1 | %----------------------------------------------------------------------
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2 | % -process LIF images
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3 | %----------------------------------------------------------------------
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4 |
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5 | %=======================================================================
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6 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
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7 | % http://www.legi.grenoble-inp.fr
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8 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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9 | %
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10 | % This file is part of the toolbox UVMAT.
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11 | %
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12 | % UVMAT is free software; you can redistribute it and/or modify
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13 | % it under the terms of the GNU General Public License as published
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14 | % by the Free Software Foundation; either version 2 of the license,
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15 | % or (at your option) any later version.
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16 | %
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17 | % UVMAT is distributed in the hope that it will be useful,
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18 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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19 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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20 | % GNU General Public License (see LICENSE.txt) for more details.
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21 | %=======================================================================
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22 |
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23 | function GUI_input=LIF_series(num_i1,num_i2,num_j1,num_j2,Series);
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24 |
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25 | %requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION)
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26 | if ~exist('num_i1','var')
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27 | GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one')
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28 | 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default)
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29 | 'RootFile';'on';... %root input file name ('on' by default)
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30 | 'FileExt';'on';... %input file extension ('on' by default)
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31 | 'NomType';'on';...%type of file indexing ('on' by default)
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32 | 'NbSlice';'on'; ...%nbre of slices ('off' by default)
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33 | 'VelTypeMenu';'one';...% menu for selecting the velocity type (civ1,..) options 'off'/'one'/'two', 'off' by default)
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34 | 'FieldMenu';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
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35 | 'CoordType';'on';...%can use a transform function 'off' by default
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36 | 'GetObject';'on';...%can use projection object ,'off' by default
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37 | %'GetMask';'on'...%can use mask option ,'off' by default
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38 | %'PARAMETER'; options: name of the user defined parameter',repeat a line for each parameter
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39 | ''};
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40 | return %exit the function
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41 | end
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42 |
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43 | %-------------------------------------------------
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44 | hseries=guidata(Series.hseries);%handles of the GUI series
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45 | WaitbarPos=get(hseries.waitbar_frame,'Position'); %positiopn of waitbar frame
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46 | %-------------------------------------------------
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47 | addpath '/fsnet/project/coriolis/2006/06ICEBOX/0_MATLAB_WORK/LIF'% define path for concentration.m
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48 | % cpath=which('series');
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49 |
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50 | %mode=''; %default
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51 | time=[];
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52 | nbviews=numel(Series.RootPath);
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53 | if nbviews<2
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54 | msgbox_uvmat('ERROR','enter both LIF and PIV series')% we introduce PIV series to improve the filtering (remove particle image)
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55 | return
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56 | end
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57 | [PD,LIFdir]=fileparts(Series.RootPath{1});
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58 |
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59 | fulldir=fullfile(PD,'Concentration');
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60 | if ~exist(fulldir,'dir')
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61 | try
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62 | mkdir(fulldir)
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63 | [xx,msg2] = fileattrib(fulldir,'+w','g'); %yield writing access (+w) to user group (g)
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64 | catch ME
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65 | msgbox_uvmat('ERROR',ME.message)
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66 | return
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67 | end
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68 | end
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69 |
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70 | filebase_LIF=fullfile(fulldir,'LIF');%root name for the merged files
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71 | RootPath=Series.RootPath{1};
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72 | filebase=fullfile(Series.RootPath{1},Series.RootFile{1});%root file name
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73 | filebase_1=fullfile(Series.RootPath{2},Series.RootFile{2});%root file name for PIV (background correction)
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74 | nbfield=numel(num_i1{1});%number of fields in the series
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75 | [XmlData,error]=imadoc2struct([filebase '.xml']);% calibration data for LIF
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76 | %[error,Heading,nom_type_read,ext_ima_read,tt,TimeUnit,mode,NbSlice,npx,npy,Calib{2}]
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77 | [XmlData_1,error]=imadoc2struct([filebase_1 '.xml']);% calibration data for PIV
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78 | if isfield(XmlData,'Time')
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79 | time=XmlData.Time;
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80 | if isfield(XmlData_1,'Time')
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81 | time_1=XmlData_1.Time;
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82 | if ~isequal(size(time),size(time_1))
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83 | msgbox_uvmat('WARNING','inconsistent time array lengths in ImaDoc fields')
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84 | end
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85 | end
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86 | end
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87 | %check coincidence in time
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88 | if size(time,1)>1
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89 | diff_time=max(max(abs(time-time_1)))
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90 | if diff_time>0
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91 | msgbox_uvmat(['times of series differ by more than ' num2str(diff_time)],'WARNING')
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92 | end
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93 | end
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94 |
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95 |
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96 | hRUN=findobj(Series.hseries,'Tag','RUN');%handles the the uicontrol 'RUN'
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97 | itime=0;
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98 | %%%%%%
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99 | %LOOP ON FILES
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100 | RootPath=fullfile(RootPath,'LIF_REF');
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101 | for ifile=1:nbfield
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102 | stopstate=get(hRUN,'BusyAction');%enable stop button
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103 | if isequal(stopstate,'queue')% enable STOP command
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104 | update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield)
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105 | %name of the current LIF input file
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106 | [inputfile,idetect]=name_generator(filebase,num_i1{1}(ifile),num_j1{1}(ifile),Series.FileExt{1},Series.NomType{1},1,num_i1{1}(ifile),num_j2{1}(ifile));
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107 | if ~idetect
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108 | msgbox_uvmat('ERROR',[inputfile ' not found'])
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109 | return
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110 | end
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111 | [Data,ParamOut,errormsg] = read_field(inputfile,'image',[]);
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112 | Data.ZIndex=num_i1{1}(ifile)-Series.NbSlice*(floor((num_i1{1}(ifile)-1)/Series.NbSlice));%second field index
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113 |
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114 |
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115 | file_ref=fullfile(RootPath,['lif_ref_' num2str(Data.ZIndex) '.nc']);
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116 | Ref=nc2struct(file_ref);%reference file
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117 | [inputfile_1,idetect]=name_generator(filebase_1,num_i1{2}(ifile),num_j1{2}(ifile),Series.FileExt{2},Series.NomType{2},1,num_i2{2}(ifile),num_j2{2}(ifile));
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118 | if ~idetect
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119 | msgbox_uvmat('ERROR',[inputfile_1 ' not found'])
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120 | return
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121 | end
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122 | Data_1=read_field(inputfile_1,'image',{[]});% read the image
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123 | Data_1.ZIndex=Data.ZIndex;
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124 | %%% transform image to concentration
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125 | [DataOut,dd,DataMask]=concentration(Data,XmlData,Data_1,XmlData_1,Ref);
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126 | % output file name (netcdf)
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127 | outputfile=name_generator(filebase_LIF,num_i1{1}(ifile),num_j1{1}(ifile),'.nc',Series.NomType{2},1,num_i2{1}(ifile),num_j2{1}(ifile));
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128 | % create a structure to prepare the result file
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129 | Resu.ListGlobalAttribute={'Project','InputFile_1','InputFile_2','Action','Time','ZIndex','z'};
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130 | [PP,Resu.Project]=fileparts(Series.PathProject);
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131 | Resu.InputFile_1=inputfile;
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132 | Resu.InputFile_2=inputfile_1;
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133 | Resu.Action=Series.Action;
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134 | if isempty(time)
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135 | Resu.Time=0;
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136 | else
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137 | Resu.Time=time(num_i1{1}(ifile),num_j1{1}(ifile));
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138 | end
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139 | Resu.ZIndex=Data.ZIndex;
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140 | Resu.z=XmlData.GeometryCalib.SliceCoord(Data.ZIndex,3);
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141 | Resu.ListVarName={'Coord_y' ,'Coord_x' ,'c','mask'};
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142 | Resu.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'},{'Coord_y','Coord_x'}};
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143 | Resu.Coord_y=[DataOut.Coord_y(1), DataOut.Coord_y(end)];
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144 | Resu.Coord_x=[DataOut.Coord_x(1), DataOut.Coord_x(end)];
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145 | Resu.c=DataOut.A;
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146 | Resu.mask=DataMask.A;%to chnge to cartesian coordinates (polar2phys)
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147 | error=struct2nc(outputfile,Resu); %save result file
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148 | if isempty(error)
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149 | display(['output file ' outputfile ' written'])
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150 | else
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151 | display( error)
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152 | end
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153 | end
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154 | end
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155 |
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