Index: /trunk/src/check_files.m =================================================================== --- /trunk/src/check_files.m (revision 511) +++ /trunk/src/check_files.m (revision 512) @@ -54,5 +54,5 @@ 'fill_GUI';...% fill a GUI with a set of parameters from a Matlab structure 'filter_tps';...% find the thin plate spline coefficients for interpolation-smoothing - 'find_field_indices';...% group the variables of a 'field object' into 'field cells' and specify their structure + 'find_field_cells';...% group the variables of a 'field object' into 'field cells' and specify their structure 'find_file_series';...%check the content of an input file and find the corresponding file series 'find_imadoc';...% find the ImaDoc xml file associated with a given input file Index: /trunk/src/civ.m =================================================================== --- /trunk/src/civ.m (revision 511) +++ /trunk/src/civ.m (revision 512) @@ -533,5 +533,5 @@ else set(handles.ImaDoc,'String',''); %xml file not used for timing - time=(i1_series(:,1)+0:size(i1_series,1)-1);% time=index i + time=(i1_series(:,1)+0:size(i1_series,3)-1);% time=index i time=time'*ones(1,size(i1_series,2),1); %makes a time matrix with the same time for all j indices TimeUnit='frame'; @@ -2533,7 +2533,5 @@ % the root name and indices may be corrected by including the first index i1 if a corresponding xml file exists [RootPath,SubDir,RootFile_1,i1_series,i2_series,j1_series,j2_series,nom_type_1,FileType,Object,i1,i2,j1,j2]=find_file_series(FilePath,[FileName Ext]); - - % [tild,tild,RootFile_1,tild,tild,tild,tild,tild,nom_type_1]=fileparts_uvmat(fileinput); - %[RootFile_1,i1_series,tild,j1_series,tild,nom_type_1,FileType,Object]=find_file_series(PathName,FileName); + %check image nom type if ~strcmp(nom_type_1,get(handles.NomType,'String')) Index: /trunk/src/find_file_series.m =================================================================== --- /trunk/src/find_file_series.m (revision 511) +++ /trunk/src/find_file_series.m (revision 512) @@ -290,4 +290,6 @@ end end - - +i1_series=permute(i1_series,[3 2 1]);% permute dimensions +i2_series=permute(i2_series,[3 2 1]);% permute dimensions +j1_series=permute(j1_series,[3 2 1]);% permute dimensions +j2_series=permute(j2_series,[3 2 1]);% permute dimensions Index: /trunk/src/get_field.m =================================================================== --- /trunk/src/get_field.m (revision 511) +++ /trunk/src/get_field.m (revision 512) @@ -218,7 +218,7 @@ set(handles.scalar,'String', Txt ) -[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Field); +[CellVarIndex,NbDim,VarType,errormsg]=find_field_cells(Field); if ~isempty(errormsg) - msgbox_uvmat('ERROR',['error in get_field/Field_input/find_field_indices: ' errormsg]) + msgbox_uvmat('ERROR',['error in get_field/Field_input/find_field_cells: ' errormsg]) return end @@ -301,5 +301,5 @@ variables_Callback(hObject, eventdata, handles) end -[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Field); +[CellVarIndex,NbDim,VarType,errormsg]=find_field_cells(Field); for icell=1:numel(CellVarIndex) VarIndex=CellVarIndex{icell}; Index: /trunk/src/mouse_down.m =================================================================== --- /trunk/src/mouse_down.m (revision 511) +++ /trunk/src/mouse_down.m (revision 512) @@ -110,6 +110,6 @@ tagaxes=get(hchild,'tag'); if isfield(FigData,tagaxes) - eval(['Field=FigData.' tagaxes ';']) - [CellVarIndex,NbDim,VarType]=find_field_indices(Field);%analyse the physical fields contained in Field + Field=FigData.(tagaxes); + [CellVarIndex,NbDim,VarType]=find_field_cells(Field);%analyse the physical fields contained in Field for icell=1:numel(CellVarIndex)%look for all physical fields if NbDim(icell)==2 % select 2D field Index: /trunk/src/mouse_motion.m =================================================================== --- /trunk/src/mouse_motion.m (revision 511) +++ /trunk/src/mouse_motion.m (revision 512) @@ -97,7 +97,7 @@ tagaxes=get(CurrentAxes,'tag'); if isfield(FigData,tagaxes) - eval(['Field=FigData.' tagaxes ';']) + Field=FigData.(tagaxes); if isfield(Field,'ListVarName') - [CellVarIndex,NbDim,VarType]=find_field_indices(Field);%analyse the physical fields contained in Field + [CellVarIndex,NbDim,VarType]=find_field_cells(Field);%analyse the physical fields contained in Field text_displ_1=''; text_displ_2=''; Index: /trunk/src/plot_field.m =================================================================== --- /trunk/src/plot_field.m (revision 511) +++ /trunk/src/plot_field.m (revision 512) @@ -6,5 +6,5 @@ % 2D vector fields are represented by arrows, 2D scalar fields by grey scale images or contour plots, 1D fields are represented by usual plot with (abscissa, ordinate). % The input field structure is first tested by check_field_structure.m, -% then split into blocks of related variables by find_field_indices.m. +% then split into blocks of related variables by find_field_cells.m. % The dimensionality of each block is obtained by this function % considering the presence of variables with the attribute .Role='coord_x' @@ -117,7 +117,7 @@ end % check the cells of fields : -[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(Data); +[CellVarIndex,NbDim,VarType,errormsg]=find_field_cells(Data); if ~isempty(errormsg) - msgbox_uvmat('ERROR',['input of plot_field/find_field_indices: ' errormsg]); + msgbox_uvmat('ERROR',['input of plot_field/find_field_cells: ' errormsg]); return end Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 511) +++ /trunk/src/proj_field.m (revision 512) @@ -36,5 +36,5 @@ % .VarAttribute: cell of structures s containing names and values of variable attributes (s.name=value) for each variable of .ListVarName % .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName -% The variables are grouped in 'fields', made of a set of variables with common dimensions (using the function find_field_indices) +% The variables are grouped in 'fields', made of a set of variables with common dimensions (using the function find_field_cells) % The variable attribute 'Role' is used to define the role for plotting: % Role = 'scalar': (default) represents a scalar field @@ -178,5 +178,5 @@ [ProjData,errormsg]=proj_heading(FieldData,ObjectData); ProjData.NbDim=0; -[CellVarIndex,NbDimCell,VarTypeCell,errormsg]=find_field_indices(FieldData); +[CellVarIndex,NbDimCell,VarTypeCell,errormsg]=find_field_cells(FieldData); if ~isempty(errormsg) errormsg=['error in proj_field/proj_points:' errormsg]; @@ -372,5 +372,5 @@ % DimVarIndex=0;%initilise list of indices for dimension variables idimvar=0; -[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(FieldData); +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_cells(FieldData); if ~isempty(errormsg) errormsg=['error in proj_field/proj_patch:' errormsg]; @@ -593,5 +593,5 @@ %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions -[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(FieldData); +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_cells(FieldData); if ~isempty(errormsg) errormsg=['error in proj_field/proj_line:' errormsg]; @@ -1008,5 +1008,5 @@ idimvar=0; -[CellVarIndex,NbDimVec,VarTypeCell,errormsg]=find_field_indices(FieldData); +[CellVarIndex,NbDimVec,VarTypeCell,errormsg]=find_field_cells(FieldData); if ~isempty(errormsg) errormsg=['error in proj_field/proj_plane:' errormsg]; @@ -1679,5 +1679,5 @@ %----------------------------------------------------------------- idimvar=0; -[CellVarIndex,NbDimVec,VarTypeCell,errormsg]=find_field_indices(FieldData); +[CellVarIndex,NbDimVec,VarTypeCell,errormsg]=find_field_cells(FieldData); if ~isempty(errormsg) errormsg=['error in proj_field/proj_plane:' errormsg]; Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 511) +++ /trunk/src/series.m (revision 512) @@ -588,18 +588,18 @@ %% display the min and max indices for all the file series -i_sum=sum(sum(i1_series,2),3);%sum of i1_series on the last index +i_sum=sum(sum(i1_series,2),1);%sum of i1_series on the last index MaxIndex_i=max(find(i_sum>0))-1;% max ref index i MinIndex_i=min(find(i_sum>0))-1;% min ref index i i2_min=[]; if ~isempty(i2_series) - i2_min=i2_series(1,2); + i2_min=i2_series(1,2,2); end j1_min=[]; if ~isempty(j1_series) - j1_min=j1_series(1,2); + j1_min=j1_series(1,2,2); end j2_min=[]; if ~isempty(j2_series) - j2_min=j2_series(1,2); + j2_min=j2_series(1,2,2); end if isequal(MinIndex_i,1) &&... @@ -607,5 +607,5 @@ MinIndex_i=0; end -j_sum=sum(sum(j1_series,1),3); +j_sum=sum(sum(j1_series,1),1); MaxIndex_j=max(find(j_sum>0))-1; MinIndex_j=min(find(j_sum>0))-1; @@ -793,6 +793,6 @@ nbview=numel(SeriesData.i1_series); for iview=1:nbview - index_min(iview)=min(find(SeriesData.i1_series{iview}(2:end,2:end,1)>0)); - index_max(iview)=max(find(SeriesData.i1_series{iview}(2:end,2:end,1)>0)); + index_min(iview)=min(find(SeriesData.i1_series{iview}(1,2:end,2:end)>0)); + index_max(iview)=max(find(SeriesData.i1_series{iview}(1,2:end,2:end)>0)); end index_min=min(index_min); @@ -808,5 +808,5 @@ ind_y=1+(iview-1)*range_y:iview*range_y; LineData=zeros(1,range_index); - x_index=find(SeriesData.i1_series{iview}(2:end,2:end,1)>0)-index_min+1; + x_index=find(SeriesData.i1_series{iview}(1,2:end,2:end)>0)-index_min+1; LineData(x_index)=1; LineData=interp1(x,LineData,xI,'nearest'); @@ -815,27 +815,4 @@ CData=cat(3,zeros(size(CData)),CData,zeros(size(CData))); set(handles.FileStatus,'CData',CData); - -% -% -% xima=0.5:pos(3)-0.5;% pixel positions on the image representing the existing file indices -% yima=0.5:pos(4)-0.5; -% [XIma,YIma]=meshgrid(xima,yima); -% nb_i=size(i1_series,1); -% nb_j=size(i1_series,2); -% ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i; -% ind_j=(0.5:nb_j-0.5)*pos(4)/nb_j; -% [Ind_i,Ind_j]=meshgrid(ind_i,ind_j); -% CData=zeros([size(XIma) 3]);%black color -% file_ima=double((i1_series(:,:,1)>0)'); -% if numel(file_ima)>=2 -% if size(file_ima,1)==1 -% CLine=interp1(ind_i,file_ima,xima,'nearest'); -% CData(:,:,2)=ones(size(yima'))*CLine; -% else -% CData(:,:,2)=interp2(Ind_i,Ind_j,file_ima,XIma,YIma,'nearest'); -% end -% set(handles.FileStatus,'CData',CData) -% end -% set(handles.FileStatus,'Units','normalized') @@ -1077,6 +1054,6 @@ % end for iview=1:numel(SeriesData.i1_series) - index_min(iview)=min(find(SeriesData.i1_series{iview}(2:end,2:end,1)>0)); - index_max(iview)=max(find(SeriesData.i1_series{iview}(2:end,2:end,1)>0)); + index_min(iview)=min(find(SeriesData.i1_series{iview}(1,2:end,2:end)>0)); + index_max(iview)=max(find(SeriesData.i1_series{iview}(1,2:end,2:end)>0)); end [index_min,iview_min]=min(index_min); @@ -2185,5 +2162,5 @@ yima=0.5:pos(4)-0.5; [XIma,YIma]=meshgrid(xima,yima); -nb_i=size(i1_series,1); +nb_i=size(i1_series,3); nb_j=size(i1_series,2); ind_i=(0.5:nb_i-0.5)*pos(3)/nb_i; Index: /trunk/src/sub_field.m =================================================================== --- /trunk/src/sub_field.m (revision 511) +++ /trunk/src/sub_field.m (revision 512) @@ -65,10 +65,10 @@ %% check the two input fields -[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_indices(Field); +[CellVarIndex,NbDim,VarTypeCell,errormsg]=find_field_cells(Field); if ~isempty(errormsg) errormsg=['invalid first input to sub_field:' errormsg]; return end -[CellVarIndex_1,NbDim_1,VarTypeCell_1,errormsg]=find_field_indices(Field_1); +[CellVarIndex_1,NbDim_1,VarTypeCell_1,errormsg]=find_field_cells(Field_1); if ~isempty(errormsg) errormsg=['invalid second input to sub_field:' errormsg]; Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 511) +++ /trunk/src/uvmat.m (revision 512) @@ -51,37 +51,36 @@ % % 1) Input filenames are determined by MenuBrowse (first field), MenuBrowse_1 -% (second field), or by the stored file names under Browse, or as an input of uvmat. -% 2) These functions call 'display_file_name.m' which detects the file series, and fills the file index boxes -% 3) Then 'update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file) -% 4) Then fields are opened and visualised by the main sub-function 'refresh_field.m' -% The function first reads the name of the input file from the edit boxes of the GUI -% A second input file can be introduced for file comparison -% It then reads the input file(s) with the appropriate function, read for -% images, read_civxdata.m for CIVx PIV data, nc2struct for other netcdf -% files. -% Main input open second input open(_1) second image (pair animation) -% | | -% | | -% Field{1} Field{2} -% | -% coord transform (phys.m) or other user defined fct acting on Field{i} | -% Field{i} -% | -% calc_field.m: calculate scalar or other derived fields (vort, div..). +% (second field), or by the stored file name .FileName_1, or as an input of uvmat. +% 2) These functions call 'uvmat/display_file_name.m' which detects the file series, and fills the file index boxes +% 3) Then 'uvmat/update_rootinfo.m' Updates information about a new field series (indices to scan, timing, calibration from an xml file) +% 4) Then fields are opened and visualised by the main sub-function 'uvmat/refresh_field.m' +% The function first reads the name of the input file(s) (one or two) from the edit boxes of the GUI +% It then reads the input file(s) with the function read_field.m and perform the following list of operations: % -% sub_field.m: combine the input Field{i} in a single set of fields (vector + scalar): -% Field{i=1->3}.X --> UvData.X | -% | -% UvData -% | -% plot histograms of the whole field -% proj_field.m: project the set of fields on the current projection objects defined by UvData.Object -% | | -% ObjectData -% | -% plot_field.m: plot the projected fields and store them as | -% UvData.PlotAxes | -% | -% AxeData +% %%%%%%%% structure of uvmat/refresh_field.m %%%%%%%% +% +% Main input open second input open_1 +% | | +% read_field.m read_field.m +% | | +% Field{1} Field{2} +% | | +% --->transform fct<--- transform (e.g. phys.m) and combine input fields +% | +% (calc_tps.m) calculate tps coefficients (for filter projection or spatial derivatives). +% | +% (calc_field.m) calculate field +% | +% UvData.Field-------------->histogram +% _____________|____________ +% | | +% proj_field.m proj_field.m project the field on the projection objects +% | | +% UvData.PlotAxes ViewData.PlotAxes (on view_field) +% | | +% plot_field.m (uvmat) plot_field.m (view_field) plot the projected fields +% +% rmq: calc_field can be performed instead at the level of proj_field when needed +% % %%%%%%%%%%%%%% SCALARS: %%%%%%%%%%%%??%%% @@ -357,5 +356,6 @@ function MenuBrowse_Callback(hObject, eventdata, handles) [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); -oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; +%oldfile=[fullfile(RootPath,SubDir,RootFile) FileIndices FileExt]; +oldfile=fullfile(RootPath,SubDir); if isempty(oldfile)||isequal(oldfile,'') %loads the previously stored file name and set it as default in the file_input box dir_perso=prefdir; @@ -371,5 +371,5 @@ fileinput=[PathName FileName];%complete file name if ~exist(fileinput,'file') - return %abandon of the browser is cancelled + return %abandon if the browser is cancelled end @@ -1014,5 +1014,5 @@ end end -[ref_i,ref_j]=find(i1_series); +[ref_j,ref_i]=find(i1_series); if ~isempty(j1_series) state_j='on'; @@ -1583,10 +1583,10 @@ if get(handles.scan_i,'Value')==1% case of scanning along index i ref_i=ref_i+step; - while ref_i>=0 && size(UvData.i1_series{1},1)>=ref_i+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0 + while ref_i>=0 && size(UvData.i1_series{1},3)>=ref_i+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0 ref_i=ref_i+step; end else % case of scanning along index j (burst numbers) ref_j=ref_j+step; - while ref_j>=0 && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(ref_i+1,ref_j+1,1)==0 + while ref_j>=0 && size(UvData.i1_series{1},2)>=ref_j+1 && UvData.i1_series{1}(1,ref_j+1,ref_i+1)==0 ref_j=ref_j+step; end @@ -1597,5 +1597,5 @@ elseif ref_j<0 errormsg='minimum j index reached'; - elseif ref_i+1>size(UvData.i1_series{1},1) + elseif ref_i+1>size(UvData.i1_series{1},3) errormsg='maximum i index reached (reload the input file to update the index bound)'; elseif ref_j+1>size(UvData.i1_series{1},2) @@ -1603,29 +1603,26 @@ end if ~isempty(errormsg),return,end - i1_subseries=UvData.i1_series{1}(ref_i+1,ref_j+1,:); - i1_subseries=i1_subseries(i1_subseries>0); - if isempty(i1_subseries)% case of pairs - i1_subseries=UvData.i1_series{1}(ref_i+1,:,:); - end - if isempty(i1_subseries),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return - else - i1=i1_subseries(end); - end + siz=size(UvData.i1_series{1}); + ref_indices=ref_i*siz(1)*siz(2)+ref_j*siz(1)+1:ref_i*siz(1)*siz(2)+(ref_j+1)*siz(1); + i1_subseries=UvData.i1_series{1}(ref_indices); + ref_indices=ref_indices(i1_subseries>0); + if isempty(ref_indices)% case of pairs (free index i) + ref_indices=ref_i*siz(1)*siz(2)+1:(ref_i+1)*siz(1)*siz(2); + i1_subseries=UvData.i1_series{1}(ref_indices); + ref_indices=ref_indices(i1_subseries>0); + end + if isempty(ref_indices),errormsg='no next frame: set num_IndexIncrement =''*'' to reach the next existing file';return + end + i1=UvData.i1_series{1}(ref_indices(end)); if ~isempty(UvData.i2_series{1}) - i2_subseries=UvData.i2_series{1}(ref_i+1,ref_j+1,:); - i2_subseries=i2_subseries(i2_subseries>0); - i2=i2_subseries(end); + i2=UvData.i2_series{1}(ref_indices(end)); end if ~isempty(UvData.j1_series{1}) - j1_subseries=UvData.j1_series{1}(ref_i+1,ref_j+1,:); - j1_subseries=j1_subseries(j1_subseries>0); - j1=j1_subseries(end); + j1=UvData.j1_series{1}(ref_indices(end)); end if ~isempty(UvData.j2_series{1}) - j2_subseries=UvData.j2_series{1}(ref_i+1,ref_j+1,:); - j2_subseries=j2_subseries(j2_subseries>0); - j2=j2_subseries(end); + j2=UvData.j2_series{1}(ref_indices(end)); end - % case of a second file series + % case of a second file series (TODO:revise) if numel(UvData.i1_series)>=2 i1_subseries=UvData.i1_series{2}(ref_i+1,ref_j+1,:); @@ -1705,5 +1702,5 @@ UvData=get(handles.uvmat,'UserData'); if isequal(FieldName,'image') - test_1=0; + index=1; [RootPath,SubDir,RootFile,FileIndices,Ext]=read_file_boxes(handles); NomType=get(handles.NomType,'String'); @@ -1713,5 +1710,5 @@ FieldName=list_fields{index_fields}; % selected field if isequal(FieldName,'image') - test_1=1; + index=2; [RootPath,tild,RootFile,FileIndex_1,Ext,NomType]=read_file_boxes_1(handles); else @@ -1739,6 +1736,10 @@ num_i2=num_i1;%repeat the index i1 by default end -% imaname_1=name_generator(filebase,num_i2,num_j2,Ext,NomType); imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,Ext,NomType,num_i2,[],num_j2); +if strcmp(NomType,'*') + num_frame=num_i2; +else + num_frame=num_j2; +end if ~exist(imaname_1,'file') msgbox_uvmat('ERROR',['second input open (-) ' imaname_1 ' not found']); @@ -1748,70 +1749,77 @@ end +%% get the first image +%Field.AName='image'; +if index==1 + Field_a=UvData.Field;% movie on the second field +else + Field_a=UvData.Field_1;% movie on the first field +end + %% read the second image -Field.AName='image'; -if test_1 - Field_a=UvData.Field_1; -else - Field_a=UvData.Field; -end -Field_b.AX=Field_a.AX; -Field_b.AY=Field_a.AY; -% z index -nbslice=str2double(get(handles.num_NbSlice,'String')); -if ~isempty(nbslice) - Field_b.ZIndex=mod(num_i2-1,nbslice)+1; -end -Field_b.CoordUnit='pixel'; - -%% determine the input file type -if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1})) - FileType='movie'; -elseif isequal(lower(Ext),'.avi') - FileType='avi'; -elseif isequal(lower(Ext),'.vol') - FileType='vol'; -else - form=imformats(Ext(2:end)); - if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab - if isequal(NomType,'*'); - FileType='multimage'; - else - FileType='image'; - end - end -end -switch FileType - case 'movie' - if test_1 - Field_b.A=read(UvData.MovieObject{2},num_i2); - else - Field_b.A=read(UvData.MovieObject{1},num_i2); - end - case 'avi' - mov=aviread(imaname_1,num_i2); - Field_b.A=frame2im(mov(1)); - case 'vol' - Field_b.A=imread(imaname_1); - case 'multimage' - Field_b.A=imread(imaname_1,num_i2); - case 'image' - Field_b.A=imread(imaname_1); -end -if get(handles.slices,'Value') - Field.ZIndex=str2double(get(handles.z_index,'String')); -end +MovieObject=[]; +if numel(UvData.MovieObject)>=index + MovieObject=UvData.MovieObject{index}; +end +[Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileType{index},MovieObject,num_frame) +% Field_b.AX=Field_a.AX; +% Field_b.AY=Field_a.AY; +% % z index +% nbslice=str2double(get(handles.num_NbSlice,'String')); +% if ~isempty(nbslice) +% Field_b.ZIndex=mod(num_i2-1,nbslice)+1; +% end +% Field_b.CoordUnit='pixel'; +% +% %% determine the input file type +% if (test_1 && isfield(UvData,'MovieObject')&& numel(UvData.MovieObject>=2))||(~test_1 && ~isempty(UvData.MovieObject{1})) +% FileType='movie'; +% elseif isequal(lower(Ext),'.avi') +% FileType='avi'; +% elseif isequal(lower(Ext),'.vol') +% FileType='vol'; +% else +% form=imformats(Ext(2:end)); +% if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab +% if isequal(NomType,'*'); +% FileType='multimage'; +% else +% FileType='image'; +% end +% end +% end +% switch FileType +% case 'movie' +% if test_1 +% Field_b.A=read(UvData.MovieObject{2},num_i2); +% else +% Field_b.A=read(UvData.MovieObject{1},num_i2); +% end +% case 'avi' +% mov=aviread(imaname_1,num_i2); +% Field_b.A=frame2im(mov(1)); +% case 'vol' +% Field_b.A=imread(imaname_1); +% case 'multimage' +% Field_b.A=imread(imaname_1,num_i2); +% case 'image' +% Field_b.A=imread(imaname_1); +% end +% if get(handles.slices,'Value') +% Field.ZIndex=str2double(get(handles.z_index,'String')); +% end %px to phys or other transform on field -menu_transform=get(handles.transform_fct,'String'); -choice_value=get(handles.transform_fct,'Value'); -transform_name=menu_transform{choice_value};%name of the transform fct given by the menu 'transform_fct' -transform_list=get(handles.transform_fct,'UserData'); -transform=transform_list{choice_value}; -if ~isequal(transform_name,'') && ~isequal(transform_name,'px') - if test_1 && isfield(UvData,'XmlData') && numel(UvData.XmlData)==2 && isfield(UvData.XmlData{2},'GeometryCalib')%use geometry calib recorded from the ImaDoc xml file as first priority - Field_a=transform(Field_a,UvData.XmlData{2});%the first field has been stored without transform - Field_b=transform(Field_b,UvData.XmlData{2}); - elseif ~test_1 && isfield(UvData,'XmlData') && isfield(UvData.XmlData{1},'GeometryCalib')%use geometry calib - Field_b=transform(Field_b,UvData.XmlData{1}); +% menu_transform=get(handles.transform_fct,'String'); +% choice_value=get(handles.transform_fct,'Value'); +% transform_name=menu_transform{choice_value};%name of the transform fct given by the menu 'transform_fct' +% transform_list=get(handles.transform_fct,'UserData'); +transform=get(handles.path_transform,'UserData'); +if ~isempty(transform) + if isfield(UvData,'XmlData') && numel(UvData.XmlData)>=index %use geometry calib recorded from the ImaDoc xml file as first priority + if index==2 + Field_a=transform(Field_a,UvData.XmlData{index});%the first field has been stored without transform + end + Field_b=transform(Field_b,UvData.XmlData{index}); end end @@ -2249,4 +2257,8 @@ %% store the current open names, fields and vel types in uvmat interface UvData.FileName_1=FileName_1; +UvData.ParamOut_1=ParamOut_1; +if numel(Field)==2 +UvData.Field_1=Field{2}; %store the second field for possible use at next RUN +end %% apply coordinate transform or other user fct @@ -2262,18 +2274,21 @@ end transform=get(handles.path_transform,'UserData'); - nbre_arg=nargin(transform); - if length(Field)==2 - if nbre_arg==4 - [Field{1},Field{2}]=transform(Field{1},XmlData,Field{2},XmlData_1); - else - Field{1}=transform(Field{1},XmlData); - Field(2)=[]; - end - else - if nbre_arg==1 - Field{1}=transform(Field{1});%transform which does not need input parameter - else - Field{1}=transform(Field{1},XmlData); - end + switch nargin(transform) + case 4 + if length(Field)==2 + UvData.Field=transform(Field{1},XmlData,Field{2},XmlData_1); + else + UvData.Field=transform(Field{1},XmlData); + end + case 3 + if length(Field)==2 + UvData.Field=transform(Field{1},XmlData,Field{2}); + else + UvData.Field=transform(Field{1},XmlData); + end + case 2 + UvData.Field=transform(Field{1},XmlData); + case 1 + UvData.Field=transform(Field{1}); end end @@ -2293,8 +2308,8 @@ check_tps=1;%tps needed to get the requested field end -if (check_tps ||check_proj_tps)&&~isfield(Field{1},'Coord_tps') - Field{1}=calc_tps(Field{1}); -end -Field{1}.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}]; +if (check_tps ||check_proj_tps)&&~isfield(UvData.Field,'Coord_tps') + UvData.Field=calc_tps(UvData.Field); +end +UvData.Field.FieldList=[{ParamOut.FieldName} {ParamOut.ColorVar}]; %% calculate scalar @@ -2302,5 +2317,5 @@ &&~strcmp(ParamOut.FieldName,'velocity') && ~strcmp(ParamOut.FieldName,'get_field...') if ~check_proj_tps - Field{1}=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],Field{1}); + UvData.Field=calc_field([{ParamOut.FieldName} {ParamOut.ColorVar}],UvData.Field); end end @@ -2314,17 +2329,4 @@ end -%% combine the two input fields (e.g. substract velocity fields) -if numel(Field)==2 - [UvData.Field,errormsg]=sub_field(Field{1},Field{2}); - UvData.Field_1=Field{2}; %store the second field for possible use at next RUN - UvData.ParamOut_1=ParamOut_1; -else - UvData.Field=Field{1}; -end -if ~isempty(errormsg) - errormsg=['error in uvmat/refresh_field/sub_field:' errormsg]; - return -end -%UvData.Field.FieldList={FieldName}; % TODO: to generalise, used for proj_field with tps interpolation %% analyse input field @@ -2336,7 +2338,7 @@ return end -[CellVarIndex,NbDim,VarType,errormsg]=find_field_indices(UvData.Field);% analyse the input field structure +[CellVarIndex,NbDim,VarType,errormsg]=find_field_cells(UvData.Field);% analyse the input field structure if ~isempty(errormsg) - errormsg=['error in uvmat/refresh_field/find_field_indices: ' errormsg];% display error + errormsg=['error in uvmat/refresh_field/find_field_cells: ' errormsg];% display error return end @@ -3513,4 +3515,5 @@ %% create the function handle of the selected fct + if isempty(list_path{ichoice})% case of no selected fct transform_handle=[]; @@ -3527,4 +3530,5 @@ set(handles.path_transform,'String',list_path{ichoice}) set(handles.path_transform,'UserData',transform_handle) +set(handles.transform_fct,'UserData',list_path) %% update the ToolTip string of the menu transform_fct with the first line of the selected fct file @@ -4806,2 +4810,9 @@ ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project source directory'); datatree_browser(ProjectDir) + + +% -------------------------------------------------------------------- +function MenuBrowseProject_Callback(hObject, eventdata, handles) +RootPath=get(handles.RootPath,'String'); +ProjectDir = uigetdir(fileparts(fileparts(RootPath)), 'select the project directory'); +datatree_browser(ProjectDir)