[1080] | 1 | %'ima2temperature': get velocity fields from LIF image series using two
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| 2 | %reference images obtained at known temperature
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| 3 |
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| 4 | %------------------------------------------------------------------------
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| 5 | % function GUI_input=ima_levels(Param)
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| 6 | %
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| 7 | %------------------------------------------------------------------------
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| 8 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
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| 9 | %
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| 10 | %OUTPUT
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| 11 | % ParamOut: sets options in the GUI series.fig needed for the function
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| 12 | %
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| 13 | %INPUT:
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| 14 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
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| 15 | % In batch mode, Param is the name of the corresponding xml file containing the same information
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| 16 | % when Param.Action.RUN=0 (as activated when the current Action is selected
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| 17 | % in series), the function ouput paramOut set the activation of the needed GUI elements
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| 18 | %
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| 19 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to
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| 20 | % see the current structure Param)
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| 21 | % .InputTable: cell of input file names, (several lines for multiple input)
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| 22 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
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| 23 | % .OutputSubDir: name of the subdirectory for data outputs
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| 24 | % .OutputDirExt: directory extension for data outputs
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| 25 | % .Action: .ActionName: name of the current activated function
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| 26 | % .ActionPath: path of the current activated function
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| 27 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct
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| 28 | % .RUN =0 for GUI input, =1 for function activation
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| 29 | % .RunMode='local','background', 'cluster': type of function use
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| 30 | %
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| 31 | % .IndexRange: set the file or frame indices on which the action must be performed
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| 32 | % .FieldTransform: .TransformName: name of the selected transform function
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| 33 | % .TransformPath: path of the selected transform function
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| 34 | % .InputFields: sub structure describing the input fields withfields
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| 35 | % .FieldName: name(s) of the field
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| 36 | % .VelType: velocity type
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| 37 | % .FieldName_1: name of the second field in case of two input series
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| 38 | % .VelType_1: velocity type of the second field in case of two input series
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| 39 | % .Coord_y: name of y coordinate variable
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| 40 | % .Coord_x: name of x coordinate variable
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| 41 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
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| 42 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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| 43 |
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| 44 | %=======================================================================
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[1107] | 45 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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[1080] | 46 | % http://www.legi.grenoble-inp.fr
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| 47 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
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| 48 | %
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| 49 | % This file is part of the toolbox UVMAT.
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| 50 | %
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| 51 | % UVMAT is free software; you can redistribute it and/or modify
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| 52 | % it under the terms of the GNU General Public License as published
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| 53 | % by the Free Software Foundation; either version 2 of the license,
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| 54 | % or (at your option) any later version.
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| 55 | %
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| 56 | % UVMAT is distributed in the hope that it will be useful,
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| 57 | % but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 58 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 59 | % GNU General Public License (see LICENSE.txt) for more details.
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| 60 | %=======================================================================
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| 61 |
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| 62 | function ParamOut=ima2temperature (Param)
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| 63 |
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| 64 | %% 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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| 65 | if isstruct(Param) && isequal(Param.Action.RUN,0)
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| 66 | ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation)
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| 67 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
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| 68 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
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| 69 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
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| 70 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default)
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| 71 | ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
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| 72 | ParamOut.FieldTransform = 'on';%can use a transform function
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| 73 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
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| 74 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default)
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| 75 | ParamOut.OutputDirExt='.temperature';%set the output dir extension
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| 76 | ParamOut.OutputFileMode='NbInput';% ='=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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| 77 | %check the type of the existence and type of the first input file:
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| 78 | Param.IndexRange.last_i=Param.IndexRange.first_i;%keep only the first index in the series
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| 79 | if isfield(Param.IndexRange,'first_j')
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| 80 | Param.IndexRange.last_j=Param.IndexRange.first_j;
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| 81 | end
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| 82 | filecell=get_file_series(Param);
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| 83 | if ~exist(filecell{1,1},'file')
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| 84 | msgbox_uvmat('WARNING','the first input file does not exist')
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| 85 | else
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| 86 | FileInfo=get_file_info(filecell{1,1});
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| 87 | FileType=FileInfo.FileType;
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| 88 | if isempty(find(strcmp(FileType,{'image','multimage','mmreader','video'})));% =1 for images
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| 89 | msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image is needed'])
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| 90 | end
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| 91 | end
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| 92 | return
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| 93 | end
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| 94 |
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| 95 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
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| 96 | %% read input parameters from an xml file if input is a file name (batch mode)
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| 97 | ParamOut=[];
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| 98 | RUNHandle=[];
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| 99 | WaitbarHandle=[];
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| 100 | checkrun=1;
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| 101 | if ischar(Param)
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| 102 | Param=xml2struct(Param);% read Param as input file (batch case)
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| 103 | checkrun=0;
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| 104 | else% interactive mode in Matlab
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| 105 | hseries=findobj(allchild(0),'Tag','series');
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| 106 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
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| 107 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
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| 108 | end
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| 109 |
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| 110 | %% subdirectory for output files
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| 111 | SubdirOut=[Param.OutputSubDir Param.OutputDirExt];
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| 112 |
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| 113 | %% root input file names and nomenclature type (cell arrays with one element)
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| 114 | RootPath=Param.InputTable(:,1);
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| 115 | RootFile=Param.InputTable(:,3);
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| 116 | SubDir=Param.InputTable(:,2);
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| 117 | NomType=Param.InputTable(:,4);
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| 118 | FileExt=Param.InputTable(:,5);
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| 119 |
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| 120 |
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| 121 | %% get the set of input file names (cell array filecell), and file indices
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| 122 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
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| 123 | % filecell{iview,fileindex}: cell array representing the list of file names
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| 124 | % iview: line in the table corresponding to a given file series
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| 125 | % fileindex: file index within the file series,
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| 126 | % 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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| 127 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
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| 128 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
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| 129 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index
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| 130 | nbfield=nbfield_j*nbfield_i; %total number of fields
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| 131 | [FileInfo{1},VideoObject{1}]=get_file_info(filecell{1,1});% type of input file
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| 132 | FileType{1}=FileInfo{1}.FileType;
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| 133 |
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| 134 | %% frame index for movie or multimage file input
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| 135 | if ~isempty(j1_series{1})
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| 136 | frame_index{1}=j1_series{1};
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| 137 | else
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| 138 | frame_index{1}=i1_series{1};
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| 139 | end
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| 140 |
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| 141 | %% calibration data and timing: read the ImaDoc files
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| 142 | %not relevant for this function
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| 143 |
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| 144 | %% check coincidence in time for several input file series
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| 145 | %not relevant for this function
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| 146 |
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| 147 | %% coordinate transform or other user defined transform
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| 148 | %not relevant for this function
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| 149 |
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| 150 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%%
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| 151 | % EDIT FROM HERE
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| 152 |
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| 153 | %% Extension and indexing nomenclature for output file
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| 154 | FileExtOut='.png'; % write result as .png images for image inputs
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| 155 | if strcmpi(NomType{1}(end),'a')
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| 156 | NomTypeOut=NomType{1};
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| 157 | else
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| 158 | NomTypeOut='_1_1';
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| 159 | end
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| 160 |
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| 161 | %% Set field names and velocity types
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| 162 | %not relevant for this function
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| 163 |
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| 164 | %% Initiate output fields
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| 165 | %not relevant for this function
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| 166 |
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| 167 | %% set processing parameters
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| 168 | % not needed for this function
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| 169 |
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| 170 | %% coordinate transform or other user defined transform:introduce the transform function phys
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| 171 | transform_fct='';%default fct handle
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| 172 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
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| 173 | currentdir=pwd;
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| 174 | cd(Param.FieldTransform.TransformPath)
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| 175 | transform_fct=str2func(Param.FieldTransform.TransformName);
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| 176 | cd (currentdir)
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| 177 | % if isfield(Param,'TransformInput')
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| 178 | % for iview=1:NbView
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| 179 | % XmlData{iview}.TransformInput=Param.TransformInput;
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| 180 | % end
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| 181 | % end
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| 182 | end
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| 183 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
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| 184 |
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| 185 | %% open the reference images
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| 186 | ImHiName=fullfile(RootPath{1},'H2mean','ref.png')%reference LIF image obtained at low uniform temperature
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| 187 | ImLowName=fullfile(RootPath{1},'H1mean','ref.png')%reference LIF image obtained at high uniform temperature
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| 188 |
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| 189 | AHi=double(imread(ImHiName));
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| 190 | ALow=double(imread(ImLowName));
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| 191 | Adiff=AHi-ALow;
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| 192 | Adiff(Adiff==0)=1;
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| 193 |
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| 194 | %% prepare the output netcdf files
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| 195 | DataOut.ListGlobalAttribute={'Conventions'};
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| 196 | DataOut.Conventions='uvmat';
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| 197 | DataOut.ListVarName={'Coord_x','Coord_y','Temperature'};
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| 198 | DataOut.VarDimName={'Coord_x','Coord_y',{'Coord_y','Coord_x'}};
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| 199 |
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| 200 | %% main loop on images,
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| 201 | j1=[];%default
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| 202 | for ifile=1:nbfield
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| 203 | update_waitbar(WaitbarHandle,ifile/nbfield)
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| 204 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
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| 205 | disp('program stopped by user')
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| 206 | return
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| 207 | end
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| 208 | if ~isempty(j1_series)&&~isequal(j1_series,{[]})
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| 209 | j1=j1_series{1}(ifile);
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| 210 | end
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| 211 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
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| 212 | %A=read_image(filename,FileType{1},VideoObject{1},frame_index{1}(ifile));
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| 213 | [Data,tild,errormsg] = read_field(filename,'image');
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| 214 | % operation on images
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| 215 | Data.A=double(Data.A);
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| 216 | Data.A=(Data.A-ALow)./Adiff;
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| 217 | Data=transform_fct(Data,XmlData{1});%transform to phys coordinates
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| 218 |
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| 219 | % write output file
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| 220 | filename_new=fullfile_uvmat(RootPath{1},SubdirOut,RootFile{1},'.nc',NomTypeOut,i1_series{1}(ifile),[],j1);
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| 221 | %imwrite(A,filename_new)
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| 222 | errormsg=struct2nc(filename_new,Data );
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| 223 | if ~isempty(errormsg)
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| 224 | disp(errormsg)
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| 225 | else
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| 226 | disp([filename_new ' written'])
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| 227 | end
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| 228 | end
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| 229 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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| 230 |
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