Index: /trunk/src/browse_data.m =================================================================== --- /trunk/src/browse_data.m (revision 1058) +++ /trunk/src/browse_data.m (revision 1059) @@ -24,5 +24,5 @@ function varargout = browse_data(varargin) -% Last Modified by GUIDE v2.5 24-Jan-2015 16:55:04 +% Last Modified by GUIDE v2.5 08-Sep-2018 19:03:40 % Begin initialization code - DO NOT EDIT @@ -47,13 +47,14 @@ %------------------------------------------------------------------------ % --- Executes just before browse_data is made visible. -function browse_data_OpeningFcn(hObject, eventdata, handles, DataSeries,EnableMirror,MultiDevices) +function browse_data_OpeningFcn(hObject, eventdata, handles, InputDir,EnableMirror,MultiDevices) %------------------------------------------------------------------------ %% Choose default command line output for browse_data -handles.output = 'Cancel'; +handles.output =hObject;% 'Cancel'; %% Update handles structure guidata(hObject, handles); set(hObject,'WindowButtonDownFcn',{'mouse_down'}) % allows mouse action with right button (zoom for uicontrol display) +set(hObject,'DeleteFcn',{@closefcn})% %% Determine the position of the dialog - centered on the screen @@ -87,11 +88,13 @@ %% initialize the GUI -if isempty(regexp(DataSeries,'^http:'))&& ~(exist('DataSeries','var') && ischar(DataSeries) && exist(DataSeries,'dir')) - DataSeries=pwd;% current dir is the starting data series by default -end -[Experiment,DataSeries,Ext]=fileparts(DataSeries); -DataSeries=[DataSeries Ext]; -[Campaign,Experiment,Ext]=fileparts(Experiment); -Experiment=[Experiment Ext]; +if isempty(regexp(InputDir,'^http:'))&& ~(exist('InputDir','var') && ischar(InputDir) && exist(InputDir,'dir')) + InputDir=pwd;% current dir is the starting data series by default +end +% [Experiment,DataSeries,Ext]=fileparts(DataSeries); +% DataSeries=[DataSeries Ext]; +% [Campaign,Experiment,Ext]=fileparts(Experiment); +% Experiment=[Experiment Ext]; +[ExpWithPath,DataSeries]=fileparts(InputDir); +[Campaign,Experiment,Ext]=fileparts(ExpWithPath); [tild,CampaignName]=fileparts(Campaign); RootXml=fullfile(Campaign,[CampaignName '.xml']); @@ -111,17 +114,19 @@ set(handles.CreateMirror,'String','create_mirror') end -errormsg=scan_campaign(handles,Campaign,Experiment,DataSeries); +errormsg=scan_campaign(handles,Campaign,Experiment,ExpWithPath); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) return end -set(handles.OK,'Visible','on') -set(handles.Cancel,'Visible','on') - -set(handles.browse_data,'WindowStyle','modal')% Make the GUI modal +% set(handles.OK,'Visible','on') +% set(handles.Cancel,'Visible','on') + +%set(handles.browse_data,'WindowStyle','modal')% Make the GUI +%modal%%%%%%%%%%%%%%%%%%%%%%% set(hObject,'Visible','on') drawnow -% UIWAIT makes GUI wait for user response (see UIRESUME) -uiwait(handles.browse_data); +% UIWAIT makes GUI wait for user response (see UIRESUME)%%%%%%%%%%%%%%%%TO +% CHECK +%uiwait(handles.browse_data); @@ -133,5 +138,5 @@ % Get default command line output from handles structure varargout{1} = handles.output; -delete(handles.browse_data) +%%%%%%%%%%%%%%%%%%delete(handles.browse_data) %------------------------------------------------------------------------ @@ -213,5 +218,5 @@ ListStruct=dir_uvmat(Campaign); %list files and dirs if numel(ListStruct)>1000% A campaign folder must contain maily a list of 'experiment' sub-folders - errormsg=[Campaign ' contains too many items (>1000) to be a Campaign folder']; + errormsg=[Campaign ' contains too many items (>1000) to be a Project folder']; return end @@ -224,7 +229,7 @@ ListFiles=sort((ListFiles(check_keep))'); index=find(strcmp(['+/' Experiment],ListFiles)); - if isempty(index), index=0; end - set(handles.ListExperiments,'String',[{'*'};ListFiles]) - set(handles.ListExperiments,'Value',index+1)% initialise the menu selection with the folder defined by the input + if isempty(index), index=1; end + set(handles.ListExperiments,'String',ListFiles) + set(handles.ListExperiments,'Value',index)% initialise the menu selection with the folder defined by the input ListExperiments_Callback([],[], handles) ListDevices=get(handles.ListDevices,'String'); @@ -252,10 +257,10 @@ ListExperiments=get(handles.ListExperiments,'String'); list_val=get(handles.ListExperiments,'Value'); -if isequal(list_val(1),1) - ListExperiments=ListExperiments(2:end); %choose all experiments if the first line '*' is selected - set(handles.ListExperiments,'Value',1) -else +% if isequal(list_val(1),1) +% ListExperiments=ListExperiments(2:end); %choose all experiments if the first line '*' is selected +% set(handles.ListExperiments,'Value',1) +% else ListExperiments=ListExperiments(list_val);%choose selected experiments -end +% end list_dataseries(handles,ListExperiments,MirrorPath) @@ -283,8 +288,8 @@ else %update the list of dataSeries [tild,msg]=fileattrib(mirror); - msg.Name=regexprep(msg.Name,'^/.','/');%remove the dot in /. at the beginning of the name - if ~strcmp(msg.Name,mirror)% if it is a link - ListFiles{ilist}=['~' ListFiles{ilist}];%mark link by '@' in the list - end +% msg.Name=regexprep(msg.Name,'^/.','/');%remove the dot in /. at the beginning of the name +% if ~strcmp(msg.Name,mirror)% if it is a link +% ListFiles{ilist}=['~' ListFiles{ilist}];%mark link by '@' in the list +% end if check_dir(ilist) ListFiles{ilist}=['+/' ListFiles{ilist}];%mark dir by '+' in the list @@ -298,4 +303,5 @@ end end +set(handles.ListDevices,'Value',1) set(handles.ListDevices,'String',sort(ListDevices)) @@ -438,170 +444,5 @@ save(t,outputfile) -% %------------------------------------------------------------------------ -% % --- Executes on button press in CampaignDoc. -% function edit_xml_Callback(hObject, eventdata, handles) -% %------------------------------------------------------------------------ -% CurrentPath=get(handles.SourceDir,'String'); -% %[CurrentPath,Name,Ext]=fileparts(CurrentDir); -% ListExperiments=get(handles.ListExperiments,'String'); -% Value=get(handles.ListExperiments,'Value'); -% if ~isequal(Value,1) -% ListExperiments=ListExperiments(Value); -% end -% ListDevices=get(handles.ListDevices,'String'); -% Value=get(handles.ListDevices,'Value'); -% if ~isequal(Value,1) -% ListDevices=ListDevices(Value); -% end -% ListRecords=get(handles.ListRecords,'String'); -% Value=get(handles.ListRecords,'Value'); -% if ~isequal(Value,1) -% ListRecords=ListRecords(Value); -% end -% [ListDevices,ListRecords,ListXml,List]=dir_scan(CurrentPath,ListExperiments,ListDevices,ListRecords); -% ListXml=get(handles.ListXml,'String'); -% Value=get(handles.ListXml,'Value'); -% set(handles.ListXml,'Value',Value(1)); -% if isequal(Value(1),1) -% msgbox_uvmat('ERROR','an xml file needs to be selected') -% return -% else -% XmlName=ListXml{Value(1)}; -% end -% for iexp=1:length(List.Experiment) -% ExpName=List.Experiment{iexp}.name; -% if isfield(List.Experiment{iexp},'Device') -% for idevice=1:length(List.Experiment{iexp}.Device) -% DeviceName=List.Experiment{iexp}.Device{idevice}.name; -% if isfield(List.Experiment{iexp}.Device{idevice},'xmlfile') -% for ixml=1:length(List.Experiment{iexp}.Device{idevice}.xmlfile) -% FileName=List.Experiment{iexp}.Device{idevice}.xmlfile{ixml}; -% if isequal(FileName,XmlName) -% editxml(fullfile(CurrentPath,ExpName,DeviceName,FileName)); -% return -% end -% end -% elseif isfield(List.Experiment{iexp}.Device{idevice},'Record') -% for irecord=1:length(List.Experiment{iexp}.Device{idevice}.Record) -% RecordName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.name; -% if isfield(List.Experiment{iexp}.Device{idevice}.Record{irecord},'xmlfile') -% for ixml=1:length(List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile) -% FileName=List.Experiment{iexp}.Device{idevice}.Record{irecord}.xmlfile{ixml}; -% if isequal(FileName,XmlName) -% editxml(fullfile(CurrentPath,ExpName,DeviceName,RecordName,FileName)); -% return -% end -% end -% end -% end -% end -% end -% end -% end -% -% -% -% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -% % CurrentPath/Campaign: root directory -% function [Title,test_mod]=check_heading(Currentpath,Campaign,Experiment,Device,Record,xmlname,testSubCampaign) -% -% %Shema for Heading: -% % Campaign -% % (SubCampaign) -% % Experiment -% % Device -% % (Record) -% % ImageName -% % DateExp -% % old: %Project: suppressed ( changed to Campaign) -% %Exp: suppressed (changed to experiment) -% %ImaNames: changed to ImageName -% if exist('Record','var') && ~isempty(Record) -% xmlfullname=fullfile(Currentpath,Campaign,Experiment,Device,Record,xmlname); -% testrecord=1; -% else -% xmlfullname=fullfile(Currentpath,Campaign,Experiment,Device,xmlname); -% testrecord=0; -% end -% if ~exist('testSubCampaign','var') -% testSubCampaign=0; -% end -% if testSubCampaign -% SubCampaign=Campaign; -% [Currentpath,Campaign,DirExt]=fileparts(Currentpath); -% Campaign=[Campaign DirExt]; -% end -% test_mod=0; %test for the modification of the xml file -% t_device=xmltree(xmlfullname); -% Title=get(t_device,1,'name'); -% uid_child=children(t_device,1); -% Heading_old=[]; -% uidheading=0; -% for ilist=1:length(uid_child) -% name=get(t_device,uid_child(ilist),'name'); -% if isequal(name,'Heading') -% uidheading=uid_child(ilist); -% end -% end -% if uidheading -% subt=branch(t_device,uidheading); -% Heading_old=convert(subt); -% else -% return % do not edit xml files without element 'Heading' -% end -% if ~(isfield(Heading_old,'Campaign')&& isequal(Heading_old.Campaign,Campaign)) -% test_mod=1; -% end -% Heading.Campaign=Campaign; -% if testSubCampaign -% if ~(isfield(Heading_old,'SubCampaign')&& isequal(Heading_old.SubCampaign,SubCampaign)) -% test_mod=1; -% end -% Heading.SubCampaign=SubCampaign; -% end -% if ~(isfield(Heading_old,'Experiment')&& isequal(Heading_old.Experiment,Experiment)) -% test_mod=1; -% end -% Heading.Experiment=Experiment; -% if ~(isfield(Heading_old,'Device')&& isequal(Heading_old.Device,Device)) -% test_mod=1; -% end -% Heading.Device=Device; -% if testrecord -% if ~(isfield(Heading_old,'Record')&& isequal(Heading_old.Record,Record)) -% test_mod=1; -% end -% Heading.Record=Record; -% end -% if isfield(Heading_old,'ImaNames') -% test_mod=1; -% if ~isempty(Heading_old.ImaNames) -% Heading.ImageName=Heading_old.ImaNames; -% end -% end -% if isfield(Heading_old,'ImageName')&& ~isempty(Heading_old.ImageName) -% Heading.ImageName=Heading_old.ImageName; -% end -% if isfield(Heading_old,'DateExp')&& ~isempty(Heading_old.DateExp) -% Heading.DateExp=Heading_old.DateExp; -% end -% if test_mod && uidheading -% uid_child=children(t_device,uidheading); -% t_device=delete(t_device,uid_child); -% t_device=struct2xml(Heading,t_device,uidheading); -% backupfile=xmlfullname; -% testexist=2; -% while testexist==2 -% backupfile=[backupfile '~']; -% testexist=exist(backupfile,'file'); -% end -% [success,message]=copyfile(xmlfullname,backupfile);%make backup -% if isequal(success,1) -% delete(xmlfullname) -% else -% return -% end -% save(t_device,xmlfullname) -% end + %------------------------------------------------------------------------ @@ -648,23 +489,43 @@ % --- Executes on button press in Cancel. %------------------------------------------------------------------------ -function Cancel_Callback(hObject, eventdata, handles) - -handles.output = get(hObject,'String'); -guidata(hObject, handles); % Update handles structure -% Use UIRESUME instead of delete because the OutputFcn needs -uiresume(handles.browse_data); +% function Cancel_Callback(hObject, eventdata, handles) +% % hseries=findobj(allchild(0),'Tag','series'); +% % if ~isempty(hseries) +% % hhh=guidata(hseries); +% % set(hhh.Replicate,'Value',0) +% % end +% % delete(get(hObject,'parent')) + +% handles.output = get(hObject,'String'); +% guidata(hObject, handles); % Update handles structure +% % Use UIRESUME instead of delete because the OutputFcn needs +% uiresume(handles.browse_data); + +%------------------------------------------------------------------------ +% --- executes when user attempts to close geometry_calib. +function browse_data_CloseRequestFcn(hObject, eventdata, handles) %------------------------------------------------------------------------ % --- Executes when user attempts to close browse_data. %------------------------------------------------------------------------ -function browse_data_CloseRequestFcn(hObject, eventdata, handles) -if isequal(get(handles.browse_data, 'waitstatus'), 'waiting') - % The GUI is still in UIWAIT, us UIRESUME - handles.output = get(hObject,'String'); - guidata(hObject, handles); % Update handles structure - uiresume(handles.browse_data); -else - % The GUI is no longer waiting, just close it - delete(handles.browse_data); +function closefcn(gcbo, eventdata) +% if isequal(get(handles.browse_data, 'waitstatus'), 'waiting') +% % The GUI is still in UIWAIT, us UIRESUME +% handles.output = get(hObject,'String'); +% guidata(hObject, handles); % Update handles structure +% uiresume(handles.browse_data); +% else +% % The GUI is no longer waiting, just close it +% delete(handles.browse_data); +% end +hseries=findobj(allchild(0),'Tag','series'); +if ~isempty(hseries) + hreplicate=findobj(hseries,'Tag','Replicate'); + set(hreplicate,'Value',0) +end +hcalib=findobj(allchild(0),'Tag','geometry_calib'); +if ~isempty(hcalib) + hreplicate=findobj(hcalib,'Tag','Replicate'); + set(hreplicate,'Value',0) end @@ -689,9 +550,30 @@ -% --- Executes on button press in Browse. -function Browse_Callback(hObject, eventdata, handles) +% --- Executes on button press in Up. +function Up_Callback(hObject, eventdata, handles) +SourceDir=get(handles.SourceDir,'String'); +% Device=ListDevices{get(handles.ListDevices,'Value')}; +% DataSeries=uigetfile_uvmat('open a data folder',Device,'uigetdir'); +% uiresume(handles.browse_data); +browse_data(SourceDir) + + +% --- Executes on button press in Down. +function Down_Callback(hObject, eventdata, handles) +SourceDir=get(handles.SourceDir,'String'); +ListExperiments=get(handles.ListExperiments,'String'); +list_val=get(handles.ListExperiments,'Value'); +SourceFolder=regexprep(ListExperiments{list_val(1)},'+',''); +set(handles.SourceDir,'String',fullfile(SourceDir,SourceFolder)) ListDevices=get(handles.ListDevices,'String'); -Device=ListDevices{get(handles.ListDevices,'Value')}; -DataSeries=uigetfile_uvmat('open a data folder',Device,'uigetdir'); -uiresume(handles.browse_data); -browse_data(DataSeries) +ValueDevice=get(handles.ListDevices,'Value'); +set(handles.ListExperiments,'String',ListDevices) +set(handles.ListExperiments,'Value',ValueDevice) +ListExperiments_Callback(hObject, [], handles) +% Device=regexprep(ListDevices{get(handles.ListDevices,'Value')},'+',''); +% Device=regexprep(Device,'~',''); +% PathDevice=fullfile(SourceDir,SourceFolder,Device); +% DirDevice=dir(PathDevice); +% NewDevice=DirDevice(end).name; +% % uiresume(handles.browse_data); +% browse_data(fullfile(PathDevice,NewDevice)) Index: /trunk/src/filter_tps.m =================================================================== --- /trunk/src/filter_tps.m (revision 1058) +++ /trunk/src/filter_tps.m (revision 1059) @@ -79,4 +79,5 @@ %% calculate tps coeff in each subdomain for isub=1:NbSubDomain + isub SubRange(1,:,isub)=[CentreX(isub)-0.55*Siz(1) CentreX(isub)+0.55*Siz(1)];%bounds of subdomain #isub in x coordinate SubRange(2,:,isub)=[CentreY(isub)-0.55*Siz(2) CentreY(isub)+0.55*Siz(2)];%bounds of subdomain #isub in y coordinate @@ -87,4 +88,5 @@ ind_sel_previous=ind_sel;% record the set of selected vector indices for next iteration ind_sel=find(Coord(:,1)>=SubRange(1,1,isub) & Coord(:,1)<=SubRange(1,2,isub) & Coord(:,2)>=SubRange(2,1,isub) & Coord(:,2)<=SubRange(2,2,isub)); + numel(ind_sel) % if no vector in the subdomain #isub, skip the subdomain if isempty(ind_sel) Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 1058) +++ /trunk/src/geometry_calib.m (revision 1059) @@ -52,5 +52,5 @@ % Edit the above text to modify the response to help geometry_calib -% Last Modified by GUIDE v2.5 16-Apr-2015 17:29:02 +% Last Modified by GUIDE v2.5 20-Sep-2018 19:04:30 % Begin initialization code - DO NOT edit @@ -108,5 +108,5 @@ set(handles.calib_type,'Position',[1 Height-40 194 30])% rank 1 set(handles.APPLY,'Position',[197 Height-40 110 30])% rank 1 -set(handles.REPLICATE,'Position',[309 Height-40 110 30])% rank 1 +set(handles.Replicate,'Position',[309 Height-40 110 30])% rank 1 set(handles.Intrinsic,'Position',[1 Height-40-2-92 418 92])% rank 2 set(handles.Extrinsic,'Position',[1 Height-40-4-92-75 418 75])% rank 3 @@ -167,234 +167,239 @@ %------------------------------------------------------------------------ % --- Executes on button press APPLY (used to launch the calibration). -function APPLY_Callback(hObject, eventdata, handles) + function APPLY_Callback(hObject, eventdata, handles) + set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) + + %------------------------------------------------------------------------ + %% look for the GUI uvmat and check for an image as input + set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation + huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat + hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat + if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') + msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') + return + end + + RootPath=''; + if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile) + RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image + SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$',''); + outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image + else + question={'save the calibration data and point coordinates in'}; + def={fullfile(RootPath,'ObjectCalib.xml')}; + options.Resize='on'; + answer=inputdlg(question,'',1,def,options); + outputfile=answer{1}; + end + + %% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image + Coord=get(handles.ListCoord,'Data'); + + + %% read the type of calibration + calib_cell=get(handles.calib_type,'String'); + val=get(handles.calib_type,'Value'); + CalibFcn=['calib_' calib_cell{val}]; + + %% read the intrinsic parameters + Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String')); + Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String')); + Intrinsic.coord_files=get(handles.ListCoordFiles,'String'); + Intrinsic.fx=str2num(get(handles.fx,'String')); + Intrinsic.fy=str2num(get(handles.fy,'String')); + Intrinsic.kc=str2num(get(handles.kc,'String')); + Intrinsic.Cx=str2num(get(handles.Cx,'String')); + Intrinsic.Cy=str2num(get(handles.Cy,'String')); + if isempty(Intrinsic.kc) + Intrinsic.kc=0; + end + if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy) + Intrinsic.Cx=Intrinsic.Npx/2; + Intrinsic.Cy=Intrinsic.Npy/2; + end + + %% apply to cropped images if requested + if get(handles.Replicate,'Value') + answer=msgbox_uvmat('INPUT_Y-N','apply to full images (not cropped)?'); + if strcmp(answer,'No') + prompt = {'npy_lower'}; + dlg_title = 'remove image the npy_lower image lines (removal of the upper line does not change calibration)'; + num_lines= 1; + def = {'0'}; + answer = inputdlg(prompt,dlg_title,num_lines,def); + npy_crop=str2num(answer{1}); + Intrinsic.Npy=Intrinsic.Npy-npy_crop; %size of the filtering window + Coord(:,5)=Coord(:,5)-npy_crop;% shift the image ordinates of the calibration points by removing the lower band + end + end + + %% Apply calibration + [GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration + + %% record the coordinate unit + unitlist=get(handles.CoordUnit,'String'); + unit=unitlist{get(handles.CoordUnit,'value')}; + GeometryCalib.CoordUnit=unit; + + %% record the coordinates of the calibration points + GeometryCalib.SourceCalib.PointCoord=Coord; + + %% display calibration results on the GUI geometry_calib + display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters + display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters + % (rotation and translation of camera with respect to the phys coordinates) + + %% set the defqult plane and display the calibration data errors for validation + answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... + ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... + ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']; + [num2str(numel(ind_removed)) ' points removed']}); + if strcmp(answer,'Yes') %store the calibration data + if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration + answer=msgbox_uvmat('INPUT_Y-N',{['Assume that the current image is in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be later modified by MenuSetSlice in the upper bar menu of uvmat'}); + SliceCoord_ref=Z_plane'*[0 0 1]; + end + else + GeometryCalib=[]; + index=1; + end + + if ~isempty(GeometryCalib) % if calibration is not cancelled + if get(handles.Replicate,'Value') + %% open the GUI browse_data + hbrowse=findobj(allchild(0),'Tag','browse_data'); + if ~isempty(hbrowse) + BrowseHandles=guidata(hbrowse); + SourceDir=get(BrowseHandles.SourceDir,'String'); + ListExperiments=get(BrowseHandles.ListExperiments,'String'); + ListValues=get(BrowseHandles.ListExperiments,'Value'); + ListExperiments=ListExperiments(ListValues); + ListDevices=get(BrowseHandles.ListDevices,'String'); + Val=get(BrowseHandles.ListDevices,'Value'); + DataFolder=ListDevices{Val}; + nbcalib=0; + for ilist=1:numel(ListExperiments) + SubDirBase=regexprep(DataFolder,'+/',''); + ListExperiments{ilist}=regexprep(ListExperiments{ilist},'+/',''); + XmlName=fullfile(SourceDir,ListExperiments{ilist},[SubDirBase '.xml']); + % copy the xml file from the old location if appropriate, then update with the calibration parameters + % if ~exist(XmlName,'file') && ~isempty(SubDirBase) + % oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']); + GeometryCalib.SliceCoord=SliceCoord_ref;%default input + if exist(XmlName,'file') + %[success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention + dispmesGeometryCalib=UvData.XmlData{1}.GeometryCalib; + else + msgbox_uvmat('ERROR','3D geometric calibration needed before defining slices') + return + end + SliceCoord=GeometryCalib.SliceCoord; + InterfaceCoord=min(SliceCoord(:,3)); + if isfield(GeometryCalib,'InterfaceCoord') + InterfaceCoord=GeometryCalib.InterfaceCoord(1,3); + end + NbSlice=size(SliceCoord,1); + CheckVolumeScan=0; + if isfield(GeometryCalib,'CheckVolumeScan') + CheckVolumeScan=GeometryCalib.CheckVolumeScan; + end + RefractionIndex=1.33; + CheckRefraction=0;% default value of the check box refraction + if isfield(GeometryCalib,'RefractionIndex') + RefractionIndex=GeometryCalib.RefractionIndex; + CheckRefraction=1; + end + SliceAngle=[0 0 0]; + if isfield(GeometryCalib,'SliceAngle') + SliceAngle=GeometryCalib.SliceAngle; + end + dispmessage=' updated with calibration parameters'; + % if ~strcmp(answer,'yes') + [XmlDataOld,warntext]=imadoc2struct(XmlName); + if isfield(XmlDataOld,'GeometryCalib') + if isfield(XmlDataOld.GeometryCalib,'SliceAngle') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.SliceAngle; + end + if isfield(XmlDataOld.GeometryCalib,'CheckRefraction') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.CheckRefraction; + end + if isfield(XmlDataOld.GeometryCalib,'RefractionIndex') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.RefractionIndex; + end + if isfield(XmlDataOld.GeometryCalib,'InterfaceCoord') + GeometryCalib.SliceAngle=XmlDataOld.GeometryCalib.InterfaceCoord; + end + end + + end + + else + dispmessage=' created with calibration parameters'; + end + errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file + if ~strcmp(errormsg,'') + msgbox_uvmat('ERROR',errormsg); + else + display([XmlName dispmessage]) + nbcalib=nbcalib+1; + end + end + + end + msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']); + else + + %% copy the xml file from the old location if appropriate, then update with the calibration parameters + if ~exist(outputfile,'file') && ~isempty(SubDirBase) + oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml']; + if exist(oldxml,'file') + [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention + end + end + errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file + if ~strcmp(errormsg,'') + msgbox_uvmat('ERROR',errormsg); + end + + %% display image with new calibration in the currently opened uvmat interface + FieldList=get(hhuvmat.FieldName,'String'); + val=get(hhuvmat.FieldName,'Value'); + if strcmp(FieldList{val},'image') + set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image + UserData=get(handles.geometry_calib,'UserData'); + UserData.XmlInputFile=outputfile;%save the current xml file name + set(handles.geometry_calib,'UserData',UserData) + uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates + PLOT_Callback(hObject, eventdata, handles) + set(handles.CoordLine,'string',num2str(index)) + Coord=get(handles.ListCoord,'Data'); + update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration + figure(handles.geometry_calib)% put the GUI geometry_calib in front + else + msgbox_uvmat('WARNING','open the image to see the effect of the new calibration') + end + end + end + set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color + +%------------------------------------------------------------------------ +% --- Executes on button press in Replicate +function Replicate_Callback(hObject, eventdata, handles) +% %------------------------------------------------------------------------ set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) -%------------------------------------------------------------------------ -%% look for the GUI uvmat and check for an image as input -set(handles.APPLY,'BackgroundColor',[1 1 0])% paint APPLY button in yellow to show activation -huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat -hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat -if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') - msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') - return -end - -RootPath=''; -if ~isempty(hhuvmat.RootPath)&& ~isempty(hhuvmat.RootFile) - RootPath=get(hhuvmat.RootPath,'String');% path to the currently displayed image - SubDirBase=regexprep(get(hhuvmat.SubDir,'String'),'\..+$',''); - outputfile=[fullfile(RootPath,SubDirBase) '.xml'];%xml file associated with the currently displayed image +if get(handles.Replicate,'Value') %open the GUI browse_data + % look for the GUI uvmat and check for an image as input + huvmat=findobj(allchild(0),'Name','uvmat'); + hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat + RootPath=get(hhuvmat.RootPath,'String'); + SubDir=get(hhuvmat.SubDir,'String'); + browse_data(fullfile(RootPath,SubDir)) else - question={'save the calibration data and point coordinates in'}; - def={fullfile(RootPath,'ObjectCalib.xml')}; - options.Resize='on'; - answer=inputdlg(question,'',1,def,options); - outputfile=answer{1}; -end - -%% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image -Coord=get(handles.ListCoord,'Data'); - - -%% read the type of calibration -calib_cell=get(handles.calib_type,'String'); -val=get(handles.calib_type,'Value'); -CalibFcn=['calib_' calib_cell{val}]; - -%% read the intrinsic parameters -Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String')); -Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String')); -Intrinsic.coord_files=get(handles.ListCoordFiles,'String'); -Intrinsic.fx=str2num(get(handles.fx,'String')); -Intrinsic.fy=str2num(get(handles.fy,'String')); -Intrinsic.kc=str2num(get(handles.kc,'String')); -Intrinsic.Cx=str2num(get(handles.Cx,'String')); -Intrinsic.Cy=str2num(get(handles.Cy,'String')); -if isempty(Intrinsic.kc) - Intrinsic.kc=0; -end -if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy) - Intrinsic.Cx=Intrinsic.Npx/2; - Intrinsic.Cy=Intrinsic.Npy/2; -end - -%% Apply calibration -[GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration - -%% record the coordinate unit -unitlist=get(handles.CoordUnit,'String'); -unit=unitlist{get(handles.CoordUnit,'value')}; -GeometryCalib.CoordUnit=unit; - -%% record the coordinates of the calibration points -GeometryCalib.SourceCalib.PointCoord=Coord; - -%% display calibration results on the GUI geometry_calib -display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters -display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters -% (rotation and translation of camera with respect to the phys coordinates) - -%% store the calibration data, by default in the xml file of the currently displayed image -answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... - ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... - ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']; - [num2str(numel(ind_removed)) ' points removed']}); -if strcmp(answer,'Yes') %store the calibration data - if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration - msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'}) - GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; - end -else - GeometryCalib=[]; - index=1; -end - -if isempty(GeometryCalib) % if calibration cancelled - set(handles.APPLY,'BackgroundColor',[1 0 1]) -else % if calibration confirmed - - %% copy the xml file from the old location if appropriate, then update with the calibration parameters - if ~exist(outputfile,'file') && ~isempty(SubDirBase) - oldxml=[fullfile(RootPath,SubDirBase,get(hhuvmat.RootFile,'String')) '.xml']; - if exist(oldxml,'file') - [success,message]=copyfile(oldxml,outputfile);%copy the old xml file to a new one with the new convention - end - end - errormsg=update_imadoc(GeometryCalib,outputfile,'GeometryCalib');% introduce the calibration data in the xml file - if ~strcmp(errormsg,'') - msgbox_uvmat('ERROR',errormsg); - end - - %% display image with new calibration in the currently opened uvmat interface - FieldList=get(hhuvmat.FieldName,'String'); - val=get(hhuvmat.FieldName,'Value'); - if strcmp(FieldList{val},'image') - set(hhuvmat.CheckFixLimits,'Value',0)% put FixedLimits option to 'off' to plot the whole image - UserData=get(handles.geometry_calib,'UserData'); - UserData.XmlInputFile=outputfile;%save the current xml file name - set(handles.geometry_calib,'UserData',UserData) - uvmat('InputFileREFRESH_Callback',hObject,eventdata,hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates - PLOT_Callback(hObject, eventdata, handles) - set(handles.CoordLine,'string',num2str(index)) - Coord=get(handles.ListCoord,'Data'); - update_calib_marker(Coord(index,:)); %indicate the point with max deviations from phys coord to calibration - figure(handles.geometry_calib)% put the GUI geometry_calib in front - set(handles.APPLY,'BackgroundColor',[1 0 0]) % set APPLY button to red color - else - msgbox_uvmat('WARNING','open the image to see the effect of the new calibration') - end -end - -%------------------------------------------------------------------------ -% --- Executes on button press in REPLICATE -function REPLICATE_Callback(hObject, eventdata, handles) -%------------------------------------------------------------------------ -set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) - -%% look for the GUI uvmat and check for an image as input -huvmat=findobj(allchild(0),'Name','uvmat'); -hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat - -%% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image -Coord=get(handles.ListCoord,'Data'); - -%% read the type of calibration -calib_cell=get(handles.calib_type,'String'); -val=get(handles.calib_type,'Value'); -CalibFcn=['calib_' calib_cell{val}]; - -%% read the intrinsic parameters -Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String')); -Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String')); -Intrinsic.coord_files=get(handles.ListCoordFiles,'String'); -Intrinsic.fx=str2num(get(handles.fx,'String')); -Intrinsic.fy=str2num(get(handles.fy,'String')); -Intrinsic.kc=str2num(get(handles.kc,'String')); -Intrinsic.Cx=str2num(get(handles.Cx,'String')); -Intrinsic.Cy=str2num(get(handles.Cy,'String')); -if isempty(Intrinsic.kc) - Intrinsic.kc=0; -end -if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy) - Intrinsic.Cx=Intrinsic.Npx/2; - Intrinsic.Cy=Intrinsic.Npy/2; -end - -%% apply to cropped images if requested -answer=msgbox_uvmat('INPUT_Y-N','apply to cropped images?'); -if strcmp(answer,'Yes') - prompt = {'npy_lower'}; - dlg_title = 'remove image the npy_lower image lines (removal of the upper linedoes not change calibration)'; - num_lines= 1; - def = {'0'}; - answer = inputdlg(prompt,dlg_title,num_lines,def); - npy_crop=str2num(answer{1}); - Intrinsic.Npy=Intrinsic.Npy-npy_crop; %size of the filtering window - Coord(:,5)=Coord(:,5)-npy_crop;% shift the image ordinates of the calibration points by removing the lower band -end - -%% Apply calibration -[GeometryCalib,index,ind_removed,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration - - -%% record the coordinate unit -unitlist=get(handles.CoordUnit,'String'); -unit=unitlist{get(handles.CoordUnit,'value')}; -GeometryCalib.CoordUnit=unit; - -%% record the coordinates of the calibration points -GeometryCalib.SourceCalib.PointCoord=Coord; - -%% display calibration results on the GUI geometry_calib -display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters -display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters -% (rotation and translation of camera with respect to the phys coordinates) - -%% store the calibration data, by default in the xml file of the currently displayed image -answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... - ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... - ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels'];... - [num2str(numel(ind_removed)) ' points removed']}); -if strcmp(answer,'Yes') %store the calibration data - if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration - msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'}) - GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; - end -else - GeometryCalib=[]; - index=1; -end - -%% open the GUI browse_data -CalibData=get(handles.geometry_calib,'UserData');%read the calibration image source on the interface userdata -if isfield(CalibData,'XmlInputFile') - InputDir=fileparts(fileparts(CalibData.XmlInputFile)); -end -DataSeries=uigetfile_uvmat('open a folder of images to calibrate',InputDir,'uigetdir'); -%SubProject=uigetfile_uvmat('open folder of subproject to calibrate',InputDir,'uigetdir'); -OutPut=browse_data(DataSeries); -nbcalib=0; -for ilist=1:numel(OutPut.Experiment) - SubDirBase=regexprep(OutPut.DataSeries{1},'\..+$',''); - XmlName=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']); - dispmessage=' created with calibration parameters'; - % copy the xml file from the old location if appropriate, then update with the calibration parameters - if ~exist(XmlName,'file') && ~isempty(SubDirBase) - oldxml=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},SubDirBase,[get(hhuvmat.RootFile,'String') '.xml']); - if exist(oldxml,'file') - [success,message]=copyfile(oldxml,XmlName);%copy the old xml file to a new one with the new convention - dispmessage=' updated with calibration parameters'; - end - end - errormsg=update_imadoc(GeometryCalib,XmlName,'GeometryCalib');% introduce the calibration data in the xml file - if ~strcmp(errormsg,'') - msgbox_uvmat('ERROR',errormsg); - else - display([XmlName dispmessage]) - nbcalib=nbcalib+1; - end -end -msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated for ' num2str(nbcalib) ' experiments']); - + hbrowse=findobj(allchild(0),'Tag','browse_data'); + if ~isempty(hbrowse) + delete(hbrowse) + end +end %------------------------------------------------------------------------ % --- activate calibration and store parameters in ouputfile . Index: /trunk/src/phys_XYZ.m =================================================================== --- /trunk/src/phys_XYZ.m (revision 1058) +++ /trunk/src/phys_XYZ.m (revision 1059) @@ -30,5 +30,5 @@ testangle=0; test_refraction=0; -if exist('Zindex','var')&& isequal(Zindex,round(Zindex))&& Zindex>0 && isfield(Calib,'SliceCoord')&&length(Calib.SliceCoord)>=Zindex +if exist('Zindex','var')&& isequal(Zindex,round(Zindex))&& Zindex>0 && isfield(Calib,'SliceCoord')&&size(Calib.SliceCoord,1)>=Zindex if isfield(Calib, 'SliceAngle') && ~isequal(Calib.SliceAngle,[0 0 0]) && ~isequal(Calib.SliceAngle(Zindex,:),[0 0 0]) testangle=1; @@ -43,5 +43,5 @@ % Z0=norm_plane*Calib.SliceCoord(Zindex,:)'/norm_plane(3); end - Z0=Calib.SliceCoord(Zindex,3);%horizontal plane z=cte + Z0=Calib.SliceCoord(Zindex,3);%horizontal plane z=cte % end Z0virt=Z0; Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1058) +++ /trunk/src/series.m (revision 1059) @@ -1,5 +1,2 @@ - - - %'series': master function associated to the GUI series.m for analysis field series %------------------------------------------------------------------------ @@ -212,9 +209,9 @@ end %get the list of previous campaigns in the upper bar menu Open campaign - if isfield(h,'MenuCampaign') - for ifile=1:min(length(h.MenuCampaign),5) - set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile}); - end - end +% if isfield(h,'MenuCampaign') +% for ifile=1:min(length(h.MenuCampaign),5) +% set(handles.(['MenuCampaign_' num2str(ifile)]),'Label',h.MenuCampaign{ifile}); +% end +% end %get the menu of actions if isfield(h,'ActionListUser') && iscell(h.ActionListUser) && isfield(h,'ActionPathListUser') && iscell(h.ActionPathListUser) @@ -498,86 +495,86 @@ end end - -OutPut=browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device -NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries); -icount=0; -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 +InputTable{1,1}='...'; set(handles.InputTable,'Data',InputTable) -REFRESH_Callback(hObject, eventdata, handles) +browse_data(oldfile,'on','on'); % open the GUI browse_data to get select a campaign dir, experiment and device +% NbLines=numel(OutPut.Experiment)*numel(OutPut.DataSeries); +% icount=0; +% 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 +%REFRESH_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- -function MenuCampaign_Callback(hObject, eventdata, handles) -% -------------------------------------------------------------------- - -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 -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) +% function MenuCampaign_Callback(hObject, eventdata, handles) +% % -------------------------------------------------------------------- +% +% 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 +% 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) @@ -742,9 +739,9 @@ %% enable other menus and uicontrols % set(handles.MenuOpenCampaign,'Enable','on') -set(handles.MenuCampaign_1,'Enable','on') -set(handles.MenuCampaign_2,'Enable','on') -set(handles.MenuCampaign_3,'Enable','on') -set(handles.MenuCampaign_4,'Enable','on') -set(handles.MenuCampaign_5,'Enable','on') +% set(handles.MenuCampaign_1,'Enable','on') +% set(handles.MenuCampaign_2,'Enable','on') +% set(handles.MenuCampaign_3,'Enable','on') +% set(handles.MenuCampaign_4,'Enable','on') +% set(handles.MenuCampaign_5,'Enable','on') set(handles.RUN, 'Enable','On') set(handles.RUN,'BackgroundColor',[1 0 0])% set RUN button to red @@ -1594,523 +1591,554 @@ end -%% create the output data directory if needed -OutputDir=''; -if isfield(Param,'OutputSubDir') - SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt]; - SubDirOutNew=SubDirOut; - detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if the dir already exist - check_create=1; % need to create the result directory by default - CheckOverwrite=1; - if isfield(Param,'CheckOverwrite') - CheckOverwrite=Param.CheckOverwrite; - end - while detect - if CheckOverwrite - comment=', possibly overwrite previous data'; +%% Look for prcessing on multiple experiments set by the GUI browse_data +NbExp=1; +ListExp=Param.InputTable(1,1); + +if get(handles.Replicate,'Value') + hh=findobj(allchild(0),'Tag','browse_data'); + BrowseData=guidata(hh); + SourceDir=get(BrowseData.SourceDir,'String'); + ListExp=get(BrowseData.ListExperiments,'String'); + ListExp=ListExp(get(BrowseData.ListExperiments,'Value')); + NbExp=numel(ListExp) % number of experiments set possibly by the GUI browse_data, =1 otherwise + for ilist=1:NbExp + ListExp{ilist}=regexprep(ListExp{ilist},'+',''); + ListExp{ilist}= [SourceDir ListExp{ilist}]; + end +end + +%%%%%%%%%%%%%%%%%%% LOOP ON EXPERIMENTS POSSIBLY SET BY THE GUI browse_data, NbExp=1 otherwise %%%%%%%%% +for iexp=1:NbExp + Param.InputTable{1,1}=ListExp{iexp}; + set(handles.InputTable,'Data',Param.InputTable) + [xx,ExpName]=fileparts(ListExp{iexp}); + Param.IndexRange.first_i=str2num(get(handles.num_first_i,'String'));%reset the firrst_i and last_i for multiple experiments, modified by the splitting into NbProcess + Param.IndexRange.last_i=str2num(get(handles.num_last_i,'String')); + %% create the output data directory if needed + OutputDir=''; + answer=''; + if isfield(Param,'OutputSubDir') + SubDirOut=[get(handles.OutputSubDir,'String') Param.OutputDirExt]; + SubDirOutNew=SubDirOut; + detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if the dir already exist + check_create=1; % need to create the result directory by default + CheckOverwrite=1; + if isfield(Param,'CheckOverwrite') + CheckOverwrite=Param.CheckOverwrite; + end + while detect + if CheckOverwrite + comment=', possibly overwrite previous data'; + else + comment=', will complement existing result files (no overwriting)'; + end + answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]); + if strcmp(answer,'Cancel') + break + elseif strcmp(answer,'Yes') + detect=0; + check_create=0; + else + r=regexp(SubDirOutNew,'(?.*\D)(?\d+)$','names'); % detect whether name ends by a number + if isempty(r) + r(1).root=[SubDirOutNew '_']; + r(1).num1='0'; + end + SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1 + detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if the dir already exists + check_create=1; + end + end + if strcmp(answer,'Cancel') + continue + end + Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,''); + Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output + set(handles.OutputDirExt,'String',Param.OutputDirExt) + OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory + if check_create % create output directory if it does not exist + [tild,msg1]=mkdir(OutputDir); + if ~strcmp(msg1,'') + errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation + return + end + end + + elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir + OutputDir=Param.ActionInput.LogPath; + end + DirXml=fullfile(OutputDir,'0_XML'); + if ~exist(DirXml,'dir') + [~,msg1]=mkdir(DirXml); + if ~strcmp(msg1,'') + errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation + return + end + end + OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files + + %% get the set of reference input field indices + first_i=1; % first i index to process + last_i=1; % last i index to process + incr_i=1; % increment step in i index + first_j=1; % first j index to process + last_j=1; % last j index to process + incr_j=1; % increment step in j index + if isfield(Param.IndexRange,'first_i') + first_i=Param.IndexRange.first_i; + incr_i=Param.IndexRange.incr_i; + last_i=Param.IndexRange.last_i; + end + if isfield(Param.IndexRange,'incr_j') + first_j=Param.IndexRange.first_j; + last_j=Param.IndexRange.last_j; + incr_j=Param.IndexRange.incr_j; + end + if last_i < first_i || last_j < first_j + errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one'; + return + end + %incr_i must be defined, =1 by default, if NbSlice is active + if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice) + incr_i=1; + set(handles.num_incr_i,'String','1') + end + % case of no increment i defined: processing is done on the available files found in i1_series + if isempty(incr_i) + if isempty(incr_j) + [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); + ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); + ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); + ref_j=ref_j-1; + ref_i=ref_i-1; else - comment=', will complement existing result files (no overwriting)'; - end - answer=msgbox_uvmat('INPUT_Y-N-Cancel',['use existing ouput directory: ' fullfile(Param.InputTable{1,1},SubDirOutNew) comment]); - if strcmp(answer,'Cancel') + ref_j=first_j:incr_j:last_j; + [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); + ref_i=ref_i-1; + ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); + end + % increment i is defined: processing is done on first_i:incr_i:last_i; + else + ref_i=first_i:incr_i:last_i; + if isempty(incr_j)% automatic finding of the existing j indices + [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); + ref_j=ref_j-1; + ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); + else + ref_j=first_j:incr_j:last_j; + end + end + CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default + if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) + CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j + end + nbfield_j=numel(ref_j); % number of j indices + BlockLength=numel(ref_i); % by default, job involves the full set of i field indices + NbProcess=1; + switch RunMode + case 'cluster' + JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax; + JobCPUTimeAdvised=SeriesData.SeriesParam.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. + BlockLength=max(BlockLength,ceil(numel(ref_i)*NbExp/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs + NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar + else + NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes + end + NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes + otherwise + if ~isempty(Param.IndexRange.NbSlice) + NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes + end + end + + %% record nbre of output files and starting time for computation for status + StatusData=get(handles.status,'UserData'); + if isfield(StatusData,'OutputFileMode') + switch StatusData.OutputFileMode + case 'NbInput' + StatusData.NbOutputFile=numel(ref_i)*nbfield_j; + case 'NbInput_i' + StatusData.NbOutputFile=numel(ref_i); + case 'NbSlice' + StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String')); + end + end + StatusData.TimeStart=now; + set(handles.status,'UserData',StatusData) + + %% case of a function in Python + if strcmp(ActionExt, '.py (in dev.)') + fprintf([ + '\n' ... + '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ... + 'The option .py is used. It is still in development.\n' ... + 'To try it, first install pyper and the most recent version of fluidimage\n' ... + '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ... + 'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ... + '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n']) + RunMode = 'python'; + end + + + %% direct processing on the current Matlab session or creation of command files + filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters + extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process + for iprocess=1:NbProcess + extxml{iprocess}='.xml'; + end + for iprocess=1:NbProcess + if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action + disp('program stopped by user') return - elseif strcmp(answer,'Yes') - detect=0; - check_create=0; - else - r=regexp(SubDirOutNew,'(?.*\D)(?\d+)$','names'); % detect whether name ends by a number - if isempty(r) - r(1).root=[SubDirOutNew '_']; - r(1).num1='0'; - end - SubDirOutNew=[r(1).root num2str(str2num(r(1).num1)+1)]; % increment the index by 1 or put 1 - detect=exist(fullfile(Param.InputTable{1,1},SubDirOutNew),'dir'); % test if the dir already exists - check_create=1; - end - end - Param.OutputDirExt=regexprep(SubDirOutNew,Param.OutputSubDir,''); - Param.OutputRootFile=Param.InputTable{1,3}; % the first sorted RootFile taken for output - set(handles.OutputDirExt,'String',Param.OutputDirExt) - OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); % full name (with path) of output directory - if check_create % create output directory if it does not exist - [tild,msg1]=mkdir(OutputDir); - if ~strcmp(msg1,'') - errormsg=['cannot create ' OutputDir ': ' msg1]; % error message for directory creation - return + end + if isempty(Param.IndexRange.NbSlice) + Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; + if Param.IndexRange.first_i>last_i + NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation + break + end + Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); + else %multislices (then incr_i is not empty) + Param.IndexRange.first_i= first_i+iprocess-1; + Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; + end + for ilist=1:size(Param.InputTable,1) + Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system + end + + if isfield(Param,'OutputSubDir') + t=struct2xml(Param); + t=set(t,1,'name','Series'); + extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,... + Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); + filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess}); + try + save(t, filexml{iprocess}); % save the xml file containing the processing parameters + catch ME + if ~strcmp (RunMode,'local') + errormsg=['error writting ' filexml{iprocess} ': ' ME.message]; + return + end + end + end + if strcmp (RunMode,'local') + switch ActionExt + case '.m' + h_fun(Param); % direct launching + + case '.sh' + switch computer + case {'PCWIN','PCWIN64'} %Windows system + filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters + system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system + case {'GLNX86','GLNXA64','MACI64'}%Linux system + system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); + end + end end end -elseif isfield(Param,'ActionInput')&&isfield(Param.ActionInput,'LogPath')% custom definition of the output dir - OutputDir=Param.ActionInput.LogPath; -end -DirXml=fullfile(OutputDir,'0_XML'); -if ~exist(DirXml,'dir') - [~,msg1]=mkdir(DirXml); - if ~strcmp(msg1,'') - errormsg=['cannot create ' DirXml ': ' msg1]; % error message for directory creation - return - end -end -OutputNomType=nomtype2pair(Param.InputTable{1,4}); % nomenclature for output files - -%% get the set of reference input field indices -first_i=1; % first i index to process -last_i=1; % last i index to process -incr_i=1; % increment step in i index -first_j=1; % first j index to process -last_j=1; % last j index to process -incr_j=1; % increment step in j index -if isfield(Param.IndexRange,'first_i') - first_i=Param.IndexRange.first_i; - incr_i=Param.IndexRange.incr_i; - last_i=Param.IndexRange.last_i; -end -if isfield(Param.IndexRange,'incr_j') - first_j=Param.IndexRange.first_j; - last_j=Param.IndexRange.last_j; - incr_j=Param.IndexRange.incr_j; -end -if last_i < first_i || last_j < first_j - errormsg= 'series/Run_Callback:last field index must be larger or equal to the first one'; - return -end -%incr_i must be defined, =1 by default, if NbSlice is active -if isempty(incr_i)&& ~isempty(Param.IndexRange.NbSlice) - incr_i=1; - set(handles.num_incr_i,'String','1') -end -% case of no increment i defined: processing is done on the available files found in i1_series -if isempty(incr_i) - if isempty(incr_j) - [ref_j,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); - ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); - ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); - ref_j=ref_j-1; - ref_i=ref_i-1; - else - ref_j=first_j:incr_j:last_j; - [tild,ref_i]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); - ref_i=ref_i-1; - ref_i=ref_i(ref_i>=first_i & ref_i<=last_i); - end - % increment i is defined: processing is done on first_i:incr_i:last_i; -else - ref_i=first_i:incr_i:last_i; - if isempty(incr_j)% automatic finding of the existing j indices - [ref_j,tild]=find(squeeze(SeriesData.i1_series{1}(1,:,:))); - ref_j=ref_j-1; - ref_j=ref_j(ref_j>=first_j & ref_j<=last_j); - else - ref_j=first_j:incr_j:last_j; - end -end -CPUTime=1; % job time estimated at 1 min per iteration (on index i and j) by default -if isfield(Param.Action, 'CPUTime') && ~isempty(Param.Action.CPUTime) - CPUTime=Param.Action.CPUTime; % Note: CpUTime for one iteration ref_i has to be multiplied by the number of j indices nbfield_j -end -nbfield_j=numel(ref_j); % number of j indices -BlockLength=numel(ref_i); % by default, job involves the full set of i field indices -NbProcess=1; -switch RunMode - case 'cluster' - JobNumberMax=SeriesData.SeriesParam.ClusterParam.JobNumberMax; - JobCPUTimeAdvised=SeriesData.SeriesParam.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 MinJobNumber. - BlockLength=max(BlockLength,ceil(numel(ref_i)/JobNumberMax)); % possibly increase the BlockLength to have less than MaxJobNumber jobs - NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar - else - NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes - end - NbCore=min(NbCore,NbProcess); % reduces the number of cores if it exceeds the number of processes - otherwise - if ~isempty(Param.IndexRange.NbSlice) - NbProcess=Param.IndexRange.NbSlice; % the parameter NbSlice sets the nbre of run processes - end -end - -%% record nbre of output files and starting time for computation for status -StatusData=get(handles.status,'UserData'); -if isfield(StatusData,'OutputFileMode') - switch StatusData.OutputFileMode - case 'NbInput' - StatusData.NbOutputFile=numel(ref_i)*nbfield_j; - case 'NbInput_i' - StatusData.NbOutputFile=numel(ref_i); - case 'NbSlice' - StatusData.NbOutputFile=str2num(get(handles.num_NbSlice,'String')); - end -end -StatusData.TimeStart=now; -set(handles.status,'UserData',StatusData) - -%% case of a function in Python -if strcmp(ActionExt, '.py (in dev.)') - fprintf([ - '\n' ... - '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n' ... - 'The option .py is used. It is still in development.\n' ... - 'To try it, first install pyper and the most recent version of fluidimage\n' ... - '(see https://bitbucket.org/fluiddyn/fluidimage).\n' ... - 'Warning: there is no direct correspondance between UVMAT and fluidimage parameters\n' ... - '!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n']) - RunMode = 'python'; -end - - -%% direct processing on the current Matlab session or creation of command files -filexml=cell(1,NbProcess); % initialisation of the names of the files containing the processing parameters -extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process -for iprocess=1:NbProcess - extxml{iprocess}='.xml'; -end -for iprocess=1:NbProcess - if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action - disp('program stopped by user') - return - end - if isempty(Param.IndexRange.NbSlice) - Param.IndexRange.first_i=first_i+(iprocess-1)*BlockLength*incr_i; - if Param.IndexRange.first_i>last_i - NbProcess=iprocess-1; % leave the loop, we are at the end of the calculation - break - end - Param.IndexRange.last_i=min(last_i,first_i+(iprocess)*BlockLength*incr_i-1); - else %multislices (then incr_i is not empty) - Param.IndexRange.first_i= first_i+iprocess-1; - Param.IndexRange.incr_i=incr_i*Param.IndexRange.NbSlice; - end - for ilist=1:size(Param.InputTable,1) - Param.InputTable{ilist,1}=regexprep(Param.InputTable{ilist,1},'\','/'); % correct path name for PCWIN system + if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python') + %% processing on a different session of the same computer (background) or cluster, create executable files + batch_file_list=cell(NbProcess,1); % initiate the list of executable files + DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files + switch computer + case {'PCWIN','PCWIN64'} %Windows system + ExeExt='.bat'; + case {'GLNX86','GLNXA64','MACI64'}%Linux system + ExeExt='.sh'; + end + %create subdirectory for executable files + if ~exist(DirExe,'dir') + [tild,msg1]=mkdir(DirExe); + if ~strcmp(msg1,'') + errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation + return + end + end + %create subdirectory for log files + DirLog=fullfile(OutputDir,'0_LOG'); + if ~exist(DirLog,'dir') + [tild,msg1]=mkdir(DirLog); + if ~strcmp(msg1,'') + errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation + return + end + end + + %create the executable file + file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,... + first_i,last_i,first_j,last_j); + file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global); + filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,... + first_i,last_i,first_j,last_j); + filelog_global=fullfile(OutputDir,'0_LOG',filelog_global); + + for iprocess=1:NbProcess + %create the executable file + batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt)); + + % set the log file name + filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log')); + end end - if isfield(Param,'OutputSubDir') - t=struct2xml(Param); - t=set(t,1,'name','Series'); - extxml{iprocess}=fullfile_uvmat('','',Param.InputTable{1,3},'.xml',OutputNomType,... - Param.IndexRange.first_i,Param.IndexRange.last_i,first_j,last_j); - filexml{iprocess}=fullfile(OutputDir,'0_XML',extxml{iprocess}); - try - save(t, filexml{iprocess}); % save the xml file containing the processing parameters - catch ME - if ~strcmp (RunMode,'local') - errormsg=['error writting ' filexml{iprocess} ': ' ME.message]; + %% launch the executable files for background or cluster processing + + switch RunMode + + case 'background' + [fid,message]=fopen(file_exe_global,'w'); + if isequal(fid,-1) + errormsg=['creation of ' file_exe_global ':' message]; return end - end - end - if strcmp (RunMode,'local') - switch ActionExt - case '.m' - h_fun(Param); % direct launching - - case '.sh' - switch computer - case {'PCWIN','PCWIN64'} %Windows system - filexml=regexprep(filexml,'\\','\\\\'); % add '\' so that '\' are left as characters - system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); % TODO: adapt to DOS system - case {'GLNX86','GLNXA64','MACI64'}%Linux system - system([ActionFullName ' ' RunTime ' ' filexml{iprocess}]); - end - end - end -end - -if ~strcmp (RunMode,'local') && ~strcmp(RunMode,'python') - %% processing on a different session of the same computer (background) or cluster, create executable files - batch_file_list=cell(NbProcess,1); % initiate the list of executable files - DirExe=fullfile(OutputDir,'0_EXE'); % directory name for executable files - switch computer - case {'PCWIN','PCWIN64'} %Windows system - ExeExt='.bat'; - case {'GLNX86','GLNXA64','MACI64'}%Linux system - ExeExt='.sh'; - end - %create subdirectory for executable files - if ~exist(DirExe,'dir') - [tild,msg1]=mkdir(DirExe); - if ~strcmp(msg1,'') - errormsg=['cannot create ' DirExe ': ' msg1]; % error message for directory creation - return - end - end - %create subdirectory for log files - DirLog=fullfile(OutputDir,'0_LOG'); - if ~exist(DirLog,'dir') - [tild,msg1]=mkdir(DirLog); - if ~strcmp(msg1,'') - errormsg=['cannot create ' DirLog ': ' msg1]; % error message for directory creation - return - end - end - - %create the executable file - file_exe_global=fullfile_uvmat('','',Param.InputTable{1,3},ExeExt,OutputNomType,... - first_i,last_i,first_j,last_j); - file_exe_global=fullfile(OutputDir,'0_EXE',file_exe_global); - filelog_global=fullfile_uvmat('','',Param.InputTable{1,3},'.log',OutputNomType,... - first_i,last_i,first_j,last_j); - filelog_global=fullfile(OutputDir,'0_LOG',filelog_global); - - for iprocess=1:NbProcess - %create the executable file - batch_file_list{iprocess}=fullfile(OutputDir,'0_EXE',regexprep(extxml{iprocess},'.xml$',ExeExt)); - - % set the log file name - filelog{iprocess}=fullfile(OutputDir,'0_LOG',regexprep(extxml{iprocess},'.xml$','.log')); - end -end - -%% launch the executable files for background or cluster processing - -switch RunMode - - case 'background' - [fid,message]=fopen(file_exe_global,'w'); - if isequal(fid,-1) - errormsg=['creation of ' file_exe_global ':' message]; - return - end - switch ActionExt - case '.m'% Matlab function - switch computer - case {'GLNX86','GLNXA64','MACI64'} - matlab_ver = ver('MATLAB'); - matlab_version = matlab_ver.Version; - cmd=[... - '#!/bin/bash\n'... - 'source /etc/profile\n'... - 'module load matlab/' matlab_version '\n'...% CHOICE OF MATLAB VERSION - 'time_start=$(date +%%s)\n'... - 'matlab -nodisplay -nosplash -nojvm -logfile ''' filelog_global ''' <','.stderr') ' '... -% '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '... -% extra_qstat ' '... -% '"oar-parexec -s -f ' ListProcess ' '... -% '-l ' ListProcess '.log"']; -% filename_oarcommand=fullfile(DirPBS,'pbs_command'); -% fid=fopen(filename_oarcommand,'w'); -% fprintf(fid,pbs_command); -% fclose(fid); -% fprintf(pbs_command); % display in command line -% %system(pbs_command); -% msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster']) - - case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct - % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs - % o?? N < 1000. - %create subdirectory for pbs command and log files - - DirSGE=fullfile(OutputDir,'0_SGE'); - if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input - curdir=pwd; - cd(DirSGE) - delete('*') - cd(curdir) - else - [tild,msg1]=mkdir(DirSGE); - if ~strcmp(msg1,'') - errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation - return - end - end - maxImgsPerJob = ceil(length(batch_file_list)/NbCore); - disp(['Max number of jobs: ' num2str(NbCore)]) - disp(['Images per job: ' num2str(maxImgsPerJob)]) - - iprocess = 1; - imgsInJob = []; - currJobIndex = 1; - done = 0; - while(~done) - if(iprocess <= length(batch_file_list)) - imgsInJob = [imgsInJob, iprocess]; - end - if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list))) - cmd=['#!/bin/sh \n'... - '#$ -cwd \n'... - 'hostname && date\n'] - for ii=1:numel(imgsInJob) - cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n']; + [tild,msg1]=mkdir(DIR_CLUSTER); + if ~strcmp(msg1,'') + errormsg=['cannot create ' DIR_CLUSTER ': ' msg1]; % error message for directory creation + return end - [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w'); - fprintf(fid, cmd); - fclose(fid); - system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh']) - sge_command=['qsub -N civ_' num2str(currJobIndex) ' '... - '-q ' qstat_Queue ' '... - '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... - '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... - fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])]; - fprintf(sge_command); % display in command line - [status, result] = system(sge_command); - fprintf(result); - currJobIndex = currJobIndex + 1; - imgsInJob = []; - end - if(iprocess == length(batch_file_list)) - done = 1; - end - iprocess = iprocess + 1; - end - msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.']) - case 'python' - command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ... - 'python -m fluidimage.run_from_xml ' filexml{iprocess}]; - fprintf(['command:\n' command '\n\n']) - system(command, '-echo'); -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 ':']; msg}); % error message for directory creation - end - end -end - + end + % create file containing the list of jobs + ListProcess=fullfile(DIR_CLUSTER,'job_list.txt'); % name of the file containing the list of executables + fid=fopen(ListProcess,'w'); % open it for writting + for iprocess=1:length(batch_file_list) + fprintf(fid,[batch_file_list{iprocess} '\n']); % write list of exe files + end + fclose(fid); + system(['chmod +x ' ListProcess]); % set the file to executable + + CPUTimeProcess=CPUTime*BlockLength*nbfield_j; % estimated CPU time for one individual process (in minutes) + LaunchCmdFcn=SeriesData.SeriesParam.ClusterParam.LaunchCmdFcn; + 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 + filename_oarcommand=fullfile(DIR_CLUSTER,'0_cluster_command'); % keep track of the command in file '0-OAR/0_cluster_command' + fid=fopen(filename_oarcommand,'w'); + fprintf(fid,oar_command); % store the command + fprintf(fid,result); % store the result (job ID number) + fclose(fid); + if status==0 + msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched for ' ExpName ' as ' num2str(NbProcess) ' processes in cluster: press STATUS to see results']) + else + msgbox_uvmat('ERROR',result) + end + % case 'cluster_pbs' % for LMFA Kepler machine: trqnsferred to fct + + % %create subdirectory for pbs command and log files + % DirPBS=fullfile(OutputDir,'0_PBS'); % todo : common name OAR/PBS + % if exist(DirPBS,'dir')% delete the content of the dir 0_LOG to allow new input + % curdir=pwd; + % cd(DirPBS) + % delete('*') + % cd(curdir) + % else + % [tild,msg1]=mkdir(DirPBS); + % if ~strcmp(msg1,'') + % errormsg=['cannot create ' DirPBS ': ' msg1]; % error message for directory creation + % return + % end + % end + % max_walltime=3600*20; % 20h max total calculation (cannot exceed 24 h) + % walltime_onejob=1800; % seconds, max estimated time for asingle file index value + % ListProcess=fullfile(DirPBS,'job_list.txt'); % create name of the global executable file + % fid=fopen(ListProcess,'w'); + % for iprocess=1:length(batch_file_list) + % fprintf(fid,[batch_file_list{iprocess} '\n']); % list of exe files + % end + % fclose(fid); + % system(['chmod +x ' ListProcess]); % set the file to executable + % pbs_command=['qsub -n CIVX '... + % '-t idempotent --checkpoint ' num2str(walltime_onejob+60) ' '... + % '-l /core=' num2str(NbCore) ','... + % 'walltime=' datestr(min(1.05*walltime_onejob/86400*max(NbProcess*BlockLength*nbfield_j,NbCore)/NbCore,max_walltime/86400),13) ' '... + % '-E ' regexprep(ListProcess,'\.txt\>','.stderr') ' '... + % '-O ' regexprep(ListProcess,'\.txt\>','.log') ' '... + % extra_qstat ' '... + % '"oar-parexec -s -f ' ListProcess ' '... + % '-l ' ListProcess '.log"']; + % filename_oarcommand=fullfile(DirPBS,'pbs_command'); + % fid=fopen(filename_oarcommand,'w'); + % fprintf(fid,pbs_command); + % fclose(fid); + % fprintf(pbs_command); % display in command line + % %system(pbs_command); + % msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster']) + + case 'cluster_sge' % for PSMN % TODO: use the standard 'cluster' config with an external fct + % Au PSMN, on ne cr??e pas 1 job avec plusieurs c??urs, mais N jobs de 1 c??urs + % o?? N < 1000. + %create subdirectory for pbs command and log files + + DirSGE=fullfile(OutputDir,'0_SGE'); + if exist(DirSGE,'dir')% delete the content of the dir 0_LOG to allow new input + curdir=pwd; + cd(DirSGE) + delete('*') + cd(curdir) + else + [tild,msg1]=mkdir(DirSGE); + if ~strcmp(msg1,'') + errormsg=['cannot create ' DirSGE ': ' msg1]; % error message for directory creation + return + end + end + maxImgsPerJob = ceil(length(batch_file_list)/NbCore); + disp(['Max number of jobs: ' num2str(NbCore)]) + disp(['Images per job: ' num2str(maxImgsPerJob)]) + + iprocess = 1; + imgsInJob = []; + currJobIndex = 1; + done = 0; + while(~done) + if(iprocess <= length(batch_file_list)) + imgsInJob = [imgsInJob, iprocess]; + end + if((numel(imgsInJob) >= maxImgsPerJob) || (iprocess == length(batch_file_list))) + cmd=['#!/bin/sh \n'... + '#$ -cwd \n'... + 'hostname && date\n'] + for ii=1:numel(imgsInJob) + cmd=[cmd ActionFullName ' /softs/matlab ' filexml{imgsInJob(ii)} '\n']; + end + [fid, message] = fopen([DirSGE '/job' num2str(currJobIndex) '.sh'], 'w'); + fprintf(fid, cmd); + fclose(fid); + system(['chmod +x ' DirSGE '/job' num2str(currJobIndex) '.sh']) + sge_command=['qsub -N civ_' num2str(currJobIndex) ' '... + '-q ' qstat_Queue ' '... + '-e ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... + '-o ' fullfile([DirSGE '/job' num2str(currJobIndex) '.out']) ' '... + fullfile([DirSGE '/job' num2str(currJobIndex) '.sh'])]; + fprintf(sge_command); % display in command line + [status, result] = system(sge_command); + fprintf(result); + currJobIndex = currJobIndex + 1; + imgsInJob = []; + end + if(iprocess == length(batch_file_list)) + done = 1; + end + iprocess = iprocess + 1; + end + msgbox_uvmat('CONFIRMATION',[num2str(currJobIndex-1) ' jobs launched on queue ' qstat_Queue '.']) + case 'python' + command = ['LD_LIBRARY_PATH=$(echo $LD_LIBRARY_PATH | pyp "l = x.split('':''); l = [s for s in l if ''matlab'' not in s]; print('':''.join(l))") ' ... + 'python -m fluidimage.run_from_xml ' filexml{iprocess}]; + fprintf(['command:\n' command '\n\n']) + system(command, '-echo'); + 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 ':']; msg}); % error message for directory creation + end + end + end +end %------------------------------------------------------------------------ function STOP_Callback(hObject, eventdata, handles) @@ -3474,10 +3502,7 @@ end -%function num_NbProcess_Callback(hObject, eventdata, handles) - function num_NbSlice_Callback(hObject, eventdata, handles) NbSlice=str2num(get(handles.num_NbSlice,'String')); -%set(handles.num_NbProcess,'String',num2str(NbSlice)) %------------------------------------------------------------------------ @@ -3520,6 +3545,6 @@ % --- Executes on mouse motion over figure - except title and menu. -function series_WindowButtonMotionFcn(hObject, eventdata, handles) -set(hObject,'Pointer','arrow'); +% function series_WindowButtonMotionFcn(hObject, eventdata, handles) +% set(hObject,'Pointer','arrow'); @@ -3736,2 +3761,13 @@ +% --- Executes on button press in Replicate. +function Replicate_Callback(hObject, eventdata, handles) +if get(handles.Replicate,'Value') +InputTable=get(handles.InputTable,'Data'); +browse_data(fullfile(InputTable{1,1},InputTable{1,2})) +else + hh=findobj(allchild(0),'Tag','browse_data'); + if ~isempty(hh) + delete(hh) + end +end Index: /trunk/src/series/extract_rdvision.m =================================================================== --- /trunk/src/series/extract_rdvision.m (revision 1058) +++ /trunk/src/series/extract_rdvision.m (revision 1059) @@ -186,16 +186,19 @@ % nbfield2=size(time,1); checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end + for iview=1:size(Param.InputTable,1) + check_xml=0; for iview_xml=1:size(Param.InputTable,1)% look for the xml files in the different data directories filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder if exist(filexml,'file') + check_xml=1; break end end - if ~exist(filexml,'file') - disp_uvmat('ERROR',[filexml ' missing'],checkrun) - return - end - + % if ~exist(filexml,'file') + % disp_uvmat('ERROR',[filexml ' missing'],checkrun) + % return + % end + newxml=fullfile(RootPath,Param.InputTable{iview,3}); newxml=regexprep(newxml,'_Master_Dalsa_4M180$','');%suppress '_Master_Dalsa_4M180' @@ -211,5 +214,7 @@ [success,errormsg] = copyfile(filename_seq,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.seq']); %copy the seq file in the upper folder [success,errormsg] = copyfile(filename_sqb,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.sqb']); %copy the sqb file in the upper folder + if check_xml [success,errormsg] = copyfile(filexml,[fullfile(RootPath,logdir,Param.InputTable{iview,3}) '.xml']); %copy the original xml file in the upper folder + end otherwise errormsg='input file extension must be .seq or .sqb'; Index: /trunk/src/set_object.m =================================================================== --- /trunk/src/set_object.m (revision 1058) +++ /trunk/src/set_object.m (revision 1059) @@ -332,5 +332,5 @@ set(handles.num_RangeY_2,'TooltipString',['num_RangeY_2: half width of the ' ObjectStyle]) case {'plane','plane_z'} -% set(handles.num_Angle_3,'Visible','on') + set(handles.num_Angle_3,'Visible','on') set(handles.num_RangeX_1,'Visible','on') set(handles.num_RangeX_2,'Visible','on') Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1058) +++ /trunk/src/uvmat.m (revision 1059) @@ -1202,6 +1202,6 @@ uicontrol('Style','pushbutton','Units','normalized', 'Position', [ii ii wwp hh],'BackgroundColor',[1 0 0],'String','APPLY','Callback',@(hObject,eventdata)set_slice_APPLY_Callback(hObject,eventdata),... 'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''APPLY'': apply the output to the current field series in uvmat'); -uicontrol('Style','pushbutton','Units','normalized', 'Position', [2*ii+wwp ii wwp hh],'BackgroundColor',[1 0 0],'String','REPLICATE','Callback',@(hObject,eventdata)set_slice_REPLICATE_Callback(hObject,eventdata),... - 'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''REPLICATE'': replicate the output for a series of experiments'); +uicontrol('Style','checkbox','Units','normalized', 'Position', [2*ii+wwp ii wwp hh],'BackgroundColor',[1 0 0],'String','Replicate','Callback',@(hObject,eventdata)set_slice_REPLICATE_Callback(hObject,eventdata),... + 'FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''Replicate'': select to replicate the output of APPLY to a series of experiments'); uicontrol('Style','pushbutton','Units','normalized', 'Position', [3*ii+2*wwp ii wwp hh],'Callback',@(hObject,eventdata)set_slice_Cancel_Callback(hObject,eventdata),... 'String','Cancel','FontWeight','bold','FontUnits','points','FontSize',12,'TooltipString','''Cancel'': quit GUI without action'); @@ -1272,4 +1272,9 @@ end +hreplicate=findobj(hObject,'Tag','Replicate'); +if get(hreplicate,'Value') + 'TEST' +else + %% store the result in the xml file used for calibration errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file @@ -1284,4 +1289,5 @@ uvmat('InputFileREFRESH_Callback',huvmat,[],hhuvmat); %file input with xml reading in uvmat, show the image in phys coordinates set(hObject,'BackgroundColor',[1 0 0]);% paint button back to red +end delete(hset_slice) @@ -1291,63 +1297,78 @@ function set_slice_REPLICATE_Callback(hObject,eventdata) %------------------------------------------------------------------------ -set(hObject,'BackgroundColor',[1 1 0]) -drawnow - -%% read the GUI set_slice -SliceData=read_GUI(get(hObject,'parent')); - -%% get info on the GUI uvmat -huvmat=findobj(allchild(0),'Tag','uvmat'); -hhuvmat=guidata(huvmat); -RootPath=read_file_boxes(hhuvmat); - -OutPutDir=uigetfile_uvmat('choose an image folder to document with slice position?',fileparts(RootPath),'uigetdir'); -OutPut=browse_data(OutPutDir,'off','on'); -nbcalib=0; -for ilist=1:numel(OutPut.Experiment) - for idevice=1:numel(OutPut.DataSeries) - SubDirBase=regexprep(OutPut.DataSeries{idevice},'\..+$',''); - XmlFile=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']); - - % read the current xml file - if exist(XmlFile,'file') - [s,errormsg]=imadoc2struct(XmlFile,'GeometryCalib'); - if ~isempty(errormsg) - msgbox_uvmat('ERROR',['error in reading ' XmlFile ': ' errormsg]) - return - end - GeometryCalib=s.GeometryCalib; - GeometryCalib.NbSlice=SliceData.NbSlice; - GeometryCalib.CheckVolumeScan=SliceData.CheckVolumeScan; - Z_plane=linspace(SliceData.Z(1),SliceData.Z(2),SliceData.NbSlice); - GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; - GeometryCalib.SliceAngle=zeros(GeometryCalib.NbSlice,3); - Angle_1=linspace(SliceData.SliceAngle_1(1),SliceData.SliceAngle_1(2),SliceData.NbSlice); - Angle_2=linspace(SliceData.SliceAngle_2(1),SliceData.SliceAngle_2(2),SliceData.NbSlice); - GeometryCalib.SliceAngle(:,1)=Angle_1';%rotation around x axis (to generalise) - GeometryCalib.SliceAngle(:,2)=Angle_2';%rotation around y axis (to generalise) - GeometryCalib.SliceAngle(:,3)=0; - if SliceData.CheckRefraction - GeometryCalib.InterfaceCoord=[0 0 SliceData.H]; - GeometryCalib.RefractionIndex=SliceData.RefractionIndex; - elseif isfield(GeometryCalib,'RefractionIndex') - GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); - GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); - end - - % update the current xml file - errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file - if ~strcmp(errormsg,'') - msgbox_uvmat('ERROR',errormsg); - else - display([XmlFile ' updated with slice positions']) - nbcalib=nbcalib+1; - end - end - end -end -set(hObject,'BackgroundColor',[1 0 0]) -msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated with slice positions for ' num2str(nbcalib) ' experiments']); - +if get(hObject,'Value') %open the GUI browse_data + % look for the GUI uvmat and check for an image as input + huvmat=findobj(allchild(0),'Name','uvmat'); + hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat + RootPath=get(hhuvmat.RootPath,'String'); + SubDir=get(hhuvmat.SubDir,'String'); + browse_data(fullfile(RootPath,SubDir)) +else + hbrowse=findobj(allchild(0),'Tag','browse_data'); + if ~isempty(hbrowse) + delete(hbrowse) + end +end + +% +% set(hObject,'BackgroundColor',[1 1 0]) +% drawnow +% +% %% read the GUI set_slice +% SliceData=read_GUI(get(hObject,'parent')); +% +% %% get info on the GUI uvmat +% huvmat=findobj(allchild(0),'Tag','uvmat'); +% hhuvmat=guidata(huvmat); +% RootPath=read_file_boxes(hhuvmat); +% +% OutPutDir=uigetfile_uvmat('choose an image folder to document with slice position?',fileparts(RootPath),'uigetdir'); +% OutPut=browse_data(OutPutDir,'off','on'); +% nbcalib=0; +% for ilist=1:numel(OutPut.Experiment) +% for idevice=1:numel(OutPut.DataSeries) +% SubDirBase=regexprep(OutPut.DataSeries{idevice},'\..+$',''); +% XmlFile=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']); +% +% % read the current xml file +% if exist(XmlFile,'file') +% [s,errormsg]=imadoc2struct(XmlFile,'GeometryCalib'); +% if ~isempty(errormsg) +% msgbox_uvmat('ERROR',['error in reading ' XmlFile ': ' errormsg]) +% return +% end +% GeometryCalib=s.GeometryCalib; +% GeometryCalib.NbSlice=SliceData.NbSlice; +% GeometryCalib.CheckVolumeScan=SliceData.CheckVolumeScan; +% Z_plane=linspace(SliceData.Z(1),SliceData.Z(2),SliceData.NbSlice); +% GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; +% GeometryCalib.SliceAngle=zeros(GeometryCalib.NbSlice,3); +% Angle_1=linspace(SliceData.SliceAngle_1(1),SliceData.SliceAngle_1(2),SliceData.NbSlice); +% Angle_2=linspace(SliceData.SliceAngle_2(1),SliceData.SliceAngle_2(2),SliceData.NbSlice); +% GeometryCalib.SliceAngle(:,1)=Angle_1';%rotation around x axis (to generalise) +% GeometryCalib.SliceAngle(:,2)=Angle_2';%rotation around y axis (to generalise) +% GeometryCalib.SliceAngle(:,3)=0; +% if SliceData.CheckRefraction +% GeometryCalib.InterfaceCoord=[0 0 SliceData.H]; +% GeometryCalib.RefractionIndex=SliceData.RefractionIndex; +% elseif isfield(GeometryCalib,'RefractionIndex') +% GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); +% GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); +% end +% +% % update the current xml file +% errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file +% if ~strcmp(errormsg,'') +% msgbox_uvmat('ERROR',errormsg); +% else +% display([XmlFile ' updated with slice positions']) +% nbcalib=nbcalib+1; +% end +% end +% end +% end +% set(hObject,'BackgroundColor',[1 0 0]) +% msgbox_uvmat('CONFIMATION',[SubDirBase ' calibrated with slice positions for ' num2str(nbcalib) ' experiments']); +% %------------------------------------------------------------------------