Index: /trunk/src/fill_GUI.m =================================================================== --- /trunk/src/fill_GUI.m (revision 1122) +++ /trunk/src/fill_GUI.m (revision 1123) @@ -60,4 +60,7 @@ hh=[]; input_data=Param.(fields{ifield}); + if isfield(Param,'Type') && isa(Param.Type,'matlab.graphics.primitive.Rectangle') + input_data='rectangle'; + end check_done=0; if isfield(handles,fields{ifield}) Index: /trunk/src/find_field_bounds.m =================================================================== --- /trunk/src/find_field_bounds.m (revision 1122) +++ /trunk/src/find_field_bounds.m (revision 1123) @@ -34,6 +34,10 @@ %% analyse input field [CellInfo,NbDimArray,errormsg]=find_field_cells(Field);% analyse the input field structure +if isempty(CellInfo) + errormsg='bad input field' + return +end if ~isempty(errormsg) - errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg];% display error + errormsg=['uvmat /refresh_field / find_field_cells / ' errormsg]% display error return end Index: /trunk/src/script_delete_rdvision.m =================================================================== --- /trunk/src/script_delete_rdvision.m (revision 1123) +++ /trunk/src/script_delete_rdvision.m (revision 1123) @@ -0,0 +1,137 @@ + +%%% extract a series of image folders from RDvision +% to run on the cluster, edit the file extract.sh in the folder TOP_view or SCANSIDE, +% Then oarsub -l "walltime=20:00:00" /fsnet/project/coriolis/2018/18ADDUCE/TOP_View/extract.sh +%%%%%%%%%%%%%% CHOOSE THE ROOT FOLDER %%%%%%%%%% + +RootDir='DATA' +%RootFolder=fullfile('/fsnet/project/coriolis/2018/18JEVERB',RootDir); +RootFolder=fullfile('/fsnet/project/edt/2021/21CORIOFARM',RootDir) +%ParamFile=fullfile(RootFolder,'extract_param.xml'); +%Param=xml2struct(ParamFile); + +ListStruct=dir(RootFolder); % get structure of the Root directory +index_dir=find(strcmp('isdir',fieldnames(ListStruct)));%detect folder info in structure ListStruct +ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray +check_dir=cell2mat(ListCells(index_dir,:));% =1 for directories, =0 for files +ListCells=ListCells(:,check_dir); +ListCells(:,1:2)=[]; +ListNames=ListCells(1,:); +List2extract={}; +List2delete={}; +List2check={}; + +%% loop on experiments +for ilist=1:numel(ListNames)%loop on experiments + ListNames{ilist} + SubFolder=fullfile(RootFolder,ListNames{ilist}); + ListStructSub=dir(SubFolder); % get structure of the Root directory + index_dir=find(strcmp('isdir',fieldnames(ListStructSub)));%detect folder info in structure ListStruct + ListCellsSub=struct2cell(ListStructSub);% transform dir struct to a cell arrray + check_dir=cell2mat(ListCellsSub(index_dir,:));% =1 for directories, =0 for files + ListCellsSub=ListCellsSub(:,check_dir); + ListCellsSub(:,1:2)=[]; + ListNamesSub=ListCellsSub(1,:); + ind_rdvision=[]; + for isub=1:numel(ListNamesSub)% loop on data folders of the current experiment + ListStructSubSub=dir(fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub})); % get structure of the Root directory + index_dir=find(strcmp('isdir',fieldnames(ListStructSubSub)));%detect folder info in structure ListStruct + ListCellsSubSub=struct2cell(ListStructSubSub);% transform dir struct to a cell arrray + check_dir=cell2mat(ListCellsSubSub(index_dir,:));% =1 for directories, =0 for files + ListCellsSubSub=ListCellsSubSub(:,check_dir); + ListCellsSubSub(:,1:2)=[]; + ListNamesSubSub=ListCellsSubSub(1,:); + ind_rdvision=[]; + for isubsub=1:numel(ListNamesSubSub) + if ~isempty(regexp(ListNamesSubSub{isubsub},'^2021-')) + ind_rdvision=[ind_rdvision isubsub];%detect rdvision folders + end + end + + %% extract the rdvision image series if it was not done + if numel(ind_rdvision)==1% + DataFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},ListNamesSubSub{ind_rdvision}); + if isempty(regexp(DataFolder,'.extract$'))% if the detected folder is not .extract + % ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']); + % mkdir(ExtractFolder) + % % if ~isempty(XmlFile) + % % copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml'])); + % % end + % seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]); + % [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]); + % Param.IndexRange.last_i=str2num(FileInfo.numberoffiles); + % Param.OutputSubDir=Param.InputTable{2}; + % Param.ActionInput.LogPath= DataFolder; + % extract_rdvision(Param)% apply the function used in series + % [ListNames{ilist} ' extracted'] + List2extract=[List2extract;DataFolder]; + end + end + + %% delete the rdvision source if the extraction has been done + Checkdelete=0; + ExtractFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub}); + status=''; + if numel(ind_rdvision)==2 + for irdvision=1:2 + CheckExtract(irdvision)=isempty(regexp(fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},ListNamesSubSub{irdvision}), '.extract$')); + end + status='extract missing'; + if numel(find(CheckExtract))==1 + ExtractFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},ListNamesSubSub{find(CheckExtract)}); + PngFolder=fullfile(RootFolder,ListNames{ilist},ListNamesSub{isub},'im'); + status='image folder not created'; + if exist(ExtractFolder,'dir') && exist(PngFolder,'dir') + filename_seq=fullfile(ExtractFolder,'im.seq'); + s=ini2struct(filename_seq); + FileInfo=s.sequenceSettings; + if isfield(s.sequenceSettings,'numberoffiles') + NumberOfFrames=str2double(s.sequenceSettings.numberoffiles); + else + status='bad seq file'; + end + DirPng=dir(PngFolder); + if numel(DirPng)==NumberOfFrames+2 + Checkdelete=1; + else + status=['extraction not finished,' num2str(numel(DirPng)-2) ' images extracted']; + end + end + end + % + % + % Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp + % ddd=dir(Param.InputTable{1}); + % Param.InputTable{2}=ddd(3).name; + % DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2}); + % ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']); + % mkdir(ExtractFolder) + % if ~isempty(XmlFile) + % copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml'])); + % end + % seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]); + % [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]); + % Param.IndexRange.last_i=str2num(FileInfo.numberoffiles); + % Param.OutputSubDir=Param.InputTable{2}; + % Param.ActionInput.LogPath= DataFolder; + % extract_rdvision(Param)% apply the function used in series + end + if Checkdelete + List2delete=[List2delete;ExtractFolder]; + %rmdir(ExtractFolder,'s') + elseif ~isempty(status) + List2check=[List2check;[ExtractFolder ' ' status]]; + end + end +end +List2extract +List2check +List2delete +if ~isempty(List2delete) + Answer = questdlg('delete listed folders(Y/N)'); + if strcmp(Answer,'Yes') + for ifolder=1:numel(List2delete) + rmdir(List2delete{ifolder},'s') + end + end +end Index: /trunk/src/script_readlvm.m =================================================================== --- /trunk/src/script_readlvm.m (revision 1122) +++ /trunk/src/script_readlvm.m (revision 1123) @@ -61,5 +61,5 @@ %% check camera signal -ind_start=find(Data.Trig_Cam>3.5,1,'first') +ind_start=find(Data.Trig_cam>3.5,1,'first') disp(['camera starts at time ' num2str(Data.Time(ind_start))]) %% transform and filter conductivity probe signals into [temperature-corrected] density Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1122) +++ /trunk/src/series.m (revision 1123) @@ -2720,4 +2720,7 @@ %% NbSlice visibility +if isfield(ParamOut,'OutputFileMode')&& strcmp(ParamOut.OutputFileMode,'NbSlice') + ParamOut.NbSlice='on'; +end if isfield(ParamOut,'NbSlice') && (strcmp(ParamOut.NbSlice,'on')||isnumeric(ParamOut.NbSlice)) set(handles.num_NbSlice,'Visible','on') Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 1122) +++ /trunk/src/series/civ_series.m (revision 1123) @@ -89,40 +89,4 @@ end end - % estimated CPUTime -% CPUtime_unit=0.01;%estimated time for a multiplication (in microsecond) -% if isfield(Param.SeriesData,'FileInfo')&&isfield(Param.SeriesData.FileInfo{1},'Height')&&isfield(Param.SeriesData.FileInfo{1},'Width') -% pixnbre=Param.SeriesData.FileInfo{1}.Height*Param.SeriesData.FileInfo{1}.Width; % total number of pxels for input images -% CPUtime=0; -% if isfield(Data.ActionInput,'Civ1') -% %BoxSize=Data.ActionInput.Civ1.CorrBoxSize(1)*Data.ActionInput.Civ1.CorrBoxSize(2); -% tic -% testboxa=rand(Data.ActionInput.Civ1.CorrBoxSize(1),Data.ActionInput.Civ1.CorrBoxSize(2)); -% testboxb=rand(Data.ActionInput.Civ1.SearchBoxSize(1),Data.ActionInput.Civ1.SearchBoxSize(2)); -% anss=conv2(testboxa,testboxb); -% CPUtime_unit=toc; -% nb_box=pixnbre/(Data.ActionInput.Civ1.Dx*Data.ActionInput.Civ1.Dy); -% %nbpos=Data.ActionInput.Civ1.SearchBoxSize-Data.ActionInput.Civ1.CorrBoxSize; -% CPUtime=2*CPUtime_unit*nb_box%*BoxSize*nbpos(1)*nbpos(2);% adjustement factor 2 used -% end -% if isfield(Data.ActionInput,'Patch1') -% CPUtime=2*CPUtime; -% end -% if isfield(Data.ActionInput,'Civ2') -% tic -% testboxa=rand(Data.ActionInput.Civ2.CorrBoxSize(1),Data.ActionInput.Civ2.CorrBoxSize(2)); -% testboxb=rand(Data.ActionInput.Civ2.SearchBoxSize(1),Data.ActionInput.Civ2.SearchBoxSize(2)); -% anss=conv2(testboxa,testboxb); -% CPUtime_unit=toc; -% nb_box=pixnbre/(Data.ActionInput.Civ2.Dx*Data.ActionInput.Civ2.Dy); -% %BoxSize=Data.ActionInput.Civ2.CorrBoxSize(1)*Data.ActionInput.Civ2.CorrBoxSize(2); -% %nbpos=Data.ActionInput.Civ2.SearchBoxSize-Data.ActionInput.Civ2.CorrBoxSize; -% CPUtime=CPUtime+2*CPUtime_unit*nb_box;%*BoxSize*nbpos(1)*nbpos(2); -% end -% if isfield(Data.ActionInput,'Patch2') -% CPUtime=(4/3)*CPUtime; -% end -% Data.CPUTime=ceil(CPUtime/6); % estimated CPU time per field pair in minute -% Data.CPUTime=Data.CPUTime/10; % displqy CPU time with 1 digit beyond dot -% end return end Index: /trunk/src/transform_field/FFT2_detrend.m =================================================================== --- /trunk/src/transform_field/FFT2_detrend.m (revision 1122) +++ /trunk/src/transform_field/FFT2_detrend.m (revision 1123) @@ -68,4 +68,5 @@ VarName=DataIn.ListVarName{ivar}; z=DataIn.(VarName); + z(isnan(z))=0;% set to 0 NaN values rhs(1) = sum(sum(x.*z)); rhs(2) = sum(sum(y.*z)); rhs(3) = sum(sum(z)); lin_coeff = inv(coeff)*rhs'; @@ -75,6 +76,6 @@ spec2 = spec2(Iy,Ix); spec2 = spec2(ss,:); - %DataOut.(VarName) = log(spec2); - DataOut.(VarName) = spec2; + DataOut.(VarName) = log10(spec2); + %DataOut.(VarName) = spec2; spec_sum=sum(sum(spec2)); kx_mean=sum(sum(spec2.*kx))/spec_sum; Index: /trunk/src/transform_field/signal_spectrum.m =================================================================== --- /trunk/src/transform_field/signal_spectrum.m (revision 1122) +++ /trunk/src/transform_field/signal_spectrum.m (revision 1123) @@ -170,5 +170,5 @@ if numel(ind_good)>WindowLength NbPos=NbPos+1; - if ~isempty(ind_bad) + if ~isempty(ind_bad)WindowLength sample=sample(ind_good); % keep only non NaN data NbNan=NbNan+numel(ind_bad); Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1122) +++ /trunk/src/uvmat.m (revision 1123) @@ -5000,5 +5000,5 @@ menu={'civ1';'filter1';'civ2';'filter2';'civ3';'filter3'}; imax=[0 1 1 2 3 3 4 5 5 6]; - imax=imax(Civ+1); + imax=imax(min(Civ+1,10)); % if isequal(Civ,0) % imax=0;