%'test_patch_tps': test the optimum value for the spline smmoothing function used in civ_series %------------------------------------------------------------------------ % Method: %open a netcdf file with civ results. % function ParamOut=test_patch_tps (Param) % %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% % %OUTPUT % ParamOut: sets input parameters when the function is selected, not activated(input Param.Action.RUN=0),=[] when the function is running % %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 % .InputFields: sub structure describing the input fields withfields % .FieldName: name(s) of the field % .VelType: velocity type %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %======================================================================= % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.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=test_patch_tps (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='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) ParamOut.NbSlice='off'; % edit box nbre of slices made active ParamOut.VelType='one';% 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';%cannot use projection object(option 'off'/'on', ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) ParamOut.OutputDirExt='.test_patch';%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 %% 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']) return else [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString); LastFileName=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 last input file ' LastFileName ' does not exist']) end end %% check the validity of input file types Data=nc2struct(FirstFileName,[]); if isfield(Data,'CivStage') switch Data.CivStage case {1,2} CivStage='civ1'; MaxDiff=1.5; SubDomainSize=250; FieldSmooth=10; %default case 3 CivStage='civ1'; MaxDiff=Data.Patch1_MaxDiff; SubDomainSize=Data.Patch1_SubDomainSize; FieldSmooth=Data.Patch1_FieldSmooth; case {4,5} CivStage='civ2'; MaxDiff=1.5; SubDomainSize=250; FieldSmooth=5; %default case 6 CivStage='civ2'; MaxDiff=Data.Patch2_MaxDiff; SubDomainSize=Data.Patch2_SubDomainSize; FieldSmooth=Data.Patch2_FieldSmooth; end else msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not a civ data']) return end %% numbers of fields incr_j=1;%default if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j) incr_j=Param.IndexRange.incr_j; end if isempty(first_j)||isempty(last_j) nbfield_j=1; else nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices) end first_i=1;last_i=1;incr_i=1;%default if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i) incr_i=Param.IndexRange.incr_i; end nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices) nbfield=nbfield_j*nbfield_i; %total number of fields %% setting of intput parameters ListParam={'CivStage';'FieldSmooth';'MaxDiff';'SubDomainSize'}; DefaultValue={CivStage;FieldSmooth;MaxDiff;SubDomainSize}; if isfield(Param,'ActionInput') ParamIn=Param.ActionInput; else ParamIn=[]; end [ParamOut.ActionInput,errormsg] = set_param_input(ListParam,DefaultValue,ParamIn); if ~isempty(errormsg) msgbox_uvmat('ERROR',errormsg) end 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 %% input preparation RootPath=Param.InputTable{:,1}; RootFile=Param.InputTable{:,3}; NomType=Param.InputTable{:,4}; [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); % if ~isempty(hdisp),delete(hdisp),end; %%%%%%%%%%%% % 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 %%%%%%%%%%%% %% output file naming FileExtOut='.nc'; % write result as .png images for image inputsFileInfo.FileType='image' NomTypeOut=NomType; OutputDir=[Param.OutputSubDir Param.OutputDirExt]; OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device); RootFileOut=RootFile; %% file index parameters Param.InputFields.VelType=Param.ActionInput.CivStage; SubDomainSize=Param.ActionInput.SubDomainSize; MaxDiff=Param.ActionInput.MaxDiff; FieldSmooth=(Param.ActionInput.FieldSmooth)*[0.1 0.2 0.5 1 2 5 10];%scan the smoothing param from 1/10 to 10 current value NbSmooth=numel(FieldSmooth); for irho=1:NbSmooth str=num2str(FieldSmooth(irho)); str=regexprep(str,'\.','p'); Ustr{irho}=['U_' str]; Vstr{irho}=['V_' str]; Xstr{irho}=['X_' str]; Ystr{irho}=['Y_' str]; Dimstr{irho}='NbVec'; str_i{irho}=str; end %% Prepare the structure of output netcdf file DataOut.ListGlobalAttribute={'CivStage','SubDomainSize','MaxDiff','CoordUnit'}; DataOut.CivStage=Param.InputFields.VelType; DataOut.SubDomainSize=SubDomainSize; DataOut.MaxDiff=MaxDiff; DataOut.CoordUnit='pixel'; DataOut.ListVarName=[{'FieldSmooth','Diff_rms','NbExclude','X','Y'} Ustr Vstr] ; DataOut.VarDimName=[{'FieldSmooth','FieldSmooth','FieldSmooth','NbVec','NbVec'} Dimstr Dimstr]; DataOut.VarAttribute{4}.Role='falseflag'; DataOut.FieldSmooth=FieldSmooth; %% MAIN LOOP for index=1:1%numel(filecell) Data=read_field(filecell{1,index},'civdata',Param.InputFields); ind_good=find(Data.FF==0|Data.FF==20);%keep good civ data, and also the ones excluded by the criterium of discrepancy betwween smoothed and raw fields (FF=20) NbGood=numel(ind_good); Xin=Data.X(ind_good); Yin=Data.Y(ind_good); Uin=Data.U(ind_good); Vin=Data.V(ind_good); tic for irho=1:NbSmooth [SubRange,NbCentres,Coord_tps,U_tps,V_tps,~,U_smooth, V_smooth,~,FFres]=... filter_tps([Xin Yin],Uin,Vin,[],SubDomainSize,FieldSmooth(irho),MaxDiff); if irho==1 DataOut.FF=zeros(size(Xin)); DataOut.X=Xin; DataOut.Y=Yin; figure(1) cla scatter(Xin,Yin,1) for irec=1:size(SubRange,3) rectangle('Position',[SubRange(:,1,irec)' SubRange(:,2,irec)'-SubRange(:,1,irec)']) end title('subdomains for thin shell splines (tps)') end ind_good=find(FFres==0); ind_false=find(FFres~=0); U_Diff=Uin(ind_good)-U_smooth(ind_good); V_Diff=Vin(ind_good)-V_smooth(ind_good); DataOut.Diff_rms(irho)=sqrt(mean(U_Diff.*U_Diff+V_Diff.*V_Diff)/2); DataOut.NbExclude(irho)=(NbGood-numel(ind_good))/NbGood; U_smooth(ind_false)=NaN; V_smooth(ind_false)=NaN; DataOut.(['U_' str_i{irho}])=U_smooth; DataOut.(['V_' str_i{irho}])=V_smooth; % DataOut.FF(ind_false)=FieldSmooth(irho); end time=toc OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1_series{1}(index),[],j1_series{1}(index),j2_series{1}(index)) errormsg=struct2nc(OutputFile,DataOut) end figure semilogx(FieldSmooth,DataOut.Diff_rms,'b',FieldSmooth,DataOut.NbExclude,'r',FieldSmooth,0.1*ones(size(FieldSmooth)),'m') grid on title( [filecell{1,1} ':' Param.InputFields.VelType]) legend({'rms vel. diff. ' ;' ratio excluded vectors';'recommended diff'},'Location','northwest') xlabel('smoothing parameter') ylabel('rms (pixels) and exclusion ratio') OutputFig=fullfile(OutputPath,OutputDir,'plot_rms_diff.png') saveas(2,OutputFig)