Index: /trunk/src/editxml.m =================================================================== --- /trunk/src/editxml.m (revision 997) +++ /trunk/src/editxml.m (revision 998) @@ -111,12 +111,12 @@ DataIn=get(heditxml,'UserData'); if ~isempty(xs) - xs_node=list.xs_uid(ind);%xs_node of the subelement #ind - [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_node); - [element,subelem]=get_xml(t,path,xs_element,NewRootUid,xs_subelem); - update_list(handles,path,xs_element,element,NewRootUid,xs_subelem,subelem); - if xs_element.subtest + xs_node=list.xs_uid(ind);%xs_node of the subelement #ind + [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_node); + [element,subelem]=get_xml(t,path,xs_element,NewRootUid,xs_subelem); + update_list(handles,path,xs_element,element,NewRootUid,xs_subelem,subelem); + if xs_element.subtest DataIn.CurrentUid=[DataIn.CurrentUid NewRootUid];%record new current uid DataIn.xs_CurrentUid=[DataIn.xs_CurrentUid xs_node];%record the new curent schema uid - end + end % %update the import file display @@ -174,6 +174,6 @@ else [xs_nodeup,path,xs_element,xs_subelem]=scan_schema(xs,xs_nodeup); - [element,subelem]=get_xml(t,path,xs_element,nodeup,xs_subelem); - update_list(handles,path,xs_element,element,nodeup,xs_subelem,subelem); + [element,subelem]=get_xml(t,path,xs_element,nodeup,xs_subelem); + update_list(handles,path,xs_element,element,nodeup,xs_subelem,subelem); %update the import file display if isfield(DataIn,'h_ref')&ishandle(DataIn.h_ref) @@ -369,7 +369,7 @@ else DataIn.xs_CurrentUid=find(xs,'/xs:schema/xs:element');%uid of the root element in the schema - [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,DataIn.xs_CurrentUid);%scan the schema at the root level - [element,subelem]=get_xml(t,path,xs_element,1,xs_subelem);% read the corresponding xml data - update_list(handles,path,xs_element,element,1,xs_subelem,subelem);%update the display of information on the interface + [nodeup,path,xs_element,xs_subelem]=scan_schema(xs,DataIn.xs_CurrentUid);%scan the schema at the root level + [element,subelem]=get_xml(t,path,xs_element,1,xs_subelem);% read the corresponding xml data + update_list(handles,path,xs_element,element,1,xs_subelem,subelem);%update the display of information on the interface end set(heditxml,'UserData',DataIn);%store the new input xml file name @@ -655,6 +655,6 @@ up=1; if node>0 - nodeup=node; - while up==1; + nodeup=node; + while up==1; nodeup=get(t,nodeup,'parent');%move up to the parent in the tree if isempty(nodeup) @@ -671,6 +671,6 @@ end end - end - element.attrup=attrup; + end + element.attrup=attrup; end %find the subelement properties in the xml file @@ -1043,5 +1043,5 @@ list_element=[]; % Data.CurrentUid=[Data.CurrentUid root_uid]%record new current uid - for iline=1:length(list_uid) + for iline=1:length(list_uid) element=get(t,list_uid(iline)); if isfield(element,'type')&isequal(element.type,'element') @@ -1071,9 +1071,9 @@ end end - end + end set(handles.list_element,'Value',1)%select the first line of list_element by default - set(handles.list_element,'String',cell2tab(list_element,' ') ) + set(handles.list_element,'String',cell2tab(list_element,' ') ) list.uid=list_uid; - set(handles.list_element,'UserData',list) + set(handles.list_element,'UserData',list) end %--------------------------------------------------------- @@ -1415,6 +1415,6 @@ % up=1 % if node>0 -% nodeup=node; -% while up==1; +% nodeup=node; +% while up==1; % nodeup=get(t,nodeup,'parent');%move up to the parent in the tree % if isempty(nodeup) @@ -1431,6 +1431,6 @@ % end % end -% end -% element.attrup=attrup; +% end +% element.attrup=attrup; % end % %find the subelement properties in the xml file Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 997) +++ /trunk/src/series.m (revision 998) @@ -3023,5 +3023,5 @@ if get(handles.EditObject,'Value') set(handles.ViewObject,'Value',0) - UserData=get(handles.series,'UserData'); + UserData=get(handles.series,'UserData'); hset_object=set_object(UserData.ProjObject); set(hset_object,'Name','edit_object_series') Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 997) +++ /trunk/src/uvmat.m (revision 998) @@ -1,3 +1,3 @@ -%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization +%'uvmat': function associated with the GUI 'uvmat.fig' for images and data field visualization %------------------------------------------------------------------------ % function huvmat=uvmat(input) @@ -52,5 +52,5 @@ % % 1) Input filenames are determined by MenuBrowse (first field), MenuBrowseCampaign -% (second field), or by the stored file name .FileName_1, or as an input of uvmat. +% (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) @@ -61,18 +61,18 @@ % %%%%%%%% structure of uvmat/refresh_field.m %%%%%%%% % -% Main input open second input open_1 -% | | +% 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 fieldname -% | +% Field{1} Field{2} +% | | +% --->transform fct<--- transform (e.g. phys.m) and combine input fieldname +% | % (tps_coeff_field.m) calculate tps coefficients (for filter projection or spatial derivatives). % | % UvData.Field-------------->Histogram % _____________|____________ -% | | -% proj_field.m proj_field.m project the field on the projection objects (use set_field_list.m) +% | | +% proj_field.m proj_field.m project the field on the projection objects (use set_field_list.m) % | | % UvData.PlotAxes ViewData.PlotAxes (on view_field) @@ -92,7 +92,7 @@ % If the scalar exists in an input open (image or scalar stored under its % name in a netcdf open), it is directly read at the level of Field{1}or Field{2}. -% Else only its name AName is recorded in Field{i}, and its field is then calculated +% Else only its name AName is recorded in Field{i}, and its field is then calculated %by the fuction calc_scal after the coordinate transform or after projection on an CheckEditObject - + % Properties attached to plotting figures (standard Matlab properties): % 'CurrentAxes'= gca or get(gcf,'CurrentAxes'); @@ -100,5 +100,5 @@ % 'CurrentCharacter'=get(gcf,'CurrentCharacter'): last character typed over the figure where the mouse is positioned % 'WindowButtonMotionFcn': function permanently called by mouse motion over the figure -% 'KeyPressFcn': function called by pressing a key on the key board +% 'KeyPressFcn': function called by pressing a key on the key board % 'WindowButtonDownFcn': function called by pressing the mouse over the figure % 'WindowButtonUpFcn': function called by releasing the mouse pressure over the figure @@ -107,5 +107,5 @@ % 'CurrentPoint'=get(gca,'CurrentPoint'); (standard Matlab) same as for the figure, but position in plot axes. % AxeData:=get(gca,'UserData'); -% AxeData.Drawing = create: create a new object +% AxeData.Drawing = create: create a new object % = deform: modify an existing object by moving its defining create % = off: no current drawing action @@ -200,5 +200,5 @@ set(hObject,'WindowButtonMotionFcn',{'mouse_motion',handles})%set mouse action functio set(hObject,'WindowButtonDownFcn',{'mouse_down'})%set mouse click action function -set(hObject,'WindowButtonUpFcn',{'mouse_up',handles}) +set(hObject,'WindowButtonUpFcn',{'mouse_up',handles}) set(hObject,'DeleteFcn',{@closefcn})% set(hObject,'ResizeFcn',{@ResizeFcn,handles})% @@ -260,5 +260,5 @@ if ishandle(handles.UVMAT_title) delete(handles.UVMAT_title) - end + end if isstruct(input) if isfield(input,'InputFile') @@ -289,5 +289,5 @@ %% check the path and date of modification of all functions in uvmat path_to_uvmat=which ('uvmat');% check the path detected for source file uvmat - [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m + [infomsg,date_str,svn_info]=check_files;%check the path of the functions called by uvmat.m date_str=['last modification: ' date_str]; if ishandle(handles.UVMAT_title) @@ -312,5 +312,5 @@ % --- Outputs from this function are returned to the command menuline. function varargout = uvmat_OutputFcn(hObject, eventdata, handles) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ varargout{1} = handles.output;% the only output argument is the handle to the GUI figure @@ -344,5 +344,5 @@ %--- activated when resizing the GUI view_field function ResizeFcn(gcbo,eventdata,handles) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ set(handles.uvmat,'Units','pixels') size_fig=get(handles.uvmat,'Position'); @@ -581,5 +581,5 @@ % -------------------------------------------------------------------- function MenuExportAxis_Callback(hObject, eventdata, handles) -% -------------------------------------------------------------------- +% -------------------------------------------------------------------- ListFig=findobj(allchild(0),'Type','figure'); nb_option=0; @@ -644,5 +644,5 @@ FileBase=fullfile(RootPath,RootFile); -%% create a fig and axis for movies +%% create a fig and axis for movies figure_movie=findobj(allchild(0),'name','figure_movie'); @@ -659,5 +659,5 @@ time_str=get(handles.TimeValue,'String'); if ~isempty(time_str) - htitle=get(newaxes,'Title'); + htitle=get(newaxes,'Title'); set(htitle,'String',['t=' time_str]) end @@ -674,5 +674,5 @@ Position(4)=Position(4)/2; hfig=findobj(allchild(0),'Tag','set_movie'); -if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI +if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI hfig=figure('name','set_movie','tag','set_movie','MenuBar','none','NumberTitle','off','Units','pixels',... 'Position',Position); @@ -714,8 +714,8 @@ hMovieSize=findobj(hset_movie,'Tag','MovieSize'); nbpix=[640 480; 720 480; 1280 720]; -SizeOption=get(hMovieSize,'Value'); -nbpix=nbpix(SizeOption,:); - -%% look for movie fig +SizeOption=get(hMovieSize,'Value'); +nbpix=nbpix(SizeOption,:); + +%% look for movie fig figure_movie=findobj(allchild(0),'name','figure_movie'); if isempty(figure_movie) @@ -726,5 +726,5 @@ newaxes=copyobj(hhuvmat.PlotAxes,figure_movie);%new plotting axes in the new figure set(newaxes,'Tag','movieaxes') - + %% display time if defined in uvmat time_str=get(hhuvmat.TimeValue,'String'); @@ -745,5 +745,5 @@ % function called by pressing APPLY in the GUI set_movie function set_movie_START_Callback(hObject,eventdata) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ %% read info from the GUI set_movie hset_movie=get(hObject,'parent'); @@ -773,13 +773,13 @@ while testexist==2 backup=[backup '~']; - testexist=exist(backup,'file'); + testexist=exist(backup,'file'); end [success,message]=copyfile(MovieName,backup);%make backup of the existing file if isequal(success,1) - delete(MovieName)%delete existing file + delete(MovieName)%delete existing file else msgbox_uvmat('ERROR',message) return - end + end end %create avi open @@ -801,5 +801,5 @@ for i=1:FrameNumber if get(hhuvmat.speed,'Value')~=0 && isequal(get(hhuvmat.MenuExportMovie,'BusyAction'),'queue') % enable STOP command - runpm(hObject,eventdata,hhuvmat,increment)% run plus + runpm(hObject,eventdata,hhuvmat,increment)% run plus drawnow time_str=get(hhuvmat.TimeValue,'String'); @@ -818,5 +818,5 @@ % function called by pressing APPLY in the GUI set_slices function set_movie_Cancel_Callback(hObject,eventdata) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ delete(hObject) @@ -937,5 +937,5 @@ %% desactivate concurrent tools set(handles.MenuRuler,'checked','off')%desactivate ruler -hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');% search the GUI geometric calibration +hgeometry_calib=findobj(allchild(0),'tag','geometry_calib');% search the GUI geometric calibration if ishandle(hgeometry_calib) hhgeometry_calib=guidata(hgeometry_calib); @@ -1005,5 +1005,5 @@ end -hset_object=set_object(data,handles);% call the GUI set_object +hset_object=set_object(data,handles);% call the GUI set_object hchild=get(hset_object,'children'); set(hchild,'enable','on') @@ -1011,5 +1011,5 @@ if check_plot hhset_object=guidata(hset_object); - set_object('REFRESH_Callback',1,[],hhset_object);% call the GUI set_object + set_object('REFRESH_Callback',1,[],hhset_object);% call the GUI set_object end set(handles.CheckViewField,'Visible','on') @@ -1058,5 +1058,5 @@ SubField_Callback(hObject, eventdata, handles) end -UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface +UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface %% suppress competing tools @@ -1064,5 +1064,5 @@ set(handles.CheckZoom,'Value',0) set(handles.CheckZoom,'BackgroundColor',[0.7 0.7 0.7]) -set(handles.ListObject,'Value',1) +set(handles.ListObject,'Value',1) %% initiate display of the GUI geometry_calib @@ -1074,5 +1074,5 @@ FileName=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt]; set(handles.view_xml,'BackgroundColor',[1 1 0])%indicate the reading of the current xml file by geometry_calib -geometry_calib(FileName);% call the geometry_calib interface +geometry_calib(FileName);% call the geometry_calib interface set(handles.view_xml,'BackgroundColor',[1 1 1])%indicate the end of reading of the current xml file by geometry_calib set(handles.MenuCalib,'checked','on')% indicate that MenuCalib is activated, test used by mouse action @@ -1089,5 +1089,5 @@ end -UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface +UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface % check=0; if isfield(UvData,'XmlData')&&isfield(UvData.XmlData{1},'GeometryCalib')&& isfield(UvData.XmlData{1}.GeometryCalib,'SliceCoord') @@ -1096,5 +1096,5 @@ msgbox_uvmat('ERROR','3D geometric calibration needed before defining slices') return -end +end SliceCoord=GeometryCalib.SliceCoord; InterfaceCoord=min(SliceCoord(:,3)); @@ -1106,11 +1106,11 @@ if isfield(GeometryCalib,'CheckVolumeScan') CheckVolumeScan=GeometryCalib.CheckVolumeScan; -end +end RefractionIndex=1.33; -CheckRefraction=0;% default value of the check box refraction +CheckRefraction=0;% default value of the check box refraction if isfield(GeometryCalib,'RefractionIndex') RefractionIndex=GeometryCalib.RefractionIndex; CheckRefraction=1; -end +end SliceAngle=[0 0 0]; if isfield(GeometryCalib,'SliceAngle') @@ -1126,5 +1126,5 @@ Bottom=ScreenSize(4)-Height-40; %put fig at top right hfig=findobj(allchild(0),'Tag','set_slice'); -if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI +if ~isempty(hfig),delete(hfig), end; %delete existing version of the GUI hfig=figure('name','set_slices','tag','set_slice','MenuBar','none','NumberTitle','off','Units','pixels','Position',[Left,Bottom,Width,Height],'UserData',GeometryCalib); BackgroundColor=get(hfig,'Color'); @@ -1197,5 +1197,5 @@ % function called by selecting CheckRefraction in the GUI set_slices function set_slice_CheckRefraction_Callback(hObject,eventdata) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ hset_slice=get(hObject,'parent'); h_refraction(1)=findobj(hset_slice,'String','surface'); @@ -1212,5 +1212,5 @@ % function called by pressing APPLY in the GUI set_slices function set_slice_APPLY_Callback(hObject,eventdata) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ set(hObject,'BackgroundColor',[1 1 0]);% paint button in yellow to indicate action drawnow @@ -1254,5 +1254,5 @@ elseif isfield(GeometryCalib,'RefractionIndex') GeometryCalib=rmfield(GeometryCalib,'RefractionIndex'); - GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); + GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); end @@ -1275,5 +1275,5 @@ % function called by pressing REPLICATE in the GUI set_slices function set_slice_REPLICATE_Callback(hObject,eventdata) -%------------------------------------------------------------------------ +%------------------------------------------------------------------------ set(hObject,'BackgroundColor',[1 1 0]) drawnow @@ -1294,5 +1294,5 @@ SubDirBase=regexprep(OutPut.DataSeries{idevice},'\..+$',''); XmlFile=fullfile(OutPut.Campaign,OutPut.Experiment{ilist},[SubDirBase '.xml']); - + % read the current xml file if exist(XmlFile,'file') @@ -1320,5 +1320,5 @@ GeometryCalib=rmfield(GeometryCalib,'InterfaceCoord'); end - + % update the current xml file errormsg=update_imadoc(GeometryCalib,XmlFile,'GeometryCalib');% introduce the calibration data in the xml file @@ -1346,5 +1346,5 @@ function MenuLIFCalib_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ -%% read UvData properties stored on the uvmat interface +%% read UvData properties stored on the uvmat interface UvData=get(handles.uvmat,'UserData'); if isfield(UvData,'XmlData')&& isfield(UvData.XmlData{1},'GeometryCalib') @@ -1394,5 +1394,5 @@ %% display the current image in polar axes with origin at the illumination source -currentdir=pwd; +currentdir=pwd; uvmatpath=fileparts(which('uvmat')); cd(fullfile(uvmatpath,'transform_field')); @@ -1464,8 +1464,8 @@ end % save the illumination origin - t=struct2xml(XmlData.Illumination,t,uid_illumination); + t=struct2xml(XmlData.Illumination,t,uid_illumination); save(t,XmlFileName); end - + @@ -1473,5 +1473,5 @@ function MenuMask_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ -UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface +UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface ListObj=UvData.ProjObject; select=zeros(1,numel(ListObj)); @@ -1568,5 +1568,5 @@ imflag=uint8(255*(0.392+0.608*flag));% =100 for flag=0 (vectors not computed when 201 @@ -2204,5 +2204,5 @@ end slices_Callback([],[], handles) - end + end end end @@ -2257,5 +2257,5 @@ set(handles.uvmat,'UserData',UvData) -%% set index navigation options +%% set index navigation options scan_option='i';%default state_j='off'; %default @@ -2269,10 +2269,10 @@ end [ref_j,ref_i]=find(squeeze(i1_series(1,:,:))); -if ~isempty(j1_series) +if ~isempty(j1_series) state_j='on'; if index==1 if isequal(ref_i,ref_i(1)*ones(size(ref_j)))% if ref_i is always equal to its first value - scan_option='j'; %scan j indext - end + scan_option='j'; %scan j indext + end end end @@ -2286,5 +2286,5 @@ end set(handles.scan_i,'Value',1) - scan_i_Callback([],[], handles); + scan_i_Callback([],[], handles); else diff_ref_j=diff(ref_j); @@ -2296,5 +2296,5 @@ end set(handles.scan_j,'Value',1) - scan_j_Callback([],[], handles); + scan_j_Callback([],[], handles); end set(handles.scan_j,'Visible',state_j) @@ -2309,5 +2309,5 @@ end -%% apply the effect of the transform fct and view the field +%% apply the effect of the transform fct and view the field transform=get(handles.TransformPath,'UserData'); if index==2 && (~isa(transform,'function_handle')||nargin(transform)<3) @@ -2373,5 +2373,5 @@ %------------------------------------------------------------------------ function update_ij(handles,index_rank) - + NomType=get(handles.NomType,'String'); @@ -2412,5 +2412,5 @@ set(handles.FileIndex_1,'BackgroundColor',[0.7 0.7 0.7])% mark the edit box in grey, then RUN0 will mark it in white for confirmation end - + %------------------------------------------------------------------------ @@ -2448,5 +2448,5 @@ for ilist=1:nbslice list_index{ilist,1}=num2str(ilist); -end +end set(handles.masklevel,'String',list_index) set(handles.masklevel,'Value',z) @@ -2465,5 +2465,5 @@ end option=get(handles.view_xml,'String'); -if isequal(option,'view .xml') +if isequal(option,'view .xml') FileXml=fullfile(RootPath,[SubDir '.xml']); if ~exist(FileXml,'file')% case of civ files , removes the extension for subdir @@ -2558,10 +2558,10 @@ %% update mask image if the mask is new -if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName)) +if ~ (isfield(UvData,'MaskName') && isequal(UvData.MaskName,MaskName)) UvData.MaskName=MaskName; %update the recorded name on UvData set(handles.uvmat,'UserData',UvData); if ~exist(MaskName,'file') if isfield(Mask,'maskhandle')&& ishandle(Mask.maskhandle) - delete(Mask.maskhandle) + delete(Mask.maskhandle) end else @@ -2592,10 +2592,10 @@ end flagmask=MaskField.A < 200; - + %make brown color image imflag(:,:,1)=0.9*flagmask; imflag(:,:,2)=0.7*flagmask; imflag(:,:,3)=zeros(size(flagmask)); - + %update mask image hmask=[]; %default @@ -2604,5 +2604,5 @@ end if ~isempty(hmask) - set(hmask,'CData',imflag) + set(hmask,'CData',imflag) set(hmask,'AlphaData',flagmask*0.6) set(hmask,'XData',MaskField.Coord_x); @@ -2611,5 +2611,5 @@ else axes(handles.PlotAxes) - hold on + hold on Mask.maskhandle=image(MaskField.Coord_x,MaskField.Coord_y,imflag,'Tag','mask','HitTest','off','AlphaData',0.6*ones(size(flagmask))); set(handles.CheckMask,'UserData',Mask) @@ -2625,5 +2625,5 @@ %------------------------------------------------------------------------ % --- Executes on button press in runplus: make one step forward and call -% --- InputFileREFRESH. The step forward is along the fieldname series 1 or 2 depending on +% --- InputFileREFRESH. The step forward is along the fieldname series 1 or 2 depending on % --- the scan_i and scan_j check box (exclusive each other) function runplus_Callback(hObject, eventdata, handles) @@ -2634,5 +2634,5 @@ increment=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to next available field index - increment='+'; + increment='+'; end errormsg=runpm(hObject,eventdata,handles,increment); @@ -2644,5 +2644,5 @@ %------------------------------------------------------------------------ % --- Executes on button press in runmin: make one step backward and call -% --- InputFileREFRESH. The step backward is along the fieldname series 1 or 2 depending on +% --- InputFileREFRESH. The step backward is along the fieldname series 1 or 2 depending on % --- the scan_i and scan_j check box (exclusive each other) function runmin_Callback(hObject, eventdata, handles) @@ -2653,5 +2653,5 @@ increment=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to previous available field index - increment='-'; + increment='-'; end errormsg=runpm(hObject,eventdata,handles,increment); @@ -2670,5 +2670,5 @@ increment=str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to next available field index - increment='+'; + increment='+'; end set(handles.STOP,'Visible','on') @@ -2700,5 +2700,5 @@ increment=-str2double(get(handles.num_IndexIncrement,'String')); %get the field increment d if isnan(increment)% case of free increment: move to next available field index - increment='-'; + increment='-'; end set(handles.STOP,'Visible','on') @@ -2799,5 +2799,5 @@ end end - + % the pair i1-i2 or j1-j2 is free (check box CheckFixPair not selected): the list of existing indices recorded in UvData is used else @@ -2870,5 +2870,5 @@ j2=UvData.j2_series{1}(ref_indices(end)); end - + % case of a second file series if sub_value @@ -2953,5 +2953,5 @@ %% update the index counters if the index move is successfull -if isempty(errormsg) +if isempty(errormsg) set(handles.i1,'String',num2stra(i1,NomType,1)); if isequal(i2,i1) @@ -2967,5 +2967,5 @@ end if strcmp(NomType,'level') - indices=num2str(i1); + indices=num2str(i1); else indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2); @@ -2981,5 +2981,5 @@ else if isempty(i2), set(handles.i2,'String',''); end % suppress the second index display if not used - if isempty(j2), set(handles.j2,'String',''); end + if isempty(j2), set(handles.j2,'String',''); end end end @@ -2998,5 +2998,5 @@ return end - + %% check the input file indexing: [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); @@ -3008,5 +3008,5 @@ filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) -set(handles.movie_pair,'BusyAction','queue')% +set(handles.movie_pair,'BusyAction','queue')% set(handles.CheckFixPair,'Value',1)% impose fixed pair (needed for function runpm) set(handles.REFRESH,'BackgroundColor',[1 1 0])%paint the command button in yellow to indicate its activity @@ -3209,9 +3209,9 @@ %------------------------------------------------------------------------ % --- read the input files and inputfilerefresh all the plots, including projection. -% OUTPUT: +% OUTPUT: % errormsg: error message char string =[] by default % INPUT: % FileName: first input file (=[] in the absence of input file) -% FileName_1: second input file (=[] in the asbsence of second input file) +% FileName_1: second input file (=[] in the asbsence of second input file) % num_i1,num_i2,num_j1,num_j2; frame indices % i1_1,i2_1,j1_1,j2_1: frame indices for the second input file (needed if FileName_1 is not empty) @@ -3273,5 +3273,5 @@ end -%% read the first input field +%% read the first input field ParamIn.ColorVar='';%default variable name for vector color frame_index=1;%default @@ -3299,5 +3299,5 @@ end case {'video','mmreader','rdvision','cine_phantom'} - ParamIn=UvData.MovieObject{1}; % movie object + ParamIn=UvData.MovieObject{1}; % movie object if strcmp(NomType,'*') frame_index=num_i1;%frame index from a single movies or multimage @@ -3327,5 +3327,5 @@ ParamIn.Npy=UvData.XmlData.Npy; ParamIn.Npx=UvData.XmlData.Npx; - else + else errormsg='Npx and Npy need to be defined in the xml file for volume images .vol'; return @@ -3348,5 +3348,5 @@ ParamIn.TimeVarName=TimeName(5:end); end - end + end end @@ -3355,5 +3355,5 @@ errormsg=['uvmat / refresh_field / read_field( ' FileName ') / ' errormsg]; return -end +end if isfield(ParamOut,'Npx')&& isfield(ParamOut,'Npy') set(handles.num_Npx,'String',num2str(ParamOut.Npx));% display image size on the interface @@ -3393,5 +3393,5 @@ list_code=get(handles.ColorScalar,'String');% list menu fields index_code=get(handles.ColorScalar,'Value');% selected string index - ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display + ParamIn_1.ColorVar= list_code{index_code}; % selected field for vector color display end end @@ -3402,5 +3402,5 @@ else frame_index_1=i1_1; - end + end case 'multimage' if strcmp(NomType_1,'*')%frame index for movies or multimage @@ -3408,5 +3408,5 @@ else frame_index_1=j1_1; - end + end case 'vol' %TODO: update if isfield(UvData.XmlData,'Npy') && isfield(UvData.XmlData,'Npx') @@ -3436,5 +3436,5 @@ ParamIn_1.Coord_x=get(handles.Coord_x,'String'); ParamIn_1.Coord_y=get(handles.Coord_y,'String'); - end + end [Field{2},ParamOut_1,errormsg] = read_field(FileName_1,UvData.FileType{2},ParamIn_1,frame_index_1); if ~isempty(errormsg) @@ -3514,5 +3514,5 @@ set(handles.FixVelType,'Visible','off') end - + %% introduce w as background image by default for a new series (only for nbdim=2) if ~isfield(UvData,'NewSeries') @@ -3537,5 +3537,5 @@ % set(handles.FieldName_1,'Visible','on'); % Field{1}.AName='w'; -% end +% end %% display time value of the current file @@ -3575,5 +3575,5 @@ abstime=Field{1}.Time; elseif ~isempty(regexp(TimeName,'^att:', 'once')) - abstime=Field{1}.(TimeName(5:end));%the time is an attribute selected by get_file + abstime=Field{1}.(TimeName(5:end));%the time is an attribute selected by get_file if isfield(Field{1},[TimeName(5:end) 'Unit']) TimeUnit=Field{1}.([TimeName(5:end) 'Unit']); @@ -3593,5 +3593,5 @@ dt=Field{2}.Dt;%dt read from the netcdf input file end -end +end set(handles.TimeValue,'String',num2str(abstime)) @@ -3619,7 +3619,7 @@ end end - + % get time in the input file of the second series, not defined in a xml file or movie - if isempty(abstime_1) && numel(Field)==2 + if isempty(abstime_1) && numel(Field)==2 if strcmp(TimeName_1,'civdata')||strcmp(TimeName_1,'civx') abstime_1=Field{2}.Time; @@ -3652,5 +3652,5 @@ set(handles.Time_title,'String',Time_title) -%% store the current open names, fieldname and vel types in uvmat interface +%% store the current open names, fieldname and vel types in uvmat interface UvData.FileName_1=FileName_1; UvData.ParamOut_1=ParamOut_1; @@ -3734,5 +3734,5 @@ else set(handles.Objects,'Visible','on') - + %% Plot the projections on the selected projection objects %if no projection object exists, create a default one @@ -3798,5 +3798,5 @@ PlotParam{1}.Vectors.ColorCode= {'rgb'}; end - + %% second projection object (view_field display) if length( IndexObj)==2 @@ -3808,6 +3808,6 @@ end end - - %% loop on the projection objects: one or two + + %% loop on the projection objects: one or two for imap=1:numel(IndexObj) iobj=IndexObj(imap); @@ -3822,9 +3822,9 @@ if iobj==1 && ~(isfield(UvData.ProjObject{iobj},'Coord') && size(UvData.ProjObject{iobj}.Coord,2)>=3 && UvData.ProjObject{iobj}.Coord(1,3)UvData.Field.ZMin) UvData.ProjObject{iobj}.Coord(1,3)=(UvData.Field.ZMin+UvData.Field.ZMax)/2;%section at a middle plane chosen - end + end end [ObjectData,errormsg]=proj_field(UvData.Field,UvData.ProjObject{iobj});% project field on the object if ~isempty(errormsg) - errormsg=['projection on ' UvData.ProjObject{iobj}.Type ': ' errormsg ]; + errormsg=['projection on ' UvData.ProjObject{iobj}.Type ': ' errormsg ]; return end @@ -3861,5 +3861,5 @@ ObjectData.A=flag_mask.*double(ObjectData.A); ObjectData.A=feval(AClass,ObjectData.A); - end + end set(handles.uvmat,'UserData',UvData) if ~isempty(ObjectData) @@ -3875,5 +3875,5 @@ hhset_object=guidata(hset_object);% set(hhset_object.ProjMode,'Value',2); - set_object('ProjMode_Callback',hset_object,[],hhset_object); + set_object('ProjMode_Callback',hset_object,[],hhset_object); end return @@ -3895,10 +3895,10 @@ end end - + %% update the mask if isequal(get(handles.CheckMask,'Value'),1)%if the mask option is on update_mask(handles); end - + %% prepare the menus of histograms and plot them (Histogram of the whole volume in 3D case) menu_histo=(UvData.Field.ListVarName)';%list of field variables to be displayed for the menu of histogram display @@ -3937,5 +3937,5 @@ menu_histo=[{[Ustring ',' Vstring]};menu_histo];% add U, V at the beginning if they exist end - + %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % display menus and plot histograms @@ -3954,5 +3954,5 @@ set(handles.CheckEditObject,'Value',1) CheckEditObject_Callback(handles.uvmat, [], handles) -end +end %ResizeFcn(handles.uvmat,[],handles) set(handles.uvmat,'Pointer',pointer) @@ -4082,5 +4082,5 @@ %------------------------------------------------------------------------ function [indx,indy]=pos2ind(x0,rangx0,nxy) -indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel +indx=1+round((nxy(2)-1)*(x0-rangx0(1))/(rangx0(2)-rangx0(1)));% index x of pixel indy=1+round((nxy(1)-1)*(y12-rangy0(1))/(rangy0(2)-rangy0(1)));% index y of pixel @@ -4144,5 +4144,5 @@ if ~test_civ2 && ~test_civ1 msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields') -end +end if test_civ2 nbname='nb_vec_2'; @@ -4159,8 +4159,8 @@ hhh=which('netcdf.open');% look for built-in matlab netcdf library if ~isequal(hhh,'')% case of builtin Matlab netcdf library - nc=netcdf.open(FileName,'NC_WRITE'); + nc=netcdf.open(FileName,'NC_WRITE'); netcdf.reDef(nc); netcdf.putAtt(nc,netcdf.getConstant('NC_GLOBAL'),'CivStage',CivStage); - dimid = netcdf.inqDimID(nc,nbname); + dimid = netcdf.inqDimID(nc,nbname); try varid = netcdf.inqVarID(nc,flagname);% look for already existing fixflag variable @@ -4170,5 +4170,5 @@ netcdf.endDef(nc); netcdf.putVar(nc,varid,UvData.PlotAxes.FF); - netcdf.close(nc); + netcdf.close(nc); else %old netcdf library netcdf_toolbox(FileName,AxeData,attrname,nbname,flagname) @@ -4185,5 +4185,5 @@ nb_vectors=size(theDim); var_FixFlag=ncvar(flagname,nc);% var_FixFlag will be written as the netcdf variable vec_FixFlag -var_FixFlag(1:nb_vectors)=AxeData.FF;% +var_FixFlag(1:nb_vectors)=AxeData.FF;% fin=close(nc); @@ -4193,5 +4193,5 @@ function SubField_Callback(hObject, eventdata, handles) -if get(handles.SubField,'Value')==0% if the subfield button is desactivated +if get(handles.SubField,'Value')==0% if the subfield button is desactivated desable_subfield(handles) transform_fct_list=get(handles.TransformName,'String'); @@ -4199,16 +4199,16 @@ if strcmp(transform_fct,'sub_field') set(handles.TransformName,'Value',1)%suppress the sub_field transform - TransformName_Callback(hObject, eventdata, handles); + TransformName_Callback(hObject, eventdata, handles); else REFRESH_Callback(hObject, eventdata, handles) - end + end else fileinput_1=uigetfile_uvmat('select a second input file:',get(handles.RootPath,'String')); if isempty(fileinput_1) set(handles.SubField,'Value',0) - else + else % refresh the current displayed field display_file_name(handles,fileinput_1,2) - + %update list of recent files in the menubar MenuFile_1=fileinput_1; @@ -4229,5 +4229,5 @@ %----------------------------------------------------------------------- function desable_subfield(handles) - + set(handles.RootPath_1,'String','') set(handles.RootFile_1,'String','') @@ -4293,5 +4293,5 @@ RootFile_1=get(handles.RootFile_1,'String'); if isequal(get(handles.RootFile_1,'Visible'),'off') || isequal(RootFile_1,'"') - RootFile_1=get(handles.RootFile,'String'); + RootFile_1=get(handles.RootFile,'String'); end RootFile_1=regexprep(RootFile_1,'\<[\\/]|[\\/]\>','');%suppress possible / or \ separator at the beginning or the end of the string @@ -4323,5 +4323,5 @@ [tild,tild,tild,i1,i2,j1,j2,tild,NomType]=fileparts_uvmat(['xxx' get(handles.FileIndex,'String') FileExt]); -switch field +switch field case 'get_field...' %% fill the axes and variables from selections in get_field @@ -4353,9 +4353,9 @@ end end - + % VelType menu desactivated set(handles.FixVelType,'visible','off') set(handles.VelType,'Visible','off') - + %read selection from get_field [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes(handles); @@ -4376,5 +4376,5 @@ ZName=GetFieldData.Coordinates.Coord_z; end - end + end CName=GetFieldData.PanelVectors.vec_color; FieldList={['vec(' UName ',' VName ')'];... @@ -4430,5 +4430,5 @@ set(handles.TimeName,'String',['dim:' GetFieldData.Time.TimeName]); set(handles.NomType,'String','*') - set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')]) + set(handles.RootFile,'String',[get(handles.RootFile,'String') get(handles.FileIndex,'String')]) set(handles.i1,'String','1')% set counter to 1 (now the time index in the input matrix) MaxIndex_i=get(handles.MaxIndex_i,'String'); @@ -4455,5 +4455,5 @@ REFRESH_Callback(hObject, eventdata, handles) end - + case 'image' %% look for image corresponding to civ data @@ -4540,9 +4540,9 @@ end end - + % VelType menu desactivated set(handles.FixVelType,'visible','off') set(handles.VelType,'Visible','off') - + %read selection from get_field [RootPath,SubDir,RootFile,FileIndices,FileExt]=read_file_boxes_1(handles); @@ -4621,5 +4621,5 @@ if ~exist(imagename,'file') imagename=uigetfile_uvmat('Pick an image file',imagename,'image'); - + end if isempty(imagename) @@ -4634,5 +4634,5 @@ set(handles.FileIndex_1,'String',get(handles.FileIndex,'String')) set(handles.FileExt_1,'String',get(handles.FileExt,'String')) - + UvData.FileType{2}=UvData.FileType{1}; UvData.XmlData{2}= UvData.XmlData{1}; @@ -4643,5 +4643,5 @@ TransformName_Callback(hObject, eventdata, handles)% activate transform_fct_Callback and refresh current plot check_refresh=0; - end + end end if ~isequal(field,'image') @@ -4651,5 +4651,5 @@ end set(handles.uvmat,'UserData',UvData) - + if check_refresh && ~(isfield(UvData,'NewSeries')&&isequal(UvData.NewSeries,1)) REFRESH_Callback(hObject, eventdata, handles) @@ -4658,5 +4658,5 @@ %------------------------------------------------------------------------ -% --- set the visibility of relevant velocity type menus: +% --- set the visibility of relevant velocity type menus: function menu=set_veltype_display(Civ,FileType) %------------------------------------------------------------------------ @@ -4720,5 +4720,5 @@ UvData=get(handles.uvmat,'UserData'); set(handles.InputFileREFRESH,'BackgroundColor',[1 1 0])%paint REFRESH button in yellow to indicate its activation -drawnow +drawnow InputFile=read_GUI(handles.InputFile);% read the input file parameters [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); @@ -4735,5 +4735,5 @@ check_refresh=1;%will refresh the current plot else% we introduce the same file (with a different field) for the second series - FileName_1=FileName;% we compare two fields in the same file + FileName_1=FileName;% we compare two fields in the same file UvData.FileType{2}=UvData.FileType{1}; UvData.XmlData{2}= UvData.XmlData{1}; @@ -4746,5 +4746,5 @@ else check_refresh=1; - end + end end @@ -4782,5 +4782,5 @@ end if exist('handle1','var')%handles of selected button - set(handle1,'BackgroundColor',[1 1 0]) + set(handle1,'BackgroundColor',[1 1 0]) end @@ -4793,5 +4793,5 @@ delete(handles.UVMAT_title) end -UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface +UvData=get(handles.uvmat,'UserData');%read UvData properties stored on the uvmat interface if isequal(get(handles.VOLUME,'Value'),1) set(handles.CheckZoom,'Value',0) @@ -4822,5 +4822,5 @@ data.RangeX=max(meshx,meshy); data.DX=max(meshx,meshy); - end + end data.ParentButton=handles.VOLUME; PlotHandles=get_plot_handles(handles);%get the handles of the interface elements setting the plotting parameters @@ -4837,5 +4837,5 @@ function edit_vect_Callback(hObject, eventdata, handles) %------------------------------------------------------- -% +% if isequal(get(handles.edit_vect,'Value'),1) VelTypeMenu=get(handles.VelType,'String'); @@ -4843,5 +4843,5 @@ if ~strcmp(VelType,'civ2') && ~strcmp(VelType,'civ1') msgbox_uvmat('ERROR','manual correction only possible for CIV1 or CIV2 velocity fields') - end + end set(handles.record,'Visible','on') set(handles.edit_vect,'BackgroundColor',[1 1 0]) @@ -4877,6 +4877,6 @@ end end - if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style') - if isequal(ObjectData.Type,'polygon') + if isfield(ObjectData,'Coord')& isfield(ObjectData,'Style') + if isequal(ObjectData.Type,'polygon') X=ObjectData.Coord(:,1); Y=ObjectData.Coord(:,2); @@ -4884,5 +4884,5 @@ [X,Y]=px_XYZ(Calib,X,Y,0);% to generalise with 3D cases end - flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside + flagobj=~inpolygon(Xi,Yi,X',Y');%=0 inside the polygon, 1 outside elseif isequal(ObjectData.Type,'ellipse') if testphys @@ -4927,5 +4927,5 @@ % imflag=uint8(255*flag);% =0 for flag=0 (vectors=0 when 20