- Timestamp:
- Mar 25, 2021, 9:37:04 AM (4 years ago)
- Location:
- trunk/src
- Files:
-
- 6 edited
-
plot_field.m (modified) (4 diffs)
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proj_field.m (modified) (10 diffs)
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series/merge_proj.m (modified) (1 diff)
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series/sliding_average.m (modified) (10 diffs)
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transform_field/phys_polar.m (modified) (10 diffs)
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uvmat.m (modified) (8 diffs)
Legend:
- Unmodified
- Added
- Removed
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trunk/src/plot_field.m
r1093 r1094 768 768 test_interp_X=0; %default, regularly meshed X coordinate 769 769 test_interp_Y=0; %default, regularly meshed Y coordinate 770 if isfield(Data,'VarAttribute')771 if numel(Data.VarAttribute)>=CellInfo{icell}.CoordIndex(end) && isfield(Data.VarAttribute{CellInfo{icell}.CoordIndex(end)},'units')772 x_units=Data.VarAttribute{CellInfo{icell}.CoordIndex(end)}.units;773 end774 if numel(Data.VarAttribute)>=CellInfo{icell}.CoordIndex(end-1) && isfield(Data.VarAttribute{CellInfo{icell}.CoordIndex(end-1)},'units')775 y_units=Data.VarAttribute{CellInfo{icell}.CoordIndex(end-1)}.units;776 end777 end770 % if isfield(Data,'VarAttribute') 771 % if numel(Data.VarAttribute)>=CellInfo{icell}.CoordIndex(end) && isfield(Data.VarAttribute{CellInfo{icell}.CoordIndex(end)},'units') 772 % x_units=Data.VarAttribute{CellInfo{icell}.CoordIndex(end)}.units; 773 % end 774 % if numel(Data.VarAttribute)>=CellInfo{icell}.CoordIndex(end-1) && isfield(Data.VarAttribute{CellInfo{icell}.CoordIndex(end-1)},'units') 775 % y_units=Data.VarAttribute{CellInfo{icell}.CoordIndex(end-1)}.units; 776 % end 777 % end 778 778 if numel(Coord_y)>2 779 779 DCoord_y=diff(Coord_y); … … 790 790 DCoord_x_min=min(DCoord_x); 791 791 DCoord_x_max=max(DCoord_x); 792 if sign(DCoord_x_min)~=sign(DCoord_x_max) ;% =1 for increasing values, 0 otherwise792 if sign(DCoord_x_min)~=sign(DCoord_x_max)% =1 for increasing values, 0 otherwise 793 793 errormsg=['errror in plot_field.m: non monotonic dimension variable ' Data.ListVarName{VarRole.coord(2)} ]; 794 794 return … … 821 821 end 822 822 %define coordinates as CoordUnits, if not defined as attribute for each variable 823 % if isfield(Data,'VarAttribute')&& numel(Data.VarAttribute)>=1 && isfield(Data.VarAttribute{1},'unit') 824 % y_units=Data.VarAttribute{1}.unit; 825 % end 823 826 if isfield(Data,'CoordUnit') 824 827 if isempty(x_units) … … 827 830 if isempty(y_units) 828 831 y_units=Data.CoordUnit; 832 end 833 elseif isfield(Data,'VarAttribute') 834 if numel(Data.VarAttribute)>=CellInfo{icell}.CoordIndex(end) && isfield(Data.VarAttribute{CellInfo{icell}.CoordIndex(end)},'units') 835 x_units=Data.VarAttribute{CellInfo{icell}.CoordIndex(end)}.units; 836 end 837 if numel(Data.VarAttribute)>=CellInfo{icell}.CoordIndex(end-1) && isfield(Data.VarAttribute{CellInfo{icell}.CoordIndex(end-1)},'units') 838 y_units=Data.VarAttribute{CellInfo{icell}.CoordIndex(end-1)}.units; 829 839 end 830 840 end -
trunk/src/proj_field.m
r1093 r1094 1125 1125 ProjMode=num2cell(blanks(numel(CellInfo))); 1126 1126 ProjMode=regexprep(ProjMode,' ',ObjectData.ProjMode); 1127 %ProjMode=cell(size(CellInfo));1128 % for icell=1:numel(CellInfo)1129 % ProjMode{icell}=ObjectData.ProjMode;% projection mode of the plane object1130 % end1131 1127 icell_grid=[];% field cell index which defines the grid 1132 1128 if strcmp(ObjectData.ProjMode,'projection') … … 1192 1188 [XI,YI]=meshgrid(coord_x_proj,coord_y_proj);%grid in the new coordinates 1193 1189 ProjData.VarDimName={AYName,AXName}; 1194 % XI=ObjectData.Coord(1,1)+(X)*cos(PlaneAngle(3))-YI*sin(PlaneAngle(3));%corresponding coordinates in the original system1195 % YI=ObjectData.Coord(1,2)+(X)*sin(PlaneAngle(3))+YI*cos(PlaneAngle(3));1196 1190 else% we use the existing grid from field cell #icell_grid 1197 1191 NbDim=NbDimArray(icell_grid); … … 1204 1198 ProjData.(AXName)=FieldData.(AXName); % new (projected ) y coordinates 1205 1199 end 1206 ProjData.ListVarName={AYName,AXName}; 1207 1200 ProjData.ListVarName={AYName,AXName}; 1208 1201 ProjData.VarAttribute{1}.Role='coord_y'; 1209 1202 ProjData.VarAttribute{2}.Role='coord_x'; 1203 YAttribute=FieldData.VarAttribute{CellInfo{icell_grid}.CoordIndex(NbDim-1)}; 1204 XAttribute=FieldData.VarAttribute{CellInfo{icell_grid}.CoordIndex(NbDim)}; 1205 if ~testangle 1206 if isfield(YAttribute,'units') 1207 ProjData.VarAttribute{1}.units=YAttribute.units; 1208 end 1209 if isfield(XAttribute,'units') 1210 ProjData.VarAttribute{2}.units=XAttribute.units; 1211 end 1212 end 1210 1213 end 1211 1214 … … 1244 1247 coord_x=FieldData.(CellInfo{icell}.XName);% initial x coordinates 1245 1248 coord_y=FieldData.(CellInfo{icell}.YName);% initial y coordinates 1246 1249 1247 1250 if check3D 1248 1251 coord_z=FieldData.(CellInfo{icell}.ZName); … … 1348 1351 VarName_FF=FieldData.ListVarName{CellInfo{icell}.VarIndex_errorflag}; 1349 1352 indsel=find(FieldData.(VarName_FF)==0); 1353 if isempty(indsel) 1354 errormsg='bad projection plane: no data found in the projection domain'; 1355 return 1356 end 1350 1357 coord_X=coord_X(indsel); 1351 1358 coord_Y=coord_Y(indsel); … … 1625 1632 end 1626 1633 [X,Y]=meshgrid(Coord{2},Coord{1});%initial coordinates 1627 %name of error flag variable 1628 % FFName='FF';%default name (if not already used) 1629 % if isfield(ProjData,'FF') 1630 % ind=1; 1631 % while isfield(ProjData,['FF_' num2str(ind)]) 1632 % ind=ind+1; 1633 % end 1634 % FFName=['FF_' num2str(ind)];% append an index to the name of error flag, FF_1,FF_2... 1635 % end 1634 1636 1635 % project all variables in the cell 1637 1636 for ivar=VarIndex … … 1656 1655 VarAttribute{length(ListVarName)+nbcoord}=FieldData.VarAttribute{ivar}; 1657 1656 end 1658 % ProjData.(FFName)=isnan(ProjData.(VarName));%detact NaN (points outside the interpolation range) 1659 % ProjData.(VarName)(ProjData.(FFName))=0; %set to 0 the NaN data 1660 end 1661 %update list of variables with error flag 1662 % ListVarName=[ListVarName FFName]; 1663 % VarDimName=[VarDimName {DimCell}]; 1664 % VarAttribute{numel(ListVarName)}.Role='errorflag'; 1657 end 1665 1658 elseif ~testangle % 3Dcase without change of angle 1666 1659 % unstructured z coordinate … … 1691 1684 Coord{2}=FieldData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex(2)});%initial y coordinates 1692 1685 Coord{3}=FieldData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex(3)});%initial x coordinates 1693 1694 1686 coord_x_proj=ObjectData.RangeX(1):InterpMesh:ObjectData.RangeX(2);% set of coordinates in the projection plane 1695 1687 coord_y_proj=ObjectData.RangeY(1):InterpMesh:ObjectData.RangeY(2); … … 1700 1692 YI_proj=M(2,1)*XI+M(2,2)*YI+ObjectData.Coord(1,2); 1701 1693 ZI_proj=M(3,1)*XI+M(3,2)*YI+ObjectData.Coord(1,3); 1702 1703 1704 1694 for ivar=VarIndex 1705 1695 VarName=FieldData.ListVarName{ivar}; … … 1763 1753 end 1764 1754 end 1765 % %prepare substraction in case of two input fields1766 % SubData.ListVarName={};1767 % SubData.VarDimName={};1768 % SubData.VarAttribute={};1769 % check_remove=zeros(size(ProjData.ListVarName));1770 % for iproj=1:numel(ProjData.VarAttribute)1771 % if isfield(ProjData.VarAttribute{iproj},'CheckSub')&&isequal(ProjData.VarAttribute{iproj}.CheckSub,1)1772 % VarName=ProjData.ListVarName{iproj};1773 % SubData.ListVarName=[SubData.ListVarName {VarName}];1774 % SubData.VarDimName=[SubData.VarDimName ProjData.VarDimName{iproj}];1775 % SubData.VarAttribute=[SubData.VarAttribute ProjData.VarAttribute{iproj}];1776 % SubData.(VarName)=ProjData.(VarName);1777 % check_remove(iproj)=1;1778 % end1779 % end1780 % if ~isempty(find(check_remove))1781 % ind_remove=find(check_remove);1782 % ProjData.ListVarName(ind_remove)=[];1783 % ProjData.VarDimName(ind_remove)=[];1784 % ProjData.VarAttribute(ind_remove)=[];1785 % ProjData=sub_field(ProjData,[],SubData);1786 % end1787 1755 1788 1756 %----------------------------------------------------------------- -
trunk/src/series/merge_proj.m
r1093 r1094 253 253 end 254 254 OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); 255 255 256 for index=1:NbField 256 257 update_waitbar(WaitbarHandle,index/NbField) -
trunk/src/series/sliding_average.m
r1093 r1094 25 25 % .RUN =0 for GUI input, =1 for function activation 26 26 % .RunMode='local','background', 'cluster': type of function use 27 % 28 % .IndexRange: set the file or frame indices on which the action must be perform ed29 % .FieldTransform: .TransformName: name of the select ed transform function27 % 900 28 % .IndexRange: set the file or frame indices on which the action must be performseriesed 29 % .FieldTransform: .TransformName: name of the select39ed transform function 30 30 % .TransformPath: path of the selected transform function 31 31 % .InputFields: sub structure describing the input fields withfields … … 34 34 % .FieldName_1: name of the second field in case of two input series 35 35 % .VelType_1: velocity type of the second field in case of two input series 36 % .Coord_y: name of y coordinate variable36 % uvmat .Coord_y: name of y coordinate variable 37 37 % .Coord_x: name of x coordinate variable 38 38 % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) 39 39 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 40 41 40 %======================================================================= 42 41 % Copyright 2008-2021, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France … … 62 61 if isstruct(Param) && isequal(Param.Action.RUN,0) 63 62 ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) 64 ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to m ax (options 'off'/'on', 'off' by default)63 ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to mseriesax (options 'off'/'on', 'off' by default) 65 64 ParamOut.NbSlice=1; %nbre of slices ('off' by default) 66 65 ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) 67 66 ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) 68 67 ParamOut.FieldTransform = 'on';%can use a transform function 69 ParamOut.ProjObject='off';%can use projection object (option 'off'/'on',68 ParamOut.ProjObject='off';%can use projection object39(option 'off'/'on', 70 69 ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) 71 70 ParamOut.OutputDirExt='.tfilter';%set the output dir extension … … 122 121 return 123 122 end 124 [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); 123 [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});900 125 124 FileType{iview}=FileInfo{iview}.FileType; 126 125 CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images … … 138 137 if size(time,1)>1 139 138 diff_time=max(max(diff(time))); 140 if diff_time>0 139 if diff_time>0series 141 140 msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) 142 141 end … … 177 176 178 177 %% Set field names and velocity types 179 InputFields{1}=[];%default (case of images) 178 InputFields{1}=[];%default (case of images)series 180 179 if isfield(Param,'InputFields') 181 180 InputFields{1}=Param.InputFields; … … 187 186 %% initialisation 188 187 T=24.2; %main wave period 188 t0=3; % time for motion start (torus at its maximum x) 189 189 NbPeriod=2; %number of periods for the sliding average 190 190 omega=2*pi/T; 191 amplitude=2.5; %oscillation amplitude 192 Lscale=15;%diameter of the torus, length scale for normalisation 193 Uscale=amplitude*omega; 191 194 192 195 DataOut.ListGlobalAttribute= {'Conventions','Time'}; 193 196 DataOut.Conventions='uvmat'; 194 DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','DUDXsin','DUDYsin','DVDXsin','DVDYsin','Ustokes','Vstokes'}; 197 DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','DUDXsin','DUDXcos','DUDYsin','DVDXsin','DVDXcos'... 198 ,'DVDYsin','Ustokes','Vstokes'}; 195 199 DataOut.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... 196 {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}}; 200 {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},... 201 {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}}; 197 202 198 203 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% … … 207 212 Time_end=Data.Time; 208 213 dt=(Time_end-Time_1)/(NbField-1); %time interval 209 NpTime=round(NbPeriod*T/dt+1) 210 214 NpTime=round(NbPeriod*T/dt+1); 215 216 OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); 217 RootFileOut=RootFile{1}; 218 NomTypeOut='_1'; 211 219 %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% 212 220 disp('loop for filtering started') … … 219 227 [Field,tild,errormsg] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index)); 220 228 221 %%%%%%%%%%% %MAIN RUNNING OPERATIONS %%%%%%%%%%%%229 %%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% 222 230 if index==1 %first field 223 DataOut.coord_x=Field.coord_x ;224 DataOut.coord_y=Field.coord_y ;231 DataOut.coord_x=Field.coord_x/Lscale; 232 DataOut.coord_y=Field.coord_y/Lscale; 225 233 npy=numel(DataOut.coord_y); 226 234 npx=numel(DataOut.coord_x); … … 229 237 Ucos=zeros(NpTime,npy,npx); 230 238 Vcos=zeros(NpTime,npy,npx); 239 DUDXcos=zeros(NpTime,npy,npx); 231 240 DUDXsin=zeros(NpTime,npy,npx); 232 241 DUDYsin=zeros(NpTime,npy,npx); 242 DVDXcos=zeros(NpTime,npy,npx); 233 243 DVDXsin=zeros(NpTime,npy,npx); 234 244 DVDYsin=zeros(NpTime,npy,npx); 235 245 end 236 Time(index)=Field.Time;246 Time(index)=Field.Time-t0;%time from the start of the motion 237 247 Umean=circshift(Umean,[-1 0 0]); %shift U by ishift along the first index 238 Vmean=circshift(Vmean,[-1 0 0]); %shift U by ishift along the first index 239 Ucos=circshift(Ucos,[-1 0 0]); %shift U by ishift along the first index 240 Vcos=circshift(Vcos,[-1 0 0]); %shift U by ishift along the first index 241 DUDXsin=circshift(DUDXsin,[-1 0 0]); 242 DUDYsin=circshift(DUDYsin,[-1 0 0]); 243 DVDXsin=circshift(DVDXsin,[-1 0 0]); 244 DVDYsin=circshift(DVDYsin,[-1 0 0]); 245 Umean(end,:,:)=Field.U; 246 Vmean(end,:,:)=Field.V; 247 Ucos(end,:,:)=Field.U*cos(omega*Time(index)); 248 Vcos(end,:,:)=Field.V*cos(omega*Time(index)); 249 DUDXsin(end,:,:)=Field.DUDX*sin(omega*Time(index)); 250 DUDYsin(end,:,:)=Field.DUDY*sin(omega*Time(index)); 251 DVDXsin(end,:,:)=Field.DVDX*sin(omega*Time(index)); 252 DVDYsin(end,:,:)=Field.DVDY*sin(omega*Time(index)); 253 DataOut.Time=Time(index)-(NpTime-1)*dt/2; 254 DataOut.Umean=squeeze(nanmean(Umean,1)); 255 DataOut.Vmean=squeeze(nanmean(Vmean,1)); 256 DataOut.Ucos=2*squeeze(nanmean(Ucos,1)); 257 DataOut.Vcos=2*squeeze(nanmean(Vcos,1)); 258 DataOut.DUDXsin=2*squeeze(nanmean(DUDXsin,1)); 259 DataOut.DUDYsin=2*squeeze(nanmean(DUDYsin,1)); 260 DataOut.DVDXsin=2*squeeze(nanmean(DVDXsin,1)); 261 DataOut.DVDYsin=2*squeeze(nanmean(DVDYsin,1)); 262 DataOut.Ustokes=(1/omega)*(DataOut.Ucos.*DataOut.DUDXsin+DataOut.Vcos.*DataOut.DUDYsin); 263 DataOut.Vstokes=(1/omega)*(DataOut.Ucos.*DataOut.DVDXsin+DataOut.Vcos.*DataOut.DVDYsin); 248 Vmean=circshift(Vmean,[-1 0 0]); %shift U by ishift along the first index 249 Ucos=circshift(Ucos,[-1 0 0]); %shift U by ishift along the first index 250 Vcos=circshift(Vcos,[-1 0 0]); %shift U by ishift along the first index 251 DUDXcos=circshift(DUDXcos,[-1 0 0]); 252 DUDXsin=circshift(DUDXsin,[-1 0 0]); 253 DUDYsin=circshift(DUDYsin,[-1 0 0]); 254 DVDXcos=circshift(DVDXcos,[-1 0 0]); 255 DVDXsin=circshift(DVDXsin,[-1 0 0]); 256 DVDYsin=circshift(DVDYsin,[-1 0 0]); 257 Umean(end,:,:)=Field.U; 258 Vmean(end,:,:)=Field.V; 259 Ucos(end,:,:)=Field.U*cos(omega*Time(index)); 260 Vcos(end,:,:)=Field.V*cos(omega*Time(index)); 261 DUDXcos(end,:,:)=Field.DUDX*cos(omega*Time(index)); 262 DUDXsin(end,:,:)=Field.DUDX*sin(omega*Time(index)); 263 DUDYsin(end,:,:)=Field.DUDY*sin(omega*Time(index));% ParamOut=[];%default output 264 265 DVDXcos(end,:,:)=Field.DVDX*cos(omega*Time(index)); 266 DVDXsin(end,:,:)=Field.DVDX*sin(omega*Time(index)); 267 DVDYsin(end,:,:)=Field.DVDY*sin(omega*Time(index)); 268 DataOut.Time=(Time(index)-(NpTime-1)*dt/2)/T;%time inperiods from the beginning of the oscillation (torus at max abscissa) 269 DataOut.Umean=(1/Uscale)*squeeze(nanmean(Umean,1)); 270 DataOut.Vmean=(1/Uscale)*squeeze(nanmean(Vmean,1)); 271 DataOut.Ucos=2*squeeze(nanmean(Ucos,1)); 272 DataOut.Vcos=2*squeeze(nanmean(Vcos,1)); 273 DataOut.DUDXcos=2*squeeze(nanmean(DUDXcos,1)); 274 DataOut.DUDXsin=2*squeeze(nanmean(DUDXsin,1)); 275 DataOut.DUDYsin=2*squeeze(nanmean(DUDYsin,1)); 276 DataOut.DVDXcos=2*squeeze(nanmean(DVDXcos,1)); 277 DataOut.DVDXsin=2*squeeze(nanmean(DVDXsin,1)); 278 DataOut.DVDYsin=2*squeeze(nanmean(DVDYsin,1)); 279 DataOut.Ustokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DUDXsin+DataOut.Vcos.*DataOut.DUDYsin); 280 DataOut.Vstokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DVDXsin+DataOut.Vcos.*DataOut.DVDYsin); 281 264 282 % writing the result file as netcdf file 265 if index-round(NpTime/2)>=1 266 OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomType{1},index-round(NpTime/2)); 267 %case of netcdf input file , determine global attributes 268 errormsg=struct2nc(OutputFile,DataOut); %save result file 269 if isempty(errormsg) 270 disp([OutputFile ' written']); 271 else 272 disp(['error in writting result file: ' errormsg]) 273 end 274 end 275 end 276 %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% 277 283 i1=i1_series{1}(index); 284 OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeOut,i1); 285 errormsg=struct2nc(OutputFile, DataOut); 286 if isempty(errormsg) 287 disp([OutputFile ' written']) 288 else 289 disp(errormsg) 290 end 291 end 292 -
trunk/src/transform_field/phys_polar.m
r1093 r1094 52 52 dlg_title = 'set the parameters for the polar coordinates'; 53 53 num_lines= 2; 54 def = { '[0 0]';' 0';'0';'+'};54 def = { '[0 0]';'';'0';'+'}; 55 55 if isfield(XmlData,'TransformInput') 56 56 if isfield(XmlData.TransformInput,'PolarCentre') … … 87 87 DataCell{2}=[];%default 88 88 checkpixel(1)=0; 89 if isfield(DataCell{1},'Coor Unit')&& strcmp(DataCell{1}.CoorUnit,'px')89 if isfield(DataCell{1},'CoordUnit')&& strcmp(DataCell{1}.CoordUnit,'pixel') 90 90 checkpixel(1)=1; 91 91 end … … 101 101 if nargin==4% case of two input fields 102 102 checkpixel(2)=0; 103 if isfield(DataCell{2},'Coor Unit')&& strcmp(DataCell{2}.CoorUnit,'px')103 if isfield(DataCell{2},'CoordUnit')&& strcmp(DataCell{2}.CoordUnit,'pixel') 104 104 checkpixel(2)=1; 105 105 end … … 124 124 end 125 125 end 126 if isfield(XmlData.TransformInput,'PolarReferenceRadius') && isnumeric(XmlData.TransformInput.PolarReferenceRadius)126 if isfield(XmlData.TransformInput,'PolarReferenceRadius') && ~isempty(XmlData.TransformInput.PolarReferenceRadius) 127 127 radius_offset=XmlData.TransformInput.PolarReferenceRadius; 128 128 end 129 129 if radius_offset > 0 130 130 angle_scale=radius_offset; %the azimuth is rescale in terms of the length along the reference radius 131 check_degree=0; %the output has the same unit as the input131 check_degree=0; %the output has the same unit as the input 132 132 else 133 133 angle_scale=180/pi; %polar angle in degrees … … 144 144 145 145 nbvar=0;%counter for the number of output variables 146 nbcoord=0;%counter for the number of variable s for radial coordiantes (case of multiple field inputs)146 nbcoord=0;%counter for the number of variablecheck_degrees for radial coordiantes (case of multiple field inputs) 147 147 nbgrid=0;%counter for the number of gridded fields (all linearly interpolated on the same output polar grid) 148 148 nbscattered=0;%counter of scattered fields … … 157 157 return 158 158 end 159 % end160 159 %transform of X,Y coordinates for vector fields 161 160 if isfield(DataCell{ifield},'ZIndex')&& ~isempty(DataCell{ifield}.ZIndex) … … 180 179 Data.VarAttribute{nbvar-1}.Role='coord_x'; 181 180 check_unit=1; 182 if isfield(DataCell{ifield},'CoordUnit')183 Data=rmfield(Data,'CoordUnit');184 Data.VarAttribute{nbvar-1}.unit=DataCell{ifield}.CoordUnit;185 elseif isfield( XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit')186 Data.VarAttribute{nbvar-1}.unit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units181 %unit of output field 182 if isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') 183 radius_unit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units 184 elseif isfield(DataCell{ifield},'CoordUnit') 185 radius_unit=DataCell{ifield}.CoordUnit; 187 186 else 188 check_unit=0; 189 end 187 radius_unit=''; 188 end 189 Data.VarAttribute{nbvar-1}.units=radius_unit; 190 if check_degree 191 Data.VarAttribute{nbvar}.units='degree'; 192 else %case of a reference radius 193 Data.VarAttribute{nbvar}.units=radius_unit; 194 Data.CoordUnit=radius_unit; 195 end 196 % if isfield(DataCell{ifield},'CoordUnit') 197 % Data=rmfield(Data,'CoordUnit'); 198 % Data.VarAttribute{nbvar-1}.unit=DataCell{ifield}.CoordUnit; 199 % elseif isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') 200 % Data.VarAttribute{nbvar-1}.unit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units 201 % else 202 % check_unit=0; 203 % end 190 204 Data.VarAttribute{nbvar}.Role='coord_y'; 191 if check_degree192 Data.VarAttribute{nbvar}.unit='degree';193 elseif check_unit194 Data.VarAttribute{nbvar}.unit=Data.VarAttribute{nbvar-1}.unit;195 end205 % if check_degree 206 % Data.VarAttribute{nbvar}.units='degree'; 207 % elseif check_unit 208 % Data.VarAttribute{nbvar}.units=Data.VarAttribute{nbvar-1}.units; 209 % end 196 210 197 211 %transform u,v into polar coordinates … … 250 264 if nbgrid==0% no gridded data yet, introduce the coordinate variables common to all gridded data 251 265 nbcoord=nbcoord+1;%add new radial coordinates for the first gridded field 252 radius_name = rename_indexing(radius_name,Data.ListVarName); 253 theta_name = rename_indexing(theta_name,Data.ListVarName); 254 Data.ListVarName = [Data.ListVarName {radius_name} {theta_name}]; 266 radius_name = rename_indexing(radius_name,Data.ListVarName);% add an index to the name, or increment an existing index, 267 theta_name = rename_indexing(theta_name,Data.ListVarName);% if the proposed Name already exists in the list 268 Data.ListVarName = [Data.ListVarName {radius_name} {theta_name}];%add polar coordinates to the list of variables 255 269 Data.VarDimName=[Data.VarDimName {radius_name} {theta_name}]; 256 270 nbvar=nbvar+2; 257 271 if check_reverse 258 259 Data.VarAttribute{nbvar}.Role='coord_x';272 Data.VarAttribute{nbvar-1}.Role='coord_y'; 273 Data.VarAttribute{nbvar}.Role='coord_x'; 260 274 else 261 Data.VarAttribute{nbvar-1}.Role='coord_x';262 Data.VarAttribute{nbvar}.Role='coord_y';275 Data.VarAttribute{nbvar-1}.Role='coord_x'; 276 Data.VarAttribute{nbvar}.Role='coord_y'; 263 277 end 264 278 check_unit=1; 265 if isfield(DataCell{ifield},'CoordUnit') 266 Data.VarAttribute{nbvar-1}.unit=DataCell{ifield}.CoordUnit; 267 elseif isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') 268 Data.VarAttribute{nbvar-1}.unit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units 279 280 if isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') 281 Data.VarAttribute{nbvar-1}.units=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units 282 elseif isfield(DataCell{ifield},'CoordUnit') 283 Data.VarAttribute{nbvar-1}.units=DataCell{ifield}.CoordUnit;%radius in coord units 269 284 else 270 285 check_unit=0; 271 286 end 272 287 if check_degree 273 Data.VarAttribute{nbvar}.unit ='degree';288 Data.VarAttribute{nbvar}.units='degree';%angle in degree 274 289 elseif check_unit 275 Data.VarAttribute{nbvar}.unit =Data.VarAttribute{nbvar-1}.unit;290 Data.VarAttribute{nbvar}.units=Data.VarAttribute{nbvar-1}.units;% angle in coord unit (normalised by reference radiuss) 276 291 end 277 292 end … … 282 297 FieldName{nbgrid}=DataCell{ifield}.ListVarName{CellInfo{icell}.VarIndex_scalar}; 283 298 A{nbgrid}=DataCell{ifield}.(FieldName{nbgrid}); 284 % Data.ListVarName=[Data.ListVarName {FieldName{nbgrid}}];285 % Data.VarDimName=[Data.VarDimName {{theta_name,radius_name}}];286 299 nbpoint(nbgrid)=numel(A{nbgrid}); 287 300 check_scalar(nbgrid)=1; … … 296 309 A{nbgrid+1}=DataCell{ifield}.(FieldName{nbgrid+1}); 297 310 A{nbgrid+2}=DataCell{ifield}.(FieldName{nbgrid+2}); 298 % Data.ListVarName=[Data.ListVarName {'U_r','U_theta'}];311 % Data.ListVarName=[Data.ListVarName {'U_r','U_theta'}]; 299 312 %Data.VarDimName=[Data.VarDimName {{theta_name,radius_name}} {{theta_name,radius_name}}]; 300 313 Data.VarAttribute{nbvar+1}.Role='vector_x'; -
trunk/src/uvmat.m
r1093 r1094 1538 1538 XmlData.LIFCalib.Ray1Coord=LineData{1}.Coord; 1539 1539 XmlData.LIFCalib.Ray2Coord=LineData{2}.Coord; 1540 if numel(LineData)<3 1541 msgbox_uvmat('ERROR','draw a reference line of direct laser illumination (without dye absorbsion)'); 1542 return 1543 end 1540 1544 XmlData.LIFCalib.RefLineCoord=LineData{3}.Coord; 1541 1545 … … 1545 1549 y=linspace(UvData.Field.Coord_y(1),UvData.Field.Coord_y(2),nby)-nby/2; 1546 1550 [X,Y]=meshgrid(x,y); 1547 coeff_quad=0.15*4/(nbx*nbx);% image luminosity reduced by 10% at the edge1548 UvData.Field.A=double(UvData.Field.A).*(1+coeff_quad*(X.*X+Y.*Y));1551 %coeff_quad=0.15*4/(nbx*nbx);% image luminosity reduced by 10% at the edge 1552 %UvData.Field.A=double(UvData.Field.A).*(1+coeff_quad*(X.*X+Y.*Y)); 1549 1553 1550 1554 %% display the current image in polar axes with origin at the illumination source … … 1564 1568 y_ref=y_ref-y0; 1565 1569 [theta_ref,r_ref] = cart2pol(x_ref,y_ref);%theta_ref and r_ref are the polar coordinates of the points on the line 1566 theta_ref=theta_ref*180/pi;% theta_ref in radians1570 theta_ref=theta_ref*180/pi;% theta_ref in degrees 1567 1571 figure(10) 1568 1572 plot(theta_ref,r_ref) … … 1570 1574 ylabel('radius from light source') 1571 1575 title('ref line in polar coordinates') 1572 azimuth_ima=linspace(DataPol.Coord_y(1),DataPol.Coord_y(2),size(DataPol.A,1)) ;%array of angular indexon the transformed image1576 azimuth_ima=linspace(DataPol.Coord_y(1),DataPol.Coord_y(2),size(DataPol.A,1))-360;%array of angular indices on the transformed image 1573 1577 dist_source = interp1(theta_ref,r_ref,azimuth_ima);% get the polar position of the reference line 1574 1578 dist_source_pixel=round(size(DataPol.A,2)*(dist_source-DataPol.Coord_x(1))/(DataPol.Coord_x(2)-DataPol.Coord_x(1))); … … 3719 3723 %% choose and read a second field FileName_1 if defined 3720 3724 ParamOut_1=[]; 3721 if numel(UvData.FileInfo)>1 3725 if ~isempty(FileName_1) 3726 if numel(UvData.FileInfo)==1 3727 UvData.FileInfo{2}=UvData.FileInfo{1}; 3728 end 3722 3729 VelType_1=[];%default 3723 3730 FieldName_1=[]; … … 3736 3743 NomType_1=get(handles.NomType,'String'); 3737 3744 end 3738 if strcmp(UvData.FileInfo{2}.Fi eldType,'image')3745 if strcmp(UvData.FileInfo{2}.FileType,'image') 3739 3746 FieldName_1='image'; 3740 3747 frame_index_1=1;%default … … 3761 3768 end 3762 3769 switch UvData.FileInfo{2}.FileType 3763 case {'civx','civdata','netcdf','pivdata_fluidimage'} ;3770 case {'civx','civdata','netcdf','pivdata_fluidimage'} 3764 3771 list_fields=get(handles.FieldName_1,'String');% list menu fields 3765 3772 FieldName_1= list_fields{get(handles.FieldName_1,'Value')}; % selected field … … 3849 3856 %% update the display menu for the second velocity type (second menuline) 3850 3857 test_veltype_1=0; 3851 if isempty(FileName_1)3852 elseif ~test_keepdata_1 3853 if strcmp(UvData.FileInfo{2}.Fi eldType,'civdata')&& ~strcmp(FieldName_1,'get_field...')3858 if ~isempty(FileName_1) 3859 3860 if strcmp(UvData.FileInfo{2}.FileType,'civdata')&& ~strcmp(FieldName_1,'get_field...') 3854 3861 test_veltype_1=1; 3855 3862 set(handles.VelType_1,'Visible','on')
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