%'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 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= function ParamOut=bed_scan (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='off';% 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 %check the type of the existence and type of the first input file: Param.IndexRange.last_i=Param.IndexRange.first_i;%keep only the first index in the series if isfield(Param.IndexRange,'first_j') Param.IndexRange.last_j=Param.IndexRange.first_j; end filecell=get_file_series(Param); if ~exist(filecell{1,1},'file') msgbox_uvmat('WARNING','the first input file does not exist') else FileInfo=get_file_info(filecell{1,1}); FileType=FileInfo.FileType; if isempty(find(strcmp(FileType,{'image','multimage','mmreader','video'})));% =1 for images msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image is needed']) end end 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{2,1}; % RootFile=Param.InputTable(:,3); % SubDir=Param.InputTable(:,2); % NomType=Param.InputTable(:,4); % FileExt=Param.InputTable(:,5); %% 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 %% frame index for movie or multimage file input %% calibration data and timing: read the ImaDoc files %not relevant for this function %% check coincidence in time for several input file series %not relevant for this function %% coordinate transform or other user defined transform %not relevant for this function %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% % EDIT FROM HERE %% Extension and indexing nomenclature for output file % name=('EXP18OS_bed_init/im/'); % name2=('EXP18OS_end/im/'); % path_proj=['/.fsnet/project/coriolis/2018/18ADDUCE/SEDIM_SCANSIDE/']; %nimages=1800; %% Load the init bed scan y=90.05-0.05*i1_series{1}; Mfiltre=ones(2,10)/20;%filter matrix for imnages tic % y=zeros(1,nimages); % X_new=zeros(4096,nimages); x=1:4096; % img=1; %filecell{1,img}= list of the images _init %filecell{2,img}= list of the images _end for img=1:nbfield_i img image=flipud(imread(filecell{2,img})); a=image(700:1900,:); % filtering a=filter2(Mfiltre,a); [imax,iy]=max(a); Z=squeeze(iy); iy(imax<50)=NaN; Z_s(:,img)=smooth(Z,40,'rloess'); % y(img)=y0-(0.05.*step); % y0=y(img); X_new(:,img)=phys_scan(x,y(img)); end toc nimages2=size(Z_s,2); %% y_y=1:size(a,1); % [Xx,Yy]=meshgrid(x,y_y); [X,Y]=meshgrid(x,y); % index=1; % [imax,iy]=max(a); % % Z=squeeze(iy); %% smooth bed init % for i=2:dim(2) % if iy(i)<300 % imax(i)=imax(i-1); % end % end % for i=1:nimages2 % Z_s(:,i)=smooth(Z(:,i),50,'rloess'); % % Z_s_new(:,i)=phys_scanz(x,Z_s(:,i)',y(i)); % % end %% Load the transit bed scan for img=1:nbfield_i img image=flipud(imread(filecell{1,img})); b=image(700:1900,:); % filtering b=filter2(Mfiltre,b); [imaxb,iyb]=max(b); Zb=squeeze(iyb); iyb(imaxb<50)=NaN; Z_sb(:,img)=smooth(Zb,20,'rloess'); end %% bed change dZ=Z_s-Z_sb; dZ_new=zeros(4096,nimages2); for img=1:nimages2 dZ_new(:,img)=phys_scanz(dZ(:,img),y(img)); end %% PLOTS coord_x=X_new(1,end):0.1:X_new(end,end); [Y_m,X_m]=meshgrid(y(1,:),coord_x); Y_new=Y'; dZ_mesh=griddata(X_new,Y_new,dZ_new,X_m,Y_m); if checkrun figure(1) hold on plot(x,Z_s+700) xlim([0 4096]) ylim([0 3000]) figure(2) hold on plot(x,Z_sb+700) xlim([0 4096]) ylim([0 3000]) figure(3) surfc(X_m,Y_m,dZ_mesh) shading interp; colorbar; caxis([0 3]); figure pcolor(X_m,Y_m,dZ_mesh); colormap; set(gca,'Xdir','reverse'); caxis([0 3]); shading flat hold on colorbar title('Dz') end save(fullfile(DirOut,'18OS_f.mat'),'dZ','dZ_new','X','Y','Z_s','Z_sb','y') % save netcdf Data.ListVarName={'coord_x','coord_y','dZ'}; Data.VarDimName={'coord_x','coord_y',{'coord_y','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(1) coord_x(end)]; Data.coord_y=[y(1) y(end)]; Data.dZ=dZ_mesh'; struct2nc(fullfile(DirOut,'dZ.nc'),Data) function F=phys_scan(X,y) F=(9.4*10^(-7)*y.^2-3.09*10^(-4)*y+0.07).*X +(-0.001023*y.^2+0.469*y+186.9); function Fz=phys_scanz(Z,y) Fz=(-1.4587*10^(-5)*y.^2 + 0.001072*y+0.0833).*Z; %+(-2.1*10^(-6)*x.^2+5.1*10^(-4)*x+0.0735).*Z;