Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 782) +++ /trunk/src/civ.m (revision 783) @@ -433,5 +433,6 @@ % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists -[RootPath,SubDirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileType,FileInfo,MovieObject]=find_file_series(FilePath,[FileName ImaExt]); +[RootPath,SubDirImages,RootFile,i1_series,tild,j1_series,tild,NomTypeIma,FileInfo,MovieObject]=find_file_series(FilePath,[FileName ImaExt]); +FileType=FileInfo.FileType; switch FileType case {'image','multimage','video','mmreader'} @@ -1204,10 +1205,14 @@ % if strcmp(Param.Program,'civ_matlab') if Param.CheckCiv1 - [Param.Civ1.FileTypeA,ImageInfoA_civ1,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); - [Param.Civ1.FileTypeB,ImageInfoB_civ1,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); + [ImageInfoA_civ1,Param.Civ1.ImageA]=get_file_type(filecell.ima1.civ1{1}); + Param.Civ1.FileTypeA=ImageInfoA_civ1.FileType; + [ImageInfoB_civ1,Param.Civ1.ImageB]=get_file_type(filecell.ima2.civ1{1}); + Param.Civ1.FileTypeB=ImageInfoB_civ1.FileType; end if Param.CheckCiv2 - [Param.Civ2.FileTypeA,ImageInfoA_civ2,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); - [Param.Civ2.FileTypeB,ImageInfoB_civ2,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); + [ImageInfoA_civ2,Param.Civ2.ImageA]=get_file_type(filecell.ima1.civ2{1}); + Param.Civ2.FileTypeA=ImageInfoA_civ2.FileType; + [ImageInfoB_civ2,Param.Civ2.ImageB]=get_file_type(filecell.ima2.civ2{1}); + Param.Civ2.FileTypeB=ImageInfoB_civ2.FileType; end % end @@ -2321,5 +2326,6 @@ if ~isequal(ext_ima,'.png') if checkbox(1) %if civ1 is performed - [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ1{1}); + [FileInfo,MovieObject]=get_file_type(filecell.ima1.civ1{1}); + FileType=FileInfo.FileType; check_j=0; if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage') @@ -2360,5 +2366,6 @@ end if checkbox(4) %if civ2 is performed - [FileType,FileInfo,MovieObject]=get_file_type(filecell.ima1.civ2{1}); + [FileInfo,MovieObject]=get_file_type(filecell.ima1.civ2{1}); + FileType=FileInfo.FileType; check_j=0; if strcmp(FileType,'mmreader')||strcmp(FileType,'VideoReader')||strcmp(FileType,'multimage') @@ -2569,6 +2576,6 @@ % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists - [RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,FileInfo,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]); - + [RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileInfo,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]); + FileType=FileInfo.FileType; %check image nom type if ~strcmp(nom_type_1,get(handles.NomType,'String')) @@ -3775,5 +3782,6 @@ Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispaly par_civ1=read_GUI(handles.Civ1); - par_civ1.FileTypeA=get_file_type(filecell.ima1.civ1{1}); + FileInfo=get_file_type(filecell.ima1.civ1{1}); + par_civ1.FileTypeA=FileInfo.FileType; par_civ1.ImageWidth=size(Data.A,2); par_civ1.ImageHeight=size(Data.A,1); Index: /trunk/src/find_file_series.m =================================================================== --- /trunk/src/find_file_series.m (revision 782) +++ /trunk/src/find_file_series.m (revision 783) @@ -1,22 +1,26 @@ %'find_file_series': check the content of an input file and find the corresponding file series %-------------------------------------------------------------------------- -% function [RootPath,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(fileinput) +% function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,Object,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml) % % OUTPUT: +% RootPath: path to the dir containing the input file +% SubDir: data dir containing the input file series % RootFile: root file detected in fileinput, possibly modified for movies (indexing is then done on image view, not file) % i1_series(pair,ref_j+1, ref_i+1),i2_series,j1_series,j2_series: set of indices (i1,i2,j1,j2) sorted by ref index ref_i, ref_j, and pairindex in case of multiple pairs with the same ref % (ref_i+1 is used to deal with the image index zero sometimes used) % NomType: nomenclature type corrected after checking the first file (problem of 0 before the number string) -% FileType: type of file, = -% = 'image', usual image as recognised by Matlab -% = 'multimage', image series stored in a single file -% = 'civx', netcdf file with civx convention -% = 'civdata', civ data with new convention -% = 'netcdf' other netcdf files -% = 'video': movie recognised by VideoReader (e;g. avi) -% MovieObject: video object (=[] otherwise) +% FileInfo: structure containing info on the input files (assumed identical on the whole series) + % FileInfo.FileType: type of file, = + % = 'image', usual image as recognised by Matlab + % = 'multimage', image series stored in a single file + % = 'civx', netcdf file with civx convention + % = 'civdata', civ data with new convention + % = 'netcdf' other netcdf files + % = 'video': movie recognised by VideoReader (e;g. avi) +% MovieObject: video object (=[] otherwise +% i1_input,i2_input,j1_input,j2_input: indices of the input file, or of the first file in the series if the input file does not exist % %INPUT -% RootPath: path to the directory to be scanned +% FilePath: path to the directory to be scanned % fileinput: name (without path) of the input file sample % checkxml: =1(default) take into account xml file existence to possibly include indexes in RootFile @@ -39,5 +43,5 @@ %AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml) +function [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput,checkxml) %------------------------------------------------------------------------ @@ -52,5 +56,5 @@ j1_series=zeros(1,1,1); j2_series=zeros(1,1,1); -[FileType,FileInfo,MovieObject]=get_file_type(fullfileinput); +[FileInfo,MovieObject]=get_file_type(fullfileinput); if ~exist(FilePath,'dir') return % don't go further if the dir path does not exist @@ -233,6 +237,6 @@ NomType=regexprep(NomType,['^' NomTypePref],''); %% update the file type if the input file does not exist (pb of 0001) - if isempty(FileType) - [FileType,FileInfo,MovieObject]=get_file_type(fullfile(FilePath,dirpair(ifile_min).name)); + if isempty(FileInfo.FileType) + [FileInfo,MovieObject]=get_file_type(fullfile(FilePath,dirpair(ifile_min).name)); end end @@ -247,31 +251,35 @@ %% introduce the frame index in case of movies or multimage type if isfield(FileInfo,'NumberOfFrames') && FileInfo.NumberOfFrames >1 - if isempty(i1_series) + if isempty(i1_series)% if there is no file index, i denotes the frame index i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 i1_input=1; NomType='*'; - else - i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames); - i1_series=[zeros(size(i1_series,1),1) i1_series]; - j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames); - j1_series=[zeros(size(i1_series,1),1) j1_series]; - % include the first index in the root name - r=regexp(NomType,'^(?_?\d+)','names');%look for a number or _1 at the beginning of NomType - if ~isempty(r) - fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput - if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected - rr=regexp(fileinput_end,'^(?\d+)','names'); - else% if a separator '_' is detected - rr=regexp(fileinput_end,'^(?_\d+)','names'); - end - if ~isempty(rr) -% RootFile=[RootFile rr.i1];% new root file -% NomTypePref=r.tiretnum; -% NomType=regexprep(NomType,['^' NomTypePref],''); - % i1_input=j1_input; - % i2_input=j2_input; - j1_input=1; - j2_input=[]; + else % if there is a file index, j denotes the frame index while i denotes the file index + if strcmp(NomType(end-1:end),'ab')% recognized as a pair + RootFile=fullfile_uvmat('','',RootFile,'',NomType,i1_input,i2_input,j1_input,j2_input);% restitute the root name without the detected indices + i1_series=zeros(FileInfo.NumberOfFrames+1,2);% first column =0 + i1_series(:,2)=(0:FileInfo.NumberOfFrames)'; % second column=frame index -1 + j1_series=[]; + i1_input=1; + NomType='*'; + else + i1_series=i1_series(:,2)*ones(1,FileInfo.NumberOfFrames);% + i1_series=[zeros(size(i1_series,1),1) i1_series]; + j1_series=ones(size(i1_series,1),1)*(1:FileInfo.NumberOfFrames);% + j1_series=[zeros(size(i1_series,1),1) j1_series]; + % include the first index in the root name + r=regexp(NomType,'^(?_?\d+)','names');%look for a number or _1 at the beginning of NomType + if ~isempty(r) + fileinput_end=regexprep(fileinput,['^' RootFile],'');%remove RootFile at the beginning of fileinput + if isempty(regexp(r.tiretnum,'^_','once'))% if a separator '_' is not detected + rr=regexp(fileinput_end,'^(?\d+)','names'); + else% if a separator '_' is detected + rr=regexp(fileinput_end,'^(?_\d+)','names'); + end + if ~isempty(rr) + j1_input=1; + j2_input=[]; + end end end Index: /trunk/src/get_file_series.m =================================================================== --- /trunk/src/get_file_series.m (revision 782) +++ /trunk/src/get_file_series.m (revision 783) @@ -62,5 +62,5 @@ FilePath=fullfile(InputTable{iview,1},InputTable{iview,2}); fileinput=[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]; - [tild,tild,tild,i1_series{iview},i2_series{iview},j1_series{iview},j2_series{iview},NomType,FileType,FileInfo,MovieObject,... + [tild,tild,tild,i1_series{iview},i2_series{iview},j1_series{iview},j2_series{iview},NomType,FileInfo,MovieObject,... i1_input,i2_input,j1_input,j2_input]=find_file_series(FilePath,fileinput); i1_series{iview}=squeeze(i1_series{iview}(1,:,:)); %select first pair index as ordered by find_file_series Index: /trunk/src/get_file_type.m =================================================================== --- /trunk/src/get_file_type.m (revision 782) +++ /trunk/src/get_file_type.m (revision 783) @@ -16,31 +16,24 @@ % INPUT: % fileinput: name, including path, of the file to analyse -function [FileType,FileInfo,VideoObject]=get_file_type(fileinput) -%%%% TODO: suppress the output argument FileType, contained in FileInfo %%%% -FileInfo=[];% will remain empty in the absence of input file +function [FileInfo,VideoObject]=get_file_type(fileinput) VideoObject=[]; if exist(fileinput,'file') FileInfo.FileName=fileinput; FileInfo.FileType='txt'; %default - FileType='txt';%default, text file else - FileType=''; + FileInfo.FileType=''; return end -[tild,tild,FileExt]=fileparts(fileinput); +[tild,tild,FileExt]=fileparts(fileinput);%get the fiel extension FileExt switch FileExt case '.fig' FileInfo.FileType='figure'; - FileType='figure'; case '.xml' FileInfo.FileType='xml'; - FileType='xml'; case '.xls' FileInfo.FileType='xls'; - FileType='xls'; case '.dat' - FileInfo.FileType='dat'; - FileType='dat'; + FileInfo.FileType='dat';; otherwise if ~isempty(FileExt)% exclude empty extension @@ -50,21 +43,18 @@ try imainfo=imfinfo(fileinput); - if length(imainfo) >1 %case of image with multiple frames - FileType='multimage'; + if length(imainfo) >1 %case of image with multiple frames FileInfo=imainfo(1);%take info from the first frame + FileInfo.FileType='multimage'; FileInfo.NumberOfFrames=length(imainfo); else - FileType='image'; FileInfo=imainfo; + FileInfo.FileType='image'; FileInfo.NumberOfFrames=1; end FileInfo.FileName=FileInfo.Filename; %correct the info given by imfinfo - FileInfo.FileType=FileType; end else error_nc=0; try - % [Data,tild,tild,errormsg]=nc2struct(fileinput,'ListGlobalAttribute','absolut_time_T0','Conventions',... - % 'CivStage','patch2','fix2','civ2','patch','fix','hart'); [Data,tild,tild,errormsg]=nc2struct(fileinput,[]); if ~isempty(errormsg) @@ -89,9 +79,9 @@ elseif isfield(Data,'Conventions') && strcmp(Data.Conventions,'uvmat/civdata') FileInfo.FileType='civdata'; % test for civx velocity fields - FileType='civdata'; % test for civx velocity fields + % FileType='civdata'; % test for civx velocity fields FileInfo.CivStage=Data.CivStage; else FileInfo.FileType='netcdf'; - FileType='netcdf'; + %FileType='netcdf'; FileInfo.ListVarName=Data.ListVarName; end @@ -105,12 +95,11 @@ VideoObject=VideoReader(fileinput); FileInfo=get(VideoObject); - FileType='video'; + FileInfo.FileType='video'; elseif exist('mmreader.m','file')% Matlab 2009a VideoObject=mmreader(fileinput); FileInfo=get(VideoObject); - FileType='mmreader'; + FileInfo.FileType='mmreader'; end FileInfo.FileName=fileinput; - FileInfo.FileType=FileType; FileInfo.BitDepth=FileInfo.BitsPerPixel/3; end Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 782) +++ /trunk/src/series.m (revision 783) @@ -424,6 +424,6 @@ if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir FileName=ListStruct(ilist).name; - FileType=get_file_type(fullfile(DirName,FileName)); - switch FileType + FileInfo=get_file_type(fullfile(DirName,FileName)); + switch FileInfo.FileType case {'image','multimage','civx','civdata','netcdf'} break @@ -477,6 +477,6 @@ if ~isequal(hdir(ilist).isdir,1)%look for files, not dir FileName=hdir(ilist).name; - FileType=get_file_type(fullfile(DirName,FileName)); - switch FileType + FileInfo=get_file_type(fullfile(DirName,FileName)); + switch FileInfo.FileType case {'image','multimage','civx','civdata','netcdf'} break @@ -553,5 +553,5 @@ RootPath=fileparts(RootPath); %will try the upper folder else %scan the input folder - [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=... + [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=... find_file_series(fullfile(InputTable{iview,1},InputTable{iview,2}),[InputTable{iview,3} InputTable{iview,4} InputTable{iview,5}]); end @@ -607,5 +607,6 @@ % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists -[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); +[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); +FileType=FileInfo.FileType; if isempty(RootFile)&&isempty(i1_series) errormsg='no input file in the series'; @@ -1024,53 +1025,4 @@ %% set length of waitbar displ_time(handles) - - -% look for netcdf data as input -% switch FileType -% case {'civx','civdata'} -% FieldList=[set_field_list('U','V');{'C'}];%standard menu for civx data -% set(handles.Coord_x,'String','X'); -% set(handles.Coord_y,'String','Y'); -% case 'netcdf' -% ind_x=find(strcmp(get(handles.Coord_x,'String'),FileInfo.ListVarName)); -% if isempty(ind_x) -% FieldList={};% new kind of file opened, we need to pick variables with get_field... -% set(handles.Coord_x,'String','') -% set(handles.Coord_y,'String','') -% else -% FileInfo.ListVarName(ind_x)=[];%remove coord-x from the list of variables to display -% ind_y=find(strcmp(get(handles.Coord_y,'String'),FileInfo.ListVarName)); -% if isempty(ind_y) -% FieldList={};% new kind of file opened, we need to pick variables with get_field... -% set(handles.Coord_x,'String','') -% set(handles.Coord_y,'String','') -% else -% FileInfo.ListVarName(ind_y)=[];%remove coord-y from the list of variables to display -% FieldList=(FileInfo.ListVarName)'; -% end -% end -% otherwise -% set(handles.FieldName,'Value',1) % set menu to 'image' -% set(handles.FieldName,'String',{'image'}) -% set(handles.Coord_x,'String','AX'); -% set(handles.Coord_y,'String','AY'); -% end -% if ismember(FileType,{'civx','civdata','netcdf'}) -% PrevMenu=get(handles.FieldName,'String'); -% PrevValue=get(handles.FieldName,'Value'); -% PrevMenu=PrevMenu(PrevValue(PrevValue<=numel(PrevMenu))); -% FieldValue=[]; -% for ilist=1:numel(PrevMenu) -% index_menu=find(strcmp(PrevMenu{ilist},FieldList)); -% if ~isempty(index_menu) -% FieldValue=[FieldValue index_menu]; -% end -% end -% if isempty(FieldValue) -% FieldValue=1; -% end -% set(handles.FieldName,'Value',FieldValue) -% set(handles.FieldName,'String',[FieldList;{'get_field...'}]) -% end @@ -3023,8 +2975,8 @@ set(htitlebox,'String',FullSelectName) elseif exist(FullSelectName,'file')%visualise the vel field if it exists - FileType=get_file_type(FullSelectName); - if strcmp(FileType,'txt') + FileInfo=get_file_type(FullSelectName); + if strcmp(FileInfo.FileType,'txt') edit(FullSelectName) - elseif strcmp(FileType,'xml') + elseif strcmp(FileInfo.FileType,'xml') editxml(FullSelectName) else Index: /trunk/src/series/aver_stat.m =================================================================== --- /trunk/src/series/aver_stat.m (revision 782) +++ /trunk/src/series/aver_stat.m (revision 783) @@ -121,5 +121,6 @@ return end - [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files Index: /trunk/src/series/aver_synchro.m =================================================================== --- /trunk/src/series/aver_synchro.m (revision 782) +++ /trunk/src/series/aver_synchro.m (revision 783) @@ -93,5 +93,6 @@ FileExt=Param.InputTable(:,5); [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); - [FileType,FileInfo]=get_file_type(filecell{1,1}); +FileInfo=get_file_type(filecell{1,1}); + FileType=FileInfo.FileType; %%%%%%%%%%%% % The cell array filecell is the list of input file names, while Index: /trunk/src/series/beam_forming.m =================================================================== --- /trunk/src/series/beam_forming.m (revision 782) +++ /trunk/src/series/beam_forming.m (revision 783) @@ -82,5 +82,6 @@ return end - [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files Index: /trunk/src/series/check_data_files.m =================================================================== --- /trunk/src/series/check_data_files.m (revision 782) +++ /trunk/src/series/check_data_files.m (revision 783) @@ -92,5 +92,6 @@ NcTypeOptions={'netcdf','civx','civdata'}; for iview=1:nbview - [FileType{iview},FileInfo{iview},Object{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},Object{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files @@ -100,12 +101,9 @@ for iview=1:nbview if isequal(FileType{iview},'mmreader')||isequal(FileType{iview},'video')||isequal(FileType{iview},'multimage') - [tild,FileInfo]=get_file_type(filecell{iview,1}); + [FileInfo]=get_file_type(filecell{iview,1}); Tabchar{1}=filecell{iview,1};%info.Filename; Tabchar{2}=''; Tabchar{3}=[num2str(FileInfo.FrameRate) ' frames/s ']; message=''; - % Tabchar{4}=''; - % Tabchar{5}=[' compression' FileInfo.VideoCompression]; - % Tabchar{6}=[ 'quality ' num2str(FileInfo.Quality)]; else Tabchar={}; @@ -133,5 +131,6 @@ end lastfield=''; - [FileType{iview},FileInfo,Object]=get_file_type(file); + [FileInfo,Object]=get_file_type(file); + FileType{iview}=FileInfo.FileType; if strcmp(FileType{iview},'civx')||strcmp(FileType{iview},'civdata') if isfield(FileInfo,'CivStage') Index: /trunk/src/series/check_peaklock.m =================================================================== --- /trunk/src/series/check_peaklock.m (revision 782) +++ /trunk/src/series/check_peaklock.m (revision 783) @@ -113,5 +113,6 @@ return end - [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 782) +++ /trunk/src/series/civ_input.m (revision 783) @@ -2068,5 +2068,6 @@ Data.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly par_civ1=read_GUI(handles.Civ1); - par_civ1.FileTypeA=get_file_type(ImageName_A); + FileInfo=get_file_type(ImageName_A); + par_civ1.FileTypeA=FileInfo.FileType; par_civ1.ImageWidth=size(Data.A,2); par_civ1.ImageHeight=size(Data.A,1); Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 782) +++ /trunk/src/series/civ_series.m (revision 783) @@ -220,5 +220,6 @@ return end - [FileType_A,FileInfo_A,VideoObject_A]=get_file_type(ImageName_A); + [FileInfo_A,VideoObject_A]=get_file_type(ImageName_A); + FileType_A=FileInfo_A.FileType; if strcmp(FileInfo_A.FileType,'netcdf') FieldName_A=Param.InputFields.FieldName; @@ -233,5 +234,6 @@ return end - [FileType_B,FileInfo_B,VideoObject_B]=get_file_type(ImageName_B); + [FileInfo_B,VideoObject_B]=get_file_type(ImageName_B); + FileType_B=FileInfo_B.FileType; if strcmp(FileInfo_B.FileType,'netcdf') FieldName_B=Param.InputFields.FieldName; @@ -255,5 +257,6 @@ return end - [FileType_B,FileInfo_B,VideoObject_B]=get_file_type(ImageName_B); + [FileInfo_B,VideoObject_B]=get_file_type(ImageName_B); + FileType_B=FileInfo_B.FileType; [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ2(1)); NbField=numel(i1_series_Civ2); Index: /trunk/src/series/float_tracking.m =================================================================== --- /trunk/src/series/float_tracking.m (revision 782) +++ /trunk/src/series/float_tracking.m (revision 783) @@ -124,5 +124,6 @@ %% check the input file type -[FileType,FileInfo,VideoObject]=get_file_type(filecell{1,1}); +[FileInfo,VideoObject]=get_file_type(filecell{1,1}); +FileType=FileInfo.FileType; ImageTypeOptions={'image','multimage','mmreader','video'}; if isempty(find(strcmp(FileType,ImageTypeOptions))) Index: /trunk/src/series/ima_levels.m =================================================================== --- /trunk/src/series/ima_levels.m (revision 782) +++ /trunk/src/series/ima_levels.m (revision 783) @@ -65,5 +65,6 @@ msgbox_uvmat('WARNING','the first input file does not exist') else - FileType=get_file_type(filecell{1,1}); + FileInfo=get_file_type(filecell{1,1}); + FileType=FileInfo.FileType; if isempty(find(strcmp(FileType,{'image','multimage','mmreader','video'})));% =1 for images msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image is needed']) @@ -106,5 +107,6 @@ nbfield_i=size(i1_series{1},2); %nb of fields for the i index nbfield=nbfield_j*nbfield_i; %total number of fields -[FileType{1},FileInfo{1},VideoObject{1}]=get_file_type(filecell{1,1});% type of input file +[FileInfo{1},VideoObject{1}]=get_file_type(filecell{1,1});% type of input file +FileType{1}=FileInfo{1}.FileType; %% frame index for movie or multimage file input Index: /trunk/src/series/merge_proj.m =================================================================== --- /trunk/src/series/merge_proj.m (revision 782) +++ /trunk/src/series/merge_proj.m (revision 783) @@ -121,5 +121,6 @@ return end - [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files Index: /trunk/src/series/merge_proj_special.m =================================================================== --- /trunk/src/series/merge_proj_special.m (revision 782) +++ /trunk/src/series/merge_proj_special.m (revision 783) @@ -114,5 +114,6 @@ return end - [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files Index: /trunk/src/series/particle_tracking.m =================================================================== --- /trunk/src/series/particle_tracking.m (revision 782) +++ /trunk/src/series/particle_tracking.m (revision 783) @@ -124,5 +124,6 @@ %% check the input file type -[FileType,FileInfo,VideoObject]=get_file_type(filecell{1,1}); +[FileInfo,VideoObject]=get_file_type(filecell{1,1}); +FileType=FileInfo.FileType; ImageTypeOptions={'image','multimage','mmreader','video'}; if isempty(find(strcmp(FileType,ImageTypeOptions))) Index: /trunk/src/series/relabel_i_j.m =================================================================== --- /trunk/src/series/relabel_i_j.m (revision 782) +++ /trunk/src/series/relabel_i_j.m (revision 783) @@ -95,5 +95,6 @@ return end -[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); +[FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); +FileType{1}=FileInfo{1}.FileType; CheckImage=~isempty(find(strcmp(FileType{1},ImageTypeOptions)));% =1 for images Index: /trunk/src/series/sub_background.m =================================================================== --- /trunk/src/series/sub_background.m (revision 782) +++ /trunk/src/series/sub_background.m (revision 783) @@ -90,5 +90,6 @@ %% check the validity of input file types ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) - FileType=get_file_type(FirstFileName); + FileInfo=get_file_type(FirstFileName); + FileType=FileInfo.FileType; CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images if ~CheckImage @@ -200,5 +201,6 @@ % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices %%%%%%%%%%%% -[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); +[FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); +FileType{1}=FileInfo{1}.FileType; if ~isempty(j1_series{1}) frame_index{1}=j1_series{1}; Index: /trunk/src/series/time_series.m =================================================================== --- /trunk/src/series/time_series.m (revision 782) +++ /trunk/src/series/time_series.m (revision 783) @@ -124,5 +124,6 @@ return end - [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; if strcmp(FileType{iview},'civdata')||strcmp(FileType{iview},'civx') if ~isfield(Param.InputFields,'VelType') Index: /trunk/src/series/turb_stat.m =================================================================== --- /trunk/src/series/turb_stat.m (revision 782) +++ /trunk/src/series/turb_stat.m (revision 783) @@ -103,5 +103,6 @@ return end - [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + [FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files Index: /trunk/src/set_grid.m =================================================================== --- /trunk/src/set_grid.m (revision 782) +++ /trunk/src/set_grid.m (revision 783) @@ -228,6 +228,6 @@ return end -[FileType,tild,VideoObject]=get_file_type(GUI.ImageA); -switch FileType +[FileInfo,VideoObject]=get_file_type(GUI.ImageA); +switch FileInfo.FileType case {'image','multimage','video','mmreader'}% case of input image or movie OK otherwise @@ -265,5 +265,5 @@ %% detect the grid points which are inside image A -A=read_image(GUI.ImageA,FileType,VideoObject,1); +A=read_image(GUI.ImageA,FileInfo.FileType,VideoObject,1); npxA=size(A,2); npyA=size(A,1); @@ -323,6 +323,6 @@ 'Pick the second image file',fileparts(fileparts(get(handles.ImageA,'String')))); ImageB=fullfile(PathName,FileName); - [FileType,tild,VideoObject]=get_file_type(ImageB); - switch FileType + [FileInfo,tild,VideoObject]=get_file_type(ImageB); + switch FileInfo.FileType case {'image','multimage','video','mmreader'}% case of input image or movie OK set(handles.ImageB,'String',ImageB) Index: /trunk/src/transform_field/ima_noise_rms.m =================================================================== --- /trunk/src/transform_field/ima_noise_rms.m (revision 783) +++ /trunk/src/transform_field/ima_noise_rms.m (revision 783) @@ -0,0 +1,55 @@ +% 'ima_noise_rms': gives the variance of relative noise by difference to the +% filered image in ppm (part per million) (for grey scale image) + +%------------------------------------------------------------------------ +%%%% Use the general syntax for transform fields with a single input and parameters %%%% +% OUTPUT: +% DataOut: output field structure + +%INPUT: +% DataIn: input field structure +% Param: matlab structure whose field Param.TransformInput contains the filter parameters +%----------------------------------- + +%------------------------------------- +function DataOut=ima_noise_rms(DataIn,Param) + +%% request input parameters +if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0) + prompt = {'npx';'npy'}; + dlg_title = 'get the filter size in x and y'; + num_lines= 2; + def = { '20';'20'}; + if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'FilterBoxSize_x')&&... + isfield(Param.TransformInput,'FilterBoxSize_y') + def={num2str(Param.TransformInput.FilterBoxSize_x);num2str(Param.TransformInput.FilterBoxSize_y)}; + end + answer = inputdlg(prompt,dlg_title,num_lines,def); + DataOut.TransformInput.FilterBoxSize_x=str2num(answer{1}); %size of the filtering window + DataOut.TransformInput.FilterBoxSize_y=str2num(answer{2}); %size of the filtering window + return +end + +DataOut=DataIn; %default + +%definition of the cos shape matrix filter +ix=[1/2-Param.TransformInput.FilterBoxSize_x/2:-1/2+Param.TransformInput.FilterBoxSize_x/2];% +iy=[1/2-Param.TransformInput.FilterBoxSize_y/2:-1/2+Param.TransformInput.FilterBoxSize_y/2];% +%del=np/3; +%fct=exp(-(ix/del).^2); +fct2_x=cos(ix/((Param.TransformInput.FilterBoxSize_x-1)/2)*pi/2); +fct2_y=cos(iy/((Param.TransformInput.FilterBoxSize_y-1)/2)*pi/2); +%Mfiltre=(ones(5,5)/5^2); +Mfiltre=fct2_y'*fct2_x; +Mfiltre=Mfiltre/(sum(sum(Mfiltre)));%normalize filter + +Atype=class(DataIn.A);% detect integer 8 or 16 bits +B=filter2(Mfiltre,DataIn.A); +B(B==0)=1; %set to 1 the zero values +C=(double(DataIn.A)-B)./B; +C=filter2(Mfiltre,C.*C);% take variance integrated in the filtering area +C=1000000*sqrt(C); % take the root and *10^6 to get an image with integer values (parts per million) +DataOut.A=feval(Atype,C);%transform to the initial image format + + + Index: /trunk/src/uigetfile_uvmat.m =================================================================== --- /trunk/src/uigetfile_uvmat.m (revision 782) +++ /trunk/src/uigetfile_uvmat.m (revision 783) @@ -147,10 +147,10 @@ uiresume(hfig) case 'status_display' - FileType=get_file_type(FullSelectName); - if strcmp(FileType,'txt') + FileInfo=get_file_type(FullSelectName); + if strcmp(FileInfo.FileType,'txt') edit(FullSelectName) - elseif strcmp(FileType,'xml') + elseif strcmp(FileInfo.FileType,'xml') editxml(FullSelectName) - elseif strcmp(FileType,'figure') + elseif strcmp(FileInfo.FileType,'figure') open(FullSelectName) else Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 782) +++ /trunk/src/uvmat.m (revision 783) @@ -643,5 +643,5 @@ [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); % detect the file type, get the movie object if relevant, and look for the corresponding file series: -[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); +[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); if isempty(i1_series) fileinput=uigetfile_uvmat('pick an input file',fullfile(RootPath,SubDir)); @@ -666,5 +666,5 @@ [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); % detect the file type, get the movie object if relevant, and look for the corresponding file series: - [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileType,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); + [RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,tild,FileInfo,MovieObject]=find_file_series(fullfile(RootPath,SubDir),[RootFile FileIndices FileExt]); if isempty(i1_series) fileinput=uigetfile_uvmat('pick an input file for the second line',fullfile(RootPath,SubDir)); @@ -737,6 +737,6 @@ % detect the file type, get the movie object if relevant, and look for the corresponding file series: % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists -[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); - +[RootPath,SubDir,RootFile,i1_series,i2_series,j1_series,j2_series,NomType,FileInfo,MovieObject,i1,i2,j1,j2]=find_file_series(FilePath,[FileName FileExt]); +FileType=FileInfo.FileType; if strcmp(FileType,'txt') try @@ -1384,5 +1384,6 @@ for ifile=1:numel(ListFiles) [tild,tild,MaskExt]=fileparts(ListFiles{1}); - [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileType]=find_file_series(MaskPath,ListFiles{ifile},0); + [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileInfo]=find_file_series(MaskPath,ListFiles{ifile},0); + MaskFileType=MaskFileInfo.FileType; if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) mdetect=1; @@ -2185,7 +2186,19 @@ case 'multimage' if ~strcmp(NomType,'*') + MaxIndex_j_cell=get(handles.MaxIndex_j,'String'); + if num_j1>str2num(MaxIndex_j_cell{1}) + errormsg='specified frame index exceeds file content'; + return + else frame_index=num_j1;%frame index for movies or multimage + end else + MaxIndex_i_cell=get(handles.MaxIndex_i,'String'); + if num_i1>str2num(MaxIndex_i_cell{1}) + errormsg='specified frame index exceeds file content'; + return + else frame_index=num_i1; + end end case 'vol' %TODO: update @@ -3877,5 +3890,5 @@ %% delete drawn objects if the output CooordUnit is different from the previous one -if ~strcmp(CoordUnit,CoordUnitPrev) +if ~isempty(CoordUnit) && ~isempty(CoordUnitPrev) && ~strcmp(CoordUnit,CoordUnitPrev) set(handles.CheckFixLimits,'Value',0) hother=findobj('Tag','proj_object');%find all the proj objects