Changeset 1129 for trunk/src/series

Timestamp:

Mar 1, 2024, 8:09:20 PM (4 months ago)

Author:

sommeria

Message:

LIF calibration update and extrct_multitif

Location:

trunk/src/series

Files:

• aver_stat.m (modified) (2 diffs)
• extract_multitif.m (modified) (1 diff)
• extract_multitif_multislice.m (added)
• stereo_input.fig (modified) (previous)
• stereo_input.m (modified) (2 diffs)
• turb_stat.m (modified) (6 diffs)

trunk/src/series/aver_stat.m

@@ -298 +298 @@
         for iview=1:NbView
             % reading input file(s)
+            filecell{iview,index}
             [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
             if ~isempty(errormsg)
@@ -469 +470 @@
     
     %% writing the result file
-    OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
+    RootPathOut=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
+    OutputDir=[Param.OutputSubDir Param.OutputDirExt];
+    OutputFile=fullfile_uvmat(RootPathOut,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
     if strcmp(FileExtOut,'.png') %case of images
         if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))

trunk/src/series/extract_multitif.m

@@ -1 +1 @@
 %'extract_multitif': read image series from PCO cameras (tiff image series) and write .png images
-%------------------------------------------------------------------------
-    
+% use a single geometric calibration, with information on the slice positions in case of 3D scanning
+%------------------------------------------------------
+% the output file indexing is based on the xml file requested by the
+% function when it is selected (or possibly inserted in this function in the section TEST)
+%  This xml file must contain the following information:
+%   NbDti: the number of 'bursts' -1
+%   NbDtj: number of frames in each burst-1, or number of repetition of a burst sequence defined by Dtj
+%   NbDtk: number of repetitions of a slice scanning process -1 (ignored by default)
+% Therefore the total number of frames is  (NbDti+1)*(NbDtj+1)*(NbDtk+1)
+% The frame series is stored in a single folder with two indices i:(NbDti+1)*(NbDtk+1) 
+%
+% To run the function in the cluster in parallel for each multitif file, indicate nb-slice_i equal to the
+% number input multitif files
+
+
 % function ParamOut=extract_multitif(Param)
 %

trunk/src/series/stereo_input.m

@@ -243 +243 @@
 %show the reference image edit box if relevant (not needed for movies or in the absence of time information
 if numel(time)>=2 % if there are at least two time values to define dt
-    if size(time,1)<MaxIndex_i;
+    if size(time,1)<MaxIndex_i
         msgbox_uvmat('WARNING','maximum i index restricted by the timing of the xml file');
     elseif size(time,2)<MaxIndex_j
@@ -2974 +2974 @@
 
 % Hint: get(hObject,'Value') returns toggle state of CheckLSM
+
+
+
+function num_resolution_Callback(hObject, eventdata, handles)
+% hObject    handle to num_resolution (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    structure with handles and user data (see GUIDATA)
+
+% Hints: get(hObject,'String') returns contents of num_resolution as text
+%        str2double(get(hObject,'String')) returns contents of num_resolution as a double
+
+
+% --- Executes during object creation, after setting all properties.
+function num_resolution_CreateFcn(hObject, eventdata, handles)
+% hObject    handle to num_resolution (see GCBO)
+% eventdata  reserved - to be defined in a future version of MATLAB
+% handles    empty - handles not created until after all CreateFcns called
+
+% Hint: edit controls usually have a white background on Windows.
+%       See ISPC and COMPUTER.
+if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
+    set(hObject,'BackgroundColor','white');
+end

trunk/src/series/turb_stat.m

@@ -1 @@
-%'aver_stat': calculate Reynolds steress components over time series
+%'aver_stat': calculate Reynolds stress components over time series
 %------------------------------------------------------------------------
 % function ParamOut=turb_stat(Param)
@@ -89 +89 @@
 RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
 WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
-
-%% define the directory for result file (with path=RootPath{1})
-OutputDir=[Param.OutputSubDir Param.OutputDirExt];
     
 %% root input file(s) name, type and index series
@@ -201 +198 @@
 Counter_1=0;
 
+if Param.IndexRange.NbSlice==1
+    interval=Param.IndexRange.incr_i% statistics is done taking into account the input index increment
+else
+    interval=Param.IndexRange.NbSlice;% statistics is done slice by slice without taking into account the input index increment
+end
+
 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
-% for i_slice=1:Param.IndexRange.NbSlice
-%     i_slice
+for i_slice=1:Param.IndexRange.NbSlice
+    i_slice
     ind_first=Param.IndexRange.first_i;
-    for index_i=ind_first:Param.IndexRange.NbSlice:Param.IndexRange.last_i
+    for index_i=ind_first:interval:Param.IndexRange.last_i
         if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
             disp('program stopped by user')
@@ -211 +214 @@
         end
         for index_j=first_j:last_j
-            InputFile=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},index_i,index_i,index_j,index_j);
-            [Field,tild,errormsg] = read_field(InputFile,FileType{iview},InputFields{iview});
-            
-            %[Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
+            InputFile=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},index_i,index_i,index_j,index_j)
+            [Field,tild,errormsg] = read_field(InputFile,FileType{iview},InputFields{iview});       
             
             %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
@@ -289 +290 @@
     
     %% writing the result file as netcdf file
-    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,ind_first,ind_first,first_j,last_j);
+    RootPathOut=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
+    OutputDir=[Param.OutputSubDir Param.OutputDirExt];
+    OutputFile=fullfile_uvmat(RootPathOut,OutputDir,RootFile{1},FileExtOut,NomTypeOut,ind_first,ind_first,first_j,last_j);
     %case of netcdf input file , determine global attributes
     errormsg=struct2nc(OutputFile,DataOut); %save result file
@@ -296 +299 @@
     else
         disp(['error in writting result file: ' errormsg])
-    end
-    
-% end
+    end    
+end
+
 %% open the result file with uvmat (in RUN mode)
 if checkrun && isequal(Param.IndexRange.NbSlice,1)