1 | %'extract_rdvision': relabel an image series with two indices, and correct errors from the RDvision transfer program |
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2 | %------------------------------------------------------------------------ |
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3 | % function ParamOut=extract_rdvision(Param) |
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4 | %------------------------------------------------------------------------ |
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5 | % |
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6 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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7 | % |
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8 | %OUTPUT |
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9 | % ParamOut: sets options in the GUI series.fig needed for the function |
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10 | % |
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11 | %INPUT: |
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12 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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13 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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14 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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15 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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16 | % |
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17 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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18 | % see the current structure Param) |
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19 | % .InputTable: cell of input file names, (several lines for multiple input) |
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20 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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21 | % .OutputSubDir: name of the subdirectory for data outputs |
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22 | % .OutputDirExt: directory extension for data outputs |
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23 | % .Action: .ActionName: name of the current activated function |
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24 | % .ActionPath: path of the current activated function |
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25 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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26 | % .RUN =0 for GUI input, =1 for function activation |
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27 | % .RunMode='local','background', 'cluster': type of function use |
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28 | % |
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29 | % .IndexRange: set the file or frame indices on which the action must be performed |
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30 | % .FieldTransform: .TransformName: name of the selected transform function |
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31 | % .TransformPath: path of the selected transform function |
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32 | % .InputFields: sub structure describing the input fields withfields |
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33 | % .FieldName: name(s) of the field |
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34 | % .VelType: velocity type |
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35 | % .FieldName_1: name of the second field in case of two input series |
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36 | % .VelType_1: velocity type of the second field in case of two input series |
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37 | % .Coord_y: name of y coordinate variable |
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38 | % .Coord_x: name of x coordinate variable |
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39 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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40 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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41 | |
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42 | %======================================================================= |
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43 | % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France |
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44 | % http://www.legi.grenoble-inp.fr |
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45 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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46 | % |
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47 | % This file is part of the toolbox UVMAT. |
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48 | % |
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49 | % UVMAT is free software; you can redistribute it and/or modify |
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50 | % it under the terms of the GNU General Public License as published |
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51 | % by the Free Software Foundation; either version 2 of the license, |
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52 | % or (at your option) any later version. |
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53 | % |
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54 | % UVMAT is distributed in the hope that it will be useful, |
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55 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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56 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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57 | % GNU General Public License (see LICENSE.txt) for more details. |
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58 | %======================================================================= |
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59 | |
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60 | function ParamOut=extract_rdvision(Param) %default output=relabel_i_j(Param) |
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61 | |
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62 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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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='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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66 | ParamOut.NbSlice='one'; ...%nbre of slices, 'one' prevents splitting in several processes, ('off' by default) |
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67 | ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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68 | ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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69 | ParamOut.FieldTransform = 'off';...%can use a transform function |
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70 | ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on', |
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71 | ParamOut.Mask='off';...%can use mask option (option 'off'/'on', 'off' by default) |
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72 | ParamOut.OutputSubDirMode='custom'; %output folder given by the program, not by the GUI series |
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73 | % detect the set of image folder |
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74 | RootPath=Param.InputTable{1,1}; |
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75 | ListStruct=dir(RootPath); |
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76 | ListCells=struct2cell(ListStruct);% transform dir struct to a cell arrray |
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77 | check_bad=strcmp('.',ListCells(1,:))|strcmp('..',ListCells(1,:));%detect the dir '.' to exclude it |
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78 | check_dir=cell2mat(ListCells(4,:));% =1 for directories, =0 for files |
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79 | ListDir=ListCells(1,find(check_dir & ~check_bad)); |
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80 | % InputTable=cell(numel(ListDir),5); |
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81 | % InputTable(:,2)=ListDir'; |
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82 | isel=0; |
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83 | for ilist=1:numel(ListDir) |
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84 | ListStructSub=dir(fullfile(RootPath,ListDir{ilist})); |
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85 | ListCellSub=struct2cell(ListStructSub);% transform dir struct to a cell arrray |
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86 | detect_seq=regexp(ListCellSub(1,:),'.seq$'); |
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87 | seq_index=find(~cellfun('isempty',detect_seq),1); |
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88 | if ~isempty(seq_index) |
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89 | % msgbox_uvmat('ERROR',['not seq file in ' ListDir{ilist} ': please check the input folders']) |
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90 | % else |
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91 | isel=isel+1; |
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92 | InputTable{isel,1}=RootPath; |
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93 | InputTable{isel,2}=ListDir{ilist}; |
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94 | RootFile=regexprep(ListCellSub{1,seq_index},'.seq$',''); |
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95 | InputTable{isel,3}=RootFile; |
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96 | InputTable{isel,4}='*'; |
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97 | InputTable{isel,5}='.seq'; |
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98 | end |
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99 | end |
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100 | hseries=findobj(allchild(0),'Tag','series');% find the parent GUI 'series' |
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101 | hhseries=guidata(hseries); %handles of the elements in 'series' |
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102 | set(hhseries.InputTable,'Data',InputTable) |
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103 | ParamOut.ActionInput.LogPath=RootPath;% indicate the path for the output info: 0_LOG .... |
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104 | return |
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105 | end |
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106 | |
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107 | ParamOut=[]; |
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108 | %%%%%%%%%%%% STANDARD PART %%%%%%%%%%%% |
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109 | %% read input parameters from an xml file if input is a file name (batch mode) |
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110 | checkrun=1; |
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111 | if ischar(Param) |
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112 | Param=xml2struct(Param);% read Param as input file (batch case) |
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113 | checkrun=0; |
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114 | end |
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115 | hseries=findobj(allchild(0),'Tag','series'); |
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116 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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117 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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118 | |
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119 | %% root input file(s) and type |
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120 | RootPath=Param.InputTable{1,1}; |
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121 | if ~isempty(find(~strcmp(RootPath,Param.InputTable(:,1))))% if the Rootpath for each camera are not identical |
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122 | disp_uvmat('ERROR','Rootpath for all cameras must be identical',checkrun) |
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123 | return |
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124 | end |
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125 | |
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126 | % get the set of input file names (cell array filecell), and the lists of |
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127 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
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128 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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129 | |
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130 | %OutputDir=[Param.OutputSubDir Param.OutputDirExt]; |
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131 | |
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132 | % numbers of slices and file indices |
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133 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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134 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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135 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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136 | |
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137 | %determine the file type on each line from the first input file |
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138 | |
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139 | FileInfo=get_file_info(filecell{1,1}); |
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140 | if strcmp(FileInfo.FileType,'rdvision') |
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141 | if ~isequal(FileInfo.NumberOfFrames,nbfield) |
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142 | msgbox_uvmat('ERROR',['the whole series of ' num2str(FileInfo.NumberOfFrames) ' images must be extracted at once']) |
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143 | %rmfield(OutputDir) |
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144 | return |
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145 | end |
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146 | %% interactive input of specific parameters (for RDvision system) |
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147 | display('converting images from RDvision system...') |
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148 | else |
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149 | msgbox_uvmat('ERROR','the input is not from rdvision: a .seq or .sqb file must be opened') |
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150 | return |
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151 | end |
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152 | t=xmltree; |
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153 | save(t,fullfile(RootPath,'Running.xml'))%create an xml file to indicate that processing takes place |
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154 | |
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155 | %% calibration data and timing: read the ImaDoc files |
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156 | mode=''; %default |
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157 | timecell={}; |
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158 | itime=0; |
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159 | NbSlice_calib={}; |
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160 | |
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161 | %SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.' |
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162 | |
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163 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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164 | %%% loop on the cameras ( #iview) |
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165 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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166 | for iview=1:size(Param.InputTable,1) |
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167 | filexml=[fullfile(RootPath,Param.InputTable{iview,3}) '.xml'];%new convention: xml at the level of the image folder |
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168 | if ~exist(filexml,'file') |
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169 | disp_uvmat('ERROR',[filexml ' missing'],checkrun) |
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170 | return |
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171 | end |
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172 | [XmlData,error]=imadoc2struct_special(filexml); |
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173 | if isfield(XmlData,'Time') |
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174 | itime=itime+1; |
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175 | timecell{itime}=XmlData.Time; |
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176 | end |
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177 | if isfield(XmlData,'GeometryCalib') && isfield(XmlData.GeometryCalib,'SliceCoord') |
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178 | NbSlice_calib{1}=size(XmlData.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
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179 | if ~isequal(NbSlice_calib{1},NbSlice_calib{1}) |
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180 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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181 | end |
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182 | end |
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183 | |
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184 | |
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185 | % correction to RDvision xml file |
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186 | t=xmltree(filexml); |
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187 | |
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188 | % correct Dtj and Dtk |
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189 | NomTypeNew='_1_1';% new file nomencalture by default |
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190 | ImageName='img_1_1.png';% first image name |
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191 | if isfield(XmlData,'NbDtj') |
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192 | uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); |
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193 | uid_value=children(t,uid_NbDtj); |
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194 | if ~isempty(uid_value) |
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195 | t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj)); |
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196 | end |
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197 | end |
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198 | if isfield(XmlData,'NbDtk') |
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199 | uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); |
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200 | uid_value=children(t,uid_NbDtk); |
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201 | if ~isempty(uid_value) |
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202 | t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk)); |
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203 | end |
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204 | end |
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205 | if isempty(j1_series{1}) && isfield(XmlData,'NbDti') |
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206 | uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti'); |
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207 | t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti)); |
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208 | uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); |
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209 | t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti)); |
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210 | uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); |
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211 | uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); |
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212 | t=delete(t,uid_NbDtj); |
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213 | t=delete(t,uid_NbDtk); |
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214 | uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj'); |
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215 | uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk'); |
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216 | t=delete(t,uid_Dtj); |
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217 | t=delete(t,uid_Dtk); |
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218 | NomTypeNew='_1'; |
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219 | ImageName='img_1.png'; |
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220 | end |
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221 | |
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222 | %update information of 'Heading' |
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223 | uid_Heading=find(t,'ImaDoc/Heading'); |
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224 | if isempty(uid_Heading) |
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225 | [t,uid_Heading]=add(t,1,'element','Heading'); |
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226 | end |
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227 | uid_SubCampaign=find(t,'ImaDoc/Heading/SubCampaign'); |
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228 | if ~isempty(uid_SubCampaign), t=delete(t,uid_SubCampaign); end |
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229 | uid_Experiment=find(t,'ImaDoc/Heading/Experiment'); |
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230 | if ~isempty(uid_Experiment), t=delete(t,uid_Experiment); end |
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231 | uid_Device=find(t,'ImaDoc/Heading/Device'); |
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232 | if ~isempty(uid_Device), t=delete(t,uid_Device); end |
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233 | uid_Record=find(t,'ImaDoc/Heading/Record'); |
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234 | if ~isempty(uid_Record), t=delete(t,uid_Record); end |
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235 | uid_DateExp=find(t,'ImaDoc/Heading/DateExp'); |
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236 | if ~isempty(uid_DateExp), t=delete(t,uid_DateExp); end |
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237 | |
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238 | %indicate the name of the first image (as a check that the xml file is not moved) |
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239 | uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); |
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240 | if isempty(uid_ImageName) |
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241 | [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); |
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242 | end |
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243 | uid_value=children(t,uid_ImageName); |
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244 | if isempty(uid_value) |
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245 | t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension |
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246 | else |
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247 | t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension |
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248 | end |
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249 | |
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250 | %indicate the date and time of the image acquisition start |
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251 | % if isfield(FileInfo,'binrepertoire') && isfield(FileInfo,'starttime') |
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252 | % sep_pos=regexp(FileInfo.binrepertoire,'T'); |
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253 | % DateTime=FileInfo.starttime; |
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254 | % if ~isempty(sep_pos) |
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255 | % DateTime=[FileInfo.binrepertoire(1:sep_pos-1) ' ' DateTime]; |
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256 | % end |
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257 | % uid_DateTime=find(t,'ImaDoc/Heading/DateTime'); |
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258 | % if isempty(uid_DateTime) |
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259 | % [t,uid_DateTime]=add(t,uid_Heading,'element','DateTime'); |
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260 | % end |
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261 | % uid_value=children(t,uid_DateTime); |
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262 | % if isempty(uid_value) |
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263 | % t=add(t,uid_DateTime,'chardata',DateTime);%indicate name of the first image, with ;png extension |
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264 | % else |
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265 | % t=set(t,uid_value(1),'value',DateTime);%indicate name of the first image, with ;png extension |
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266 | % end |
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267 | % end |
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268 | |
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269 | %% backup the previous xml file and save the corrected one |
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270 | % [success,message]=copyfile(filexml,[filexml '~']);%make backup |
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271 | % if success~=1 |
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272 | % disp(['errror in xml file backup: ' message]); |
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273 | % return |
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274 | % end |
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275 | save(t,filexml) |
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276 | nbfield2=1; |
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277 | if isfield(XmlData,'Time') |
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278 | nbfield2=size(XmlData.Time,2); |
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279 | end |
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280 | |
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281 | %% get the names of .seq and .sqb files |
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282 | switch Param.InputTable{iview,5} |
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283 | case {'.seq','.sqb'} |
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284 | filename_seq=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.seq']); |
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285 | filename_sqb=fullfile(RootPath,Param.InputTable{iview,2},[Param.InputTable{iview,3} '.sqb']); |
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286 | otherwise |
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287 | errormsg='input file extension must be .seq or .sqb'; |
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288 | end |
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289 | if ~exist(filename_seq,'file') |
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290 | errormsg=[filename_seq ' does not exist']; |
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291 | return |
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292 | end |
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293 | |
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294 | %% get data from .seq file |
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295 | s=ini2struct(filename_seq); |
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296 | SeqData=s.sequenceSettings; |
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297 | SeqData.width=str2double(SeqData.width); |
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298 | SeqData.height=str2double(SeqData.height); |
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299 | SeqData.bytesperpixel=str2double(SeqData.bytesperpixel); |
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300 | SeqData.nb_frames=str2double(s.sequenceSettings.numberoffiles); |
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301 | if isempty(SeqData.binrepertoire)%used when binrepertoire empty, strange feature of rdvision |
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302 | SeqData.binrepertoire=regexprep(s.sequenceSettings.bindirectory,'\\$','');%tranform Windows notation to Linux |
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303 | SeqData.binrepertoire=regexprep(SeqData.binrepertoire,'\','/'); |
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304 | [tild,binrepertoire,DirExt]=fileparts(SeqData.binrepertoire); |
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305 | SeqData.binrepertoire=[SeqData.binrepertoire DirExt]; |
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306 | end |
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307 | % PathDir=fileparts(PathDir); |
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308 | |
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309 | %% reading the .sqb file |
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310 | m = memmapfile(filename_sqb,'Format', { 'uint32' [1 1] 'offset'; ... |
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311 | 'uint32' [1 1] 'garbage1';... |
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312 | 'double' [1 1] 'timestamp';... |
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313 | 'uint32' [1 1] 'file_idx';... |
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314 | 'uint32' [1 1] 'garbage2' },'Repeat',SeqData.nb_frames); |
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315 | %%%%%%%BRICOLAGE in case of unreadable .sqb file |
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316 | % ind=[60 63:152];%indices of bin files |
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317 | % lengthimage=w*h*bpp;% lengthof an image record on the binary file |
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318 | % for ii=1:32*numel(ind) |
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319 | % data(ii).offset=mod(ii-1,32)*2*lengthimage+lengthimage;%Dalsa_2 |
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320 | % %data(ii).offset=mod(ii-1,32)*2*lengthimage;%Dalsa_1 |
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321 | % data(ii).file_idx=ind(ceil(ii/32)); |
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322 | % data(ii).timestamp=0.2*(ii-1); |
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323 | % end |
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324 | %%%%%%% |
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325 | for ii=1: numel(m.Data) |
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326 | timestamp(ii)=m.Data(ii).timestamp; |
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327 | end |
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328 | timestamp %todo: check withDt from the xml file |
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329 | [BinSize,errormsg]=binread_rdv_series(RootPath,SeqData,m.Data,nbfield2,NomTypeNew) |
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330 | if ~isempty(errormsg) |
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331 | disp_uvmat('ERROR',errormsg,checkrun) |
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332 | return |
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333 | end |
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334 | end |
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335 | delete(fullfile(RootPath,'Running.xml'))%delete the xml file to indicate that processing is finished |
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336 | |
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337 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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338 | %--------- reads a series of bin files |
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339 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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340 | function [BinSize,errormsg]=binread_rdv_series(PathDir,SeqData,SqbData,nbfield2,NomTypeNew) |
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341 | % BINREAD_RDV Permet de lire les fichiers bin gᅵnᅵrᅵs par Hiris ᅵ partir du |
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342 | % fichier seq associᅵ. |
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343 | % [IMGS,TIMESTAMPS,NB_FRAMES] = BINREAD_RDV(FILENAME,FRAME_IDX) lit |
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344 | % l'image d'indice FRAME_IDX de la sï¿œquence FILENAME. |
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345 | % |
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346 | % Entrï¿œes |
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347 | % ------- |
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348 | % FILENAME : Nom du fichier sï¿œquence (.seq). |
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349 | % FRAME_IDX : Indice de l'image ᅵ lire. Si FRAME_IDX vaut -1 alors la |
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350 | % sï¿œquence est entiï¿œrement lue. Si FRAME_IDX est un tableau d'indices |
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351 | % alors toutes les images d'incides correspondant sont lues. Si FRAME_IDX |
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352 | % est un tableau vide alors aucune image n'est lue mais le nombre |
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353 | % d'images et tous les timestamps sont renvoyᅵs. Les indices commencent ᅵ |
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354 | % 1 et se termines ᅵ NB_FRAMES. |
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355 | % |
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356 | % Sorties |
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357 | % ------- |
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358 | % IMGS : Images de sortie. |
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359 | % TIMESTAMPS : Timestaps des images lues. |
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360 | % NB_FRAMES : Nombres d'images dans la sï¿œquence. |
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361 | NbBinFile=0; |
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362 | BinSize=0; |
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363 | fid=0; |
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364 | errormsg=''; |
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365 | classname=sprintf('uint%d',SeqData.bytesperpixel*8); |
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366 | |
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367 | classname=['*' classname]; |
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368 | BitDepth=8*SeqData.bytesperpixel;%needed to write images (8 or 16 bits) |
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369 | binrepertoire=fullfile(PathDir,SeqData.binrepertoire); |
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370 | OutputDir=fullfile(PathDir,SeqData.sequencename); |
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371 | if ~exist(OutputDir,'dir') |
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372 | % errormsg=[OutputDir ' already exist, delete it first']; |
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373 | % return |
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374 | % end |
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375 | [s,errormsg]=mkdir(OutputDir); |
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376 | |
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377 | if s==0 |
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378 | disp(errormsg) |
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379 | return%not able to create new image dir |
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380 | end |
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381 | end |
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382 | for ii=1:SeqData.nb_frames |
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383 | j1=[]; |
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384 | if ~isequal(nbfield2,1) |
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385 | j1=mod(ii-1,nbfield2)+1; |
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386 | end |
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387 | i1=floor((ii-1)/nbfield2)+1; |
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388 | OutputFile=fullfile_uvmat(PathDir,SeqData.sequencename,'img','.png',NomTypeNew,i1,[],j1);% TODO: set NomTypeNew from SeqData.mode |
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389 | fname=fullfile(binrepertoire,sprintf('%s%.5d.bin',SeqData.binfile,SqbData(ii).file_idx)); |
---|
390 | if exist(OutputFile,'file') |
---|
391 | fid=0; |
---|
392 | else |
---|
393 | if fid==0 || ~strcmp(fname,fname_prev) % open the bin file if not in use |
---|
394 | if fid~=0 |
---|
395 | fclose(fid);%close the previous bin file if relevant |
---|
396 | end |
---|
397 | [fid,msg]=fopen(fname,'rb'); |
---|
398 | if isequal(fid,-1) |
---|
399 | disp(['error in opening ' fname ': ' msg]) |
---|
400 | else |
---|
401 | disp([fname ' opened for reading']) |
---|
402 | end |
---|
403 | fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file |
---|
404 | NbBinFile=NbBinFile+1;%counter of binary files (for checking purpose) |
---|
405 | BinSize(NbBinFile)=0;% strat counter for new bin file |
---|
406 | else |
---|
407 | % fclose(fid);%close the previous bin file |
---|
408 | % fid=fopen(fname,'rb');% open the new bin file |
---|
409 | fseek(fid,SqbData(ii).offset,-1);%look at the right starting place in the bin file |
---|
410 | end |
---|
411 | fname_prev=fname; |
---|
412 | A=reshape(fread(fid,SeqData.width*SeqData.height,classname),SeqData.width,SeqData.height);%read the current image |
---|
413 | A=A'; |
---|
414 | BinSize(NbBinFile)=BinSize(NbBinFile)+SeqData.width*SeqData.height*SeqData.bytesperpixel*8; %record bits read |
---|
415 | try |
---|
416 | imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images |
---|
417 | disp([OutputFile ' written']); |
---|
418 | % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a') |
---|
419 | % if ~s |
---|
420 | % % disp_uvmat('ERROR',errormsg,checkrun); |
---|
421 | % return |
---|
422 | % end |
---|
423 | catch ME |
---|
424 | errormsg=ME.message; |
---|
425 | return |
---|
426 | end |
---|
427 | end |
---|
428 | end |
---|
429 | if fid~=0 |
---|
430 | fclose(fid) |
---|
431 | end |
---|
432 | |
---|
433 | |
---|
434 | |
---|
435 | |
---|
436 | % for ifile=1:nbfield |
---|
437 | % update_waitbar(WaitbarHandle,ifile/nbfield) |
---|
438 | % if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue') |
---|
439 | % disp('program stopped by user') |
---|
440 | % break |
---|
441 | % end |
---|
442 | % [A,FileInfo,timestamps]=read_rdvision(filename,ifile); |
---|
443 | % if ifile==1 |
---|
444 | % classA=class(A); |
---|
445 | % if strcmp(classA,'uint8') |
---|
446 | % BitDepth=8; |
---|
447 | % else |
---|
448 | % BitDepth=16; |
---|
449 | % end |
---|
450 | % end |
---|
451 | % j1=[]; |
---|
452 | % if ~isequal(nbfield2,1) |
---|
453 | % j1=mod(ifile-1+first_label,nbfield2)+1; |
---|
454 | % end |
---|
455 | % i1=floor((ifile-1+first_label)/nbfield2)+1; |
---|
456 | % OutputFile=fullfile_uvmat(RootPath{1},OutputDir,'img','.png',NomTypeNew,i1,[],j1); |
---|
457 | % try |
---|
458 | % imwrite(A,OutputFile,'BitDepth',BitDepth) % case of 16 bit images |
---|
459 | % disp([OutputFile ' written']); |
---|
460 | % [s,errormsg] = fileattrib(OutputFile,'-w','a'); %set images to read only '-w' for all users ('a') |
---|
461 | % if ~s |
---|
462 | % disp_uvmat('ERROR',errormsg,checkrun); |
---|
463 | % return |
---|
464 | % end |
---|
465 | % catch ME |
---|
466 | % disp_uvmat('ERROR',ME.message,checkrun); |
---|
467 | % return |
---|
468 | % end |
---|
469 | % |
---|
470 | % end |
---|
471 | |
---|
472 | %'imadoc2struct_special': reads the xml file for image documentation |
---|
473 | %------------------------------------------------------------------------ |
---|
474 | % function [s,errormsg]=imadoc2struct_special(ImaDoc,option) |
---|
475 | % |
---|
476 | % OUTPUT: |
---|
477 | % s: structure representing ImaDoc |
---|
478 | % s.Heading: information about the data hierarchical structure |
---|
479 | % s.Time: matrix of times |
---|
480 | % s.TimeUnit |
---|
481 | % s.GeometryCalib: substructure containing the parameters for geometric calibration |
---|
482 | % errormsg: error message |
---|
483 | % |
---|
484 | % INPUT: |
---|
485 | % ImaDoc: full name of the xml input file with head key ImaDoc |
---|
486 | % option: ='GeometryCalib': read the data of GeometryCalib, including source point coordinates |
---|
487 | |
---|
488 | function [s,errormsg]=imadoc2struct_special(ImaDoc,option) |
---|
489 | |
---|
490 | %% default input and output |
---|
491 | if ~exist('option','var') |
---|
492 | option='*'; |
---|
493 | end |
---|
494 | errormsg=[];%default |
---|
495 | s.Heading=[];%default |
---|
496 | s.Time=[]; %default |
---|
497 | s.TimeUnit=[]; %default |
---|
498 | s.GeometryCalib=[]; |
---|
499 | tsai=[];%default |
---|
500 | |
---|
501 | %% opening the xml file |
---|
502 | if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist |
---|
503 | try |
---|
504 | t=xmltree(ImaDoc); |
---|
505 | catch |
---|
506 | errormsg={[ImaDoc ' is not a valid xml file']; lasterr}; |
---|
507 | display(errormsg); |
---|
508 | return |
---|
509 | end |
---|
510 | uid_root=find(t,'/ImaDoc'); |
---|
511 | if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file |
---|
512 | |
---|
513 | |
---|
514 | %% Heading |
---|
515 | uid_Heading=find(t,'/ImaDoc/Heading'); |
---|
516 | if ~isempty(uid_Heading), |
---|
517 | uid_Campaign=find(t,'/ImaDoc/Heading/Campaign'); |
---|
518 | uid_Exp=find(t,'/ImaDoc/Heading/Experiment'); |
---|
519 | uid_Device=find(t,'/ImaDoc/Heading/Device'); |
---|
520 | uid_Record=find(t,'/ImaDoc/Heading/Record'); |
---|
521 | uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName'); |
---|
522 | s.Heading.Campaign=get(t,children(t,uid_Campaign),'value'); |
---|
523 | s.Heading.Experiment=get(t,children(t,uid_Exp),'value'); |
---|
524 | s.Heading.Device=get(t,children(t,uid_Device),'value'); |
---|
525 | if ~isempty(uid_Record) |
---|
526 | s.Heading.Record=get(t,children(t,uid_Record),'value'); |
---|
527 | end |
---|
528 | s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value'); |
---|
529 | end |
---|
530 | |
---|
531 | %% Camera and timing |
---|
532 | if strcmp(option,'*') || strcmp(option,'Camera') |
---|
533 | uid_Camera=find(t,'/ImaDoc/Camera'); |
---|
534 | if ~isempty(uid_Camera) |
---|
535 | uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize'); |
---|
536 | if ~isempty(uid_ImageSize); |
---|
537 | ImageSize=get(t,children(t,uid_ImageSize),'value'); |
---|
538 | xindex=findstr(ImageSize,'x'); |
---|
539 | if length(xindex)>=2 |
---|
540 | s.Npx=str2double(ImageSize(1:xindex(1)-1)); |
---|
541 | s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1)); |
---|
542 | end |
---|
543 | end |
---|
544 | uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit'); |
---|
545 | if ~isempty(uid_TimeUnit) |
---|
546 | s.TimeUnit=get(t,children(t,uid_TimeUnit),'value'); |
---|
547 | end |
---|
548 | uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming'); |
---|
549 | if ~isempty(uid_BurstTiming) |
---|
550 | for k=1:length(uid_BurstTiming) |
---|
551 | subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming |
---|
552 | % reading Dtk |
---|
553 | Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1); |
---|
554 | Dtj=get_value(subt,'/BurstTiming/Dtj',[]); |
---|
555 | Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') |
---|
556 | NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]); |
---|
557 | %%%% correction RDvision %%%% |
---|
558 | % NbDtj=NbDtj/numel(Dtj); |
---|
559 | % s.NbDtj=NbDtj; |
---|
560 | % %%%% |
---|
561 | Dti=get_value(subt,'/BurstTiming/Dti',[]); |
---|
562 | NbDti=get_value(subt,'/BurstTiming/NbDti',1); |
---|
563 | %%%% correction RDvision %%%% |
---|
564 | if isempty(Dti)% series |
---|
565 | Dti=Dtj; |
---|
566 | NbDti=NbDtj; |
---|
567 | Dtj=[]; |
---|
568 | s.Dti=Dti; |
---|
569 | s.NbDti=NbDti; |
---|
570 | else |
---|
571 | % NbDtj=NbDtj/numel(Dtj);%bursts |
---|
572 | if ~isempty(NbDtj) |
---|
573 | s.NbDtj=NbDtj/numel(Dtj);%bursts; |
---|
574 | else |
---|
575 | s.NbDtj=1; |
---|
576 | end |
---|
577 | end |
---|
578 | %%%% %%%% |
---|
579 | Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') |
---|
580 | |
---|
581 | Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit |
---|
582 | if ~isempty(Dti) |
---|
583 | Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times |
---|
584 | Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti |
---|
585 | end |
---|
586 | if ~isempty(Dtj) |
---|
587 | Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times |
---|
588 | Dtj=[0 Dtj]; |
---|
589 | Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj |
---|
590 | end |
---|
591 | % reading Dtk |
---|
592 | Dtk=get_value(subt,'/BurstTiming/Dtk',[]); |
---|
593 | NbDtk=get_value(subt,'/BurstTiming/NbDtk',1); |
---|
594 | %%%% correction RDvision %%%% |
---|
595 | if ~isequal(NbDtk,1) |
---|
596 | NbDtk=-1+(NbDtk+1)/(NbDti+1); |
---|
597 | end |
---|
598 | s.NbDtk=NbDtk; |
---|
599 | %%%%% |
---|
600 | if isempty(Dtk) |
---|
601 | s.Time=[s.Time;Time_val]; |
---|
602 | else |
---|
603 | for kblock=1:NbDtk+1 |
---|
604 | Time_val_k=Time_val+(kblock-1)*Dtk; |
---|
605 | s.Time=[s.Time;Time_val_k]; |
---|
606 | end |
---|
607 | end |
---|
608 | end |
---|
609 | end |
---|
610 | end |
---|
611 | end |
---|
612 | |
---|
613 | %% motor |
---|
614 | if strcmp(option,'*') || strcmp(option,'GeometryCalib') |
---|
615 | uid_subtree=find(t,'/ImaDoc/TranslationMotor'); |
---|
616 | if length(uid_subtree)==1 |
---|
617 | subt=branch(t,uid_subtree);%subtree under GeometryCalib |
---|
618 | [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]); |
---|
619 | end |
---|
620 | end |
---|
621 | %% geometric calibration |
---|
622 | if strcmp(option,'*') || strcmp(option,'GeometryCalib') |
---|
623 | uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib'); |
---|
624 | if ~isempty(uid_GeometryCalib) |
---|
625 | if length(uid_GeometryCalib)>1 |
---|
626 | errormsg=['More than one GeometryCalib in ' filecivxml]; |
---|
627 | return |
---|
628 | end |
---|
629 | subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib |
---|
630 | cont=get(subt,1,'contents'); |
---|
631 | if ~isempty(cont) |
---|
632 | uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType'); |
---|
633 | if isequal(length(uid_CalibrationType),1) |
---|
634 | tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value'); |
---|
635 | end |
---|
636 | uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit'); |
---|
637 | if isequal(length(uid_CoordUnit),1) |
---|
638 | tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value'); |
---|
639 | end |
---|
640 | uid_fx_fy=find(subt,'/GeometryCalib/fx_fy'); |
---|
641 | focal=[];%default fro old convention (Reg Wilson) |
---|
642 | if isequal(length(uid_fx_fy),1) |
---|
643 | tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value')); |
---|
644 | else %old convention (Reg Wilson) |
---|
645 | uid_focal=find(subt,'/GeometryCalib/focal'); |
---|
646 | uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy'); |
---|
647 | uid_sx=find(subt,'/GeometryCalib/sx'); |
---|
648 | if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx) |
---|
649 | dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value')); |
---|
650 | sx=str2num(get(subt,children(subt,uid_sx),'value')); |
---|
651 | focal=str2num(get(subt,children(subt,uid_focal),'value')); |
---|
652 | tsai.fx_fy(1)=sx*focal/dpx_dpy(1); |
---|
653 | tsai.fx_fy(2)=focal/dpx_dpy(2); |
---|
654 | end |
---|
655 | end |
---|
656 | uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy'); |
---|
657 | if ~isempty(uid_Cx_Cy) |
---|
658 | tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value')); |
---|
659 | end |
---|
660 | uid_kc=find(subt,'/GeometryCalib/kc'); |
---|
661 | if ~isempty(uid_kc) |
---|
662 | tsai.kc=str2double(get(subt,children(subt,uid_kc),'value')); |
---|
663 | else %old convention (Reg Wilson) |
---|
664 | uid_kappa1=find(subt,'/GeometryCalib/kappa1'); |
---|
665 | if ~isempty(uid_kappa1)&& ~isempty(focal) |
---|
666 | kappa1=str2double(get(subt,children(subt,uid_kappa1),'value')); |
---|
667 | tsai.kc=-kappa1*focal*focal; |
---|
668 | end |
---|
669 | end |
---|
670 | uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz'); |
---|
671 | if ~isempty(uid_Tx_Ty_Tz) |
---|
672 | tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value')); |
---|
673 | end |
---|
674 | uid_R=find(subt,'/GeometryCalib/R'); |
---|
675 | if ~isempty(uid_R) |
---|
676 | RR=get(subt,children(subt,uid_R),'value'); |
---|
677 | if length(RR)==3 |
---|
678 | tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})]; |
---|
679 | end |
---|
680 | end |
---|
681 | |
---|
682 | %look for laser plane definitions |
---|
683 | uid_Angle=find(subt,'/GeometryCalib/PlaneAngle'); |
---|
684 | uid_Pos=find(subt,'/GeometryCalib/SliceCoord'); |
---|
685 | if isempty(uid_Pos) |
---|
686 | uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention |
---|
687 | end |
---|
688 | if ~isempty(uid_Angle) |
---|
689 | tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value')); |
---|
690 | end |
---|
691 | if ~isempty(uid_Pos) |
---|
692 | for j=1:length(uid_Pos) |
---|
693 | tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value')); |
---|
694 | end |
---|
695 | uid_DZ=find(subt,'/GeometryCalib/SliceDZ'); |
---|
696 | uid_NbSlice=find(subt,'/GeometryCalib/NbSlice'); |
---|
697 | if ~isempty(uid_DZ) && ~isempty(uid_NbSlice) |
---|
698 | DZ=str2double(get(subt,children(subt,uid_DZ),'value')); |
---|
699 | NbSlice=get(subt,children(subt,uid_NbSlice),'value'); |
---|
700 | if isequal(NbSlice,'volume') |
---|
701 | tsai.NbSlice='volume'; |
---|
702 | NbSlice=NbDtj+1; |
---|
703 | else |
---|
704 | tsai.NbSlice=str2double(NbSlice); |
---|
705 | end |
---|
706 | tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1]; |
---|
707 | end |
---|
708 | end |
---|
709 | tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]); |
---|
710 | tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n'); |
---|
711 | tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]); |
---|
712 | tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1); |
---|
713 | |
---|
714 | if strcmp(option,'GeometryCalib') |
---|
715 | tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]); |
---|
716 | end |
---|
717 | s.GeometryCalib=tsai; |
---|
718 | end |
---|
719 | end |
---|
720 | end |
---|
721 | |
---|
722 | %-------------------------------------------------- |
---|
723 | % read a subtree |
---|
724 | % INPUT: |
---|
725 | % t: xltree |
---|
726 | % head_element: head elelemnt of the subtree |
---|
727 | % Data, structure containing |
---|
728 | % .Key: element name |
---|
729 | % .Type: type of element ('charg', 'float'....) |
---|
730 | % .NbOccur: nbre of occurrence, NaN for un specified number |
---|
731 | function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest) |
---|
732 | %-------------------------------------------------- |
---|
733 | s=[];%default |
---|
734 | errormsg=''; |
---|
735 | head_element=get(subt,1,'name'); |
---|
736 | cont=get(subt,1,'contents'); |
---|
737 | if ~isempty(cont) |
---|
738 | for ilist=1:length(Data) |
---|
739 | uid_key=find(subt,[head_element '/' Data{ilist}]); |
---|
740 | if ~isequal(length(uid_key),NbOccur(ilist)) |
---|
741 | errormsg=['wrong number of occurence for ' Data{ilist}]; |
---|
742 | return |
---|
743 | end |
---|
744 | for ival=1:length(uid_key) |
---|
745 | val=get(subt,children(subt,uid_key(ival)),'value'); |
---|
746 | if ~NumTest(ilist) |
---|
747 | eval(['s.' Data{ilist} '=val;']); |
---|
748 | else |
---|
749 | eval(['s.' Data{ilist} '=str2double(val);']) |
---|
750 | end |
---|
751 | end |
---|
752 | end |
---|
753 | end |
---|
754 | |
---|
755 | |
---|
756 | %-------------------------------------------------- |
---|
757 | % read an xml element |
---|
758 | function val=get_value(t,label,default) |
---|
759 | %-------------------------------------------------- |
---|
760 | val=default; |
---|
761 | uid=find(t,label);%find the element iud(s) |
---|
762 | if ~isempty(uid) %if the element named label exists |
---|
763 | uid_child=children(t,uid);%find the children |
---|
764 | if ~isempty(uid_child) |
---|
765 | data=get(t,uid_child,'type');%get the type of child |
---|
766 | if iscell(data)% case of multiple element |
---|
767 | for icell=1:numel(data) |
---|
768 | val_read=str2num(get(t,uid_child(icell),'value')); |
---|
769 | if ~isempty(val_read) |
---|
770 | val(icell,:)=val_read; |
---|
771 | end |
---|
772 | end |
---|
773 | % val=val'; |
---|
774 | else % case of unique element value |
---|
775 | val_read=str2num(get(t,uid_child,'value')); |
---|
776 | if ~isempty(val_read) |
---|
777 | val=val_read; |
---|
778 | else |
---|
779 | val=get(t,uid_child,'value');%char string data |
---|
780 | end |
---|
781 | end |
---|
782 | end |
---|
783 | end |
---|
784 | |
---|
785 | |
---|
786 | |
---|
787 | |
---|