Changeset 453 for trunk

Timestamp:

Jun 13, 2012, 5:03:06 PM (13 years ago)

Author:

sommeria

Message:

series adapted to BATCH mode. Tests still needed.

Location:

trunk/src

Files:

• get_file_series.m (modified) (2 diffs)
• read_image.m (added)
• series.m (modified) (6 diffs)
• struct2xml.m (modified) (1 diff)
• xml2struct.m (modified) (1 diff)

trunk/src/get_file_series.m

@@ -7 +7 @@
 %        iview: line in the table corresponding to a given file series
 %        fileindex: file index within  the file series, 
-% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
-% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
+% i1_series{iview}(ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j 
+% i1_series{iview}(fileindex) expresses the same indices as a 1D array in file indices
 
 % INPUT:
@@ -50 +50 @@
         r(1).mode='';
     end
-    [i1_series_iview,i2_series_iview,j1_series_iview,j2_series_iview]=find_file_indices(ref_i,ref_j,str2num(r.num1),str2num(r.num2),r.mode);
+    [i1_series{iview},i2_series{iview},j1_series{iview},j2_series{iview}]=find_file_indices(ref_i,ref_j,str2num(r.num1),str2num(r.num2),r.mode);
     %case of pairs (.nc files)
     i2=[];j1=[];j2=[];
-    for ifile=1:numel(i1_series_iview)
-        i1=i1_series_iview(ifile);
-        if ~isempty(i2_series_iview)
-            i2=i2_series_iview(ifile);
+    for ifile=1:numel(i1_series{iview})
+        i1=i1_series{iview}(ifile);
+        if ~isempty(i2_series{iview})
+            i2=i2_series{iview}(ifile);
         end
-        if ~isempty(j1_series_iview)
-            j1=j1_series_iview(ifile);
+        if ~isempty(j1_series{iview})
+            j1=j1_series{iview}(ifile);
         end
-        if ~isempty(j2_series_iview)
-            j2=j2_series_iview(ifile);
+        if ~isempty(j2_series{iview})
+            j2=j2_series{iview}(ifile);
         end
         filecell{iview,ifile}=fullfile_uvmat(InputTable{iview,1},InputTable{iview,2},InputTable{iview,3},InputTable{iview,5},InputTable{iview,4}...
             ,i1,i2,j1,j2);
     end
-    i1_series(iview,:,:)=i1_series_iview;
-    i2_series(iview,:,:)=i2_series_iview;
-    j1_series(iview,:,:)=j1_series_iview;
-    j2_series(iview,:,:)=j2_series_iview;
 end
 

trunk/src/series.m

@@ -1259 +1259 @@
 set(handles.RUN, 'Enable','Off')
 set(handles.RUN,'BackgroundColor',[0.831 0.816 0.784])
-[h_fun,Series,errormsg]=prepare_jobs(handles);
+[h_fun,Series,filexml,errormsg]=prepare_jobs(handles);
 if ~isempty(errormsg)
     msgbox_uvmat('ERROR',errormsg)
 else
+   Series.Specific=h_fun(Series,0);   
+   t=struct2xml(Series);
+    t=set(t,1,'name','Series');
+    save(t,filexml);
     h_fun(Series);
 end
@@ -1283 +1287 @@
 set(handles.BATCH, 'Enable','Off')
 set(handles.BATCH,'BackgroundColor',[0.831 0.816 0.784])
-[h_fun,Series,errormsg]=prepare_jobs(handles);
+[h_fun,Series,filexml,errormsg]=prepare_jobs(handles);
 if ~isempty(errormsg)
     msgbox_uvmat('ERROR',errormsg)
     return
 end
+% update the xml file after interactive input with the function
+Series.Specific=h_fun(Series,0);   
+t=struct2xml(Series);
+t=set(t,1,'name','Series');
+save(t,filexml);
 path_series=fileparts(which('series'));
 filename_xml=fullfile(Series.OutputDir,[Series.OutputRootFile '.xml']);
@@ -1296 +1305 @@
     return
 end
+fctpath=get(handles.ActionPath,'String');
 text_matlabscript=[...
     '#!/bin/bash \n'...
@@ -1301 +1311 @@
     'matlab -nodisplay -nosplash -nojvm <<END_MATLAB \n'...
     'cd(''' path_series '''); \n'...
+    'addpath(''' fctpath '''); \n'...
     '' Series.Action  '( ''' filename_xml '''); \n'...
     'exit \n'...
@@ -1323 +1334 @@
 %------------------------------------------------------------------------
 % --- Main lauch command, called by RUN and BATCH
-function [h_fun,Series,errormsg]=prepare_jobs(handles)
+function [h_fun,Series,filexml,errormsg]=prepare_jobs(handles)
 %------------------------------------------------------------------------
 errormsg='';
@@ -1688 +1699 @@
          delete(hget_field)%delete opened versions of get_field
      end
-     [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(read_GUI(handles.series));
+     filecell=get_file_series(read_GUI(handles.series));
      if exist(filecell{1,1},'file')
         get_field(filecell{1,1})

trunk/src/struct2xml.m

@@ -48 +48 @@
      [t,new_uid]=add(t,uid,'element',key);
      [t]=add(t,new_uid,'chardata',val);
- elseif isnumeric(val)
+ elseif isnumeric(val)||islogical(val)
        siz=size(val);
        if length(siz)<=2 %do not translate matrices with more than 2 indices

trunk/src/xml2struct.m

@@ -39 +39 @@
     case 'cell'
         for ilist=1:numel(ss)
+            if ~isempty(str2num(ss{ilist}))
             out(ilist,:)=str2num(ss{ilist});
+            end
         end
     otherwise