Changeset 922


Ignore:
Timestamp:
Nov 24, 2015, 10:48:46 AM (5 years ago)
Author:
sommeria
Message:

corrections quentin

Location:
trunk/src
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/phys_ima.m

    r892 r922  
    4040Rangy(1)=max(ycorner);
    4141test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
    42 npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images)
    43 npY=1+round((Rangy(1)-Rangy(2))/min(dy));
     42% npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images)
     43% npY=1+round((Rangy(1)-Rangy(2))/min(dy));
     44
     45npX=1+round((Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images)
     46npY=1+round((Rangy(1)-Rangy(2))/max(dy));
     47
     48
    4449x=linspace(Rangx(1),Rangx(2),npX);
    4550y=linspace(Rangy(1),Rangy(2),npY);
     
    6974%            end
    7075        end
    71         xima=0.5:npx-0.5;%image coordinates of corners
    72         yima=npy-0.5:-1:0.5;
     76        xima=0.5:npx(icell)-0.5;%image coordinates of corners
     77        yima=npy(icell)-0.5:-1:0.5;
    7378        [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates
    7479        [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,zphys);% image coordinates for each point in the real
  • trunk/src/plot_object.m

    r908 r922  
    386386            if nbpoints>length(PlotData.DeformPoint)
    387387                for ipt=length(PlotData.DeformPoint)+1:nbpoints
    388                     PlotData.DeformPoint(ipt)=line(xline(ipt),yline(ipt),'Color',col,'LineStyle','.','Tag','DeformPoint',...
     388                    PlotData.DeformPoint(ipt)=line(xline(ipt),yline(ipt),'Color',col,'LineStyle','-','Tag','DeformPoint',...
    389389                        'SelectionHighlight','off','UserData',hplot);
    390390                end
  • trunk/src/series.m

    r919 r922  
    17681768extxml=cell(1,NbProcess); % initialisation of the set of labels used for the files documenting each process
    17691769for iprocess=1:NbProcess
     1770    extxml{iprocess}='.xml';
     1771end
     1772for iprocess=1:NbProcess
    17701773    if ~strcmp(get(handles.RUN,'BusyAction'),'queue')% allow for STOP action
    17711774        disp('program stopped by user')
     
    18281831                    case {'PCWIN','PCWIN64'} %Windows system
    18291832                        filexml=regexprep(filexml,'\\','\\\\');% add '\' so that '\' are left as characters
    1830                         system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
     1833                        system([ActionFullName ' ' RunTime ' ' filexml]);% TODO: adapt to DOS system
    18311834                    case {'GLNX86','GLNXA64','MACI64'}%Linux  system
    1832                         system([fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml]);
     1835                        system([ActionFullName ' ' RunTime ' ' filexml]);
    18331836                end
    18341837        end
     
    19411944                                'hostname && date \n '...
    19421945                                'umask 002 \n'...
    1943                                 fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml];%allow writting access to created files for user group
     1946                                ActionFullName ' ' RunTime ' ' filexml];%allow writting access to created files for user group
    19441947                            fprintf(fid,cmd);%fill the executable file with the  char string cmd
    19451948                            fclose(fid);% close the executable file
     
    19511954                    end
    19521955                end
    1953                 msgbox_uvmat('CONFIRMATION',[ActionName ' launched in background: press STATUS to see results'])
     1956                msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched in background: press STATUS to see results'])
    19541957        end
    19551958       
     
    19671970                'hostname && date \n '...
    19681971                'umask 002 \n'...
    1969                 fullfile(ActionPath,[ActionName '.sh']) ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
     1972                ActionFullName ' ' RunTime ' ' filexml{iprocess}];%allow writting access to created files for user group
    19701973            else
    19711974                cmd=[...
     
    20212024        WallTimeOneJob=min(4*JobTime+10,WallTimeTotal*60/2);% estimated max time of an individual job for checkpoint
    20222025        disp(['WallTimeOneJob: ' num2str(WallTimeOneJob) ' minutes'])
    2023         oar_command=['oarsub -n UVmat_' ActionName ' '...
     2026        oar_command=['oarsub -n UVmat_' ActionFullName ' '...
    20242027            '-t idempotent --checkpoint ' num2str(WallTimeOneJob*60) ' '...
    20252028            '-l /core=' num2str(NbCore) ','...
     
    20282031            '-O ' filename_log ' '...
    20292032            extra_oar ' '...
    2030             '"oar-parexec -s -f ' filename_joblist ' '...
     2033           '"oar-parexec -s -f ' filename_joblist ' '...
    20312034            '-l ' filename_joblist '.log"'];
     2035       
     2036
     2037       
    20322038        fprintf(oar_command);% display  system command on the Matlab command window
    20332039        [status,result]=system(oar_command)% execute system command and show the result (ID number of the launched job) on the Matlab command window
     
    20372043        fprintf(fid,result);% store the result (job ID number)
    20382044        fclose(fid);
    2039         msgbox_uvmat('CONFIRMATION',[ActionName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
     2045        msgbox_uvmat('CONFIRMATION',[ActionFullName ' launched as  ' num2str(NbProcess) ' processes in cluster: press STATUS to see results'])
    20402046       
    20412047    case 'cluster_pbs' % for LMFA Kepler machine
     
    20782084        fprintf(pbs_command);% display in command line
    20792085        %system(pbs_command);
    2080         msgbox_uvmat('CONFIRMATION',[ActionName ' command ready to be launched in cluster'])
     2086        msgbox_uvmat('CONFIRMATION',[ActionFullName ' command ready to be launched in cluster'])
    20812087    case 'python'
    20822088        command = [
  • trunk/src/series/extract_rdvision.m

    r909 r922  
    7070    ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
    7171    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
    72     ParamOut.OutputSubDirMode='custom'; %output folder given by the program, not by the GUI series
     72     ParamOut.OutputDirExt='.extract';%set the output dir extension
     73    ParamOut.OutputSubDirMode='one'; %output folder given by the program, not by the GUI series
    7374     % detect the set of image folder
    7475    RootPath=Param.InputTable{1,1};
     
    143144        msgbox_uvmat('ERROR',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once'])
    144145        %rmfield(OutputDir)
    145         return
     146%         return
    146147    end
    147148    %% interactive input of specific parameters (for RDvision system)
     
    183184checkpreserve=0;% if =1, will npreserve the original images, else it erases them at the end
    184185for iview=1:size(Param.InputTable,1)
    185     filexml=[fullfile(RootPath,Param.InputTable{iview,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
     186    for iview_xml=1:size(Param.InputTable,1)% loojk for the xml files in the different data directories
     187    filexml=[fullfile(RootPath,Param.InputTable{iview_xml,2},Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder
     188    if exist(filexml,'file')
     189        break
     190    end
     191    end
    186192    if ~exist(filexml,'file')
    187193        disp_uvmat('ERROR',[filexml ' missing'],checkrun)
     
    275281    time_diff_min=min(diff_time');
    276282    if max(time_diff_max)>0.005
    277         disp_uvmat('WARNING',['timestamps exceeds xml time by' num2str(max(time_diff_max))],checkrun)
     283        disp(['WARNING:timestamps exceeds xml time by' num2str(max(time_diff_max))])
    278284        checkpreserve=1;
    279285    elseif min(time_diff_min)<-0.005
    280         disp_uvmat('WARNING',['timestamps is lower than xml time by' num2str(min(time_diff_min))],checkrun)
     286        disp(['timestamps is lower than xml time by' num2str(min(time_diff_min))])
    281287        checkpreserve=1;
    282288    else
    283         disp_uvmat('CONFIRMATION','time from xml file correct within better than 5 ms',checkrun)
     289        disp('CONFIRMATION:time from xml file correct within better than 5 ms')
    284290    end
    285291    if checkpreserve
     
    303309    % check images
    304310   
    305     delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
    306     if ~checkpreserve
    307         for ibin=1:numel(BinList)
    308             delete(BinList{ibin})
    309         end
    310         rmdir(fullfile(RootPath,Param.InputTable{iview,2}))
    311     end
    312 end
     311%     delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
     312%     if ~checkpreserve
     313%         for ibin=1:numel(BinList)
     314%             delete(BinList{ibin})
     315%         end
     316%         rmdir(fullfile(RootPath,Param.InputTable{iview,2}))
     317%     end
     318end
     319delete(fullfile(RootPath,'Running.xml'))%delete the  xml file to indicate that processing is finished
    313320
    314321%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  • trunk/src/set_object.m

    r912 r922  
    391391        end       
    392392    end
    393     if isempty(str2num(get(handles.num_RangeInterp,'String')))
     393    if isempty(str2num(get(handles.num_RangeInterp,'String'))) && isfield(UvData,'Field')
    394394     set(handles.num_RangeInterp,'String',num2str(3*UvData.Field.CoordMesh))% default interpolationlength= 3 meshes
    395395    end
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