Changeset 456 for trunk

Timestamp:

Jun 17, 2012, 10:50:20 PM (13 years ago)

Author:

sommeria

Message:

various bugs corrected

Location:

trunk/src

Files:

• find_file_series.m (modified) (1 diff)
• imadoc2struct.m (modified) (2 diffs)
• mouse_down.m (modified) (2 diffs)
• read_imatext.m (deleted)
• series.fig (modified) (previous)
• series.m (modified) (14 diffs)
• uvmat.m (modified) (5 diffs)

trunk/src/find_file_series.m

@@ -235 +235 @@
     end
     %[tild,ifile_min]=min(ref_ij(ref_ij>0));
-    ifile_min=find(ref_ij>0 , 1);
-    if isempty(ifile_min)
+    ind_select=find(ref_ij>0);
+    if isempty(ind_select)
         %         RootPath='';
         RootFile='';
         NomType='';
     else
+        [tild,ifile_min]=min(ref_ij(ind_select));
         [tild,tild,tild,tild,tild,tild,tild,tild,NomType]=fileparts_uvmat(dirpair(ifile_min).name);% update the representation of indices (number of 0 before the number)
         NomType=regexprep(NomType,['^' NomTypePref],'');

trunk/src/imadoc2struct.m

@@ -28 +28 @@
 
 %% opening the xml file
-if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist
+[tild,tild,FileExt]=fileparts(ImaDoc);
+if strcmp(FileExt,'.civ')
+    [errormsg,time,TimeUnit,mode,npx,npy,XmlData{iview}.GeometryCalib]=read_imatext(ImaDoc);
+    return
+end
 try
     t=xmltree(ImaDoc);
-catch
-    errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
+catch ME
+    errormsg={['error reading ' ImaDoc ': ']; ME.message};
     display(errormsg);
     return
 end
 uid_root=find(t,'/ImaDoc');
-if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file
-
+if isempty(uid_root), return; end;%not an ImaDoc .xml file
 
 %% Heading
@@ -283 +286 @@
    end
 end
+
+%------------------------------------------------------------------------
+%'read_imatext': reads the .civ file for image documentation (obsolete)
+% fileinput: name of the documentation file 
+% time: matrix of times for the set of images
+%pxcmx: scale along x in pixels/cm
+%pxcmy: scale along y in pixels/cm
+function [error,time,TimeUnit,mode,npx,npy,GeometryCalib]=read_imatext(fileinput)
+%------------------------------------------------------------------------
+error=0;%default
+time=[]; %default
+TimeUnit='s';
+mode='pairs';
+npx=[]; %default
+npy=[]; %default
+pxcmx=1;%default
+pxcmy=1;%default
+if exist(fileinput,'file')~=2, error=2, return;end;%input file does not exist
+dotciv=textread(fileinput);
+sizdot=size(dotciv);
+if ~isequal(sizdot(1)-8,dotciv(1,1));
+    error=1; %inconsistent number of bursts
+end
+nbfield=sizdot(1)-8;
+npx=(dotciv(2,1));
+npy=(dotciv(2,2));
+pxcmx=(dotciv(6,1));% pixels/cm in the .civ file 
+pxcmy=(dotciv(6,2));
+% nburst=dotciv(3,1); % nbre of bursts
+abs_time1=dotciv([9:nbfield+8],2);
+dtime=dotciv(5,1)*(dotciv([9:nbfield+8],[3:end-1])+1);
+timeshift=[abs_time1 dtime];
+time=cumsum(timeshift,2);
+
+GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
+GeometryCalib.Tx=0;
+GeometryCalib.Ty=0;
+GeometryCalib.Tz=1;
+GeometryCalib.dpx=1;
+GeometryCalib.dpy=1;
+GeometryCalib.sx=1;
+GeometryCalib.Cx=0;
+GeometryCalib.Cy=0;
+GeometryCalib.f=1;
+GeometryCalib.kappa1=0;
+GeometryCalib.CoordUnit='cm';

trunk/src/mouse_down.m

@@ -132 +132 @@
                 if isequal(get(hObject,'SelectionType'),'alt')  && isequal(get(hchild,'Visible'),'on') && ~isequal(get(hchild,'tag'),'frame_object')&&...
                         ~isequal(get(hchild,'tag'),'ListObject') 
-%                     if strcmp(get(hchild,'Visible'),'on')
                     if ~strcmp(get(hchild,'Style'),'frame')%do not visualisaze frames
                         msg_pos(1:2)=GUI_pos(1:2)+obj_pos(1:2).*GUI_pos(3:4);
@@ -159 +158 @@
                 end
         end
+        if ~isempty(output_str)
+            break   %leave the current loop if a uicontrol has been selected
+        end
     end
 end

trunk/src/series.m

@@ -539 +539 @@
 MinIndex=get(handles.MinIndex,'Data');%retrieve the min indices in the table MinIndex
 MaxIndex=get(handles.MaxIndex,'Data');%retrieve the max indices in the table MaxIndex
-i_sum=sum(sum(i1_series,2),3);
+i_sum=sum(sum(i1_series,2),3);%sum of i1_series on the last index
 MaxIndex_i=max(find(i_sum>0))-1;
-MinIndex_i=min(find(i_sum>0))-1;
-j_sum=sum(sum(i1_series,1),3);
+if isequal(i1_series(1),0)
+    MinIndex_i=0;
+else
+    MinIndex_i=min(find(i_sum>0))-1;
+end
+j_sum=sum(sum(j1_series,1),3);
 MaxIndex_j=max(find(j_sum>0))-1;
 MinIndex_j=min(find(j_sum>0))-1;
@@ -650 +654 @@
 
 %% update time table
+if ~isempty(time)
 TimeTable=get(handles.TimeTable,'Data');
 if isempty(MinIndex_j)
+    if MinIndex_i>0
     TimeTable{iview,1}=time(MinIndex_i);
+    end
     TimeTable{iview,2}=time(first_i);
     TimeTable{iview,3}=time(last_i);
     TimeTable{iview,4}=time(MaxIndex_i);
 elseif ~isempty(time)
+    if MinIndex_i>0
     TimeTable{iview,1}=time(MinIndex_i,MinIndex_j);
+    end
     TimeTable{iview,2}=time(first_i,first_j);
     TimeTable{iview,3}=time(last_i,last_j);
@@ -663 +672 @@
 end
 set(handles.TimeTable,'Data',TimeTable)
+end
 
 %% number of slices
@@ -1108 +1118 @@
 else
     enable_i(handles,'On')
-    enable_j(handles,'On')
+    if isempty(j1_series)
+         enable_j(handles,'Off')
+    else
+        enable_j(handles,'On')
+    end
 end
 fill_ListPair(handles,i1_series,i2_series,j1_series,j2_series,time)
@@ -1259 +1273 @@
 set(handles.RUN, 'Enable','Off')
 set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
+drawnow
 [h_fun,Series,filexml,errormsg]=prepare_jobs(handles);
 if ~isempty(errormsg)
     msgbox_uvmat('ERROR',errormsg)
 else
-   Series.Specific=h_fun(Series,0);   
+  %Series.Specific=h_fun(Series);   
+   Series=h_fun(Series);  
    t=struct2xml(Series);
     t=set(t,1,'name','Series');
     save(t,filexml);
-    h_fun(Series);
+%     h_fun(Series);
 end
 set(handles.RUN, 'Enable','On')
@@ -1293 +1309 @@
 end
 % update the xml file after interactive input with the function
-Series.Specific=h_fun(Series,0);   
+Series.Specific=h_fun('input?');   
 t=struct2xml(Series);
 t=set(t,1,'name','Series');
@@ -1305 +1321 @@
     return
 end
-fctpath=get(handles.ActionPath,'String');
+path_fct=get(handles.ActionPath,'String');
 text_matlabscript=[...
     '#!/bin/bash \n'...
@@ -1311 +1327 @@
     'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
     'cd(''' path_series '''); \n'...
-    'addpath(''' fctpath '''); \n'...
+    'addpath(''' path_fct '''); \n'...
     '' Series.Action  '( ''' filename_xml '''); \n'...
     'exit \n'...
@@ -1318 +1334 @@
 fclose(fid);
 if isunix
-    system(['chmod +x ' filename_bat]);
+    system(['chmod +x ' filename_bat]);% set the file to executable
+    system(['. ' filename_bat]);%execute fct
 end
 set(handles.BATCH, 'Enable','On')
 set(handles.BATCH,'BackgroundColor',[1 0 0])
+
 %------------------------------------------------------------------------
 % --- Executes on button press in BIN.
@@ -1333 +1351 @@
     
 %------------------------------------------------------------------------
-% --- Main lauch command, called by RUN and BATCH
+% --- Main launch command, called by RUN and BATCH
 function [h_fun,Series,filexml,errormsg]=prepare_jobs(handles)
 %------------------------------------------------------------------------
+filexml='';
 errormsg='';
 %% Read parameters from series
@@ -1343 +1362 @@
 end
 
-%% read root name and field type
+%% read index ranges
 first_i=1;
 last_i=1;
@@ -1463 +1482 @@
     end
     filexml=fullfile(Series.OutputDir,[Series.InputTable{1,3} '.xml']);% name of the parameter xml file set in this directory
-    t=struct2xml(Series);
-    t=set(t,1,'name','Series');
-    save(t,filexml);
+%     t=struct2xml(Series);
+%     t=set(t,1,'name','Series');
+%     save(t,filexml);
 end
 
@@ -1573 +1592 @@
     InputText=textscan(fid,'%s',1,'delimiter','\n');
     fclose(fid)
-    set(handles.ActionName,'ToolTipString',InputText{1}{1})
+    set(handles.ActionName,'ToolTipString',InputText{1}{1})% put the first line of the selected function as tooltip help
 end
 if ~isequal(path_series,PathName)
@@ -1617 +1636 @@
                 SeriesData.AllowInputSort=1;
                 set(handles.series,'UserData',SeriesData)
-            end              
+            end                      
+        case 'WholeIndexRange'
+            if isequal(lower(varargout{ilist+1}),'on')% sort the input table by alphabetical order of the SubDir
+                MinIndex=get(handles.MinIndex,'Data');
+                MaxIndex=get(handles.MaxIndex,'Data');
+                if ~isempty(MinIndex)
+                    set(handles.num_first_i,'String',num2str(MinIndex{1}))
+                    set(handles.num_last_i,'String',num2str(MaxIndex{1}))
+                    set(handles.num_incr_i,'String','1')
+                    if size(MinIndex,2)>=2
+                        set(handles.num_first_j,'String',num2str(MinIndex{1,2}))
+                        set(handles.num_last_j,'String',num2str(MaxIndex{1,2}))
+                        set(handles.num_incr_j,'String','1')
+                    end
+                end
+            end            
         case 'NbSlice'   %hidden by default
             if isequal(lower(varargout{ilist+1}),'on')

trunk/src/uvmat.m

@@ -597 +597 @@
 % read the current input file name:
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles);
+if ~exist(fullfile(RootPath,SubDir),'dir')
+    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
+    return
+end
 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
 [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
@@ -608 +612 @@
 % update_rootinfo_1(hObject,eventdata,handles)
 [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles);
+if ~exist(fullfile(RootPath,SubDir),'dir')
+    msgbox_uvmat('ERROR',['directory ' fullfile(RootPath,SubDir) ' does not exist'])
+    return
+end
 % detect the file type, get the movie object if relevant, and look for the corresponding file series:
 [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]);
@@ -908 +916 @@
 SubDirBase=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.'
 filexml=fullfile(RootPath,[SubDirBase '.xml']);% new convention: xml above the image dir
+DocExt='.xml';
 if ~exist(filexml,'file')
     filexml=fullfile(RootPath,SubDir,[RootFile '.xml']);%old convention: xml within the image directroy
+    if ~exist(filexml,'file')
+        filexml=fullfile(RootPath,SubDir,[RootFile '.civ']); % very old convention: .civ file
+        if ~exist(filexml,'file')
+            DocExt='.civ';
+        else
+            filexml='';
+        end
+    end
 end
 warntext='';%default warning message
 NbSlice=1;%default
 set(handles.RootPath,'BackgroundColor',[1 1 1])
-if exist(filexml,'file')
+if ~isempty(filexml)
     set(handles.view_xml,'Visible','on')
     set(handles.view_xml,'BackgroundColor',[1 1 0])
     set(handles.view_xml,'String','view .xml')
     drawnow
-    [XmlData,warntext]=imadoc2struct(filexml);
+    [XmlDataRead,warntext]=imadoc2struct(filexml);
     if ~isempty(warntext)
-        display(warntext)
-%         msgbox_uvmat('WARNING',warntext)
-    end
-    if isfield(XmlData,'TimeUnit')
-        if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
-            TimeUnit=XmlData.TimeUnit;
-        end
-    end
-    set(handles.view_xml,'BackgroundColor',[1 1 1])
-    drawnow
-    if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
-        if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
-            set (handles.nb_slice,'String','volume')
-        end
-        hgeometry_calib=findobj('tag','geometry_calib');
-        if ~isempty(hgeometry_calib)
-            GUserData=get(hgeometry_calib,'UserData');
-            if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
-                answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
-                if strcmp(answer,'Yes')
-                    geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
+        msgbox_uvmat('WARNING',warntext)
+    end
+    if isempty(XmlDataRead)
+        set(handles.view_xml,'Visible','off')
+    else
+        set(handles.view_xml,'String',['view ' DocExt])   
+        XmlData=XmlDataRead;
+        if isfield(XmlData,'TimeUnit')
+            if isfield(XmlData,'TimeUnit')&& ~isempty(XmlData.TimeUnit)
+                TimeUnit=XmlData.TimeUnit;
+            end
+        end
+        set(handles.view_xml,'BackgroundColor',[1 1 1])
+        drawnow
+        if isfield(XmlData, 'GeometryCalib') && ~isempty(XmlData.GeometryCalib)
+            if isfield(XmlData.GeometryCalib,'VolumeScan') && isequal(XmlData.GeometryCalib.VolumeScan,'y')
+                set (handles.nb_slice,'String','volume')
+            end
+            hgeometry_calib=findobj('tag','geometry_calib');
+            if ~isempty(hgeometry_calib)
+                GUserData=get(hgeometry_calib,'UserData');
+                if ~(isfield(GUserData,'XmlInputFile') && strcmp(GUserData.XmlInputFile,filexml))
+                    answer=msgbox_uvmat('INPUT_Y-N','replace the display of geometry_calib with the new input data?');
+                    if strcmp(answer,'Yes')
+                        geometry_calib(filexml);%diplay the new calibration points and parameters in geometry_calib
+                    end
                 end
             end
         end
-    end  
-else
-    fileciv=fullfile(RootPath,SubDir,[RootFile '.civ']);
-    if exist(fileciv,'file')% if .civ file found (very old convention)
-        [error,XmlData.Time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext(fileciv);
-        GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0];
-        GeometryCalib.Tx=0;
-        GeometryCalib.Ty=0;
-        GeometryCalib.Tz=1;
-        GeometryCalib.dpx=1;
-        GeometryCalib.dpy=1;
-        GeometryCalib.sx=1;
-        GeometryCalib.Cx=0;
-        GeometryCalib.Cy=0;
-        GeometryCalib.f=1;
-        GeometryCalib.kappa1=0;
-        GeometryCalib.CoordUnit='cm';
-        XmlData.GeometryCalib=GeometryCalib;
-        if error==2, warntext=['no file ' fileciv];
-        elseif error==1, warntext='inconsistent number of fields in the .civ file';
-        end
-        set(handles.num_Npx,'String',num2str(npx));%fills nbre of pixels x box
-        set(handles.num_Npy,'String',num2str(npy));%fills nbre of pixels y box
-        set(handles.pxcm,'String',num2str(pxcmx));%fills scale x (pixel/cm) box
-        set(handles.pycm,'String',num2str(pxcmy));%fills scale y (pixel/cm) box
-        set(handles.pxcm,'Visible','on');%fills scale x (pixel/cm) box
-        set(handles.pycm,'Visible','on');%fills scale y (pixel/cm) box
-        set(handles.view_xml,'Visible','on')
-        set(handles.view_xml,'String','view .civ')
-    else
-        set(handles.view_xml,'Visible','off')
     end
 end
@@ -991 +982 @@
     %transform .Time to a column vector if it is a line vector the nomenclature uses a single index
     if isequal(size(XmlData.Time,1),1)
-%     if isequal(nbfield,1) && ~isequal(nbfield_j,1)% .Time is a line vector
         NomType=get(handles.NomType,'String');
-%         if isempty(nbfield_j)
-%         if numel(NomType)>=2 &&(strcmp(NomType,'_i')||strcmp(NomType(1:2),'%0')||strcmp(NomType(1:2),'_%'))
-            XmlData.Time=(XmlData.Time)';
+        XmlData.Time=(XmlData.Time)';
     end
 end
@@ -2327 +2315 @@
       abstime_1=[];
 end  
-set(handles.abs_time,'String',num2str(abstime,4))
-set(handles.abs_time_1,'String',num2str(abstime_1,4))
+set(handles.abs_time,'String',num2str(abstime,5))
+set(handles.abs_time_1,'String',num2str(abstime_1,5))
 % if testimedoc && isfield(UvData,'dt')
 %     dt=UvData.dt;