Index: /trunk/src/geometry_calib.m =================================================================== --- /trunk/src/geometry_calib.m (revision 1000) +++ /trunk/src/geometry_calib.m (revision 1001) @@ -168,4 +168,6 @@ % --- Executes on button press APPLY (used to launch the calibration). function APPLY_Callback(hObject, eventdata, handles) +set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) + %------------------------------------------------------------------------ %% look for the GUI uvmat and check for an image as input @@ -173,4 +175,8 @@ huvmat=findobj(allchild(0),'Name','uvmat');% look for the GUI uvmat hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat +if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') + msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') + return +end RootPath=''; @@ -186,5 +192,60 @@ outputfile=answer{1}; end -[GeometryCalib,index]=calibrate(handles,hhuvmat);% apply calibration + +%% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image +Coord=get(handles.ListCoord,'Data'); + + +%% read the type of calibration +calib_cell=get(handles.calib_type,'String'); +val=get(handles.calib_type,'Value'); +CalibFcn=['calib_' calib_cell{val}]; + +%% read the intrinsic parameters +Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String')); +Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String')); +Intrinsic.coord_files=get(handles.ListCoordFiles,'String'); +Intrinsic.f1=str2num(get(handles.fx,'String')); +Intrinsic.f2=str2num(get(handles.fy,'String')); +Intrinsic.k=str2num(get(handles.kc,'String')); +Intrinsic.Cx=str2num(get(handles.Cx,'String')); +Intrinsic.Cy=str2num(get(handles.Cy,'String')); +if isempty(Intrinsic.k) + Intrinsic.k=0; +end +if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy) + Intrinsic.Cx=Intrinsic.Npx/2; + Intrinsic.Cy=Intrinsic.Npy/2; +end + +%% Apply calibration +[GeometryCalib,index,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration + +%% record the coordinate unit +unitlist=get(handles.CoordUnit,'String'); +unit=unitlist{get(handles.CoordUnit,'value')}; +GeometryCalib.CoordUnit=unit; + +%% record the coordinates of the calibration points +GeometryCalib.SourceCalib.PointCoord=Coord; + +%% display calibration results on the GUI geometry_calib +display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters +display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters +% (rotation and translation of camera with respect to the phys coordinates) + +%% store the calibration data, by default in the xml file of the currently displayed image +answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... + ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... + ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']}); +if strcmp(answer,'Yes') %store the calibration data + if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration + msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'}) + GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; + end +else + GeometryCalib=[]; + index=1; +end if isempty(GeometryCalib) % if calibration cancelled @@ -228,9 +289,78 @@ function REPLICATE_Callback(hObject, eventdata, handles) %------------------------------------------------------------------------ +set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) %% look for the GUI uvmat and check for an image as input huvmat=findobj(allchild(0),'Name','uvmat'); hhuvmat=guidata(huvmat);%handles of elements in the GUI uvmat -GeometryCalib=calibrate(handles,hhuvmat);% apply calibration + +%% read coordinates of the calibration poinnts: Coord(:,1-3) in phys, Coord(:,4-5) image +Coord=get(handles.ListCoord,'Data'); + +%% read the type of calibration +calib_cell=get(handles.calib_type,'String'); +val=get(handles.calib_type,'Value'); +CalibFcn=['calib_' calib_cell{val}]; + +%% read the intrinsic parameters +Intrinsic.Npx=str2num(get(hhuvmat.num_Npx,'String')); +Intrinsic.Npy=str2num(get(hhuvmat.num_Npy,'String')); +Intrinsic.coord_files=get(handles.ListCoordFiles,'String'); +Intrinsic.f1=str2num(get(handles.fx,'String')); +Intrinsic.f2=str2num(get(handles.fy,'String')); +Intrinsic.k=str2num(get(handles.kc,'String')); +Intrinsic.Cx=str2num(get(handles.Cx,'String')); +Intrinsic.Cy=str2num(get(handles.Cy,'String')); +if isempty(Intrinsic.k) + Intrinsic.k=0; +end +if isempty(Intrinsic.Cx)||isempty(Intrinsic.Cy) + Intrinsic.Cx=Intrinsic.Npx/2; + Intrinsic.Cy=Intrinsic.Npy/2; +end + +%% apply to cropped images if requested +answer=msgbox_uvmat('INPUT_Y-N','apply to cropped images?'); +if strcmp(answer,'Yes') + prompt = {'npy_lower'}; + dlg_title = 'remove image the npy_lower image lines (removal of the upper linedoes not change calibration)'; + num_lines= 1; + def = {'0'}; + answer = inputdlg(prompt,dlg_title,num_lines,def); + npy_crop=str2num(answer{1}); + Intrinsic.Npy=Intrinsic.Npy-npy_crop; %size of the filtering window + Coord(:,5)=Coord(:,5)-npy_crop;% shift the image ordinates of the calibration points by removing the lower band +end + +%% Apply calibration +[GeometryCalib,index,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic);% apply calibration + + +%% record the coordinate unit +unitlist=get(handles.CoordUnit,'String'); +unit=unitlist{get(handles.CoordUnit,'value')}; +GeometryCalib.CoordUnit=unit; + +%% record the coordinates of the calibration points +GeometryCalib.SourceCalib.PointCoord=Coord; + +%% display calibration results on the GUI geometry_calib +display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters +display_extrinsic(GeometryCalib,handles)%display calibration extrinsic parameters +% (rotation and translation of camera with respect to the phys coordinates) + +%% store the calibration data, by default in the xml file of the currently displayed image +answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... + ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... + ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']}); +if strcmp(answer,'Yes') %store the calibration data + if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration + msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'}) + GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; + end +else + GeometryCalib=[]; + index=1; +end %% open the GUI browse_data @@ -265,18 +395,14 @@ %------------------------------------------------------------------------ % --- activate calibration and store parameters in ouputfile . -function [GeometryCalib,index]=calibrate(handles,hhuvmat) -%------------------------------------------------------------------------ -set(handles.CheckEnableMouse,'Value',0)% desactivate mouse (to avoid spurious creation of new points) -%% read the current calibration points +function [GeometryCalib,index,Z_plane]=calibrate(Coord,CalibFcn,Intrinsic) +%------------------------------------------------------------------------ + index=[]; -Coord=get(handles.ListCoord,'Data'); -Coord(:,6)=[]; + % apply the calibration, whose type is selected in handles.calib_type -GeometryCalib=[]; if ~isempty(Coord) - calib_cell=get(handles.calib_type,'String'); - val=get(handles.calib_type,'Value'); - GeometryCalib=feval(['calib_' calib_cell{val}],Coord,handles); + GeometryCalib=feval(CalibFcn,Coord,Intrinsic); else + GeometryCalib=[]; msgbox_uvmat('ERROR','No calibration points, abort') end @@ -306,39 +432,9 @@ end end -%set the coordinate unit -unitlist=get(handles.CoordUnit,'String'); -unit=unitlist{get(handles.CoordUnit,'value')}; -GeometryCalib.CoordUnit=unit; -%record the points -GeometryCalib.SourceCalib.PointCoord=Coord; -display_intrinsic(GeometryCalib,handles)%display calibration intrinsic parameters - -% Display extrinsinc parameters (rotation and translation of camera with respect to the phys coordiantes) -set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4)) -set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4)) -set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4)) -set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4)) -set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4)) -set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4)) - -%% store the calibration data, by default in the xml file of the currently displayed image -answer=msgbox_uvmat('INPUT_Y-N',{'store calibration data';... - ['Error rms (along x,y)=' num2str(GeometryCalib.ErrorRms) ' pixels'];... - ['Error max (along x,y)=' num2str(GeometryCalib.ErrorMax) ' pixels']}); -if strcmp(answer,'Yes') %store the calibration data - if strcmp(calib_cell{val}(1:2),'3D')%set the plane position for 3D (projection) calibration - msgbox_uvmat('CONFIRMATION',{['The current image series is assumed by default in the plane of the calib points z=' num2str(Z_plane) ] ; 'can be modified by MenuSetSlice in the upper bar menu of uvmat'}) - GeometryCalib.SliceCoord=Z_plane'*[0 0 1]; - end - -else - GeometryCalib=[]; - index=1; -end %------------------------------------------------------------------------ % --- determine the parameters for a calibration by an affine function (rescaling and offset, no rotation) -function GeometryCalib=calib_rescale(Coord,handles) +function GeometryCalib=calib_rescale(Coord,Intrinsic) %------------------------------------------------------------------------ X=Coord(:,1); @@ -358,5 +454,5 @@ %------------------------------------------------------------------------ % --- determine the parameters for a calibration by a linear transform matrix (rescale and rotation) -function GeometryCalib=calib_linear(Coord,handles) +function GeometryCalib=calib_linear(Coord,Intrinsic) %------------------------------------------------------------------------ X=Coord(:,1); @@ -388,5 +484,5 @@ % --- determine the tsai parameters for a view normal to the grid plane % NOT USED -function GeometryCalib=calib_normal(Coord,handles) +function GeometryCalib=calib_normal(Coord,Intrinsic) %------------------------------------------------------------------------ Calib.f1=str2num(get(handles.fx,'String')); @@ -451,12 +547,8 @@ %------------------------------------------------------------------------ -function GeometryCalib=calib_3D_linear(Coord,handles) -%------------------------------------------------------------------------ -path_uvmat=which('uvmat');% check the path detected for source file uvmat -path_UVMAT=fileparts(path_uvmat); %path to UVMAT -huvmat=findobj(allchild(0),'Tag','uvmat'); -hhuvmat=guidata(huvmat); -coord_files=get(handles.ListCoordFiles,'String'); -if ischar(coord_files) +function GeometryCalib=calib_3D_linear(Coord,Intrinsic) +%------------------------------------------------------------------------ +coord_files=Intrinsic.coord_files; +if ischar(Intrinsic.coord_files) coord_files={coord_files}; end @@ -466,10 +558,7 @@ %retrieve the calibration points stored in the files listed in the popup list ListCoordFiles x_1=Coord(:,4:5)';%px coordinates of the ref points -if ~strcmp(get(hhuvmat.Scalar,'Visible'),'on') - msgbox_uvmat('ERROR','An image needs to be opened in uvmat for calibration') - return -end -nx=str2num(get(hhuvmat.num_Npx,'String')); -ny=str2num(get(hhuvmat.num_Npy,'String')); + +nx=Intrinsic.Npx; +ny=Intrinsic.Npy; x_1(2,:)=ny-x_1(2,:);%reverse the y image coordinates X_1=Coord(:,1:3)';%phys coordinates of the ref points @@ -1221,12 +1310,23 @@ set(handles.kc,'String',num2str(kc,'%1.4f')) - -% --- Executes when user attempts to close geometry_calib. +%------------------------------------------------------------------------ +% ---display calibration extrinsic parameters +function display_extrinsic(GeometryCalib,handles) +%------------------------------------------------------------------------ +set(handles.Tx,'String',num2str(GeometryCalib.Tx_Ty_Tz(1),4)) +set(handles.Ty,'String',num2str(GeometryCalib.Tx_Ty_Tz(2),4)) +set(handles.Tz,'String',num2str(GeometryCalib.Tx_Ty_Tz(3),4)) +set(handles.Phi,'String',num2str(GeometryCalib.omc(1),4)) +set(handles.Theta,'String',num2str(GeometryCalib.omc(2),4)) +set(handles.Psi,'String',num2str(GeometryCalib.omc(3),4)) + +%------------------------------------------------------------------------ +% --- executes when user attempts to close geometry_calib. function geometry_calib_CloseRequestFcn(hObject, eventdata, handles) - +%------------------------------------------------------------------------ delete(hObject); % closes the figure %------------------------------------------------------------------------ -% --- Executes on button press in PLOT. +% --- executes on button press in PLOT. %------------------------------------------------------------------------ function PLOT_Callback(hObject, eventdata, handles) Index: /trunk/src/nc2struct.m =================================================================== --- /trunk/src/nc2struct.m (revision 1000) +++ /trunk/src/nc2struct.m (revision 1001) @@ -1,2 +1,3 @@ + %'nc2struct': transform a NetCDF file in a corresponding matlab structure % it reads all the global attributes and all variables, or a selected list. Index: /trunk/src/plot_field.m =================================================================== --- /trunk/src/plot_field.m (revision 1000) +++ /trunk/src/plot_field.m (revision 1001) @@ -696,12 +696,12 @@ vec_U=Data.(Data.ListVarName{CellInfo{icell}.VarIndex_vector_x}); vec_V=Data.(Data.ListVarName{CellInfo{icell}.VarIndex_vector_y}); + XName=Data.ListVarName{CellInfo{icell}.CoordIndex(end)}; + YName=Data.ListVarName{CellInfo{icell}.CoordIndex(end-1)}; if strcmp(CellInfo{icell}.CoordType,'scattered')%2D field with unstructured coordinates - XName=Data.ListVarName{CellInfo{icell}.CoordIndex(end)}; - YName=Data.ListVarName{CellInfo{icell}.CoordIndex(end-1)}; vec_X=reshape(Data.(XName),[],1); %transform vectors in column matlab vectors vec_Y=reshape(Data.(YName),[],1); elseif strcmp(CellInfo{icell}.CoordType,'grid')%2D field with structured coordinates - y=Data.(Data.ListVarName{CellInfo{icell}.CoordIndex(end-1)}); - x=Data.(Data.ListVarName{CellInfo{icell}.CoordIndex(end)}); + y=Data.(YName); + x=Data.(XName); if numel(y)==2 % y defined by first and last values on aregular mesh y=linspace(y(1),y(2),size(vec_U,1)); @@ -744,6 +744,6 @@ XName=Data.ListVarName{ivar_X}; YName=Data.ListVarName{ivar_Y}; - eval(['Coord_x=reshape(Data.' XName ',1,[]);']) - eval(['Coord_y=reshape(Data.' YName ',1,[]);']) + Coord_x=reshape(Data.(XName),1,[]); + Coord_y=reshape(Data.(YName),1,[]); [A,Coord_x,Coord_y]=proj_grid(Coord_x',Coord_y',A',[],[],'np>256'); % interpolate on a grid if isfield(Data,'VarAttribute') @@ -757,6 +757,7 @@ elseif strcmp(CellInfo{icell}.CoordType,'grid')%2D field with structured coordinates YName=Data.ListVarName{CellInfo{icell}.CoordIndex(end-1)}; + XName=Data.ListVarName{CellInfo{icell}.CoordIndex(end)}; Coord_y=Data.(YName); - Coord_x=Data.(Data.ListVarName{CellInfo{icell}.CoordIndex(end)}); + Coord_x=Data.(XName); test_interp_X=0; %default, regularly meshed X coordinate test_interp_Y=0; %default, regularly meshed Y coordinate @@ -774,5 +775,5 @@ DCoord_y_max=max(DCoord_y); if sign(DCoord_y_min)~=sign(DCoord_y_max);% =1 for increasing values, 0 otherwise - errormsg=['errror in plot_field.m: non monotonic dimension variable ' Data.ListVarName{VarRole.coord(1)} ]; + errormsg=['errror in plot_field.m: non monotonic dimension variable ' YName ]; return end Index: /trunk/src/read_field.m =================================================================== --- /trunk/src/read_field.m (revision 1000) +++ /trunk/src/read_field.m (revision 1001) @@ -152,5 +152,5 @@ [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeVarName',ParamIn.TimeVarName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]); if numel(num)~=1 - NbCoord=NbCoord+1;% adds time coordinate, except if q single time hqs been selected + NbCoord=NbCoord+1;% adds time coordinate, except if a single time has been selected end else @@ -160,5 +160,6 @@ return end - %scan all the variables beyond the two first ones, ParamIn.Coord_x and ParamIn.Coord_y. + CheckStructured=1; + %scan all the variables beyond the two first NbCoord ones describing the coordinates. for ilist=NbCoord+1:numel(Field.VarDimName) if isequal(Field.VarDimName{1},Field.VarDimName{ilist}) % if a variable has the same dimension as the coordinate, it denotes a field with unstructured coordinates @@ -168,7 +169,21 @@ Field.VarAttribute{3}.Role='coord_z'; end + CheckUnstructured=0; break end end + if CheckStructured + for ilist=NbCoord+1:numel(Field.VarDimName) + rank(1)=find(strcmp(ParamIn.Coord_x,Field.VarDimName{ilist})); + rank(2)=find(strcmp(ParamIn.Coord_y,Field.VarDimName{ilist})); + if NbCoord==3 + rank(3)=find(strcmp(ParamIn.Coord_z,Field.VarDimName{ilist})); + end + rank=flip(rank); + VarName=Field.ListVarName{ilist}; + Field.(VarName)=permute(Field.(VarName),rank); + Field.VarDimName{ilist}=Field.VarDimName{ilist}(rank);% permute the order of dimensions + end + end NormName=''; UName=''; @@ -225,4 +240,5 @@ Field.VarAttribute=[cell(1,numel(Field.ListDimName)) Field.VarAttribute]; end + end case 'video' Index: /trunk/src/series.m =================================================================== --- /trunk/src/series.m (revision 1000) +++ /trunk/src/series.m (revision 1001) @@ -1,2 +1,5 @@ + + + %'series': master function associated to the GUI series.m for analysis field series %------------------------------------------------------------------------ @@ -185,4 +188,5 @@ TransformPathList=cell(NbBuiltinTransform,1); % initiate the cell matrix of Action fct paths TransformPathList(:)={path_transform_fct}; % set the default path to series fcts to all list members +SeriesData.TransformPath=path_transform_fct;% store the standard path for trqnsform functions (needed for compilation) %% get the user defined functions stored in the personal file uvmat_perso.mat @@ -1526,6 +1530,19 @@ if strcmp(ActionExt,'.sh') TransformPath=''; - if ~isempty(get(handles.ActionExt,'UserData')) - TransformPath=get(handles.ActionExt,'UserData'); + if isfield(SeriesData,'TransformPath') + TransformPath=SeriesData.TransformPath; + if isfield(SeriesData,'TransformList') + TransformList=get(handles.TransformName,'String'); + TransformIndex=get(handles.TransformName,'Value'); + TransformName=TransformList{TransformIndex}; + if ~ismember(TransformName,SeriesData.TransformList) + TransformPath=''; + end + end + end + if ~isempty(TransformPath)&&... + ~strcmp(TransformPath,get(handles.TransformPath,'String'))% if the transform is not in paths set for compilation + msgbox_uvmat('ERROR', 'compilation not available for this transform function, select .m') + return end set(handles.series,'Pointer','watch') % set the mouse pointer to 'watch' @@ -2552,12 +2569,17 @@ FieldTransformVisible='off'; %hidden by default if isfield(ParamOut,'FieldTransform') - FieldTransformVisible=ParamOut.FieldTransform; + if ~strcmp(ParamOut.FieldTransform,'off') + FieldTransformVisible='on'; + end + if iscell(ParamOut.FieldTransform) + SeriesData.TransformList=ParamOut.FieldTransform; + end TransformName_Callback([],[], handles) end set(handles.FieldTransform,'Visible',FieldTransformVisible) -if isfield(ParamOut,'TransformPath') - set(handles.ActionExt,'UserData',ParamOut.TransformPath) +if isfield(ParamOut,'TransformPath');% record the path of transform function requested for compilation + set(handles.TransformPath,'UserData',ParamOut.TransformPath) else - set(handles.ActionExt,'UserData',[]) + set(handles.TransformPath,'UserData',[]) end Index: /trunk/src/series/time_series.m =================================================================== --- /trunk/src/series/time_series.m (revision 1000) +++ /trunk/src/series/time_series.m (revision 1001) @@ -67,6 +67,10 @@ ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) - ParamOut.FieldTransform = 'on';%can use a transform function - ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) + ParamOut.FieldTransform = {'phys','phys_polar'};%can use a transform function, proposed list (needed for compilation) + ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) + if 1==2 % loop used to enforce compilation of transform fct, never entered. + phys + phys_polar + end ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) @@ -217,7 +221,7 @@ transform_fct=[];%default if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) - addpath(Param.FieldTransform.TransformPath) + %addpath(Param.FieldTransform.TransformPath) transform_fct=str2func(Param.FieldTransform.TransformName); - rmpath(Param.FieldTransform.TransformPath) + %rmpath(Param.FieldTransform.TransformPath) if isfield(Param,'TransformInput') XmlData{1}.TransformInput=Param.TransformInput; Index: unk/src/series/turb_correlation.m =================================================================== --- /trunk/src/series/turb_correlation.m (revision 1000) +++ (revision ) @@ -1,308 +1,0 @@ -%'aver_stat': calculate Reynolds steress components over time series -%------------------------------------------------------------------------ -% function ParamOut=turb_stat(Param) -% -%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% -% -%OUTPUT -% ParamOut: sets options in the GUI series.fig needed for the function -% -%INPUT: -% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. -% In batch mode, Param is the name of the corresponding xml file containing the same information -% when Param.Action.RUN=0 (as activated when the current Action is selected -% in series), the function ouput paramOut set the activation of the needed GUI elements -% -% Param contains the elements:(use the menu bar command 'export/GUI config' in series to -% see the current structure Param) -% .InputTable: cell of input file names, (several lines for multiple input) -% each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} -% .OutputSubDir: name of the subdirectory for data outputs -% .OutputDirExt: directory extension for data outputs -% .Action: .ActionName: name of the current activated function -% .ActionPath: path of the current activated function -% .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct -% .RUN =0 for GUI input, =1 for function activation -% .RunMode='local','background', 'cluster': type of function use -% -% .IndexRange: set the file or frame indices on which the action must be performed -% .FieldTransform: .TransformName: name of the selected transform function -% .TransformPath: path of the selected transform function -% .InputFields: sub structure describing the input fields withfields -% .FieldName: name(s) of the field -% .VelType: velocity type -% .FieldName_1: name of the second field in case of two input series -% .VelType_1: velocity type of the second field in case of two input series -% .Coord_y: name of y coordinate variable -% .Coord_x: name of x coordinate variable -% .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) -%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% - -%======================================================================= -% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France -% http://www.legi.grenoble-inp.fr -% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr -% -% This file is part of the toolbox UVMAT. -% -% UVMAT is free software; you can redistribute it and/or modify -% it under the terms of the GNU General Public License as published -% by the Free Software Foundation; either version 2 of the license, -% or (at your option) any later version. -% -% UVMAT is distributed in the hope that it will be useful, -% but WITHOUT ANY WARRANTY; without even the implied warranty of -% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -% GNU General Public License (see LICENSE.txt) for more details. -%======================================================================= - -function ParamOut=turb_stat(Param) - -%% set the input elements needed on the GUI series when the action is selected in the menu ActionName -if isstruct(Param) && isequal(Param.Action.RUN,0) - ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) - ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) - ParamOut.NbSlice='off'; %nbre of slices ('off' by default) - ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) - ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) - ParamOut.FieldTransform = 'on';%can use a transform function - ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', - ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) - ParamOut.OutputDirExt='.staturb';%set the output dir extension - ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice -% filecell=get_file_series(Param);%check existence of the first input file -% if ~exist(filecell{1,1},'file') -% msgbox_uvmat('WARNING','the first input file does not exist') -% end - return -end - -%%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% -ParamOut=[];%default output -%% read input parameters from an xml file if input is a file name (batch mode) -checkrun=1; -if ischar(Param) - Param=xml2struct(Param);% read Param as input file (batch case) - checkrun=0; -end -hseries=findobj(allchild(0),'Tag','series'); -RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series -WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series - -%% define the directory for result file (with path=RootPath{1}) -OutputDir=[Param.OutputSubDir Param.OutputDirExt]; - -%% root input file(s) name, type and index series -RootPath=Param.InputTable(:,1); -RootFile=Param.InputTable(:,3); -SubDir=Param.InputTable(:,2); -NomType=Param.InputTable(:,4); -FileExt=Param.InputTable(:,5); -[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); -%%%%%%%%%%%% -% The cell array filecell is the list of input file names, while -% filecell{iview,fileindex}: -% iview: line in the table corresponding to a given file series -% fileindex: file index within the file series, -% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j -% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices -%%%%%%%%%%%% NbView=1 : a single input series -NbView=numel(i1_series);%number of input file series (lines in InputTable) -NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) -NbField_i=size(i1_series{1},2); %nb of fields for the i index -NbField=NbField_j*NbField_i; %total number of fields - -%% determine the file type on each line from the first input file -ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; -NcTypeOptions={'netcdf','civx','civdata'}; -for iview=1:NbView - if ~exist(filecell{iview,1}','file') - msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) - return - end - [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); - FileType{iview}=FileInfo{iview}.FileType; - CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images - CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files - if ~isempty(j1_series{iview}) - frame_index{iview}=j1_series{iview}; - else - frame_index{iview}=i1_series{iview}; - end -end - -%% calibration data and timing: read the ImaDoc files -XmlData=[]; -[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); -if size(time,1)>1 - diff_time=max(max(diff(time))); - if diff_time>0 - msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) - end -end - -%% coordinate transform or other user defined transform -transform_fct='';%default -if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) - addpath(Param.FieldTransform.TransformPath) - transform_fct=str2func(Param.FieldTransform.TransformName); - rmpath(Param.FieldTransform.TransformPath) -end - -%%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% - % EDIT FROM HERE - -%% check the validity of input file types -if CheckImage{1} - FileExtOut='.png'; % write result as .png images for image inputs -elseif CheckNc{1} - FileExtOut='.nc';% write result as .nc files for netcdf inputs -else - msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) - return -end - - -%% settings for the output file -NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file -first_i=i1_series{1}(1); -last_i=i1_series{1}(end); -if isempty(j1_series{1})% if there is no second index j - first_j=1;last_j=1; -else - first_j=j1_series{1}(1); - last_j=j1_series{1}(end); -end - -%% Set field names and velocity types -InputFields{1}=[];%default (case of images) -if isfield(Param,'InputFields') - InputFields{1}=Param.InputFields; -end - -nbfiles=0; -nbmissing=0; - -%initialisation -DataOut.ListGlobalAttribute= {'Conventions'}; -DataOut.Conventions= 'uvmat'; -DataOut.ListVarName={'coord_y', 'coord_x' ,'UMean' , 'VMean','u2Mean','v2Mean','u2Mean_1','v2Mean_1','uvMean','Counter'}; -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'}}; -DataOut.UMean=0; -DataOut.VMean=0; -DataOut.u2Mean=0; -DataOut.v2Mean=0; -DataOut.u2Mean_1=0; -DataOut.v2Mean_1=0; -DataOut.uvMean=0; -DataOut.Counter=0; -U2Mean=0; -V2Mean=0; -UVMean=0; -U2Mean_1=0; -V2Mean_1=0; -Counter_1=0; - -%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% -for index=1:NbField - update_waitbar(WaitbarHandle,index/NbField) - if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') - disp('program stopped by user') - break - end - [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); - - %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% - if index==1 %first field - DataOut=Field; - DataOut.coord_y=Field.coord_y; - DataOut.coord_x=Field.coord_x; - Uprev=Field.U; - Vprev=Field.V; - if isfield(Field,'FF') - FFprev=Field.FF; - else - FFprev=true(size(Field.U)); - end - [npy,npx]=size(Field.U); - DataOut.Ucorr=zeros(npy,npx); - end - FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U - UMean=sum(Field.U,2); - UMean=sum(FF,2); - UMean=UMean./UMean; - Field.U=Field.U-ones(npy,1)*UMean;% substract mean U at each position y - Field.U(FF)=0;% set to 0 the nan values - Field.V(FF)=0; - Ucorr=zeros(npy,npx); - for ishift=-(npx-1):(npx-1)% calculate the field U shifted - U_shift=shiftdim(Field.U,[0 -ishift]); - if ishift<0 - U_shift(:,1:-ishift)=0; - FF_shift(:,1:-ishift)=1; - elseif ishift>0 - U_shift(:,end-ishift:end)=0; - FF_shift(:,1:end-ishift:end)=1; - end - UCorr(:,ishift+npx)=sum(Field.U.*U_shift,2); - nonNaNcounter=sum(~FF.*~FF_shift,2); - UCorr(:,ishift+npx)=UCorr(:,ishift+npx)./nonNaNcounter; - end - DataOut.UCorr=DataOut.UCorr+UCorr; - - %% continuer - - DataOut.UMean=DataOut.UMean+Field.U; %increment the sum - DataOut.VMean=DataOut.VMean+Field.V; %increment the sum - U2Mean=U2Mean+(Field.U).*(Field.U); %increment the U squared sum - V2Mean=V2Mean+(Field.V).*(Field.V); %increment the V squared sum - UVMean=UVMean+(Field.U).*(Field.V); %increment the sum - U2Mean_1=U2Mean_1+(Field.U).*Uprev; %increment the U squared sum - V2Mean_1=V2Mean_1+(Field.V).*Vprev; %increment the V squared sum - Uprev=Field.U; %store for next iteration - Vprev=Field.V; - FFprev=FF; -end -%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% -DataOut.UCorr=DataOut.UCorr/NbField; -%DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero -% DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean -% DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean -% U2Mean=U2Mean./DataOut.Counter; % normalize the mean -% V2Mean=V2Mean./DataOut.Counter; % normalize the mean -% UVMean=UVMean./DataOut.Counter; % normalize the mean -% U2Mean_1=U2Mean_1./Counter_1; % normalize the mean -% V2Mean_1=V2Mean_1./Counter_1; % normalize the mean -% DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the mean -% DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean -% DataOut.uvMean=UVMean-DataOut.UMean.*DataOut.VMean; % normalize the mean \ -% DataOut.u2Mean_1=U2Mean_1-DataOut.UMean.*DataOut.UMean; % normalize the mean -% DataOut.v2Mean_1=V2Mean_1-DataOut.VMean.*DataOut.VMean; % normalize the mean - - -%% calculate the profiles -% npx=numel(DataOut.coord_x); -% band=ceil(npx/5) :floor(4*npx/5);% keep only the central band -% for ivar=3:numel(DataOut.ListVarName)-1 -% VarName=DataOut.ListVarName{ivar};% name of the variable -% DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Profile']}];%append the name of the profile variable -% DataOut.VarDimName=[DataOut.VarDimName {'coord_y'}]; -% DataOut.([VarName 'Profile'])=mean(DataOut.(VarName)(:,band),2); %take the mean profile of U, excluding the edges -% end - -%% writing the result file as netcdf file -OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); - %case of netcdf input file , determine global attributes - errormsg=struct2nc(OutputFile,DataOut); %save result file - if isempty(errormsg) - disp([OutputFile ' written']); - else - disp(['error in writting result file: ' errormsg]) - end - - -%% open the result file with uvmat (in RUN mode) -if checkrun - uvmat(OutputFile)% open the last result file with uvmat -end Index: /trunk/src/series/turb_correlation_time.m =================================================================== --- /trunk/src/series/turb_correlation_time.m (revision 1001) +++ /trunk/src/series/turb_correlation_time.m (revision 1001) @@ -0,0 +1,350 @@ +%'turb_correlation_time': calculate the time correlation function at each point +%------------------------------------------------------------------------ +% function ParamOut=turb_correlation_time(Param) +% +%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% +% +%OUTPUT +% ParamOut: sets options in the GUI series.fig needed for the function +% +%INPUT: +% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. +% In batch mode, Param is the name of the corresponding xml file containing the same information +% when Param.Action.RUN=0 (as activated when the current Action is selected +% in series), the function ouput paramOut set the activation of the needed GUI elements +% +% Param contains the elements:(use the menu bar command 'export/GUI config' in series to +% see the current structure Param) +% .InputTable: cell of input file names, (several lines for multiple input) +% each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} +% .OutputSubDir: name of the subdirectory for data outputs +% .OutputDirExt: directory extension for data outputs +% .Action: .ActionName: name of the current activated function +% .ActionPath: path of the current activated function +% .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct +% .RUN =0 for GUI input, =1 for function activation +% .RunMode='local','background', 'cluster': type of function use +% +% .IndexRange: set the file or frame indices on which the action must be performed +% .FieldTransform: .TransformName: name of the selected transform function +% .TransformPath: path of the selected transform function +% .InputFields: sub structure describing the input fields withfields +% .FieldName: name(s) of the field +% .VelType: velocity type +% .FieldName_1: name of the second field in case of two input series +% .VelType_1: velocity type of the second field in case of two input series +% .Coord_y: name of y coordinate variable +% .Coord_x: name of x coordinate variable +% .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%======================================================================= +% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% http://www.legi.grenoble-inp.fr +% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr +% +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published +% by the Free Software Foundation; either version 2 of the license, +% or (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (see LICENSE.txt) for more details. +%======================================================================= + +function ParamOut=turb_stat(Param) + +%% set the input elements needed on the GUI series when the action is selected in the menu ActionName +if isstruct(Param) && isequal(Param.Action.RUN,0) + ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) + ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + ParamOut.NbSlice='off'; %nbre of slices ('off' by default) + ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldTransform = 'on';%can use a transform function + ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', + ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) + ParamOut.OutputDirExt='.corr_t';%set the output dir extension + ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice +% filecell=get_file_series(Param);%check existence of the first input file +% if ~exist(filecell{1,1},'file') +% msgbox_uvmat('WARNING','the first input file does not exist') +% end + return +end + +%%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% +ParamOut=[];%default output +%% read input parameters from an xml file if input is a file name (batch mode) +checkrun=1; +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +end + +hseries=findobj(allchild(0),'Tag','series'); +RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series +WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series + +%% define the directory for result file (with path=RootPath{1}) +OutputDir=[Param.OutputSubDir Param.OutputDirExt]; + +%% root input file(s) name, type and index series +RootPath=Param.InputTable(:,1); +RootFile=Param.InputTable(:,3); +SubDir=Param.InputTable(:,2); +NomType=Param.InputTable(:,4); +FileExt=Param.InputTable(:,5); +[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); +%%%%%%%%%%%% +% The cell array filecell is the list of input file names, while +% filecell{iview,fileindex}: +% iview: line in the table corresponding to a given file series +% fileindex: file index within the file series, +% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j +% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices +%%%%%%%%%%%% NbView=1 : a single input series +NbView=numel(i1_series);%number of input file series (lines in InputTable) +NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) +NbField_i=size(i1_series{1},2); %nb of fields for the i index +NbField=NbField_j*NbField_i; %total number of fields +NpTime=256;% max number of times for each side of the time correlation fct +NpTime=min(NpTime,floor(NbField/4)); %nbre of points for the correlation fct on each side of 0 + +%% determine the file type on each line from the first input file +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; +NcTypeOptions={'netcdf','civx','civdata'}; +for iview=1:NbView + if ~exist(filecell{iview,1}','file') + msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) + return + end + [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; + CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images + CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files + if ~isempty(j1_series{iview}) + frame_index{iview}=j1_series{iview}; + else + frame_index{iview}=i1_series{iview}; + end +end + +%% calibration data and timing: read the ImaDoc files +XmlData=[]; +[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); +if size(time,1)>1 + diff_time=max(max(diff(time))); + if diff_time>0 + msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) + end +end + +%% coordinate transform or other user defined transform +transform_fct='';%default +if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) + addpath(Param.FieldTransform.TransformPath) + transform_fct=str2func(Param.FieldTransform.TransformName); + rmpath(Param.FieldTransform.TransformPath) +end + +%%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% + % EDIT FROM HERE + +%% check the validity of input file types +if CheckImage{1} + FileExtOut='.png'; % write result as .png images for image inputs +elseif CheckNc{1} + FileExtOut='.nc';% write result as .nc files for netcdf inputs +else + msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) + return +end + + +%% settings for the output file +NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file +first_i=i1_series{1}(1); +last_i=i1_series{1}(end); +if isempty(j1_series{1})% if there is no second index j + first_j=1;last_j=1; +else + first_j=j1_series{1}(1); + last_j=j1_series{1}(end); +end + +%% Set field names and velocity types +InputFields{1}=[];%default (case of images) +if isfield(Param,'InputFields') + InputFields{1}=Param.InputFields; +end + +nbfiles=0; +nbmissing=0; + +%initialisation +DataOut.ListGlobalAttribute= {'Conventions'}; +DataOut.Conventions='uvmat'; +DataOut.ListVarName={'delta_t','coord_y','coord_x','UUCorr' , 'VVCorr','UVCorr','Counter'}; +DataOut.VarDimName={'delta_t','coord_y','coord_x',... + {'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'},{'delta_t','coord_y','coord_x'}}; + +%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% +% First get mean values % +disp('loop for mean started') +Time=zeros(1,NbField); +for index=1:NbField + update_waitbar(WaitbarHandle,index/NbField) + if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + break + end + [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); + if index==1 %first field + if ~isempty(errormsg) + disp_uvmat('ERROR',errormsg,checkrun) + return + elseif ~isfield(Field,'U')||~isfield(Field,'V') + disp_uvmat('ERROR','this function requires the velocity components U and V as input',checkrun) + return + elseif ~isfield(Field,'Time') + disp_uvmat('ERROR','the attribute Time needs to be defined as input',checkrun) + return + end + [npy,npx]=size(Field.U); + UMean=zeros(npy,npx); + VMean=zeros(npy,npx); + Counter=false(npy,npx); + % transcripts the global attributes + if isfield(Field,'ListGlobalAttribute') + DataOut.ListGlobalAttribute= Field.ListGlobalAttribute; + for ilist=1:numel(Field.ListGlobalAttribute) + AttrName=Field.ListGlobalAttribute{ilist}; + DataOut.(AttrName)=Field.(AttrName); + end + end + end + Time(index)=Field.Time; + FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U + Field.U(FF)=0;% set to 0 the nan values, + Field.V(FF)=0; + UMean=UMean+Field.U; + VMean=VMean+Field.V; + Counter=Counter+~FF; +end +UMean=UMean./Counter; +VMean=VMean./Counter; + + +%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% +disp('loop for correlation started') +for index=1:NbField + update_waitbar(WaitbarHandle,index/NbField) + if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + break + end + [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); + + %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% + if index==1 %first field + [npy,npx]=size(Field.U); + dt=diff(Time); + Maxdt=max(dt); Mindt=min(dt); + if Maxdt-Mindt>0.001*Maxdt + disp_uvmat('ERROR','the time increment between fields is not constant',checkrun) + return + else + dt=(Maxdt+Mindt)/2; + end + DataOut.delta_t=(0:dt:dt*NpTime)'; + DataOut.coord_x=Field.coord_x; + DataOut.coord_y=Field.coord_y; + DataOut.UUCorr=zeros(NpTime+1,npy,npx); + DataOut.VVCorr=zeros(NpTime+1,npy,npx); + DataOut.UVCorr=zeros(NpTime+1,npy,npx); + DataOut.Counter=zeros(NpTime+1,npy,npx); + U_shift=zeros(NpTime+1,npy,npx); + V_shift=zeros(NpTime+1,npy,npx); + FF_shift=zeros(NpTime+1,npy,npx); + UUCorr=zeros(NpTime+1,npy,npx); + VVCorr=zeros(NpTime+1,npy,npx); + UVCorr=zeros(NpTime+1,npy,npx); + FFCorr=false(NpTime+1,npy,npx); + end + FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U + Field.U(FF)=0;% set to 0 the nan values,'delta_x' + Field.V(FF)=0; + Field.U=Field.U-UMean; + Field.V=Field.V-VMean; + if index<=NpTime+1 + U_shift(index,:,:)=Field.U; + V_shift(index,:,:)=Field.V; + FF_shift(index,:,:)=FF; + else + U_shift=circshift(U_shift,[-1 0 0]); %shift U by ishift along the first index + V_shift=circshift(V_shift,[-1 0 0]); %shift U by ishift along the first index + FF_shift=circshift(FF_shift,[-1 0 0]); %shift U by ishift along the first index + U_shift(NpTime+1,:,:)=Field.U; + V_shift(NpTime+1,:,:)=Field.V; + FF_shift(NpTime+1,:,:)=FF; + end + for ishift=1:NpTime% calculate the field U shifted + UUCorr(ishift,:,:)=Field.U.*U_shift(ishift,:,:); + VVCorr(ishift,:,:)=Field.V.*V_shift(ishift,:,:); + UVCorr(ishift,:,:)=Field.U.*V_shift(ishift,:,:); + FFCorr(ishift,:,:)=FF | FF_shift; + end + DataOut.UUCorr=DataOut.UUCorr+UUCorr; + DataOut.VVCorr=DataOut.VVCorr+VVCorr; + DataOut.UVCorr=DataOut.UVCorr+UVCorr; + DataOut.Counter=DataOut.Counter+~FFCorr; +end +%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% +% DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter; +% DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter; +% DataOut.VUVCorr=DataOut.UVCorr./DataOut.Counter; +%DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero +% DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean +% DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean +% U2Mean=U2Mean./DataOut.Counter; % normalize the mean +% V2Mean=V2Mean./DataOut.Counter; % normalize the mean +% UVMean=UVMean./DataOut.Counter; % normalize the mean +% U2Mean_1=U2Mean_1./Counter_1; % normalize the mean +% V2Mean_1=V2Mean_1./Counter_1; % normalize the mean +% DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the meanFFCorr +% DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean +% DataOut.uvMean=UVMean-DataOut.UMean.*DataOut.VMean; % normalize the mean \ +% DataOut.u2Mean_1=U2Mean_1-DataOut.UMean.*DataOut.UMean; % normalize the mean +% DataOut.v2Mean_1=V2Mean_1-DataOut.VMean.*DataOut.VMean; % normalize the mean + + +%% calculate the profiles +% npx=numel(DataOut.coord_x); +% band=ceil(npx/5) :floor(4*npx/5);% keep only the central band +% for ivar=3:numel(DataOut.ListVarName)-1 +% VarName=DataOut.ListVarName{ivar};% name of the variable +% DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Profile']}];%append the name of the profile variable +% DataOut.VarDimName=[DataOut.VarDimName {'coord_y'}]; +% DataOut.([VarName 'Profile'])=mean(DataOut.(VarName)(:,band),2); %take the mean profile of U, excluding the edges +% end + +%% writing the result file as netcdf file +OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); + %case of netcdf input file , determine global attributes + errormsg=struct2nc(OutputFile,DataOut); %save result file + if isempty(errormsg) + disp([OutputFile ' written']); + else + disp(['error in writting result file: ' errormsg]) + end + + +%% open the result file with uvmat (in RUN mode) +if checkrun + uvmat(OutputFile)% open the last result file with uvmat +end Index: /trunk/src/series/turb_correlation_x.m =================================================================== --- /trunk/src/series/turb_correlation_x.m (revision 1001) +++ /trunk/src/series/turb_correlation_x.m (revision 1001) @@ -0,0 +1,332 @@ +%'turb_correlation_x': calculate the x wise correlation function at each point +%------------------------------------------------------------------------ +% function ParamOut=turb_correlation_x(Param) +% +%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% +% +%OUTPUT +% ParamOut: sets options in the GUI series.fig needed for the function +% +%INPUT: +% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. +% In batch mode, Param is the name of the corresponding xml file containing the same information +% when Param.Action.RUN=0 (as activated when the current Action is selected +% in series), the function ouput paramOut set the activation of the needed GUI elements +% +% Param contains the elements:(use the menu bar command 'export/GUI config' in series to +% see the current structure Param) +% .InputTable: cell of input file names, (several lines for multiple input) +% each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} +% .OutputSubDir: name of the subdirectory for data outputs +% .OutputDirExt: directory extension for data outputs +% .Action: .ActionName: name of the current activated function +% .ActionPath: path of the current activated function +% .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct +% .RUN =0 for GUI input, =1 for function activation +% .RunMode='local','background', 'cluster': type of function use +% +% .IndexRange: set the file or frame indices on which the action must be performed +% .FieldTransform: .TransformName: name of the selected transform function +% .TransformPath: path of the selected transform function +% .InputFields: sub structure describing the input fields withfields +% .FieldName: name(s) of the field +% .VelType: velocity type +% .FieldName_1: name of the second field in case of two input series +% .VelType_1: velocity type of the second field in case of two input series +% .Coord_y: name of y coordinate variable +% .Coord_x: name of x coordinate variable +% .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +%======================================================================= +% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France +% http://www.legi.grenoble-inp.fr +% Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr +% +% This file is part of the toolbox UVMAT. +% +% UVMAT is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published +% by the Free Software Foundation; either version 2 of the license, +% or (at your option) any later version. +% +% UVMAT is distributed in the hope that it will be useful, +% but WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +% GNU General Public License (see LICENSE.txt) for more details. +%======================================================================= + +function ParamOut=turb_stat(Param) + +%% set the input elements needed on the GUI series when the action is selected in the menu ActionName +if isstruct(Param) && isequal(Param.Action.RUN,0) + ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) + ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + ParamOut.NbSlice='off'; %nbre of slices ('off' by default) + ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldTransform = 'on';%can use a transform function + ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', + ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) + ParamOut.OutputDirExt='.corr_x';%set the output dir extension + ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice +% filecell=get_file_series(Param);%check existence of the first input file +% if ~exist(filecell{1,1},'file') +% msgbox_uvmat('WARNING','the first input file does not exist') +% end + return +end + +%%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% +ParamOut=[];%default output +%% read input parameters from an xml file if input is a file name (batch mode) +checkrun=1; +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +end +hseries=findobj(allchild(0),'Tag','series'); +RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series +WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series + +%% define the directory for result file (with path=RootPath{1}) +OutputDir=[Param.OutputSubDir Param.OutputDirExt]; + +%% root input file(s) name, type and index series +RootPath=Param.InputTable(:,1); +RootFile=Param.InputTable(:,3); +SubDir=Param.InputTable(:,2); +NomType=Param.InputTable(:,4); +FileExt=Param.InputTable(:,5); +[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); +%%%%%%%%%%%% +% The cell array filecell is the list of input file names, while +% filecell{iview,fileindex}: +% iview: line in the table corresponding to a given file series +% fileindex: file index within the file series, +% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j +% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices +%%%%%%%%%%%% NbView=1 : a single input series +NbView=numel(i1_series);%number of input file series (lines in InputTable) +NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) +NbField_i=size(i1_series{1},2); %nb of fields for the i index +NbField=NbField_j*NbField_i; %total number of fields + +%% determine the file type on each line from the first input file +ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; +NcTypeOptions={'netcdf','civx','civdata'}; +for iview=1:NbView + if ~exist(filecell{iview,1}','file') + msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) + return + end + [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); + FileType{iview}=FileInfo{iview}.FileType; + CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images + CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files + if ~isempty(j1_series{iview}) + frame_index{iview}=j1_series{iview}; + else + frame_index{iview}=i1_series{iview}; + end +end + +%% calibration data and timing: read the ImaDoc files +XmlData=[]; +[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); +if size(time,1)>1 + diff_time=max(max(diff(time))); + if diff_time>0 + msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) + end +end + +%% coordinate transform or other user defined transform +transform_fct='';%default +if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) + addpath(Param.FieldTransform.TransformPath) + transform_fct=str2func(Param.FieldTransform.TransformName); + rmpath(Param.FieldTransform.TransformPath) +end + +%%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% + % EDIT FROM HERE + +%% check the validity of input file types +if CheckImage{1} + FileExtOut='.png'; % write result as .png images for image inputs +elseif CheckNc{1} + FileExtOut='.nc';% write result as .nc files for netcdf inputs +else + msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) + return +end + + +%% settings for the output file +NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file +first_i=i1_series{1}(1); +last_i=i1_series{1}(end); +if isempty(j1_series{1})% if there is no second index j + first_j=1;last_j=1; +else + first_j=j1_series{1}(1); + last_j=j1_series{1}(end); +end + +%% Set field names and velocity types +InputFields{1}=[];%default (case of images) +if isfield(Param,'InputFields') + InputFields{1}=Param.InputFields; +end + +nbfiles=0; +nbmissing=0; + +%initialisation +DataOut.ListGlobalAttribute= {'Conventions'}; +DataOut.Conventions= 'uvmat'; +DataOut.ListVarName={'delta_x','coord_y','coord_x','UUCorr' , 'VVCorr','UVCorr','Counter'}; +DataOut.VarDimName={'delta_x','coord_y','coord_x',... + {'delta_x','coord_y','coord_x'},{'delta_x','coord_y','coord_x'},{'delta_x','coord_y','coord_x'},{'delta_x','coord_y','coord_x'}}; +DataOut.UUCorr=0; +DataOut.Counter=0; + +%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% +% First get mean values % +disp('loop for mean started') +for index=1:NbField + update_waitbar(WaitbarHandle,index/NbField) + if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + break + end + [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); + if index==1 %first field + if ~isfield(Field,'U')||~isfield(Field,'V') + disp_uvmat('ERROR','this function requires the velocity components U and V as input',checkrun) + return + end + [npy,npx]=size(Field.U); + UMean=zeros(npy,npx); + VMean=zeros(npy,npx); + Counter=false(npy,npx); + % transcripts the global attributes + if isfield(Field,'ListGlobalAttribute') + DataOut.ListGlobalAttribute= Field.ListGlobalAttribute; + for ilist=1:numel(Field.ListGlobalAttribute) + AttrName=Field.ListGlobalAttribute{ilist}; + DataOut.(AttrName)=Field.(AttrName); + end + end + end + FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U + Field.U(FF)=0;% set to 0 the nan values, + Field.V(FF)=0; + UMean=UMean+Field.U; + VMean=VMean+Field.V; + Counter=Counter+~FF; +end +UMean=UMean./Counter; +VMean=VMean./Counter; + + +%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% +disp('loop for correlation started') +for index=1:NbField + update_waitbar(WaitbarHandle,index/NbField) + if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + break + end + [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); + + %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% + if index==1 %first field + [npy,npx]=size(Field.U); + npcorr=floor(npx/4); %nbre of points for the correlation fct on each side of 0 + dx=(Field.coord_x(end)-Field.coord_x(1))/(numel(Field.coord_x)-1); + DataOut.delta_x=(-dx*npcorr:dx:dx*npcorr)'; + DataOut.coord_x=Field.coord_x; + DataOut.coord_y=Field.coord_y; + DataOut.UUCorr=zeros(2*npcorr+1,npy,npx); + DataOut.VVCorr=zeros(2*npcorr+1,npy,npx); + DataOut.UVCorr=zeros(2*npcorr+1,npy,npx); + DataOut.Counter=zeros(2*npcorr+1,npy,npx); + end + FF=isnan(Field.U);%|Field.U<-60|Field.U>30;% threshold on U + Field.U(FF)=0;% set to 0 the nan values,'delta_x' + Field.V(FF)=0; + Field.U=Field.U-UMean; + Field.V=Field.V-VMean; + UUCorr=zeros(2*npcorr+1,npy,npx); + VVCorr=zeros(2*npcorr+1,npy,npx); + UVCorr=zeros(2*npcorr+1,npy,npx); + FFCorr=false(2*npcorr+1,npy,npx); + for ishift=-npcorr:npcorr% calculate the field U shifted + U_shift=circshift(Field.U,[0 -ishift]); %shift U by ishift along the index x + V_shift=circshift(Field.V,[0 -ishift]); %shift U by ishift along the index x + FF_shift=circshift(FF,[0 -ishift]); %shift U by ishift along the index x + if ishift<0 + U_shift(:,1:-ishift)=0; + V_shift(:,1:-ishift)=0; + FF_shift(:,1:-ishift)=1; + elseif ishift>0 + U_shift(:,end-ishift:end)=0; + V_shift(:,end-ishift:end)=0; + FF_shift(:,end-ishift:end)=1; + end + UUCorr(ishift+npcorr+1,:,:)=Field.U.*U_shift; + VVCorr(ishift+npcorr+1,:,:)=Field.V.*V_shift; + UVCorr(ishift+npcorr+1,:,:)=Field.U.*V_shift; + FFCorr(ishift+npcorr+1,:,:)=FF | FF_shift; + end + DataOut.UUCorr=DataOut.UUCorr+UUCorr; + DataOut.VVCorr=DataOut.VVCorr+VVCorr; + DataOut.UVCorr=DataOut.UVCorr+UVCorr; + DataOut.Counter=DataOut.Counter+~FFCorr; +end +%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% +DataOut.UUCorr=DataOut.UUCorr./DataOut.Counter; +DataOut.VVCorr=DataOut.VVCorr./DataOut.Counter; +DataOut.VUVCorr=DataOut.UVCorr./DataOut.Counter; +%DataOut.Counter(DataOut.Counter==0)=1;% put counter to 1 when it is zero +% DataOut.UMean=DataOut.UMean./DataOut.Counter; % normalize the mean +% DataOut.VMean=DataOut.VMean./DataOut.Counter; % normalize the mean +% U2Mean=U2Mean./DataOut.Counter; % normalize the mean +% V2Mean=V2Mean./DataOut.Counter; % normalize the mean +% UVMean=UVMean./DataOut.Counter; % normalize the mean +% U2Mean_1=U2Mean_1./Counter_1; % normalize the mean +% V2Mean_1=V2Mean_1./Counter_1; % normalize the mean +% DataOut.u2Mean=U2Mean-DataOut.UMean.*DataOut.UMean; % normalize the meanFFCorr +% DataOut.v2Mean=V2Mean-DataOut.VMean.*DataOut.VMean; % normalize the mean +% DataOut.uvMean=UVMean-DataOut.UMean.*DataOut.VMean; % normalize the mean \ +% DataOut.u2Mean_1=U2Mean_1-DataOut.UMean.*DataOut.UMean; % normalize the mean +% DataOut.v2Mean_1=V2Mean_1-DataOut.VMean.*DataOut.VMean; % normalize the mean + + +%% calculate the profiles +% npx=numel(DataOut.coord_x); +% band=ceil(npx/5) :floor(4*npx/5);% keep only the central band +% for ivar=3:numel(DataOut.ListVarName)-1 +% VarName=DataOut.ListVarName{ivar};% name of the variable +% DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Profile']}];%append the name of the profile variable +% DataOut.VarDimName=[DataOut.VarDimName {'coord_y'}]; +% DataOut.([VarName 'Profile'])=mean(DataOut.(VarName)(:,band),2); %take the mean profile of U, excluding the edges +% end + +%% writing the result file as netcdf file +OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j); + %case of netcdf input file , determine global attributes + errormsg=struct2nc(OutputFile,DataOut); %save result file + if isempty(errormsg) + disp([OutputFile ' written']); + else + disp(['error in writting result file: ' errormsg]) + end + + +%% open the result file with uvmat (in RUN mode) +if checkrun + uvmat(OutputFile)% open the last result file with uvmat +end Index: /trunk/src/set_object.m =================================================================== --- /trunk/src/set_object.m (revision 1000) +++ /trunk/src/set_object.m (revision 1001) @@ -380,22 +380,24 @@ % set default values read in the plot of uvmat to initiate the mesh if isequal(ProjMode,'interp_lin')|| isequal(ProjMode,'interp_tps') - huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle + huvmat=findobj('Tag','uvmat');%find the current uvmat interface handle + if ~isempty(huvmat) UvData=get(huvmat,'UserData');%Data associated to the current uvmat interface - if isempty(str2num(get(handles.num_DX,'String')))||isempty(str2num(get(handles.num_DY,'String'))); -% Field=UvData.Field; - if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh) - set(handles.num_DX,'String',num2str(UvData.Field.CoordMesh)) - set(handles.num_DY,'String',num2str(UvData.Field.CoordMesh)) - set(handles.num_RangeX_1,'String',num2str(UvData.Field.XMin)) - set(handles.num_RangeX_2,'String',num2str(UvData.Field.XMax)) - set(handles.num_RangeY_1,'String',num2str(UvData.Field.YMin)) - set(handles.num_RangeY_2,'String',num2str(UvData.Field.YMax)) - end - if isempty(get(handles.CoordUnit,'String'))&& isfield(UvData.Field,'CoordUnit') - set(handles.CoordUnit,'String',UvData.Field.CoordUnit) - end + if isempty(str2num(get(handles.num_DX,'String')))||isempty(str2num(get(handles.num_DY,'String'))); + % Field=UvData.Field; + if isfield(UvData.Field,'CoordMesh')&&~isempty(UvData.Field.CoordMesh) + set(handles.num_DX,'String',num2str(UvData.Field.CoordMesh)) + set(handles.num_DY,'String',num2str(UvData.Field.CoordMesh)) + set(handles.num_RangeX_1,'String',num2str(UvData.Field.XMin)) + set(handles.num_RangeX_2,'String',num2str(UvData.Field.XMax)) + set(handles.num_RangeY_1,'String',num2str(UvData.Field.YMin)) + set(handles.num_RangeY_2,'String',num2str(UvData.Field.YMax)) + end + if isempty(get(handles.CoordUnit,'String'))&& isfield(UvData.Field,'CoordUnit') + set(handles.CoordUnit,'String',UvData.Field.CoordUnit) + end + end end if isempty(str2num(get(handles.num_RangeInterp,'String'))) && isfield(UvData,'Field') - set(handles.num_RangeInterp,'String',num2str(3*UvData.Field.CoordMesh))% default interpolationlength= 3 meshes + set(handles.num_RangeInterp,'String',num2str(3*UvData.Field.CoordMesh))% default interpolationlength= 3 meshes end end Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1000) +++ /trunk/src/uvmat.m (revision 1001) @@ -422,7 +422,7 @@ %% reset position and scale of axis pos(1)=0.2*size_fig(3)+35; -pos(2)=35; +pos(2)=50; pos(3)=0.77*size_fig(3)-1.2*ColumnWidth; -pos(4)=size_fig(4)-60; +pos(4)=size_fig(4)-100; set(handles.PlotAxes,'Units','pixels') set(handles.PlotAxes,'Position',pos)