Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 909) +++ /trunk/src/series.m (revision 910) @@ -1481,23 +1481,16 @@ errormsg='';%default error message xmlfile=fullfile(path_series,'PARAM.xml'); -test_batch=0;%default: ,no batch mode available +%test_batch=0;%default: ,no batch mode available if ~exist(xmlfile,'file') [success,message]=copyfile(fullfile(path_series,'PARAM.xml.default'),xmlfile); end -% RunTime=''; if strcmp(ActionExt,'.sh') if exist(xmlfile,'file') s=xml2struct(xmlfile); if strcmp(RunMode,'cluster_oar') && isfield(s,'BatchParam') -% if isfield(s.BatchParam,'RunTime') -% RunTime=s.BatchParam.RunTime; -% end if isfield(s.BatchParam,'NbCore') NbCore=s.BatchParam.NbCore; end elseif (strcmp(RunMode,'background')||strcmp(RunMode,'local')) && isfield(s,'RunParam') -% if isfield(s.RunParam,'RunTime') -% RunTime=s.RunParam.RunTime; -% end if isfield(s.RunParam,'NbCore') NbCore=s.RunParam.NbCore; @@ -1505,8 +1498,4 @@ end end -% if isempty(RunTime) && strcmp(RunMode,'cluster_oar') -% errormsg='RunTime name not found in PARAM.xml, compiled version .sh cannot run on cluster'; -% return -% end end @@ -1727,19 +1716,17 @@ end nbfield_j=numel(ref_j); % number of j indices -BlockLength=numel(ref_i);%default -if isempty(Param.IndexRange.NbSlice) - NbProcess=NbCore;% choose one process per core by default if NbSlice is not imposed - switch RunMode - case 'cluster_oar' - BlockLength= ceil(20/(CPUTime*nbfield_j));% short iterations are grouped such that the minimum time of a process is 20 min. - NbProcess=ceil(numel(ref_i)/BlockLength) ; % nbre of processes sent to oar - end -else - NbProcess=Param.IndexRange.NbSlice;% the parameter NbSlice sets the nbre of run processes - NbCore=min(NbCore,NbProcess);% reduces the number of cores if it exceeds the number of processes -end - -%BlockLength=ceil(numel(ref_i)/NbProcess);% nbre of input fields in each process -%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_oar','cluster_pbs'} + if isempty(Param.IndexRange.NbSlice)% if NbSlice is not defined + BlockLength= ceil(20/(CPUTime*nbfield_j));% short iterations are grouped such that the minimum time of a process is 20 min. + BlockLength=max(BlockLength,ceil(numel(ref_i)/1000));% possibly increase the BlockLength to have less than 1000 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 + NbCore=min(NbCore,NbProcess);% reduces the number of cores if it exceeds the number of processes + end +end %% record nbre of output files and starting time for computation for status Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 909) +++ /trunk/src/series/civ_input.m (revision 910) @@ -130,6 +130,8 @@ return end + if isfield(Data,'.Civ1_ImageA') [PathCiv1_ImageA,Civ1_ImageA,FileExtA]=fileparts(Data.Civ1_ImageA);%look for the source image A [PathCiv1_ImageB,Civ1_ImageB,FileExtA]=fileparts(Data.Civ1_ImageB);%look for the source image B + end if isfield(Data,'Civ2_ImageA') [PathCiv2_ImageA,Civ2_ImageA,FileExtA]=fileparts(Data.Civ2_ImageA); @@ -137,8 +139,15 @@ end if size(Param.InputTable,1)==1 + if isfield(Data,'.Civ1_ImageA') series('display_file_name',hhseries,Data.Civ1_ImageA,'append');%append the image series to the input list - end - [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ1_ImageA); + [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ1_ImageA); [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ1_ImageB); + else + series('display_file_name',hhseries,Data.Civ2_ImageA,'append');%append the image series to the input list + [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaA]=fileparts_uvmat(Data.Civ2_ImageA); + [RootPath,SubDir,RootFile,i1,i2,j1,j2,FileExt,NomTypeImaB]=fileparts_uvmat(Data.Civ2_ImageB); + end + end + iview_image=2;%line # for the input images case 'civxdata'% case of civx data, Index: /trunk/src/series/civ_series.m =================================================================== --- /trunk/src/series/civ_series.m (revision 909) +++ /trunk/src/series/civ_series.m (revision 910) @@ -1024,4 +1024,6 @@ if sizemask > 1/2% eliminate point if more than half of the correlation box is masked F(ivec)=3; % + utable(ivec)=0; + vtable(ivec)=0; else image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) @@ -1042,5 +1044,8 @@ F(ivec)=3; end - if F(ivec)~=3 + if F(ivec)==3 + utable(ivec)=0; + vtable(ivec)=0; + else %mask if checkmask @@ -1099,4 +1104,5 @@ catch ME F(ivec)=3; + disp(ME.message) end else @@ -1127,5 +1133,5 @@ %http://urapiv.wordpress.com peaky = y; -if y <= npy-1 && y >= 1 +if y <= npy-1 && y > 1 f0 = log(result_conv(y,x)); f1 = log(result_conv(y-1,x)); @@ -1136,5 +1142,5 @@ end peakx=x; -if x <= npx-1 && x >= 1 +if x <= npx-1 && x > 1 f0 = log(result_conv(y,x)); f1 = log(result_conv(y,x-1)); Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 909) +++ /trunk/src/uvmat.m (revision 910) @@ -1469,6 +1469,6 @@ flag=1; if ~isfield(UvData.Field,'A') - msgbox_uvmat('ERROR','an image needs to be opened to set the mask size'); - return + msgbox_uvmat('ERROR','an image needs to be opened to set the mask size'); + return end npx=size(UvData.Field.A,2); @@ -1477,62 +1477,62 @@ yi=0.5:npy-0.5; [Xi,Yi]=meshgrid(xi,yi); - for iobj=1:length(UvData.ProjObject) - ObjectData=UvData.ProjObject{iobj}; - if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside')); - flagobj=1; - testphys=0; %coordinates in pixels by default - if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel') - if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib') - Calib=UvData.XmlData{1}.GeometryCalib; - testphys=1; + for iobj=1:length(UvData.ProjObject) + ObjectData=UvData.ProjObject{iobj}; + if isfield(ObjectData,'ProjMode') &&(isequal(ObjectData.ProjMode,'mask_inside')||isequal(ObjectData.ProjMode,'mask_outside')); + flagobj=1; + testphys=0; %coordinates in pixels by default + if isfield(ObjectData,'CoordUnit') && ~isequal(ObjectData.CoordUnit,'pixel') + if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib') + Calib=UvData.XmlData{1}.GeometryCalib; + testphys=1; + end + end + if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type') + if isequal(ObjectData.Type,'polygon') + X=ObjectData.Coord(:,1); + Y=ObjectData.Coord(:,2); + if testphys + pos=[X Y zeros(size(X))]; + if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3 + if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0]) + om=norm(Calib.SliceAngle);%norm of rotation angle in radians + OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis + cos_om=cos(pi*om/180); + sin_om=sin(pi*om/180); + pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis; + end + pos(:,1)=pos(:,1)+Calib.SliceCoord(1); + pos(:,2)=pos(:,2)+Calib.SliceCoord(2); + pos(:,3)=pos(:,3)+Calib.SliceCoord(3); + end + [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3)); end + flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside + elseif isequal(ObjectData.Type,'ellipse') + if testphys + %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys + end + RangeX=max(ObjectData.RangeX); + RangeY=max(ObjectData.RangeY); + X2Max=RangeX*RangeX; + Y2Max=RangeY*RangeY; + distX=(Xi-ObjectData.Coord(1,1)); + distY=(Yi-ObjectData.Coord(1,2)); + flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1; + elseif isequal(ObjectData.Type,'rectangle') + if testphys + %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys + end + distX=abs(Xi-ObjectData.Coord(1,1)); + distY=abs(Yi-ObjectData.Coord(1,2)); + flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY); end - if isfield(ObjectData,'Coord')&& isfield(ObjectData,'Type') - if isequal(ObjectData.Type,'polygon') - X=ObjectData.Coord(:,1); - Y=ObjectData.Coord(:,2); - if testphys - pos=[X Y zeros(size(X))]; - if isfield(Calib,'SliceCoord') && length(Calib.SliceCoord)>=3 - if isfield(Calib,'SliceAngle')&&~isequal(Calib.SliceAngle,[0 0 0]) - om=norm(Calib.SliceAngle);%norm of rotation angle in radians - OmAxis=Calib.SliceAngle/om; %unit vector marking the rotation axis - cos_om=cos(pi*om/180); - sin_om=sin(pi*om/180); - pos=cos_om*pos+sin_om*cross(OmAxis,pos)+(1-cos_om)*(OmAxis*pos')*OmAxis; - end - pos(:,1)=pos(:,1)+Calib.SliceCoord(1); - pos(:,2)=pos(:,2)+Calib.SliceCoord(2); - pos(:,3)=pos(:,3)+Calib.SliceCoord(3); - end - [X,Y]=px_XYZ(Calib,pos(:,1),pos(:,2),pos(:,3)); - end - flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside - elseif isequal(ObjectData.Type,'ellipse') - if testphys - %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys - end - RangeX=max(ObjectData.RangeX); - RangeY=max(ObjectData.RangeY); - X2Max=RangeX*RangeX; - Y2Max=RangeY*RangeY; - distX=(Xi-ObjectData.Coord(1,1)); - distY=(Yi-ObjectData.Coord(1,2)); - flagobj=(distX.*distX/X2Max+distY.*distY/Y2Max)>1; - elseif isequal(ObjectData.Type,'rectangle') - if testphys - %[X,Y]=px_XYZ(Calib,X,Y,0);% TODO:create a polygon boundary and transform to phys - end - distX=abs(Xi-ObjectData.Coord(1,1)); - distY=abs(Yi-ObjectData.Coord(1,2)); - flagobj=distX>max(ObjectData.RangeX) | distY>max(ObjectData.RangeY); - end - if isequal(ObjectData.ProjMode,'mask_outside') - flagobj=~flagobj; - end - flag=flag & flagobj; + if isequal(ObjectData.ProjMode,'mask_outside') + flagobj=~flagobj; end - end - end + flag=flag & flagobj; + end + end + end %mask name RootPath=get(handles.RootPath,'String'); @@ -1548,5 +1548,5 @@ imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 20