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