Changeset 1184 for trunk/src/series.m

Timestamp:

Nov 6, 2025, 7:03:02 PM (4 weeks ago)

Author:

sommeria

Message:

bed-scan updated and many updates

File:

• trunk/src/series.m (modified) (31 diffs)

trunk/src/series.m

@@ -134 +134 @@
 %% Read the parameter file series.xml, or created from series.xml.default if it does not exist
 SeriesData=[];
-[path_series,name,ext]=fileparts(which('series'));% path to the GUI series
+path_series=fileparts(which('series'));% path to the GUI series
 xmlfile=fullfile(path_series,'series.xml');
 if ~exist(xmlfile,'file')
@@ -157 +157 @@
 NbBuiltinAction=numel(ActionList);
 set(handles.Action,'UserData',NbBuiltinAction)
-path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
-[path_series,name,ext]=fileparts(which('series')); % path to the GUI series
+%path_series_fct=fullfile(path_series,'series');%path of the functions in subdirectroy 'series'
+[path_series]=fileparts(which('series')); % path to the GUI series
 path_series_fct=fullfile(path_series,'series'); % path of the functions in subdirectroy 'series'
 ActionExtList={'.m';'.sh';'fluidimage'}; % default choice of extensions (Matlab fct .m or compiled version .sh
@@ -166 +166 @@
 if isfield(SeriesData.ClusterParam, 'ExistenceTest')
     oarcommand=SeriesData.ClusterParam.ExistenceTest;
-    [s,w]=system(oarcommand); % look for cluster system presence
+    s=system(oarcommand); % look for cluster system presence
     if isequal(s,0)% cluster detected
         RunModeList=[RunModeList;{'cluster'}];
@@ -275 +275 @@
     %% fill the list of input file series
     InputTable=[{Param.InputFile.RootPath},{Param.InputFile.SubDir},{Param.InputFile.RootFile},{Param.InputFile.NomType},{Param.InputFile.FileExt}];
-    if isempty(find(cellfun('isempty',InputTable)==0)) % if there is no input file, do not introduce input info
+    if isempty(find(cellfun('isempty',InputTable)==0,1)) % if there is no input file, do not introduce input info
         set(handles.REFRESH,'BackgroundColor',[1 0 1])% set REFRESH button to magenta color to indicate that input refresh is needed
         return
     end
-    TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
+   % TimeTable=[{Param.InputFile.TimeName},{[]},{[]},{[]},{[]}];
     if isfield(Param.InputFile,'RootPath_1')
         InputTable=[InputTable;[{Param.InputFile.RootPath_1},{Param.InputFile.SubDir_1},{Param.InputFile.RootFile_1},{Param.InputFile.NomType_1},{Param.InputFile.FileExt_1}]];
-        TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
+       % TimeTable=[TimeTable; [{Param.InputFile.TimeName_1},{[]},{[]},{[]},{[]}]];
     end
     set(handles.InputTable,'Data',InputTable)
@@ -291 +291 @@
     set(handles.Device,'String',[Device DeviceExt])
     set(handles.Experiment,'String',[Experiment ExperimentExt])
-    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)'))
+    if ~isempty(regexp(InputTable{1,1},'(^http://)|(^https://)','once'))
     set(handles.OutputPathBrowse,'Value',1)% an output folder needs to be specified for OpenDAP data
     end
@@ -308 +308 @@
     %% determine the selected reference field indices for pair display
 
-    [tild,tild,tild,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
-    if isempty(i1)
-        i1=1;
-    end
-    if isempty(i2)
-        i2=i1;
-    end
+  %  [~,~,~,i1,i2,j1,j2]=fileparts_uvmat(Param.InputFile.FileIndex);
+  i1=1;j1=1;%default
+    if isfield(Param,'i1')
+        i1=Param.i1;
+    end
+    if isfield(Param,'j1')
+        j1=Param.j1;
+    end
+    if isfield(Param,'i2')
+        i2=Param.i2;
+    end
+    if isfield(Param,'j2')
+        j2=Param.j2;
+    end
+    
     ref_i=floor((i1+i2)/2); % reference image number corresponding to the file
     % set(handles.num_ref_i,'String',num2str(ref_i));
@@ -609 +617 @@
 %% update MinIndex_i and MaxIndex_i if the input table content has been reduced in line nbre
 MinIndex_i_table=get(handles.MinIndex_i,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MinIndex_i_table)
 set(handles.MinIndex_i,'Data',MinIndex_i_table(1:nbview,:));
-end
 MinIndex_j_table=get(handles.MinIndex_j,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MinIndex_j_table)
 set(handles.MinIndex_j,'Data',MinIndex_j_table(1:nbview,:));
-end
 MaxIndex_i_table=get(handles.MaxIndex_i,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MaxIndex_i_table)
+
 set(handles.MaxIndex_i,'Data',MaxIndex_i_table(1:nbview,:));
-end
 MaxIndex_j_table=get(handles.MaxIndex_j,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(MaxIndex_j_table)
 set(handles.MaxIndex_j,'Data',MaxIndex_j_table(1:nbview,:));
-end
 PairString=get(handles.PairString,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(PairString)
 set(handles.PairString,'Data',PairString(1:nbview,:));
-end
 TimeTable=get(handles.TimeTable,'Data'); % retrieve the min indices in the table MinIndex
-if ~isempty(TimeTable)
 set(handles.TimeTable,'Data',TimeTable(1:nbview,:));
-end
 
 %% set length of waitbar
@@ -861 +858 @@
 
 %% display the min and max indices for the whole file series
-if size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
+if isempty(i1_series)
+    MinIndex_j=1;MaxIndex_j=1;MinIndex_i=1;MaxIndex_i=1;
+elseif size(i1_series,2)==2 && min(min(i1_series(:,1,:)))==0
     MinIndex_j=1; % index j set to 1 by default
     MaxIndex_j=1;
@@ -988 +987 @@
 XmlData=[];
 check_calib=0;
-
 XmlFileName=find_imadoc(InputTable{iview,1},InputTable{iview,2});
 if ~isempty(XmlFileName)
@@ -996 +994 @@
     end
     % read time if available
-    if isfield(XmlData,'Time') && strcmp(FileInfo.FieldType,'image')
+    if isfield(XmlData,'Time')
         Time=XmlData.Time;
         TimeName='xml';
@@ -1310 +1308 @@
 end
 PairString=get(handles.PairString,'Data');
-ref_i_1=str2num(get(handles.num_first_i,'String')); % first reference index
-ref_i_2=str2num(get(handles.num_last_i,'String')); % last reference index
-ref_j_1=[];ref_j_2=[];
+ref_i_1=str2double(get(handles.num_first_i,'String')); % first reference index
+if isnan(ref_i_1)
+ref_i_1=1;
+end
+ref_i_2=str2double(get(handles.num_last_i,'String')); % last reference index
+if isnan(ref_i_2)
+ref_i_2=1;
+end
+ref_j_1=NaN;ref_j_2=NaN;
 if strcmp(get(handles.num_first_j,'Visible'),'on')
-ref_j_1=str2num(get(handles.num_first_j,'String'));
-ref_j_2=str2num(get(handles.num_last_j,'String'));
+    ref_j_1=str2double(get(handles.num_first_j,'String'));
+    ref_j_2=str2double(get(handles.num_last_j,'String'));
 end
 [i1_1,i2_1,j1_1,j2_1] = get_file_index(ref_i_1,ref_j_1,PairString);
@@ -1429 +1433 @@
 
 function errormsg=launch_action(handles)
-errormsg=''; % default
+%errormsg=''; % default
 
 %% read the data on the GUI series
@@ -1637 +1641 @@
         end
     end
-    [xx,ExpName]=fileparts(Param.InputTable{1,1});
-    Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
-    Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String'));
+    [~,ExpName]=fileparts(Param.InputTable{1,1});
+    Param.IndexRange.first_i=str2double(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess
+    Param.IndexRange.last_i=str2double(get(handles.num_last_i,'String'));
 
     %% create the output data directory if needed, after checking its existence
@@ -1655 +1659 @@
         else
             PathExpOut=fullfile(PathOut,get(handles.Experiment,'String'));
-            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'))
+            PathExpDeviceOut=fullfile(PathExpOut,get(handles.Device,'String'));
         end
         if ~exist(PathExpOut,'dir')
-            [tild,msg1]=mkdir(PathExpOut);
+            [~,msg1]=mkdir(PathExpOut);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' PathExpOut ': ' msg1]; % error message for directory creation
@@ -1665 +1669 @@
         end
         if ~exist(PathExpDeviceOut,'dir')
-            [tild,msg1]=mkdir(PathExpDeviceOut);
+            [~,msg1]=mkdir(PathExpDeviceOut);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' PathExpDeviceOut ': ' msg1]; % error message for directory creation
@@ -1710 +1714 @@
         OutputDir=fullfile(PathExpDeviceOut,[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory
         if check_create    % create output directory if it does not exist
-            [tild,msg1]=mkdir(OutputDir);
+            [~,msg1]=mkdir(OutputDir);
             if ~strcmp(msg1,'')
                 errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation
@@ -1784 +1788 @@
         else
             ref_j=first_j:incr_j:last_j;
-            [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
+            [~,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
             ref_i=ref_i-1;
             ref_i=ref_i(ref_i>=first_i & ref_i<=last_i);
@@ -1792 +1796 @@
         ref_i=first_i:incr_i:last_i;
         if isempty(incr_j)% automatic finding of the existing j indices
-            [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
+            ref_j=find(squeeze(SeriesData.i1_series{1}(1,:,:)));
             ref_j=ref_j-1;
             ref_j=ref_j(ref_j>=first_j & ref_j<=last_j);
@@ -1809 +1813 @@
             else
                 answer=msgbox_uvmat('INPUT_TXT','estimate the CPU time(in minutes) for each value of index i:' ,'');
-                CPUTime=str2num(answer);
+                CPUTime=str2double(answer);
                 set(handles.num_CPUTime,'String',answer)
                 Param.Action.CPUTime=CPUTime;
@@ -2091 +2095 @@
                 cd(curdir)
             else
-                [tild,msg1]=mkdir(DIR_CLUSTER);
+                [~,msg1]=mkdir(DIR_CLUSTER);
                 if ~strcmp(msg1,'')
                     errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation
@@ -2186 +2190 @@
                 cd(curdir)
             else
-                [tild,msg1]=mkdir(DirSGE);
+                [~,msg1]=mkdir(DirSGE);
                 if ~strcmp(msg1,'')
                     errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation
@@ -2211 +2215 @@
                         cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n'];
                     end
-                    [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
+                    fid = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w');
                     fprintf(fid, cmd);
                     fclose(fid);
@@ -2221 +2225 @@
                         fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])];
                     fprintf(sge_command); % display in command line
-                    [status, result] = system(sge_command);
+                    [~, result] = system(sge_command);
                     fprintf(result);
                     currJobIndex = currJobIndex + 1;
@@ -2235 +2239 @@
             command = ['python -m fluidimage.run_from_xml ' filexml{iprocess}];
             fprintf(['command:\n' command '\n\n'])
-            [status, result] = call_command_clean(command);
+          %  [status, result] = call_command_clean(command);
     end
     if exist(OutputDir,'dir')
-        [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir);
+        [~,MESSAGE] = fileattrib (OutputDir);
         if MESSAGE.GroupWrite~=1
             [success,msg] = fileattrib(OutputDir,'+w','g','s'); % allow writing access for the group of users, recursively in the folder
@@ -2393 +2397 @@
 %% Put the first line of the selected Action fct as tooltip help
 try
-    [fid,errormsg] =fopen([fullfile(ActionPath,ActionName) '.m']);
+    fid=fopen([fullfile(ActionPath,ActionName) '.m']);
     InputText=textscan(fid,'%s',1,'delimiter','\n');
     fclose(fid);
@@ -2877 +2881 @@
         set(handles.FieldName,'String',[FieldListInit; FieldList; {'add_field...'}]);
         if ~strcmp(GetFieldData.FieldOption,'civdata...')
-           if ~isempty(regexp(FieldList{1},'^vec'))
+           if ~isempty(regexp(FieldList{1},'^vec', 'once'))
                 set(handles.FieldName,'Value',1)
            else
@@ -3031 +3035 @@
             datepair(imulti)=datenum(dirpair(ind_pairs(imulti)).date); % dates of creation
         end
-        [datenew,indsort2]=sort(datepair); % sort the multiplet by creation date
+        [~,indsort2]=sort(datepair); % sort the multiplet by creation date
         ind_s=indsort2(1:end-1); %
         ind_remove=[ind_remove ind_pairs(ind_s)]; % remove these indices, leave the last one
@@ -3058 +3062 @@
     num_j1=meshgrid(num_j,ones(size(num_i1_line)));
     num_j2=meshgrid(num_j,ones(size(num_i1_line)));
-    [xx,num_i1]=meshgrid(num_j,num_i1_line);
-    [xx,num_i2]=meshgrid(num_j,num_i2_line);
+    [~,num_i1]=meshgrid(num_j,num_i1_line);
+    [~,num_i2]=meshgrid(num_j,num_i2_line);
 elseif isequal (mode,'series(Dj)')||isequal (mode,'bursts')
     if isequal(mode,'bursts') %case of bursts (png_old or png_2D)
@@ -3200 +3204 @@
     MaskTable=cell(NbView,2);
     
-    RootPath=Param.InputTable{1,1};
+    %RootPath=Param.InputTable{1,1};
     first_j=[];% note that the function will propose to cover the whole range of indices
     if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
-    last_j=[];
+   %last_j=[];
     if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
     PairString='';
@@ -3214 +3218 @@
             Param.InputTable{iview,5},Param.InputTable{iview,4},i1,i2,j1,j2);
         
-        [FileInfo,VideoObject]=get_file_info(FirstFileName);
+       % [FileInfo,VideoObject]=get_file_info(FirstFileName);
         
         
@@ -3422 +3426 @@
 %% use a browser to choose the xml file containing the processing config
 InputTable=get(handles.InputTable,'Data');
-oldfile='';
-if isempty(InputTable)
-    oldfile='';
-else
 oldfile=InputTable{1,1}; % current path in InputTable
-end
 if isempty(oldfile)
     % use a file name stored in prefdir