Index: trunk/src/read_image.m
===================================================================
--- trunk/src/read_image.m	(revision 822)
+++ trunk/src/read_image.m	(revision 823)
@@ -43,4 +43,5 @@
     num=1;
 end
+A=[];
 ObjectOut=VideoObject;%default
 switch FileType
Index: trunk/src/series/avi2png.m
===================================================================
--- trunk/src/series/avi2png.m	(revision 822)
+++ 	(revision )
@@ -1,118 +1,0 @@
-% 'avi2png': copy an avi movie to a series of B/W .png images (take the average of green and blue color components)
-%----------------------------------------------------------------------
-
-%=======================================================================
-% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
-%   http://www.legi.grenoble-inp.fr
-%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
-%
-%     This file is part of the toolbox UVMAT.
-%
-%     UVMAT is free software; you can redistribute it and/or modify
-%     it under the terms of the GNU General Public License as published
-%     by the Free Software Foundation; either version 2 of the license,
-%     or (at your option) any later version.
-%
-%     UVMAT is distributed in the hope that it will be useful,
-%     but WITHOUT ANY WARRANTY; without even the implied warranty of
-%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-%     GNU General Public License (see LICENSE.txt) for more details.
-%=======================================================================
-
-function GUI_input=avi2png(num_i1,num_i2,num_j1,num_j2,Series)
-%% INPUT PARAMETERS (to edit)
-increment=4% frame increment: the frequency of the png images will be (initial frequency)/increment.
-colorweight=[0 0.5 0.5]; % relative weight of color components [r g b] for the resulting B/W image
-colorweight=colorweight/sum(colorweight)
-
-%% default output (set the input options in the GUI series)
-if ~exist('num_i1','var')
-    GUI_input={};
-        return
-end
-hh=guidata(Series.hseries);
-set(hh.incr_i,'String',num2str(increment))% preset the increment in the GUI
-
-%% set file names
-nbfield=length(num_i1);
-aviname=fullfile(Series.RootPath,[Series.RootFile Series.FileExt]);
-rootname=fullfile(Series.RootPath,Series.RootFile);
-if ~exist(rootname,'dir')
-    mkdir(rootname)% will put the extracted images in a subdirectory with the same lname as the avi file (without extension)
-end
-basename=fullfile(rootname,'frame');
-
-%% enable waitbar and stop buttons on the series interface:
-hRUN=findobj(Series.hseries,'Tag','RUN');% handle of the RUN button
-hwaitbar=findobj(Series.hseries,'Tag','waitbar');%handle of the waitbar
-waitbarpos(1)=Series.WaitbarPos(1);%x position of the waitbar
-waitbarpos(3)=Series.WaitbarPos(3);% width of the waitbar
-
-%% read the movie object
-if isequal(lower(Series.FileExt),'.avi')
-    display('opening the avi movie ...')
-    hhh=which('mmreader');%look for the existence of 'mmreader'for movie reading
-    if ~isequal(hhh,'')&& mmreader.isPlatformSupported()
-        MovieObject=mmreader(aviname);
-        FileType='movie';
-    else
-        FileType='avi';
-    end
-end
-
-%% main loop on frames
-for ifile=1:nbfield
-     stopstate=get(hRUN,'BusyAction');
-     if isequal(stopstate,'queue')% if STOP command is not activated
-        waitbarpos(4)=(ifile/nbfield)*Series.WaitbarPos(4);
-        waitbarpos(2)=Series.WaitbarPos(4)+Series.WaitbarPos(2)-waitbarpos(4);
-        set(hwaitbar,'Position',waitbarpos)%update waitbar on the series interface
-        drawnow
-        A=read_image(aviname,'movie',num_i1(ifile),MovieObject);
-        if ndims(A)==3% convert color image to B/W
-            A=double(A);
-            A=colorweight(1)*A(:,:,1)+colorweight(2)*A(:,:,2)+colorweight(3)*A(:,:,3);
-            A=uint8(A);% transform to 8 bit integers
-        end
-        new_index=1+floor((num_i1(ifile)-num_i1(1))/increment);
-        filename=[basename '_' num2str(new_index) '.png'];%create image name
-        imwrite(A,filename,'BitDepth',8);%write image
-        display(['new frame '  num2str(new_index) ' written as png image'])
-     end
-end
-
-%% create xml file with timing: 
-info=aviinfo(aviname);
-t=xmltree;
-t=set(t,1,'name','ImaDoc');
-[t,uid]=add(t,1,'element','Heading');
-% A AJOUTER
-% Heading.Project='';
-Heading.ImageName='frame_1.png';
-t=struct2xml(Heading,t,uid);
-[t,uid]=add(t,1,'element','Camera');
-Camera.TimeUnit='s';
-% Camera.BurstTiming.FrameFrequency=info.FramesPerSecond/increment;
-Camera.BurstTiming.Dti=increment/info.FramesPerSecond;
-Camera.BurstTiming.NbDti=numel(num_i1)-1;
-Camera.BurstTiming.Time=(num_i1(1)-1)/info.FramesPerSecond;%time of the first frame of the avi movie
-t=struct2xml(Camera,t,uid);
-save(t,[basename '.xml'])
-
-%------------------------------------------------------------------------
-%--read images and convert them to the uint16 format used for PIV
-function A=read_image(filename,type_ima,num,MovieObject)
-%------------------------------------------------------------------------
-%num is the view number needed for an avi movie
-switch type_ima
-    case 'movie'
-        A=read(MovieObject,num);
-    case 'avi'
-        mov=aviread(filename,num);
-        A=frame2im(mov(1));
-    case 'multimage'
-        A=imread(filename,num);
-    case 'image'    
-        A=imread(filename);
-end
-
Index: trunk/src/series/movie2png.m
===================================================================
--- trunk/src/series/movie2png.m	(revision 823)
+++ trunk/src/series/movie2png.m	(revision 823)
@@ -0,0 +1,174 @@
+% 'movie2png': copy a movie to a series of grey scale .png images 
+%------------------------------------------------------------------------
+% function ParamOut=movie2png(Param)
+%------------------------------------------------------------------------
+%
+%OUTPUT
+% ParamOut: sets options in the GUI series.fig needed for the function
+%
+%INPUT:
+% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
+% In batch mode, Param is the name of the corresponding xml file containing the same information
+% when Param.Action.RUN=0 (as activated when the current Action is selected
+% in series), the function ouput paramOut set the activation of the needed GUI elements
+%
+% Param contains the elements:(use the menu bar command 'export/GUI config' in series to 
+% see the current structure Param)
+%    .InputTable: cell of input file names, (several lines for multiple input)
+%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
+%    .OutputSubDir: name of the subdirectory for data outputs
+%    .OutputDirExt: directory extension for data outputs
+%    .Action: .ActionName: name of the current activated function
+%             .ActionPath:   path of the current activated function
+%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
+%             .RUN =0 for GUI input, =1 for function activation
+%             .RunMode='local','background', 'cluster': type of function  use
+%             
+%    .IndexRange: set the file or frame indices on which the action must be performed
+%    .FieldTransform: .TransformName: name of the selected transform function
+%                     .TransformPath:   path  of the selected transform function
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%=======================================================================
+% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
+%   http://www.legi.grenoble-inp.fr
+%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
+%
+%     This file is part of the toolbox UVMAT.
+%
+%     UVMAT is free software; you can redistribute it and/or modify
+%     it under the terms of the GNU General Public License as published
+%     by the Free Software Foundation; either version 2 of the license,
+%     or (at your option) any later version.
+%
+%     UVMAT is distributed in the hope that it will be useful,
+%     but WITHOUT ANY WARRANTY; without even the implied warranty of
+%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%     GNU General Public License (see LICENSE.txt) for more details.
+%=======================================================================
+function ParamOut=movie2png(Param)
+
+%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
+if isstruct(Param) && isequal(Param.Action.RUN,0)
+    ParamOut.FieldTransform = 'on';%can use a transform function
+    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
+    ParamOut.OutputDirExt='.png';%set the output dir extension
+    ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
+    
+    first_j=[];
+    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
+    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,'');
+    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
+        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
+    if ~exist(FirstFileName,'file')
+        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
+    end
+    return
+end
+
+%% INPUT PARAMETERS (to edit)
+increment=Param.IndexRange.incr_i;% frame increment: the frequency of the png images will be (initial frequency)/increment.
+colorweight=[1 1 1] % relative weight of color components [r g b] for the resulting B/W image
+
+%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
+ParamOut=[]; %default output
+%% 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
+hseries=findobj(allchild(0),'Tag','series');
+RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
+WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
+
+%% define the directory for result file (with path=RootPath{1})
+OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
+if ~isfield(Param,'InputFields')
+    Param.InputFields.FieldName='';
+end
+%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
+ % EDIT FROM HERE
+ 
+%% root input file type
+RootPath=Param.InputTable{1,1};
+RootFile=Param.InputTable{1,3};
+SubDir=Param.InputTable{1,2};
+NomType=Param.InputTable{1,4};
+FileExt=Param.InputTable{1,5};
+    first_j=[];
+    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
+    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,'');
+    InputFileName=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1,i2,j1,j2);
+[FileInfo,VideoObject]=get_file_info(InputFileName);
+
+%% determine the file type on each line from the first input file 
+if isempty(find(strcmp(FileInfo.FileType,{'mmreader','video'})));% =1 for images
+    disp_uvmat('ERROR','the input is not a movie or image series',checkrun)
+end
+FileExtOut='.png'; %image output (input and proj result = image)
+NomTypeOut='_1';% output file index will indicate the first and last ref index in the series
+RootFileOut=RootFile;
+NbField=floor((Param.IndexRange.last_i-Param.IndexRange.first_i+1)/increment);
+%% create xml file with timing: 
+%info=aviinfo(aviname);
+t=xmltree;
+t=set(t,1,'name','ImaDoc');
+[t,uid]=add(t,1,'element','Heading');
+% A AJOUTER
+% Heading.Project='';
+Heading.ImageName='frame_1.png';
+t=struct2xml(Heading,t,uid);
+[t,uid]=add(t,1,'element','Camera');
+Camera.TimeUnit='s';
+% Camera.BurstTiming.FrameFrequency=info.FramesPerSecond/increment;
+Camera.BurstTiming.Dti=1/FileInfo.FrameRate;
+Camera.BurstTiming.NbDti=NbField*increment;
+Camera.BurstTiming.Time=i1/FileInfo.FrameRate;%time of the first frame of the avi movie
+t=struct2xml(Camera,t,uid);
+save(t,[fileparts(InputFileName) '.xml'])
+
+%% LOOP ON FRAMES
+
+for index=Param.IndexRange.first_i:increment:Param.IndexRange.last_i
+    update_waitbar(WaitbarHandle,(index-Param.IndexRange.first_i)/NbField)
+    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
+        disp('program stopped by user')
+        return
+    end
+    A=read_image(InputFileName,FileInfo.FileType,VideoObject,index);
+    if ndims(A)==3% convert color image to B/W
+        A=double(A);
+        A=colorweight(1)*A(:,:,1)+colorweight(2)*A(:,:,2)+colorweight(3)*A(:,:,3);
+        A=uint16(A);% transform to 16 bit integers
+    end
+    %new_index=1+floor((index-Param.IndexRange.first_i)/increment);
+    OutputFileName=fullfile_uvmat(RootPath,OutputDir,RootFile,FileExtOut,NomTypeOut,index);
+    %filename=[basename '_' num2str(new_index) '.png'];%create image name
+    imwrite(A,OutputFileName,'BitDepth',16);%write image
+    disp(['new frame '  num2str(index) ' written as png image'])
+end
+
+%% main loop on frames
+% for ifile=1:nbfield
+%      stopstate=get(hRUN,'BusyAction');
+%      if isequal(stopstate,'queue')% if STOP command is not activated
+%         waitbarpos(4)=(ifile/nbfield)*Series.WaitbarPos(4);
+%         waitbarpos(2)=Series.WaitbarPos(4)+Series.WaitbarPos(2)-waitbarpos(4);
+%         set(hwaitbar,'Position',waitbarpos)%update waitbar on the series interface
+%         drawnow
+%         A=read_image(aviname,'movie',num_i1(ifile),MovieObject);
+%         if ndims(A)==3% convert color image to B/W
+%             A=double(A);
+%             A=colorweight(1)*A(:,:,1)+colorweight(2)*A(:,:,2)+colorweight(3)*A(:,:,3);
+%             A=uint8(A);% transform to 8 bit integers
+%         end
+%         new_index=1+floor((num_i1(ifile)-num_i1(1))/increment);
+%         filename=[basename '_' num2str(new_index) '.png'];%create image name
+%         imwrite(A,filename,'BitDepth',8);%write image
+%         display(['new frame '  num2str(new_index) ' written as png image'])
+%      end
+% end
+
+
+
Index: trunk/src/transform_field/ima_color2BW.m
===================================================================
--- trunk/src/transform_field/ima_color2BW.m	(revision 823)
+++ trunk/src/transform_field/ima_color2BW.m	(revision 823)
@@ -0,0 +1,34 @@
+% 'ima_color2BW': transform a color image to grey scale image 
+%------------------------------------------------------------------------
+%%%%  Use the general syntax for transform fields with a single input %%%%
+% OUTPUT: 
+% DataOut:   output field structure 
+%
+%INPUT:
+% DataIn:  first input field structure
+
+%=======================================================================
+% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
+%   http://www.legi.grenoble-inp.fr
+%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
+%
+%     This file is part of the toolbox UVMAT.
+%
+%     UVMAT is free software; you can redistribute it and/or modify
+%     it under the terms of the GNU General Public License as published
+%     by the Free Software Foundation; either version 2 of the license,
+%     or (at your option) any later version.
+%
+%     UVMAT is distributed in the hope that it will be useful,
+%     but WITHOUT ANY WARRANTY; without even the implied warranty of
+%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%     GNU General Public License (see LICENSE.txt) for more details.
+%=======================================================================
+
+function DataOut=ima_color2BW(DataIn)
+
+DataOut=DataIn; %default
+if ndims(DataOut.A)==3
+    DataOut.A=uint16(sum(double(DataOut.A,3)));%sum on color components, transform in 16 bit BW images
+end
+ 
