(regexp('Param','.xml$'))) |
---|
46 | Param=xml2struct(Param); |
---|
47 | checkrun=0; |
---|
48 | else % RUN case: parameters introduced as the input structure Param |
---|
49 | hseries=guidata(Param.hseries);%handles of the GUI series |
---|
50 | WaitbarPos=get(hseries.waitbar_frame,'Position'); |
---|
51 | checkrun=1; |
---|
52 | end |
---|
53 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
---|
54 | |
---|
55 | %% projection object |
---|
56 | test_object=get(hseries.GetObject,'Value'); |
---|
57 | if test_object%isfield(Series,'sethandles') |
---|
58 | hset_object=findobj(allchild(0),'tag','set_object'); |
---|
59 | ProjObject=read_GUI(hset_object); |
---|
60 | answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type ' before averaging']); |
---|
61 | if ~isequal(answeryes,'Yes') |
---|
62 | return |
---|
63 | end |
---|
64 | end |
---|
65 | |
---|
66 | %% root input file and type |
---|
67 | RootPath=Param.InputTable(:,1); |
---|
68 | RootFile=Param.InputTable(:,3); |
---|
69 | SubDir=Param.InputTable(:,2); |
---|
70 | NomType=Param.InputTable(:,4); |
---|
71 | FileExt=Param.InputTable(:,5); |
---|
72 | ext=FileExt{1}; |
---|
73 | form=imformats(ext([2:end]));%test valid Matlab image formats |
---|
74 | testima=0; |
---|
75 | if ~isempty(form)||isequal(lower(ext),'.avi')||isequal(lower(ext),'.vol') |
---|
76 | testima(1)=1; |
---|
77 | end |
---|
78 | if length(FileExt)>=2 |
---|
79 | ext_1=FileExt{2}; |
---|
80 | form=imformats(ext_1([2:end]));%test valid Matlab image formats |
---|
81 | if ~isempty(form)||isequal(lower(ext_1),'.avi')||isequal(lower(ext_1),'.vol') |
---|
82 | testima(2)=1; |
---|
83 | end |
---|
84 | if testima(2)~=testima(1) |
---|
85 | msgbox_uvmat('ERROR','images and netcdf files cannot be compared') |
---|
86 | return |
---|
87 | end |
---|
88 | end |
---|
89 | |
---|
90 | |
---|
91 | %% Number of input series: this function accepts two input file series at most (then it operates on the difference of fields) |
---|
92 | nbview=length(RootPath); |
---|
93 | if nbview>2 |
---|
94 | RootPath=RootPath(1:2); |
---|
95 | set(hseries.RootPath,'String',RootPath) |
---|
96 | SubDir=SubDir(1:2); |
---|
97 | set(hseries.SubDir,'String',SubDir) |
---|
98 | RootFile=RootFile(1:2); |
---|
99 | set(hseries.RootFile,'String',RootFile) |
---|
100 | NomType=NomType(1:2); |
---|
101 | FileExt=FileExt(1:2); |
---|
102 | set(hseries.FileExt,'String',FileExt) |
---|
103 | nbview=2; |
---|
104 | end |
---|
105 | |
---|
106 | %% determine image type |
---|
107 | hhh=which('mmreader'); |
---|
108 | for iview=1:nbview |
---|
109 | if isequal(FileExt{iview},'.nc')||isequal(FileExt{iview},'.cdf') |
---|
110 | FileType{iview}='netcdf'; |
---|
111 | elseif isequal(lower(FileExt{iview}),'.avi') |
---|
112 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported() |
---|
113 | MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); |
---|
114 | FileType{iview}='movie'; |
---|
115 | else |
---|
116 | FileType{iview}='avi'; |
---|
117 | end |
---|
118 | elseif isequal(lower(FileExt{iview}),'.vol') |
---|
119 | FileType{iview}='vol'; |
---|
120 | else |
---|
121 | form=imformats(FileExt{iview}(2:end)); |
---|
122 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
---|
123 | if isequal(NomType{iview},'*'); |
---|
124 | FileType{iview}='multimage'; |
---|
125 | else |
---|
126 | FileType{iview}='image'; |
---|
127 | end |
---|
128 | end |
---|
129 | end |
---|
130 | end |
---|
131 | |
---|
132 | %% number of slices |
---|
133 | NbSlice=Param.IndexRange.NbSlice; |
---|
134 | |
---|
135 | %% Field and velocity type (the same for the two views) |
---|
136 | Field_str=get(hseries.FieldMenu,'String'); |
---|
137 | FieldName=[]; %default |
---|
138 | testfield=get(hseries.FieldMenu,'Visible'); |
---|
139 | if isequal(testfield,'on') |
---|
140 | val=get(hseries.FieldMenu,'Value'); |
---|
141 | FieldName=Field_str(val);%the same set of fields for all views |
---|
142 | if isequal(FieldName,{'get_field...'}) |
---|
143 | hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI |
---|
144 | if length(hget_field)>1 |
---|
145 | delete(hget_field(2:end)) |
---|
146 | elseif isempty(hget_field) |
---|
147 | filename=... |
---|
148 | name_generator(fullfile(RootPath{1},RootFile{1}),i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),num_j2{1}(1),SubDir{1}); |
---|
149 | get_field(filename); |
---|
150 | return |
---|
151 | end |
---|
152 | SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI |
---|
153 | end |
---|
154 | end |
---|
155 | |
---|
156 | %% get the velocity type |
---|
157 | testcivx=0; |
---|
158 | if ~isequal(FieldName,{'get_field...'}) |
---|
159 | testcivx=isequal(FileType{1},'netcdf'); |
---|
160 | end |
---|
161 | if testcivx |
---|
162 | VelType_str=get(hseries.VelTypeMenu,'String'); |
---|
163 | VelType_val=get(hseries.VelTypeMenu,'Value'); |
---|
164 | VelType{1}=VelType_str{VelType_val}; |
---|
165 | if nbview==2 |
---|
166 | VelType_str=get(hseries.VelTypeMenu_1,'String'); |
---|
167 | VelType_val=get(hseries.VelTypeMenu_1,'Value'); |
---|
168 | VelType{2}=VelType_str{VelType_val}; |
---|
169 | end |
---|
170 | end |
---|
171 | |
---|
172 | %% Calibration data and timing: read the ImaDoc files |
---|
173 | mode=''; %default |
---|
174 | timecell={}; |
---|
175 | itime=0; |
---|
176 | NbSlice_calib={}; |
---|
177 | for iview=1:nbview%Loop on views |
---|
178 | XmlData{iview}=[];%default |
---|
179 | filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); |
---|
180 | if exist([filebase{iview} '.xml'],'file') |
---|
181 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
---|
182 | if isfield(XmlData{iview},'Time') |
---|
183 | itime=itime+1; |
---|
184 | timecell{itime}=XmlData{iview}.Time; |
---|
185 | end |
---|
186 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
---|
187 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
---|
188 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
---|
189 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
---|
190 | end |
---|
191 | end |
---|
192 | elseif exist([filebase{iview} '.civ'],'file') |
---|
193 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
---|
194 | itime=itime+1; |
---|
195 | timecell{itime}=time; |
---|
196 | XmlData{iview}.Time=time; |
---|
197 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
---|
198 | GeometryCalib.Tx=0; |
---|
199 | GeometryCalib.Ty=0; |
---|
200 | GeometryCalib.Tz=1; |
---|
201 | GeometryCalib.dpx=1; |
---|
202 | GeometryCalib.dpy=1; |
---|
203 | GeometryCalib.sx=1; |
---|
204 | GeometryCalib.Cx=0; |
---|
205 | GeometryCalib.Cy=0; |
---|
206 | GeometryCalib.f=1; |
---|
207 | GeometryCalib.kappa1=0; |
---|
208 | GeometryCalib.CoordUnit='cm'; |
---|
209 | XmlData{iview}.GeometryCalib=GeometryCalib; |
---|
210 | if error==1 |
---|
211 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
---|
212 | end |
---|
213 | end |
---|
214 | end |
---|
215 | |
---|
216 | %% check coincidence in time for several input file series |
---|
217 | multitime=0; |
---|
218 | if isempty(timecell) |
---|
219 | time=[]; |
---|
220 | elseif length(timecell)==1 |
---|
221 | time=timecell{1}; |
---|
222 | elseif length(timecell)>1 |
---|
223 | multitime=1; |
---|
224 | for icell=1:length(timecell) |
---|
225 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
---|
226 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
---|
227 | time=timecell{1}; |
---|
228 | multitime=0; |
---|
229 | break |
---|
230 | end |
---|
231 | end |
---|
232 | end |
---|
233 | if multitime |
---|
234 | for icell=1:length(timecell) |
---|
235 | time(icell,:,:)=timecell{icell}; |
---|
236 | end |
---|
237 | diff_time=max(max(diff(time))); |
---|
238 | if diff_time>0 |
---|
239 | msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) |
---|
240 | end |
---|
241 | end |
---|
242 | if size(time,2) < i2_series{1}(end) || size(time,3) < num_j2{1}(end)% time array absent or too short in ImaDoc xml file' |
---|
243 | time=[]; |
---|
244 | end |
---|
245 | |
---|
246 | %% Name(s) of output file(s) |
---|
247 | filebase_out=filebase{1};% the result file has the same root name as the input file series (and the first one is chosen in case of two input series) |
---|
248 | %file extension of the result |
---|
249 | if testima %case of images |
---|
250 | ext_out='.png'; |
---|
251 | else |
---|
252 | ext_out='.nc'; |
---|
253 | end |
---|
254 | subdir_result=[SubDir{1} '.stat'];%subdirectory for the results |
---|
255 | pathdir=RootPath{1};% full subdirectory name, including path |
---|
256 | checkdetect=1; |
---|
257 | while checkdetect %create a new subdir if the netcdf files already exist |
---|
258 | checkdetect=exist(fullfile(pathdir,subdir_result)); |
---|
259 | if checkdetect% if a nesult dir already exists |
---|
260 | r=regexp(subdir_result,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number |
---|
261 | if isempty(r) |
---|
262 | r(1).root=[subdir_result '_']; |
---|
263 | r(1).num1='0'; |
---|
264 | end |
---|
265 | subdir_result=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1 |
---|
266 | end |
---|
267 | end |
---|
268 | NomTypeOut='_1-2'; |
---|
269 | fileresult{1}=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},ext_out,NomTypeOut,i1_series{1}(1),i1_series{1}(end),[],[]); |
---|
270 | |
---|
271 | % A REPRNDRE CAS MULTI-NIVEAU: |
---|
272 | % pathdir=fullfile(RootPath{1},subdir_result);% full subdirectory name, including path |
---|
273 | % if NbSlice==1% keep track of the first and lsat indices of the input files |
---|
274 | % %NomTypeOut=nomtype2pair(Param.InputTable{1,4},i2_series{end}(end)-i1_series{1}(1),j2_series{end}(end)-j1_series{1}(1)); |
---|
275 | % NomTypeOut='_1-2'; |
---|
276 | % fileresult{1}=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},ext_out,NomTypeOut,i1_series{1}(1),i1_series{1}(end),[],[]); |
---|
277 | % testexist=exist(fileresult{1},'file'); |
---|
278 | % else % simplified indexing with i_slice for multiple slices |
---|
279 | % testexist=0; |
---|
280 | % for i_slice=1:NbSlice |
---|
281 | % fileresult{1}=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},ext_out,NomTypeOut,i_slice,[],[],[]); |
---|
282 | % if exist(fileresult{i_slice},'file') |
---|
283 | % testexist=1; |
---|
284 | % break |
---|
285 | % end |
---|
286 | % end |
---|
287 | % end |
---|
288 | % if testexist |
---|
289 | % subdir_result=[subdir_result '.0']; |
---|
290 | % end |
---|
291 | % end |
---|
292 | % create result directory if needed |
---|
293 | if ~exist(fullfile(RootPath{1},subdir_result),'dir') |
---|
294 | [m1,m2,m3]=mkdir(fullfile(RootPath{1},subdir_result)); |
---|
295 | if ~isequal(m2,'') |
---|
296 | msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation |
---|
297 | end |
---|
298 | end |
---|
299 | [xx,msg2] = fileattrib(fullfile(RootPath{1},subdir_result),'+w','g'); %yield writing access (+w) to user group (g) |
---|
300 | if ~strcmp(msg2,'') |
---|
301 | msgbox_uvmat('ERROR',['pb of permission for ' fullfile(RootPath{1},subdir_result) ': ' msg2])%error message for writting access |
---|
302 | return |
---|
303 | end |
---|
304 | |
---|
305 | %% coordinate transform or other user defined transform |
---|
306 | transform_fct='';%default |
---|
307 | if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'fct_handle') |
---|
308 | transform_fct=Param.FieldTransform.fct_handle; |
---|
309 | end |
---|
310 | |
---|
311 | %% main loop |
---|
312 | siz=size(i1_series{1}); |
---|
313 | nbfield2=siz(1); %nb of consecutive fields at each level(burst |
---|
314 | nbfield=siz(1)*siz(2); |
---|
315 | nbfield=floor(nbfield/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices) |
---|
316 | |
---|
317 | % loop on slices |
---|
318 | for i_slice=1:NbSlice |
---|
319 | for ifield=1:nbfield |
---|
320 | indselect(:,ifield)=((ifield-1)*NbSlice+(i_slice-1))*nbfield2+[1:nbfield2]';%selected indices on the list of files of a slice |
---|
321 | end |
---|
322 | S=0; %initiate the image sum S |
---|
323 | nbfiles=0; |
---|
324 | nbmissing=0; |
---|
325 | % averaging loop |
---|
326 | for index=1:nbfield*nbfield2 |
---|
327 | % stopstate=get(hseries.RUN,'BusyAction'); |
---|
328 | % if isequal(stopstate,'queue') % enable STOP command |
---|
329 | % update_waitbar(hseries.waitbar,WaitbarPos,index/(nbfield*nbfield2)) |
---|
330 | if checkrun |
---|
331 | update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield*nbfield2)) |
---|
332 | stopstate=get(hseries.RUN,'BusyAction'); |
---|
333 | else |
---|
334 | stopstate='queue'; |
---|
335 | end |
---|
336 | ifile=indselect(index); |
---|
337 | % reading input file(s) |
---|
338 | for iview=1:nbview |
---|
339 | filename=filecell{iview,index}; |
---|
340 | if ~isequal(FileType{iview},'netcdf') |
---|
341 | Data{iview}.ListVarName={'A'}; |
---|
342 | Data{iview}.AName='image'; |
---|
343 | switch FileType{iview} |
---|
344 | case 'movie' |
---|
345 | A=read(MovieObject{iview},i1_series{iview}(ifile)); |
---|
346 | case 'avi' |
---|
347 | mov=aviread(filename,i1_series{iview}(ifile)); |
---|
348 | A=frame2im(mov(1)); |
---|
349 | case 'vol' |
---|
350 | A=imread(filename); |
---|
351 | case 'multimage' |
---|
352 | A=imread(filename,i1_series{iview}(ifile)); |
---|
353 | case 'image' |
---|
354 | A=imread(filename); |
---|
355 | end |
---|
356 | Data{iview}.ListVarName={'AY','AX','A'}; % |
---|
357 | Atype{iview}=class(A); |
---|
358 | npy=size(A,1); |
---|
359 | npx=size(A,2); |
---|
360 | nbcolor=size(A,3); |
---|
361 | if nbcolor==3 |
---|
362 | Data{iview}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; |
---|
363 | else |
---|
364 | Data{iview}.VarDimName={'AY','AX',{'AY','AX'}}; |
---|
365 | end |
---|
366 | Data{iview}.AY=[npy-0.5 0.5]; |
---|
367 | Data{iview}.AX=[0.5 npx-0.5]; |
---|
368 | Data{iview}.A=double(A); |
---|
369 | Data{iview}.CoordUnit='pixel'; |
---|
370 | elseif testcivx |
---|
371 | [Data{iview},VelTypeOut,errormsg]=read_civxdata(filename,FieldName,VelType); |
---|
372 | if ~isempty(errormsg) |
---|
373 | msgbox_uvmat('ERROR',['error of input reading: ' errormsg]) |
---|
374 | return |
---|
375 | end |
---|
376 | else |
---|
377 | [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
---|
378 | Data{iview}.VarAttribute=SubField.VarAttribute; |
---|
379 | end |
---|
380 | if isfield(Data{iview},'Txt') |
---|
381 | msgbox_uvmat('ERROR',['error of input reading: ' Data{iview}.Txt]) |
---|
382 | return |
---|
383 | end |
---|
384 | end |
---|
385 | |
---|
386 | % coordinate transform (or other user defined transform) |
---|
387 | if ~isempty(transform_fct) |
---|
388 | if ~isempty(NbSlice_calib) |
---|
389 | Data{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1;%Zindex for phys transform |
---|
390 | end |
---|
391 | if nbview==2 |
---|
392 | [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
---|
393 | if isempty(Data{2}) |
---|
394 | Data(2)=[]; |
---|
395 | end |
---|
396 | else |
---|
397 | Data{1}=transform_fct(Data{1},XmlData{1}); |
---|
398 | end |
---|
399 | end |
---|
400 | |
---|
401 | % field calculation (vort, div...) |
---|
402 | if testcivx |
---|
403 | Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) |
---|
404 | end |
---|
405 | |
---|
406 | % field substration (for two input file series) |
---|
407 | if length(Data)==2 |
---|
408 | [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields |
---|
409 | if ~isempty(errormsg) |
---|
410 | msgbox_uvmat('ERROR',['error in aver_stat/sub_field:' errormsg]) |
---|
411 | return |
---|
412 | end |
---|
413 | else |
---|
414 | Field=Data{1}; |
---|
415 | end |
---|
416 | if test_object |
---|
417 | [Field,errormsg]=proj_field(Field,ProjObject); |
---|
418 | if ~isempty(errormsg) |
---|
419 | msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg]) |
---|
420 | return |
---|
421 | end |
---|
422 | end |
---|
423 | nbfiles=nbfiles+1; |
---|
424 | if nbfiles==1 %first field |
---|
425 | time_1=[]; |
---|
426 | if isfield(Field,'Time') |
---|
427 | time_1=Field.Time(1); |
---|
428 | end |
---|
429 | DataMean=Field;%default |
---|
430 | else |
---|
431 | for ivar=1:length(Field.ListVarName) |
---|
432 | VarName=Field.ListVarName{ivar}; |
---|
433 | eval(['sizmean=size(DataMean.' VarName ');']); |
---|
434 | eval(['siz=size(Field.' VarName ');']); |
---|
435 | if ~isequal(siz,sizmean) |
---|
436 | msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid']) |
---|
437 | return |
---|
438 | else |
---|
439 | eval(['DataMean.' VarName '=DataMean.' VarName '+ Field.' VarName ';']); % update the sum |
---|
440 | end |
---|
441 | end |
---|
442 | end |
---|
443 | % end |
---|
444 | end |
---|
445 | %end averaging loop |
---|
446 | for ivar=1:length(Field.ListVarName) |
---|
447 | VarName=Field.ListVarName{ivar}; |
---|
448 | eval(['DataMean.' VarName '=DataMean.' VarName '/nbfiles;']); % normalize the mean |
---|
449 | end |
---|
450 | if nbmissing~=0 |
---|
451 | msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted']) |
---|
452 | end |
---|
453 | if isempty(time) % time read from files prevails |
---|
454 | if isfield(Field,'Time') |
---|
455 | time_end=Field.Time(1);%last time read |
---|
456 | if ~isempty(time_1) |
---|
457 | DataMean.Time=time_1; |
---|
458 | DataMean.Time_end=time_end; |
---|
459 | end |
---|
460 | end |
---|
461 | else % time from ImaDoc prevails |
---|
462 | DataMean.Time=time(1,i1_series{1}(1),j1_series{1}(1)); |
---|
463 | DataMean.Time_end=time(end,i1_series{end}(end),j1_series{end}(end)); |
---|
464 | end |
---|
465 | |
---|
466 | %writing the result file |
---|
467 | if testima %case of images |
---|
468 | if isequal(Atype{1},'uint16') |
---|
469 | imwrite(uint16(DataMean.A),fileresult{i_slice},'BitDepth',16); % case of 16 bit images |
---|
470 | else |
---|
471 | imwrite(uint8(DataMean.A),fileresult{i_slice},'BitDepth',8); % case of 8 bit images |
---|
472 | end |
---|
473 | display([fileresult{i_slice} ' written']); |
---|
474 | else %case of netcdf input file , determine global attributes |
---|
475 | if isempty(strcmp('Conventions',DataMean.ListGlobalAttribute)) |
---|
476 | DataMean.ListGlobalAttribute=['Conventions' DataMean.ListGlobalAttribute]; |
---|
477 | end |
---|
478 | DataMean.Conventions='uvmat'; |
---|
479 | DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {Param.Action}]; |
---|
480 | ActionKey='Action'; |
---|
481 | while isfield(DataMean,ActionKey) |
---|
482 | ActionKey=[ActionKey '_1']; |
---|
483 | end |
---|
484 | DataMean.(ActionKey)=Param.Action; |
---|
485 | DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {ActionKey}]; |
---|
486 | if isfield(DataMean,'Time') |
---|
487 | DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {'Time','Time_end'}]; |
---|
488 | end |
---|
489 | errormsg=struct2nc(fileresult{i_slice},DataMean); %save result file |
---|
490 | if isempty(errormsg) |
---|
491 | display([fileresult{i_slice} ' written']); |
---|
492 | else |
---|
493 | msgbox_uvmat('ERROR',['error in writting result file: ' errormsg]) |
---|
494 | display(errormsg) |
---|
495 | end |
---|
496 | end % end averaging loop |
---|
497 | end % end loop on slices |
---|
498 | |
---|
499 | %% reproduce ImaDoc/GeometryCalib for image series |
---|
500 | if isfield(XmlData{1},'GeometryCalib') && ~isempty(XmlData{1}.GeometryCalib) |
---|
501 | [tild,RootFile]=fileparts(filebase_out); |
---|
502 | outputxml=fullfile(pathdir,[RootFile '.xml']); |
---|
503 | errormsg=update_imadoc(XmlData{1}.GeometryCalib,outputxml);% introduce the calibration data in the xml file |
---|
504 | if strcmp(errormsg,'') |
---|
505 | display(['GeometryCalib transferred to ' outputxml]) |
---|
506 | else |
---|
507 | msgbox_uvmat('ERROR',errormsg); |
---|
508 | end |
---|
509 | end |
---|
510 | |
---|
511 | %% open the result file with uvmat |
---|
512 | hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI |
---|
513 | delete(hget_field) |
---|
514 | uvmat(fileresult{end}) |
---|