Changeset 1051 for trunk/src

Timestamp:

Jun 27, 2018, 11:20:37 PM (6 years ago)

Author:

sommeria

Message:

psmsn cluster command updated, pb with multimask solved...

Location:

trunk/src

Files:

• batch_extract_rdvision.m (added)
• check_files.m (modified) (1 diff)
• cluster_command_psmn.m (modified) (2 diffs)
• series.m (modified) (2 diffs)
• series/extract_rdvision.m (modified) (2 diffs)
• uvmat.m (modified) (4 diffs)

trunk/src/check_files.m

@@ -167 +167 @@
         svn_info.cur_rev=str2double(t.rev); %version nbre of the current package
     end
-    [tild,result]=system(['svn info -r ''HEAD'' '  pathuvmat]);
+    %[tild,result]=system(['svn info -r ''HEAD'' '  pathuvmat]);
+    [tild,result]=system(['svn info ''HEAD'' '  pathuvmat]);
     t=regexp(result,'R.vision\s*:\s*(?<rev>\d+)','names');
     if ~isempty(t)

trunk/src/cluster_command_psmn.m

@@ -17 +17 @@
 function cmd=cluster_command_psmn(ListProcessFile, ActionFullName, DirLog, NbProcess, NbCore, CPUTimeProcess)
     SubmitScriptFile = regexprep(ListProcessFile, '\job_list.txt\>', 'submit_script.sh');
-    fid_list = fopen(ListProcessFile, 'r');
+        fid_list = fopen(ListProcessFile, 'r');
     fid_submit = fopen(SubmitScriptFile, 'w');
     i=1;
-    while(true)
-        process = fgets(fid_list);
+        while(true)
+                process = fgets(fid_list);
         if(process == -1)
-            break
+                        break
         end
         n = numel(process);
@@ -31 +31 @@
                             '-e ' LogFile ' '...
                             '-o ' LogFile ' '...
-                            '-q piv_debian '...
+                            '-q piv_debian* '...
+                            '-P PIV '...
                             '-N UVmat_' num2str(i) ' '...
                             process char(10)]);
         i=i+1;
-    end
-    fclose(fid_list);
+        end
+        fclose(fid_list);
     fclose(fid_submit);
     system(['chmod +x ' SubmitScriptFile]);

trunk/src/series.m

@@ -1464 +1464 @@
     RunMode=Param.Action.RunMode;
     Param.Action=rmfield(Param.Action,'RunMode'); % remove from the recorded xml file to avoid interference during ImportConfig
+    Param.RunMode=RunMode; % keep track of the mode
 end
 ActionExt='.m'; % default
@@ -2321 +2322 @@
     set(handles.VelType_title,'Visible','on')
     FieldList=set_field_list('U','V'); % standard menu for civx data
-    %CheckList=1;
+    if max(get(handles.FieldName,'Value'))>numel(FieldList)
     set(handles.FieldName,'Value',1); % velocity vector choice by default
+    end
     if  VelTypeRequest_1 && numel(iview_civ)>=2
         menu=set_veltype_display(SeriesData.FileInfo{iview_civ(2)}.CivStage,SeriesData.FileType{iview_civ(2)});

trunk/src/series/extract_rdvision.m

@@ -111 +111 @@
 %%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
 %% read input parameters from an xml file if input is a file name (batch mode)
-checkrun=1;
+
 if ischar(Param)
     Param=xml2struct(Param);% read Param as input file (batch case)
-    checkrun=0;
-end
+%     checkrun=0;
+end
+disp(Param)
+checkrun=strcmp(Param.RunMode,'local')
 hseries=findobj(allchild(0),'Tag','series');
 RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
@@ -527 +529 @@
 
 %% adjust Dti
+if NbDti+1>size(timestamp,1)
+    NbDti=size(timestamp,1)-1;
+end
 Dti_stamp=(timestamp(1+NbDti,1)-timestamp(1,1))/NbDti;
 t=set(t,uid_content_Dti,'value',num2str(Dti_stamp));%corret Dti

trunk/src/uvmat.m

@@ -2615 +2615 @@
         RootPath=MaskPath;
     end
-    if mdetect==0
+    if mdetect==0 % if no mask is detected in the current folder
         MaskFullName=uigetfile_uvmat('pick a mask image file:',RootPath,'image');
         if isempty(MaskFullName)
@@ -2633 +2633 @@
     else
         Mask.File=MaskFile{1};
+    end
+    Mask.NbSlice_i=1;
+    Mask.NbSlice_j=1;
+    if isempty(j1_series)
+        Mask.NbSlice_i=i1_series(1,2,end);
+    else
+        Mask.NbSlice_j=j1_series(1,end,2);
     end
     Mask.Ext=MaskExt;
@@ -2657 +2664 @@
 errormsg=[];%default
 Mask=get(handles.CheckMask,'UserData');
-MaskIndex=1;
 if strcmp(get(handles.z_index,'Visible'),'on')
-    MaskIndex=str2num(get(handles.z_index,'String'));
+    MaskIndex_i=str2num(get(handles.z_index,'String'));
+else
+    MaskIndex_i=mod(str2num(get(handles.i1,'String')),Mask.NbSlice_i);
+end
+if Mask.NbSlice_j>1
+    MaskIndex_j=str2num(get(handles.j1,'String'));
+else
+    MaskIndex_j=1;
 end
 if isfield(Mask,'maskhandle')&& ishandle(Mask.maskhandle)
     uistack(Mask.maskhandle,'top');
 end
-MaskName=fullfile_uvmat(Mask.Path,'',Mask.File,Mask.Ext,Mask.NomType,MaskIndex);
+MaskName=fullfile_uvmat(Mask.Path,'',Mask.File,Mask.Ext,Mask.NomType,MaskIndex_i,[],MaskIndex_j);
 UvData=get(handles.uvmat,'UserData');
 
@@ -2689 +2702 @@
             return
         end
-        MaskField.ZIndex=MaskIndex;
+        MaskField.ZIndex=MaskIndex_i;
         %px to phys or other transform on field
          menu_transform=get(handles.TransformName,'String');