Changeset 843 for trunk

Timestamp:

Dec 12, 2014, 1:21:45 PM (9 years ago)

Author:

sommeria

Message:

 

File:

• trunk/src/series/extract_rdvision.m (modified) (8 diffs)

trunk/src/series/extract_rdvision.m

@@ -78 +78 @@
     check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files
     ListDir=ListCells(1,find(check_dir & ~check_bad));
-    InputTable=cell(numel(ListDir),5);
-    InputTable(:,2)=ListDir';
+%     InputTable=cell(numel(ListDir),5);
+%     InputTable(:,2)=ListDir';
     isel=0;
     for ilist=1:numel(ListDir)
@@ -91 +91 @@
            isel=isel+1;
            InputTable{isel,1}=RootPath;
+           InputTable{isel,2}=ListDir{ilist};
             RootFile=regexprep(ListCellSub{1,seq_index},'.seq$','');
             InputTable{isel,3}=RootFile;
-        end
         InputTable{isel,4}='*';
         InputTable{isel,5}='.seq';
+    end
     end
     hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series'
@@ -267 +268 @@
     
     %% backup the previous xml file and save the corrected one
-    [success,message]=copyfile(filexml,[filexml '~']);%make backup
-    if success~=1
-        dips(['errror in xml file backup: ' message]);
-        return
-    end
+%    [success,message]=copyfile(filexml,[filexml '~']);%make backup
+%     if success~=1
+%         disp(['errror in xml file backup: ' message]);
+%         return
+%     end
     save(t,filexml)
     nbfield2=1;
@@ -338 +339 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 function [BinSize,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew)
-% BINREAD_RDV Permet de lire les fichiers bin générés par Hiris à partir du
-% fichier seq associé.
+% BINREAD_RDV Permet de lire les fichiers bin gￜnￜrￜs par Hiris ￜ partir du
+% fichier seq associￜ.
 %   [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit
-%   l'image d'indice FRAME_IDX de la séquence FILENAME.
-%
-%   Entrées
+%   l'image d'indice FRAME_IDX de la sï¿œquence FILENAME.
+%
+%   Entrï¿œes
 %   -------
-%   FILENAME  : Nom du fichier séquence (.seq).
-%   FRAME_IDX : Indice de l'image à lire. Si FRAME_IDX vaut -1 alors la
-%   séquence est entièrement lue. Si FRAME_IDX est un tableau d'indices
+%   FILENAME  : Nom du fichier sï¿œquence (.seq).
+%   FRAME_IDX : Indice de l'image ￜ lire. Si FRAME_IDX vaut -1 alors la
+%   sï¿œquence est entiï¿œrement lue. Si FRAME_IDX est un tableau d'indices
 %   alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX
 %   est un tableau vide alors aucune image n'est lue mais le nombre
-%   d'images et tous les timestamps sont renvoyés. Les indices commencent à
-%   1 et se termines à NB_FRAMES.
+%   d'images et tous les timestamps sont renvoyￜs. Les indices commencent ￜ
+%   1 et se termines ￜ NB_FRAMES.
 %
 %   Sorties
@@ -357 +358 @@
 %   IMGS        : Images de sortie.
 %   TIMESTAMPS  : Timestaps des images lues.
-%   NB_FRAMES   : Nombres d'images dans la séquence.
+%   NB_FRAMES   : Nombres d'images dans la sï¿œquence.
 NbBinFile=0;
 BinSize=0;
@@ -366 +367 @@
 BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits)
 binrepertoire=fullfile(PathDir,SeqData.binrepertoire);
-tic
-OutputDir=fullfile(PathDir,SeqData.sequencename)
-if exist(OutputDir,'dir')
-    errormsg=[OutputDir ' already exist, delete it first'];
-    return
-end
-[s,errormsg]=mkdir(OutputDir);
-if s==0
-    return%not able to create new image dir
+OutputDir=fullfile(PathDir,SeqData.sequencename);
+if ~exist(OutputDir,'dir')
+    %     errormsg=[OutputDir ' already exist, delete it first'];
+    %     return
+    % end
+    [s,errormsg]=mkdir(OutputDir);
+    
+    if s==0
+        disp(errormsg)
+        return%not able to create new image dir
+    end
 end
 for ii=1:SeqData.nb_frames
-    OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode 
-    fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
-    if ii==1 || ~strcmp(fname,fname_prev) % open the bin file if not in use
-        fid=fopen(fname,'rb');
-        fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
-        NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
-        
-        BinSize(NbBinFile)=0;% strat counter for new bin file
-    else
-        fclose(fid);%close the previous bin file
-        fid=fopen(fname,'rb');% open the new bin file
-        fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
-    end
-    fname_prev=fname;
-    A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
-    A=A';
-    BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
     j1=[];
     if ~isequal(nbfield2,1)
@@ -399 +385 @@
     end
     i1=floor((ii-1)/nbfield2)+1;
-    try
-        imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
-        disp([OutputFile ' written']);
-       % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
-%         if ~s
-% %             disp_uvmat('ERROR',errormsg,checkrun);
-%             return
-%         end
-    catch ME
-        errormsg=ME.message;
-        return
-    end
-end
+    OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode
+    fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx));
+    if exist(OutputFile,'file')
+        fid=0;
+    else
+        if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use
+            if fid~=0
+                fclose(fid);%close the previous bin file if relevant
+            end
+            [fid,msg]=fopen(fname,'rb');
+            if isequal(fid,-1)
+                disp(['error in opening ' fname ': ' msg])
+            else
+                disp([fname ' opened for reading'])
+            end
+            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
+            NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose)
+            BinSize(NbBinFile)=0;% strat counter for new bin file
+        else
+            %             fclose(fid);%close the previous bin file
+            %             fid=fopen(fname,'rb');% open the new bin file
+            fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file
+        end
+        fname_prev=fname;
+        A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image
+        A=A';
+        BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read
+        try
+            imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images
+            disp([OutputFile ' written']);
+            % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a')
+            %         if ~s
+            % %             disp_uvmat('ERROR',errormsg,checkrun);
+            %             return
+            %         end
+        catch ME
+            errormsg=ME.message;
+            return
+        end
+    end
+end
+if fid~=0
 fclose(fid)
-toc
+end
+
 
 
@@ -450 +466 @@
 %         return
 %     end
-%     
+%
 % end
 
-%'imadoc2struct_special': reads the xml file for image documentation 
+%'imadoc2struct_special': reads the xml file for image documentation
 %------------------------------------------------------------------------
-% function [s,errormsg]=imadoc2struct_special(ImaDoc,option) 
+% function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
 %
 % OUTPUT: