Changeset 1002 for trunk/src/series

Timestamp:

Feb 28, 2017, 10:41:54 AM (8 years ago)

Author:

sommeria

Message:

correlation_time and correlation_x corrected

Location:

trunk/src/series

Files:

• extract_multitif.m (modified) (6 diffs)
• extract_multitif_parallel.m (deleted)
• turb_correlation_time.m (modified) (4 diffs)
• turb_correlation_x.m (modified) (2 diffs)

trunk/src/series/extract_multitif.m

@@ -59 +59 @@
 %=======================================================================
 
-function ParamOut=extract_multitif(Param)
+function ParamOut=extract_multitif_parallel(Param)
 
 %%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
@@ -65 +65 @@
     ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
     ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
-    ParamOut.NbSlice=1; % impose calculation in a single process (no parallel processing to avoid 'holes'))
+    ParamOut.NbSlice='off'; % impose calculation in a single process (no parallel processing to avoid 'holes'))
     ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
     ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
@@ -73 +73 @@
     ParamOut.OutputDirExt='.png';%set the output dir extension
     ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
-     ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
+      ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
     %% root input file(s) and type
     % check the existence of the first file in the series
@@ -95 +95 @@
         return
     end
-    xmlinput=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml');
-    [tild,ParamOut.ActionInput.XmlFile]=fileparts(xmlinput);
-    ParamOut.ActionInput.XmlFile
-    
+    ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml');  
     return
 end
@@ -111 +108 @@
     checkrun=0;
 else
-hseries=findobj(allchild(0),'Tag','series');
-RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
-WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
+    hseries=findobj(allchild(0),'Tag','series');
+    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
+    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
 end
 
 %% list of input images
-DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2});
-ListStruct=dir(DirImages);   
-ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
-check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it
-check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
-ListFile=ListCells(1,find(~check_dir & ~check_bad));
+% DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2});
+% ListStruct=dir(DirImages);
+% ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
+% check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it
+% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
+% ListFile=ListCells(1,find(~check_dir & ~check_bad));
 
 %% check file names
-RootName=regexprep(ListFile{1},'.tif$','')
-for ilist=2:numel(ListFile)
-    rank=regexprep(ListFile{ilist},'.tif$','');
-    rank=regexprep(rank,['^' RootName '@'],'');
-    if ~isequal(str2num(rank),ilist-1)
-        disp(['error in the list of input file # ' num2str(ilist-1)])
-        return
-    end
-end
+% RootName=regexprep(ListFile{1},'.tif$','')
+% rank(1)=1;
+% for ilist=2:numel(ListFile)
+%     rank_str=regexprep(ListFile{ilist},'.tif$','');
+%     rank(ilist)=regexprep(rank_str,['^' RootName '@'],'');
+% %     if ~isequal(str2num(rank),ilist-1)
+% %         disp(['error in the list of input file # ' num2str(ilist-1)])
+% %         return
+% %     end
+% end
 
 %% output directory
- OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);
- 
-%% Timing 
-XmlInputFile=fullfile(Param.InputTable{1,1},[Param.ActionInput.XmlFile '.xml'])
-XmlInput=imadoc2struct(XmlInputFile,'Camera');
+OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]);
+
+%% Timing
+XmlInputFile=Param.ActionInput.XmlFile;
+[XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera');
+if ~isempty(errormsg)
+    disp(['bad xml input file: ' errormsg])
+    return
+end
+ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices
+
+%% create the xml file of PCO camera if it does not exist
+Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']);
+if ~exist(Newxml,'file')
+XmlInput.Camera.CameraName='PCO';
+XmlInput=rmfield(XmlInput,'Time');
+XmlInput=rmfield(XmlInput,'TimeUnit');
+t=struct2xml(XmlInput);
+t=set(t,1,'name','ImaDoc');
+save(t,Newxml);
+end
 
 %% Main loop
 
-ImagesPerLevel=size(XmlInput.Time,2)-1;%100;
-count=0;
+
+% count=0;
 %count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1
 %count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images
-%% loop on the files  
-for ifile=1:numel(ListFile)
-    update_waitbar(WaitbarHandle,ifile/numel(ListFile))
-    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
-        disp('program stopped by user')
-        break
-    end
-    ImageName=fullfile(DirImages,ListFile{ifile});
+%% loop on the files
+% include the first tiff file with no index in the first iteration
+if Param.IndexRange.first_i==1% first slice of processing
+    firstindex=0;
+   count=0;
+else
+    firstindex=Param.IndexRange.first_i;
+    ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif');
     NbFrames=numel(imfinfo(ImageName));
-    % loop on the frames within the tiff file
-    for iframe=1:NbFrames       
+   count=Param.IndexRange.first_i*NbFrames;
+end
+for ifile=firstindex:Param.IndexRange.last_i
+    if firstindex==0 && ifile==0% first slice of processing
+        ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif')
+    else
+        ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif'])
+    end
+    NbFrames=numel(imfinfo(ImageName));
+    for iframe=1:NbFrames
+        iframe
         if isequal(ImagesPerLevel,1)% mode series
-            i_index=count+1;
             OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']);
         else % indices i and j
@@ -178 +200 @@
 end
 
-% for ifile=1:numel(ListFile)
-%     update_waitbar(WaitbarHandle,ifile/numel(ListFile))
-%     if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
-%         disp('program stopped by user')
-%         break
-%     end
-%     ImageName=fullfile(DirImages,ListFile{ifile});
-%     NbFrames=numel(imfinfo(ImageName));
-%     % loop on the frames within the tiff file
-%     for iframe=1:NbFrames      
-%         A=imread(ImageName,iframe);
-% 
-%         if isequal(ImagesPerLevel,1)% mode series 
-%             i_index=count+1;
-%             OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']);
-%         else % indices i and j 
-%             i_index=fix(count/ImagesPerLevel)+1;
-%             j_index=mod(count,ImagesPerLevel)+1;
-%             OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']);
-%         end
-%         imwrite(A,OutputFile,'BitDepth',16)
-%         count=count+1;
-%     end
-% end
-
-%% create the xml file of PCO camera
-XmlInput.Camera.CameraName='PCO';
-t=struct2xml(XmlInput.Camera);
-t=set(t,1,'name','ImaDoc');
-save(t,fullfile(Param.InputTable{1,1},'PCO.xml'))
-
-%% remove initial files if transfer OK
-%     if i_index== (size(XmlInput.Time,1)-1)
-% 
-%         [SUCCESS,MESSAGE]=rmdir(DirImages,'s')
-%        
-%     end
+
+

trunk/src/series/turb_correlation_time.m

@@ -57 +57 @@
 %=======================================================================
 
-function ParamOut=turb_stat(Param)
+function ParamOut=turb_correlation_time(Param)
 
 %% set the input elements needed on the GUI series when the action is selected in the menu ActionName
@@ -63 +63 @@
     ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
     ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
-    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
+    ParamOut.NbSlice=1; %nbre of slices ('off' by default)
     ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
     ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
@@ -277 +277 @@
         FFCorr=false(NpTime+1,npy,npx);
     end
+    Field.U=Field.U-UMean;
+    Field.V=Field.V-VMean;
     FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U
     Field.U(FF)=0;% set to 0 the nan values,'delta_x'
     Field.V(FF)=0;
-    Field.U=Field.U-UMean;
-    Field.V=Field.V-VMean;
     if index<=NpTime+1
-        U_shift(index,:,:)=Field.U;
-        V_shift(index,:,:)=Field.V;
-        FF_shift(index,:,:)=FF;
+        U_shift(NpTime+2-index,:,:)=Field.U;
+        V_shift(NpTime+2-index,:,:)=Field.V;
+        FF_shift(NpTime+2-index,:,:)=FF;
     else
-        U_shift=circshift(U_shift,[-1 0 0]); %shift U by ishift along the first index
-        V_shift=circshift(V_shift,[-1 0 0]); %shift U by ishift along the first index
-        FF_shift=circshift(FF_shift,[-1 0 0]); %shift U by ishift along the first index
-        U_shift(NpTime+1,:,:)=Field.U;
-        V_shift(NpTime+1,:,:)=Field.V;
-        FF_shift(NpTime+1,:,:)=FF;
-    end
-    for ishift=1:NpTime% calculate the field U shifted
-        UUCorr(ishift,:,:)=Field.U.*U_shift(ishift,:,:);
-        VVCorr(ishift,:,:)=Field.V.*V_shift(ishift,:,:);
-        UVCorr(ishift,:,:)=Field.U.*V_shift(ishift,:,:);
-        FFCorr(ishift,:,:)=FF | FF_shift;
+        U_shift=circshift(U_shift,[1 0 0]); %shift U by ishift along the first index
+        V_shift=circshift(V_shift,[1 0 0]); %shift U by ishift along the first index
+        FF_shift=circshift(FF_shift,[1 0 0]); %shift U by ishift along the first index
+        U_shift(1,:,:)=Field.U;
+        V_shift(1,:,:)=Field.V;
+        FF_shift(1,:,:)=FF;
+    end
+    for ishift=1:NpTime+1% calculate the field U shifted
+        UUCorr(ishift,:,:)=Field.U.*squeeze(U_shift(ishift,:,:));
+        VVCorr(ishift,:,:)=Field.V.*squeeze(V_shift(ishift,:,:));
+        UVCorr(ishift,:,:)=Field.U.*squeeze(V_shift(ishift,:,:));
+        FFCorr(ishift,:,:)=FF | squeeze(FF_shift(ishift,:,:));
     end
     DataOut.UUCorr=DataOut.UUCorr+UUCorr;
@@ -306 +306 @@
 end
 %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
-% DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter;
-% DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter;
-% DataOut.VUVCorr=DataOut.UVCorr./DataOut.Counter;
-%DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero
+DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero (to avoid NaN)
+DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter;
+DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter;
+DataOut.UVCorr=DataOut.UVCorr./DataOut.Counter;
+
 % DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean
 % DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean

trunk/src/series/turb_correlation_x.m

@@ -57 +57 @@
 %=======================================================================
 
-function ParamOut=turb_stat(Param)
+function ParamOut=turb_correlation_x(Param)
 
 %% set the input elements needed on the GUI series when the action is selected in the menu ActionName
@@ -290 +290 @@
 DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter;
 DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter;
-DataOut.VUVCorr=DataOut.UVCorr./DataOut.Counter;
+DataOut.UVCorr=DataOut.UVCorr./DataOut.Counter;
 %DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero
 % DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean