source: trunk/src/series/bed_scan.m @ 1055

Last change on this file since 1055 was 1055, checked in by sommeria, 3 years ago

bed_scan updated

File size: 10.1 KB
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1%'bed_scan': get the bed shape from laser ipact
2
3%------------------------------------------------------------------------
4% function GUI_input=bed_scan(Param)
5%
6%------------------------------------------------------------------------
7%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
8%
9%OUTPUT
10% ParamOut: sets options in the GUI series.fig needed for the function
11%
12%INPUT:
13% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
14% In batch mode, Param is the name of the corresponding xml file containing the same information
15% when Param.Action.RUN=0 (as activated when the current Action is selected
16% in series), the function ouput paramOut set the activation of the needed GUI elements
17%
18% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
19% see the current structure Param)
20%    .InputTable: cell of input file names, (several lines for multiple input)
21%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
22%    .OutputSubDir: name of the subdirectory for data outputs
23%    .OutputDirExt: directory extension for data outputs
24%    .Action: .ActionName: name of the current activated function
25%             .ActionPath:   path of the current activated function
26%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
27%             .RUN =0 for GUI input, =1 for function activation
28%             .RunMode='local','background', 'cluster': type of function  use
29%             
30%    .IndexRange: set the file or frame indices on which the action must be performed
31%    .FieldTransform: .TransformName: name of the selected transform function
32%                     .TransformPath:   path  of the selected transform function
33%    .InputFields: sub structure describing the input fields withfields
34%              .FieldName: name(s) of the field
35%              .VelType: velocity type
36%              .FieldName_1: name of the second field in case of two input series
37%              .VelType_1: velocity type of the second field in case of two input series
38%              .Coord_y: name of y coordinate variable
39%              .Coord_x: name of x coordinate variable
40%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
41%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
42
43%=======================================================================
44% Copyright 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
45%   http://www.legi.grenoble-inp.fr
46%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
47%
48%     This file is part of the toolbox UVMAT.
49%
50%     UVMAT is free software; you can redistribute it and/or modify
51%     it under the terms of the GNU General Public License as published
52%     by the Free Software Foundation; either version 2 of the license,
53%     or (at your option) any later version.
54%
55%     UVMAT is distributed in the hope that it will be useful,
56%     but WITHOUT ANY WARRANTY; without even the implied warranty of
57%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
58%     GNU General Public License (see LICENSE.txt) for more details.
59%=======================================================================
60
61function ParamOut=bed_scan (Param)
62
63%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
64if isstruct(Param) && isequal(Param.Action.RUN,0)
65    ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation)
66    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
67    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
68    ParamOut.NbSlice=1; %nbre of slices ('off' by default)
69    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
70    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
71    ParamOut.FieldTransform = 'off';%can use a transform function
72    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
73    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
74    ParamOut.OutputDirExt='.bed';%set the output dir extension
75    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
76    %check the type of the existence and type of the first input file:
77    Param.IndexRange.last_i=Param.IndexRange.first_i;%keep only the first index in the series
78    if isfield(Param.IndexRange,'first_j')
79    Param.IndexRange.last_j=Param.IndexRange.first_j;
80    end
81    filecell=get_file_series(Param);
82    if ~exist(filecell{1,1},'file')
83        msgbox_uvmat('WARNING','the first input file does not exist')
84    else
85        FileInfo=get_file_info(filecell{1,1});
86        FileType=FileInfo.FileType;
87        if isempty(find(strcmp(FileType,{'image','multimage','mmreader','video'})));% =1 for images
88            msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image is needed'])
89        end
90    end
91return
92end
93
94%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
95%% read input parameters from an xml file if input is a file name (batch mode)
96ParamOut=[];
97RUNHandle=[];
98WaitbarHandle=[];
99checkrun=1;
100if ischar(Param)% case of batch: Param is the name of the xml file containing the input parameters
101    Param=xml2struct(Param);% read Param as input file (batch case)
102    checkrun=0;
103else% interactive mode in Matlab
104    hseries=findobj(allchild(0),'Tag','series');
105    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
106    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
107end
108
109%% root input file names and nomenclature type (cell arrays with one element)
110RootPath=Param.InputTable{2,1};
111% RootFile=Param.InputTable(:,3);
112% SubDir=Param.InputTable(:,2);
113% NomType=Param.InputTable(:,4);
114% FileExt=Param.InputTable(:,5);
115
116%% directory for output files
117DirOut=fullfile(RootPath,[Param.OutputSubDir Param.OutputDirExt]);
118
119%% get the set of input file names (cell array filecell), and file indices
120[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
121% filecell{iview,fileindex}: cell array representing the list of file names
122%        iview: line in the table corresponding to a given file series
123%        fileindex: file index within  the file series,
124% 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
125% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
126nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
127nbfield_i=size(i1_series{1},2); %nb of fields for the i index
128
129%% frame index for movie or multimage file input 
130
131%% calibration data and timing: read the ImaDoc files
132%not relevant for this function
133
134%% check coincidence in time for several input file series
135%not relevant for this function
136
137%% coordinate transform or other user defined transform
138%not relevant for this function
139
140%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
141 % EDIT FROM HERE
142
143 %% Extension and indexing nomenclature for output file
144
145% name=('EXP18OS_bed_init/im/');
146% name2=('EXP18OS_end/im/');
147% path_proj=['/.fsnet/project/coriolis/2018/18ADDUCE/SEDIM_SCANSIDE/']; 
148
149%nimages=1800;
150
151%% Load the init bed scan
152
153y=90.05-0.05*i1_series{1};
154Mfiltre=ones(2,10)/20;%filter matrix for imnages
155tic
156% y=zeros(1,nimages);
157% X_new=zeros(4096,nimages);
158x=1:4096;
159% img=1;
160%filecell{1,img}= list of the images _init
161%filecell{2,img}= list of the images _end
162for img=1:nbfield_i
163     img
164    image=flipud(imread(filecell{2,img}));
165    a=image(700:1900,:);
166    % filtering
167    a=filter2(Mfiltre,a);
168    [imax,iy]=max(a);
169    Z=squeeze(iy);
170    iy(imax<50)=NaN;
171    Z_s(:,img)=smooth(Z,40,'rloess');
172%     y(img)=y0-(0.05.*step);
173%     y0=y(img);
174    X_new(:,img)=phys_scan(x,y(img));
175end
176
177toc
178
179nimages2=size(Z_s,2);
180%%
181y_y=1:size(a,1);
182
183% [Xx,Yy]=meshgrid(x,y_y);
184[X,Y]=meshgrid(x,y);
185
186% index=1;
187% [imax,iy]=max(a);
188%
189% Z=squeeze(iy);
190
191%%  smooth bed init
192% for i=2:dim(2)
193% if iy(i)<300
194%     imax(i)=imax(i-1);
195% end
196% end
197
198% for i=1:nimages2
199% Z_s(:,i)=smooth(Z(:,i),50,'rloess');
200% % Z_s_new(:,i)=phys_scanz(x,Z_s(:,i)',y(i));
201%
202% end
203
204%% Load the transit bed scan
205for img=1:nbfield_i
206    img
207     image=flipud(imread(filecell{1,img}));
208    b=image(700:1900,:);
209        % filtering
210    b=filter2(Mfiltre,b);
211    [imaxb,iyb]=max(b);
212    Zb=squeeze(iyb);
213    iyb(imaxb<50)=NaN;
214    Z_sb(:,img)=smooth(Zb,20,'rloess');
215end
216
217
218%% bed change
219dZ=Z_s-Z_sb;
220dZ_new=zeros(4096,nimages2);
221for img=1:nimages2 
222    dZ_new(:,img)=phys_scanz(dZ(:,img),y(img));
223end
224
225
226%% PLOTS
227coord_x=X_new(1,end):0.1:X_new(end,end);
228[Y_m,X_m]=meshgrid(y(1,:),coord_x);
229Y_new=Y';
230dZ_mesh=griddata(X_new,Y_new,dZ_new,X_m,Y_m);
231
232if checkrun
233    figure(1)
234    hold on
235    plot(x,Z_s+700)
236    xlim([0 4096])
237    ylim([0 3000])
238   
239    figure(2)
240    hold on
241    plot(x,Z_sb+700)
242    xlim([0 4096])
243    ylim([0 3000])
244   
245    figure(3)
246    surfc(X_m,Y_m,dZ_mesh)
247    shading interp;
248    colorbar;
249    caxis([0 3]);
250   
251    figure
252    pcolor(X_m,Y_m,dZ_mesh);
253    colormap;
254    set(gca,'Xdir','reverse');
255    caxis([0 3]);
256    shading flat
257    hold on
258    colorbar
259    title('Dz')
260end
261
262save(fullfile(DirOut,'18OS_f.mat'),'dZ','dZ_new','X','Y','Z_s','Z_sb','y')
263
264% save netcdf
265Data.ListVarName={'coord_x','coord_y','dZ'};
266Data.VarDimName={'coord_x','coord_y',{'coord_y','coord_x'}};
267Data.VarAttribute{1}.Role='coord_x';
268Data.VarAttribute{1}.unit='cm';
269Data.VarAttribute{2}.Role='coord_y';
270Data.VarAttribute{2}.unit='cm';
271Data.VarAttribute{3}.Role='scalar';
272Data.VarAttribute{3}.unit='cm';
273Data.coord_x=[coord_x(1) coord_x(end)];
274Data.coord_y=[y(1) y(end)];
275Data.dZ=dZ_mesh';
276struct2nc(fullfile(DirOut,'dZ.nc'),Data)
277
278function F=phys_scan(X,y)
279F=(9.4*10^(-7)*y.^2-3.09*10^(-4)*y+0.07).*X +(-0.001023*y.^2+0.469*y+186.9);
280
281function Fz=phys_scanz(Z,y)
282Fz=(-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;
283
284 
285
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