Changeset 1129 for trunk

Timestamp:

Mar 1, 2024, 8:09:20 PM (10 months ago)

Author:

sommeria

Message:

LIF calibration update and extrct_multitif

Location:

trunk/src

Files:

• phys_ima.m (modified) (3 diffs)
• series/aver_stat.m (modified) (2 diffs)
• series/extract_multitif.m (modified) (1 diff)
• series/extract_multitif_multislice.m (added)
• series/stereo_input.fig (modified) (previous)
• series/stereo_input.m (modified) (2 diffs)
• series/turb_stat.m (modified) (6 diffs)
• uvmat.m (modified) (6 diffs)

trunk/src/phys_ima.m

@@ -11 +11 @@
 % XmlData: cell array of structures defining the calibration parameters for each image
 % ZIndex: index of the reference plane used to define the phys position in 3D
-
-function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex)
+% resolution_factor: factor to control the number of pixels of the new image, default value =1 : same nbre of pixels as the original
+function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex,resolution_factor)
 xcorner=[];
 ycorner=[];
@@ -21 +21 @@
 if isstruct(XmlData)
     XmlData={XmlData};
+end
+if ~exist('resolution_factor','var')
+resolution_factor=1;
 end
 
@@ -50 +53 @@
 test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
 
-npX=1+round((Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images)
-npY=1+round((Rangy(1)-Rangy(2))/max(dy));
+npX=1+round(resolution_factor*(Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images)
+npY=1+round(resolution_factor*(Rangy(1)-Rangy(2))/max(dy));
 
 x=linspace(Rangx(1),Rangx(2),npX);

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)

trunk/src/uvmat.m

@@ -1657 +1657 @@
 
 %% rescale the image
-[nby,nbx]=size(UvData.Field.A);
-x=linspace(UvData.Field.Coord_x(1),UvData.Field.Coord_x(2),nbx)-nbx/2;
-y=linspace(UvData.Field.Coord_y(1),UvData.Field.Coord_y(2),nby)-nby/2;
-[X,Y]=meshgrid(x,y);
+% [nby,nbx]=size(UvData.Field.A);
+% x=linspace(UvData.Field.Coord_x(1),UvData.Field.Coord_x(2),nbx)-nbx/2;
+% y=linspace(UvData.Field.Coord_y(1),UvData.Field.Coord_y(2),nby)-nby/2;
+% [X,Y]=meshgrid(x,y);
 %coeff_quad=0.15*4/(nbx*nbx);% image luminosity reduced by 10% at the edge
 %UvData.Field.A=double(UvData.Field.A).*(1+coeff_quad*(X.*X+Y.*Y));
@@ -1686 +1686 @@
     ylabel('radius from light source')
     title('ref line in polar coordinates')
-    azimuth_ima=linspace(DataPol.Coord_y(1),DataPol.Coord_y(2),size(DataPol.A,1))-360;%array of angular indices on the transformed image
-    dist_source = interp1(theta_ref,r_ref,azimuth_ima);% get the polar position of the reference line
-    dist_source_pixel=round(size(DataPol.A,2)*(dist_source-DataPol.Coord_x(1))/(DataPol.Coord_x(2)-DataPol.Coord_x(1)));
+    %azimuth_ima=linspace(DataPol.Coord_y(1),DataPol.Coord_y(2),size(DataPol.A,1));%array of angular indices on the transformed image
+   % dist_source = interp1(theta_ref,r_ref,azimuth_ima);% get the polar position of the reference line
+    dist_source = interp1(theta_ref,r_ref,DataPol.theta);% get the polar position of the reference line
+    dist_source_pixel=floor(size(DataPol.A,2)*(dist_source-DataPol.radius(1))/(DataPol.radius(end)-DataPol.radius(1)))+1;
     line_nan= isnan(dist_source);
     dist_source_pixel(line_nan)=1;
@@ -1710 +1711 @@
 %% get the image A*r
 [npy,npx]=size(Anorm);
-AX=DataPol.Coord_x;
-AY=DataPol.Coord_y;
-dX=(AX(2)-AX(1))/(npx-1);
-dY=(AY(1)-AY(2))/(npy-1);%mesh of new pixels
-[R,Theta]=meshgrid(linspace(AX(1),AX(2),npx),linspace(AY(1),AY(2),npy));
+AX=DataPol.radius;
+AY=DataPol.theta;
+% dX=(AX(2)-AX(1))/(npx-1);
+% dY=(AY(1)-AY(2))/(npy-1);%mesh of new pixels
+[R,Theta]=meshgrid(linspace(AX(1),AX(end),npx),linspace(AY(1),AY(end),npy));%matrix of radius and angles with the same size as DataPol
 A=R.*Anorm;
 A=(A<=0).*ones(npy,npx)+(A>0).*A; %replaces zeros by ones
@@ -1734 +1735 @@
 gamma_coeff=NaN(1,npy);
 fitlength=NaN(1,npy);
+%[ThetaMask,RMask] = cart2pol(MaskData.Coord(:,1)-x0,MaskData.Coord(:,2)-y0);
+%ThetaMask=ThetaMask*180/pi
 for iY=1:npy% loop on the y index of the image in polar coordinate
     ALine=A(iY,:);%profile of image luminosity log (vs radial index)
@@ -1752 +1755 @@
     p = polyfit(RLine,ALine,1);
     gamma_coeff(iY)=-p(1);
-    fitlength(iY)=numel(find(check_good));
-end
+   fitlength(iY)=numel(find(check_good));
+end
+
+%% plot the decay coef versus theta
+figure(13)
+plot(Theta(:,1),100*gamma_coeff)
+xlabel('angle(degree)')
+ylabel('decay coeff(m-1)')
+
 
 %% show and store the rescaled image
@@ -1760 +1770 @@
 view_field(DataPol);
 imwrite(DataPol.A,NewImageName,'BitDepth',16)
-figure(13)
-plot(Theta(:,1),100*gamma_coeff)
-xlabel('angle(degree)')
-ylabel('decay coeff(m-1)')
+
 
 %% keep the average of gamma_coeff