Changeset 1097 for trunk/src/series

Timestamp:

Apr 11, 2021, 10:03:02 PM (3 years ago)

Author:

sommeria

Message:

various bug repairs

Location:

trunk/src/series

Files:

• aver_stat.m (modified) (2 diffs)
• civ_input.m (modified) (4 diffs)
• civ_series.m (modified) (3 diffs)
• merge_proj.m (modified) (1 diff)
• sliding_average.m (modified) (1 diff)
• sub_background_special.m (added)

trunk/src/series/aver_stat.m

@@ -225 +225 @@
 
 %% settings for the output file
+OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
+OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
 NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
 first_i=i1_series{1}(1);
@@ -467 +469 @@
     
     %% writing the result file
-    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out);
+    OutputFile=fullfile_uvmat(OutputPath,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/civ_input.m

@@ -249 +249 @@
 set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms)
 set(handles.TimeUnit,'String',TimeUnit);
-%set(handles.CoordUnit,'String',CoordUnit)
 set(handles.SearchRange,'UserData', pxcm_search);
 
@@ -319 +318 @@
 %% set the menu and default choice of civ pairs
 if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs
-    set(handles.ListPairMode,'Value',1)
     PairMenu={'series(Di)'};
 elseif  MaxIndex_i==1 && MaxIndex_j>1% simple series in j
     PairMenu={'pair j1-j2';'series(Dj)'};
-    if  MaxIndex_j <= 10
-        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
-    end
 else
     PairMenu={'pair j1-j2';'series(Dj)';'series(Di)'};%multiple choice
-    if strcmp(NomTypeNc,'_1-2_1')
-        set(handles.ListPairMode,'Value',3)% advise 'series(Di)'
-    elseif  MaxIndex_j <= 10
-        set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large
-    end
 end
 set(handles.ListPairMode,'String',PairMenu)
 
 %% set default choice of pair mode
-PairIndex=1;
+PairIndex=[];
 if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'PairIndices')
-    PairIndex=find(strcmp(Param.ActionInput.PairIndices.ListPairMode,PairMenu));
+    PairIndex=find(strcmp(Param.ActionInput.PairIndices.ListPairMode,PairMenu));%retrieve the previous option
 end
 if isempty(PairIndex)
@@ -353 +343 @@
         elseif  MaxIndex_j <= 10
             PairIndex=1;% advice 'pair j1-j2' except in MaxIndex_j is large
+        else
+            PairIndex=2;% advice 'Dj' 
         end
     end
@@ -1748 +1740 @@
      ImageData.ListVarName={'ny','nx','A'};
      ImageData.VarDimName= {'ny','nx',{'ny','nx'}};
+     ImageData.VarAttribute{1}.Role='coord_y';
+     ImageData.VarAttribute{2}.Role='coord_x';
+     ImageData.VarAttribute{3}.Role='scalar';
      ImageData.A=imread(Data.Civ1_ImageA); % read the first image
      if ndims(ImageData.A)==3 %case of color image

trunk/src/series/civ_series.m

@@ -71 +71 @@
     Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar)
     Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
-    if isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
+    if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2')
         if isfield(Data.ActionInput.PairIndices,'ListPairCiv2')
             str_civ=Data.ActionInput.PairIndices.ListPairCiv2;
@@ -90 +90 @@
     end
     % estimated CPUTime
-    CPUtime_unit=0.01;%estimated time for a multiplication (in microsecond)
-    if isfield(Param.SeriesData,'FileInfo')&&isfield(Param.SeriesData.FileInfo{1},'Height')&&isfield(Param.SeriesData.FileInfo{1},'Width')
-        pixnbre=Param.SeriesData.FileInfo{1}.Height*Param.SeriesData.FileInfo{1}.Width; % total number of pxels for input images  
-        CPUtime=0;
-        if isfield(Data.ActionInput,'Civ1')
-            %BoxSize=Data.ActionInput.Civ1.CorrBoxSize(1)*Data.ActionInput.Civ1.CorrBoxSize(2);
-            tic
-            testboxa=rand(Data.ActionInput.Civ1.CorrBoxSize(1),Data.ActionInput.Civ1.CorrBoxSize(2));
-            testboxb=rand(Data.ActionInput.Civ1.SearchBoxSize(1),Data.ActionInput.Civ1.SearchBoxSize(2));
-            anss=conv2(testboxa,testboxb);
-            CPUtime_unit=toc;
-            nb_box=pixnbre/(Data.ActionInput.Civ1.Dx*Data.ActionInput.Civ1.Dy);    
-            %nbpos=Data.ActionInput.Civ1.SearchBoxSize-Data.ActionInput.Civ1.CorrBoxSize;
-            CPUtime=2*CPUtime_unit*nb_box%*BoxSize*nbpos(1)*nbpos(2);% adjustement factor 2 used
-        end
-        if isfield(Data.ActionInput,'Patch1')
-            CPUtime=2*CPUtime;
-        end
-        if isfield(Data.ActionInput,'Civ2')
-            tic
-            testboxa=rand(Data.ActionInput.Civ2.CorrBoxSize(1),Data.ActionInput.Civ2.CorrBoxSize(2));
-            testboxb=rand(Data.ActionInput.Civ2.SearchBoxSize(1),Data.ActionInput.Civ2.SearchBoxSize(2));
-            anss=conv2(testboxa,testboxb);
-            CPUtime_unit=toc;
-            nb_box=pixnbre/(Data.ActionInput.Civ2.Dx*Data.ActionInput.Civ2.Dy);
-            %BoxSize=Data.ActionInput.Civ2.CorrBoxSize(1)*Data.ActionInput.Civ2.CorrBoxSize(2);
-            %nbpos=Data.ActionInput.Civ2.SearchBoxSize-Data.ActionInput.Civ2.CorrBoxSize;
-            CPUtime=CPUtime+2*CPUtime_unit*nb_box;%*BoxSize*nbpos(1)*nbpos(2);
-        end
-        if isfield(Data.ActionInput,'Patch2')
-            CPUtime=(4/3)*CPUtime;
-        end
-        Data.CPUTime=ceil(CPUtime/6); % estimated CPU time per field pair in minute
-        Data.CPUTime=Data.CPUTime/10; % displqy CPU time with 1 digit beyond dot
-    end
+%     CPUtime_unit=0.01;%estimated time for a multiplication (in microsecond)
+%     if isfield(Param.SeriesData,'FileInfo')&&isfield(Param.SeriesData.FileInfo{1},'Height')&&isfield(Param.SeriesData.FileInfo{1},'Width')
+%         pixnbre=Param.SeriesData.FileInfo{1}.Height*Param.SeriesData.FileInfo{1}.Width; % total number of pxels for input images  
+%         CPUtime=0;
+%         if isfield(Data.ActionInput,'Civ1')
+%             %BoxSize=Data.ActionInput.Civ1.CorrBoxSize(1)*Data.ActionInput.Civ1.CorrBoxSize(2);
+%             tic
+%             testboxa=rand(Data.ActionInput.Civ1.CorrBoxSize(1),Data.ActionInput.Civ1.CorrBoxSize(2));
+%             testboxb=rand(Data.ActionInput.Civ1.SearchBoxSize(1),Data.ActionInput.Civ1.SearchBoxSize(2));
+%             anss=conv2(testboxa,testboxb);
+%             CPUtime_unit=toc;
+%             nb_box=pixnbre/(Data.ActionInput.Civ1.Dx*Data.ActionInput.Civ1.Dy);    
+%             %nbpos=Data.ActionInput.Civ1.SearchBoxSize-Data.ActionInput.Civ1.CorrBoxSize;
+%             CPUtime=2*CPUtime_unit*nb_box%*BoxSize*nbpos(1)*nbpos(2);% adjustement factor 2 used
+%         end
+%         if isfield(Data.ActionInput,'Patch1')
+%             CPUtime=2*CPUtime;
+%         end
+%         if isfield(Data.ActionInput,'Civ2')
+%             tic
+%             testboxa=rand(Data.ActionInput.Civ2.CorrBoxSize(1),Data.ActionInput.Civ2.CorrBoxSize(2));
+%             testboxb=rand(Data.ActionInput.Civ2.SearchBoxSize(1),Data.ActionInput.Civ2.SearchBoxSize(2));
+%             anss=conv2(testboxa,testboxb);
+%             CPUtime_unit=toc;
+%             nb_box=pixnbre/(Data.ActionInput.Civ2.Dx*Data.ActionInput.Civ2.Dy);
+%             %BoxSize=Data.ActionInput.Civ2.CorrBoxSize(1)*Data.ActionInput.Civ2.CorrBoxSize(2);
+%             %nbpos=Data.ActionInput.Civ2.SearchBoxSize-Data.ActionInput.Civ2.CorrBoxSize;
+%             CPUtime=CPUtime+2*CPUtime_unit*nb_box;%*BoxSize*nbpos(1)*nbpos(2);
+%         end
+%         if isfield(Data.ActionInput,'Patch2')
+%             CPUtime=(4/3)*CPUtime;
+%         end
+%         Data.CPUTime=ceil(CPUtime/6); % estimated CPU time per field pair in minute
+%         Data.CPUTime=Data.CPUTime/10; % displqy CPU time with 1 digit beyond dot
+%     end
     return
 end
@@ -474 +474 @@
             Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param];
             Data.CivStage=1;
+        else
+            i1=Param.ActionInput.PairIndices.ref_i; %case of TESTmode
         end
         % set the list of variables

trunk/src/series/merge_proj.m

@@ -239 +239 @@
 %% MAIN LOOP ON FIELDS
 %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
-% for i_slice=1:NbSlice
-%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
-%     NbFiles=0;
-%     nbmissing=0;
 
     %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%

trunk/src/series/sliding_average.m

@@ -205 +205 @@
 end
 NbPeriod=2; %number of periods for the sliding average
-omega=2*pi/T;
+omega=2*2*pi/T;%harmonic
 Lscale=15;%diameter of the torus, length scale for normalisation
 Uscale=amplitude*omega;