Changeset 1150

Timestamp:

Jun 24, 2024, 6:38:26 PM (4 months ago)

Author:

sommeria

Message:

browse_data improved

Location:

trunk/src

Files:

• browse_data.fig (modified) (previous)
• browse_data.m (modified) (4 diffs)
• civ_3D.m (deleted)
• geometry_calib.m (modified) (4 diffs)
• imadoc2struct.m (modified) (1 diff)
• series.m (modified) (1 diff)
• series/civ_3D.m (modified) (1 diff)
• xml2struct.m (modified) (1 diff)
• xmlburst2time.m (modified) (3 diffs)

trunk/src/browse_data.m

@@ -426 +426 @@
                 ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray
                 ListFiles=ListCells(1,:);
-                check_xml=~cellfun('isempty',regexp(ListFiles,'(\.xml|~)$'));% detect non xml files and files not marked by ~
+                check_xml=~cellfun('isempty',regexp(ListFiles,'\.xml$'));% detect  xml files
+                check_tild=~cellfun('isempty',regexp(ListFiles,'~$'));% detect  ~  files
                 index_isdir=find(strcmp('isdir',fieldnames(ListStruct)));
                 check_dir=cell2mat(ListCells(index_isdir,:));% =1 for directories, =0 for files
-                nbfiles=numel(find(~check_xml & ~check_dir));% number of non xml files
+                nbfiles=numel(find(~check_xml & ~check_dir & ~check_tild));% number of non xml files
                 check_dir=check_dir & cellfun('isempty', regexp(ListFiles,'^(-|\.|\+/\.)'));% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . )
                 ListFiles(check_dir)=regexprep(ListFiles(check_dir),'^.+','+/$0');% put '+/' in front of dir name display
@@ -477 +478 @@
         ListCells=struct2cell(ListStruct);%transform dir struct to a cell arrray
         ListFiles=ListCells(1,:);%list of dir and file  names
-        cell_remove=regexp(ListFiles,'^(-|\.|\+/\.)');% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . )
+        cell_remove=regexp(ListFiles,'^((-|\.|\+/\.))');% detect strings beginning by '-' ,'.' or '+/.'(dir beginning by . )
         check_keep=cellfun('isempty', cell_remove);
         index_isdir=find(strcmp('isdir',fieldnames(ListStruct)));
@@ -721 +722 @@
 ListDevices=get(handles.ListDevices,'String');
 DeviceIndices=get(handles.ListDevices,'Value');
-set(handles.DataSeries,'String',ListDevices);
+set(handles.DataSeries,'String',ListDevices);%transfer list of devices to DataSeries
 set(handles.DataSeries,'Value',DeviceIndices);
 
 ListExperiments=get(handles.ListExperiments,'String');
 ExpIndices=get(handles.ListExperiments,'Value');
-set(handles.ListDevices,'String',ListExperiments);
+set(handles.ListDevices,'String',ListExperiments);%transfer list of experiments to devices 
 set(handles.ListDevices,'Value',ExpIndices);
 
@@ -740 +741 @@
 % set(handles.ListExperiments,'String',DataSeries)
 % set(handles.ListExperiments,'Value',ValueDevice)
-% ListExperiments_Callback(hObject, [], handles)
-
-
-% % --- Executes on selection change in DataSeries.
-% function DataSeries_Callback(hObject, eventdata, handles)
-% SourceDir=get(handles.SourceDir,'String');
-% ListData=get(handles.DataSeries,'String');
-% Folder=ListData{get(handles.DataSeries,'Value')};
-% if ~isempty(regexp(Folder,'^\+/'))% if a folder is selected
-%     Folder=regexprep(Folder,'\+/','');
-%     ListExperiments=get(handles.ListExperiments,'String');
-%     list_val=get(handles.ListExperiments,'Value');
-%     for iexp=1:numel(list_val)
-%         ExpName=regexprep(ListExperiments{list_val(iexp)},'\+/','');
-%         FullName=fullfile(SourceDir,ExpName,Folder);
-%         dd=dir(FullName);
-%         check_sub=1;
-%         for idir=1:numel(dd)
-%             ListData{ilist}=dd(ilist).name;
-%             if dd(ilist).isdir && ~strcmp(dd(ilist).name,'.')&& ~strcmp(dd(ilist).name,'..')&& isempty(regexp(dd(ilist).name,'^_LOG'))...
-%                     && isempty(regexp(dd(ilist).name,'^_LOG'))&& isempty(regexp(dd(ilist).name,'^_XML'))
-%                check_sub=1;
-%                ListData{ilist}=['+/' dd(ilist).name];
-%             end
-%         end
-%         if check_sub
-%         set(handles.ListDevices,'String',ListData);
-%                 set(handles.ListDevices,'Visible','on');
-%                 set(handles.DataSeries,'String',ListData)
-%                 break
-%         end
-%     end
-% end
-
-% % --- Executes on button press in CheckDevices.
-% function CheckDevices_Callback(hObject, eventdata, handles)
-% if get(handles.CheckDevices,'Value')
-%     set(handles.ListDevices,'Visible','on')
-%     ListDevices=get(handles.DataSeries,'String');
-%     Index=get(handles.DataSeries,'Value');
-%     set(handles.ListDevices,'String',ListDevices)
-%     set(handles.ListDevices,'Value',Index)
-%     set(handles.DataSeries,'Value',1)
-%     if strcmp(get(handles.MirrorDir,'Visible'),'on')
-%     MirrorPath=get(handles.MirrorDir,'String');
-%     else
-%     MirrorPath=get(handles.SourceDir,'String');
-%     end
-%     IndexExperiment=get(handles.ListExperiments,'Value');
-%     ListExperiment=get(handles.ListExperiments,'String');
-%     Experiment=ListExperiment{get(handles.ListExperiments,'Value')};
-%     Experiment=regexprep(Experiment,'^\+/','');% remove the +/ used to mark dir
-%     Experiment=regexprep(Experiment,'^~','');% remove the ~ used to mark symbolic link
-%     Device=regexprep(ListDevices{Index},'^\+/','');% remove the +/ used to mark dir
-%     Device=regexprep(Device,'^~','');% remove the ~ used to mark symbolic link
-%     DataSeries=dir(fullfile(MirrorPath,Experiment,Device));
-%     DataSeriesCell=struct2cell(DataSeries);
-%     set(handles.DataSeries,'String',DataSeriesCell(1,:)')
-% else
-%     ListDevices=get(handles.ListDevices,'String');
-%     Index=get(handles.ListDevices,'Value');
-%     set(handles.ListDevices,'Visible','off')
-%     set(handles.DataSeries,'String',ListDevices)
-%     set(handles.DataSeries,'Value',Index)
-% end
+ListExperiments_Callback(hObject, [], handles)
+SourceDir_Callback(hObject, [], handles)
 
 

trunk/src/geometry_calib.m

@@ -346 +346 @@
                         display([XmlName ' updated with calibration parameters' dispmessage])
                     else
-                        display([XmlName ' created with calibration parameters' dispmessage])
+                        display([XmlName ' created with calibration parameters: no timing defined' dispmessage])
                     end
                 end
@@ -396 +396 @@
 %------------------------------------------------------------------------
 % --- Executes on button press in Replicate
-    function Replicate_Callback(hObject, eventdata, handles)
-        % %------------------------------------------------------------------------
-        set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
-        
-        if get(handles.Replicate,'Value') %open the GUI browse_data
-            % look for the GUI uvmat and check for an image as input
-            huvmat=findobj(allchild(0),'Name','uvmat');
-            hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
-            RootPath=get(hhuvmat.RootPath,'String');
-            SubDir=get(hhuvmat.SubDir,'String');
-            browse_data(fullfile(RootPath,SubDir))
-        else
-            hbrowse=findobj(allchild(0),'Tag','browse_data');
-            if ~isempty(hbrowse)
-                delete(hbrowse)
-            end
-        end
+function Replicate_Callback(hObject, eventdata, handles)
+% %------------------------------------------------------------------------
+set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points)
+
+if get(handles.Replicate,'Value') %open the GUI browse_data
+    % look for the GUI uvmat and check for an image as input
+    huvmat=findobj(allchild(0),'Name','uvmat');
+    hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat
+    RootPath=get(hhuvmat.RootPath,'String');
+    SubDir=get(hhuvmat.SubDir,'String');
+    browse_data(fullfile(RootPath,SubDir))
+else
+    hbrowse=findobj(allchild(0),'Tag','browse_data');
+    if ~isempty(hbrowse)
+        delete(hbrowse)
+    end
+end
 %------------------------------------------------------------------------
 % --- activate calibration and store parameters in ouputfile .
@@ -1294 +1294 @@
     Heading=s.Heading;
 end
-
+if isfield (s,'GeometryCalib')
 GeometryCalib=s.GeometryCalib;
 fx=1;fy=1;Cx=0;Cy=0;kc=0; %default
@@ -1341 +1341 @@
     set(handles.CheckEnableMouse,'BackgroundColor',[0.7 0.7 0.7])
 end
-
+end
 %------------------------------------------------------------------------
 %---display calibration intrinsic parameters

trunk/src/imadoc2struct.m

@@ -70 +70 @@
         s.Camera.FirstFrameIndexI=1; %first index assumed equl to 1 by default
     end
-    Timing=s.Camera.BurstTiming;
-    if ~iscell(Timing)
-        Timing={Timing};
-    end
+    s.Time=xmlburst2time(s.Camera.BurstTiming,s.Camera.FirstFrameIndexI);
+end
 
-    s.Time=[];
-    for k=1:length(Timing)
-        Frequency=1;
-        if isfield(Timing{k},'FrameFrequency')
-            Frequency=Timing{k}.FrameFrequency;
-        end
-        Dtj=[];
-        if isfield(Timing{k},'Dtj')
-            Dtj=Timing{k}.Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's');
-        end
-        NbDtj=1;
-        if isfield(Timing{k},'NbDtj')&&~isempty(Timing{k}.NbDtj)
-            NbDtj=Timing{k}.NbDtj;
-        end
-        Dti=[];
-        if isfield(Timing{k},'Dti')
-            Dti=Timing{k}.Dti/Frequency;%Dti converted from frame unit to TimeUnit (e.g. 's');
-        end
-        NbDti=1;
-        if isfield(Timing{k},'NbDti')&&~isempty(Timing{k}.NbDti)
-            NbDti=Timing{k}.NbDti;
-        end
-        Time_val=Timing{k}.Time;%time in TimeUnit
-        if ~isempty(Dti)
-            Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
-            Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals  Dti
-        end
-        if ~isempty(Dtj)
-            Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
-            Dtj=[0 Dtj];
-            Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
-        end
-        % reading Dtk
-        Dtk=[];%default
-        NbDtk=1;%default
-        if isfield(Timing{k},'Dtk')
-            Dtk=Timing{k}.Dtk;
-        end
-        if isfield(Timing{k},'NbDtk')&&~isempty(Timing{k}.NbDtk)
-            NbDtk=Timing{k}.NbDtk;
-        end
-        if isempty(Dtk)
-            s.Time=[s.Time;Time_val];
-        else
-            for kblock=1:NbDtk+1
-                Time_val_k=Time_val+(kblock-1)*Dtk;
-                s.Time=[s.Time;Time_val_k];
-            end
-        end
-    end
-   
-    s.Time=[zeros(size(s.Time,1),1) s.Time]; %insert a vertical line of zeros (to deal with zero file indices)
-    if s.Camera.FirstFrameIndexI~=0
-    s.Time=[zeros(s.Camera.FirstFrameIndexI,size(s.Time,2)); s.Time]; %insert a horizontal line of zeros
-    end
-end
 
 function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)

trunk/src/series.m

@@ -1420 +1420 @@
 %% create the Action fct handle if RunMode option = 'local'
 if strcmp(RunMode,'local')
-    if ~isequal(ActionPath,path_series)
-        eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
-        if ~exist(ActionPath,'dir')
-            errormsg=['The prescribed function path ' ActionPath ' does not exist'];
-            return
-        end
-        if ~isequal(spath,ActionPath)
-            addpath(ActionPath)% add the prescribed path if not the current one
-        end
-    end
-    eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
-    if ~isequal(ActionPath,path_series)
-        rmpath(ActionPath)% add the prescribed path if not the current one
-    end
-end
+    current_dir=pwd; % current working dir
+cd(ActionPath)
+h_fun=str2func(ActionName);% create the function handle for the function ActionName
+cd(current_dir)
+    % if ~isequal(ActionPath,path_series)
+    % 
+    %     %eval(['spath=which(''' ActionName ''');']) %spath = current path of the selected function ACTION
+    %     if ~exist(ActionPath,'dir')
+    %         errormsg=['The prescribed function path ' ActionPath ' does not exist'];
+    %         return
+    %     end
+    %     spath=fileparts(which(ActionName));
+    %     if ~strcmp(spath,ActionPath)
+    %         addpath(ActionPath)% add the prescribed path if not the current one
+    %     end
+    % end
+    % eval(['h_fun=@' ActionName ';'])%create a function handle for ACTION
+    % if ~isequal(ActionPath,path_series)
+    %     rmpath(ActionPath)% add the prescribed path if not the current one
+    % end
+ end
 
 %% Get  parameters from series.xml

trunk/src/series/civ_3D.m

@@ -290 +290 @@
         par_civ1.ImageB=zeros(2*SearchRange_z+1,npy,npx);
 
-        for islice=ceil(par_civ1.Dz/2):par_civ1.Dz:NbSlice
-            if par_civ1.Dz<2*SearchRange_z+1
+        for islice=par_civ1.Dz:NbSlice
+            if par_civ1.Dz<2*SearchRange_z+1 
             par_civ1.ImageA=circshift(par_civ1.ImageA,-par_civ1.Dz);
             par_civ1.ImageB=circshift(par_civ1.ImageA,-par_civ1.Dz);
             end
               for iz=1:par_civ1.Dz
-            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield,islice));
+            ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(1,ifield),[],j1_series_Civ1(islice+SearchRange_z-iz+1,1));
             A= read_image(ImageName_A,FileType_A);
-            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield,islice));
+            ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(1,ifield),[],j1_series_Civ1(islice+SearchRange_z-iz+1,1));
             B= read_image(ImageName_B,FileType_B);
             par_civ1.ImageA(2*SearchRange_z+2-iz,:,:) = A;

trunk/src/xml2struct.m

@@ -59 +59 @@
         else
         tsub=branch(t,uid_sub);
+        if ~isempty(get(tsub,1,'contents'))
         ss=convert(tsub);
         s.(varargin{isub})=convert_string(ss);
+        end
         end
     end

trunk/src/xmlburst2time.m

@@ -5 +5 @@
 if ~iscell(BurstTiming)
     BurstTiming={BurstTiming};
-    BurstTiming{1}.Time=0;%time origin set to zero by default
 end
 TimeMatrix=[];
@@ -12 +11 @@
     if isfield(BurstTiming{k},'FrameFrequency')
         Frequency=BurstTiming{k}.FrameFrequency;
+    end
+    if isfield(BurstTiming{k},'Time')
+        BurstTiming{k}.Time=0;%time origin set to zero by default
     end
     Dtj=[];
@@ -58 +60 @@
 end
 TimeMatrix=[zeros(size(TimeMatrix,1),1) TimeMatrix]; %insert a vertical line of zeros (to deal with zero file indices)
-    if FirstFrameIndexI~=0
+if FirstFrameIndexI~=0
     TimeMatrix=[zeros(FirstFrameIndexI,size(TimeMatrix,2)); TimeMatrix]; %insert a horizontal line of zeros
-    end
+end