%'bed_scan': get the bed shape from laser impact % firts line input files = active images % second line, reference images for the initial bed %------------------------------------------------------------------------ % 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 2008-2024, 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=bed_scan_init (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=1; %nbre of slices ('off' by default) ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) ParamOut.FieldName='one';% 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='.bed';%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 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 %% root input file names and nomenclature type (cell arrays with one element) RootPath=Param.InputTable{1,1}; %% directory for output files DirOut=fullfile(RootPath,[Param.OutputSubDir Param.OutputDirExt]); %% get the set of input file names (cell array filecell), and file indices [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); % filecell{iview,fileindex}: cell array representing the list of file names % 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 %nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) nbfield_i=size(i1_series{1},2); %nb of fields for the i index %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%%fullfile( % EDIT FROM HERE %% set of y positions nb_scan=400;% nbre of planes for a scan if nbfield_i<400 nb_scan=nbfield_i; end %ycalib=[-51 -1 49];% calibration planes y_scan=-51+0.25*(1:nb_scan);% transverse position given by the translating system: first view at y=-51, view 400 at y=+49 coord_x=0.25:0.25:450;%% coord x in phys coordinates for final projection %%%%%%%% A GENERALISER pour plusieurs scans Mfiltre=ones(2,10)/20;%filter matrix for imnages %% calibration data and timing: read the ImaDoc files [RootRoot,CamName]=fileparts(RootPath); RootRoot=fileparts(RootRoot); CalibFolder=fullfile(RootRoot,'EXP_INIT',CamName); XmlData_A=xml2struct(fullfile(CalibFolder,'planeA.xml')); XmlData_B=xml2struct(fullfile(CalibFolder,'planeB.xml')); XmlData_C=xml2struct(fullfile(CalibFolder,'planeC.xml')); ycalib=[-51 -1 49];% the three y positions for calibration= fx(1)=XmlData_C.GeometryCalib.fx_fy(1); fx(2)=XmlData_B.GeometryCalib.fx_fy(1); fx(3)=XmlData_A.GeometryCalib.fx_fy(1); fy(1)=XmlData_C.GeometryCalib.fx_fy(2); fy(2)=XmlData_B.GeometryCalib.fx_fy(2); fy(3)=XmlData_A.GeometryCalib.fx_fy(2); Tx(1)=XmlData_C.GeometryCalib.Tx_Ty_Tz(1); Tx(2)=XmlData_B.GeometryCalib.Tx_Ty_Tz(1); Tx(3)=XmlData_A.GeometryCalib.Tx_Ty_Tz(1); Ty(1)=XmlData_C.GeometryCalib.Tx_Ty_Tz(2); Ty(2)=XmlData_B.GeometryCalib.Tx_Ty_Tz(2); Ty(3)=XmlData_A.GeometryCalib.Tx_Ty_Tz(2); R11(1)=XmlData_C.GeometryCalib.R(1,1); R11(2)=XmlData_B.GeometryCalib.R(1,1); R11(3)=XmlData_A.GeometryCalib.R(1,1); R12(1)=XmlData_C.GeometryCalib.R(1,2); R12(2)=XmlData_B.GeometryCalib.R(1,2); R12(3)=XmlData_A.GeometryCalib.R(1,2); R21(1)=XmlData_C.GeometryCalib.R(2,1); R21(2)=XmlData_B.GeometryCalib.R(2,1); R21(3)=XmlData_A.GeometryCalib.R(2,1); R22(1)=XmlData_C.GeometryCalib.R(2,2); R22(2)=XmlData_B.GeometryCalib.R(2,2); R22(3)=XmlData_A.GeometryCalib.R(2,2); pfx=polyfit(ycalib,fx,1);%get thfield_ie linear interpolation of each parameter of the three calibrations pfy=polyfit(ycalib,fy,1); pTx=polyfit(ycalib,Tx,1); pTy=polyfit(ycalib,Ty,1); p11=polyfit(ycalib,R11,1); p12=polyfit(ycalib,R12,1); p21=polyfit(ycalib,R21,1); p22=polyfit(ycalib,R22,1); %get the calibration parameters at each position y by interpolation of the 3 calibration parameters for img=1:nb_scan Calib(img).fx_fy(1)=pfx(1)*y_scan(img)+pfx(2); Calib(img).fx_fy(2)=pfy(1)*y_scan(img)+pfy(2); Calib(img).Tx_Ty_Tz(1)=pTx(1)*y_scan(img)+pTx(2); Calib(img).Tx_Ty_Tz(2)=pTy(1)*y_scan(img)+pTy(2); Calib(img).Tx_Ty_Tz(3)=1; Calib(img).R=zeros(3,3); Calib(img).R(3,3)=-1; Calib(img).R(1,2)=p12(1)*y_scan(img)+p12(2); Calib(img).R(1,1)=p11(1)*y_scan(img)+p11(2); Calib(img).R(1,2)=p12(1)*y_scan(img)+p12(2); Calib(img).R(2,1)=p21(1)*y_scan(img)+p21(2); Calib(img).R(2,2)=p22(1)*y_scan(img)+p22(2); end %% check coincdence in time for several input file series %not relevant for this function %% coordinate transform or other user defined transform %not relevant for this function %% Load the init bed scan tic %for img=1:nbfield_i for img=1:nb_scan%nbfield_i img a=flipud(imread(filecell{1,img+400}));%image of the initial bed [X_b_new(img,:),Z_b_new(img,:)]=phys_XYZ(Calib(img),[],x,Z_sb(img,:)) if img==1 [nby,nbx]=size(a); x_ima=1:nbx;%image absissa in pixel coordinates % X_new=zeros(nb_scan,size(a,2));% initialise the x po400sitions in phys coordinates % Z_s=zeros(nb_scan,size(a,2));% initialise the image index of max luminosity (dependning on x) for the reference scan X_phys=zeros(nb_scan,nbx); Z_phys=zeros(nb_scan,nbx); end % filtering amean=mean(a,2); [~,ind_max]=max(amean);% get the max of the image averaged along x, to restrict the search region ind_range=max(1,ind_max-30):min(nby,ind_max+30);% search band to find the line a=filter2(Mfiltre,a);%smoothed image % [~,iy]=max(a);% find the max along the first coordinate Z_s_new=zeros(nb_scan,size(Z_s,2)); y, max values imax and the corresponding y index iy along the first coordinate y z_ima=get_max(a(ind_range,:))+ind_range(1)-1;% get the max in the search band and shift to express it in indices of the original image % z_ima=iy'; z_ima=smooth(z_ima,20,'rloess');%smooth Z, the image index of max luminosity (dependning on x) [X_phys(img,:),Z_phys(img,:)]=phys_XYZ(Calib(mod(img-1,nb_scan)+1),[],x_ima,z_ima'); end %% interpolate on a regular grid %coord_x=X_phys(end,1):0.1:X_phys(end,end);%% coord x in phys coordinates based in the last view plane (the last) %y_scan_2=y_scan(1:400); [X_m,Y_m]=meshgrid(coord_x,y_scan); Y=y_scan'*ones(1,nbx);%initialisation of X, Y final topography map Data.Z_init=griddata(X_phys,Y,Z_phys,X_m,Y_m);% dZ interpolated on the regular ph1ys grid X_m,Y_m %Data.Z_init=0.5*(Data.Z_init(1:nb_scan,:)+Data.Z_init(nb_scan+1:2*nb_scan,:)); toc % save netcdf Data.ListVarName={'coord_x','y_scan','Z_init'}; Data.VarDimName={'coord_x','y_scan',{'y_scan','coord_x'}}; Data.VarAttribute{1}.Role='coord_x'; Data.VarAttribute{1}.unit='cm'; Data.VarAttribute{2}.Role='coord_y'; Data.VarAttribute{2}.unit='cm'; Data.VarAttribute{3}.Role='scalar'; Data.VarAttribute{3}.unit='cm'; Data.coord_x=coord_x; Data.y_scan=y_scan; struct2nc(fullfile(DirOut,'Z_init.nc'),Data) %%%%% function iy=get_max(a)% get the max with sub picel resolution [a_max,iy]=max(a); [Nby,Nbx]=size(a); for ind_x=1:Nbx if iy(ind_x)>1 && iy(ind_x)0 iy(ind_x)=iy(ind_x)+0.5*(a_plus-a_min)/denom;%adjust the position of the max with a quadratic fit of the three points around the max end end end