 Timestamp:
 Jun 25, 2016, 11:20:40 AM (8 years ago)
 Location:
 trunk/src/series
 Files:

 3 edited
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 Unmodified
 Added
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trunk/src/series/aver_stat.m
r959 r960 14 14 % in series), the function ouput paramOut set the activation of the needed GUI elements 15 15 % 16 % Param contains the elements:(use the menu bar command 'export/GUI config' in series to 16 % Param contains the elements:(use the menu bar command 'export/GUI config' in series to 17 17 % see the current structure Param) 18 18 % .InputTable: cell of input file names, (several lines for multiple input) … … 25 25 % .RUN =0 for GUI input, =1 for function activation 26 26 % .RunMode='local','background', 'cluster': type of function use 27 % 27 % 28 28 % .IndexRange: set the file or frame indices on which the action must be performed 29 29 % .FieldTransform: .TransformName: name of the selected transform function … … 70 70 ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) 71 71 ParamOut.OutputDirExt='.stat';%set the output dir extension 72 ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1file per slice73 72 ParamOut.OutputFileMode='NbSlice';% '=NbInput': one output file per input file index, '=NbInput_i': one file per input file index i, '=NbSlice': one file per slice 73 % check for selection of a projection object 74 74 hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series 75 75 if ~isfield(Param,'ProjObject') … … 106 106 [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); 107 107 LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... 108 Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);108 Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); 109 109 if ~exist(LastFileName,'file') 110 110 msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist']) 111 111 end 112 112 end 113 113 % determine volume scan mode 114 114 prompt = {'volume scan mode (Yes/No)'}; 115 115 dlg_title = 'determine volume scan'; 116 116 num_lines= 1; 117 117 def = { 'No'}; 118 119 % answer = inputdlg(prompt,dlg_title,num_lines,def);118 answer=msgbox_uvmat('INPUT_YN','volume scan mode (OK/No)?'); 119 % answer = inputdlg(prompt,dlg_title,num_lines,def); 120 120 if isempty(answer) 121 121 return 122 122 end 123 123 %check input consistency 124 if strcmp(answer,'Yes') 125 126 124 if strcmp(answer,'Yes') 125 ParamOut.NbSlice=1;% set NbSlice to 1 ( for i index) 126 ParamOut.ActionInput.CheckVolume=1; 127 127 end 128 128 return … … 143 143 %% define the directory for result file (with path=RootPath{1}) 144 144 OutputDir=[Param.OutputSubDir Param.OutputDirExt]; 145 145 146 146 %% root input file(s) name, type and index series 147 147 RootPath=Param.InputTable(:,1); … … 150 150 NomType=Param.InputTable(:,4); 151 151 FileExt=Param.InputTable(:,5); 152 152 153 hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); 154 % gives the series of input file names and indices set by the input parameters: 153 155 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); 154 if ~isempty(hdisp),delete(hdisp),end;155 %%%%%%%%%%%%156 % The cell array filecell is the list of input file names, while157 156 % filecell{iview,fileindex}: 158 157 % iview: line in the table corresponding to a given file series 159 % fileindex: file index with in the file series,160 % 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 158 % fileindex: file index with i and j reshaped as a 1D array 159 % 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 161 160 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices 162 %%%%%%%%%%%% 161 if ~isempty(hdisp),delete(hdisp),end;%end the waiting display 162 163 163 NbView=numel(i1_series);%number of input file series (lines in InputTable) 164 164 NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) … … 166 166 NbField=NbField_j*NbField_i; %total number of fields 167 167 168 %% determine the file type on each line from the first input file 168 %% determine the file type on each line from the first input file 169 169 ImageTypeOptions={'image','multimage','mmreader','video'}; 170 170 NcTypeOptions={'netcdf','civx','civdata'}; … … 191 191 if diff_time>0 192 192 disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) 193 end 193 end 194 194 end 195 195 … … 201 201 rmpath(Param.FieldTransform.TransformPath) 202 202 if isfield(Param,'TransformInput') 203 204 end 203 XmlData{1}.TransformInput=Param.TransformInput; 204 end 205 205 end 206 206 207 207 %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% 208 208 % EDIT FROM HERE 209 209 210 210 %% check the validity of input file types and set the output file type … … 222 222 end 223 223 if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane') 224 224 FileExtOut='.nc';% write result as .nc files (even for image input) 225 225 end 226 226 … … 253 253 end 254 254 end 255 nbfiles=0;%counter of the successfully read files (bad files are skipped) 255 256 256 VarMesh=[]; 257 257 if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}) 258 if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms 259 VarMesh=Param.ActionInput.VarMesh;258 if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms 259 VarMesh=Param.ActionInput.VarMesh; 260 260 else 261 VarMesh=[]; 262 disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun) 263 end 264 end 265 266 %% set volume scan 267 NbSlice_j=1; 261 VarMesh=[]; 262 disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun) 263 end 264 end 265 266 NbSlice_j=1;% number of j slices =1 except fo volume scan 268 267 index_series=1:size(filecell,2); 269 first_j_out=first_j; 270 last_j_out=last_j; 268 index_j=1; 269 270 %% set volume scan if requested 271 first_j_out=first_j;%first j index to use for the output file name 272 last_j_out=last_j;%last j index to use for the output file name 271 273 if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'CheckVolume') ... 272 274 && Param.ActionInput.CheckVolume 273 index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j;274 NbSlice_j=numel(index_j);275 index_i=index_series(1:NbSlice_j:end);276 end 277 278 %% % loop onslices (volume scan)275 index_j=Param.IndexRange.first_j:Param.IndexRange.incr_j:Param.IndexRange.last_j; 276 NbSlice_j=numel(index_j); 277 index_series=1:NbSlice_j:size(filecell,2); 278 end 279 280 %% loop on j slices (volume scan) 279 281 for islice=index_j 282 nbfiles=0;%counter of the successfully read files (bad files are skipped) 280 283 if NbSlice_j>1 281 first_j_out=islice; 282 last_j_out=islice; 283 284 first_j_out=islice;%first and last j index to use for the output file name are the current j index 285 last_j_out=islice; 284 286 end 285 287 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 286 288 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% 287 for index=index_ i+index_j(islice)289 for index=index_series+index_j(islice)index_j(1) 288 290 update_waitbar(WaitbarHandle,index/NbField) 289 291 if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') … … 295 297 for iview=1:NbView 296 298 % reading input file(s) 297 %InputFile=fullfile_uvmat(RootPath{iview},SubDir{iview},RootFile{iview},FileExt{iview},NomType{iview},first_i,last_i,first_j_out,last_j_out);298 299 [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); 299 300 if ~isempty(errormsg) 300 301 errormsg=['error of input reading: ' errormsg]; 301 break 302 break% leave the loop on views in case of error 302 303 end 303 304 if ~isempty(NbSlice_calib) … … 307 308 %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%% 308 309 309 if isempty(errormsg) 310 Field=Data{1}; % default input field structure 311 nbfiles=nbfiles+1; %increment the file counter 312 %% coordinate transform (or other user defined transform) 313 if ~isempty(transform_fct) 314 switch nargin(transform_fct) 315 case 4 316 if length(Data)==2 317 Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); 318 else 319 Field=transform_fct(Data{1},XmlData{1}); 320 end 321 case 3 322 if length(Data)==2 323 Field=transform_fct(Data{1},XmlData{1},Data{2}); 324 else 325 Field=transform_fct(Data{1},XmlData{1}); 326 end 327 case 2 310 if ~isempty(errormsg) 311 disp(errormsg) 312 continue % go to next input field in case of error (file skipped in the average) 313 end 314 Field=Data{1}; % default input field structure 315 nbfiles=nbfiles+1; %increment the file counter 316 317 %% coordinate transform (or other user defined transform) 318 if ~isempty(transform_fct) 319 switch nargin(transform_fct) 320 case 4 321 if length(Data)==2 322 Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); 323 else 328 324 Field=transform_fct(Data{1},XmlData{1}); 329 case 1 330 Field=transform_fct(Data{1}); 325 end 326 case 3 327 if length(Data)==2 328 Field=transform_fct(Data{1},XmlData{1},Data{2}); 329 else 330 Field=transform_fct(Data{1},XmlData{1}); 331 end 332 case 2 333 Field=transform_fct(Data{1},XmlData{1}); 334 case 1 335 Field=transform_fct(Data{1}); 336 end 337 end 338 339 %% field projection on an object 340 if Param.CheckObject 341 if strcmp(Param.ProjObject.ProjMode,'interp_tps') 342 Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed 343 end 344 [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh); 345 if ~isempty(errormsg) 346 disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun) 347 return 348 end 349 end 350 351 %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% 352 if nbfiles==1 %first field 353 time_1=[]; 354 if isfield(Field,'Time') 355 time_1=Field.Time(1); 356 end 357 DataOut=Field;%outcome reproduces the first (projected) field by default 358 DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files 359 if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms 360 for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram) 361 VarName=Field.ListVarName{ivar}; 362 if isfield(Data{1},VarName) 363 DataOut.(VarName)=Field.(VarName); 364 DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName))); 365 VarMesh=DataOut.(VarName)(2)DataOut.(VarName)(1); 366 end 331 367 end 332 end 333 334 %% field projection on an object 335 if Param.CheckObject 336 if strcmp(Param.ProjObject.ProjMode,'interp_tps') 337 Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed 338 end 339 [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh); 340 if ~isempty(errormsg) 341 disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun) 342 return 343 end 344 end 345 346 %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% 347 if nbfiles==1 %first field 348 time_1=[]; 349 if isfield(Field,'Time') 350 time_1=Field.Time(1); 351 end 352 DataOut=Field;%outcome reproduces the first (projected) field by default 353 DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files 354 if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms 355 for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram) 368 disp(['mesh for histogram = ' num2str(VarMesh)]) 369 else 370 errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable 371 if isfield(Field,'VarAttribute') 372 for ivar=1:numel(Field.ListVarName) 356 373 VarName=Field.ListVarName{ivar}; 357 if isfield(Data{1},VarName) 358 DataOut.(VarName)=Field.(VarName); 359 DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName))); 360 VarMesh=DataOut.(VarName)(2)DataOut.(VarName)(1); 361 end 362 end 363 disp(['mesh for histogram = ' num2str(VarMesh)]) 364 else 365 errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable 366 if isfield(Field,'VarAttribute') 367 for ivar=1:numel(Field.ListVarName) 368 VarName=Field.ListVarName{ivar}; 369 DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero 370 NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero 371 372 for iivar=1:length(Field.VarAttribute) 373 if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')... 374 && strcmp(Field.VarAttribute{iivar}.Role,'errorflag') 375 errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar 376 end 374 DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero 375 NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero 376 377 for iivar=1:length(Field.VarAttribute) 378 if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')... 379 && strcmp(Field.VarAttribute{iivar}.Role,'errorflag') 380 errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar 377 381 end 378 382 end 379 DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result 380 DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result 381 DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result 383 end 384 DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result 385 DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result 386 DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result 387 else 388 for ivar=1:numel(Field.ListVarName) 389 VarName=Field.ListVarName{ivar}; 390 DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero 391 NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero 392 end 393 end 394 395 end 396 end %current field 397 for ivar=1:length(DataOut.ListVarName) 398 VarName=DataOut.ListVarName{ivar}; 399 sizmean=size(DataOut.(VarName)); 400 siz=size(Field.(VarName)); 401 if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}) 402 if isfield(Data{1},VarName) 403 MaxValue=max(DataOut.(VarName));% current max of histogram absissa 404 MinValue=min(DataOut.(VarName));% current min of histogram absissa 405 % VarMesh=Field.VarAttribute{ivar}.Mesh; 406 MaxIndex=round(MaxValue/VarMesh); 407 MinIndex=round(MinValue/VarMesh); 408 MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field 409 MinIndex_new=round(min(Field.(VarName)/VarMesh)); 410 if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one 411 DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values 412 DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_newMaxIndex)]; % append the new histo values 413 end 414 if MinIndex_new <= MinIndex1 415 DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex1) DataOut.(VarName)];% insert the new variable values 416 DataOut.([VarName 'Histo'])=[zeros(1,MinIndexMinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values 417 ind_start=1; 382 418 else 383 for ivar=1:numel(Field.ListVarName) 384 VarName=Field.ListVarName{ivar}; 385 DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero 386 NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero 387 end 388 end 389 419 ind_start=MinIndex_newMinIndex+1; 420 end 421 DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_newMinIndex_new)=... 422 DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_newMinIndex_new)+Field.([VarName 'Histo']); 390 423 end 391 end %current field 392 for ivar=1:length(DataOut.ListVarName) 393 VarName=DataOut.ListVarName{ivar}; 394 sizmean=size(DataOut.(VarName)); 395 siz=size(Field.(VarName)); 396 if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}) 397 if isfield(Data{1},VarName) 398 MaxValue=max(DataOut.(VarName));% current max of histogram absissa 399 MinValue=min(DataOut.(VarName));% current min of histogram absissa 400 % VarMesh=Field.VarAttribute{ivar}.Mesh; 401 MaxIndex=round(MaxValue/VarMesh); 402 MinIndex=round(MinValue/VarMesh); 403 MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field 404 MinIndex_new=round(min(Field.(VarName)/VarMesh)); 405 if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one 406 DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values 407 DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_newMaxIndex)]; % append the new histo values 408 end 409 if MinIndex_new <= MinIndex1 410 DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex1) DataOut.(VarName)];% insert the new variable values 411 DataOut.([VarName 'Histo'])=[zeros(1,MinIndexMinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values 412 ind_start=1; 413 else 414 ind_start=MinIndex_newMinIndex+1; 415 end 416 DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_newMinIndex_new)=... 417 DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_newMinIndex_new)+Field.([VarName 'Histo']); 418 end 419 elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean) 420 disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid'],checkrun) 421 return 424 elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean) 425 disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid'],checkrun) 426 return 427 else 428 if errorvar(ivar)==0 429 check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else 422 430 else 423 if errorvar(ivar)==0 424 check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else 425 else 426 check_bad=isnan(Field.(VarName))  Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else 427 end 428 Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag 429 DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum 430 NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point 431 check_bad=isnan(Field.(VarName))  Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else 431 432 end 432 end 433 %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%% 433 Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag 434 DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum 435 NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point 436 end 437 end 438 %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%% 439 end 440 %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% 441 442 if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})) 443 for ivar=1:length(Field.ListVarName) 444 VarName=Field.ListVarName{ivar}; 445 DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean 446 end 447 end 448 nbmissing=numel(index_series+index_j(islice)index_j(1))nbfiles; 449 if nbmissing~=0 450 if NbSlice_j==1 451 disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun) 434 452 else 435 disp(errormsg) 436 end 437 end 438 %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% 439 440 if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})) 441 for ivar=1:length(Field.ListVarName) 442 VarName=Field.ListVarName{ivar}; 443 DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean 444 end 445 end 446 nbmissing=NbFieldnbfiles; 447 if nbmissing~=0 448 disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun) 449 end 450 if isempty(time) % time is read from files 451 if isfield(Field,'Time') 452 time_end=Field.Time(1);%last time read 453 if ~isempty(time_1) 454 DataOut.Time=time_1; 455 DataOut.Time_end=time_end; 456 end 457 end 458 else % time from ImaDoc prevails if it exists 459 DataOut.Time=time(1); 460 DataOut.Time_end=time(end); 461 end 462 463 %% writing the result file 464 OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out); 465 if strcmp(FileExtOut,'.png') %case of images 466 if isequal(FileInfo{1}.BitDepth,16)(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) 467 DataOut.A=uint16(DataOut.A); 468 imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images 469 else 470 DataOut.A=uint8(DataOut.A); 471 imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images 472 end 473 disp([OutputFile ' written']); 474 else %case of netcdf file , determine global attributes 475 errormsg=struct2nc(OutputFile,DataOut); %save result file 476 if isempty(errormsg) 453 disp(['WARNING: ' num2str(nbmissing) ' input files are missing or skipped in slice ' num2str(islice)]) 454 end 455 end 456 if isempty(time) % time is read from files 457 if isfield(Field,'Time') 458 time_end=Field.Time(1);%last time read 459 if ~isempty(time_1) 460 DataOut.Time=time_1; 461 DataOut.Time_end=time_end; 462 end 463 end 464 else % time from ImaDoc prevails if it exists 465 DataOut.Time=time(1); 466 DataOut.Time_end=time(end); 467 end 468 469 %% writing the result file 470 OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out); 471 if strcmp(FileExtOut,'.png') %case of images 472 if isequal(FileInfo{1}.BitDepth,16)(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) 473 DataOut.A=uint16(DataOut.A); 474 imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images 475 else 476 DataOut.A=uint8(DataOut.A); 477 imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images 478 end 477 479 disp([OutputFile ' written']); 478 else 479 disp(['error in writting result file: ' errormsg]) 480 end 481 end % end averaging loop 480 else %case of netcdf file , determine global attributes 481 errormsg=struct2nc(OutputFile,DataOut); %save result file 482 if isempty(errormsg) 483 disp([OutputFile ' written']); 484 else 485 disp(['error in writting result file: ' errormsg]) 486 end 487 end % end averaging loop 482 488 end 483 489 
trunk/src/series/merge_proj.m
r959 r960 111 111 end 112 112 113 %% root input file type113 %% root input file(s) name, type and index series 114 114 RootPath=Param.InputTable(:,1); 115 115 RootFile=Param.InputTable(:,3); … … 117 117 NomType=Param.InputTable(:,4); 118 118 FileExt=Param.InputTable(:,5); 119 120 hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); 121 % gives the series of input file names and indices set by the input parameters: 119 122 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); 120 %%%%%%%%%%%%121 % The cell array filecell is the list of input file names, while122 123 % filecell{iview,fileindex}: 123 124 % iview: line in the table corresponding to a given file series 124 % fileindex: file index with in the file series,125 % fileindex: file index with i and j reshaped as a 1D array 125 126 % 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 126 127 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices 127 %%%%%%%%%%%% 128 % NbSlice=1;%default 129 % if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) 130 % NbSlice=Param.IndexRange.NbSlice; 131 % end 128 if ~isempty(hdisp),delete(hdisp),end;%end the waiting display 129 132 130 NbView=numel(i1_series);%number of input file series (lines in InputTable) 133 131 NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) 
trunk/src/series/time_series.m
r924 r960 153 153 NomType=Param.InputTable(:,4); 154 154 FileExt=Param.InputTable(:,5); 155 155 156 hdisp=disp_uvmat('WAITING...','checking the file series',checkrun); 157 % gives the series of input file names and indices set by the input parameters: 156 158 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); 157 if ~isempty(hdisp),delete(hdisp),end;158 %%%%%%%%%%%%159 % The cell array filecell is the list of input file names, while160 159 % filecell{iview,fileindex}: 161 160 % iview: line in the table corresponding to a given file series 162 % fileindex: file index with in the file series,163 % 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 161 % fileindex: file index with i and j reshaped as a 1D array 162 % 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 164 163 % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices 165 %%%%%%%%%%%% 166 nbview=numel(i1_series);%number of input file series (lines in InputTable) 167 nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) 168 nbfield_i=size(i1_series{1},2); %nb of fields for the i index 169 nbfield=nbfield_j*nbfield_i; %total number of fields 164 if ~isempty(hdisp),delete(hdisp),end;%end the waiting display 165 166 NbView=numel(i1_series);%number of input file series (lines in InputTable) 167 NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) 168 NbField_i=size(i1_series{1},2); %nb of fields for the i index 169 NbField=NbField_j*NbField_i; %total number of fields 170 170 171 171 %% determine the file type on each line from the first input file
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