Index: /trunk/src/batch_extract_rdvision.m =================================================================== --- /trunk/src/batch_extract_rdvision.m (revision 1052) +++ /trunk/src/batch_extract_rdvision.m (revision 1053) @@ -3,12 +3,9 @@ % to run on the cluster, edit the file extract.sh in the folder TOP_view or SCANSIDE, % Then oarsub -l "walltime=20:00:00" /fsnet/project/coriolis/2018/18ADDUCE/TOP_View/extract.sh -function batch_extract_rdvision(RootDir,FirstFolder) -%%%%%%%%%%%%%% CHOOSE THE ROOT FOLDER %%%%%%%%%% -%RootDir='TOP_View' -%RootDir='SCANSIDE';% -%%%%%%%%%%%%%%%%%%%%%%% +function batch_extract_rdvision(RootDir) + RootFolder=fullfile('/fsnet/project/coriolis/2018/18ADDUCE',RootDir); ParamFile=fullfile(RootFolder,'extract_param.xml'); -%XmlFile='/fsnet/project/coriolis/2018/18ADDUCE/TOP_View/im.xml'; +XmlFile=fullfile(RootFolder,'im.xml'); Param=xml2struct(ParamFile); switch RootDir @@ -26,7 +23,8 @@ check_dir=cell2mat(ListCells(index_dir,:));% =1 for directories, =0 for files ListDir=ListNames(check_dir); -FirstFolder -first=find(strcmp(FirstFolder,ListDir)) -NbFolders=1%5; %totql number of folders to process +ind_bad=[find(strcmp('.',ListDir)) find(strcmp('..',ListDir))]; +ListDir(ind_bad)=[]; + +%NbFolders=1%5; %totql number of folders to process % first=9;% #3 is the first folder in the list (#1='.', #2='..') % disp('first folder') @@ -36,21 +34,45 @@ % dd(last).name -for ilist=first:first+NbFolders-1 - Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp - ddd=dir(Param.InputTable{1}); - Param.InputTable{2}=ddd(3).name; - DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2}); - ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']); - mkdir(ExtractFolder) - if ~isempty(XmlFile) - copyfile(fullfile(RootFolder,XmlFile),fullfile(DataFolder,[Param.OutputRootFile '.xml'])); +%for ilist=first:first+NbFolders-1 +for ilist=1:numel(ListDir) + disp([ListDir{ilist} ' opened']) + ddd=dir(fullfile(RootFolder,ListDir{ilist})); + dddCells=struct2cell(ddd);% transform dir struct to a cell arrray + dddNames=dddCells(1,:);%list of file names + checkdone=false; + checkrdvision=0; + for iname=1:numel(dddNames) + checkdone=~isempty(regexp(dddNames{iname},'.extract$')); + if checkdone + disp('already extracted') + break + end + checkrdvision=checkrdvision+isequal(regexp(dddNames{iname},'^2018-'),1) end - seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]); - [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]); - Param.IndexRange.last_i=str2num(FileInfo.numberoffiles); - Param.OutputSubDir=Param.InputTable{2}; - Param.ActionInput.LogPath= DataFolder; - extract_rdvision(Param)% apply the function used in series + if ~checkdone + if checkrdvision==0 + disp('no rdvision folder') + elseif checkrdvision>1 + disp('multiple rdvision folders, no extraction') + else + Param.InputTable{1}=fullfile(RootFolder,ListDir{ilist});%folder exp + Param.InputTable{2}=ddd(3).name; + DataFolder=fullfile(Param.InputTable{1},Param.InputTable{2}); + ExtractFolder=fullfile(Param.InputTable{1},[Param.InputTable{2} '.extract']); + mkdir(ExtractFolder) + if ~isempty(XmlFile) + copyfile(XmlFile,fullfile(DataFolder,[Param.OutputRootFile '.xml'])); + end + seqname=fullfile(DataFolder,[Param.InputTable{3} Param.InputTable{5}]); + [A,FileInfo,timestamps,errormsg]=read_rdvision(seqname,[]); + Param.IndexRange.last_i=str2num(FileInfo.numberoffiles); + Param.OutputSubDir=Param.InputTable{2}; + Param.ActionInput.LogPath= DataFolder; + extract_rdvision(Param)% apply the function used in series + disp([ListDir{ilist} ' extracted']) + end + end end +'PROGRAM END' %%%%% COMMAND CLUSTER %oarsub -l "walltime=10:00:00" /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/extract.sh -E /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/error -O /fsnet/project/coriolis/2018/18ADDUCE/SCANSIDE/stdout 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; + + +