Index: trunk/src/series/civ_3D.m =================================================================== --- trunk/src/series/civ_3D.m (revision 1089) +++ trunk/src/series/civ_3D.m (revision 1089) @@ -0,0 +1,1412 @@ +%'civ_3D': PIV function activated by the general GUI series +% --- call the sub-functions: +% civ: PIV function itself +% fix: removes false vectors after detection by various criteria +% filter_tps: make interpolation-smoothing +%------------------------------------------------------------------------ +% function [Data,errormsg,result_conv]= civ_series(Param) +% +%OUTPUT +% Data=structure containing the PIV results and information on the processing parameters +% errormsg=error message char string, decd ..fault='' +% resul_conv: image inter-correlation function for the last grid point (used for tests) +% +%INPUT: +% Param: Matlab structure of input parameters +% Param contains info of the GUI series using the fct read_GUI. +% Param.Action.RUN = 0 (to set the status of the GUI series) or =1 to RUN the computation +% Param.InputTable: sets the input file(s) +% if absent, the fct looks for input data in Param.ActionInput (test mode) +% Param.OutputSubDir: sets the folder name of output file(s, +% if absent no file is produced, result in the output structure Data (test mode) +% Param.ActionInput: substructure with the parameters provided by the GUI civ_input +% .Civ1: parameters for civ1 +% .Fix1: parameters for fix1 +% .Patch1: +% .Civ2: for civ2 +% .Fix2: +% .Patch2: + +%======================================================================= +% Copyright 2008-2020, 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 [Data,errormsg,result_conv]= civ_3D(Param) +errormsg=''; + +%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed +if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN + path_series=fileparts(which('series')); + addpath(fullfile(path_series,'series')) + Data=civ_input_3D(Param);% introduce the civ parameters using the GUI civ_input + %Data=civ_input_App(Param);% introduce the civ parameters using the GUI + %civ_input %%%% TO MOVE + if isempty(Data) + Data=Param;% if civ_input has been cancelled, keep previous parameters + end + Data.Program=mfilename;%gives the name of the current function + Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) + Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) + Data.NbSlice='off'; %nbre of slices ('off' by default) + Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) + Data.FieldName='on';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) + Data.FieldTransform = 'off';%can use a transform function + Data.ProjObject='off';%can use projection object(option 'off'/'on', + Data.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) + Data.OutputDirExt='.civ';%set the output dir extension + Data.OutputSubDirMode='last'; %select the last subDir in the input table as root of the output subdir name (option 'all'/'first'/'last', 'all' by default) + Data.OutputFileMode='NbInput_i';% one output file expected per value of i index (used for waitbar) + Data.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) + if isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') + if isfield(Data.ActionInput.PairIndices,'ListPairCiv2') + str_civ=Data.ActionInput.PairIndices.ListPairCiv2; + else + str_civ=Data.ActionInput.PairIndices.ListPairCiv1; + end + r=regexp(str_civ,'^j= (?[a-z])-(?[a-z])','names'); + if isempty(r) + r=regexp(str_civ,'^j= (?[A-Z])-(?[A-Z])','names'); + if isempty(r) + r=regexp(str_civ,'^j= (?\d+)-(?\d+)','names'); + end + end + if ~isempty(r) + Data.j_index_1=stra2num(r.num1); + Data.j_index_2=stra2num(r.num2); + end + end + % estimated CPUTime + CPUtime_unit=0.01;%estimated time for a multiplication (in microsecond) + if isfield(Param.SeriesData,'FileInfo')&&isfield(Param.SeriesData.FileInfo{1},'Height')&&isfield(Param.SeriesData.FileInfo{1},'Width') + pixnbre=Param.SeriesData.FileInfo{1}.Height*Param.SeriesData.FileInfo{1}.Width; % total number of pxels for input images + CPUtime=0; + if isfield(Data.ActionInput,'Civ1') + %BoxSize=Data.ActionInput.Civ1.CorrBoxSize(1)*Data.ActionInput.Civ1.CorrBoxSize(2); + tic + testboxa=rand(Data.ActionInput.Civ1.CorrBoxSize(1),Data.ActionInput.Civ1.CorrBoxSize(2)); + testboxb=rand(Data.ActionInput.Civ1.SearchBoxSize(1),Data.ActionInput.Civ1.SearchBoxSize(2)); + anss=conv2(testboxa,testboxb); + CPUtime_unit=toc; + nb_box=pixnbre/(Data.ActionInput.Civ1.Dx*Data.ActionInput.Civ1.Dy); + %nbpos=Data.ActionInput.Civ1.SearchBoxSize-Data.ActionInput.Civ1.CorrBoxSize; + CPUtime=2*CPUtime_unit*nb_box%*BoxSize*nbpos(1)*nbpos(2);% adjustement factor 2 used + end + if isfield(Data.ActionInput,'Patch1') + CPUtime=2*CPUtime; + end + if isfield(Data.ActionInput,'Civ2') + tic + testboxa=rand(Data.ActionInput.Civ2.CorrBoxSize(1),Data.ActionInput.Civ2.CorrBoxSize(2)); + testboxb=rand(Data.ActionInput.Civ2.SearchBoxSize(1),Data.ActionInput.Civ2.SearchBoxSize(2)); + anss=conv2(testboxa,testboxb); + CPUtime_unit=toc; + nb_box=pixnbre/(Data.ActionInput.Civ2.Dx*Data.ActionInput.Civ2.Dy); + %BoxSize=Data.ActionInput.Civ2.CorrBoxSize(1)*Data.ActionInput.Civ2.CorrBoxSize(2); + %nbpos=Data.ActionInput.Civ2.SearchBoxSize-Data.ActionInput.Civ2.CorrBoxSize; + CPUtime=CPUtime+2*CPUtime_unit*nb_box;%*BoxSize*nbpos(1)*nbpos(2); + end + if isfield(Data.ActionInput,'Patch2') + CPUtime=(4/3)*CPUtime; + end + Data.CPUTime=ceil(CPUtime/6); % estimated CPU time per field pair in minute + Data.CPUTime=Data.CPUTime/10; % displqy CPU time with 1 digit beyond dot + end + return +end + +%% 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 + +%% test input +if ~isfield(Param,'ActionInput') + disp_uvmat('ERROR','no parameter set for PIV',checkrun) + return +end +iview_A=0;%default values +NbField=1; +RUNHandle=[]; +CheckInputFile=isfield(Param,'InputTable');%= 1 in test use for TestCiv (no nc file involved) +CheckOutputFile=isfield(Param,'OutputSubDir');%= 1 in test use for TestPatch (no nc file produced) + +%% input files and indexing (skipped in Test mode) +if CheckInputFile + 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 + MaxIndex_i=Param.IndexRange.MaxIndex_i; + MinIndex_i=Param.IndexRange.MinIndex_i; + MaxIndex_j=ones(size(MaxIndex_i));MinIndex_j=ones(size(MinIndex_i)); + if isfield(Param.IndexRange,'MaxIndex_j')&& isfield(Param.IndexRange,'MinIndex_j') + MaxIndex_j=Param.IndexRange.MaxIndex_j; + MinIndex_j=Param.IndexRange.MinIndex_j; + end + if isfield(Param,'InputTable') + [tild,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); + iview_A=0;% series index (iview) for the first image series + iview_B=0;% series index (iview) for the second image series (only non zero for option 'shift' comparing two image series ) + if Param.ActionInput.CheckCiv1 + iview_A=1;% usual PIV, the image series is on the first line of the table + elseif Param.ActionInput.CheckCiv2 % civ2 is performed without Civ1, a netcdf file series is needed in the first table line + iview_A=2;% the second line is used for the input images of Civ2 + end +% if strcmp(Param.ActionInput.ListCompareMode,'shift') +% iview_B=iview_A+1; % the second image series is on the next line of the input table +% end + if iview_A~=0 + RootPath_A=Param.InputTable{iview_A,1}; + RootFile_A=Param.InputTable{iview_A,3}; + SubDir_A=Param.InputTable{iview_A,2}; + NomType_A=Param.InputTable{iview_A,4}; + FileExt_A=Param.InputTable{iview_A,5}; + if iview_B==0 + iview_B=iview_A;% the second image series is the same as the first + end + RootPath_B=Param.InputTable{iview_B,1}; + RootFile_B=Param.InputTable{iview_B,3}; + SubDir_B=Param.InputTable{iview_B,2}; + NomType_B=Param.InputTable{iview_B,4}; + FileExt_B=Param.InputTable{iview_B,5}; + end + + PairCiv2=''; + switch Param.ActionInput.ListCompareMode + case 'PIV' + PairCiv1=Param.ActionInput.PairIndices.ListPairCiv1; + if isfield(Param.ActionInput.PairIndices,'ListPairCiv2') + PairCiv2=Param.ActionInput.PairIndices.ListPairCiv2;%string which determines the civ2 pair + end + if iview_A==1% if Civ1 is performed + [i1_series_Civ1,i2_series_Civ1,j1_series_Civ1,j2_series_Civ1,check_bounds,NomTypeNc]=... + find_pair_indices(PairCiv1,i1_series{1},j1_series{1},MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j); + if ~isempty(PairCiv2) + [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds_Civ2]=... + find_pair_indices(PairCiv2,i1_series{1},j1_series{1},MinIndex_i(1),MaxIndex_i(1),MinIndex_j(1),MaxIndex_j(1)); + check_bounds=check_bounds | check_bounds_Civ2; + end + else% we start from an existing Civ1 file + i1_series_Civ1=i1_series{1}; + i2_series_Civ1=i2_series{1}; + j1_series_Civ1=j1_series{1}; + j2_series_Civ1=j2_series{1}; + NomTypeNc=Param.InputTable{1,4}; + if ~isempty(PairCiv2) + [i1_series_Civ2,i2_series_Civ2,j1_series_Civ2,j2_series_Civ2,check_bounds,NomTypeNc]=... + find_pair_indices(PairCiv2,i1_series{2},j1_series{2},MinIndex_i(2),MaxIndex_i(2),MinIndex_j(2),MaxIndex_j(2)); + end + end + case 'displacement' + if isfield(Param.ActionInput,'OriginIndex') + i1_series_Civ1=Param.ActionInput.OriginIndex*ones(size(i1_series{1})); + else + i1_series_Civ1=ones(size(i1_series{1})); + end + i1_series_Civ2=i1_series_Civ1; + i2_series_Civ1=i1_series{1}; + i2_series_Civ2=i1_series{1}; + j1_series_Civ1=[];% no j index variation for the ref image + j1_series_Civ2=[]; + if isempty(j1_series{1}) + j2_series_Civ1=ones(size(i1_series_Civ1)); + else + j2_series_Civ1=j1_series{1};% if j index exist + end + j2_series_Civ2=j2_series_Civ1; + NomTypeNc='_1'; + case 'PIV volume' + % TODO, TODO + end + %determine frame indices for input with movie or other multiframe input file + if isempty(j1_series_Civ1)% simple movie with index i + FrameIndex_A_Civ1=i1_series_Civ1; + FrameIndex_B_Civ1=i2_series_Civ1; + j1_series_Civ1=ones(size(i1_series_Civ1)); + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + j2_series_Civ1=ones(size(i1_series_Civ1)); + end + else % movie for each burst or volume (index j) + FrameIndex_A_Civ1=j1_series_Civ1; + FrameIndex_B_Civ1=j2_series_Civ1; + end + if isempty(PairCiv2) + FrameIndex_A_Civ2=FrameIndex_A_Civ1; + FrameIndex_B_Civ2=FrameIndex_B_Civ1; + else + if isempty(j1_series_Civ2) + FrameIndex_A_Civ2=i1_series_Civ2; + FrameIndex_B_Civ2=i2_series_Civ2; + j1_series_Civ2=ones(size(i1_series_Civ2)); + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + j2_series_Civ2=ones(size(i1_series_Civ2)); + end + else + FrameIndex_A_Civ2=j1_series_Civ2; + FrameIndex_B_Civ2=j2_series_Civ2; + end + end + if isempty(i1_series_Civ1)||(~isempty(PairCiv2) && isempty(i1_series_Civ2)) + disp_uvmat('ERROR','no image pair for civ in the input file index range',checkrun) + return + end + end + + %% check the first image pair + if Param.ActionInput.CheckCiv1% Civ1 is performed + NbField=numel(i1_series_Civ1); + elseif Param.ActionInput.CheckCiv2 % Civ2 is performed without Civ1 + NbField=numel(i1_series_Civ2); + else + NbField=numel(i1_series_Civ1);% no image used (only fix or patch) TO CHECK + end + + %% Output directory + OutputDir=''; + if CheckOutputFile + OutputDir=[Param.OutputSubDir Param.OutputDirExt]; + end +end + +%% prepare output Data +ListGlobalAttribute={'Conventions','Program','CivStage'}; +Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes +Data.Program='civ_series'; +Data.CivStage=0;%default +check_civx=0;%default + +%% get timing from the ImaDoc file or input video +if iview_A~=0 + XmlFileName=find_imadoc(RootPath_A,SubDir_A,RootFile_A,FileExt_A); + Time=[]; + if ~isempty(XmlFileName) + XmlData=imadoc2struct(XmlFileName); + if isfield(XmlData,'Time') + Time=XmlData.Time; + end + if isfield(XmlData,'Camera') + if isfield(XmlData.Camera,'NbSlice')&& ~isempty(XmlData.Camera.NbSlice) + NbSlice_calib{iview}=XmlData.Camera.NbSlice;% Nbre of slices for Zindex in phys transform + if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) + msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); + end + end + if isfield(XmlData.Camera,'TimeUnit')&& ~isempty(XmlData.Camera.TimeUnit) + TimeUnit=XmlData.Camera.TimeUnit; + end + end + end +end + +%%%%% MAIN LOOP %%%%%% +maskoldname='';% initiate the mask name +FileType_A=''; +FileType_B=''; +CheckOverwrite=1;%default +if isfield(Param,'CheckOverwrite') + CheckOverwrite=Param.CheckOverwrite; +end +for ifield=1:NbField + tic + if ~isempty(RUNHandle)% update the waitbar in interactive mode with GUI series (checkrun=1) + update_waitbar(WaitbarHandle,ifield/NbField) + if checkrun && ~strcmp(get(RUNHandle,'BusyAction'),'queue') + disp('program stopped by user') + break + end + end + if CheckInputFile + if iview_A==0 % no nc file has been entered + ncfile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},... + NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + else% an existing nc file has been entered + if iview_A==1% if Civ1 is performed + Civ1Dir=OutputDir; + else + Civ1Dir=Param.InputTable{1,2}; + end + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),... + j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + else + ncfile=fullfile_uvmat(RootPath_A,Civ1Dir,RootFile_A,'.nc',NomTypeNc,i2_series_Civ1(ifield),[],... + j1_series_Civ1(ifield),j2_series_Civ1(ifield)); + end + end + ncfile_out=ncfile;% by default + if isfield (Param.ActionInput,'Civ2') + i1_civ2=i1_series_Civ2(ifield); + i2_civ2=i1_civ2; + if ~isempty(i2_series_Civ2) + i2_civ2=i2_series_Civ2(ifield); + end + j1_civ2=1; + if ~isempty(j1_series_Civ2) + j1_civ2=j1_series_Civ2(ifield); + end + j2_civ2=i1_civ2; + if ~isempty(j2_series_Civ2) + j2_civ2=j2_series_Civ2(ifield); + end + if strcmp(Param.ActionInput.ListCompareMode,'PIV') + ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i1_civ2,i2_civ2,j1_civ2,j2_civ2); + else % displacement + ncfile_out=fullfile_uvmat(RootPath_A,OutputDir,RootFile_A,'.nc',NomTypeNc,i2_civ2,[],j2_civ2); + end + end + if ~CheckOverwrite && exist(ncfile_out,'file') + disp(['existing output file ' ncfile_out ' already exists, skip to next field']) + continue% skip iteration if the mode overwrite is desactivated and the result file already exists + end + end + %% Civ1 + % if Civ1 computation is requested + if isfield (Param.ActionInput,'Civ1') + if CheckInputFile + disp('civ1 started') + end + par_civ1=Param.ActionInput.Civ1;% parameters for civ1 + if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) + try + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + ImageName_A=Param.ActionInput.RefFile; + else + ImageName_A=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield)); + end + if strcmp(FileExt_A,'.nc')% case of input images in format netcdf + FieldName_A=Param.InputFields.FieldName; + [DataIn,tild,tild,errormsg]=nc2struct(ImageName_A,{FieldName_A}); + par_civ1.ImageA=DataIn.(FieldName_A); + else % usual image formats for image A + if isempty(FileType_A)% open the image object if not already done in case of movie input + [FileInfo_A,VideoObject_A]=get_file_info(ImageName_A); + FileType_A=FileInfo_A.FileType; + if isempty(Time) && ~isempty(find(strcmp(FileType_A,{'mmreader','video','cine_phantom'})))% case of video input + Time=zeros(FileInfo_A.NumberOfFrames+1,2); + Time(:,2)=(0:1/FileInfo_A.FrameRate:(FileInfo_A.NumberOfFrames)/FileInfo_A.FrameRate)'; + end + if ~isempty(FileType_A) && isempty(Time)% Time = index i +0.001 index j by default + MaxIndex_i=max(i2_series_Civ1); + MaxIndex_j=max(j2_series_Civ1); + Time=(1:MaxIndex_i)'*ones(1,MaxIndex_j); + Time=Time+0.001*ones(MaxIndex_i,1)*(1:MaxIndex_j); + Time=[zeros(1,MaxIndex_j);Time];% insert a first line of zeros + Time=[zeros(MaxIndex_i+1,1) Time];% insert a first column of zeros + end + end + if ~exist(ImageName_A,'file') + disp([ImageName_A ' missing']) + continue + end + [par_civ1.ImageA,VideoObject_A] = read_image(ImageName_A,FileType_A,VideoObject_A,FrameIndex_A_Civ1(ifield)); + end + ImageName_B=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield)); + if strcmp(FileExt_B,'.nc') % case of input images in format netcdf + FieldName_B=Param.InputFields.FieldName; + [DataIn,tild,tild,errormsg]=nc2struct(ImageName_B,{FieldName_B}); + par_civ1.ImageB=DataIn.(FieldName_B); + else % usual image formats for image B + if isempty(FileType_B) + [FileInfo_B,VideoObject_B]=get_file_info(ImageName_B); + FileType_B=FileInfo_B.FileType; + end + if ~exist(ImageName_B,'file') + disp([ImageName_B ' missing']) + continue + end + [par_civ1.ImageB,VideoObject_B] = read_image(ImageName_B,FileType_B,VideoObject_B,FrameIndex_B_Civ1(ifield)); + end + catch ME % display errors in reading input images + if ~isempty(ME.message) + disp_uvmat('ERROR', ['error reading input image: ' ME.message],checkrun) + continue + end + end + par_civ1.ImageWidth=size(par_civ1.ImageA,2); + par_civ1.ImageHeight=size(par_civ1.ImageA,1); + list_param=(fieldnames(Param.ActionInput.Civ1))'; + list_param(strcmp('TestCiv1',list_param))=[];% remove the parameter TestCiv1 from the list + Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before each string in list_param + Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images + %indicate the values of all the global attributes in the output data + Data.Civ1_ImageA=ImageName_A; + Data.Civ1_ImageB=ImageName_B; + i1=i1_series_Civ1(ifield); + i2=i1; + if ~isempty(i2_series_Civ1) + i2=i2_series_Civ1(ifield); + end + j1=1; + if ~isempty(j1_series_Civ1) + j1=j1_series_Civ1(ifield); + end + j2=j1; + if ~isempty(j2_series_Civ1) + j2=j2_series_Civ1(ifield); + end + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + Data.Civ1_Time=Time(i2+1,j2+1);% the Time is the Time of the secodn image + Data.Civ1_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading + else + Data.Civ1_Time=(Time(i2+1,j2+1)+Time(i1+1,j1+1))/2;% the Time is the Time at the middle of the image pair + Data.Civ1_Dt=Time(i2+1,j2+1)-Time(i1+1,j1+1); + end + for ilist=1:length(list_param) + Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist}); + end + Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; + Data.CivStage=1; + end + % set the list of variables + Data.ListVarName={'Civ1_X','Civ1_Y','Civ1_U','Civ1_V','Civ1_F','Civ1_C'};% cell array containing the names of the fields to record + Data.VarDimName={'nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1','nb_vec_1'}; + Data.VarAttribute{1}.Role='coord_x'; + Data.VarAttribute{2}.Role='coord_y'; + Data.VarAttribute{3}.Role='vector_x'; + Data.VarAttribute{4}.Role='vector_y'; + Data.VarAttribute{5}.Role='warnflag'; + % case of mask + if par_civ1.CheckMask&&~isempty(par_civ1.Mask) + if isfield(par_civ1,'NbSlice') + [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ1.Mask); + i1_mask=mod(i1-1,par_civ1.NbSlice)+1; + maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); + else + maskname=Param.ActionInput.Civ1.Mask; + end + if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 + par_civ1.Mask=mask; %use mask already opened + else + if exist(maskname,'file') + try + par_civ1.Mask=imread(maskname);%update the mask, an store it for future use + catch ME + if ~isempty(ME.message) + errormsg=['error reading input image: ' ME.message]; + disp_uvmat('ERROR',errormsg,checkrun) + return + end + end + else + par_civ1.Mask=[]; + end + mask=par_civ1.Mask; + maskoldname=maskname; + end + end + if strcmp(Param.ActionInput.ListCompareMode, 'PIV volume') + Data.ListVarName=[Data.ListVarName 'Civ1_Z']; + Data.Civ1_X=[];Data.Civ1_Y=[];Data.Civ1_Z=[]; + Data.Civ1_U=[];Data.Civ1_V=[];Data.Civ1_C=[];Data.Civ1_F=[]; + for ivol=1:NbSlice + % caluclate velocity data (y and v in indices, reverse to y component) + [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); + if ~isempty(errormsg) + disp_uvmat('ERROR',errormsg,checkrun) + return + end + Data.Civ1_X=[Data.Civ1_X reshape(xtable,[],1)]; + Data.Civ1_Y=[Data.Civ1_Y reshape(Param.Civ1.ImageHeight-ytable+1,[],1)]; + Data.Civ1_Z=[Data.Civ1_Z ivol*ones(numel(xtable),1)];% z=image index in image coordinates + Data.Civ1_U=[Data.Civ1_U reshape(utable,[],1)]; + Data.Civ1_V=[Data.Civ1_V reshape(-vtable,[],1)]; + Data.Civ1_C=[Data.Civ1_C reshape(ctable,[],1)]; + Data.Civ1_F=[Data.Civ1_C reshape(F,[],1)]; + end + else %usual PIV + % caluclate velocity data (y and v in indices, reverse to y component) + [xtable, ytable, utable, vtable, ctable, F, result_conv, errormsg] = civ (par_civ1); + if ~isempty(errormsg) + disp_uvmat('ERROR',errormsg,checkrun) + return + end + Data.Civ1_X=reshape(xtable,[],1); + Data.Civ1_Y=reshape(par_civ1.ImageHeight-ytable+1,[],1); + Data.Civ1_U=reshape(utable,[],1); + Data.Civ1_V=reshape(-vtable,[],1); + Data.Civ1_C=reshape(ctable,[],1); + Data.Civ1_F=reshape(F,[],1); + end + else% we use existing Civ1 data + if exist('ncfile','var') + CivFile=ncfile; + [Data,tild,tild,errormsg]=nc2struct(CivFile,'ListGlobalAttribute','absolut_time_T0'); %look for the constant 'absolut_time_T0' to detect old civx data format + if ~isempty(errormsg) + disp_uvmat('ERROR',errormsg,checkrun) + return + end + [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file + elseif isfield(Param,'Civ1_X') + Data.ListGlobalAttribute={}; + Data.ListVarName={}; + Data.VarDimName={}; + Data.Civ1_X=Param.Civ1_X; + Data.Civ1_Y=Param.Civ1_Y; + Data.Civ1_U=Param.Civ1_U; + Data.Civ1_V=Param.Civ1_V; + Data.Civ1_FF=Param.Civ1_FF; + end + end + + %% Fix1 + if isfield (Param.ActionInput,'Fix1') + disp('fix1 started') + if ~isfield (Param.ActionInput,'Civ1')% if we use existing Civ1, remove previous data beyond Civ1 + Fix1_attr=find(strcmp('Fix1',Data.ListGlobalAttribute)); + Data.ListGlobalAttribute(Fix1_attr)=[]; + for ilist=1:numel(Fix1_attr) + Data=rmfield(Data,Data.ListGlobalAttribute{Fix1_attr(ilist)}); + end + end + list_param=fieldnames(Param.ActionInput.Fix1)'; + Fix1_param=regexprep(list_param,'^.+','Fix1_$0');% insert 'Fix1_' before each string in ListFixParam + %indicate the values of all the global attributes in the output data + for ilist=1:length(list_param) + Data.(Fix1_param{ilist})=Param.ActionInput.Fix1.(list_param{ilist}); + end + Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix1_param]; + Data.ListVarName=[Data.ListVarName {'Civ1_FF'}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_1'}]; + nbvar=length(Data.ListVarName); + Data.VarAttribute{nbvar}.Role='errorflag'; + Data.Civ1_FF=int8(fix(Param.ActionInput.Fix1,Data.Civ1_F,Data.Civ1_C,Data.Civ1_U,Data.Civ1_V)); + Data.CivStage=2; + end + %% Patch1 + if isfield (Param.ActionInput,'Patch1') + disp('patch1 started') + if check_civx + errormsg='Civ Matlab input needed for patch'; + disp_uvmat('ERROR',errormsg,checkrun) + return + end + + % record the processing parameters of Patch1 as global attributes in the result nc file + list_param=fieldnames(Param.ActionInput.Patch1)'; + list_param(strcmp('TestPatch1',list_param))=[];% remove 'TestPatch1' from the list of parameters + Patch1_param=regexprep(list_param,'^.+','Patch1_$0');% insert 'Patch1_' before each parameter name + for ilist=1:length(list_param) + Data.(Patch1_param{ilist})=Param.ActionInput.Patch1.(list_param{ilist}); + end + Data.CivStage=3;% record the new state of processing + Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch1_param]; + + % list the variables to record + nbvar=length(Data.ListVarName); + Data.ListVarName=[Data.ListVarName {'Civ1_U_smooth','Civ1_V_smooth','Civ1_SubRange','Civ1_NbCentres','Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps'}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_1','nb_vec_1',{'nb_coord','nb_bounds','nb_subdomain_1'},'nb_subdomain_1',... + {'nb_tps_1','nb_coord','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'},{'nb_tps_1','nb_subdomain_1'}}]; + Data.VarAttribute{nbvar+1}.Role='vector_x'; + Data.VarAttribute{nbvar+2}.Role='vector_y'; + Data.VarAttribute{nbvar+5}.Role='coord_tps'; + Data.VarAttribute{nbvar+6}.Role='vector_x'; + Data.VarAttribute{nbvar+7}.Role='vector_y'; + Data.Civ1_U_smooth=Data.Civ1_U; % zeros(size(Data.Civ1_X)); + Data.Civ1_V_smooth=Data.Civ1_V; %zeros(size(Data.Civ1_X)); + if isfield(Data,'Civ1_FF') + ind_good=find(Data.Civ1_FF==0); + else + ind_good=1:numel(Data.Civ1_X); + end + + % perform Patch calculation using the UVMAT fct 'filter_tps' + [Data.Civ1_SubRange,Data.Civ1_NbCentres,Data.Civ1_Coord_tps,Data.Civ1_U_tps,Data.Civ1_V_tps,tild,Ures, Vres,tild,FFres]=... + filter_tps([Data.Civ1_X(ind_good) Data.Civ1_Y(ind_good)],Data.Civ1_U(ind_good),Data.Civ1_V(ind_good),[],Data.Patch1_SubDomainSize,Data.Patch1_FieldSmooth,Data.Patch1_MaxDiff); + Data.Civ1_U_smooth(ind_good)=Ures;% take the interpolated (smoothed) velocity values for good vectors, keep civ1 data for the other + Data.Civ1_V_smooth(ind_good)=Vres; + Data.Civ1_FF(ind_good)=int8(FFres); + disp('patch1 performed') + end + + %% Civ2 + if isfield (Param.ActionInput,'Civ2') + disp('civ2 started') + par_civ2=Param.ActionInput.Civ2; + if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) + par_civ2.ImageA=[]; + par_civ2.ImageB=[]; + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + ImageName_A_Civ2=Param.ActionInput.RefFile; + else + ImageName_A_Civ2=fullfile_uvmat(RootPath_A,SubDir_A,RootFile_A,FileExt_A,NomType_A,i1_civ2,[],j1_civ2); + end + if strcmp(ImageName_A_Civ2,ImageName_A) && isequal(FrameIndex_A_Civ1(ifield),FrameIndex_A_Civ2(ifield)) + par_civ2.ImageA=par_civ1.ImageA; + else + [par_civ2.ImageA,VideoObject_A] = read_image(ImageName_A_Civ2,FileType_A,VideoObject_A,FrameIndex_A_Civ2(ifield)); + end + ImageName_B_Civ2=fullfile_uvmat(RootPath_B,SubDir_B,RootFile_B,FileExt_B,NomType_B,i2_civ2,[],j2_civ2); + if strcmp(ImageName_B_Civ2,ImageName_B) && isequal(FrameIndex_B_Civ1(ifield),FrameIndex_B_Civ2) + par_civ2.ImageB=par_civ1.ImageB; + else + [par_civ2.ImageB,VideoObject_B] = read_image(ImageName_B_Civ2,FileType_B,VideoObject_B,FrameIndex_B_Civ2(ifield)); + end + par_civ2.ImageWidth=FileInfo_A.Width; + par_civ2.ImageHeight=FileInfo_A.Height; + if isfield(par_civ2,'Grid')% grid points set as input file + if ischar(par_civ2.Grid)%read the grid file if the input is a file name + par_civ2.Grid=dlmread(par_civ2.Grid); + par_civ2.Grid(1,:)=[];%the first line must be removed (heading in the grid file) + end + else% automatic grid + minix=floor(par_civ2.Dx/2)-0.5; + maxix=minix+par_civ2.Dx*floor((par_civ2.ImageWidth-1)/par_civ2.Dx); + miniy=floor(par_civ2.Dy/2)-0.5; + maxiy=minix+par_civ2.Dy*floor((par_civ2.ImageHeight-1)/par_civ2.Dy); + [GridX,GridY]=meshgrid(minix:par_civ2.Dx:maxix,miniy:par_civ2.Dy:maxiy); + par_civ2.Grid(:,1)=reshape(GridX,[],1); + par_civ2.Grid(:,2)=reshape(GridY,[],1); + end + end + + % get the guess from patch1 or patch2 (case 'CheckCiv3') + if CheckInputFile % read input images (except in mode Test where it is introduced directly in Param.ActionInput.Civ1.ImageNameA and B) + if isfield (par_civ2,'CheckCiv3') && par_civ2.CheckCiv3 %get the guess from patch2 + SubRange= Data.Civ2_SubRange; + NbCentres=Data.Civ2_NbCentres; + Coord_tps=Data.Civ2_Coord_tps; + U_tps=Data.Civ2_U_tps; + V_tps=Data.Civ2_V_tps; + CivStage=Data.CivStage;%store the current CivStage + Civ1_Dt=Data.Civ2_Dt; + Data=[];%reinitialise the result structure Data + Data.ListGlobalAttribute={'Conventions','Program','CivStage'}; + Data.Conventions='uvmat/civdata';% states the conventions used for the description of field variables and attributes + Data.Program='civ_series'; + Data.CivStage=CivStage+1;%update the current civStage after reinitialisation of Data + Data.ListVarName={}; + Data.VarDimName={}; + else % get the guess from patch1 + SubRange= Data.Civ1_SubRange; + NbCentres=Data.Civ1_NbCentres; + Coord_tps=Data.Civ1_Coord_tps; + U_tps=Data.Civ1_U_tps; + V_tps=Data.Civ1_V_tps; + Civ1_Dt=Data.Civ1_Dt; + Data.CivStage=4; + end + else + SubRange= par_civ2.Civ1_SubRange; + NbCentres=par_civ2.Civ1_NbCentres; + Coord_tps=par_civ2.Civ1_Coord_tps; + U_tps=par_civ2.Civ1_U_tps; + V_tps=par_civ2.Civ1_V_tps; + Civ1_Dt=par_civ2.Civ1_Dt; + Civ2_Dt=par_civ2.Civ1_Dt; + Data.ListVarName={}; + Data.VarDimName={}; + end + Shiftx=zeros(size(par_civ2.Grid,1),1);% shift expected from civ1 data + Shifty=zeros(size(par_civ2.Grid,1),1); + nbval=zeros(size(par_civ2.Grid,1),1);% nbre of interpolated values at each grid point (from the different patch subdomains) + if par_civ2.CheckDeformation + DUDX=zeros(size(par_civ2.Grid,1),1); + DUDY=zeros(size(par_civ2.Grid,1),1); + DVDX=zeros(size(par_civ2.Grid,1),1); + DVDY=zeros(size(par_civ2.Grid,1),1); + end + NbSubDomain=size(SubRange,3); + for isub=1:NbSubDomain% for each sub-domain of Patch1 + nbvec_sub=NbCentres(isub);% nbre of Civ vectors in the subdomain + ind_sel=find(par_civ2.Grid(:,1)>=SubRange(1,1,isub) & par_civ2.Grid(:,1)<=SubRange(1,2,isub) &... + par_civ2.Grid(:,2)>=SubRange(2,1,isub) & par_civ2.Grid(:,2)<=SubRange(2,2,isub));% grid points in the subdomain + if ~isempty(ind_sel) + epoints = par_civ2.Grid(ind_sel,:);% coordinates of interpolation sites (measurement grids) + ctrs=Coord_tps(1:nbvec_sub,:,isub) ;%(=initial points) ctrs + nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for each interpolation point (in case of subdomain overlap) + EM = tps_eval(epoints,ctrs);% thin plate spline (tps) coefficient + Shiftx(ind_sel)=Shiftx(ind_sel)+EM*U_tps(1:nbvec_sub+3,isub);%velocity shift estimated by tps from civ1 + Shifty(ind_sel)=Shifty(ind_sel)+EM*V_tps(1:nbvec_sub+3,isub); + if par_civ2.CheckDeformation + [EMDX,EMDY] = tps_eval_dxy(epoints,ctrs);%2D matrix of distances between extrapolation points epoints and spline centres (=site points) ctrs + DUDX(ind_sel)=DUDX(ind_sel)+EMDX*U_tps(1:nbvec_sub+3,isub); + DUDY(ind_sel)=DUDY(ind_sel)+EMDY*U_tps(1:nbvec_sub+3,isub); + DVDX(ind_sel)=DVDX(ind_sel)+EMDX*V_tps(1:nbvec_sub+3,isub); + DVDY(ind_sel)=DVDY(ind_sel)+EMDY*V_tps(1:nbvec_sub+3,isub); + end + end + end + if par_civ2.CheckMask&&~isempty(par_civ2.Mask) + if isfield(par_civ2,'NbSlice') + [RootPath_mask,SubDir_mask,RootFile_mask,i1_mask,i2_mask,j1_mask,j2_mask,Ext_mask]=fileparts_uvmat(Param.ActionInput.Civ2.Mask); + i1_mask=mod(i1-1,par_civ2.NbSlice)+1; + maskname=fullfile_uvmat(RootPath_mask,SubDir_mask,RootFile_mask,Ext_mask,'_1',i1_mask); + else + maskname=Param.ActionInput.Civ2.Mask; + end + if strcmp(maskoldname,maskname)% mask exist, not already read in civ1 + par_civ2.Mask=mask; %use mask already opened + else + if exist(maskname,'file') + try + par_civ2.Mask=imread(maskname);%update the mask, an store it for future use + catch ME + if ~isempty(ME.message) + errormsg=['error reading input image: ' ME.message]; + disp_uvmat('ERROR',errormsg,checkrun) + return + end + end + else + par_civ2.Mask=[]; + end + mask=par_civ2.Mask; + maskoldname=maskname; + end + end + + if CheckInputFile % else Dt given by par_civ2 + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + Civ1_Dt=1; + Civ2_Dt=1; + else + Civ2_Dt=Time(i2_civ2+1,j2_civ2+1)-Time(i1_civ2+1,j1_civ2+1); + end + end + par_civ2.SearchBoxShift=(Civ2_Dt/Civ1_Dt)*[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)]; + % shift the grid points by half the expected shift to provide the correlation box position in image A + par_civ2.Grid=[par_civ2.Grid(nbval>=1,1)-par_civ2.SearchBoxShift(:,1)/2 par_civ2.Grid(nbval>=1,2)-par_civ2.SearchBoxShift(:,2)/2]; + if par_civ2.CheckDeformation + par_civ2.DUDX=DUDX(nbval>=1)./nbval(nbval>=1); + par_civ2.DUDY=DUDY(nbval>=1)./nbval(nbval>=1); + par_civ2.DVDX=DVDX(nbval>=1)./nbval(nbval>=1); + par_civ2.DVDY=DVDY(nbval>=1)./nbval(nbval>=1); + end + + % calculate velocity data (y and v in image indices, reverse to y component) + [xtable, ytable, utable, vtable, ctable, F,result_conv,errormsg] = civ (par_civ2); + + list_param=(fieldnames(Param.ActionInput.Civ2))'; + list_param(strcmp('TestCiv2',list_param))=[];% remove the parameter TestCiv2 from the list + Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before each string in list_param + Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images + %indicate the values of all the global attributes in the output data + if exist('ImageName_A','var') + Data.Civ2_ImageA=ImageName_A; + Data.Civ2_ImageB=ImageName_B; + if strcmp(Param.ActionInput.ListCompareMode,'displacement') + Data.Civ2_Time=Time(i2_civ2+1,j2_civ2+1);% the Time is the Time of the secodn image + Data.Civ2_Dt=1;% Time interval is 1, to yield displacement instead of velocity=displacement/Dt at reading + else + Data.Civ2_Time=(Time(i2_civ2+1,j2_civ2+1)+Time(i1_civ2+1,j1_civ2+1))/2; + Data.Civ2_Dt=Civ2_Dt; + end + end + for ilist=1:length(list_param) + Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist}); + end + Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param]; + + nbvar=numel(Data.ListVarName); + % define the Civ2 variable (if Civ2 data are not replaced from previous calculation) + if isempty(find(strcmp('Civ2_X',Data.ListVarName),1)) + Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];% cell array containing the names of the fields to record + Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2','nb_vec_2'}]; + Data.VarAttribute{nbvar+1}.Role='coord_x'; + Data.VarAttribute{nbvar+2}.Role='coord_y'; + Data.VarAttribute{nbvar+3}.Role='vector_x'; + Data.VarAttribute{nbvar+4}.Role='vector_y'; + Data.VarAttribute{nbvar+5}.Role='warnflag'; + end + Data.Civ2_X=reshape(xtable,[],1); + Data.Civ2_Y=reshape(size(par_civ2.ImageA,1)-ytable+1,[],1); + Data.Civ2_U=reshape(utable,[],1); + Data.Civ2_V=reshape(-vtable,[],1); + Data.Civ2_C=reshape(ctable,[],1); + Data.Civ2_F=reshape(F,[],1); + disp('civ2 performed') + elseif ~isfield(Data,'ListVarName') % we start there, using existing Civ2 data + if exist('ncfile','var') + CivFile=ncfile; + [Data,tild,tild,errormsg]=nc2struct(CivFile);%read civ1 and fix1 data in the existing netcdf file + if ~isempty(errormsg) + disp_uvmat('ERROR',errormsg,checkrun) + return + end + elseif isfield(Param,'Civ2_X')% use Civ2 data as input in Param (test mode) + Data.ListGlobalAttribute={}; + Data.ListVarName={}; + Data.VarDimName={}; + Data.Civ2_X=Param.Civ2_X; + Data.Civ2_Y=Param.Civ2_Y; + Data.Civ2_U=Param.Civ2_U; + Data.Civ2_V=Param.Civ2_V; + Data.Civ2_FF=Param.Civ2_FF; + end + end + + %% Fix2 + if isfield (Param.ActionInput,'Fix2') + disp('fix2 started') + list_param=fieldnames(Param.ActionInput.Fix2)'; + Fix2_param=regexprep(list_param,'^.+','Fix2_$0');% insert 'Fix1_' before each string in ListFixParam + %indicate the values of all the global attributes in the output data + for ilist=1:length(list_param) + Data.(Fix2_param{ilist})=Param.ActionInput.Fix2.(list_param{ilist}); + end + Data.ListGlobalAttribute=[Data.ListGlobalAttribute Fix2_param]; + % + % ListFixParam=fieldnames(Param.ActionInput.Fix2); + % for ilist=1:length(ListFixParam) + % ParamName=ListFixParam{ilist}; + % ListName=['Fix2_' ParamName]; + % eval(['Data.ListGlobalAttribute=[Data.ListGlobalAttribute ''' ParamName '''];']) + % eval(['Data.' ListName '=Param.ActionInput.Fix2.' ParamName ';']) + % end + if check_civx + if ~isfield(Data,'fix2') + Data.ListGlobalAttribute=[Data.ListGlobalAttribute 'fix2']; + Data.fix2=1; + Data.ListVarName=[Data.ListVarName {'vec2_FixFlag'}]; + Data.VarDimName=[Data.VarDimName {'nb_vectors2'}]; + end + Data.vec_FixFlag=fix(Param.Fix2,Data.vec2_F,Data.vec2_C,Data.vec2_U,Data.vec2_V,Data.vec2_X,Data.vec2_Y); + else + Data.ListVarName=[Data.ListVarName {'Civ2_FF'}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_2'}]; + nbvar=length(Data.ListVarName); + Data.VarAttribute{nbvar}.Role='errorflag'; + Data.Civ2_FF=double(fix(Param.ActionInput.Fix2,Data.Civ2_F,Data.Civ2_C,Data.Civ2_U,Data.Civ2_V)); + Data.CivStage=Data.CivStage+1; + end + end + + %% Patch2 + if isfield (Param.ActionInput,'Patch2') + disp('patch2 started') + list_param=fieldnames(Param.ActionInput.Patch2)'; + list_param(strcmp('TestPatch2',list_param))=[];% remove the parameter TestCiv1 from the list + Patch2_param=regexprep(list_param,'^.+','Patch2_$0');% insert 'Fix1_' before each string in ListFixParam + %indicate the values of all the global attributes in the output data + for ilist=1:length(list_param) + Data.(Patch2_param{ilist})=Param.ActionInput.Patch2.(list_param{ilist}); + end + Data.ListGlobalAttribute=[Data.ListGlobalAttribute Patch2_param]; + + nbvar=length(Data.ListVarName); + Data.ListVarName=[Data.ListVarName {'Civ2_U_smooth','Civ2_V_smooth','Civ2_SubRange','Civ2_NbCentres','Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps'}]; + Data.VarDimName=[Data.VarDimName {'nb_vec_2','nb_vec_2',{'nb_coord','nb_bounds','nb_subdomain_2'},{'nb_subdomain_2'},... + {'nb_tps_2','nb_coord','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'},{'nb_tps_2','nb_subdomain_2'}}]; + + Data.VarAttribute{nbvar+1}.Role='vector_x'; + Data.VarAttribute{nbvar+2}.Role='vector_y'; + Data.VarAttribute{nbvar+5}.Role='coord_tps'; + Data.VarAttribute{nbvar+6}.Role='vector_x'; + Data.VarAttribute{nbvar+7}.Role='vector_y'; + Data.Civ2_U_smooth=Data.Civ2_U; + Data.Civ2_V_smooth=Data.Civ2_V; + if isfield(Data,'Civ2_FF') + ind_good=find(Data.Civ2_FF==0); + else + ind_good=1:numel(Data.Civ2_X); + end + [Data.Civ2_SubRange,Data.Civ2_NbCentres,Data.Civ2_Coord_tps,Data.Civ2_U_tps,Data.Civ2_V_tps,tild,Ures,Vres,tild,FFres]=... + filter_tps([Data.Civ2_X(ind_good) Data.Civ2_Y(ind_good)],Data.Civ2_U(ind_good),Data.Civ2_V(ind_good),[],Data.Patch2_SubDomainSize,Data.Patch2_FieldSmooth,Data.Patch2_MaxDiff); + Data.Civ2_U_smooth(ind_good)=Ures; + Data.Civ2_V_smooth(ind_good)=Vres; + Data.Civ2_FF(ind_good)=FFres; + Data.CivStage=Data.CivStage+1; + disp('patch2 performed') + end + + %% write result in a netcdf file if requested + if CheckOutputFile + errormsg=struct2nc(ncfile_out,Data); + if isempty(errormsg) + disp([ncfile_out ' written']) + %[success,msg] = fileattrib(ncfile_out ,'+w','g');% done in struct2nc + else + disp(errormsg) + end + disp(['ellapsed time ' num2str(toc/60,2) ' minutes']) + end +end + + +% 'civ': function piv.m adapted from PIVlab http://pivlab.blogspot.com/ +%-------------------------------------------------------------------------- +% function [xtable ytable utable vtable typevector] = civ (image1,image2,ibx,iby step, subpixfinder, mask, roi) +% +% OUTPUT: +% xtable: set of x coordinates +% ytable: set of y coordiantes +% utable: set of u displacements (along x) +% vtable: set of v displacements (along y) +% ctable: max image correlation for each vector +% typevector: set of flags, =1 for good, =0 for NaN vectors +% +%INPUT: +% par_civ: structure of input parameters, with fields: +% .ImageA: first image for correlation (matrix) +% .ImageB: second image for correlation(matrix) +% .CorrBoxSize: 1,2 vector giving the size of the correlation box in x and y +% .SearchBoxSize: 1,2 vector giving the size of the search box in x and y +% .SearchBoxShift: 1,2 vector or 2 column matrix (for civ2) giving the shift of the search box in x and y +% .CorrSmooth: =1 or 2 determines the choice of the sub-pixel determination of the correlation max +% .ImageWidth: nb of pixels of the image in x +% .Dx, Dy: mesh for the PIV calculation +% .Grid: grid giving the PIV calculation points (alternative to .Dx .Dy): centres of the correlation boxes in Image A +% .Mask: name of a mask file or mask image matrix itself +% .MinIma: thresholds for image luminosity +% .MaxIma +% .CheckDeformation=1 for subpixel interpolation and image deformation (linear transform) +% .DUDX: matrix of deformation obtained from patch at each grid point +% .DUDY +% .DVDX: +% .DVDY + +function [xtable,ytable,utable,vtable,ctable,F,result_conv,errormsg] = civ (par_civ) + +%% prepare measurement grid +if isfield(par_civ,'Grid')% grid points set as input, central positions of the sub-images in image A + if ischar(par_civ.Grid)%read the grid file if the input is a file name (grid in x, y image coordinates) + par_civ.Grid=dlmread(par_civ.Grid); + par_civ.Grid(1,:)=[];%the first line must be removed (heading in the grid file) + end + % else par_civ.Grid is already an array, no action here +else% automatic grid in x, y image coordinates + minix=floor(par_civ.Dx/2)-0.5; + maxix=minix+par_civ.Dx*floor((par_civ.ImageWidth-1)/par_civ.Dx); + miniy=floor(par_civ.Dy/2)-0.5;% first automatic grid point at half the mesh Dy + maxiy=minix+par_civ.Dy*floor((par_civ.ImageHeight-1)/par_civ.Dy); + [GridX,GridY]=meshgrid(minix:par_civ.Dx:maxix,miniy:par_civ.Dy:maxiy); + par_civ.Grid(:,1)=reshape(GridX,[],1); + par_civ.Grid(:,2)=reshape(GridY,[],1);% increases with array index +end +nbvec=size(par_civ.Grid,1); + +%% prepare correlation and search boxes +ibx2=floor(par_civ.CorrBoxSize(1)/2); +iby2=floor(par_civ.CorrBoxSize(2)/2); +isx2=floor(par_civ.SearchBoxSize(1)/2); +isy2=floor(par_civ.SearchBoxSize(2)/2); +shiftx=round(par_civ.SearchBoxShift(:,1));%use the input shift estimate, rounded to the next integer value +shifty=-round(par_civ.SearchBoxShift(:,2));% sign minus because image j index increases when y decreases +if numel(shiftx)==1% case of a unique shift for the whole field( civ1) + shiftx=shiftx*ones(nbvec,1); + shifty=shifty*ones(nbvec,1); +end + +%% Array initialisation and default output if par_civ.CorrSmooth=0 (just the grid calculated, no civ computation) +xtable=round(par_civ.Grid(:,1)+0.5)-0.5; +ytable=round(par_civ.ImageHeight-par_civ.Grid(:,2)+0.5)-0.5;% y index corresponding to the position in image coordiantes +utable=shiftx;%zeros(nbvec,1); +vtable=shifty;%zeros(nbvec,1); +ctable=zeros(nbvec,1); +F=zeros(nbvec,1); +result_conv=[]; +errormsg=''; + +%% prepare mask +if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) + if strcmp(par_civ.Mask,'all') + return % get the grid only, no civ calculation + elseif ischar(par_civ.Mask) + par_civ.Mask=imread(par_civ.Mask);% read the mask if not allready done + end +end +check_MinIma=isfield(par_civ,'MinIma');% test for image luminosity threshold +check_MaxIma=isfield(par_civ,'MaxIma') && ~isempty(par_civ.MaxIma); + +par_civ.ImageA=sum(double(par_civ.ImageA),3);%sum over rgb component for color images +par_civ.ImageB=sum(double(par_civ.ImageB),3); +[npy_ima npx_ima]=size(par_civ.ImageA); +if ~isequal(size(par_civ.ImageB),[npy_ima npx_ima]) + errormsg='image pair with unequal size'; + return +end + +%% Apply mask +% Convention for mask IDEAS TO IMPLEMENT ? +% mask >200 : velocity calculated +% 200 >=mask>150;velocity not calculated, interpolation allowed (bad spots) +% 150>=mask >100: velocity not calculated, nor interpolated +% 100>=mask> 20: velocity not calculated, impermeable (no flux through mask boundaries) +% 20>=mask: velocity=0 +checkmask=0; +MinA=min(min(par_civ.ImageA)); +%MinB=min(min(par_civ.ImageB)); +%check_undefined=false(size(par_civ.ImageA)); +if isfield(par_civ,'Mask') && ~isempty(par_civ.Mask) + checkmask=1; + if ~isequal(size(par_civ.Mask),[npy_ima npx_ima]) + errormsg='mask must be an image with the same size as the images'; + return + end + check_undefined=(par_civ.Mask<200 & par_civ.Mask>=20 ); + % par_civ.ImageA(check_undefined)=0;% put image A to zero (i.e. the min image value) in the undefined area + % par_civ.ImageB(check_undefined)=0;% put image B to zero (i.e. the min image value) in the undefined area +end + +%% compute image correlations: MAINLOOP on velocity vectors +corrmax=0; +sum_square=1;% default +mesh=1;% default +CheckDeformation=isfield(par_civ,'CheckDeformation')&& par_civ.CheckDeformation==1; +if CheckDeformation + mesh=0.25;%mesh in pixels for subpixel image interpolation (x 4 in each direction) + par_civ.CorrSmooth=2;% use SUBPIX2DGAUSS (take into account more points near the max) +end + +if par_civ.CorrSmooth~=0 % par_civ.CorrSmooth=0 implies no civ computation (just input image and grid points given) + for ivec=1:nbvec + iref=round(par_civ.Grid(ivec,1)+0.5);% xindex on the image A for the middle of the correlation box + jref=round(par_civ.ImageHeight-par_civ.Grid(ivec,2)+0.5);% j index for the middle of the correlation box in the image A + F(ivec)=0; + subrange1_x=iref-ibx2:iref+ibx2;% x indices defining the first subimage + subrange1_y=jref-iby2:jref+iby2;% y indices defining the first subimage + subrange2_x=iref+shiftx(ivec)-isx2:iref+shiftx(ivec)+isx2;%x indices defining the second subimage + subrange2_y=jref+shifty(ivec)-isy2:jref+shifty(ivec)+isy2;%y indices defining the second subimage + image1_crop=MinA*ones(numel(subrange1_y),numel(subrange1_x));% default value=min of image A + image2_crop=MinA*ones(numel(subrange2_y),numel(subrange2_x));% default value=min of image A + check1_x=subrange1_x>=1 & subrange1_x<=par_civ.ImageWidth;% check which points in the subimage 1 are contained in the initial image 1 + check1_y=subrange1_y>=1 & subrange1_y<=par_civ.ImageHeight; + check2_x=subrange2_x>=1 & subrange2_x<=par_civ.ImageWidth;% check which points in the subimage 2 are contained in the initial image 2 + check2_y=subrange2_y>=1 & subrange2_y<=par_civ.ImageHeight; + image1_crop(check1_y,check1_x)=par_civ.ImageA(subrange1_y(check1_y),subrange1_x(check1_x));%extract a subimage (correlation box) from image A + image2_crop(check2_y,check2_x)=par_civ.ImageB(subrange2_y(check2_y),subrange2_x(check2_x));%extract a larger subimage (search box) from image B + if checkmask + mask1_crop=ones(numel(subrange1_y),numel(subrange1_x));% default value=1 for mask + mask2_crop=ones(numel(subrange2_y),numel(subrange2_x));% default value=1 for mask + mask1_crop(check1_y,check1_x)=check_undefined(subrange1_y(check1_y),subrange1_x(check1_x));%extract a mask subimage (correlation box) from image A + mask2_crop(check2_y,check2_x)=check_undefined(subrange2_y(check2_y),subrange2_x(check2_x));%extract a mask subimage (search box) from image B + sizemask=sum(sum(mask1_crop))/(numel(subrange1_y)*numel(subrange1_x));%size of the masked part relative to the correlation sub-image + if sizemask > 1/2% eliminate point if more than half of the correlation box is masked + F(ivec)=3; % + utable(ivec)=0; + vtable(ivec)=0; + else + image1_crop=image1_crop.*~mask1_crop;% put to zero the masked pixels (mask1_crop='true'=1) + image2_crop=image2_crop.*~mask2_crop; + image1_mean=mean(mean(image1_crop))/(1-sizemask); + image2_mean=mean(mean(image2_crop))/(1-sizemask); + end + else + image1_mean=mean(mean(image1_crop)); + image2_mean=mean(mean(image2_crop)); + end + %threshold on image minimum + if F(ivec)~=3 + if check_MinIma && (image1_mean < par_civ.MinIma || image2_mean < par_civ.MinIma) + F(ivec)=3; + %threshold on image maximum + elseif check_MaxIma && (image1_mean > par_civ.MaxIma || image2_mean > par_civ.MaxIma) + F(ivec)=3; + end + if F(ivec)==3 + utable(ivec)=0; + vtable(ivec)=0; + else + %mask + if checkmask + image1_crop=(image1_crop-image1_mean).*~mask1_crop;%substract the mean, put to zero the masked parts + image2_crop=(image2_crop-image2_mean).*~mask2_crop; + else + image1_crop=(image1_crop-image1_mean); + image2_crop=(image2_crop-image2_mean); + end + %deformation + if CheckDeformation + xi=(1:mesh:size(image1_crop,2)); + yi=(1:mesh:size(image1_crop,1))'; + [XI,YI]=meshgrid(xi-ceil(size(image1_crop,2)/2),yi-ceil(size(image1_crop,1)/2)); + XIant=XI-par_civ.DUDX(ivec)*XI+par_civ.DUDY(ivec)*YI+ceil(size(image1_crop,2)/2); + YIant=YI+par_civ.DVDX(ivec)*XI-par_civ.DVDY(ivec)*YI+ceil(size(image1_crop,1)/2); + image1_crop=interp2(image1_crop,XIant,YIant); + image1_crop(isnan(image1_crop))=0; + xi=(1:mesh:size(image2_crop,2)); + yi=(1:mesh:size(image2_crop,1))'; + image2_crop=interp2(image2_crop,xi,yi,'*spline'); + image2_crop(isnan(image2_crop))=0; + end + sum_square=sum(sum(image1_crop.*image1_crop)); + %reference: Oliver Pust, PIV: Direct Cross-Correlation + result_conv= conv2(image2_crop,flipdim(flipdim(image1_crop,2),1),'valid'); + corrmax= max(max(result_conv)); + result_conv=(result_conv/corrmax)*255; %normalize, peak=always 255 + %Find the correlation max, at 255 + [y,x] = find(result_conv==255,1); + subimage2_crop=image2_crop(y:y+2*iby2/mesh,x:x+2*ibx2/mesh);%subimage of image 2 corresponding to the optimum displacement of first image + sum_square=sum_square*sum(sum(subimage2_crop.*subimage2_crop));% product of variances of image 1 and 2 + sum_square=sqrt(sum_square);% srt of the variance product to normalise correlation + if ~isempty(y) && ~isempty(x) + try + if par_civ.CorrSmooth==1 + [vector,F(ivec)] = SUBPIXGAUSS (result_conv,x,y); + elseif par_civ.CorrSmooth==2 + [vector,F(ivec)] = SUBPIX2DGAUSS (result_conv,x,y); + else + [vector,F(ivec)] = quadr_fit(result_conv,x,y); + end + utable(ivec)=vector(1)*mesh+shiftx(ivec); + vtable(ivec)=vector(2)*mesh+shifty(ivec); + xtable(ivec)=iref+utable(ivec)/2-0.5;% convec flow (velocity taken at the point middle from imgae 1 and 2) + ytable(ivec)=jref+vtable(ivec)/2-0.5;% and position of pixel 1=0.5 (convention for image coordinates=0 at the edge) + iref=round(xtable(ivec)+0.5);% nearest image index for the middle of the vector + jref=round(ytable(ivec)+0.5); + % eliminate vectors located in the mask + if checkmask && (iref<1 || jref<1 ||iref>npx_ima || jref>npy_ima ||( par_civ.Mask(jref,iref)<200 && par_civ.Mask(jref,iref)>=100)) + utable(ivec)=0; + vtable(ivec)=0; + F(ivec)=3; + end + ctable(ivec)=corrmax/sum_square;% correlation value + catch ME + F(ivec)=3; + disp(ME.message) + end + else + F(ivec)=3; + end + end + end + end +end +result_conv=result_conv*corrmax/(255*sum_square);% keep the last correlation matrix for output + +%------------------------------------------------------------------------ +% --- Find the maximum of the correlation function after interpolation +% OUPUT: +% vector = optimum displacement vector with subpixel correction +% F =flag: =0 OK +% =-2 , warning: max too close to the edge of the search box (1 pixel margin) +% INPUT: +% x,y: position of the maximum correlation at integer values + +function [vector,F] = SUBPIXGAUSS (result_conv,x,y) +%------------------------------------------------------------------------ +% vector=[0 0]; %default +F=0; +[npy,npx]=size(result_conv); +result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (=0 by discretisation, to avoid divergence in the log) +%the following 8 lines are copyright (c) 1998, Uri Shavit, Roi Gurka, Alex Liberzon, Technion ??? Israel Institute of Technology +%http://urapiv.wordpress.com +peaky = y; +if y < npy && y > 1 + f0 = log(result_conv(y,x)); + f1 = log(result_conv(y-1,x)); + f2 = log(result_conv(y+1,x)); + peaky = peaky+ (f1-f2)/(2*f1-4*f0+2*f2); +else + F=-2; % warning flag for vector truncated by the limited search box +end +peakx=x; +if x < npx-1 && x > 1 + f0 = log(result_conv(y,x)); + f1 = log(result_conv(y,x-1)); + f2 = log(result_conv(y,x+1)); + peakx = peakx+ (f1-f2)/(2*f1-4*f0+2*f2); +else + F=-2; % warning flag for vector truncated by the limited search box +end +vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; + +%------------------------------------------------------------------------ +% --- Find the maximum of the correlation function after interpolation +function [vector,F] = SUBPIX2DGAUSS (result_conv,x,y) +%------------------------------------------------------------------------ +% vector=[0 0]; %default +F=-2; +peaky=y; +peakx=x; +result_conv(result_conv<1)=1; %set to 1 correlation values smaller than 1 (to avoid divergence in the log) +[npy,npx]=size(result_conv); +if (x < npx) && (y < npy) && (x > 1) && (y > 1) + F=0; + for i=-1:1 + for j=-1:1 + %following 15 lines based on + %H. Nobach ??? M. Honkanen (2005) + %Two-dimensional Gaussian regression for sub-pixel displacement + %estimation in particle image velocimetry or particle position + %estimation in particle tracking velocimetry + %Experiments in Fluids (2005) 38: 511???515 + c10(j+2,i+2)=i*log(result_conv(y+j, x+i)); + c01(j+2,i+2)=j*log(result_conv(y+j, x+i)); + c11(j+2,i+2)=i*j*log(result_conv(y+j, x+i)); + c20(j+2,i+2)=(3*i^2-2)*log(result_conv(y+j, x+i)); + c02(j+2,i+2)=(3*j^2-2)*log(result_conv(y+j, x+i)); + end + end + c10=(1/6)*sum(sum(c10)); + c01=(1/6)*sum(sum(c01)); + c11=(1/4)*sum(sum(c11)); + c20=(1/6)*sum(sum(c20)); + c02=(1/6)*sum(sum(c02)); + deltax=(c11*c01-2*c10*c02)/(4*c20*c02-c11^2); + deltay=(c11*c10-2*c01*c20)/(4*c20*c02-c11^2); + if abs(deltax)<1 + peakx=x+deltax; + end + if abs(deltay)<1 + peaky=y+deltay; + end +end +vector=[peakx-floor(npx/2)-1 peaky-floor(npy/2)-1]; + +%------------------------------------------------------------------------ +% --- Find the maximum of the correlation function after quadratic interpolation +function [vector,F] = quadr_fit(result_conv,x,y) +[npy,npx]=size(result_conv); +if x<4 || y<4 || npx-x<4 ||npy-y <4 + F=-2; + vector=[x y]; +else + F=0; + x_ind=x-4:x+4; + y_ind=y-4:y+4; + x_vec=0.25*(x_ind-x); + y_vec=0.25*(y_ind-y); + [X,Y]=meshgrid(x_vec,y_vec); + coord=[reshape(X,[],1) reshape(Y,[],1)]; + result_conv=reshape(result_conv(y_ind,x_ind),[],1); + + + % n=numel(X); + % x=[X Y]; + % X=X-0.5; + % Y=Y+0.5; + % y = (X.*X+2*Y.*Y+X.*Y+6) + 0.1*rand(n,1); + p = polyfitn(coord,result_conv,2); + A(1,1)=2*p.Coefficients(1); + A(1,2)=p.Coefficients(2); + A(2,1)=p.Coefficients(2); + A(2,2)=2*p.Coefficients(4); + vector=[x y]'-A\[p.Coefficients(3) p.Coefficients(5)]'; + vector=vector'-[floor(npx/2) floor(npy/2)]-1 ; + % zg = polyvaln(p,coord); + % figure + % surf(x_vec,y_vec,reshape(zg,9,9)) + % hold on + % plot3(X,Y,reshape(result_conv,9,9),'o') + % hold off +end + +%'RUN_FIX': function for fixing velocity fields: +%----------------------------------------------- +% RUN_FIX(filename,field,flagindex,thresh_vecC,thresh_vel,iter,flag_mask,maskname,fileref,fieldref) +% +%filename: name of the netcdf file (used as input and output) +%field: structure specifying the names of the fields to fix (depending on civ1 or civ2) +%.vel_type='civ1' or 'civ2'; +%.nb=name of the dimension common to the field to fix ('nb_vectors' for civ1); +%.fixflag=name of fix flag variable ('vec_FixFlag' for civ1) +%flagindex: flag specifying which values of vec_f are removed: +% if flagindex(1)=1: vec_f=-2 vectors are removed +% if flagindex(2)=1: vec_f=3 vectors are removed +% if flagindex(3)=1: vec_f=2 vectors are removed (if iter=1) or vec_f=4 vectors are removed (if iter=2) +%iter=1 for civ1 fields and iter=2 for civ2 fields +%thresh_vecC: threshold in the image correlation vec_C +%flag_mask: =1 mask used to remove vectors (0 else) +%maskname: name of the mask image file for fix +%thresh_vel: threshold on velocity, or on the difference with the reference file fileref if exists +%inf_sup=1: remove values smaller than threshold thresh_vel, =2, larger than threshold +%fileref: .nc file name for a reference velocity (='': refrence 0 used) +%fieldref: 'civ1','filter1'...feld used in fileref + +function FF=fix(Param,F,C,U,V,X,Y) +FF=zeros(size(F));%default + +%criterium on warn flags +FlagName={'CheckFmin2','CheckF2','CheckF3','CheckF4'}; +FlagVal=[-2 2 3 4]; +for iflag=1:numel(FlagName) + if isfield(Param,FlagName{iflag}) && Param.(FlagName{iflag}) + FF=(FF==1| F==FlagVal(iflag)); + end +end +%criterium on correlation values +if isfield (Param,'MinCorr') + FF=FF==1 | C(Param.MaxVel*Param.MaxVel); + end +end + + +%------------------------------------------------------------------------ +% --- determine the list of index pairs of processing file +function [i1_series,i2_series,j1_series,j2_series,check_bounds,NomTypeNc]=... + find_pair_indices(str_civ,i_series,j_series,MinIndex_i,MaxIndex_i,MinIndex_j,MaxIndex_j) +%------------------------------------------------------------------------ +i1_series=i_series;% set of first image indexes +i2_series=i_series; +j1_series=j_series;%ones(size(i_series));% set of first image numbers +j2_series=j_series;%ones(size(i_series)); +r=regexp(str_civ,'^\D(?[i|j])=( -| )(?\d+)\|(?\d+)','names'); +if ~isempty(r) + mode=['D' r.ind]; + ind1=str2num(r.num1); + ind2=str2num(r.num2); +else + mode='j1-j2'; + r=regexp(str_civ,'^j= (?[a-z])-(?[a-z])','names'); + if ~isempty(r) + NomTypeNc='_1ab'; + else + r=regexp(str_civ,'^j= (?[A-Z])-(?[A-Z])','names'); + if ~isempty(r) + NomTypeNc='_1AB'; + else + r=regexp(str_civ,'^j= (?\d+)-(?\d+)','names'); + if ~isempty(r) + NomTypeNc='_1_1-2'; + end + end + end + if isempty(r) + display('wrong pair mode input option') + else + ind1=stra2num(r.num1); + ind2=stra2num(r.num2); + end +end +switch mode + case 'Di' + i1_series=i_series-ind1;% set of first image numbers + i2_series=i_series+ind2; + check_bounds=i1_seriesMaxIndex_i; + if isempty(j_series) + NomTypeNc='_1-2'; + else + j1_series=j_series; + j2_series=j_series; + NomTypeNc='_1-2_1'; + end + case 'Dj' + j1_series=j_series-ind1; + j2_series=j_series+ind2; + check_bounds=j1_seriesMaxIndex_j; + NomTypeNc='_1_1-2'; + otherwise %bursts + i1_series=i_series(1,:);% do not sweep the j index + i2_series=i_series(1,:); + j1_series=ind1*ones(1,size(i_series,2));% j index is fixed by pair choice + j2_series=ind2*ones(1,size(i_series,2)); + check_bounds=zeros(size(i1_series));% no limitations due to min-max indices +end + + + + Index: trunk/src/series/civ_series.m =================================================================== --- trunk/src/series/civ_series.m (revision 1088) +++ trunk/src/series/civ_series.m (revision 1089) @@ -54,4 +54,5 @@ addpath(fullfile(path_series,'series')) Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input + %Data=civ_input_App(Param);% introduce the civ parameters using the GUI civ_input if isempty(Data) Data=Param;% if civ_input has been cancelled, keep previous parameters Index: trunk/src/series/ima2vol.m =================================================================== --- trunk/src/series/ima2vol.m (revision 1088) +++ trunk/src/series/ima2vol.m (revision 1089) @@ -137,5 +137,5 @@ end VolData.A(jfile,:,:)=Data.A;%concacene along y - VolData.Coord_z(jfile)=Data.PlaneCoord(3); + VolData.Coord_z(jfile)=XmlData{1}.GeometryCalib.SliceCoord(jfile,3); end % npx=size(Data.A,2);