Index: trunk/src/series/aver_stat.m =================================================================== --- trunk/src/series/aver_stat.m (revision 1096) +++ trunk/src/series/aver_stat.m (revision 1097) @@ -225,4 +225,6 @@ %% settings for the output file +OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files +OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device)); NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file first_i=i1_series{1}(1); @@ -467,5 +469,5 @@ %% writing the result file - OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out); + OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j_out,last_j_out); if strcmp(FileExtOut,'.png') %case of images if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) Index: trunk/src/series/civ_input.m =================================================================== --- trunk/src/series/civ_input.m (revision 1096) +++ trunk/src/series/civ_input.m (revision 1097) @@ -249,5 +249,4 @@ set(handles.dt_unit,'String',['dt in m' TimeUnit]);%display dt in unit 10-3 of the time (e.g ms) set(handles.TimeUnit,'String',TimeUnit); -%set(handles.CoordUnit,'String',CoordUnit) set(handles.SearchRange,'UserData', pxcm_search); @@ -319,25 +318,16 @@ %% set the menu and default choice of civ pairs if ~isfield(Param.IndexRange,'first_j')||isequal(MaxIndex_j,MinIndex_j)% no possibility of j pairs - set(handles.ListPairMode,'Value',1) PairMenu={'series(Di)'}; elseif MaxIndex_i==1 && MaxIndex_j>1% simple series in j PairMenu={'pair j1-j2';'series(Dj)'}; - if MaxIndex_j <= 10 - set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large - end else PairMenu={'pair j1-j2';'series(Dj)';'series(Di)'};%multiple choice - if strcmp(NomTypeNc,'_1-2_1') - set(handles.ListPairMode,'Value',3)% advise 'series(Di)' - elseif MaxIndex_j <= 10 - set(handles.ListPairMode,'Value',1)% advice 'pair j1-j2' except in MaxIndex_j is large - end end set(handles.ListPairMode,'String',PairMenu) %% set default choice of pair mode -PairIndex=1; +PairIndex=[]; if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'PairIndices') - PairIndex=find(strcmp(Param.ActionInput.PairIndices.ListPairMode,PairMenu)); + PairIndex=find(strcmp(Param.ActionInput.PairIndices.ListPairMode,PairMenu));%retrieve the previous option end if isempty(PairIndex) @@ -353,4 +343,6 @@ elseif MaxIndex_j <= 10 PairIndex=1;% advice 'pair j1-j2' except in MaxIndex_j is large + else + PairIndex=2;% advice 'Dj' end end @@ -1748,4 +1740,7 @@ ImageData.ListVarName={'ny','nx','A'}; ImageData.VarDimName= {'ny','nx',{'ny','nx'}}; + ImageData.VarAttribute{1}.Role='coord_y'; + ImageData.VarAttribute{2}.Role='coord_x'; + ImageData.VarAttribute{3}.Role='scalar'; ImageData.A=imread(Data.Civ1_ImageA); % read the first image if ndims(ImageData.A)==3 %case of color image Index: trunk/src/series/civ_series.m =================================================================== --- trunk/src/series/civ_series.m (revision 1096) +++ trunk/src/series/civ_series.m (revision 1097) @@ -71,5 +71,5 @@ 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') && isfield(Data.ActionInput,'PairIndices') && strcmp(Data.ActionInput.PairIndices.ListPairMode,'pair j1-j2') if isfield(Data.ActionInput.PairIndices,'ListPairCiv2') str_civ=Data.ActionInput.PairIndices.ListPairCiv2; @@ -90,39 +90,39 @@ 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 +% 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 @@ -474,4 +474,6 @@ Data.ListGlobalAttribute=[ListGlobalAttribute Civ1_param]; Data.CivStage=1; + else + i1=Param.ActionInput.PairIndices.ref_i; %case of TESTmode end % set the list of variables Index: trunk/src/series/merge_proj.m =================================================================== --- trunk/src/series/merge_proj.m (revision 1096) +++ trunk/src/series/merge_proj.m (revision 1097) @@ -239,8 +239,4 @@ %% MAIN LOOP ON FIELDS %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% -% for i_slice=1:NbSlice -% index_slice=i_slice:NbSlice:NbField;% select file indices of the slice -% NbFiles=0; -% nbmissing=0; %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% Index: trunk/src/series/sliding_average.m =================================================================== --- trunk/src/series/sliding_average.m (revision 1096) +++ trunk/src/series/sliding_average.m (revision 1097) @@ -205,5 +205,5 @@ end NbPeriod=2; %number of periods for the sliding average -omega=2*pi/T; +omega=2*2*pi/T;%harmonic Lscale=15;%diameter of the torus, length scale for normalisation Uscale=amplitude*omega; Index: trunk/src/series/sub_background_special.m =================================================================== --- trunk/src/series/sub_background_special.m (revision 1097) +++ trunk/src/series/sub_background_special.m (revision 1097) @@ -0,0 +1,157 @@ +%'bed_scan': get the bed shape from laser ipact + +%------------------------------------------------------------------------ +% function GUI_input=bed_scan(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 2008-2021, 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=sub_background_special (Param) + +%% 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) + ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation) + 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'; %nbre of slices ('off' by default) + 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='.sback';%set the output dir extension + ParamOut.OutputFileMode='NbInput';% ='=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice + %check the type of the existence and type of the first input file: +return +end + +%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% +%% read input parameters from an xml file if input is a file name (batch mode) +ParamOut=[]; +RUNHandle=[]; +WaitbarHandle=[]; +checkrun=1; +if ischar(Param)% case of batch: Param is the name of the xml file containing the input parameters + Param=xml2struct(Param);% read Param as input file (batch case) + checkrun=0; +else% interactive mode in Matlab + 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 +%% estimate the position of bottom and mask for each Z Index +BottomIndex=[1900 1800 1700 1650 1650 1600 1600 1600 1600 1600 1600]; +MaxIndex=BottomIndex+100; +MinIndex=BottomIndex-100; +maskindex=[665 1080];% range of x index perturbed by shadows +NbSlice=11; +Bfilter=ones(1,20)/20; +%% root input file names and nomenclature type (cell arrays with one element) +OutputDir=[Param.OutputSubDir Param.OutputDirExt]; +nbj=numel(Param.IndexRange.first_i:Param.IndexRange.last_i); +for i_ind=Param.IndexRange.first_i:Param.IndexRange.last_i + ZIndex=mod(i_ind-1,NbSlice)+1; + for j_ind=Param.IndexRange.first_j:Param.IndexRange.last_j + % read the current image + InputFile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); + A=imread(InputFile); + % get the bottom as the max of luminosity along vertical lines + IndexMax=ones(1,size(A,2));%initiate the index position of the bottom + if j_ind==Param.IndexRange.first_j + indexMax_j=ones(nbj,size(A,2));%initiate the matrix of index position of the bottom + end + for icolumn=1:maskindex(1) + [M,IndexMax(icolumn)] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),icolumn),[],1); + end + [M,IndexMax(maskindex(2))] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),maskindex(2)),[],1); + for icolumn=maskindex(1)+1:maskindex(2)-1 % linear interpolation in the masked region + IndexMax(icolumn)= IndexMax(maskindex(1))*(maskindex(2)-icolumn)+IndexMax(maskindex(2))*(icolumn-maskindex(1)); + IndexMax(icolumn)=IndexMax(icolumn)/(maskindex(2)-maskindex(1)); + end + for icolumn=maskindex(2)+1:size(A,2) + [M,IndexMax(icolumn)] = max(A(MinIndex(ZIndex)+1:MaxIndex(ZIndex),icolumn),[],1); + end + IndexFilt=filter(Bfilter,1,IndexMax);% smoothed IndexMax + peakdetect=find(abs(IndexFilt-IndexMax)>5);% detect strong departures from the filtered values + IndexMax(peakdetect)=IndexFilt(peakdetect);%replace the peaks by the filtered values + IndexMax_j(j_ind,:)=round(filter(Bfilter,1,IndexMax));%filter again and take the closest integer + % get the background image as the min at each point in the j series + if j_ind==Param.IndexRange.first_j + Amin=A; + else + Amin=min(Amin,A); + end + end + + for j_ind=Param.IndexRange.first_j:Param.IndexRange.last_j + InputFile=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); + A=imread(InputFile); + A=A-Amin; + for icolumn=1:size(A,2) + A(MinIndex(ZIndex)+IndexMax_j(j_ind,icolumn):end,icolumn)=0; + end + OutputFile=fullfile_uvmat(Param.InputTable{1,1},OutputDir,Param.InputTable{1,3},Param.InputTable{1,5},Param.InputTable{1,4},i_ind,i_ind,j_ind); + imwrite(A,OutputFile) + disp([OutputFile ' written']) + end +end + + + + + + + +