Changeset 922

Timestamp:

Nov 24, 2015, 10:48:46 AM (9 years ago)

Author:

sommeria

Message:

corrections quentin

Location:

trunk/src

Files:

• phys_ima.m (modified) (2 diffs)
• plot_object.m (modified) (1 diff)
• series.m (modified) (9 diffs)
• series/extract_rdvision.m (modified) (5 diffs)
• set_object.m (modified) (1 diff)

trunk/src/phys_ima.m

@@ -40 +40 @@
 Rangy(1)=max(ycorner);
 test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
-npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images)
-npY=1+round((Rangy(1)-Rangy(2))/min(dy));
+% npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images)
+% npY=1+round((Rangy(1)-Rangy(2))/min(dy));
+
+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));
+
+
 x=linspace(Rangx(1),Rangx(2),npX);
 y=linspace(Rangy(1),Rangy(2),npY);
@@ -69 +74 @@
 %            end
         end
-        xima=0.5:npx-0.5;%image coordinates of corners
-        yima=npy-0.5:-1:0.5;
+        xima=0.5:npx(icell)-0.5;%image coordinates of corners
+        yima=npy(icell)-0.5:-1:0.5;
         [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates
         [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,zphys);% image coordinates for each point in the real

trunk/src/plot_object.m

@@ -386 +386 @@
             if nbpoints>length(PlotData.DeformPoint)
                 for ipt=length(PlotData.DeformPoint)+1:nbpoints
-                    PlotData.DeformPoint(ipt)=line(xline(ipt),yline(ipt),'Color',col,'LineStyle','.','Tag','DeformPoint',...
+                    PlotData.DeformPoint(ipt)=line(xline(ipt),yline(ipt),'Color',col,'LineStyle','-','Tag','DeformPoint',...
                         'SelectionHighlight','off','UserData',hplot);
                 end

trunk/src/series.m

@@ -1768 +1768 @@
 extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
 for iprocess=1:NbProcess
+    extxml{iprocess}='.xml';
+end
+for iprocess=1:NbProcess
     if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
         disp('program stopped by user')
@@ -1828 +1831 @@
                     case {'PCWIN','PCWIN64'} %Windows system
                         filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
-                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
+                        system([ActionFullName ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
                     case {'GLNX86','GLNXA64','MACI64'}%Linux  system
-                        system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
+                        system([ActionFullName ' ' RunTime ' ' filexml]);
                 end
         end
@@ -1941 +1944 @@
                                 'hostname && date \n '...
                                 'umask 002 \n'...
-                                fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group
+                                ActionFullName ' ' RunTime ' ' filexml];%allow writting access to created files for user group
                             fprintf(fid,cmd);%fill the executable file with the  char string cmd
                             fclose(fid);% close the executable file
@@ -1951 +1954 @@
                     end
                 end
-                msgbox_uvmat('CONFIRMATION',[ActionName ' launched in background: press STATUS to see results'])
+                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
         end
         
@@ -1967 +1970 @@
                 'hostname && date \n '...
                 'umask 002 \n'...
-                fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
+                ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
             else
                 cmd=[...
@@ -2021 +2024 @@
         WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint
         disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes'])
-        oar_command=['oarsub -n UVmat_' ActionName ' '...
+        oar_command=['oarsub -n UVmat_' ActionFullName ' '...
             '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '...
             '-l /core=' num2str(NbCore) ','...
@@ -2028 +2031 @@
             '-O ' filename_log ' '...
             extra_oar ' '...
-            '"oar-parexec -s -f ' filename_joblist ' '...
+           '"oar-parexec -s -f ' filename_joblist ' '...
             '-l ' filename_joblist '.log"'];
+        
+
+        
         fprintf(oar_command);% display  system command on the Matlab command window
         [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
@@ -2037 +2043 @@
         fprintf(fid,result);% store the result (job ID number)
         fclose(fid);
-        msgbox_uvmat('CONFIRMATION',[ActionName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
+        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
         
     case 'cluster_pbs' % for LMFA Kepler machine
@@ -2078 +2084 @@
         fprintf(pbs_command);% display in command line
         %system(pbs_command);
-        msgbox_uvmat('CONFIRMATION',[ActionName ' command ready to be launched in cluster'])
+        msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
     case 'python'
         command = [

trunk/src/series/extract_rdvision.m

@@ -70 +70 @@
     ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
     ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
-    ParamOut.OutputSubDirMode='custom'; %output folder given by the program, not by the GUI series
+     ParamOut.OutputDirExt='.extract';%set the output dir extension
+    ParamOut.OutputSubDirMode='one'; %output folder given by the program, not by the GUI series
      % detect the set of image folder
     RootPath=Param.InputTable{1,1};
@@ -143 +144 @@
         msgbox_uvmat('ERROR',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once'])
         %rmfield(OutputDir)
-        return
+%         return
     end
     %% interactive input of specific parameters (for RDvision system)
@@ -183 +184 @@
 checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end
 for iview=1:size(Param.InputTable,1)
-    filexml=[fullfile(RootPath,Param.InputTable{iview,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
+    for iview_xml=1:size(Param.InputTable,1)% loojk for the xml files in the different data directories
+    filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
+    if exist(filexml,'file')
+        break
+    end
+    end 
     if ~exist(filexml,'file')
         disp_uvmat('ERROR',[filexml ' missing'],checkrun)
@@ -275 +281 @@
     time_diff_min=min(diff_time');
     if max(time_diff_max)>0.005
-        disp_uvmat('WARNING',['timestamps exceeds xml time by' num2str(max(time_diff_max))],checkrun)
+        disp(['WARNING:timestamps exceeds xml time by' num2str(max(time_diff_max))])
         checkpreserve=1;
     elseif min(time_diff_min)<-0.005
-        disp_uvmat('WARNING',['timestamps is lower than xml time by' num2str(min(time_diff_min))],checkrun)
+        disp(['timestamps is lower than xml time by' num2str(min(time_diff_min))])
         checkpreserve=1;
     else
-        disp_uvmat('CONFIRMATION','time from xml file correct within better than 5 ms',checkrun)
+        disp('CONFIRMATION:time from xml file correct within better than 5 ms')
     end
     if checkpreserve
@@ -303 +309 @@
     % check images
     
-    delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
-    if ~checkpreserve
-        for ibin=1:numel(BinList)
-            delete(BinList{ibin})
-        end
-        rmdir(fullfile(RootPath,Param.InputTable{iview,2}))
-    end
-end
+%     delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
+%     if ~checkpreserve
+%         for ibin=1:numel(BinList)
+%             delete(BinList{ibin})
+%         end
+%         rmdir(fullfile(RootPath,Param.InputTable{iview,2}))
+%     end
+end
+delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

trunk/src/set_object.m

@@ -391 +391 @@
         end       
     end
-    if isempty(str2num(get(handles.num_RangeInterp,'String')))
+    if isempty(str2num(get(handles.num_RangeInterp,'String'))) && isfield(UvData,'Field')
      set(handles.num_RangeInterp,'String',num2str(3*UvData.Field.CoordMesh))% default interpolationlength= 3 meshes
     end