Index: trunk/src/series/bed_scan.m
===================================================================
--- trunk/src/series/bed_scan.m	(revision 1053)
+++ trunk/src/series/bed_scan.m	(revision 1053)
@@ -0,0 +1,285 @@
+%'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{1,1};
+% 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
+
+y0=90.05;
+Mfiltre=ones(2,10);%filter matrix for imnages
+tic
+% y=zeros(1,nimages);
+% X_new=zeros(4096,nimages);
+x=1:4096;
+step=Param.IndexRange.incr_i;
+% 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{1,img}));
+    a=image(700:1900,:);
+    % filtering
+    a=filter2(Mfiltre,a);
+    [~,iy]=max(a);
+    Z=squeeze(iy);
+    Z_s(:,img)=smooth(Z,50,'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{2,img}));
+    b=image(700:1900,:);
+        % filtering
+    b=filter2(Mfiltre,b);
+    [imaxb,iyb]=max(b);
+    Zb=squeeze(iyb);
+    Z_sb(:,img)=smooth(Zb,40,'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
+[Y_m,X_m]=meshgrid(y(1,:),X_new(:,1));
+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=X_new(:,1);
+Data.coord_y=y(1,:);
+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;
+
+ 
+
