Index: /trunk/src/find_file_series.m =================================================================== --- /trunk/src/find_file_series.m (revision 934) +++ /trunk/src/find_file_series.m (revision 935) @@ -68,5 +68,5 @@ i1_series=[];i2_series=[];j1_series=[];j2_series=[]; i1_input=1;i2_input=[];j1_input=[];j2_input=[]; - if ~exist(fullfileinput,'file') + if exist(fullfileinput,'file')~=2 RootFile=''; return Index: /trunk/src/get_file_info.m =================================================================== --- /trunk/src/get_file_info.m (revision 934) +++ /trunk/src/get_file_info.m (revision 935) @@ -37,5 +37,5 @@ function [FileInfo,VideoObject]=get_file_info(fileinput) VideoObject=[]; -if exist(fileinput,'file') +if exist(fileinput,'file')==2 FileInfo.FileName=fileinput; FileInfo.FileType='txt'; %default Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 934) +++ /trunk/src/proj_field.m (revision 935) @@ -951,6 +951,6 @@ PlaneAngle=[0 0 0]; norm_plane=[0 0 1]; -cos_om=1; -sin_om=0; +%cos_om=1; +%sin_om=0; test90x=0;%=1 for 90 degree rotation alround x axis test90y=0;%=1 for 90 degree rotation alround y axis @@ -1052,8 +1052,8 @@ ProjData.CoordMesh=FieldData.CoordMesh; end -error=0;%default -flux=0; -testfalse=0; -ListIndex={}; +%error=0;%default +%flux=0; +%testfalse=0; +%ListIndex={}; %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions @@ -1340,4 +1340,56 @@ if strcmp(ProjMode{icell},'interp_tps') Coord=FieldData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex}); + + + coord_x=Coord(:,1,:);% initial x coordinates + coord_y=Coord(:,2,:);% initial y coordinates + check3D=(numel(CellInfo{icell}.CoordIndex)==3); + if check3D + coord_z=Coord(:,3,:); + end + + % translate initial coordinates to account for the new origin + coord_x=coord_x-ObjectData.Coord(1,1); + coord_y=coord_y-ObjectData.Coord(1,2); + if check3D + coord_z=coord_z-ObjectData.Coord(1,3); + end + + % selection of the vectors in the projection range (3D case) + if check3D && width > 0 + %components of the unitiy vector normal to the projection plane + fieldZ=norm_plane(1)*coord_x + norm_plane(2)*coord_y+ norm_plane(3)*coord_z;% distance to the plane + indcut=find(abs(fieldZ) <= width); + for ivar=VarIndex + VarName=FieldData.ListVarName{ivar}; + FieldData.(VarName)=FieldData.(VarName)(indcut); + end + coord_x=coord_x(indcut); + coord_y=coord_y(indcut); + coord_z=coord_z(indcut); + end + + %rotate coordinates if needed: coord_X,coord_Y= = coordinates in the new plane + Psi=PlaneAngle(1); + Theta=PlaneAngle(2); + Phi=PlaneAngle(3); + if testangle && ~test90y && ~test90x;%=1 for slanted plane + coord_X=(coord_x *cos(Phi) + coord_y* sin(Phi)); + coord_Y=(-coord_x *sin(Phi) + coord_y *cos(Phi))*cos(Theta); + coord_Y=coord_Y+coord_z *sin(Theta); + coord_X=(coord_X *cos(Psi) - coord_Y* sin(Psi));%A VERIFIER + coord_Y=(coord_X *sin(Psi) + coord_Y* cos(Psi)); + else + coord_X=coord_x; + coord_Y=coord_y; + end + + %restriction to the range of X and Y if imposed by the projection object + + + Coord(:,1,:)=coord_X;% initial x coordinates + Coord(:,2,:)=coord_Y;% initial y coordinates + + NbCentres=FieldData.(FieldData.ListVarName{CellInfo{icell}.NbCentres_tps}); SubRange=FieldData.(FieldData.ListVarName{CellInfo{icell}.SubRange_tps}); Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 934) +++ /trunk/src/series.m (revision 935) @@ -518,100 +518,77 @@ set(handles.InputTable,'Data',InputTable) REFRESH_Callback(hObject, eventdata, handles) -% DataSeries=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); -% fileinput=uigetfile_uvmat('pick an input file',DataSeries); -% hh=dir(fileinput); -% if numel(hh)>1 -% msgbox_uvmat('ERROR','invalid input, probably a broken link'); + + +% %------------------------------------------------------------------------ +% % --- fct activated by the browser under 'Open campaign/Browse...' +% %------------------------------------------------------------------------ +% function MenuBrowseCampaignAppend_Callback(hObject, eventdata, handles) +% append='append'; +% browse_campaign(handles,append); + +% %------------------------------------------------------------------------ +% function browse_campaign(handles,append); +% +% %% look for the previously opened file 'oldfile' +% +% % +% % +% % InputTable=get(handles.InputTable,'Data'); +% % RootPath=InputTable{1,1}; +% % CampaignPath=fileparts(fileparts(RootPath)); +% % DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir'); +% % if ~ischar(DirFull)|| ~exist(DirFull,'dir') +% % return +% % end +% OutPut=browse_data(oldfile);% open the GUI browse_data to get select a campaign dir, experiment and device +% if ~isfield(OutPut,'Campaign') +% return +% end +% DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); +% ListStruct=dir(DirName); %list files and the dir DataSeries +% % select the first appropriate file in the dir +% FileName=''; +% for ilist=1:numel(ListStruct) +% if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir +% FileName=ListStruct(ilist).name; +% FileInfo=get_file_info(fullfile(DirName,FileName)); +% switch FileInfo.FileType +% case {'image','multimage','civx','civdata','netcdf'} +% break +% end +% end +% end +% if isempty(FileName) +% msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)]) % return % end % -% -% -% %% launch the browser -% fileinput=uigetfile_uvmat('pick an input file in the series',oldfile); -% hh=dir(fileinput); -% if numel(hh)>1 -% msgbox_uvmat('ERROR','invalid input, probably a broken link'); -% else -% if ~isempty(fileinput) -% display_file_name(handles,fileinput,'one') +% %% update the list of campaigns in the menubar +% MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};... +% {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}]; +% check_dir=isempty(find(strcmp(DirName,MenuCampaign))); +% if check_dir %insert the new campaign in the list if it is not found +% MenuCampaign(end)=[]; %suppress the last item +% MenuCampaign=[{DirName};MenuCampaign];%insert the new campaign +% for ilist=1:numel(MenuCampaign) +% set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist}) +% end +% % save the list for future opening: +% dir_perso=prefdir; +% profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); +% if exist(profil_perso,'file') +% save (profil_perso,'MenuCampaign','-append'); %store the file names for future opening of uvmat +% else +% save (profil_perso,'MenuCampaign','-V6'); %store the file names for future opening of uvmat % end % end -% append='one'; -% set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) -% drawnow -% browse_campaign(handles,append); - -%------------------------------------------------------------------------ -% --- fct activated by the browser under 'Open campaign/Browse...' -%------------------------------------------------------------------------ -function MenuBrowseCampaignAppend_Callback(hObject, eventdata, handles) -append='append'; -browse_campaign(handles,append); - -%------------------------------------------------------------------------ -function browse_campaign(handles,append); - -%% look for the previously opened file 'oldfile' - % -% -% InputTable=get(handles.InputTable,'Data'); -% RootPath=InputTable{1,1}; -% CampaignPath=fileparts(fileparts(RootPath)); -% DirFull=uigetfile_uvmat('define this path as the Campaign folder:',CampaignPath,'uigetdir'); -% if ~ischar(DirFull)|| ~exist(DirFull,'dir') -% return +% %% display the selected field and related information +% if get(handles.CheckAppend,'Value') +% display_file_name(handles,fullfile(DirName,FileName),'append') +% else +% display_file_name(handles,fullfile(DirName,FileName),'one') % end -OutPut=browse_data(oldfile);% open the GUI browse_data to get select a campaign dir, experiment and device -if ~isfield(OutPut,'Campaign') - return -end -DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); -ListStruct=dir(DirName); %list files and the dir DataSeries -% select the first appropriate file in the dir -FileName=''; -for ilist=1:numel(ListStruct) - if ~isequal(ListStruct(ilist).isdir,1)%look for files, not dir - FileName=ListStruct(ilist).name; - FileInfo=get_file_info(fullfile(DirName,FileName)); - switch FileInfo.FileType - case {'image','multimage','civx','civdata','netcdf'} - break - end - end -end -if isempty(FileName) - msgbox_uvmat('ERROR',['no appropriate input file in the DataSeries folder ' fullfile(DirName)]) - return -end - -%% update the list of campaigns in the menubar -MenuCampaign=[{get(handles.MenuCampaign_1,'Label')};{get(handles.MenuCampaign_2,'Label')};... - {get(handles.MenuCampaign_3,'Label')};{get(handles.MenuCampaign_4,'Label')};{get(handles.MenuCampaign_5,'Label')}]; -check_dir=isempty(find(strcmp(DirName,MenuCampaign))); -if check_dir %insert the new campaign in the list if it is not found - MenuCampaign(end)=[]; %suppress the last item - MenuCampaign=[{DirName};MenuCampaign];%insert the new campaign - for ilist=1:numel(MenuCampaign) - set(handles.(['MenuCampaign_' num2str(ilist)]),'Label',MenuCampaign{ilist}) - end - % save the list for future opening: - dir_perso=prefdir; - profil_perso=fullfile(dir_perso,'uvmat_perso.mat'); - if exist(profil_perso,'file') - save (profil_perso,'MenuCampaign','-append'); %store the file names for future opening of uvmat - else - save (profil_perso,'MenuCampaign','-V6'); %store the file names for future opening of uvmat - end -end - -%% display the selected field and related information -if get(handles.CheckAppend,'Value') - display_file_name(handles,fullfile(DirName,FileName),'append') -else - display_file_name(handles,fullfile(DirName,FileName),'one') -end -set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) +% set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) % -------------------------------------------------------------------- @@ -619,26 +596,64 @@ % -------------------------------------------------------------------- set(handles.MenuOpenCampaign,'ForegroundColor',[1 1 0]) -OutPut=browse_data(get(hObject,'Label'));% open the GUI browse_data to get select a campaign dir, experiment and device +OutPut=browse_data(get(hObject,'Label'),'on','on');% open the GUI browse_data to get select a campaign dir, experiment and device if ~isfield(OutPut,'Campaign') return end -DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); -hdir=dir(DirName); %list files and dirs -for ilist=1:numel(hdir) - if ~isequal(hdir(ilist).isdir,1)%look for files, not dir - FileName=hdir(ilist).name; - FileInfo=get_file_info(fullfile(DirName,FileName)); - switch FileInfo.FileType - case {'image','multimage','civx','civdata','netcdf'} - break - end - end -end -if get(handles.CheckAppend,'Value') - display_file_name(handles,fullfile(DirName,FileName),'append') -else - display_file_name(handles,fullfile(DirName,FileName),'one') -end -set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) +NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries); +icount=0; +InputTable=get(handles.InputTable,'Data'); +for iexp=1:numel(OutPut.Experiment) + for idevice=1:numel(OutPut.DataSeries) + icount=icount+1; + InputTable{icount,1}=fullfile(OutPut.Campaign,OutPut.Experiment{iexp}); + InputTable{icount,2}=OutPut.DataSeries{idevice}; + if isempty(InputTable{icount,3}) + if icount>1 + InputTable{icount,3}=InputTable{icount-1,3}; + else + InputTable{icount,3}=''; + end + end + if isempty(InputTable{icount,4}) + if icount>1 + InputTable{icount,4}=InputTable{icount-1,4}; + else + InputTable{icount,4}=''; + end + end + if isempty(InputTable{icount,5}) + if icount>1 + InputTable{icount,5}=InputTable{icount-1,5}; + else + InputTable{icount,5}=''; + end + end + end +end +if size(InputTable,1)>icount + InputTable(icount+1:size(InputTable,1),:)=[]; +end +set(handles.InputTable,'Data',InputTable) +REFRESH_Callback(hObject, eventdata, handles) + + +% DirName=fullfile(OutPut.Campaign,OutPut.Experiment{1},OutPut.DataSeries{1}); +% hdir=dir(DirName); %list files and dirs +% for ilist=1:numel(hdir) +% if ~isequal(hdir(ilist).isdir,1)%look for files, not dir +% FileName=hdir(ilist).name; +% FileInfo=get_file_info(fullfile(DirName,FileName)); +% switch FileInfo.FileType +% case {'image','multimage','civx','civdata','netcdf'} +% break +% end +% end +% end +% if get(handles.CheckAppend,'Value') +% display_file_name(handles,fullfile(DirName,FileName),'append') +% else +% display_file_name(handles,fullfile(DirName,FileName),'one') +% end +% set(handles.MenuOpenCampaign,'ForegroundColor',[0 0 0]) @@ -1610,13 +1625,14 @@ NbCore=1;% no need to split the calculation case 'cluster_oar' - if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) - NbCore=1;% one core used only (limitation of Matlab licences) - answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?'); - if ~strcmp(answer,'Yes') - errormsg='Action launch interrupted by user'; - return - end - extra_oar=''; - else + %%%%% TEST A REMETTRE%%%%% + % if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) +% NbCore=1;% one core used only (limitation of Matlab licences) +% answer=msgbox_uvmat('INPUT_Y-N','Number of cores =1: select the compiled version .sh for multi-core processing. Proceed with the .m version?'); +% if ~strcmp(answer,'Yes') +% errormsg='Action launch interrupted by user'; +% return +% end +% extra_oar=''; + % else answer=inputdlg({'Number of cores (max 36)','extra oar options'},'oarsub parameter',1,{'12',''}); if isempty(answer) @@ -1626,5 +1642,5 @@ NbCore=str2double(answer{1}); extra_oar=answer{2}; - end + % end case 'cluster_pbs' if strcmp(ActionExt,'.m')% case of Matlab function (uncompiled) @@ -1698,5 +1714,5 @@ DirXml=fullfile(OutputDir,'0_XML'); if ~exist(DirXml,'dir') - [tild,msg1]=mkdir(DirXml); + [~,msg1]=mkdir(DirXml); if ~strcmp(msg1,'') errormsg=['cannot create ' DirXml ': ' msg1];%error message for directory creation @@ -2113,7 +2129,10 @@ end if exist(OutputDir,'dir') + [SUCCESS,MESSAGE,MESSAGEID] = fileattrib (OutputDir) + if MESSAGE.GroupWrite~=1 [success,msg] = fileattrib(OutputDir,'+w','g','s');% allow writing access for the group of users, recursively in the folder if success==0 - msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg1});%error message for directory creation + msgbox_uvmat('WARNING',{['unable to set group write access to ' OutputDir ':']; msg});%error message for directory creation + end end end Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 934) +++ /trunk/src/series/extract_rdvision.m (revision 935) @@ -469,11 +469,12 @@ NbDti=size(timestamp,1); %default for series or burst uid_motor_nbslice=find(t,'ImaDoc/TranslationMotor/Nbslice'); -if ~isempty(uid_motor_nbslice) +uid_nbDtk=find(t,'ImaDoc/TranslationMotor/NbDtk'); +if ~isempty(uid_motor_nbslice)&& ~isempty(uid_nbDtk) uid_content=get(t,uid_motor_nbslice,'contents'); NbSlice=str2num(get(t,uid_content,'value')); NbDti=NbSlice-1; -uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); -uid_content=get(t,uid_NbDti,'contents'); -t=set(t,uid_content,'value',num2str(NbDti)); + uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); + uid_content=get(t,uid_NbDti,'contents'); + t=set(t,uid_content,'value',num2str(NbDti)); end @@ -510,5 +511,5 @@ [success,msg] = fileattrib(newxml,'+w','g');% allow writing access for the group of users if success==0 - msgbox_uvmat('WARNING',{['unable to set group write access to ' newxml ':']; msg1});%error message for directory creation + msgbox_uvmat('WARNING',{['unable to set group write access to ' newxml ':']; msg});%error message for directory creation end Index: /trunk/src/transform_field/phys_polar.m =================================================================== --- /trunk/src/transform_field/phys_polar.m (revision 934) +++ /trunk/src/transform_field/phys_polar.m (revision 935) @@ -67,4 +67,7 @@ DataOut.TransformInput.PolarReferenceRadius=str2num(answer{2}); DataOut.TransformInput.PolarReferenceAngle=str2num(answer{3}); + if isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') + DataOut.CoordUnit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units + end return end Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 934) +++ /trunk/src/uvmat.m (revision 935) @@ -3585,4 +3585,7 @@ if isfield(UvData,'XmlData')%use geometry calib recorded from the ImaDoc xml file as first priority XmlData=UvData.XmlData{1}; + if isfield(UvData,'TransformInput') + XmlData.TransformInput=UvData.TransformInput; + end if numel(UvData.XmlData)==2 XmlData_1=UvData.XmlData{2}; @@ -4949,4 +4952,7 @@ XmlData=UvData.XmlData{1}; end + if isfield(UvData,'TransformInput') + XmlData.TransformInput=UvData.TransformInput; + end UvData.Field.Action.RUN=0;% indicate that the transform fct is called only to get input param DataOut=feval(transform_handle,UvData.Field,XmlData);% execute the transform fct to get the required conditions @@ -4958,5 +4964,5 @@ end if isfield(DataOut,'TransformInput')% used to add transform parameters at selection of the transform fct - UvData.XmlData{1}.TransformInput=DataOut.TransformInput; + UvData.TransformInput=DataOut.TransformInput; end end