Index: /trunk/src/get_file_info.m =================================================================== --- /trunk/src/get_file_info.m (revision 1169) +++ /trunk/src/get_file_info.m (revision 1170) @@ -127,4 +127,14 @@ FileInfo.BitDepth=BitmapInfoHeader.biBitCount; FileInfo.TimeName='video'; + case '.hcc' + %cd 'TelopsToolbox_20230707(r20340)' + installToolboxIRCAM + [~,InfoArray]=readIRCam(fileinput,'HeadersOnly',true); + FileInfo.FileType='telopsIR'; + FileInfo.Height=InfoArray(1).Height; + FileInfo.Width=InfoArray(1).Width; + FileInfo.FrameRate=InfoArray(1).AcquisitionFrameRate; + FileInfo.NumberOfFrames=numel(InfoArray); + FileInfo.TimeName='video'; otherwise if ~isempty(FileExt)% exclude empty extension @@ -253,5 +263,5 @@ FileInfo.FieldType=FileInfo.FileType;%default switch FileInfo.FileType - case {'image','multimage','video','mmreader','rdvision','image_DaVis','cine_phantom'} + case {'image','multimage','video','mmreader','rdvision','image_DaVis','cine_phantom','telopsIR'} FileInfo.FieldType='image'; case {'civx','civdata','pivdata_fluidimage'} Index: /trunk/src/installToolboxIRCAM.m =================================================================== --- /trunk/src/installToolboxIRCAM.m (revision 1170) +++ /trunk/src/installToolboxIRCAM.m (revision 1170) @@ -0,0 +1,58 @@ +function installToolbox +% configure MATLAB paths for the Telops Toolbox. +% installToolbox +% +% Drop this file into MATLAB command line window. It will configure the +% required paths to run with the Telops Toolbox. + +% moveright Telops 2009 +% $Revision: 9106 $ +% $Author: ssavary $ +% $LastChangedDate: 2014-11-03 14:16:48 -0500 (lun., 03 nov. 2014) $ +if ~exist('readIRCam.p','file') + if ~exist('Library_IRCAM','dir') + unzip('Library_IRCAM.zip') + disp('Library_IRCAM created') + end + root = fileparts(mfilename('fullpath')); + + D = [{root}; extractSubTree(root)]; + + v2007_exceptions = {'GUILayout'}; + exceptions = {'Documentation', 'ReleasePackages'}; + + disp('installToolbox: Installing Toolbox...') + disp('installToolbox: Adding directories to the MATLAB path:') + + V = ver('matlab'); + for ii=1:length(D) + if ~isempty(V) && (str2double(V.Version(1)) == 7 && str2double(V.Version(3:end)) < 10) && ... + any(arrayfun(@(x)~isempty(strfind(D{ii},x{1})), v2007_exceptions)) || ... + any(arrayfun(@(x)~isempty(strfind(D{ii},x{1})), exceptions)) || ... + any(D{ii} == '+') + else + disp(['path ' D{ii} ' added']) + addpath(D{ii}) + end + end + + disp('installToolbox: Installation complete.') +end + + +function D = extractSubTree(root) +% Recursively build the list of subdirectories under 'root'. +% extractSubTree +% + +DD = dir(root); + +idx = find([DD.isdir]); +D = []; +for ii=idx + if strncmp(DD(ii).name,'.',1)==0 && isempty(strfind(DD(ii).name,'@')) && isempty(strfind(DD(ii).name,'private')) + % skip '.', '..', and invisible folders + subdir = fullfile(root, DD(ii).name); + D = [D; {subdir}; extractSubTree(subdir)]; %#ok + end +end Index: /trunk/src/read_field.m =================================================================== --- /trunk/src/read_field.m (revision 1169) +++ /trunk/src/read_field.m (revision 1170) @@ -239,4 +239,8 @@ A=read(ParamOut,frame_index); end + case 'telopsIR' + [A,Header]=readIRCam(FileName,'Frames',frame_index); + A=(reshape(A,Header(1).Width,Header(1).Height))'; + A=flip(A,1); case 'mmreader' if isa(ParamIn,'mmreader') Index: /trunk/src/read_image.m =================================================================== --- /trunk/src/read_image.m (revision 1169) +++ /trunk/src/read_image.m (revision 1170) @@ -79,3 +79,7 @@ A=Input.Frames{num}.Components{1}.Planes{1}'; end + case 'telopsIR' + [A,Header]=readIRCam(FileName,'Frames',num); + A=(reshape(A,Header(1).Width,Header(1).Height))'; + A=flip(A,1); end Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1169) +++ /trunk/src/series.m (revision 1170) @@ -140,11 +140,11 @@ end if exist(xmlfile,'file') - SeriesData.SeriesParam=xml2struct(xmlfile); - if ~(isfield(SeriesData.SeriesParam,'ClusterParam')&& isfield(SeriesData.SeriesParam.ClusterParam,'LaunchCmdFcn')) + SeriesData=xml2struct(xmlfile); + if ~(isfield(SeriesData,'ClusterParam')&& isfield(SeriesData.ClusterParam,'LaunchCmdFcn')) [success,message]=copyfile(xmlfile,fullfile(path_series,'series_old.xml'));% update the file series.xml inot correctly documented delete(xmlfile); [success,message]=copyfile(fullfile(path_series,'series.xml.default'),xmlfile); end - SeriesData.SeriesParam=xml2struct(xmlfile); + SeriesData=xml2struct(xmlfile); end @@ -160,5 +160,10 @@ ActionPathList(:)={path_series_fct}; % set the default path to series fcts to all list members RunModeList={'local';'background'}; % default choice of extensions (Matlab fct .m or compiled version .sh) -[s,w]=system(SeriesData.SeriesParam.ClusterParam.ExistenceTest); % look for cluster system presence +if isfield(SeriesData.ClusterParam.ExistenceTest,'Text') + oarcommand=SeriesData.ClusterParam.ExistenceTest.Text; +else + oarcommand=SeriesData.ClusterParam.ExistenceTest; +end +[s,w]=system(oarcommand); % look for cluster system presence if isequal(s,0) RunModeList=[RunModeList;{'cluster'}]; @@ -1533,6 +1538,6 @@ % case 'cluster' % %proposed number of cores to reserve in the cluster -% NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised; -% NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax); +% NbCoreAdvised=SeriesData.ClusterParam.NbCoreAdvised; +% NbCoreMax=min(NbProcess,SeriesData.ClusterParam.NbCoreMax); % if NbCoreMax~=1 % if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) @@ -1824,6 +1829,6 @@ Param.Action.CPUTime=CPUTime; end - JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax; - JobCPUTimeAdvised=SeriesData.SeriesParam.ClusterParam.JobCPUTimeAdvised; + JobNumberMax=SeriesData.ClusterParam.JobNumberMax; + JobCPUTimeAdvised=SeriesData.ClusterParam.JobCPUTimeAdvised; if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined BlockLength= ceil(JobCPUTimeAdvised/(CPUTime*nbfield_j)); % iterations are grouped in sets with length BlockLength such that the typical CPU time of a job is JobCPUTimeAdvised. @@ -1835,6 +1840,6 @@ % %proposed number of cores to reserve in the cluster - NbCoreAdvised=SeriesData.SeriesParam.ClusterParam.NbCoreAdvised; - NbCoreMax=min(NbProcess,SeriesData.SeriesParam.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes + NbCoreAdvised=SeriesData.ClusterParam.NbCoreAdvised; + NbCoreMax=min(NbProcess,SeriesData.ClusterParam.NbCoreMax);% reduces the number of cores if it exceeds the number of processes if NbCoreMax~=1 if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) @@ -2101,5 +2106,5 @@ end CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes) - LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn;% command obtained from the function + LaunchCmdFcn=SeriesData.ClusterParam.LaunchCmdFcn;% command obtained from the function oar_command=feval(LaunchCmdFcn,ListProcess,ActionFullName,DirLog,NbProcess, NbCore,CPUTimeProcess) [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window @@ -2632,29 +2637,4 @@ end end - -% status_j='on'; % default -% if isfield(SeriesData,'j1_series') && isempty(find(~cellfun(@isempty,SeriesData.j1_series), 1)) % case of empty j indices -% status_j='off'; % no j index needed -% elseif strcmp(get(handles.PairString,'Visible'),'on') -% check_burst=cellfun(@isempty,regexp(get(handles.PairString,'Data'),'^j')); % =0 for burst case, 1 otherwise -% if isempty(find(check_burst, 1))% if all pair string begins by j (burst) -% status_j='off'; % no j index needed for bust case -% end -% end -% enable_j(handles,status_j) % no j index needed -% if isfield(ParamOut,'j_index_1')&& isfield(ParamOut,'j_index_2')%strcmp(ParamOut.Desable_j_index,'on') -% %status_j='off'; -% set(handles.num_first_j,'String',num2str(ParamOut.j_index_1)) -% set(handles.num_last_j,'String',num2str(ParamOut.j_index_2)) -% % set(handles.num_first_j,'enable','off') -% % set(handles.num_last_j,'enable','off') -% set(handles.num_first_j,'visible','off') -% set(handles.num_last_j,'visible','off') -% set(handles.num_incr_j,'visible','off') -% else -% set(handles.num_first_j,'visible','on') -% set(handles.num_last_j,'visible','on') -% set(handles.num_incr_j,'visible',status_j) -% end %% NbSlice visibility @@ -3963,5 +3943,5 @@ function DiskQuota_Callback(hObject, eventdata, handles) SeriesData=get(handles.series,'UserData'); -system(SeriesData.SeriesParam.DiskQuotaCmd) +system(SeriesData.DiskQuotaCmd) Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 1169) +++ /trunk/src/series/civ_input.m (revision 1170) @@ -877,5 +877,11 @@ ref_j=[]; if isequal(mode_selected,'pair j1-j2')%|isequal(mode,'st_pair j1-j2') - ref_j=0; + ref_j=0; + MinIndex_j=str2num(get(handles.MinIndex_j,'String')); + MaxIndex_j=str2num(get(handles.MaxIndex_j,'String')); + if MaxIndex_j-MinIndex_j>10 + mode_selected= 'series(Dj)'; + ref_j= str2double(get(handles.ref_j,'String')); + end elseif strcmp(get(handles.ref_j,'Visible'),'on') ref_j=str2double(get(handles.ref_j,'String')); @@ -935,6 +941,10 @@ end case 'pair j1-j2'%case of pairs - MinIndex_j=str2num(get(handles.MinIndex_j,'String')); - MaxIndex_j=str2num(get(handles.MaxIndex_j,'String')); +% MinIndex_j=str2num(get(handles.MinIndex_j,'String')); +% MaxIndex_j=str2num(get(handles.MaxIndex_j,'String')); +% if MaxIndex_j-MinIndex_j>10 +% disp('too many pairs, switch to mode series(Dj)') +% return +% end index_pair=0; %get all the Time intervals in bursts Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 1169) +++ /trunk/src/series/civ_series.m (revision 1170) @@ -73,5 +73,5 @@ Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) - if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') + if isfield(Data,'ActionInput') && isfield(Data.ActionInput,'PairIndices') && isequal(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') Data.IndexRange_j='off';%no j index display in series else @@ -346,7 +346,10 @@ [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); FileType_A=FileInfo_A.FileType; - if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'}), 1))% case of video input - Time=zeros(FileInfo_A.NumberOfFrames+1,2); + if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom','telopsIR'}), 1))% case of video input + Time=zeros(FileInfo_A.NumberOfFrames+1,2); Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; + if ~isempty(j1_series_Civ1) && j1_series_Civ1~=1 + Time=Time'; + end end if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default