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: unk/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 +