1 | %'merge_proj': concatene several images from series, adjust their luminosity, can project them on a regular grid in phys coordinates |
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2 | %------------------------------------------------------------------------ |
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3 | % function ParamOut=merge_proj(Param) |
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4 | %------------------------------------------------------------------------ |
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5 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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6 | % |
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7 | %OUTPUT |
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8 | % ParamOut: sets options in the GUI series.fig needed for the function |
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9 | % |
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10 | %INPUT: |
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11 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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12 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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13 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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14 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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15 | % |
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16 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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17 | % see the current structure Param) |
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18 | % .InputTable: cell of input file names, (several lines for multiple input) |
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19 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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20 | % .OutputSubDir: name of the subdirectory for data outputs |
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21 | % .OutputDirExt: directory extension for data outputs |
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22 | % .Action: .ActionName: name of the current activated function |
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23 | % .ActionPath: path of the current activated function |
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24 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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25 | % .RUN =0 for GUI input, =1 for function activation |
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26 | % .RunMode='local','background', 'cluster': type of function use |
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27 | % |
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28 | % .IndexRange: set the file or frame indices on which the action must be performed |
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29 | % .FieldTransform: .TransformName: name of the selected transform function |
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30 | % .TransformPath: path of the selected transform function |
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31 | % .InputFields: sub structure describing the input fields withfields |
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32 | % .FieldName: name(s) of the field |
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33 | % .VelType: velocity type |
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34 | % .FieldName_1: name of the second field in case of two input series |
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35 | % .VelType_1: velocity type of the second field in case of two input series |
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36 | % .Coord_y: name of y coordinate variable |
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37 | % .Coord_x: name of x coordinate variable |
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38 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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39 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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40 | |
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41 | %======================================================================= |
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42 | % Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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43 | % http://www.legi.grenoble-inp.fr |
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44 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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45 | % |
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46 | % This file is part of the toolbox UVMAT. |
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47 | % |
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48 | % UVMAT is free software; you can redistribute it and/or modify |
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49 | % it under the terms of the GNU General Public License as published |
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50 | % by the Free Software Foundation; either version 2 of the license, |
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51 | % or (at your option) any later version. |
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52 | % |
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53 | % UVMAT is distributed in the hope that it will be useful, |
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54 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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55 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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56 | % GNU General Public License (see LICENSE.txt) for more details. |
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57 | %======================================================================= |
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58 | |
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59 | function ParamOut=merge_proj(Param) |
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60 | |
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61 | %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed |
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62 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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63 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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64 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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65 | ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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66 | ParamOut.NbSlice='off'; %nbre of slices ('off' by default) |
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67 | ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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68 | ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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69 | ParamOut.FieldTransform = 'on';%can use a transform function |
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70 | ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only) |
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71 | ParamOut.ProjObject='on';%can use projection object(option 'off'/'on', |
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72 | ParamOut.Mask='on';%can use mask option (option 'off'/'on', 'off' by default) |
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73 | ParamOut.OutputDirExt='.mproj';%set the output dir extension |
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74 | 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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75 | first_j=[]; |
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76 | if isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject') |
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77 | msgbox_uvmat('WARNING','You need a projection object of type plane for merge_proj') |
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78 | end |
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79 | if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end |
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80 | PairString=''; |
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81 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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82 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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83 | |
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84 | for iview=1:size(Param.InputTable,1) |
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85 | FirstFileName=fullfile_uvmat(Param.InputTable{iview,1},Param.InputTable{iview,2},Param.InputTable{iview,3},... |
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86 | Param.InputTable{iview,5},Param.InputTable{iview,4},i1,i2,j1,j2); |
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87 | if ~exist(FirstFileName,'file') |
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88 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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89 | end |
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90 | FileInfo=get_file_info(FirstFileName); |
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91 | CheckImage=~isempty(find(strcmp(FileInfo.FileType,ImageTypeOptions)));% =1 for images |
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92 | if ~CheckImage |
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93 | msgbox_uvmat('WARNING',['the input file ' FirstFileName ' is not an image']) |
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94 | end |
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95 | end |
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96 | return |
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97 | end |
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98 | |
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99 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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100 | ParamOut=[]; %default output |
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101 | %% read input parameters from an xml file if input is a file name (batch mode) |
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102 | checkrun=1; |
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103 | if ischar(Param) |
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104 | Param=xml2struct(Param);% read Param as input file (batch case) |
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105 | checkrun=0; |
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106 | end |
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107 | hseries=findobj(allchild(0),'Tag','series'); |
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108 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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109 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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110 | |
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111 | %% define the directory for result file (with path=RootPath{1}) |
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112 | OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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113 | |
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114 | if ~isfield(Param,'InputFields') |
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115 | Param.InputFields.FieldName=''; |
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116 | end |
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117 | |
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118 | %% root input file type |
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119 | RootPath=Param.InputTable(:,1); |
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120 | RootFile=Param.InputTable(:,3); |
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121 | SubDir=Param.InputTable(:,2); |
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122 | NomType=Param.InputTable(:,4); |
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123 | FileExt=Param.InputTable(:,5); |
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124 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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125 | %%%%%%%%%%%% |
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126 | % The cell array filecell is the list of input file names, while |
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127 | % filecell{iview,fileindex}: |
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128 | % iview: line in the table corresponding to a given file series |
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129 | % fileindex: file index within the file series, |
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130 | % 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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131 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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132 | %%%%%%%%%%%% |
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133 | % NbSlice=1;%default |
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134 | % if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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135 | % NbSlice=Param.IndexRange.NbSlice; |
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136 | % end |
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137 | NbView=numel(i1_series);%number of input file series (lines in InputTable) |
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138 | NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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139 | NbField_i=size(i1_series{1},2); %nb of fields for the i index |
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140 | NbField=NbField_j*NbField_i; %total number of fields |
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141 | |
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142 | %% determine the file type on each line from the first input file |
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143 | ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'}; |
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144 | NcTypeOptions={'netcdf','civx','civdata'}; |
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145 | for iview=1:NbView |
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146 | if ~exist(filecell{iview,1}','file') |
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147 | disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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148 | return |
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149 | end |
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150 | [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1}); |
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151 | FileType{iview}=FileInfo{iview}.FileType; |
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152 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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153 | |
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154 | if ~isempty(j1_series{iview}) |
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155 | frame_index{iview}=j1_series{iview}; |
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156 | else |
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157 | frame_index{iview}=i1_series{iview}; |
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158 | end |
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159 | end |
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160 | |
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161 | %% calibration data and timing: read the ImaDoc files |
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162 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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163 | if size(time,1)>1 |
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164 | diff_time=max(max(diff(time))); |
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165 | if diff_time>0 |
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166 | disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun) |
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167 | end |
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168 | end |
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169 | if ~isempty(errormsg) |
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170 | disp_uvmat('WARNING',errormsg,checkrun) |
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171 | end |
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172 | time=mean(time,1); %averaged time taken for the merged field |
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173 | |
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174 | %% coordinate transform or other user defined transform |
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175 | transform_fct='';%default fct handle |
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176 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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177 | currentdir=pwd; |
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178 | cd(Param.FieldTransform.TransformPath) |
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179 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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180 | cd (currentdir) |
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181 | end |
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182 | |
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183 | %% output file type (8 bits) |
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184 | |
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185 | FileExtOut='.png'; %image output (input and proj result = image) |
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186 | % for iview=1:NbView |
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187 | % BitDepth(iview)=FileInfo{iview}.BitDepth; |
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188 | % end |
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189 | % BitDepth=max(BitDepth); |
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190 | BitDepth=8; |
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191 | |
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192 | NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series |
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193 | RootFileOut=RootFile{1}; |
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194 | for iview=2:NbView |
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195 | if ~strcmp(RootFile{iview},RootFile{1}) |
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196 | RootFileOut='mproj'; |
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197 | break |
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198 | end |
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199 | end |
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200 | |
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201 | %% mask |
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202 | MaskData=cell(NbView,1); |
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203 | if Param.CheckMask |
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204 | if ischar(Param.MaskTable)% case of a single mask (char chain) |
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205 | Param.MaskTable={Param.MaskTable}; |
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206 | end |
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207 | for iview=1:numel(Param.MaskTable) |
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208 | if exist(Param.MaskTable{iview},'file') |
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209 | [MaskData{iview},tild,errormsg] = read_field(Param.MaskTable{iview},'image'); |
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210 | if ~isempty(transform_fct) && nargin(transform_fct)>=2 |
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211 | MaskData{iview}=transform_fct(MaskData{iview},XmlData{iview}); |
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212 | end |
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213 | end |
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214 | end |
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215 | end |
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216 | |
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217 | %% Set field names and velocity types |
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218 | %use Param.InputFields for all views |
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219 | |
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220 | %% MAIN LOOP ON FIELDS |
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221 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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222 | % for i_slice=1:NbSlice |
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223 | % index_slice=i_slice:NbSlice:NbField;% select file indices of the slice |
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224 | % NbFiles=0; |
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225 | % nbmissing=0; |
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226 | |
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227 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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228 | for index=1:NbField |
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229 | update_waitbar(WaitbarHandle,index/NbField) |
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230 | if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
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231 | disp('program stopped by user') |
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232 | return |
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233 | end |
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234 | |
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235 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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236 | Data=cell(1,NbView);%initiate the set Data |
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237 | timeread=zeros(1,NbView); |
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238 | for iview=1:NbView |
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239 | %% reading input file(s) |
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240 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index)); |
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241 | if ~isempty(errormsg) |
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242 | disp(['ERROR in merge_proj/read_field/' errormsg]) |
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243 | return |
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244 | end |
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245 | % get the time defined in the current file if not already defined from the xml file |
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246 | if ~isempty(time) && isfield(Data{iview},'Time') |
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247 | timeread(iview)=Data{iview}.Time; |
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248 | end |
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249 | if ~isempty(NbSlice_calib) |
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250 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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251 | end |
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252 | |
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253 | %% transform the input field (e.g; phys) if requested (no transform involving two input fields) |
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254 | if ~isempty(transform_fct) |
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255 | if nargin(transform_fct)>=2 |
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256 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); |
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257 | else |
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258 | Data{iview}=transform_fct(Data{iview}); |
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259 | end |
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260 | end |
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261 | |
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262 | %% CUSTOM ADJUSTMENT OF LUMINOSITY ANDCONTRAST%%%%%%%%%%% |
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263 | if iview==1 |
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264 | Data{iview}.A=Data{iview}.A-100; %remove offset on Dalsa1 |
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265 | else |
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266 | Data{iview}.A=Data{iview}.A-60; %remove offset on Dalsa2 |
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267 | Data{iview}.A=Data{iview}.A*3;%adjust luminosity of Dalsa2 |
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268 | Data{iview}.A=filter2(ones(2,2)/4,Data{iview}.A); %filter image Dalsa2 to fit with the projection grid resolution |
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269 | end |
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270 | |
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271 | %% projection on object (gridded plane) |
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272 | if Param.CheckObject |
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273 | [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject); |
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274 | if ~isempty(errormsg) |
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275 | disp(['ERROR in merge_proge/proj_field: ' errormsg]) |
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276 | return |
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277 | end |
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278 | end |
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279 | |
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280 | %% mask |
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281 | if Param.CheckMask && ~isempty(MaskData{iview}) |
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282 | [Data{iview},errormsg]=mask_proj(Data{iview},MaskData{iview}); |
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283 | end |
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284 | end |
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285 | %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%% |
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286 | |
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287 | %% merge the NbView fields |
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288 | MergeData=merge_field(Data); |
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289 | if isfield(MergeData,'Txt') |
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290 | disp(MergeData.Txt); |
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291 | return |
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292 | end |
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293 | |
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294 | %% time of the merged field: take the average of the different views |
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295 | if ~isempty(time) |
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296 | timeread=time(index); |
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297 | elseif ~isempty(find(timeread))% time defined from ImaDoc |
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298 | timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined) |
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299 | else |
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300 | timeread=index;% take time=file index |
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301 | end |
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302 | |
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303 | %% generating the name of the merged field |
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304 | i1=i1_series{1}(index); |
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305 | if ~isempty(i2_series{end}) |
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306 | i2=i2_series{end}(index); |
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307 | else |
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308 | i2=i1; |
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309 | end |
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310 | j1=1; |
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311 | j2=1; |
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312 | if ~isempty(j1_series{1}) |
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313 | j1=j1_series{1}(index); |
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314 | if ~isempty(j2_series{end}) |
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315 | j2=j2_series{end}(index); |
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316 | else |
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317 | j2=j1; |
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318 | end |
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319 | end |
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320 | OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,FileExtOut,NomType{1},i1,i2,j1,j2); |
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321 | |
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322 | %% recording the merged field |
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323 | |
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324 | if BitDepth==8 |
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325 | imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8) |
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326 | else |
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327 | imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16) |
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328 | end |
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329 | if index==1 |
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330 | %write xml calibration file, using the first file |
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331 | siz=size(MergeData.A); |
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332 | npy=siz(1); |
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333 | npx=siz(2); |
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334 | if isfield(MergeData,'coord_x') && isfield(MergeData,'coord_y') |
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335 | Rangx=MergeData.coord_x; |
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336 | Rangy=MergeData.coord_y; |
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337 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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338 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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339 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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340 | else |
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341 | Rangx=[0.5 npx-0.5]; |
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342 | Rangy=[npy-0.5 0.5];%default |
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343 | end |
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344 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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345 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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346 | T_x=-pxcmx*Rangx(1)+0.5; |
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347 | T_y=-pxcmy*Rangy(2)+0.5; |
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348 | GeometryCal.CalibrationType='rescale'; |
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349 | GeometryCal.CoordUnit=MergeData.CoordUnit; |
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350 | GeometryCal.focal=1; |
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351 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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352 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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353 | ImaDoc.GeometryCalib=GeometryCal; |
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354 | t=struct2xml(ImaDoc); |
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355 | t=set(t,1,'name','ImaDoc'); |
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356 | save(t,[fileparts(OutputFile) '.xml']) |
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357 | end |
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358 | end |
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359 | |
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360 | |
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361 | |
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362 | %'merge_field': concatene fields |
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363 | %------------------------------------------------------------------------ |
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364 | function [MergeData,errormsg]=merge_field(Data) |
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365 | %% default output |
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366 | if isempty(Data)||~iscell(Data) |
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367 | MergeData=[]; |
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368 | return |
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369 | end |
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370 | errormsg=''; |
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371 | MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field |
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372 | NbView=length(Data); |
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373 | if NbView==1 |
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374 | return |
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375 | end |
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376 | |
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377 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
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378 | [CellInfo,NbDim,errormsg]=find_field_cells(Data{1}); |
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379 | if ~isempty(errormsg) |
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380 | return |
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381 | end |
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382 | |
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383 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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384 | for icell=1:length(CellInfo) |
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385 | if NbDim(icell)~=1 % skip field cells which are of dim 1 |
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386 | switch CellInfo{icell}.CoordType |
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387 | case 'scattered' %case of input fields with unstructured coordinates: just concacene data |
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388 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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389 | VarName=Data{1}.ListVarName{ivar}; |
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390 | %MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field |
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391 | for iview=2:NbView |
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392 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
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393 | end |
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394 | end |
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395 | case 'grid' %case of fields defined on a structured grid |
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396 | FFName=''; |
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397 | if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag) |
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398 | FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable |
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399 | end |
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400 | % select good data on each view |
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401 | for ivar=CellInfo{icell}.VarIndex % indices of the selected variables in the list FieldData.ListVarName |
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402 | VarName=Data{1}.ListVarName{ivar}; |
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403 | for iview=1:NbView |
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404 | if isempty(FFName) |
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405 | check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else |
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406 | else |
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407 | check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else |
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408 | end |
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409 | Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or masked data |
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410 | if iview==1 |
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411 | MergeData.(VarName)=Data{1}.(VarName);% correct the field of MergeData |
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412 | NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point |
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413 | elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName)) |
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414 | errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object'; |
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415 | return |
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416 | else |
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417 | MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName);%add data |
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418 | NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else |
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419 | end |
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420 | end |
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421 | MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point |
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422 | end |
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423 | end |
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424 | if isempty(FFName) |
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425 | FFName='FF'; |
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426 | end |
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427 | MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data |
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428 | MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data |
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429 | end |
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430 | end |
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431 | |
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432 | |
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433 | |
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434 | |
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