1 | %'time_series': extract a time series, used with series.fig |
---|
2 | % this function can be used as a template for applying a global operation on a series of input fields |
---|
3 | %------------------------------------------------------------------------ |
---|
4 | % function GUI_input=time_series(Param) |
---|
5 | % |
---|
6 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
7 | % |
---|
8 | % This function is used in four modes by the GUI series: |
---|
9 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
---|
10 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
---|
11 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
---|
12 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
---|
13 | % |
---|
14 | % This function is used in four modes by the GUI series: |
---|
15 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
---|
16 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
---|
17 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
---|
18 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
---|
19 | % |
---|
20 | %OUTPUT |
---|
21 | % GUI_input=list of options in the GUI series.fig needed for the function |
---|
22 | % |
---|
23 | %INPUT: |
---|
24 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
---|
25 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
---|
26 | % In the absence of input (as activated when the current Action is selected |
---|
27 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
---|
28 | % |
---|
29 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
---|
30 | % .InputTable: cell of input file names, (several lines for multiple input) |
---|
31 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
---|
32 | % .OutputSubDir: name of the subdirectory for data outputs |
---|
33 | % .OutputDir: directory for data outputs, including path |
---|
34 | % .Action: .ActionName: name of the current activated function |
---|
35 | % .ActionPath: path of the current activated function |
---|
36 | % .IndexRange: set the file or frame indices on which the action must be performed |
---|
37 | % .FieldTransform: .TransformName: name of the selected transform function |
---|
38 | % .TransformPath: path of the selected transform function |
---|
39 | % .TransformHandle: corresponding function handle |
---|
40 | % .InputFields: sub structure describing the input fields withfields |
---|
41 | % .FieldName: name of the field |
---|
42 | % .VelType: velocity type |
---|
43 | % .FieldName_1: name of the second field in case of two input series |
---|
44 | % .VelType_1: velocity type of the second field in case of two input series |
---|
45 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
---|
46 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
47 | % |
---|
48 | function ParamOut=time_series(Param) |
---|
49 | |
---|
50 | %% requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) |
---|
51 | if ~exist('Param','var') |
---|
52 | ParamOut={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') |
---|
53 | 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) |
---|
54 | 'RootFile';'on';... %root input file name ('on' by default) |
---|
55 | 'FileExt';'on';... %input file extension ('on' by default) |
---|
56 | 'NomType';'on';...%type of file indexing ('on' by default) |
---|
57 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
---|
58 | 'VelTypeMenu';'two';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default) |
---|
59 | 'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
---|
60 | 'CoordType';'on';...%can use a transform function 'off' by default |
---|
61 | 'GetObject';'on';...%can use projection object ,'off' by default |
---|
62 | 'OutputDirExt';'.series'... |
---|
63 | %'GetMask';'on'...%can use mask option ,'off' by default |
---|
64 | %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter |
---|
65 | ''}; |
---|
66 | return %exit the function |
---|
67 | end |
---|
68 | |
---|
69 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
---|
70 | %% select different modes, RUN, parameter input, BATCH |
---|
71 | % BATCH case: read the xml file for batch case |
---|
72 | ParamOut=Param; %default output |
---|
73 | if ischar(Param) |
---|
74 | if strcmp(Param,'input?') |
---|
75 | checkrun=1;% will inly search input parameters (preparation of BATCH mode) |
---|
76 | else |
---|
77 | Param=xml2struct(Param); |
---|
78 | checkrun=0; |
---|
79 | end |
---|
80 | % RUN case: parameters introduced as the input structure Param |
---|
81 | else |
---|
82 | hseries=guidata(Param.hseries);%handles of the GUI series |
---|
83 | WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series |
---|
84 | checkrun=2; % indicate the RUN option is used |
---|
85 | end |
---|
86 | |
---|
87 | %% root input file(s) and type |
---|
88 | RootPath=Param.InputTable(:,1); |
---|
89 | RootFile=Param.InputTable(:,3); |
---|
90 | SubDir=Param.InputTable(:,2); |
---|
91 | NomType=Param.InputTable(:,4); |
---|
92 | FileExt=Param.InputTable(:,5); |
---|
93 | |
---|
94 | % get the set of input file names (cell array filecell), and the lists of |
---|
95 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
---|
96 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
---|
97 | % filecell{iview,fileindex}: cell array representing the list of file names |
---|
98 | % iview: line in the table corresponding to a given file series |
---|
99 | % fileindex: file index within the file series, |
---|
100 | % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j |
---|
101 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
---|
102 | % set of frame indices used for movie or multimage input |
---|
103 | % numbers of slices and file indices |
---|
104 | |
---|
105 | NbSlice=1;%default |
---|
106 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
---|
107 | NbSlice=Param.IndexRange.NbSlice; |
---|
108 | end |
---|
109 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
---|
110 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
---|
111 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
---|
112 | nbfield=nbfield_j*nbfield_i; %total number of fields |
---|
113 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
---|
114 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
---|
115 | |
---|
116 | %determine the file type on each line from the first input file |
---|
117 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
---|
118 | NcTypeOptions={'netcdf','civx','civdata'}; |
---|
119 | for iview=1:nbview |
---|
120 | if ~exist(filecell{iview,1}','file') |
---|
121 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
---|
122 | return |
---|
123 | end |
---|
124 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); |
---|
125 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
---|
126 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
---|
127 | if ~isempty(j1_series{iview}) |
---|
128 | frame_index{iview}=j1_series{iview}; |
---|
129 | else |
---|
130 | frame_index{iview}=i1_series{iview}; |
---|
131 | end |
---|
132 | end |
---|
133 | |
---|
134 | %% calibration data and timing: read the ImaDoc files |
---|
135 | mode=''; %default |
---|
136 | timecell={}; |
---|
137 | itime=0; |
---|
138 | NbSlice_calib={}; |
---|
139 | XmlData=cell(1,nbview);%initiate the structures containing the data from the xml file (calibration and timing) |
---|
140 | for iview=1:nbview%Loop on views |
---|
141 | SubDirBase=regexprep(SubDir{iview},'\..*','');%take the root part of SubDir, before the first dot '.' |
---|
142 | filexml=[fullfile(RootPath{iview},SubDirBase) '.xml'];%new convention: xml at the level of the image folder |
---|
143 | if ~exist(filexml,'file') |
---|
144 | filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.xml']; % old convention: xml inside the image folder |
---|
145 | if ~exist(filexml,'file') |
---|
146 | filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.civ']; % very old convention: .civ file |
---|
147 | if ~exist(filexml,'file') |
---|
148 | filexml=''; |
---|
149 | end |
---|
150 | end |
---|
151 | end |
---|
152 | if ~isempty(filexml) |
---|
153 | [XmlData{iview},error]=imadoc2struct(filexml); |
---|
154 | end |
---|
155 | if isfield(XmlData{iview},'Time') |
---|
156 | itime=itime+1; |
---|
157 | timecell{itime}=XmlData{iview}.Time; |
---|
158 | end |
---|
159 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
---|
160 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
---|
161 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
---|
162 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
---|
163 | end |
---|
164 | end |
---|
165 | end |
---|
166 | |
---|
167 | %% check coincidence in time for several input file series |
---|
168 | multitime=0; |
---|
169 | if isempty(timecell) |
---|
170 | time=[]; |
---|
171 | elseif length(timecell)==1 |
---|
172 | time=timecell{1}; |
---|
173 | elseif length(timecell)>1 |
---|
174 | multitime=1; |
---|
175 | for icell=1:length(timecell) |
---|
176 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
---|
177 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
---|
178 | time=timecell{1}; |
---|
179 | multitime=0; |
---|
180 | break |
---|
181 | end |
---|
182 | end |
---|
183 | end |
---|
184 | if multitime |
---|
185 | for icell=1:length(timecell) |
---|
186 | time(icell,:,:)=timecell{icell}; |
---|
187 | end |
---|
188 | diff_time=max(max(diff(time))); |
---|
189 | if diff_time>0 |
---|
190 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
---|
191 | end |
---|
192 | end |
---|
193 | if size(time,2) < i2_series{1}(end) ||( ~isempty(j2_series{1}) && size(time,3) < j2_series{1}(end))% time array absent or too short in ImaDoc xml file' |
---|
194 | time=[]; |
---|
195 | end |
---|
196 | |
---|
197 | %% coordinate transform or other user defined transform |
---|
198 | transform_fct='';%default |
---|
199 | if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'TransformHandle') |
---|
200 | transform_fct=Param.FieldTransform.TransformHandle; |
---|
201 | end |
---|
202 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
---|
203 | % EDIT FROM HERE |
---|
204 | |
---|
205 | %% check the validity of input file types |
---|
206 | if CheckImage{1} |
---|
207 | FileExtOut='.png'; % write result as .png images for image inputs |
---|
208 | elseif CheckNc{1} |
---|
209 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
---|
210 | else |
---|
211 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
---|
212 | return |
---|
213 | end |
---|
214 | if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) |
---|
215 | msgbox_uvmat('ERROR','input must be two image series or two netcdf file series') |
---|
216 | return |
---|
217 | end |
---|
218 | NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series |
---|
219 | if NbSlice~=nbfield_j |
---|
220 | answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); |
---|
221 | if ~strcmp(answer,'Yes') |
---|
222 | return |
---|
223 | end |
---|
224 | end |
---|
225 | |
---|
226 | %% Set field names and velocity types |
---|
227 | InputFields{1}=[];%default (case of images) |
---|
228 | if isfield(Param,'InputFields') |
---|
229 | InputFields{1}=Param.InputFields; |
---|
230 | end |
---|
231 | if nbview==2 |
---|
232 | InputFields{2}=[];%default (case of images) |
---|
233 | if isfield(Param,'InputFields') |
---|
234 | InputFields{2}=Param.InputFields{1};%default |
---|
235 | if isfield(Param.InputFields,'FieldName_1') |
---|
236 | InputFields{2}.FieldName=Param.InputFields.FieldName_1; |
---|
237 | if isfield(Param.InputFields,'VelType_1') |
---|
238 | InputFields{2}.VelType=Param.InputFields.VelType_1; |
---|
239 | end |
---|
240 | end |
---|
241 | end |
---|
242 | end |
---|
243 | %%% TO UPDATE |
---|
244 | if isequal(FieldName,'get_field...') |
---|
245 | hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI |
---|
246 | if numel(hget_field)>1 |
---|
247 | delete(hget_field(2:end)) % delete multiple occurerence of the GUI get_fioeld |
---|
248 | elseif isempty(hget_field) |
---|
249 | filename=filecell{1,1}; |
---|
250 | % filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),num_j2{1}(1),SubDir{1}); |
---|
251 | idetect(iview)=exist(filename,'file'); |
---|
252 | hget_field=get_field(filename); |
---|
253 | return |
---|
254 | end |
---|
255 | SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI |
---|
256 | if isempty(SubField) |
---|
257 | delete(hget_field) |
---|
258 | filename=filecell{1,1}; |
---|
259 | %filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),j2_series{1}(1),SubDir{1}); |
---|
260 | hget_field=get_field(filename); |
---|
261 | SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI |
---|
262 | end |
---|
263 | end |
---|
264 | %%%%%%% |
---|
265 | |
---|
266 | %% Initiate output fields |
---|
267 | %initiate the output structure as a copy of the first input one (reproduce fields) |
---|
268 | [DataOut,ParamOut,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1); |
---|
269 | if ~isempty(errormsg) |
---|
270 | msgbox_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg]) |
---|
271 | return |
---|
272 | end |
---|
273 | time_1=[]; |
---|
274 | if isfield(DataOut,'Time') |
---|
275 | time_1=DataOut.Time(1); |
---|
276 | end |
---|
277 | if CheckNc{iview} |
---|
278 | if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute)) |
---|
279 | DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute]; |
---|
280 | end |
---|
281 | DataOut.Conventions='uvmat'; |
---|
282 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}]; |
---|
283 | ActionKey='Action'; |
---|
284 | while isfield(DataOut,ActionKey) |
---|
285 | ActionKey=[ActionKey '_1']; |
---|
286 | end |
---|
287 | DataOut.(ActionKey)=Param.Action; |
---|
288 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}]; |
---|
289 | if isfield(DataOut,'Time') |
---|
290 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}]; |
---|
291 | end |
---|
292 | end |
---|
293 | |
---|
294 | |
---|
295 | |
---|
296 | |
---|
297 | %% detect whether the two files are 'images' or 'netcdf' |
---|
298 | testcivx=0; |
---|
299 | % FileExt=get(hseries.FileExt,'String'); |
---|
300 | if ~isequal(FieldName,{'get_field...'}) |
---|
301 | testcivx=isequal(FileType{1},'netcdf'); |
---|
302 | end |
---|
303 | % VelType_str=get(hseries.VelTypeMenu,'String'); |
---|
304 | % VelType_val=get(hseries.VelTypeMenu,'Value'); |
---|
305 | % VelType{1}=VelType_str{VelType_val}; |
---|
306 | % if nbview==2 |
---|
307 | % VelType_str=get(hseries.VelTypeMenu_1,'String'); |
---|
308 | % VelType_val=get(hseries.VelTypeMenu_1,'Value'); |
---|
309 | % VelType{2}=VelType_str{VelType_val}; |
---|
310 | % end |
---|
311 | |
---|
312 | %% LOOP ON SLICES |
---|
313 | nbmissing=0; %number of undetected files |
---|
314 | for i_slice=1:NbSlice |
---|
315 | dt=[]; |
---|
316 | %%%%%%%%%%%%%%%%%%%%%%%%%%%% LOOP ON FIELDS WITHIN A SLICE |
---|
317 | filecounter=0; |
---|
318 | for ifile=i_slice:NbSlice:nbfield |
---|
319 | if checkrun |
---|
320 | update_waitbar(hseries.waitbar_frame,WaitbarPos,ifile/nbfield) |
---|
321 | stopstate=get(hseries.RUN,'BusyAction'); |
---|
322 | else |
---|
323 | stopstate='queue'; |
---|
324 | end |
---|
325 | errormsg=''; |
---|
326 | if isequal(stopstate,'queue')% enable STOP command |
---|
327 | % loop on views (in case of multiple input series) |
---|
328 | for iview=1:nbview |
---|
329 | filename=filecell{iview,ifile}; |
---|
330 | % filename=name_generator(filebase{iview},... |
---|
331 | % i1_series{iview}(ifile),j1_series{iview}(ifile),FileExt{iview},NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile),SubDir{iview}); |
---|
332 | if exist(filename,'file') |
---|
333 | try |
---|
334 | Data{iview}=[]; %default |
---|
335 | if ~isequal(FileType{iview},'netcdf') |
---|
336 | Data{iview}.ListVarName={'A'}; |
---|
337 | Data{iview}.AName='image'; |
---|
338 | switch FileType{iview} |
---|
339 | case 'movie' |
---|
340 | A=read(MovieObject{iview},i1_series{iview}(ifile)); |
---|
341 | case 'avi' |
---|
342 | mov=aviread(filename,i1_series{iview}(ifile)); |
---|
343 | A=frame2im(mov(1)); |
---|
344 | case 'vol' |
---|
345 | A=imread(filename); |
---|
346 | case 'multimage' |
---|
347 | A=imread(filename,i1_series{iview}(ifile)); |
---|
348 | case 'image' |
---|
349 | A=imread(filename); |
---|
350 | end |
---|
351 | Data{iview}.ListVarName={'AY','AX','A'}; % |
---|
352 | npy=size(A,1); |
---|
353 | npx=size(A,2); |
---|
354 | nbcolor=size(A,3); |
---|
355 | if nbcolor==3 |
---|
356 | Data{iview}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; |
---|
357 | else |
---|
358 | Data{iview}.VarDimName={'AY','AX',{'AY','AX'}}; |
---|
359 | end |
---|
360 | Data{iview}.AY=[npy-0.5 0.5]; |
---|
361 | Data{iview}.AX=[0.5 npx-0.5]; |
---|
362 | Data{iview}.A=double(A); |
---|
363 | Data{iview}.CoordUnit='pixel'; |
---|
364 | elseif testcivx |
---|
365 | [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); |
---|
366 | if ~isequal(FieldName,{''}) |
---|
367 | Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) |
---|
368 | end |
---|
369 | else |
---|
370 | [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
---|
371 | Data{iview}.VarAttribute=SubField.VarAttribute; |
---|
372 | end |
---|
373 | if ~isempty(NbSlice_calib) % z index |
---|
374 | Data{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1; |
---|
375 | end |
---|
376 | catch ME |
---|
377 | errormsg=ME.message; |
---|
378 | end |
---|
379 | else |
---|
380 | errormsg=[filename ' is missing']; |
---|
381 | end |
---|
382 | if isempty(errormsg) |
---|
383 | % coordinate transform (or other user defined transform) |
---|
384 | if ~isempty(transform_fct) |
---|
385 | if nbview==2 |
---|
386 | [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
---|
387 | if isempty(Data{2}) |
---|
388 | Data(2)=[]; |
---|
389 | end |
---|
390 | else |
---|
391 | Data{1}=transform_fct(Data{1},XmlData{1}); |
---|
392 | end |
---|
393 | end |
---|
394 | if length(Data)==2 |
---|
395 | [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields |
---|
396 | else |
---|
397 | Field=Data{1}; |
---|
398 | end |
---|
399 | if test_object |
---|
400 | [Field,errormsg]=proj_field(Field,ProjObject); |
---|
401 | end |
---|
402 | end |
---|
403 | filecounter=filecounter+1; |
---|
404 | |
---|
405 | % initiate the time series at the first iteration |
---|
406 | if filecounter==1 |
---|
407 | % stop program if the first field reading is in error |
---|
408 | if ~isempty(errormsg) |
---|
409 | msgbox_uvmat('ERROR',['error in time_series/sub_field:' errormsg]) |
---|
410 | return |
---|
411 | end |
---|
412 | RecordData=Field;%default |
---|
413 | RecordData.NbDim=Field.NbDim+1; %add the time dimension for plots |
---|
414 | nbvar=length(Field.ListVarName); |
---|
415 | if nbvar==0 |
---|
416 | msgbox_uvmat('ERROR','no input variable selected in get_field') |
---|
417 | return |
---|
418 | end |
---|
419 | testsum=2*ones(1,nbvar);%initiate flag for action on each variable |
---|
420 | if isfield(Field,'VarAttribute') % look for coordinate and flag variables |
---|
421 | for ivar=1:nbvar |
---|
422 | if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') |
---|
423 | var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable |
---|
424 | if isequal(var_role,'errorflag') |
---|
425 | msgbox_uvmat('ERROR','do not handle error flags in time series') |
---|
426 | return |
---|
427 | end |
---|
428 | if isequal(var_role,'warnflag') |
---|
429 | testsum(ivar)=0; % not recorded variable |
---|
430 | eval(['RecordData=rmfield(RecordData,''' Field.ListVarName{ivar} ''');']);%remove variable |
---|
431 | end |
---|
432 | if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|... |
---|
433 | isequal(var_role,'coord_z')|isequal(var_role,'coord') |
---|
434 | testsum(ivar)=1; %constant coordinates, record without time evolution |
---|
435 | end |
---|
436 | end |
---|
437 | % check whether the variable ivar is a dimension variable |
---|
438 | DimCell=Field.VarDimName{ivar}; |
---|
439 | if ischar(DimCell) |
---|
440 | DimCell={DimCell}; |
---|
441 | end |
---|
442 | if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables |
---|
443 | testsum(ivar)=1; |
---|
444 | end |
---|
445 | end |
---|
446 | end |
---|
447 | for ivar=1:nbvar |
---|
448 | if testsum(ivar)==2 |
---|
449 | eval(['RecordData.' Field.ListVarName{ivar} '=[];']) |
---|
450 | end |
---|
451 | end |
---|
452 | RecordData.ListVarName=[{'Time'} RecordData.ListVarName]; |
---|
453 | end |
---|
454 | |
---|
455 | % add data to the current field |
---|
456 | for ivar=1:length(Field.ListVarName) |
---|
457 | VarName=Field.ListVarName{ivar}; |
---|
458 | VarVal=Field.(VarName); |
---|
459 | if testsum(ivar)==2% test for recorded variable |
---|
460 | if isempty(errormsg) |
---|
461 | if isequal(ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode |
---|
462 | if isempty(VarVal) |
---|
463 | msgbox_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(ifile))]) |
---|
464 | return |
---|
465 | end |
---|
466 | VarVal=mean(VarVal,1); |
---|
467 | end |
---|
468 | VarVal=shiftdim(VarVal,-1); %shift dimension |
---|
469 | RecordData.(VarName)=cat(1,RecordData.(VarName),VarVal);%concanete the current field to the time series |
---|
470 | else |
---|
471 | RecordData.(VarName)=cat(1,RecordData.(VarName),0);% put each variable to 0 in case of input reading error |
---|
472 | end |
---|
473 | elseif testsum(ivar)==1% variable representing fixed coordinates |
---|
474 | eval(['VarInit=RecordData.' VarName ';']); |
---|
475 | if isempty(errormsg) && ~isequal(VarVal,VarInit) |
---|
476 | msgbox_uvmat('ERROR',['time series requires constant coordinates ' VarName]) |
---|
477 | return |
---|
478 | end |
---|
479 | end |
---|
480 | end |
---|
481 | |
---|
482 | % record the time: |
---|
483 | if isempty(time)% time read in ncfiles |
---|
484 | if isfield(Field,'Time') |
---|
485 | RecordData.Time(filecounter,1)=Field.Time; |
---|
486 | else |
---|
487 | RecordData.Time(filecounter,1)=ifile;%default |
---|
488 | end |
---|
489 | else % time from ImaDoc prevails TODO: correct |
---|
490 | % RecordData.Time(filecounter,1)=time{1}(i1_series{1})(ifile),j1_series{1}(ifile))+time(end,i2_series{end}(ifile),j2_series{end}(ifile)))/2; |
---|
491 | RecordData.Time(filecounter,1)=i1_series{1}(ifile);% TODO : generalise |
---|
492 | end |
---|
493 | |
---|
494 | % record the number of missing input fields |
---|
495 | if ~isempty(errormsg) |
---|
496 | nbmissing=nbmissing+1; |
---|
497 | display(['ifile=' num2str(ifile) ':' errormsg]) |
---|
498 | end |
---|
499 | end |
---|
500 | end |
---|
501 | end |
---|
502 | %%%%%%% END OF LOOP WITHIN A SLICE |
---|
503 | |
---|
504 | %remove time for global attributes if exists |
---|
505 | Time_index=find(strcmp('Time',RecordData.ListGlobalAttribute)); |
---|
506 | if ~isempty(Time_index) |
---|
507 | RecordData.ListGlobalAttribute(Time_index)=[]; |
---|
508 | end |
---|
509 | RecordData.Conventions='uvmat'; |
---|
510 | for ivar=1:numel(RecordData.ListVarName) |
---|
511 | VarName=RecordData.ListVarName{ivar}; |
---|
512 | eval(['RecordData.' VarName '=squeeze(RecordData.' VarName ');']) %remove singletons |
---|
513 | end |
---|
514 | |
---|
515 | % add time dimension |
---|
516 | for ivar=1:length(Field.ListVarName) |
---|
517 | DimCell=Field.VarDimName(ivar); |
---|
518 | if testsum(ivar)==2%variable used as time series |
---|
519 | RecordData.VarDimName{ivar}=[{'Time'} DimCell]; |
---|
520 | elseif testsum(ivar)==1 |
---|
521 | RecordData.VarDimName{ivar}=DimCell; |
---|
522 | end |
---|
523 | end |
---|
524 | indexremove=find(~testsum); |
---|
525 | if ~isempty(indexremove) |
---|
526 | RecordData.ListVarName(1+indexremove)=[]; |
---|
527 | RecordData.VarDimName(indexremove)=[]; |
---|
528 | if isfield(RecordData,'Role') && ~isempty(RecordData.Role{1})%generaliser aus autres attributs |
---|
529 | RecordData.Role(1+indexremove)=[]; |
---|
530 | end |
---|
531 | end |
---|
532 | |
---|
533 | %shift variable attributes |
---|
534 | if isfield(RecordData,'VarAttribute') |
---|
535 | RecordData.VarAttribute=[{[]} RecordData.VarAttribute]; |
---|
536 | end |
---|
537 | RecordData.VarDimName=[{'Time'} RecordData.VarDimName]; |
---|
538 | RecordData.Action=Param.Action;%name of the processing programme |
---|
539 | test_time=diff(RecordData.Time)>0;% test that the readed time is increasing (not constant) |
---|
540 | if ~test_time |
---|
541 | RecordData.Time=[1:filecounter]; |
---|
542 | end |
---|
543 | |
---|
544 | % display nbmissing |
---|
545 | if ~isequal(nbmissing,0) |
---|
546 | msgbox_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display']) |
---|
547 | end |
---|
548 | |
---|
549 | %name of result file |
---|
550 | % [filemean]=... |
---|
551 | % name_generator(filebase_out,i1_series{1}(i_slice),j1_series{1}(i_slice),'.nc','_i1-i2_j1-j2',1,i2_series{end}(ifile),j2_series{end}(ifile),subdir_result); |
---|
552 | filemean=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},'.nc','_1',i1_series{1}(i_slice)); |
---|
553 | errormsg=struct2nc(filemean,RecordData); %save result file |
---|
554 | if isempty(errormsg) |
---|
555 | display([filemean ' written']) |
---|
556 | else |
---|
557 | msgbox_uvmat('ERROR',['error in Series/struct2nc: ' errormsg]) |
---|
558 | end |
---|
559 | end |
---|
560 | |
---|
561 | %% plot the time series (the last one in case of multislices) |
---|
562 | figure |
---|
563 | haxes=axes; |
---|
564 | plot_field(RecordData,haxes) |
---|
565 | |
---|
566 | %% display the result file using the GUI get_field |
---|
567 | hget_field=findobj(allchild(0),'name','get_field'); |
---|
568 | if ~isempty(hget_field) |
---|
569 | delete(hget_field) |
---|
570 | end |
---|
571 | get_field(filemean,RecordData) |
---|
572 | |
---|
573 | %------------------------------------------------------------------------ |
---|
574 | % --- Executes on selection change in CoordType. |
---|
575 | function CoordType_Callback(hObject, eventdata, handles) |
---|
576 | %------------------------------------------------------------------------ |
---|
577 | menu_str=get(handles.CoordType,'String'); |
---|
578 | ind_coord=get(handles.CoordType,'Value'); |
---|
579 | coord_option=menu_str{ind_coord}; |
---|
580 | if isequal(coord_option,'more...'); |
---|
581 | fct_name=''; |
---|
582 | if exist('./TMP/current_usr_fct.mat','file')% if a file is found |
---|
583 | h=load('./TMP/current_usr_fct.mat'); |
---|
584 | if isfield(h,'fct_name'); |
---|
585 | fct_name=h.fct_name; |
---|
586 | end |
---|
587 | end |
---|
588 | prompt = {'Enter the name of the transform function'}; |
---|
589 | dlg_title = 'user defined transform'; |
---|
590 | num_lines= 1; |
---|
591 | [FileName, PathName, filterindex] = uigetfile( ... |
---|
592 | {'*.m', ' (*.m)'; |
---|
593 | '*.m', '.m files '; ... |
---|
594 | '*.*', 'All Files (*.*)'}, ... |
---|
595 | 'Pick a file', fct_name); |
---|
596 | fct_name=fullfile(PathName,FileName); |
---|
597 | addpath(PathName);%add the path to the selected fct |
---|
598 | [errormsg,date_str]=check_functions;%check whether new functions can oversed the uvmat package A UTILISER |
---|
599 | if ~exist(fct_name,'file') |
---|
600 | warndlg(['image procesing fct ' fct_name ' not found']) |
---|
601 | else |
---|
602 | transform=FileName(1:end-2);% |
---|
603 | update_menu(handles.CoordType,transform)%add the selected fct to the menu |
---|
604 | % set(handles.mouse_coord,'String',menu([1:end-1])')%update the mouse coord menu |
---|
605 | %save ('./TMP/current_usr_fct.mat','fct_name'); |
---|
606 | end |
---|
607 | end |
---|
608 | ind_coord=get(handles.CoordType,'Value'); |
---|
609 | |
---|
610 | %--------------------------------------------------------------------- |
---|
611 | % % --- Executes on selection change in ProjObject. |
---|
612 | % function ProjObject_Callback(hObject, eventdata, handles) |
---|
613 | % |
---|
614 | % list_object=get(handles.ProjObject,'String'); |
---|
615 | % index=get(handles.ProjObject,'Value'); |
---|
616 | % hseries=get(handles.ProjObject,'Parent'); |
---|
617 | % SeriesData=get(hseries,'UserData'); |
---|
618 | % Obj=SeriesData.ProjObject{index}; |
---|
619 | % [SeriesData.hset_object,SeriesData.sethandles]=set_object(SeriesData.ProjObject{index}); |
---|
620 | % set(hseries,'UserData',SeriesData); |
---|
621 | |
---|