Changeset 599 for trunk/src/series/time_series.m
 Timestamp:
 Apr 3, 2013, 10:21:53 AM (11 years ago)
 File:

 1 edited
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trunk/src/series/time_series.m
r596 r599 45 45 if isstruct(Param) && isequal(Param.Action.RUN,0) 46 46 ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) 47 ParamOut.WholeIndexRange='off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)48 ParamOut.NbSlice='on'; ...%nbre of slices ('off' by default)49 ParamOut.VelType='two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default)50 ParamOut.FieldName='two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)51 ParamOut.FieldTransform = 'on';...%can use a transform function52 ParamOut.ProjObject='on';...%can use projection object(option 'off'/'on',53 ParamOut.Mask='off';...%can use mask option (option 'off'/'on', 'off' by default)54 ParamOut.OutputDirExt='.tseries';%set the output dir extension55 return47 ParamOut.WholeIndexRange='off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) 48 ParamOut.NbSlice='on'; ...%nbre of slices ('off' by default) 49 ParamOut.VelType='two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) 50 ParamOut.FieldName='two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) 51 ParamOut.FieldTransform = 'on';...%can use a transform function 52 ParamOut.ProjObject='on';...%can use projection object(option 'off'/'on', 53 ParamOut.Mask='off';...%can use mask option (option 'off'/'on', 'off' by default) 54 ParamOut.OutputDirExt='.tseries';%set the output dir extension 55 return 56 56 end 57 57 … … 78 78 % filecell{iview,fileindex}: 79 79 % iview: line in the table corresponding to a given file series 80 % fileindex: file index within the file series, 81 % 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 80 % fileindex: file index within the file series, 81 % 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 82 82 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices 83 83 %%%%%%%%%%%% … … 90 90 nbfield_i=size(i1_series{1},2); %nb of fields for the i index 91 91 nbfield=nbfield_j*nbfield_i; %total number of fields 92 nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) 92 nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) 93 93 nbfield=nbfield_i*NbSlice; %total number of fields after adjustement 94 94 95 %determine the file type on each line from the first input file 95 %determine the file type on each line from the first input file 96 96 ImageTypeOptions={'image','multimage','mmreader','video'}; 97 97 NcTypeOptions={'netcdf','civx','civdata'}; … … 117 117 if diff_time>0 118 118 displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) 119 end 119 end 120 120 time=time(1,:);% choose the time data from the first sequence 121 121 end … … 130 130 131 131 %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% 132 132 % EDIT FROM HERE 133 133 134 134 %% check the validity of ctinput file types … … 137 137 elseif CheckNc{1} 138 138 FileExtOut='.nc';% write result as .nc files for netcdf inputs 139 else 139 else 140 140 displ_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) 141 141 return 142 142 end 143 143 if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) 144 144 displ_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun) 145 145 return 146 146 end … … 196 196 end 197 197 198 %% LOOP ON SLICES199 198 nbmissing=0; %number of undetected files 200 for i_slice=1:NbSlice 201 index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice 202 nbfile=0; 203 nbmissing=0; 204 205 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% 206 for index=index_slice 207 if checkrun 208 stopstate=get(Param.RUNHandle,'BusyAction'); 209 update_waitbar(Param.WaitbarHandle,index/nbfield) 210 else 211 stopstate='queue'; 212 end 213 if isequal(stopstate,'queue')% enable STOP command 214 Data=cell(1,nbview);%initiate the set Data; 215 nbtime=0; 216 dt=[]; 217 %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% 218 for iview=1:nbview 219 % reading input file(s) 220 [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); 221 if ~isempty(errormsg) 222 errormsg=['time_series / read_field / ' errormsg]; 223 display(errormsg) 224 break 199 % for i_slice=1:NbSlice 200 %index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice 201 nbfile=0; 202 nbmissing=0; 203 204 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% 205 for index=1:nbfield 206 if checkrun 207 stopstate=get(Param.RUNHandle,'BusyAction'); 208 update_waitbar(Param.WaitbarHandle,index/nbfield) 209 else 210 stopstate='queue'; 211 end 212 if ~isequal(stopstate,'queue')% enable STOP command 213 break 214 end 215 Data=cell(1,nbview);%initiate the set Data; 216 nbtime=0; 217 dt=[]; 218 %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% 219 for iview=1:nbview 220 % reading input file(s) 221 [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); 222 if ~isempty(errormsg) 223 errormsg=['time_series / read_field / ' errormsg]; 224 display(errormsg) 225 break 226 end 227 if ~isempty(NbSlice_calib) 228 Data{iview}.ZIndex=mod(i1_series{iview}(index)1,NbSlice_calib{iview})+1;%Zindex for phys transform 229 end 230 end 231 if isempty(errormsg) 232 Field=Data{1}; % default input field structure 233 % coordinate transform (or other user defined transform) 234 if ~isempty(transform_fct) 235 switch nargin(transform_fct) 236 case 4 237 if length(Data)==2 238 Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); 239 else 240 Field=transform_fct(Data{1},XmlData{1}); 241 end 242 case 3 243 if length(Data)==2 244 Field=transform_fct(Data{1},XmlData{1},Data{2}); 245 else 246 Field=transform_fct(Data{1},XmlData{1}); 247 end 248 case 2 249 Field=transform_fct(Data{1},XmlData{1}); 250 case 1 251 Field=transform_fct(Data{1}); 252 end 253 end 254 255 % calculate tps coefficients if needed 256 if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps') 257 Field=tps_coeff_field(Field,check_proj_tps); 258 end 259 260 %field projection on an object 261 if Param.CheckObject 262 [Field,errormsg]=proj_field(Field,Param.ProjObject); 263 if ~isempty(errormsg) 264 msgbox_uvmat('ERROR',['time_series / proj_field / ' errormsg]) 265 return 266 end 267 end 268 nbfile=nbfile+1; 269 270 % initiate the time series at the first iteration 271 if nbfile==1 272 % stop program if the first field reading is in error 273 if ~isempty(errormsg) 274 displ_uvmat('ERROR',['time_series / sub_field / ' errormsg],checkrun) 275 return 276 end 277 DataOut=Field;%default 278 DataOut.NbDim=Field.NbDim+1; %add the time dimension for plots 279 nbvar=length(Field.ListVarName); 280 if nbvar==0 281 displ_uvmat('ERROR','no input variable selected',checkrun) 282 return 283 end 284 testsum=2*ones(1,nbvar);%initiate flag for action on each variable 285 if isfield(Field,'VarAttribute') % look for coordinate and flag variables 286 for ivar=1:nbvar 287 if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') 288 var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable 289 if isequal(var_role,'errorflag') 290 displ_uvmat('ERROR','do not handle error flags in time series',checkrun) 291 return 292 end 293 if isequal(var_role,'warnflag') 294 testsum(ivar)=0; % not recorded variable 295 eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable 296 end 297 if isequal(var_role,'coord_x') isequal(var_role,'coord_y')... 298 isequal(var_role,'coord_z')isequal(var_role,'coord') 299 testsum(ivar)=1; %constant coordinates, record without time evolution 300 end 301 end 302 % check whether the variable ivar is a dimension variable 303 DimCell=Field.VarDimName{ivar}; 304 if ischar(DimCell) 305 DimCell={DimCell}; 306 end 307 if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables 308 testsum(ivar)=1; 309 end 225 310 end 226 if ~isempty(NbSlice_calib) 227 Data{iview}.ZIndex=mod(i1_series{iview}(index)1,NbSlice_calib{iview})+1;%Zindex for phys transform 311 end 312 for ivar=1:nbvar 313 if testsum(ivar)==2 314 eval(['DataOut.' Field.ListVarName{ivar} '=[];']) 228 315 end 229 316 end 230 if isempty(errormsg) 231 Field=Data{1}; % default input field structure 232 % coordinate transform (or other user defined transform) 233 if ~isempty(transform_fct) 234 switch nargin(transform_fct) 235 case 4 236 if length(Data)==2 237 Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); 238 else 239 Field=transform_fct(Data{1},XmlData{1}); 317 DataOut.ListVarName=[{'Time'} DataOut.ListVarName]; 318 end 319 320 % add data to the current field 321 for ivar=1:length(Field.ListVarName) 322 VarName=Field.ListVarName{ivar}; 323 VarVal=Field.(VarName); 324 if testsum(ivar)==2% test for recorded variable 325 if isempty(errormsg) 326 if isequal(Param.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode 327 if isempty(VarVal) 328 displ_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(index))],checkrun) 329 return 240 330 end 241 case 3 242 if length(Data)==2 243 Field=transform_fct(Data{1},XmlData{1},Data{2}); 244 else 245 Field=transform_fct(Data{1},XmlData{1}); 246 end 247 case 2 248 Field=transform_fct(Data{1},XmlData{1}); 249 case 1 250 Field=transform_fct(Data{1}); 331 VarVal=mean(VarVal,1); 332 end 333 VarVal=shiftdim(VarVal,1); %shift dimension 334 DataOut.(VarName)=cat(1,DataOut.(VarName),VarVal);%concanete the current field to the time series 335 else 336 DataOut.(VarName)=cat(1,DataOut.(VarName),0);% put each variable to 0 in case of input reading error 251 337 end 252 end 253 254 % calculate tps coefficients if needed 255 if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps') 256 Field=tps_coeff_field(Field,check_proj_tps); 257 end 258 259 %field projection on an object 260 if Param.CheckObject 261 [Field,errormsg]=proj_field(Field,Param.ProjObject); 262 if ~isempty(errormsg) 263 msgbox_uvmat('ERROR',['time_series / proj_field / ' errormsg]) 338 elseif testsum(ivar)==1% variable representing fixed coordinates 339 VarInit=DataOut.(VarName); 340 if isempty(errormsg) && ~isequal(VarVal,VarInit) 341 displ_uvmat('ERROR',['time series requires constant coordinates ' VarName],checkrun) 264 342 return 265 343 end 266 344 end 267 nbfile=nbfile+1; 268 269 % initiate the time series at the first iteration 270 if nbfile==1 271 % stop program if the first field reading is in error 272 if ~isempty(errormsg) 273 displ_uvmat('ERROR',['time_series / sub_field / ' errormsg],checkrun) 274 return 275 end 276 DataOut=Field;%default 277 DataOut.NbDim=Field.NbDim+1; %add the time dimension for plots 278 nbvar=length(Field.ListVarName); 279 if nbvar==0 280 displ_uvmat('ERROR','no input variable selected',checkrun) 281 return 282 end 283 testsum=2*ones(1,nbvar);%initiate flag for action on each variable 284 if isfield(Field,'VarAttribute') % look for coordinate and flag variables 285 for ivar=1:nbvar 286 if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') 287 var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable 288 if isequal(var_role,'errorflag') 289 displ_uvmat('ERROR','do not handle error flags in time series',checkrun) 290 return 291 end 292 if isequal(var_role,'warnflag') 293 testsum(ivar)=0; % not recorded variable 294 eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable 295 end 296 if isequal(var_role,'coord_x') isequal(var_role,'coord_y')... 297 isequal(var_role,'coord_z')isequal(var_role,'coord') 298 testsum(ivar)=1; %constant coordinates, record without time evolution 299 end 300 end 301 % check whether the variable ivar is a dimension variable 302 DimCell=Field.VarDimName{ivar}; 303 if ischar(DimCell) 304 DimCell={DimCell}; 305 end 306 if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables 307 testsum(ivar)=1; 308 end 309 end 310 end 311 for ivar=1:nbvar 312 if testsum(ivar)==2 313 eval(['DataOut.' Field.ListVarName{ivar} '=[];']) 314 end 315 end 316 DataOut.ListVarName=[{'Time'} DataOut.ListVarName]; 317 end 318 319 % add data to the current field 320 for ivar=1:length(Field.ListVarName) 321 VarName=Field.ListVarName{ivar}; 322 VarVal=Field.(VarName); 323 if testsum(ivar)==2% test for recorded variable 324 if isempty(errormsg) 325 if isequal(Param.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode 326 if isempty(VarVal) 327 displ_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(index))],checkrun) 328 return 329 end 330 VarVal=mean(VarVal,1); 331 end 332 VarVal=shiftdim(VarVal,1); %shift dimension 333 DataOut.(VarName)=cat(1,DataOut.(VarName),VarVal);%concanete the current field to the time series 334 else 335 DataOut.(VarName)=cat(1,DataOut.(VarName),0);% put each variable to 0 in case of input reading error 336 end 337 elseif testsum(ivar)==1% variable representing fixed coordinates 338 VarInit=DataOut.(VarName); 339 if isempty(errormsg) && ~isequal(VarVal,VarInit) 340 displ_uvmat('ERROR',['time series requires constant coordinates ' VarName],checkrun) 341 return 342 end 343 end 344 end 345 346 % record the time: 347 if isempty(time)% time not set by xml filer(s) 348 if isfield(Data{1},'Time') 349 DataOut.Time(nbfile,1)=Field.Time; 350 else 351 DataOut.Time(nbfile,1)=index;%default 352 end 353 else % time from ImaDoc prevails TODO: correct 354 DataOut.Time(nbfile,1)=time(index);% 355 end 356 357 % record the number of missing input fields 358 if ~isempty(errormsg) 359 nbmissing=nbmissing+1; 360 display(['index=' num2str(index) ':' errormsg]) 361 end 362 end 363 end 364 end 365 %%%%%%% END OF LOOP WITHIN A SLICE 345 end 346 347 % record the time: 348 if isempty(time)% time not set by xml filer(s) 349 if isfield(Data{1},'Time') 350 DataOut.Time(nbfile,1)=Field.Time; 351 else 352 DataOut.Time(nbfile,1)=index;%default 353 end 354 else % time from ImaDoc prevails TODO: correct 355 DataOut.Time(nbfile,1)=time(index);% 356 end 357 358 % record the number of missing input fields 359 if ~isempty(errormsg) 360 nbmissing=nbmissing+1; 361 display(['index=' num2str(index) ':' errormsg]) 362 end 363 end 366 364 367 %remove time for global attributes if exists 368 Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute)); 369 if ~isempty(Time_index) 370 DataOut.ListGlobalAttribute(Time_index)=[]; 371 end 372 DataOut.Conventions='uvmat'; 373 for ivar=1:numel(DataOut.ListVarName) 374 VarName=DataOut.ListVarName{ivar}; 375 eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons 376 end 377 378 % add time dimension 379 for ivar=1:length(Field.ListVarName) 380 DimCell=Field.VarDimName(ivar); 381 if testsum(ivar)==2%variable used as time series 382 DataOut.VarDimName{ivar}=[{'Time'} DimCell]; 383 elseif testsum(ivar)==1 384 DataOut.VarDimName{ivar}=DimCell; 385 end 386 end 387 indexremove=find(~testsum); 388 if ~isempty(indexremove) 389 DataOut.ListVarName(1+indexremove)=[]; 390 DataOut.VarDimName(indexremove)=[]; 391 if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs 392 DataOut.Role(1+indexremove)=[]; 393 end 394 end 395 396 %shift variable attributes 397 if isfield(DataOut,'VarAttribute') 398 DataOut.VarAttribute=[{[]} DataOut.VarAttribute]; 399 end 400 DataOut.VarDimName=[{'Time'} DataOut.VarDimName]; 401 DataOut.Action=Param.Action;%name of the processing programme 402 test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant) 403 if ~test_time 404 DataOut.Time=1:filecounter; 405 end 406 407 % display nbmissing 408 if ~isequal(nbmissing,0) 409 displ_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun) 410 end 411 412 %name of result file 413 OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]); 414 errormsg=struct2nc(OutputFile,DataOut); %save result file 415 if isempty(errormsg) 416 display([OutputFile ' written']) 417 else 418 displ_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun) 419 end 420 end 365 end 366 %%%%%%% END OF LOOP WITHIN A SLICE 367 368 %remove time for global attributes if exists 369 Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute)); 370 if ~isempty(Time_index) 371 DataOut.ListGlobalAttribute(Time_index)=[]; 372 end 373 DataOut.Conventions='uvmat'; 374 for ivar=1:numel(DataOut.ListVarName) 375 VarName=DataOut.ListVarName{ivar}; 376 eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons 377 end 378 379 % add time dimension 380 for ivar=1:length(Field.ListVarName) 381 DimCell=Field.VarDimName(ivar); 382 if testsum(ivar)==2%variable used as time series 383 DataOut.VarDimName{ivar}=[{'Time'} DimCell]; 384 elseif testsum(ivar)==1 385 DataOut.VarDimName{ivar}=DimCell; 386 end 387 end 388 indexremove=find(~testsum); 389 if ~isempty(indexremove) 390 DataOut.ListVarName(1+indexremove)=[]; 391 DataOut.VarDimName(indexremove)=[]; 392 if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs 393 DataOut.Role(1+indexremove)=[]; 394 end 395 end 396 397 %shift variable attributes 398 if isfield(DataOut,'VarAttribute') 399 DataOut.VarAttribute=[{[]} DataOut.VarAttribute]; 400 end 401 DataOut.VarDimName=[{'Time'} DataOut.VarDimName]; 402 DataOut.Action=Param.Action;%name of the processing programme 403 test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant) 404 if ~test_time 405 DataOut.Time=1:filecounter; 406 end 407 408 % display nbmissing 409 if ~isequal(nbmissing,0) 410 displ_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun) 411 end 412 413 %name of result file 414 OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]); 415 errormsg=struct2nc(OutputFile,DataOut); %save result file 416 if isempty(errormsg) 417 display([OutputFile ' written']) 418 else 419 displ_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun) 420 end 421 421 422 422 423 %% plot the time series (the last one in case of multislices) … … 425 426 haxes=axes; 426 427 plot_field(DataOut,haxes) 427 428 428 429 %% display the result file using the GUI get_field 429 430 hget_field=findobj(allchild(0),'name','get_field');
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