Fixes and use of syntactic sugars.

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@167 4c865b51-4357-4376-afb4-474e03ccb993

1_preprocessing/gtCopyCorrectUndistortCondor.m

@@ -114,38 +114,36 @@ while counter<100
     end
 
     %sort files by date order to copy in order
-    sfdates=[];
-    for n=1:length(sfiles)
-        sfdates(n)=sfiles(n).datenum;
-    end
-    [sfdates,i]=sort(sfdates);
+    [~,indx] = sort( {sfiles.('datenum')} );
 
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     %   try to copy files
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-    for n=1:length(sfiles)
-        sfname=sfiles(i(n)).name;
+    for n = 1:length(sfiles)
+        sfname = sfiles(indx(n)).name;
 
         %check if sfname has already been taken by another condor job
-        test=0;
         try
-            test=mym(sprintf('insert into %s (filename) values ("%s")', filetable, sfname));
+            test = mym(sprintf('insert into %s (filename) values ("%s")', filetable, sfname));
+        catch Mexc
+            gtPrintException(Mexc)
+            rethrow(Mexc)
         end
-        if test==1 %no other job is copying this file, do copy
 
-            disp(sprintf('working on %s',sfname))
+        if test %no other job is copying this file, do copy
+            disp(['working on ' sfname])
 
             if isfield(parameters.acq, 'interlaced_turns') && parameters.acq.interlaced_turns>0
                 %if using interlaced turns, may need some renaming
-                fnamein  = fullfile(sourcedir, sfiles(i(n)).name);
-                newfname = sfRename(sfiles(i(n)).name); %determine how file should be renamed
+                fnamein  = fullfile(sourcedir, sfiles(indx(n)).name);
+                newfname = sfRename(sfiles(indx(n)).name); %determine how file should be renamed
                 fnameout = fullfile(destdir, newfname);
-                fnameout_orig = fullfile(destdir_orig, sfiles(i(n)).name); %keep original data as collected
+                fnameout_orig = fullfile(destdir_orig, sfiles(indx(n)).name); %keep original data as collected
             else %standard routine
-                fnamein  = fullfile(sourcedir, sfiles(i(n)).name);
+                fnamein  = fullfile(sourcedir, sfiles(indx(n)).name);
                 newfname = 1; %flag to do copy in this case
-                fnameout = fullfile(destdir, sfiles(i(n)).name);
-                fnameout_orig = fullfile(destdir_orig, sfiles(i(n)).name);
+                fnameout = fullfile(destdir, sfiles(indx(n)).name);
+                fnameout_orig = fullfile(destdir_orig, sfiles(indx(n)).name);
             end
 
             if ~isempty(newfname)

1_preprocessing/gtCopyCorrectUndistortWrapper.m

@@ -82,11 +82,15 @@ disp('Can add other things that should be copied first')
 % calculate how many jobs to launch
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %count files in source dir, nfiles
-sfiles=dir([sourcedir '/*']);
-cfiles=dir([destdir '/*']);
-for n=1:length(cfiles)
-    cfnames{n}=cfiles(n).name;
-end
+sfiles = dir(fullfile(sourcedir, '*'));
+cfiles = dir(fullfile(destdir, '*'));
+% This can be quicker and faster:
+cfnames = {cfiles.('name')};
+% Slower and more tedious:
+%for n = 1:length(cfiles)
+%    cfnames{n} = cfiles(n).name;
+%end
+
 n=1;
 %go through the source list, remove directories, parameters.mat,
 %and anything else already copied

1_preprocessing/gtCreateAbsLive.m

@@ -149,7 +149,7 @@ for ii=first_img:last_img
         %  % keep a record of the mean intensity
         %  mean_vals(ii+1)=gtImgMeanValue2(im(:,[1:prep.margin,end-prep.margin+1:end]));
 
-        %% check if we need ot update the reference images
+        % check if we need ot update the reference images
         index1 = floor(ii/acq.refon)*acq.refon;
         refname1 = fullfile(datadir, sprintf('refHST%04d.edf', index1) );
 
@@ -157,7 +157,7 @@ for ii=first_img:last_img
         if ( isfield(acq,'mono_tune') && acq.mono_tune ~= 0 ... % sabine if mono_tune
            && mod(ceil(ii/acq.refon)*acq.refon,acq.mono_tune) == 0 )
             index2 = ceil(ii/acq.refon)*acq.refon-1;
-            index2 = max(0, index);
+            index2 = max(0, index2);
             refname2 = fullfile(datadir, sprintf('refHST%04d.edf', index2));
         else
             index2 = ceil(ii/acq.refon)*acq.refon;

zUtil_EDF/edf_read.m

@@ -26,17 +26,17 @@ function [img, varargout] = edf_read(filename, GT_bb, dispmes, info)
   %% File Error Checking
   if isempty(edfFile)
     Mexc = MException('EDF:fileNotFound', ['Could not find ' filename]);
-    throw(Mexc)
+    throw(Mexc);
   end
 
   if edfFile.isdir == true
     Mexc = MException('EDF:fileIsDirectory', [ filename ' is a directory instead of a file.']);
-    throw(Mexc)
+    throw(Mexc);
   end
 
   if edfFile.bytes == 0
     Mexc = MException('EDF:fileIsEmpty', [ filename ' is an empty file.']);
-    throw(Mexc)
+    throw(Mexc);
   end
 
   % Let's read the header
@@ -50,14 +50,14 @@ function [img, varargout] = edf_read(filename, GT_bb, dispmes, info)
   else
     if info.dim_3 > 1 && (exist('GT_bb','var') && ~isempty(GT_bb))
       Mexc = MException('EDF:roiIn3d', 'Cannot use an ROI on 3D EDF file');
-      throw(Mexc)
+      throw(Mexc);
     end
   end
 
   fid = fopen(filename,'r',info.byteorder);
   if fid == -1
     Mexc = MException('EDF:fileNotFound', ['Could not open ' fname]);
-    throw(Mexc)
+    throw(Mexc);
   end
   fseek(fid, info.headerlength, 'bof');
 
@@ -101,7 +101,7 @@ function [img, varargout] = edf_read(filename, GT_bb, dispmes, info)
                       '  Expected: ' num2str(dim_1*dim_2*info.dim_3) ...
                       ', Got: ' num2str(count)];
     Mexc = MException('EDF:fileCorrupted', report_string );
-    throw(Mexc)
+    throw(Mexc);
   end
 
   %% Let's reshape to the real format of the matrix

zUtil_EDF/edf_wait_read.m

@@ -17,7 +17,7 @@ function [img, varargout] = edf_wait_read(fname, bb, waitfortranslated)
 % and then from peter's pfWaitToRead(fname, bb, waitfortranslated)
 % Modified by Nicola Vigano, 2011-2012, nicola.vigano@esrf.fr
 
-  %handle inputs
+  %% handle input
   if ~exist('bb', 'var')
     bb=[];
   end
@@ -28,18 +28,22 @@ function [img, varargout] = edf_wait_read(fname, bb, waitfortranslated)
   %  disp(sprintf('waiting for images to have been translated %d times', waitfortranslated))
   end
 
-  % wait for file to appear
+  %% wait for file to appear
   if ~exist(fname,'file')
-    fprintf('Waiting for %s',fname);
+    seconds = 0;
+    fprintf('Waiting for "%s"\n',fname);
     while ~exist(fname,'file')
       pause(2)
+      seconds = seconds + 2;
     end
 
-    fprintf('Found it!\n');
+    minutes = floor(seconds/60);
+    hours = floor(minutes/60);
+    fprintf('Found it (in %dh:%dm:%ds)!\n', hours, minutes, seconds);
     pause(2)
   end
 
-  % check whether file has been translated 
+  %% check whether file has been translated 
   % (by gtApplyDrifts.m)
   firsttime = true;
   if waitfortranslated
@@ -47,7 +51,7 @@ function [img, varargout] = edf_wait_read(fname, bb, waitfortranslated)
     while ~translated
       try
         info = edf_info(fname);
-        if isfield(info, 'istranslated') && str2num(info.istranslated)==waitfortranslated
+        if isfield(info, 'istranslated') && (str2double(info.istranslated) == waitfortranslated)
           translated = true;
           %disp('file has been translated!')
         else
@@ -68,7 +72,7 @@ function [img, varargout] = edf_wait_read(fname, bb, waitfortranslated)
     end
   end
 
-  % try to read file
+  %% try to read file
   while (true)
     try
       if ~exist('info', 'var')