Index: /trunk/src/find_field_cells.m =================================================================== --- /trunk/src/find_field_cells.m (revision 1047) +++ /trunk/src/find_field_cells.m (revision 1048) @@ -328,5 +328,5 @@ end for ivar=ind_coord_y - if check_coord_names(ivar) + if check_coord_names(ivar) DimRank=find(strcmp(Data.VarDimName{ivar},DimCell_var)); check_coord=~isempty(DimRank); @@ -396,8 +396,9 @@ CellInfo{icell}.CoordSize=numel(Data.(CellInfo{icell}.XName)); case 'grid' + VarName=Data.ListVarName{CellInfo{icell}.VarIndex(1)}; if NbDim(icell)==3 - CellInfo{icell}.CoordSize=[numel(Data.(CellInfo{icell}.XName)) numel(Data.(CellInfo{icell}.YName)) numel(Data.(CellInfo{icell}.YName))]; + CellInfo{icell}.CoordSize=[size(Data.(VarName),3) size(Data.(VarName),2) size(Data.(VarName),1)]; else - CellInfo{icell}.CoordSize=[numel(Data.(CellInfo{icell}.XName)) numel(Data.(CellInfo{icell}.YName))]; + CellInfo{icell}.CoordSize=[size(Data.(VarName),2) size(Data.(VarName),1)]; end case 'tps' @@ -469,15 +470,23 @@ Cell1DPlot{icell}.XIndex=ind_coord_x(icell); Cell1DPlot{icell}.XName=Data.ListVarName{ind_coord_x(icell)}; + Cell1DPlot{icell}.YIndex=[]; + Cell1DPlot{icell}.YIndex_discrete=[]; DimCell_x=Data.VarDimName{ind_coord_x(icell)}; - for ivar=[ind_coord_y ind_discrete] + for ivar=ind_coord_y DimCell=Data.VarDimName{ivar}; if numel(DimCell)==1 && strcmp(DimCell_x{1},DimCell{1}) y_nbre(icell)=y_nbre(icell)+1; Cell1DPlot{icell}.YIndex(y_nbre(icell))=ivar; - break - end - end - end - Cell1DPlot(find(y_nbre==0))=[]; + end + end + for ivar=ind_discrete + DimCell=Data.VarDimName{ivar}; + if numel(DimCell)==1 && strcmp(DimCell_x{1},DimCell{1}) + y_nbre(icell)=y_nbre(icell)+1; + Cell1DPlot{icell}.YIndex_discrete(y_nbre(icell))=ivar; + end + end + end + Cell1DPlot(y_nbre==0)=[]; CellInfo=[CellInfo Cell1DPlot]; NbDim=[NbDim ones(1,numel(Cell1DPlot))]; Index: /trunk/src/plot_field.m =================================================================== --- /trunk/src/plot_field.m (revision 1047) +++ /trunk/src/plot_field.m (revision 1048) @@ -410,5 +410,5 @@ %loop on input fields for icell=1:numel(CellInfo) - VarIndex=CellInfo{icell}.YIndex;% indices of the selected variables in the list data.ListVarName + VarIndex=[CellInfo{icell}.YIndex CellInfo{icell}.YIndex_discrete];% indices of the selected variables in the list data.ListVarName coord_x_index=CellInfo{icell}.XIndex; coord_x_name{icell}=data.ListVarName{coord_x_index}; @@ -442,5 +442,5 @@ end end - if isfield(CellInfo{icell},'VarIndex_discrete') + if isfield(CellInfo{icell},'YIndex_discrete')&& ~isempty(CellInfo{icell}.YIndex_discrete) charplot_0='''+'''; else Index: /trunk/src/proj_field.m =================================================================== --- /trunk/src/proj_field.m (revision 1047) +++ /trunk/src/proj_field.m (revision 1048) @@ -539,5 +539,4 @@ end % default output -errormsg='';%default Xline=[]; flux=0; @@ -545,6 +544,4 @@ liny=ObjectData.Coord(:,2); NbPoints=size(ObjectData.Coord,1); -testfalse=0; -ListIndex={}; %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions @@ -556,10 +553,6 @@ CellInfo=CellInfo(NbDim>=2); %keep only the 2D or 3D cells cell_select=true(size(CellInfo)); - for icell=1:length(CellInfo) if isfield(CellInfo{icell},'ProjModeRequest') -% if ~strcmp(CellInfo{icell}.ProjModeRequest, ProjMode) -% cell_select(icell)=0; -% end if strcmp(ProjMode,'interp_tps')&& ~strcmp(CellInfo{icell}.CoordType,'tps') cell_select(icell)=0; @@ -567,5 +560,5 @@ end end -if isempty(find(cell_select)) +if isempty(find(cell_select,1)) errormsg=[' invalid projection mode ''' ProjMode ''': use ''interp_tps'' to interpolate spatial derivatives']; return @@ -598,8 +591,4 @@ end CheckClosedLine=~isempty(find(strcmp(ObjectData.Type,{'rectangle','ellipse','polygon'}))); - -% x = a \ \cosh \mu \ \cos \nu -% -% y = a \ \sinh \mu \ \sin \nu %% angles of the polyline and boundaries of action for mode 'projection' @@ -694,10 +683,8 @@ %case of unstructured coordinates case 'scattered' - % XName= FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}; - % YName= FieldData.ListVarName{CellInfo{icell}.CoordIndex(end-1)}; coord_x=FieldData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex(end)}); coord_y=FieldData.(FieldData.ListVarName{CellInfo{icell}.CoordIndex(end-1)}); - if isequal(ProjMode,'projection') + if strcmp(ProjMode,'projection') if width==0 errormsg='range of the projection object is missing'; @@ -707,4 +694,5 @@ ProjData.VarDimName=[ProjData.VarDimName FieldData.ListVarName(CellInfo{icell}.CoordIndex(end))]; nbvar=numel(ProjData.ListVarName); + ProjData.VarAttribute{nbvar}.Role='coord_x'; ProjData.VarAttribute{nbvar}.long_name='abscissa along line'; % select the (non false) input data located in the band of projection @@ -742,4 +730,5 @@ ProjData.VarDimName=[ProjData.VarDimName {XName}]; nbvar=numel(ProjData.ListVarName); + ProjData.VarAttribute{nbvar}.Role='coord_x'; ProjData.VarAttribute{nbvar}.long_name='abscissa along line'; check_abscissa=1; % define abcissa only once @@ -769,5 +758,5 @@ end end - ProjData.VarAttribute{ivar+nbvar}.Role='continuous';% will promote plots of the profiles with continuous lines + ProjData.VarAttribute{ivar+nbvar}.Role='coord_y';% will promote plots of the profiles with continuous lines ProjData.(ListFieldProj{ivar})=ProjVar{ivar}; end @@ -778,6 +767,6 @@ NbCentres=FieldData.(FieldData.ListVarName{CellInfo{icell}.NbCentres_tps}); SubRange=FieldData.(FieldData.ListVarName{CellInfo{icell}.SubRange_tps}); - if isfield(CellInfo{icell},'VarIndex_vector_x_tps')&&isfield(CellInfo{icell},'VarIndex_vector_y_tps') - FieldVar=cat(3,FieldData.(FieldData.ListVarName{CellInfo{icell}.VarIndex_vector_x_tps}),FieldData.(FieldData.ListVarName{CellInfo{icell}.VarIndex_vector_y_tps})); + if isfield(CellInfo{icell},'VarIndex_vector_x')&&isfield(CellInfo{icell},'VarIndex_vector_y') + FieldVar=cat(3,FieldData.(FieldData.ListVarName{CellInfo{icell}.VarIndex_vector_x}),FieldData.(FieldData.ListVarName{CellInfo{icell}.VarIndex_vector_y})); end [DataOut,VarAttribute,errormsg]=calc_field_tps(Coord,NbCentres,SubRange,FieldVar,CellInfo{icell}.FieldName,cat(3,XI,YI)); @@ -786,4 +775,5 @@ ProjData.X=Xproj; nbvar=numel(ProjData.ListVarName); + ProjData.VarAttribute{nbvar}.Role='coord_x'; ProjData.VarAttribute{nbvar}.long_name='abscissa along line'; ProjVarName=(fieldnames(DataOut))'; @@ -799,5 +789,5 @@ end end - ProjData.VarAttribute{ivar+nbvar}.Role='continuous';% will promote plots of the profiles with continuous lines + ProjData.VarAttribute{ivar+nbvar}.Role='coord_y';% will promote plots of the profiles with continuous lines ProjData.(ProjVarName{ivar})=DataOut.(ProjVarName{ivar}); end @@ -1107,6 +1097,4 @@ %error=0;%default %flux=0; -%testfalse=0; -%ListIndex={}; %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions Index: /trunk/src/series/civ_input.m =================================================================== --- /trunk/src/series/civ_input.m (revision 1047) +++ /trunk/src/series/civ_input.m (revision 1048) @@ -337,5 +337,5 @@ %% set default choice of pair mode -PairIndex=[]; +PairIndex=1; if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'PairIndices') PairIndex=find(strcmp(Param.ActionInput.PairIndices.ListPairMode,PairMenu)); Index: /trunk/src/series/extract_multitif_special.m =================================================================== --- /trunk/src/series/extract_multitif_special.m (revision 1048) +++ /trunk/src/series/extract_multitif_special.m (revision 1048) @@ -0,0 +1,231 @@ +%'ima2netcdf': read image series and transform to netcdf +%------------------------------------------------------------------------ + + +% function ParamOut=ima2netcdf(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 2008-2018, 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=extract_multitif_parallel(Param) + +%%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% +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='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + ParamOut.NbSlice='off'; % impose calculation in a single process (no parallel processing to avoid 'holes')) + ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + ParamOut.FieldTransform = 'off';%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='.png';%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 + ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) + %% root input file(s) and type + % check the existence of the first file in the series + first_j=[];% note that the function will propose to cover the whole range of indices + if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end + last_j=[]; + if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end + PairString=''; + if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end + [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); + FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... + Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); + if ~exist(FirstFileName,'file') + msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) + end + + %% check the validity of input file types + FileInfo=get_file_info(FirstFileName); + if ~strcmp(FileInfo.FileType,'multimage') + msgbox_uvmat('ERROR',['invalid file type input: ' FileInfo.FileType ' not an image']) + return + end + %ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); + return +end +%%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% + +%% read input parameters from an xml file if input is a file name (batch mode) +checkrun=1; +RUNHandle=[]; +WaitbarHandle=[]; +if ischar(Param) + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +else + 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 +end + +%% list of input images +% DirImages=fullfile(Param.InputTable{1,1},Param.InputTable{1,2}); +% ListStruct=dir(DirImages); +% ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray +% check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it +% check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files +% ListFile=ListCells(1,find(~check_dir & ~check_bad)); + +%% check file names +% RootName=regexprep(ListFile{1},'.tif$','') +% rank(1)=1; +% for ilist=2:numel(ListFile) +% rank_str=regexprep(ListFile{ilist},'.tif$',''); +% rank(ilist)=regexprep(rank_str,['^' RootName '@'],''); +% % if ~isequal(str2num(rank),ilist-1) +% % disp(['error in the list of input file # ' num2str(ilist-1)]) +% % return +% % end +% end + +%% output directory +OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); + +%% Timing +% XmlInputFile=Param.ActionInput.XmlFile; +% [XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera'); +% if ~isempty(errormsg) +% disp(['bad xml input file: ' errormsg]) +% return +% end +%ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices +ImagesPerLevel=450;% total number of images per position, ImagesPerLevel-Nbj images skiiped during motion between two positions +Nbj=400; %Nbre of images kept at a given position +%% create the xml file of PCO camera if it does not exist +Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']); +if ~exist(Newxml,'file') + XmlInput.Camera.CameraName='PCO'; + XmlInput.Camera.TimeUnit='s'; + XmlInput.Camera.BurstTiming.FrameFrequency=1; + % XmlInput.Camera.BurstTiming.Time=-1;% for 180 + XmlInput.Camera.BurstTiming.Time=0;% for 200 + XmlInput.Camera.BurstTiming.Dtj=0.05; + XmlInput.Camera.BurstTiming.NbDtj=199; + XmlInput.Camera.BurstTiming.Dti=12.5; + XmlInput.Camera.BurstTiming.NbDti=10; + XmlInput.Camera.BurstTiming.Dtk=157; + XmlInput.Camera.BurstTiming.NbDtk=2; + %XmlInput=rmfield(XmlInput,'Time'); + %XmlInput=rmfield(XmlInput,'TimeUnit'); + t=struct2xml(XmlInput); + t=set(t,1,'name','ImaDoc'); + save(t,Newxml); +end + +%% Main loop + + +% count=0; +%count=316;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP08: 4684 images -> start at 316 start 67->_11_1 +%count=1934%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%CORRECTION EXP07: 3066 images +%% loop on the files +% include the first tiff file with no index in the first iteration +if Param.IndexRange.first_i==1% first slice of processing + firstindex=0; + count=0; +else + firstindex=Param.IndexRange.first_i; + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif'); + NbFrames=numel(imfinfo(ImageName)); + count=Param.IndexRange.first_i*NbFrames; +end +for ifile=firstindex:Param.IndexRange.last_i + if firstindex==0 && ifile==0% first slice of processing + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') + else + ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif']) + end + NbFrames=numel(imfinfo(ImageName)); + for iframe=1:NbFrames + iframe% = frame number inside a tif multimage + checkkeep=1; + count=count+1; + if count<=ImagesPerLevel*11 % first scan of 11 levels + i_index=fix((count-1)/ImagesPerLevel)+1; + j_index=mod(count-1,ImagesPerLevel)+1; + elseif count<=ImagesPerLevel*11+400 %skip 400 images during return + checkkeep=0; + elseif count<=ImagesPerLevel*22+400 % =5930 second scan + i_index=fix((count-401)/ImagesPerLevel)+1; + j_index=mod(count-401,ImagesPerLevel)+1; + elseif count<=ImagesPerLevel*22+800 %skip images during second return, from 2763 to 3167 + checkkeep=0; + elseif count<=ImagesPerLevel*33+800 % =5930 third scan + i_index=fix((count-801)/ImagesPerLevel)+1; + j_index=mod(count-801,ImagesPerLevel)+1; + end + if checkkeep + if j_index>Nbj + OutputFile=''; + else + OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); + end + if ~isempty(OutputFile) + if Param.CheckOverwrite ||~exist(OutputFile,'file') + A=imread(ImageName,iframe); + imwrite(A,OutputFile,'BitDepth',16); + disp([OutputFile ' written']) + else + disp([OutputFile ' already exists']) + end + end + end + end +end + + + Index: /trunk/src/uvmat.m =================================================================== --- /trunk/src/uvmat.m (revision 1047) +++ /trunk/src/uvmat.m (revision 1048) @@ -4164,12 +4164,12 @@ test_v=0; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% A REMETTRE -% if ~isempty(menu_histo) -% set(handles.HistoMenu,'Value',1) -% set(handles.HistoMenu,'String',menu_histo) -% set(handles.Histogram,'Visible','on') -% set(handles.HistoMenu,'Visible','on') -% set(handles.HistoAxes,'Visible','on') -% HistoMenu_Callback(handles.HistoMenu, [], handles)% plot first histogram -% end + if ~isempty(menu_histo) + set(handles.HistoMenu,'Value',1) + set(handles.HistoMenu,'String',menu_histo) + set(handles.Histogram,'Visible','on') + set(handles.HistoMenu,'Visible','on') + set(handles.HistoAxes,'Visible','on') + HistoMenu_Callback(handles.HistoMenu, [], handles)% plot first histogram + end end % open the set_object for interactive plane projection in 3D case @@ -4262,4 +4262,6 @@ end end + Histo.VarAttribute{1}.Role='coord_x'; + Histo.VarAttribute{2}.Role='coord_y'; if ~isempty(units) Histo.VarAttribute{1}.units=units;