- Timestamp:
- Dec 13, 2024, 8:57:14 PM (12 months ago)
- Location:
- trunk/src
- Files:
-
- 6 edited
-
civ.m (modified) (7 diffs)
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mouse_motion.m (modified) (5 diffs)
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read_civdata.m (modified) (1 diff)
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series/civ_input.m (modified) (5 diffs)
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series/civ_series.m (modified) (22 diffs)
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uvmat.m (modified) (5 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/src/civ.m
r1168 r1169 44 44 %% prepare measurement grid if not given as input 45 45 if ~isfield(par_civ,'Grid')% grid points defining central positions of the sub-images in image A 46 % if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates)47 % par_civ.Grid=dlmread(par_civ.Grid);48 % par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file)49 % end50 % % else par_civ.Grid is already an array, no action here51 % else% automatic grid in x, y image coordinates52 46 nbinterv_x=floor((npx_ima-1)/par_civ.Dx); 53 47 gridlength_x=nbinterv_x*par_civ.Dx; … … 114 108 checkmask=0; 115 109 MinA=min(min(par_civ.ImageA)); 116 %MinB=min(min(par_civ.ImageB));117 %check_undefined=false(size(par_civ.ImageA));118 110 if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) 119 111 checkmask=1; … … 126 118 127 119 %% compute image correlations: MAINLOOP on velocity vectors 128 corrmax=0;129 120 sum_square=1;% default 130 121 mesh=1;% default … … 134 125 par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) 135 126 end 136 127 137 128 if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) 138 129 for ivec=1:nbvec … … 141 132 FF(ivec)=0; 142 133 ibx2=floor(CorrBoxSizeX(ivec)/2); 143 iby2=floor(CorrBoxSizeY(ivec)/2);144 isx2=ibx2+ceil(par_civ.SearchRange(1));145 isy2=iby2+ceil(par_civ.SearchRange(2));134 iby2=floor(CorrBoxSizeY(ivec)/2); 135 isx2=ibx2+ceil(par_civ.SearchRange(1)); 136 isy2=iby2+ceil(par_civ.SearchRange(2)); 146 137 subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage 147 138 subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage … … 216 207 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 217 208 corrmax= max(max(result_conv)); 218 209 219 210 %result_conv=(result_conv/corrmax); %normalize, peak=always 255 220 211 %Find the correlation max, at 255 … … 280 271 peaky = y; peakx=x; 281 272 if y < npy && y > 1 && x < npx-1 && x > 1 282 FF=false; % no error by the limited search box273 FF=false; % no error by the limited search box 283 274 max_conv=result_conv(y,x);% max correlation 284 275 %peak2noise= max(4,max_conv/std(reshape(result_conv,1,[])));% ratio of max conv to standard deviation of correlations (estiamtion of noise level), set to value 4 if it is too low 285 276 peak2noise=100;% TODO: make this threshold more precise, depending on the image noise 286 result_conv=result_conv*peak2noise/max_conv;% renormalise the correlation with respect to the noise 277 result_conv=result_conv*peak2noise/max_conv;% renormalise the correlation with respect to the noise 287 278 result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (=0 by discretisation, to avoid divergence in the log) 288 279 -
trunk/src/mouse_motion.m
r1168 r1169 238 238 if test_piv 239 239 [dd,ind_pt]=min(abs(Field.X-xy(1,1))+abs(Field.Y-xy(1,2))); 240 if isfield(hhciv,'TestCiv2') && strcmp(get(hhciv.Civ2,'Visible'),'on')&& ...241 strcmp(get(hhciv.TestCiv2,'Visible'),'on')&& get(hhciv.TestCiv2,'Value')% if TestCiv2 is activated242 CivOption='Civ2';243 Param.CheckCiv1=0;244 par_civ=read_GUI(hhciv.Civ2);%read the Civ2 panel in civ_input245 par_civ.Civ1_SubRange=Field.Civ1_SubRange;% get the subranges used for patch246 par_civ.Civ1_NbCentres=Field.Civ1_NbCentres;% get the nbre of civ1 data points in each subrange247 par_civ.Civ1_Coord_tps=Field.Civ1_Coord_tps;% get the positions of the centres (Civ1 data)248 par_civ.Civ1_U_tps=Field.Civ1_U_tps;% get the tps coefficients for spline, U component249 par_civ.Civ1_V_tps=Field.Civ1_V_tps;% get the tps coefficients for spline, V component250 par_civ.Civ1_Dt=Field.Civ1_Dt;251 par_civ.Civ2_Dt=Field.Civ2_Dt;252 shiftx=Field.ShiftX(ind_pt);% get field info stored in the cuirrent figure253 shifty=Field.ShiftY(ind_pt);254 else255 CivOption='Civ1';256 240 Param.CheckCiv2=0; 257 241 par_civ=read_GUI(hhciv.Civ1);%read the Civ1 panel in civ_input 258 242 shiftx=par_civ.SearchBoxShift(1); 259 243 shifty=par_civ.SearchBoxShift(2); 260 end261 244 xround=Field.X(ind_pt); 262 245 yround=Field.Y(ind_pt); … … 284 267 285 268 % perform the PIV calculation as the single point xround yround 286 Param.ActionInput.CheckCiv1=1;287 % Param.CheckFix1=0;288 % Param.CheckPatch1=0;%desactivate all calculations except Civ2 or Civ1289 Param.Action.RUN=1;290 Param.ActionInput.ListCompareMode='PIV';291 Param.ActionInput.PairIndices=read_GUI(hhciv.PairIndices);292 269 par_civ.ImageA=Field.A; 293 270 par_civ.ImageB=Field.B; … … 295 272 par_civ.ImageWidth=size(par_civ.ImageA,2); 296 273 par_civ.Grid=[xround yround];% PIV calculation with a single point 297 Param.ActionInput.(CivOption)=par_civ; 298 [Data,errormsg,result_conv]= civ_series(Param); 274 [~,~,utable,vtable,~,~,result_conv,errormsg]= civ(par_civ); 299 275 if ~isempty(errormsg) 300 276 text_displ_5=errormsg; 301 277 else 302 % rangx(1)=-(isx2-ibx2)+shiftx;303 % rangx(2)=isx2-ibx2+shiftx;304 % rangy(1)=-(isy2-iby2)-shifty;305 % rangy(2)=(isy2-iby2)-shifty;306 278 rangx(1)=-isx2+shiftx; 307 279 rangx(2)=isx2+shiftx; … … 320 292 set(0,'CurrentFigure',corrfig(1)) 321 293 AxeData.CurrentCorrImage=imagesc(rangx,-rangy,result_conv,[0 1]);% plot the correlation map, with full colormap from 0 to 1 322 AxeData.CurrentVector=line([0 Data.([CivOption '_U'])],[0 Data.([CivOption '_V'])],'Tag','vector');294 AxeData.CurrentVector=line([0 utable],[0 vtable],'Tag','vector'); 323 295 AxeData.TitleHandle=title(['[x,y]= ' num2str(par_civ.Grid) ' px']); 324 296 colorbar … … 339 311 set(ParentAxe,'XLim',rangx) 340 312 set(ParentAxe,'YLim',[-rangy(2) -rangy(1)]) 341 set(AxeData.CurrentVector,'XData',[0 Data.([CivOption '_U'])],'YData',[0 Data.([CivOption '_V'])]);313 set(AxeData.CurrentVector,'XData',[0 utable],'YData',[0 vtable]); 342 314 set(AxeData.TitleHandle,'String',['[x,y]= ' num2str(par_civ.Grid) ' px']) 343 315 end -
trunk/src/read_civdata.m
r1162 r1169 93 93 94 94 %% reading data 95 [Data,tild,tild,errormsg]=nc2struct(FileName,'ListGlobalAttribute','Conventions','CivStage'); 95 [Data,tild,tild,errormsg]=nc2struct(FileName,'ListGlobalAttribute','Conventions','CivStage');% read the global attributes to get Data.CivStage 96 96 if ~isempty(errormsg) 97 97 errormsg=['read_civdata: ' errormsg]; -
trunk/src/series/civ_input.m
r1167 r1169 1532 1532 drawnow 1533 1533 if get(handles.TestCiv1,'Value') 1534 set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch 1534 set(handles.TestCiv1,'BackgroundColor',[1 1 0])% paint TestCiv1 button to yellow to confirm civ launch 1535 1535 set(handles.CheckFix1,'value',0)% desactivate next step 1536 1536 set(handles.CheckPatch1,'value',0)% desactivate next step … … 1539 1539 set(handles.CheckPatch2,'value',0)% desactivate next step 1540 1540 update_CivOptions(handles,0) 1541 hseries=findobj(allchild(0),'Tag','series'); 1542 Param=read_GUI(hseries); 1543 Param.Action.RUN=1; 1544 Param.ActionInput=read_GUI(handles.civ_input); 1545 if isfield(Param.ActionInput,'Fix1') 1546 Param.ActionInput=rmfield(Param.ActionInput,'Fix1'); 1547 end 1548 if isfield(Param.ActionInput,'Patch1') 1549 Param.ActionInput=rmfield(Param.ActionInput,'Patch1'); 1550 end 1551 if isfield(Param.ActionInput,'Civ2')%remove options that may be selected beyond Patch1 1552 Param.ActionInput=rmfield(Param.ActionInput,'Civ2'); 1553 end 1554 if isfield(Param.ActionInput,'Fix2') 1555 Param.ActionInput=rmfield(Param.ActionInput,'Fix2'); 1556 end 1557 if isfield(Param.ActionInput,'Patch2') 1558 Param.ActionInput=rmfield(Param.ActionInput,'Patch2'); 1559 end 1560 if isfield(Param,'OutputSubDir') 1561 Param=rmfield(Param,'OutputSubDir'); %remove output file option from civ_series 1562 end 1563 Param.ActionInput.Civ1.CorrSmooth=0;% launch Civ1 with no data point (to get the image names for A and B) 1564 Param.IndexRange.first_i=str2num(get(handles.ref_i,'String')); 1565 Param.IndexRange.last_i=str2num(get(handles.ref_i,'String')); 1566 if strcmp(get(handles.ref_j,'Visible'),'on') 1567 Param.IndexRange.first_j=str2num(get(handles.ref_j,'String')); 1568 Param.IndexRange.last_j=Param.IndexRange.first_j; 1569 else 1570 Param.IndexRange.first_j=1; 1571 Param.IndexRange.last_j=1; 1572 end 1573 [Data,errormsg]=civ_series(Param);% get the civ1+fix1 results 1574 if ~isempty(errormsg), return, end % rmq: error msg displayed in civ_series 1575 1576 %% create image data ImageData for display 1577 ImageData.ListVarName={'ny','nx','A'}; 1578 ImageData.VarDimName= {'ny','nx',{'ny','nx'}}; 1579 ImageData.VarAttribute{1}.Role='coord_y'; 1580 ImageData.VarAttribute{2}.Role='coord_x'; 1581 ImageData.VarAttribute{3}.Role='scalar'; 1582 ImageData.A=imread(Data.Civ1_ImageA); % read the first image 1583 if ndims(ImageData.A)==3 %case of color image 1584 ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; 1585 end 1586 ImageData.ny=[size(ImageData.A,1) 1]; 1587 ImageData.nx=[1 size(ImageData.A,2)]; 1588 ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly 1589 1590 %% create the figure view_field for image visualization 1591 hview_field=view_field(ImageData); %view the image in the GUI view_field 1592 set(0,'CurrentFigure',hview_field) 1593 hhview_field=guihandles(hview_field); 1594 set(hview_field,'CurrentAxes',hhview_field.PlotAxes) 1595 ViewData=get(hview_field,'UserData'); 1596 ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field 1597 ViewData.PlotAxes.X=Data.Civ1_X'; 1598 ViewData.PlotAxes.Y=Data.Civ1_Y'; 1599 ViewData.PlotAxes.B=imread(Data.Civ1_ImageB);%store the second image in the UserData of the GUI view_field 1600 set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field 1541 % get info from the GUI 'series' 1542 hseries=findobj(allchild(0),'Tag','series'); 1543 Param=read_GUI(hseries); 1544 Param.Action.RUN=1; 1545 Param.ActionInput=read_GUI(handles.civ_input); 1546 i1=str2num(get(handles.ref_i,'String')); %references indices 1547 i2=i1; 1548 j1=1; 1549 if strcmp(get(handles.ref_j,'Visible'),'on') 1550 j1=str2num(get(handles.ref_j,'String')); 1551 end 1552 j2=j1; 1553 str_civ=Param.ActionInput.PairIndices.ListPairCiv1; 1554 r=regexp(str_civ,'^\D(?<ind>[i|j])=( -| )(?<num1>\d+)\|(?<num2>\d+)','names'); 1555 if ~isempty(r) 1556 if strmp(r.ind,'i') 1557 i1=i1-str2num(r.num1); 1558 i2=i2 +str2num(r.num2); 1559 elseif strmp(r.ind,'j') 1560 j1=j1-str2num(r.num1); 1561 j2=j2 +str2num(r.num2); 1562 end 1563 else % mode='j1-j2'; 1564 r=regexp(str_civ,'^j= (?<num1>[a-z])-(?<num2>[a-z])','names'); 1565 if isempty(r) 1566 r=regexp(str_civ,'^j= (?<num1>[A-Z])-(?<num2>[A-Z])','names'); 1567 if isempty(r) 1568 r=regexp(str_civ,'^j= (?<num1>\d+)-(?<num2>\d+)','names'); 1569 end 1570 end 1571 if isempty(r) 1572 disp('wrong pair mode input option') 1573 else 1574 j1=stra2num(r.num1); 1575 j2=stra2num(r.num2); 1576 end 1577 end 1578 1579 par_civ1=Param.ActionInput.Civ1; 1580 1581 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 1582 ImageName_A=Param.ActionInput.RefFile; 1583 else 1584 RootPath_A=Param.InputTable{1,1}; 1585 SubDir_A=Param.InputTable{1,2}; 1586 RootFile_A=Param.InputTable{1,3}; 1587 NomType_A=Param.InputTable{1,4}; 1588 FileExt_A=Param.InputTable{1,5}; 1589 ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1,[],j1); 1590 ImageName_B=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i2,[],j2); 1591 end 1592 par_civ1.ImageA = read_image(ImageName_A); 1593 par_civ1.ImageB = read_image(ImageName_B); 1594 par_civ1.CorrSmooth=0;% will give only the grid of data points expected for PIV, computations will be activated by the fct mouse_motion.m 1595 [Data.Civ1_X,Data.Civ1_Y,Data.Civ1_U,Data.Civ1_V,Data.Civ1_C,Data.Civ1_FF, ~, errormsg]=civ(par_civ1); 1596 if ~isempty(errormsg) 1597 disp(errormsg) 1598 return 1599 end % rmq: error msg displayed in civ_series 1600 1601 %% create image data ImageData for display 1602 ImageData.ListVarName={'ny','nx','A'}; 1603 ImageData.VarDimName= {'ny','nx',{'ny','nx'}}; 1604 ImageData.VarAttribute{1}.Role='coord_y'; 1605 ImageData.VarAttribute{2}.Role='coord_x'; 1606 ImageData.VarAttribute{3}.Role='scalar'; 1607 ImageData.A=par_civ1.ImageA; % get the first image 1608 if ndims(ImageData.A)==3 %case of color image 1609 ImageData.VarDimName= {'ny','nx',{'ny','nx','rgb'}}; 1610 end 1611 ImageData.ny=[size(ImageData.A,1) 1]; 1612 ImageData.nx=[1 size(ImageData.A,2)]; 1613 ImageData.CoordUnit='pixel';% used to set equal scaling for x and y in image dispa=ly 1614 1615 %% create the figure view_field for image visualization 1616 hview_field=view_field(ImageData); %view the image in the GUI view_field 1617 set(0,'CurrentFigure',hview_field) 1618 hhview_field=guihandles(hview_field); 1619 set(hview_field,'CurrentAxes',hhview_field.PlotAxes) 1620 ViewData=get(hview_field,'UserData'); 1621 ViewData.CivHandle=handles.civ_input;% indicate the handle of the civ GUI in view_field 1622 ViewData.PlotAxes.X=Data.Civ1_X'; 1623 ViewData.PlotAxes.Y=Data.Civ1_Y'; 1624 ViewData.PlotAxes.B=par_civ1.ImageB;%store the second image in the UserData of the GUI view_field 1625 set(hview_field,'UserData',ViewData)% store the info in the UserData of image view_field, to be used by mouse_motion.m 1601 1626 1602 1627 %% look for a current figure for image correlation display … … 1623 1648 if ~isempty(hview_field) 1624 1649 delete(hview_field) 1625 end 1650 end 1626 1651 end 1627 1652 … … 1636 1661 %--------------------------------------------------------------------- 1637 1662 function NomTypeNc=nomtype2pair(NomTypeIma,mode_selected) 1638 %--------------------------------------------------------------------- 1663 %--------------------------------------------------------------------- 1639 1664 % OUTPUT: 1640 1665 % NomTypeNc … … 1645 1670 NomTypeNc=NomTypeIma;%default 1646 1671 switch mode_selected 1647 case 'pair j1-j2' 1648 if ~isempty(regexp(NomTypeIma,'a$'))1649 NomTypeNc=[NomTypeIma 'b'];1650 elseif ~isempty(regexp(NomTypeIma,'A$'))1651 NomTypeNc=[NomTypeIma 'B'];1652 else1653 r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');1654 if ~isempty(r)1655 NomTypeNc='_1_1-2';1656 end1657 end1658 case 'series(Dj)' 1659 % r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names');1660 % if ~isempty(r)1661 1662 % end1663 case 'series(Di)'1672 case 'pair j1-j2' 1673 if ~isempty(regexp(NomTypeIma,'a$')) 1674 NomTypeNc=[NomTypeIma 'b']; 1675 elseif ~isempty(regexp(NomTypeIma,'A$')) 1676 NomTypeNc=[NomTypeIma 'B']; 1677 else 1678 r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); 1679 if ~isempty(r) 1680 NomTypeNc='_1_1-2'; 1681 end 1682 end 1683 case 'series(Dj)' 1684 % r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); 1685 % if ~isempty(r) 1686 NomTypeNc='_1_1-2'; 1687 % end 1688 case 'series(Di)' 1664 1689 r=regexp(NomTypeIma,'(?<num1>\d+)_(?<num2>\d+)$','names'); 1665 1690 if ~isempty(r) -
trunk/src/series/civ_series.m
r1168 r1169 3 3 % civ: PIV function itself 4 4 % detect_false: put a flag to false vectors after detection by various criteria 5 % filter_tps: make interpolation-smoothing 5 % filter_tps: make interpolation-smoothing 6 6 %------------------------------------------------------------------------ 7 7 % function [Data,errormsg,result_conv]= civ_series(Param) … … 15 15 % Param: Matlab structure of input parameters 16 16 % Param contains info of the GUI series using the fct read_GUI. 17 % Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation 17 % Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation 18 18 % Param.InputTable: sets the input file(s) 19 19 % if absent, the fct looks for input data in Param.ActionInput (test mode) … … 93 93 return 94 94 end 95 iview_A=0;%default values95 %iview_A=0;%default values 96 96 NbField=1; 97 97 RUNHandle=[]; 98 CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved)99 CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced)98 % CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) 99 % CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) 100 100 101 101 %% input files and indexing (skipped in Test mode) 102 if CheckInputFile 103 hseries=findobj(allchild(0),'Tag','series'); 104 RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series 105 WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series 106 MaxIndex_i=Param.IndexRange.MaxIndex_i; 107 MinIndex_i=Param.IndexRange.MinIndex_i; 108 MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); 109 if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') 110 MaxIndex_j=Param.IndexRange.MaxIndex_j; 111 MinIndex_j=Param.IndexRange.MinIndex_j; 112 end 113 if isfield(Param,'InputTable') 114 [~,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); 115 iview_A=0;% series index (iview) for the first image series 116 iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) 117 if Param.ActionInput.CheckCiv1 118 iview_A=1;% usual PIV, the image series is on the first line of the table 119 else % Civ1 has been already stored in a netcdf file input 120 iview_A=2;% the second line is used for the input images 121 end 122 if iview_A~=0 123 RootPath_A=Param.InputTable{iview_A,1}; 124 RootFile_A=Param.InputTable{iview_A,3}; 125 SubDir_A=Param.InputTable{iview_A,2}; 126 NomType_A=Param.InputTable{iview_A,4}; 127 FileExt_A=Param.InputTable{iview_A,5}; 128 if iview_B==0 129 iview_B=iview_A;% the second image series is the same as the first 130 end 131 RootPath_B=Param.InputTable{iview_B,1}; 132 RootFile_B=Param.InputTable{iview_B,3}; 133 SubDir_B=Param.InputTable{iview_B,2}; 134 NomType_B=Param.InputTable{iview_B,4}; 135 FileExt_B=Param.InputTable{iview_B,5}; 136 end 137 138 PairCiv2=''; 139 switch Param.ActionInput.ListCompareMode 140 case 'PIV' 141 PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; 142 if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') 143 PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair 102 hseries=findobj(allchild(0),'Tag','series'); 103 RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series 104 WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series 105 MaxIndex_i=Param.IndexRange.MaxIndex_i; 106 MinIndex_i=Param.IndexRange.MinIndex_i; 107 MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); 108 if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') 109 MaxIndex_j=Param.IndexRange.MaxIndex_j; 110 MinIndex_j=Param.IndexRange.MinIndex_j; 111 end 112 if isfield(Param,'InputTable') 113 [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); 114 % iview_A=0;% series index (iview) for the first image series 115 iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) 116 if Param.ActionInput.CheckCiv1 117 iview_A=1;% usual PIV, the image series is on the first line of the table 118 else % Civ1 has been already stored in a netcdf file input 119 iview_A=2;% the second line is used for the input images 120 end 121 % if iview_A~=0 122 RootPath_A=Param.InputTable{iview_A,1}; 123 RootFile_A=Param.InputTable{iview_A,3}; 124 SubDir_A=Param.InputTable{iview_A,2}; 125 NomType_A=Param.InputTable{iview_A,4}; 126 FileExt_A=Param.InputTable{iview_A,5}; 127 if iview_B==0 128 iview_B=iview_A;% the second image series is the same as the first 129 end 130 RootPath_B=Param.InputTable{iview_B,1}; 131 RootFile_B=Param.InputTable{iview_B,3}; 132 SubDir_B=Param.InputTable{iview_B,2}; 133 NomType_B=Param.InputTable{iview_B,4}; 134 FileExt_B=Param.InputTable{iview_B,5}; 135 PairCiv2=''; 136 137 switch Param.ActionInput.ListCompareMode 138 case 'PIV' 139 PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; 140 if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') 141 PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair 142 end 143 if iview_A==1% if Civ1 is performed 144 [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... 145 find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); 146 if ~isempty(PairCiv2) 147 [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... 148 find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); 149 check_bounds=check_bounds | check_bounds_Civ2; 144 150 end 145 if iview_A==1% if Civ1 is performed 146 [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... 147 find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); 148 if ~isempty(PairCiv2) 149 [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... 150 find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); 151 check_bounds=check_bounds | check_bounds_Civ2; 152 end 153 else% we start from an existing Civ1 file 154 i1_series_Civ1=i1_series{1}; 155 i2_series_Civ1=i2_series{1}; 156 j1_series_Civ1=j1_series{1}; 157 j2_series_Civ1=j2_series{1}; 158 NomTypeNc=Param.InputTable{1,4}; 159 if ~isempty(PairCiv2) 160 [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... 161 find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); 162 end 151 else% we start from an existing Civ1 file 152 i1_series_Civ1=i1_series{1}; 153 i2_series_Civ1=i2_series{1}; 154 j1_series_Civ1=j1_series{1}; 155 j2_series_Civ1=j2_series{1}; 156 NomTypeNc=Param.InputTable{1,4}; 157 if ~isempty(PairCiv2) 158 [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... 159 find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); 163 160 end 164 case 'displacement' 165 if isfield(Param.ActionInput,'OriginIndex') 161 end 162 case 'displacement' 163 if isfield(Param.ActionInput,'OriginIndex') 166 164 i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); 167 else 168 i1_series_Civ1=ones(size(i1_series{1})); 169 end 170 i1_series_Civ2=i1_series_Civ1; 171 i2_series_Civ1=i1_series{1}; 172 i2_series_Civ2=i1_series{1}; 173 j1_series_Civ1=[];% no j index variation for the ref image 174 j1_series_Civ2=[]; 175 if isempty(j1_series{1}) 176 j2_series_Civ1=ones(size(i1_series_Civ1)); 177 else 178 j2_series_Civ1=j1_series{1};% if j index exist 179 end 180 j2_series_Civ2=j2_series_Civ1; 181 NomTypeNc='_1'; 182 end 183 %determine frame indices for input with movie or other multiframe input file 184 if isempty(j1_series_Civ1)% simple movie with index i 185 FrameIndex_A_Civ1=i1_series_Civ1; 186 FrameIndex_B_Civ1=i2_series_Civ1; 187 j1_series_Civ1=ones(size(i1_series_Civ1)); 165 else 166 i1_series_Civ1=ones(size(i1_series{1})); 167 end 168 i1_series_Civ2=i1_series_Civ1; 169 i2_series_Civ1=i1_series{1}; 170 i2_series_Civ2=i1_series{1}; 171 j1_series_Civ1=[];% no j index variation for the ref image 172 j1_series_Civ2=[]; 173 if isempty(j1_series{1}) 174 j2_series_Civ1=ones(size(i1_series_Civ1)); 175 else 176 j2_series_Civ1=j1_series{1};% if j index exist 177 end 178 j2_series_Civ2=j2_series_Civ1; 179 NomTypeNc='_1'; 180 end 181 %determine frame indices for input with movie or other multiframe input file 182 if isempty(j1_series_Civ1)% simple movie with index i 183 FrameIndex_A_Civ1=i1_series_Civ1; 184 FrameIndex_B_Civ1=i2_series_Civ1; 185 j1_series_Civ1=ones(size(i1_series_Civ1)); 186 if strcmp(Param.ActionInput.ListCompareMode,'PIV') 187 j2_series_Civ1=ones(size(i1_series_Civ1)); 188 end 189 else % movie for each burst or volume (index j) 190 FrameIndex_A_Civ1=j1_series_Civ1; 191 FrameIndex_B_Civ1=j2_series_Civ1; 192 end 193 if isempty(PairCiv2) 194 FrameIndex_A_Civ2=FrameIndex_A_Civ1; 195 FrameIndex_B_Civ2=FrameIndex_B_Civ1; 196 else 197 if isempty(j1_series_Civ2) 198 FrameIndex_A_Civ2=i1_series_Civ2; 199 FrameIndex_B_Civ2=i2_series_Civ2; 200 j1_series_Civ2=ones(size(i1_series_Civ2)); 188 201 if strcmp(Param.ActionInput.ListCompareMode,'PIV') 189 j2_series_Civ1=ones(size(i1_series_Civ1)); 190 end 191 else % movie for each burst or volume (index j) 192 FrameIndex_A_Civ1=j1_series_Civ1; 193 FrameIndex_B_Civ1=j2_series_Civ1; 194 end 195 if isempty(PairCiv2) 196 FrameIndex_A_Civ2=FrameIndex_A_Civ1; 197 FrameIndex_B_Civ2=FrameIndex_B_Civ1; 202 j2_series_Civ2=ones(size(i1_series_Civ2)); 203 end 198 204 else 199 if isempty(j1_series_Civ2) 200 FrameIndex_A_Civ2=i1_series_Civ2; 201 FrameIndex_B_Civ2=i2_series_Civ2; 202 j1_series_Civ2=ones(size(i1_series_Civ2)); 203 if strcmp(Param.ActionInput.ListCompareMode,'PIV') 204 j2_series_Civ2=ones(size(i1_series_Civ2)); 205 end 206 else 207 FrameIndex_A_Civ2=j1_series_Civ2; 208 FrameIndex_B_Civ2=j2_series_Civ2; 209 end 210 end 211 if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) 212 disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) 213 return 214 end 215 end 216 217 %% check the first image pair 218 if Param.ActionInput.CheckCiv1% Civ1 is performed 219 NbField=numel(i1_series_Civ1); 220 elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 221 NbField=numel(i1_series_Civ2); 222 else 223 NbField=numel(i1_series_Civ1);% no image used (only detect_false or patch) TO CHECK 224 end 225 226 %% Output directory 227 OutputDir=''; 228 if CheckOutputFile 229 OutputDir=[Param.OutputSubDir Param.OutputDirExt]; 230 end 205 FrameIndex_A_Civ2=j1_series_Civ2; 206 FrameIndex_B_Civ2=j2_series_Civ2; 207 end 208 end 209 if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) 210 disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) 211 return 212 end 213 end 214 215 %% check the first image pair 216 if Param.ActionInput.CheckCiv1% Civ1 is performed 217 NbField=numel(i1_series_Civ1); 218 elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 219 NbField=numel(i1_series_Civ2); 220 else 221 NbField=numel(i1_series_Civ1);% no image used (only detect_false or patch) TO CHECK 231 222 end 232 223 233 224 %% prepare output Data 225 OutputDir=[Param.OutputSubDir Param.OutputDirExt]; 234 226 ListGlobalAttribute={'Conventions','Program','CivStage'}; 235 227 Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes … … 241 233 242 234 %% get timing from the ImaDoc file or input video 243 if iview_A~=0244 245 246 247 XmlData=imadoc2struct(XmlFileName);248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 end235 % if iview_A~=0 236 XmlFileName=find_imadoc(RootPath_A,SubDir_A); 237 Time=[]; 238 if ~isempty(XmlFileName) 239 XmlData=imadoc2struct(XmlFileName);%read the time from XmlFileName 240 if isfield(XmlData,'Time') 241 Time=XmlData.Time; 242 end 243 if isfield(XmlData,'Camera') 244 if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) 245 NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform 246 if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) 247 msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); 248 end 249 end 250 if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) 251 TimeUnit=XmlData.Camera.TimeUnit; 252 end 253 end 254 end 255 % end 264 256 265 257 %%%%% MAIN LOOP %%%%%% … … 284 276 end 285 277 end 286 % if CheckInputFile287 if CheckOutputFile288 289 if iview_A==0 % no nc file has been entered290 ncfile=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},...291 NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield));292 else% an existing nc file has been entered293 if iview_A==1% if Civ1 is performed294 Civ1Dir=OutputDir;295 else296 Civ1Dir=Param.InputTable{1,2};297 end298 299 ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...300 301 302 ncfile=fullfile_uvmat(OutputPath,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],...303 304 305 end306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 end278 % % if CheckInputFile 279 % if CheckOutputFile 280 OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); 281 % if iview_A==0 % no nc file has been entered 282 % ncfile=fullfile_uvmat(OutputPath,Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... 283 % NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); 284 % else% an existing nc file has been entered 285 % if iview_A==1% if Civ1 is performed 286 % Civ1Dir=OutputDir; 287 % else 288 % Civ1Dir=Param.InputTable{1,2}; 289 % end 290 if strcmp(Param.ActionInput.ListCompareMode,'PIV') 291 ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... 292 j1_series_Civ1(ifield),j2_series_Civ1(ifield)); 293 else 294 ncfile=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... 295 j1_series_Civ1(ifield),j2_series_Civ1(ifield)); 296 end 297 % end 298 ncfile_out=ncfile;% by default 299 300 if isfield (Param.ActionInput,'Civ2') 301 i1_civ2=i1_series_Civ2(ifield); 302 i2_civ2=i1_civ2; 303 if ~isempty(i2_series_Civ2) 304 i2_civ2=i2_series_Civ2(ifield); 305 end 306 j1_civ2=1; 307 if ~isempty(j1_series_Civ2) 308 j1_civ2=j1_series_Civ2(ifield); 309 end 310 j2_civ2=i1_civ2; 311 if ~isempty(j2_series_Civ2) 312 j2_civ2=j2_series_Civ2(ifield); 313 end 314 if strcmp(Param.ActionInput.ListCompareMode,'PIV') 315 ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); 316 else % displacement 317 ncfile_out=fullfile_uvmat(OutputPath,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); 318 end 319 end 320 if ~CheckOverwrite && exist(ncfile_out,'file') 321 disp(['existing output file ' ncfile_out ' already exists, skip to next field']) 322 continue% skip iteration if the mode overwrite is desactivated and the result file already exists 323 end 324 % end 333 325 ImageName_A='';ImageName_B='';%default 334 326 VideoObject_A=[];VideoObject_B=[]; … … 337 329 % if Civ1 computation is requested 338 330 if Param.ActionInput.CheckCiv1 339 if CheckInputFile 340 disp('civ1 started') 341 end 331 disp('civ1 started') 342 332 par_civ1=Param.ActionInput.Civ1;% parameters for civ1 343 if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) 344 try 345 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 346 ImageName_A=Param.ActionInput.RefFile; 347 else 348 ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); 333 %if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) 334 try 335 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 336 ImageName_A=Param.ActionInput.RefFile; 337 else 338 ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); 339 end 340 if strcmp(FileExt_A,'.nc')% case of input images in format netcdf 341 FieldName_A=Param.InputFields.FieldName; 342 [DataIn,~,~,errormsg]=nc2struct(ImageName_A,{FieldName_A}); 343 par_civ1.ImageA=DataIn.(FieldName_A); 344 else % usual image formats for image A 345 if isempty(FileType_A)% open the image object if not already done in case of movie input 346 [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); 347 FileType_A=FileInfo_A.FileType; 348 if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'}), 1))% case of video input 349 Time=zeros(FileInfo_A.NumberOfFrames+1,2); 350 Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; 351 end 352 if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default 353 MaxIndex_i=max(i2_series_Civ1); 354 MaxIndex_j=max(j2_series_Civ1); 355 Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); 356 Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); 357 Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros 358 Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros 359 end 349 360 end 350 if strcmp(FileExt_A,'.nc')% case of input images in format netcdf 351 FieldName_A=Param.InputFields.FieldName; 352 [DataIn,~,~,errormsg]=nc2struct(ImageName_A,{FieldName_A}); 353 par_civ1.ImageA=DataIn.(FieldName_A); 354 else % usual image formats for image A 355 if isempty(FileType_A)% open the image object if not already done in case of movie input 356 [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); 357 FileType_A=FileInfo_A.FileType; 358 if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'}), 1))% case of video input 359 Time=zeros(FileInfo_A.NumberOfFrames+1,2); 360 Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; 361 end 362 if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default 363 MaxIndex_i=max(i2_series_Civ1); 364 MaxIndex_j=max(j2_series_Civ1); 365 Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); 366 Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); 367 Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros 368 Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros 369 end 370 end 371 if isempty(regexp(ImageName_A,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_A,'file') 372 disp([ImageName_A ' missing']) 373 continue 374 end 375 tsart_input=tic; 376 [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); 377 time_input=toc(tsart_input); 378 end 379 ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); 380 if isempty(FileType_B)% determine the image type for the first field 381 [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); 382 FileType_B=FileInfo_B.FileType; 383 end 384 if isempty(regexp(ImageName_B,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_B,'file') 385 disp([ImageName_B ' missing']) 361 if isempty(regexp(ImageName_A,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_A,'file') 362 disp([ImageName_A ' missing']) 386 363 continue 387 364 end 388 [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); 389 catch ME % display errors in reading input images 390 if ~isempty(ME.message) 391 disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) 392 continue 393 end 394 end 395 396 % par_civ1.ImageWidth=size(par_civ1.ImageA,2); 397 % par_civ1.ImageHeight=size(par_civ1.ImageA,1); 398 list_param=(fieldnames(Param.ActionInput.Civ1))'; 399 list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list 400 Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param 401 Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images 402 %indicate the values of all the global attributes in the output data 403 Data.Civ1_ImageA=ImageName_A; 404 Data.Civ1_ImageB=ImageName_B; 405 i1=i1_series_Civ1(ifield); 406 i2=i1; 407 if ~isempty(i2_series_Civ1) 408 i2=i2_series_Civ1(ifield); 409 end 410 j1=1; 411 if ~isempty(j1_series_Civ1) 412 j1=j1_series_Civ1(ifield); 413 end 414 j2=j1; 415 if ~isempty(j2_series_Civ1) 416 j2=j2_series_Civ1(ifield); 417 end 418 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 419 Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image 420 Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading 421 else 422 Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair 423 Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); 424 end 425 for ilist=1:length(list_param) 426 Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); 427 end 428 Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; 429 430 Data.CivStage=1; 365 tsart_input=tic; 366 [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); 367 time_input=toc(tsart_input); 368 end 369 ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); 370 if isempty(FileType_B)% determine the image type for the first field 371 [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); 372 FileType_B=FileInfo_B.FileType; 373 end 374 if isempty(regexp(ImageName_B,'(^http://)|(^https://)', 'once')) && ~exist(ImageName_B,'file') 375 disp([ImageName_B ' missing']) 376 continue 377 end 378 [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); 379 catch ME % display errors in reading input images 380 if ~isempty(ME.message) 381 disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) 382 continue 383 end 384 end 385 386 % par_civ1.ImageWidth=size(par_civ1.ImageA,2); 387 % par_civ1.ImageHeight=size(par_civ1.ImageA,1); 388 list_param=(fieldnames(Param.ActionInput.Civ1))'; 389 list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list 390 Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param 391 Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images 392 %indicate the values of all the global attributes in the output data 393 Data.Civ1_ImageA=ImageName_A; 394 Data.Civ1_ImageB=ImageName_B; 395 i1=i1_series_Civ1(ifield); 396 i2=i1; 397 if ~isempty(i2_series_Civ1) 398 i2=i2_series_Civ1(ifield); 399 end 400 j1=1; 401 if ~isempty(j1_series_Civ1) 402 j1=j1_series_Civ1(ifield); 403 end 404 j2=j1; 405 if ~isempty(j2_series_Civ1) 406 j2=j2_series_Civ1(ifield); 407 end 408 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 409 Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the second image 410 Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading 431 411 else 432 i1=Param.ActionInput.PairIndices.ref_i; %case of TESTmode 433 end 412 Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair 413 Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); 414 end 415 for ilist=1:length(list_param) 416 Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); 417 end 418 Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; 419 Data.CivStage=1; 420 434 421 % set the list of variables 435 422 Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_C','Civ1_FF'};% cell array containing the names of the fields to record … … 489 476 490 477 % caluclate velocity data 491 % tstart_civ1=tic;492 478 [Data.Civ1_X,Data.Civ1_Y,Data.Civ1_U,Data.Civ1_V,Data.Civ1_C,Data.Civ1_FF, result_conv, errormsg] = civ (par_civ1); 493 479 if ~isempty(errormsg) … … 495 481 return 496 482 end 497 % 498 % if exist('ncfile','var') 499 % CivFile=ncfile; 500 % % [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format 501 % % if ~isempty(errormsg) 502 % % disp_uvmat('ERROR',errormsg,checkrun) 503 % % return 504 % % end 505 % [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file 506 % if ~isempty(errormsg) 507 % disp(errormsg) 508 % return 509 % end 510 % elseif isfield(Param,'Civ1_X') 511 % Data.ListGlobalAttribute={}; 512 % Data.ListVarName={}; 513 % Data.VarDimName={}; 514 % Data.Civ1_X=Param.Civ1_X; 515 % Data.Civ1_Y=Param.Civ1_Y; 516 % Data.Civ1_U=Param.Civ1_U; 517 % Data.Civ1_V=Param.Civ1_V; 518 % Data.Civ1_FF=Param.Civ1_FF; 519 % end 520 end 521 483 end 484 522 485 523 486 %% Fix1 … … 542 505 end 543 506 %% Patch1 544 if isfield (Param.ActionInput,'Patch1')507 if Param.ActionInput.CheckPatch1 && isfield (Param.ActionInput,'Patch1') 545 508 disp('patch1 started') 546 547 509 tstart_patch1=tic; 510 548 511 % record the processing parameters of Patch1 as global attributes in the result nc file 549 512 list_param=fieldnames(Param.ActionInput.Patch1)'; … … 574 537 end 575 538 if isempty(ind_good) 576 577 578 end 579 539 disp_uvmat('ERROR','all vectors of civ1 are bad, check input parameters' ,checkrun) 540 return 541 end 542 580 543 % perform Patch calculation using the UVMAT fct 'filter_tps' 581 544 [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,~,Ures, Vres,~,FFres]=... … … 593 556 tstart_civ2=tic; 594 557 par_civ2=Param.ActionInput.Civ2; 595 if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) 596 par_civ2.ImageA=[]; 597 par_civ2.ImageB=[]; 598 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 599 ImageName_A_Civ2=Param.ActionInput.RefFile; 600 else 601 ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); 602 end 603 if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) 604 par_civ2.ImageA=par_civ1.ImageA; 605 else 606 [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); 607 end 608 ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); 609 if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) 610 par_civ2.ImageB=par_civ1.ImageB; 611 else 612 [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); 613 end 614 [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2); 615 [npy_ima,npx_ima]=size(par_civ2.ImageA(:,:)); 616 % par_civ2.ImageWidth=FileInfo_A.Width; 617 % par_civ2.ImageHeight=FileInfo_A.Height; 618 619 if par_civ2.CheckGrid &&~isempty(par_civ2.Grid) % case of input grid 620 GridData=nc2struct(Param.ActionInput.Civ2.Grid); 621 par_civ2.Grid=GridData.Grid; 622 par_civ2.CorrBoxSize=GridData.CorrBox; 623 624 else% automatic grid 625 nbinterv_x=floor((npx_ima-1)/par_civ2.Dx); 626 gridlength_x=nbinterv_x*par_civ2.Dx; 627 minix=ceil((npx_ima-gridlength_x)/2); 628 nbinterv_y=floor((npy_ima-1)/par_civ2.Dy); 629 gridlength_y=nbinterv_y*par_civ2.Dy; 630 miniy=ceil((npy_ima-gridlength_y)/2); 631 [GridX,GridY]=meshgrid(minix:par_civ2.Dx:npx_ima-1,miniy:par_civ2.Dy:npy_ima-1); 632 par_civ2.Grid=zeros(numel(GridX),2); 633 par_civ2.Grid(:,1)=reshape(GridX,[],1); 634 par_civ2.Grid(:,2)=reshape(GridY,[],1);% increases with array index 635 636 end 637 end 638 558 % if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) 559 par_civ2.ImageA=[]; 560 par_civ2.ImageB=[]; 561 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 562 ImageName_A_Civ2=Param.ActionInput.RefFile; 563 else 564 ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); 565 end 566 if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) 567 par_civ2.ImageA=par_civ1.ImageA; 568 else 569 [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); 570 end 571 ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); 572 if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) 573 par_civ2.ImageB=par_civ1.ImageB; 574 else 575 [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); 576 end 577 % [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A_Civ2); 578 npy_ima=size(par_civ2.ImageA,1); 579 npx_ima=size(par_civ2.ImageA,2); 580 if par_civ2.CheckGrid &&~isempty(par_civ2.Grid) % case of input grid 581 GridData=nc2struct(Param.ActionInput.Civ2.Grid); 582 par_civ2.Grid=GridData.Grid; 583 par_civ2.CorrBoxSize=GridData.CorrBox; 584 else% automatic grid 585 nbinterv_x=floor((npx_ima-1)/par_civ2.Dx); 586 gridlength_x=nbinterv_x*par_civ2.Dx; 587 minix=ceil((npx_ima-gridlength_x)/2); 588 nbinterv_y=floor((npy_ima-1)/par_civ2.Dy); 589 gridlength_y=nbinterv_y*par_civ2.Dy; 590 miniy=ceil((npy_ima-gridlength_y)/2); 591 [GridX,GridY]=meshgrid(minix:par_civ2.Dx:npx_ima-1,miniy:par_civ2.Dy:npy_ima-1); 592 par_civ2.Grid=zeros(numel(GridX),2); 593 par_civ2.Grid(:,1)=reshape(GridX,[],1); 594 par_civ2.Grid(:,2)=reshape(GridY,[],1);% increases with array index 595 end 596 639 597 % get the guess from patch1 or patch2 (case 'CheckCiv3') 640 % if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) 641 if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 642 SubRange= Data.Civ2_SubRange; 643 NbCentres=Data.Civ2_NbCentres; 644 Coord_tps=Data.Civ2_Coord_tps; 645 U_tps=Data.Civ2_U_tps; 646 V_tps=Data.Civ2_V_tps; 647 CivStage=Data.CivStage;%store the current CivStage 648 Civ1_Dt=Data.Civ2_Dt; 598 if iview_A==2 && isfield (par_civ2,'CheckCiv3') && strcmp(par_civ2.CheckCiv3,'iterate(civ3)') %get the guess from patch2% Civ1 data read in a netcdf file 599 [DataIn,~,~,errormsg]=nc2struct(filecell{1,ifield}); 600 if ~isempty(errormsg) 601 disp(errormsg) 602 return 603 end 604 SubRange= DataIn.Civ2_SubRange; 605 NbCentres=DataIn.Civ2_NbCentres; 606 Coord_tps=DataIn.Civ2_Coord_tps; 607 U_tps=DataIn.Civ2_U_tps; 608 V_tps=DataIn.Civ2_V_tps; 609 %CivStage=DataIn.CivStage;%store the current CivStage 610 Civ1_Dt=DataIn.Civ2_Dt; 649 611 Data=[];%reinitialise the result structure Data 650 612 Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; 651 613 Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes 652 614 Data.Program='civ_series'; 653 Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data615 % Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data 654 616 Data.ListVarName={}; 655 617 Data.VarDimName={}; … … 661 623 V_tps=Data.Civ1_V_tps; 662 624 Civ1_Dt=Data.Civ1_Dt; 663 Data.CivStage=4;664 end 665 % else666 % SubRange= par_civ2.Civ1_SubRange;667 % NbCentres=par_civ2.Civ1_NbCentres;668 % Coord_tps=par_civ2.Civ1_Coord_tps;669 % U_tps=par_civ2.Civ1_U_tps;670 % V_tps=par_civ2.Civ1_V_tps;671 % Civ1_Dt=par_civ2.Civ1_Dt;672 % Civ2_Dt=par_civ2.Civ1_Dt;673 % Data.ListVarName={};674 % Data.VarDimName={};675 % end676 Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data625 % Data.CivStage=4; 626 end 627 Data.CivStage=4; 628 % SubRange= par_civ2.Civ1_SubRange; 629 % NbCentres=par_civ2.Civ1_NbCentres; 630 % Coord_tps=par_civ2.Civ1_Coord_tps; 631 % U_tps=par_civ2.Civ1_U_tps; 632 % V_tps=par_civ2.Civ1_V_tps; 633 % Civ1_Dt=par_civ2.Civ1_Dt; 634 % Civ2_Dt=par_civ2.Civ1_Dt; 635 % Data.ListVarName={}; 636 % Data.VarDimName={}; 637 % end 638 Shiftx=zeros(size(par_civ2.Grid,1),1);% initialise the shift expected from civ1 data 677 639 Shifty=zeros(size(par_civ2.Grid,1),1); 678 640 nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains) … … 713 675 Shiftx(nbval>0)=Shiftx(nbval>0)./nbval(nbval>0); 714 676 Shifty(nbval>0)=Shifty(nbval>0)./nbval(nbval>0); 715 677 716 678 % introduce mask 717 679 if par_civ2.CheckMask && ~isempty(par_civ2.Mask) … … 753 715 end 754 716 end 755 756 if CheckInputFile % else Dt given by par_civ2 757 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 758 Civ1_Dt=1; 759 Civ2_Dt=1; 760 else 761 Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); 762 end 717 718 719 if strcmp(Param.ActionInput.ListCompareMode,'displacement') 720 Civ1_Dt=1; 721 Civ2_Dt=1; 722 else 723 Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); 763 724 end 764 725 par_civ2.SearchBoxShift=zeros(size(par_civ2.Grid)); 765 par_civ2.SearchBoxShift(:,1)=(Civ2_Dt/Civ1_Dt)*Shiftx; 726 par_civ2.SearchBoxShift(:,1)=(Civ2_Dt/Civ1_Dt)*Shiftx;%rescale the shift in case of Dt different for Civ1 and Civ2 766 727 par_civ2.SearchBoxShift(:,2)=(Civ2_Dt/Civ1_Dt)*Shifty; 767 % shift the grid points by half the expected shift to provide the correlation box position in image A 768 %par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2]; 769 728 770 729 if par_civ2.CheckDeformation 771 730 par_civ2.DUDX(nbval>0)=DUDX(nbval>0)./nbval(nbval>0); … … 774 733 par_civ2.DVDY(nbval>0)=DVDY(nbval>0)./nbval(nbval>0); 775 734 end 776 735 777 736 % calculate velocity data (y and v in image indices, reverse to y component) 778 737 779 738 [Data.Civ2_X,Data.Civ2_Y,Data.Civ2_U,Data.Civ2_V,Data.Civ2_C,Data.Civ2_FF,~, errormsg] = civ (par_civ2); 780 739 781 740 list_param=(fieldnames(Param.ActionInput.Civ2))'; 782 741 list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list … … 799 758 end 800 759 Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; 801 760 802 761 nbvar=numel(Data.ListVarName); 803 762 % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) … … 817 776 if exist('ncfile','var') 818 777 CivFile=ncfile; 819 [Data, tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and detect_false1 data in the existing netcdf file778 [Data,~,~,errormsg]=nc2struct(CivFile);%read civ1 and detect_false1 data in the existing netcdf file 820 779 if ~isempty(errormsg) 821 780 disp_uvmat('ERROR',errormsg,checkrun) … … 824 783 end 825 784 end 826 785 827 786 %% Fix2 828 if isfield (Param.ActionInput,'Fix2')787 if Param.ActionInput.CheckFix2 && isfield (Param.ActionInput,'Fix2')% if Fix2 computation is requested 829 788 disp('detect_false2 started') 830 789 list_param=fieldnames(Param.ActionInput.Fix2)'; … … 840 799 841 800 %% Patch2 842 if isfield (Param.ActionInput,'Patch2') 801 if Param.ActionInput.CheckPatch2 && isfield (Param.ActionInput,'Patch2')% if Patch2 computation is requested 802 843 803 disp('patch2 started') 844 804 tstart_patch2=tic; … … 869 829 ind_good=1:numel(Data.Civ2_X); 870 830 end 871 872 873 874 875 831 if isempty(ind_good) 832 disp_uvmat('ERROR','all vectors of civ2 are bad, check input parameters' ,checkrun) 833 return 834 end 835 876 836 [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=... 877 837 filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff); … … 884 844 end 885 845 886 %% write result in a netcdf file if requested887 if CheckOutputFile888 errormsg=struct2nc(ncfile_out,Data);889 if isempty(errormsg)890 disp([ncfile_out ' written'])891 else892 disp(errormsg)893 end894 time_total=toc(tstart);895 disp(['ellapsed time ' num2str(time_total/60,2) ' minutes'])896 disp(['time civ1 ' num2str(time_civ1,2) ' s'])897 disp(['time patch1 ' num2str(time_patch1,2) ' s'])898 disp(['time civ2 ' num2str(time_civ2,2) ' s'])899 disp(['time patch2 ' num2str(time_patch2,2) ' s'])900 if exist('time_input','var')901 disp(['time image reading ' num2str(time_input,2) ' s'])902 disp(['time other ' num2str((time_total-time_input-time_civ1-time_patch1-time_civ2-time_patch2),2) ' s'])903 904 end 905 end 846 %% write result in a netcdf file 847 errormsg=struct2nc(ncfile_out,Data); 848 if isempty(errormsg) 849 disp([ncfile_out ' written']) 850 else 851 disp(errormsg) 852 end 853 time_total=toc(tstart); 854 disp(['ellapsed time ' num2str(time_total/60,2) ' minutes']) 855 disp(['time civ1 ' num2str(time_civ1,2) ' s']) 856 disp(['time patch1 ' num2str(time_patch1,2) ' s']) 857 disp(['time civ2 ' num2str(time_civ2,2) ' s']) 858 disp(['time patch2 ' num2str(time_patch2,2) ' s']) 859 if exist('time_input','var') 860 disp(['time image reading ' num2str(time_input,2) ' s']) 861 disp(['time other ' num2str((time_total-time_input-time_civ1-time_patch1-time_civ2-time_patch2),2) ' s']) 862 end 863 end 864 865 906 866 907 867 %------------------------------------------------------------------------ … … 967 927 end 968 928 929 %------------------------------------------------------------------------ 930 % --- set the flag for false vectors 969 931 function FF=detect_false(Param,C,U,V,FFIn) 970 932 FF=FFIn;%default, good vectors -
trunk/src/uvmat.m
r1168 r1169 2898 2898 %case of view mask selection 2899 2899 if isequal(get(handles.CheckMask,'Value'),1) 2900 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); 2901 % if isempty(regexp(RootPath,'^http://')) 2902 % fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) 2903 % else 2904 % fileinput=[RootPath '/' SubDir '/' RootFile FileIndex FileExt];% 2905 % end 2906 % FileInfo=get_file_info(fileinput); 2907 2908 % MaskSubDir=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' 2909 % MaskPath=fullfile(RootPath,[MaskSubDir '.mask']); 2910 mdetect=0; 2911 % if exist(MaskPath,'dir') 2912 % ListStruct=dir(MaskPath);%look for a mask file 2913 % ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray 2914 % check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files 2915 % ListFiles=ListCells(1,:);%list of file and dri names 2916 % ListFiles=ListFiles(~check_dir);%list of file names (excluding dir) 2917 % if ~isempty(ListFiles) 2918 % for ifile=1:numel(ListFiles) 2919 % [tild,tild,MaskExt]=fileparts(ListFiles{1}); 2920 % [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileInfo]=find_file_series(MaskPath,ListFiles{ifile},0); 2921 % MaskFileType=MaskFileInfo.FileType; 2922 % if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) 2923 % mdetect=1; 2924 % end 2925 % if ~strcmp(MaskFile{ifile},MaskFile{1}) 2926 % mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection 2927 % break 2928 % end 2929 % end 2930 % end 2931 % RootPath=MaskPath; 2932 % end 2933 filemask= uigetfile_uvmat('pick a mask image file:',RootPath,'image'); 2900 [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); 2901 if isempty(regexp(RootPath,'^http://')) 2902 fileinput=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) 2903 else 2904 fileinput=[RootPath '/' SubDir '/' RootFile FileIndex FileExt];% 2905 end 2906 FileInfo=get_file_info(fileinput); 2907 if isfield(FileInfo,'MaskFile')&& exist(FileInfo.MaskFile,'file') 2908 filemask=FileInfo.MaskFile; 2909 else 2910 % MaskSubDir=regexprep(SubDir,'\..*','');%take the root part of SubDir, before the first dot '.' 2911 % MaskPath=fullfile(RootPath,[MaskSubDir '.mask']); 2912 % mdetect=0; 2913 % if exist(MaskPath,'dir') 2914 % ListStruct=dir(MaskPath);%look for a mask file 2915 % ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray 2916 % check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files 2917 % ListFiles=ListCells(1,:);%list of file and dri names 2918 % ListFiles=ListFiles(~check_dir);%list of file names (excluding dir) 2919 % if ~isempty(ListFiles) 2920 % for ifile=1:numel(ListFiles) 2921 % [tild,tild,MaskExt]=fileparts(ListFiles{1}); 2922 % [tild,tild,MaskFile{ifile},i1_series,i2_series,j1_series,j2_series,MaskNomType,MaskFileInfo]=find_file_series(MaskPath,ListFiles{ifile},0); 2923 % MaskFileType=MaskFileInfo.FileType; 2924 % if strcmp(MaskFileType,'image') && isempty(i2_series) && isempty(j2_series) 2925 % mdetect=1; 2926 % end 2927 % if ~strcmp(MaskFile{ifile},MaskFile{1}) 2928 % mdetect=0;% cancel detection test in case of multiple masks, use the brower for selection 2929 % break 2930 % end 2931 % end 2932 % end 2933 % RootPath=MaskPath; 2934 % end 2935 filemask= uigetfile_uvmat('pick a mask image file:',RootPath,'image'); 2936 end 2934 2937 if ~isempty(filemask) 2935 2938 [MaskPath,FileName,FileExt]=fileparts(filemask); … … 2949 2952 errormsg=update_mask(handles); 2950 2953 if ~isempty(errormsg) 2951 2954 msgbox_uvmat(['ERROR','error in displaying mask, ' errormsg]); 2952 2955 end 2953 2956 testmask=1; … … 2956 2959 MaskData=get(handles.CheckMask,'UserData'); 2957 2960 if isfield(MaskData,'maskhandle') && ishandle(MaskData.maskhandle) 2958 delete(MaskData.maskhandle) 2961 % delete(MaskData.maskhandle) 2962 set(MaskData.maskhandle,'Visible','off') 2959 2963 end 2960 2964 set(handles.CheckMask,'UserData',[]) … … 3037 3041 if ~isempty(hmask) 3038 3042 set(hmask,'CData',imflag) 3039 set(hmask,'AlphaData',flagmask*0. 6)3043 set(hmask,'AlphaData',flagmask*0.3) 3040 3044 set(hmask,'XData',MaskField.Coord_x); 3041 3045 set(hmask,'YData',MaskField.Coord_y); … … 3044 3048 axes(handles.PlotAxes) 3045 3049 hold on 3046 MaskInfo.maskhandle=image(MaskField.Coord_x,MaskField.Coord_y,imflag,'Tag','mask','HitTest','off','AlphaData',0. 6*ones(size(flagmask)));3050 MaskInfo.maskhandle=image(MaskField.Coord_x,MaskField.Coord_y,imflag,'Tag','mask','HitTest','off','AlphaData',0.3*ones(size(flagmask))); 3047 3051 set(handles.CheckMask,'UserData',MaskInfo) 3048 3052 end
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