Index: /trunk/src/@xmltree/xmltree.m =================================================================== --- /trunk/src/@xmltree/xmltree.m (revision 1094) +++ /trunk/src/@xmltree/xmltree.m (revision 1095) @@ -38,21 +38,25 @@ % Input argument is an XML string if (~exist(varargin{1},'file') && ... - ~isempty(xml_findstr(varargin{1},'<',1,1))) + ~isempty(xml_findstr(varargin{1},'<',1,1))) tree.tree = xml_parser(varargin{1}); tree.filename = ''; - % Input argument is an XML filename + % Input argument is an XML filename else - fid = fopen(varargin{1},'rt'); - if (fid == -1) - error(['[XMLTree] Cannot open ' varargin{1}]); + if isempty(regexp(varargin{1},'^http://'))%ordinary file (not OpenDAP) + fid = fopen(varargin{1},'rt'); + if (fid == -1) + error(['[XMLTree] Cannot open ' varargin{1}]); + end + xmlstr = fread(fid,'*char')'; + %xmlstr = fscanf(fid,'%c'); + fclose(fid); + else + xmlstr=webread(varargin{1});%OpenDAP case end - xmlstr = fread(fid,'*char')'; - %xmlstr = fscanf(fid,'%c'); - fclose(fid); tree.tree = xml_parser(xmlstr); - tree.filename = varargin{1}; + tree.filename = varargin{1}; end tree = class(tree,'xmltree'); - else + else error('[XMLTree] Bad input argument'); end Index: /trunk/src/find_field_bounds.m =================================================================== --- /trunk/src/find_field_bounds.m (revision 1094) +++ /trunk/src/find_field_bounds.m (revision 1095) @@ -119,7 +119,7 @@ FieldOut.ProjModeRequest='interp_tps'; end - if strcmp(CellInfo{imax(ind)}.ProjModeRequest,'interp_lin')&& ~strcmp(FieldOut.ProjModeRequest,'interp_tps') - FieldOut.ProjModeRequest='interp_lin'; - end +% if strcmp(CellInfo{imax(ind)}.ProjModeRequest,'interp_lin')&& ~strcmp(FieldOut.ProjModeRequest,'interp_tps') +% FieldOut.ProjModeRequest='interp_lin'; +% end end end Index: /trunk/src/find_field_cells.m =================================================================== --- /trunk/src/find_field_cells.m (revision 1094) +++ /trunk/src/find_field_cells.m (revision 1095) @@ -149,6 +149,4 @@ %% initate cells around each scalar field with different coordinates -% index_remove=[]; -% index_coord_x=zeros(size(ind_coord_x)); cell_counter=0; DimCell={}; Index: /trunk/src/get_field.m =================================================================== --- /trunk/src/get_field.m (revision 1094) +++ /trunk/src/get_field.m (revision 1095) @@ -79,5 +79,10 @@ if ischar(filename) % input file name set(handles.inputfile,'String',filename)% fill the input file name + if ~isempty(regexp(filename,'.mat$'))%case of .mat file + Field=mat2struct(filename); + errormsg=''; + else [Field,tild,tild,errormsg]=nc2struct(filename,[]);% reads the field structure, without the variables + end else msgbox_uvmat('ERROR','get_field requires a file name as input')% display error message for input file reading @@ -405,10 +410,4 @@ case '1D plot' set(handles.Coordinates,'Visible','on') - %set(handles.PanelOrdinate,'Visible','on') - %pos=get(handles.PanelOrdinate,'Position'); -% pos(1)=2; -% pos_coord=get(handles.Coordinates,'Position'); -% pos(2)=pos_coord(2)-pos(4)-2; - %set(handles.PanelOrdinate,'Position',pos) set(handles.PanelScalar,'Visible','off') set(handles.PanelVectors,'Visible','off') @@ -419,10 +418,7 @@ set(handles.Z_title,'Visible','off') set(handles.Coord_x,'String',Field.Display.ListVarName') - Coord_x_Callback(hObject, VarName, handles) - %set(handles.Coord_y,'String',Field.Display.ListVarName') - %Coord_x_Callback(hObject, VarName, handles) + Coord_x_Callback(hObject, VarName, handles) case {'scalar'} set(handles.Coordinates,'Visible','on') - %set(handles.PanelOrdinate,'Visible','off') set(handles.PanelScalar,'Visible','on') set(handles.PanelVectors,'Visible','off') @@ -469,4 +465,5 @@ set(handles.Coord_y,'Visible','on') set(handles.Y_title,'Visible','on') + set(handles.Coord_x,'Visible','on') %default vector selection vector_x_value=get(handles.vector_x,'UserData'); @@ -770,4 +767,5 @@ update_field(handles,VarName) end + %------------------------------------------------------------------------ % --- Executes on selection change in vector_x or vector_y @@ -803,5 +801,5 @@ var_coord=find(test_coord);% % list of variable indices elligible as structured coordinates var_component(var_component==vector_x_index|var_component==vector_y_index)=[]; - var_coord(var_coord==vector_x_index|var_coord==vector_y_index)=[];% remove vector components form te possible list of coordinates + var_coord(var_coord==vector_x_index|var_coord==vector_y_index)=[];% remove vector components from the possible list of coordinates ListCoord=Field.Display.ListVarName([var_coord var_component]); @@ -844,6 +842,6 @@ coord_val=[1 2 3]; end - set(handles.Coord_x,'Value',coord_val(end)) - set(handles.Coord_y,'Value',coord_val(end-1)) + set(handles.Coord_x,'Value',min(coord_val(end),numel(ListCoord))) + set(handles.Coord_y,'Value',min(coord_val(end-1),numel(ListCoord))) if numel(coord_val)>=3 set(handles.Coord_z,'Value',coord_val(end-2)) @@ -887,5 +885,5 @@ %------------------------------------------------------------------------ function Coord_x_Callback(hObject, DimCell, handles) -DimCell + index=get(handles.Coord_x,'Value'); string=get(handles.Coord_x,'String'); Index: /trunk/src/mat2struct.m =================================================================== --- /trunk/src/mat2struct.m (revision 1095) +++ /trunk/src/mat2struct.m (revision 1095) @@ -0,0 +1,39 @@ +%'mat2struct': read a matlab file .mat as a structure similar to the output +%of nc2struct +%---------------------------------------------------------------------- +function Field=mat2struct(filename,ListFieldName) + +Field=load(filename);%case of .mat data file +if ~exist('ListFieldName','var') + ListFieldName=fieldnames(Field); +end +ivar=0; +Field.DimValue=[]; +Field.ListGlobalAttribute={}; +Field.ListVarName={}; +ndim=0; +for ilist=1:numel(ListFieldName) + if isnumeric(Field.(ListFieldName{ilist})) && numel(Field.(ListFieldName{ilist}))>=2 + ivar=ivar+1; + Field.ListVarName=[Field.ListVarName ListFieldName{ilist}]; + ndim_var=0; + for idim=1:ndims(Field.(ListFieldName{ilist})) + sizevar=size(Field.(ListFieldName{ilist}),idim); + if sizevar>1% avoid singleton dimensions + ndim_var=ndim_var+1; + prevdim_index=find(Field.DimValue==sizevar);%look for the same value of dimension + if isempty(prevdim_index)% new dimension detected + ndim=ndim+1; + Field.DimValue(ndim)=sizevar; + Field.ListDimName{ndim}=num2str(sizevar); + Field.VarDimName{ivar}{ndim_var}=Field.ListDimName{ndim}; + else + Field.VarDimName{ivar}{ndim_var}=Field.ListDimName{prevdim_index}; + end + end + end + Field.VarType(ivar)=5;%for double variable + else + Field.ListGlobalAttribute=[Field.ListGlobalAttribute ListFieldName{ilist}]; + end +end Index: /trunk/src/nc2struct.m =================================================================== --- /trunk/src/nc2struct.m (revision 1094) +++ /trunk/src/nc2struct.m (revision 1095) @@ -1,4 +1,5 @@ %'nc2struct': transform a NetCDF file in a corresponding matlab structure +% or directly read the a matlab data file .mat (calling the fct mat2struct.m) % it reads all the global attributes and all variables, or a selected list. % The corresponding dimensions and variable attributes are then extracted @@ -60,245 +61,248 @@ varargin{1}='*'; end -hhh=which('netcdf.open');% look for built-in matlab NetCDF library - -if ~isempty(hhh) - %% default output - Data=[];%default - var_detect=[];%default - ichoice=[];%default - - %% open the NetCDF file for reading - if ischar(nc) - if exist(nc,'file') + +%% default output +Data=[];%default +var_detect=[];%default +ichoice=[];%default + +%% open the NetCDF (or .mat) file for reading +if ischar(nc) + testfile=1; + if exist(nc,'file') + if ~isempty(regexp(nc,'.mat$')) + Data=mat2struct(nc,varargin{1}); + return + else try nc=netcdf.open(nc,'NC_NOWRITE'); - testfile=1; catch ME errormsg=['ERROR opening ' nc ': ' ME.message]; return end + end + else %case of OpenDAP files + if regexp(nc,'^http://') + try + nc=netcdf.open(nc,'NC_NOWRITE'); + catch ME + errormsg=['ERROR opening ' nc ': ' ME.message]; + return + end else - if regexp(nc,'^http://') - nc=netcdf.open(nc,'NC_NOWRITE'); - testfile=1; - else errormsg=['ERROR:file ' nc ' does not exist']; return - end - end + end + end +else + testfile=0; +end + +%% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute' +if isequal(varargin{1},'ListGlobalAttribute') + for ilist=2:numel(varargin) + valuestr=[];%default + try + valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist}); + catch ME + end + eval(['Data.' varargin{ilist} '=valuestr;']) + end + netcdf.close(nc) + return +end + +%% time variable or dimension +input_index=1; +CheckTimeVar=0; +TimeVarName=''; +if isequal(varargin{1},'TimeVarName') + TimeVarName=varargin{2}; + CheckTimeVar=1; + TimeIndex=varargin{3}; + input_index=4;% list of variables to read is at fourth argument +elseif isequal(varargin{1},'TimeDimName') + TimeDimName=varargin{2}; + TimeIndex=varargin{3}; + input_index=4; +end + +%% full reading: get the nbre of dimensions, variables, global attributes +ListVarName=varargin{input_index}; +[ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the NetCDF file + +%% -------- read all global attributes (constants)----------- +Data.ListGlobalAttribute={};%default +att_key=cell(1,ngatts);%default +for iatt=1:ngatts + keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1); + valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr); + keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists + if strcmp(keystr(1),'_') + keystr(1)=[]; + end + try + if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters + eval(['Data.' keystr '=''' valuestr ''';']) + elseif isnumeric(valuestr) + eval(['Data.' keystr '=valuestr;']) + else + eval(['Data.' keystr '='';']) + end + att_key{iatt}=keystr; + catch ME + att_key{iatt}=['attr_' num2str(iatt)]; + Data.(att_key{iatt})=[]; + end +end +Data.ListGlobalAttribute=att_key; + +%% -------- read dimension names----------- +ListDimNameNetcdf=cell(1,ndims); +dim_value=zeros(1,ndims); +for idim=1:ndims %loop on the dimensions of the NetCDF file + [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension +end +if ~isempty(ListDimNameNetcdf) + flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused) +end +if isequal(varargin{1},'TimeDimName')% time dimension introduced + TimeDimIndex=find(strcmp(TimeDimName,ListDimNameNetcdf)); + if isempty(TimeDimIndex) + errormsg=['requested time dimension ' varargin{2} ' not found']; + return + end + if dim_value(TimeDimIndex)1 %multiple choice of variable ranked by order of priority + for iline=1:size(ListVarName,1) + search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of NetCDF variables + if ~isempty(search_index) + break % go to the next line + end + end + ichoice=iline-1;%selected line number in the list of input names of variables else - testfile=0; - end - - %% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute' - if isequal(varargin{1},'ListGlobalAttribute') - for ilist=2:numel(varargin) - valuestr=[];%default - try - valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist}); - catch ME - end - eval(['Data.' varargin{ilist} '=valuestr;']) - end - netcdf.close(nc) - return - end - - %% time variable or dimension - input_index=1; - CheckTimeVar=0; - TimeVarName=''; - if isequal(varargin{1},'TimeVarName') - TimeVarName=varargin{2}; - CheckTimeVar=1; - TimeIndex=varargin{3}; - input_index=4;% list of variables to read is at fourth argument - elseif isequal(varargin{1},'TimeDimName') - TimeDimName=varargin{2}; - TimeIndex=varargin{3}; - input_index=4; - end - - %% full reading: get the nbre of dimensions, variables, global attributes - ListVarName=varargin{input_index}; - [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the NetCDF file - - %% -------- read all global attributes (constants)----------- - Data.ListGlobalAttribute={};%default - att_key=cell(1,ngatts);%default - for iatt=1:ngatts - keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1); - valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr); - keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists - if strcmp(keystr(1),'_') - keystr(1)=[]; + iline=1; + end + %ListVarName=ListVarName(iline,:);% select the appropriate option for input variable (lin ein the input name matrix) + if CheckTimeVar + TimeVarIndex=find(strcmp(TimeVarName,ListVarNameNetcdf),1); %look for the index of the time variable in the netcdf list + if isempty(TimeVarIndex) + errormsg='requested variable for time is missing'; + return + end + TimeDimIndex=dimids{TimeVarIndex}(1)+1; + ListVarName=[ListVarName {TimeVarName}]; + end + var_index=zeros(1,size(ListVarName,2));%default list of variable indices + for ivar=1:size(ListVarName,2) + search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of NetCDF file + if ~isempty(search_index) + var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar + end + end + var_detect=(var_index~=0);%=1 for detected variables + list_index=find(var_index);% indices in the input list corresponding to a detected variable + var_index=var_index(list_index);% NetCDF variable indices corresponding to the output list of read variable + Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables +end + +%% get the dimensions and attributes associated to variables +var_dim=cell(size(var_index));% initiate list of dimensions for variables +for ivar=1:length(var_index) + var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar + Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar}); + flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions + for iatt=1:nbatt(var_index(ivar)) + attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1); + valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname); + attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove '\','.' or '-' if exists + if strcmp(attname(1),'_') + attname(1)=[]; end try - if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters - eval(['Data.' keystr '=''' valuestr ''';']) - elseif isnumeric(valuestr) - eval(['Data.' keystr '=valuestr;']) - else - eval(['Data.' keystr '='';']) - end - att_key{iatt}=keystr; + if ~isempty(valuestr) + Data.VarAttribute{ivar}.(attname)=valuestr; + end catch ME - att_key{iatt}=['attr_' num2str(iatt)]; - Data.(att_key{iatt})=[]; - end - end - Data.ListGlobalAttribute=att_key; - - %% -------- read dimension names----------- - ListDimNameNetcdf=cell(1,ndims); - dim_value=zeros(1,ndims); - for idim=1:ndims %loop on the dimensions of the NetCDF file - [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension - end - if ~isempty(ListDimNameNetcdf) - flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused) - end - if isequal(varargin{1},'TimeDimName')% time dimension introduced - TimeDimIndex=find(strcmp(TimeDimName,ListDimNameNetcdf)); - if isempty(TimeDimIndex) - errormsg=['requested time dimension ' varargin{2} ' not found']; - return - end - if dim_value(TimeDimIndex)1 %multiple choice of variable ranked by order of priority - for iline=1:size(ListVarName,1) - search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of NetCDF variables - if ~isempty(search_index) - break % go to the next line + display(attname) + display(valuestr) + display(ME.message) + Data.VarAttribute{ivar}.(['atrr_' num2str(iatt)])='not read'; + end + end +end + +%% select the dimensions used for the set of input variables +if ~isempty(var_index) + dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions + Data.ListDimName=ListDimNameNetcdf(dim_index); + Data.DimValue=dim_value(dim_index); + if input_index==4% if a dimension is selected as time + Data.DimValue(TimeDimIndex)=numel(TimeIndex); + end +end + +%% get the values of the input variables +if ~isempty(ListVarName) + for ivar=1:length(var_index) + VarName=Data.ListVarName{ivar}; + VarName=regexprep(VarName,'-','_'); %suppress '-' if it exists in the NetCDF variable name (leads to errors in matlab) + % CheckSub=0; + if input_index==4% if a dimension is selected as time + ind_vec=zeros(1,numel(var_dim{ivar}));% vector with zeros corresponding to al the dimensions of the variable VarName + ind_size=dim_value(var_dim{ivar});% vector giving the size (for each dimension) of the variable VarName + index_time=find(var_dim{ivar}==TimeDimIndex); + if ~isempty(index_time) + if ind_size(index_time)1 diff_time=max(max(diff(time))); - if diff_time>0series + if diff_time>0 msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) end @@ -185,5 +185,5 @@ %% initialisation -T=24.2; %main wave period +T=24.4; %main wave period t0=3; % time for motion start (torus at its maximum x) NbPeriod=2; %number of periods for the sliding average @@ -195,9 +195,9 @@ DataOut.ListGlobalAttribute= {'Conventions','Time'}; DataOut.Conventions='uvmat'; -DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','DUDXsin','DUDXcos','DUDYsin','DVDXsin','DVDXcos'... +DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','Usin','Vsin','DUDXsin','DUDXcos','DUDYsin','DVDXsin','DVDXcos'... ,'DVDYsin','Ustokes','Vstokes'}; DataOut.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... - {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}}; + {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}}; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% @@ -237,4 +237,6 @@ Ucos=zeros(NpTime,npy,npx); Vcos=zeros(NpTime,npy,npx); + Usin=zeros(NpTime,npy,npx); + Vsin=zeros(NpTime,npy,npx); DUDXcos=zeros(NpTime,npy,npx); DUDXsin=zeros(NpTime,npy,npx); @@ -249,4 +251,6 @@ Ucos=circshift(Ucos,[-1 0 0]); %shift U by ishift along the first index Vcos=circshift(Vcos,[-1 0 0]); %shift U by ishift along the first index + Usin=circshift(Usin,[-1 0 0]); %shift U by ishift along the first index + Vsin=circshift(Vsin,[-1 0 0]); %shift U by ishift along the first index DUDXcos=circshift(DUDXcos,[-1 0 0]); DUDXsin=circshift(DUDXsin,[-1 0 0]); @@ -259,4 +263,6 @@ Ucos(end,:,:)=Field.U*cos(omega*Time(index)); Vcos(end,:,:)=Field.V*cos(omega*Time(index)); + Usin(end,:,:)=Field.U*sin(omega*Time(index)); + Vsin(end,:,:)=Field.V*sin(omega*Time(index)); DUDXcos(end,:,:)=Field.DUDX*cos(omega*Time(index)); DUDXsin(end,:,:)=Field.DUDX*sin(omega*Time(index)); @@ -269,6 +275,8 @@ DataOut.Umean=(1/Uscale)*squeeze(nanmean(Umean,1)); DataOut.Vmean=(1/Uscale)*squeeze(nanmean(Vmean,1)); - DataOut.Ucos=2*squeeze(nanmean(Ucos,1)); - DataOut.Vcos=2*squeeze(nanmean(Vcos,1)); + DataOut.Ucos=2*(1/Uscale)*squeeze(nanmean(Ucos,1)); + DataOut.Vcos=2*(1/Uscale)*squeeze(nanmean(Vcos,1)); + DataOut.Usin=2*(1/Uscale)*squeeze(nanmean(Usin,1)); + DataOut.Vsin=2*(1/Uscale)*squeeze(nanmean(Vsin,1)); DataOut.DUDXcos=2*squeeze(nanmean(DUDXcos,1)); DataOut.DUDXsin=2*squeeze(nanmean(DUDXsin,1)); Index: /trunk/src/series/turb_stat.m =================================================================== --- /trunk/src/series/turb_stat.m (revision 1094) +++ /trunk/src/series/turb_stat.m (revision 1095) @@ -303,5 +303,5 @@ %% open the result file with uvmat (in RUN mode) -if checkrun +if checkrun && isequal(Param.IndexRange.NbSlice,1) uvmat(OutputFile)% open the last result file with uvmat end Index: /trunk/src/uigetfile_uvmat.m =================================================================== --- /trunk/src/uigetfile_uvmat.m (revision 1094) +++ /trunk/src/uigetfile_uvmat.m (revision 1095) @@ -54,5 +54,5 @@ elseif exist(InputName,'file') [InputDir,InputFileName,Ext]=fileparts(InputName); - if isempty(InputFileName)% if InputName is already the root + if isempty(InputFileName)% if InputName is alr2eady the root InputFileName=InputDir; if ~isempty(strcmp (computer, {'PCWIN','PCWIN64'}))%case of Windows systems @@ -308,5 +308,6 @@ FullSelectName=[DirName '/' SelectName]; end -end +end% end +% end if CheckSubDir%exist(FullSelectName,'dir')% a directory has been selected set(hObject,'BackgroundColor',[1 1 0])% paint list in yellow to indicate action @@ -344,9 +345,5 @@ index_dir=find(strcmp('isdir',fieldnames(ListStruct))); check_dir=cell2mat(ListCells(index_dir,:));% =1 for directories, =0 for files -% for ilist=1:numel(check_dir) -% if check_dir(ilist) ListFiles(check_dir)=regexprep(ListFiles(check_dir),'^.+','+/$0');% put '+/' in front of dir name display -% end -% end if exist('filter_ext','var') && ~strcmp(filter_ext,'*') &&~strcmp(filter_ext,'uigetdir') if strcmp(filter_ext,'image') Index: /trunk/src/update_imadoc.m =================================================================== --- /trunk/src/update_imadoc.m (revision 1094) +++ /trunk/src/update_imadoc.m (revision 1095) @@ -90,8 +90,8 @@ %% save the output file -t=struct2xml(Struct,t,uid_calib); +t=struct2xml(Struct,t,uid_calib); try -save(t,outputfile); + save(t,outputfile); catch ME - errormsg=['error in update_imadoc' ME.message]; + errormsg=['error in saving ' outputfile ': ' ME.message]; end Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1094) +++ /trunk/src/uvmat.m (revision 1095) @@ -2198,12 +2198,12 @@ editxml(fileinput); return - case 'mat'% matlab data file - global Data_uvmat -Data_uvmat.Field=load(fileinput); -evalin('base','global Data_uvmat')%make CurData global in the workspace -disp('Data_uvmat.Field=') -evalin('base','Data_uvmat.Field') %display CurData in the workspace -commandwindow; %brings the Matlab command window to the front -return +% case 'mat'% matlab data file +% % global Data_uvmat +% Data_uvmat.Field=load(fileinput); +% evalin('base','global Data_uvmat')%make CurData global in the workspace +% disp('Data_uvmat.Field=') +% evalin('base','Data_uvmat.Field') %display CurData in the workspace +% commandwindow; %brings the Matlab command window to the front +% return otherwise set(handles_RootPath,'String',RootPath); @@ -2278,5 +2278,4 @@ %enable other menus -% set(handles.MenuOpenCampaign,'Enable','on') set(handles.MenuExport,'Enable','on') set(handles.MenuExportFigure,'Enable','on') @@ -2355,5 +2354,5 @@ if isfield(FileInfo,'FrameRate')% frame rate given in the file (case of video data) TimeUnit='s'; - if isempty(j1_series); %frame index along i + if isempty(j1_series) %frame index along i XmlData.Time=zeros(FileInfo.NumberOfFrames+1,2); XmlData.Time(:,2)=(0:1/FileInfo.FrameRate:(FileInfo.NumberOfFrames)/FileInfo.FrameRate)'; @@ -2552,5 +2551,5 @@ set(handles.Coord_x,'String','X'); set(handles.Coord_y,'String','Y'); - case 'netcdf' + case {'netcdf','mat'} set(handles_Fields,'Value',1) set(handles_Fields,'String',{'get_field...'}) @@ -3019,5 +3018,5 @@ pause(1.02-get(handles.speed,'Value'))% wait for next image end -if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj), +if isfield(UvData,'aviobj') && ~isempty( UvData.aviobj) UvData.aviobj=close(UvData.aviobj); set(handles.uvmat,'UserData',UvData); @@ -3063,5 +3062,4 @@ set(handles.MovieBackward,'BusyAction','Cancel') set(handles.MenuExportMovie,'BusyAction','Cancel') -%set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command buttonback to red set(handles.Movie,'BackgroundColor',[1 0 0])%paint the command buttonback to red set(handles.MovieBackward,'BackgroundColor',[1 0 0])%paint the command buttonback to red @@ -3073,8 +3071,8 @@ errormsg='';%default %% check for movie pair status -movie_status=get(handles.movie_pair,'Value'); -if movie_status - STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active -end +% movie_status=get(handles.movie_pair,'Value'); +% if movie_status +% STOP_Callback(hObject, eventdata, handles)%interrupt movie pair if active +% end %% read the current input file name(s) and field indices @@ -3090,10 +3088,10 @@ j1=str2num(get(handles.j1,'String'));%case of indexed movie end -if movie_status% we read the second index from the edit box - i2=str2num(get(handles.i2,'String'));%read the field indices (for movie, it is not given by the file name) - if strcmp(get(handles.j2,'Visible'),'on') - j2=str2num(get(handles.j2,'String'));% - end -end +% if movie_status% we read the second index from the edit box +% i2=str2num(get(handles.i2,'String'));%read the field indices (for movie, it is not given by the file name) +% if strcmp(get(handles.j2,'Visible'),'on') +% j2=str2num(get(handles.j2,'String'));% +% end +% end sub_value= get(handles.SubField,'Value'); if sub_value % a second input file has been entered @@ -3113,5 +3111,5 @@ set(handles.CheckFixPair,'Value',0) end -CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&&isempty(j2)); +CheckFixPair=get(handles.CheckFixPair,'Value')||(isempty(i2)&& isempty(j2)); % the pair i1-i2 or j1-j2 is imposed (check box CheckFixPair selected) @@ -3132,6 +3130,6 @@ 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 + + % 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 UvData=get(handles.uvmat,'UserData'); @@ -3154,5 +3152,4 @@ end else % free increment - % runaction=get(gcbo,'tag'); if strcmp(increment,'+')% if runplus or movie is activated step=1; @@ -3203,5 +3200,5 @@ j2=UvData.j2_series{1}(ref_indices(end)); end - + % case of a second file series if sub_value @@ -3300,7 +3297,7 @@ end if strcmp(NomType,'level') - indices=num2str(i1); + indices=num2str(i1); else - indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2); + indices=fullfile_uvmat('','','','',NomType,i1,i2,j1,j2); end set(handles.FileIndex,'String',indices); @@ -3309,11 +3306,6 @@ set(handles.FileIndex_1,'String',indices_1); end - if isequal(movie_status,1) - set(handles.movie_pair,'Value',1) - movie_pair_Callback(hObject, eventdata, handles); %reactivate moviepair if it was activated - 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 - end + if isempty(i2), set(handles.i2,'String',''); end % suppress the second index display if not used + if isempty(j2), set(handles.j2,'String',''); end end @@ -3352,11 +3344,11 @@ msgbox_uvmat('ERROR',errormsg); end - - % set(hima,'CData',Field_b.A); %TODO: generalise to other kinds of fields pause(1.02-get(handles.speed,'Value'));% wait for next image errormsg=runpm(hObject,eventdata,handles,-increment); - - % set(hima,'CData',Field_a.A); + if ~isempty(errormsg) + msgbox_uvmat('ERROR',errormsg); + end pause(1.02-get(handles.speed,'Value'));% wait for next image + get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue') end set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red @@ -3364,164 +3356,6 @@ set(handles.Dt_txt,'String','') - - - set(handles.runplus,'BackgroundColor',[1 0 0])%paint the command button back in red -% -% set(handles.runmin,'BackgroundColor',[1 1 0])%paint the command button in yellow -% drawnow -% 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='-'; -% end -% errormsg=runpm(hObject,eventdata,handles,increment); -% if ~isempty(errormsg) -% msgbox_uvmat('ERROR',errormsg); -% end -% set(handles.runmin,'BackgroundColor',[1 0 0])%paint the command button back in red -% -% %% check the input file indexing: -% [RootPath,SubDir,RootFile,FileIndex,FileExt]=read_file_boxes(handles); -% NomType=get(handles.NomType,'String'); -% if ~isempty(find(regexp(NomType,'-'))) -% msgbox_uvmat('ERROR','The movie pair requires file series with a single index on the first input line') -% return -% end -% filename=[fullfile(RootPath,SubDir,RootFile) FileIndex FileExt];% build the input file name (first line) -% -% 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 -% set(handles.movie_pair,'BackgroundColor',[1 1 0])%paint the command button in yellow to indicate its activity -% drawnow -% -% num_i1=str2num(get(handles.i1,'String')); -% num_j1=stra2num(get(handles.j1,'String')); -% num_i2=str2num(get(handles.i2,'String')); -% num_j2=stra2num(get(handles.j2,'String')); -% -% %% determine the name 'imaname_1' of the second file in the pair -% imaname_1=''; -% if isempty(num_j2)% no second j index indicated -% if isempty(num_i2) -% if strcmp(get(handles.j2,'Visible'),'on') %if the j box is visible -% imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,num_i1,[],num_j1+1); -% end -% if exist(imaname_1,'file') -% num_j2=num_j1+1;% look by default for the next j index as the second file -% set(handles.j2,'String',num2stra(num_j2,NomType)); -% else -% imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,num_i1+1,[],num_j1); -% if exist(imaname_1,'file') -% num_i2=num_i1+1; -% set(handles.i2,'String',num2str(num_i2)); -% else -% msgbox_uvmat('ERROR', 'a second image index i2 or j2 is needed to show the pair as a movie') -% set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red -% set(handles.movie_pair,'Value',0) -% return -% end -% end -% else -% num_j2=num_j1;%repeat the index i1 by default -% end -% end -% if isempty(num_i2) -% num_i2=num_i1;%repeat the index i1 by default -% end -% if isempty(num_j1) -% num_j1=1; -% end -% if isempty(num_j2) -% num_j2=num_j1;%repeat the index i1 by default -% end -% imaname_1=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,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']); -% set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red -% set(handles.movie_pair,'Value',0) -% return -% end -% -% %% display the first field in the pair (including possibly a background field from second line input filename_1) -% filename_1='';%default -% FileIndex_1=''; -% if get(handles.SubField,'Value') -% [RootPath_1,SubDir_1,RootFile_1,FileIndex_1,FileExt_1]=read_file_boxes_1(handles); -% filename_1=[fullfile(RootPath_1,SubDir_1,RootFile_1) FileIndex_1 FileExt_1]; -% end -% [tild,tild,tild,i1_1,i2_1,j1_1,j2_1]=fileparts_uvmat(FileIndex_1);% get the indices of the second series from the string FileIndex_1 -% if isempty(j1_1)% case of movies, the index is not given by file index -% j1_1=num_j1; -% end -% -% errormsg=refresh_field(handles,filename,filename_1,num_i1,num_i2,num_j1,num_j2,i1_1,i2_1,j1_1,j2_1); -% -% if isempty(errormsg) -% set(handles.REFRESH,'BackgroundColor',[1 0 0])% set button color to red, update successfull -% else -% msgbox_uvmat('ERROR',errormsg); -% set(handles.REFRESH,'BackgroundColor',[1 0 1])% keep button color magenta, input not succesfull -% end -% UvData=get(handles.uvmat,'UserData'); -% Field_a=UvData.Field;% movie on the field defined by the second input line -% -% %% display time interval for the image pair -% if isfield(UvData,'XmlData')&&isfield(UvData.XmlData{1},'Time')... -% && size(UvData.XmlData{1}.Time,1)>=num_i2+1 && size(UvData.XmlData{1}.Time,2)>=num_j2+1 -% dt=(UvData.XmlData{1}.Time(num_i2+1,num_j2+1)-UvData.XmlData{1}.Time(num_i1+1,num_j1+1)); -% if isfield(UvData,'TimeUnit') -% set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' m' UvData.TimeUnit] ) -% else -% set(handles.Dt_txt,'String',['Dt=' num2str(1000*dt,3) ' 10^(-3)'] ) -% end -% else -% set(handles.Dt_txt,'String','') -% end -% -% %% read the second field -% if isempty(UvData.MovieObject) -% [Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileInfo{index}.FileType,[],num_frame); -% else -% [Field_b,ParamOut,errormsg] = read_field(imaname_1,UvData.FileInfo{1}.FileType,UvData.MovieObject{1},num_frame); -% end -% if ~isempty(errormsg) -% msgbox_uvmat('ERROR',['Error in reading second image: ' errormsg]) -% return -% end -% -% %% apply phys or other transform on the two input fields -% transform=get(handles.TransformPath,'UserData'); -% if ~isempty(transform) -% if isfield(UvData,'XmlData') && ~isempty(UvData.XmlData) %use geometry calib recorded from the ImaDoc xml file as first priority -% if nargin(transform)>=2 -% Field_b=transform(Field_b,UvData.XmlData{1}); -% else -% Field_b=transform(Field_b); -% end -% end -% end -% -% %% make movie until movie speed is set to 0 or STOP is activated -% hima=findobj(handles.PlotAxes,'Tag','ima');% %handles.PlotAxes =main plotting window (A GENERALISER) -% set(handles.STOP,'Visible','on') -% set(handles.speed,'Visible','on') -% set(handles.speed_txt,'Visible','on') -% while get(handles.speed,'Value')~=0 && isequal(get(handles.movie_pair,'BusyAction'),'queue') % enable STOP command -% % read and plot the series of images in non erase mode -% set(hima,'CData',Field_b.A); %TODO: generalise to other kinds of fields -% pause(1.02-get(handles.speed,'Value'));% wait for next image -% set(hima,'CData',Field_a.A); -% pause(1.02-get(handles.speed,'Value'));% wait for next image -% end -% set(handles.movie_pair,'BackgroundColor',[1 0 0])%paint the command button in red -% set(handles.movie_pair,'Value',0) -% set(handles.Dt_txt,'String','') %------------------------------------------------------------------------ @@ -3660,8 +3494,11 @@ end switch UvData.FileInfo{1}.FieldType - case {'civdata','netcdf'} + case {'civdata','netcdf','mat'} list_fields=get(handles.FieldName,'String');% list menu fields FieldName= list_fields{get(handles.FieldName,'Value')}; % selected field - if ~strcmp(FieldName,'get_field...') + if strcmp(FieldName,'get_field...') + FieldName_Callback(hObject, eventdata, handles) + return + else if get(handles.FixVelType,'Value') VelTypeList=get(handles.VelType,'String'); @@ -3697,5 +3534,4 @@ end ParamIn.Coord_z=get(handles.Coord_z,'String'); - %ParamIn.CheckCoordIndex=strcmp(get(handles.SwitchCoordIndex,'String'),'dim'); TimeName=get(handles.TimeName,'String'); r=regexp(TimeName,'^(?(dim:)|(var:))','names');%look for 'var:' or 'dim:' at the beginning of time name @@ -3768,5 +3604,5 @@ end switch UvData.FileInfo{2}.FileType - case {'civx','civdata','netcdf','pivdata_fluidimage'} + case {'civx','civdata','netcdf','pivdata_fluidimage','mat'} list_fields=get(handles.FieldName_1,'String');% list menu fields FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field @@ -4170,5 +4006,5 @@ break end - if UvData.Field.NbDim==3 + if isfield(UvData.Field,'NbDim') && UvData.Field.NbDim==3 UvData.ProjObject{iobj}.NbDim=3;%test for 3D objects if ~isfield(UvData.ProjObject{iobj},'RangeZ') @@ -5356,5 +5192,5 @@ prev_path=fullfile(fileparts(which('uvmat')),'transform_field'); end -if strcmp(transform_name,'more...'); +if strcmp(transform_name,'more...') transform_fct_chosen=uigetfile_uvmat('Pick the transform function',prev_path,'.m'); if ~isempty(transform_fct_chosen) @@ -5444,7 +5280,4 @@ %% delete drawn objects if the output CooordUnit is different from the previous one if ~strcmp(CoordUnit,CoordUnitPrev) -% for iobj=1:numel(UvData.ProjObject) -% delete_object(iobj) -% end set(handles.CheckFixLimits,'Value',0) hother=findobj('Tag','proj_object');%find all the proj objects @@ -5834,5 +5667,5 @@ AxeData=[]; if isfield(UvData,'PlotAxes') -AxeData=UvData.PlotAxes;% retrieve the current plotted data + AxeData=UvData.PlotAxes;% retrieve the current plotted data end PlotParam=read_GUI(handles.uvmat); Index: /trunk/src/xml2struct.m =================================================================== --- /trunk/src/xml2struct.m (revision 1094) +++ /trunk/src/xml2struct.m (revision 1095) @@ -29,5 +29,5 @@ % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. -%======================================================================= +%=======================================================================UVMAT-https function [s,RootTag,errormsg]=xml2struct(filename,varargin)