1 | %'extract_multitif': read image series from PCO cameras (tiff image series) and write .png images |
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2 | % use a single geometric calibration, with information on the slice positions in case of 3D scanning |
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3 | %------------------------------------------------------ |
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4 | % the output file indexing is based on the xml file requested by the |
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5 | % function when it is selected (or possibly inserted in this function in the section TEST) |
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6 | % This xml file must contain the following information: |
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7 | % NbDti: the number of 'bursts' -1 |
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8 | % NbDtj: number of frames in each burst-1, or number of repetition of a burst sequence defined by Dtj |
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9 | % NbDtk: number of repetitions of a slice scanning process -1 (ignored by default) |
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10 | % Therefore the total number of frames is (NbDti+1)*(NbDtj+1)*(NbDtk+1) |
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11 | % The frame series is stored in a single folder with two indices i:(NbDti+1)*(NbDtk+1) |
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12 | % |
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13 | % To run the function in the cluster in parallel for each multitif file, indicate nb-slice_i equal to the |
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14 | % number input multitif files |
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15 | |
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16 | |
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17 | % function ParamOut=extract_multitif(Param) |
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18 | % |
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19 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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20 | % |
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21 | %OUTPUT |
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22 | % ParamOut: sets options in the GUI series.fig needed for the function |
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23 | % |
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24 | %INPUT: |
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25 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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26 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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27 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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28 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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29 | % |
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30 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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31 | % see the current structure Param) |
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32 | % .InputTable: cell of input file names, (several lines for multiple input) |
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33 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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34 | % .OutputSubDir: name of the subdirectory for data outputs |
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35 | % .OutputDirExt: directory extension for data outputs |
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36 | % .Action: .ActionName: name of the current activated function |
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37 | % .ActionPath: path of the current activated function |
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38 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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39 | % .RUN =0 for GUI input, =1 for function activation |
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40 | % .RunMode='local','background', 'cluster': type of function use |
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41 | % |
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42 | % .IndexRange: set the file or frame indices on which the action must be performed |
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43 | % .FieldTransform: .TransformName: name of the selected transform function |
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44 | % .TransformPath: path of the selected transform function |
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45 | % .InputFields: sub structure describing the input fields withfields |
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46 | % .FieldName: name(s) of the field |
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47 | % .VelType: velocity type |
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48 | % .FieldName_1: name of the second field in case of two input series |
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49 | % .VelType_1: velocity type of the second field in case of two input series |
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50 | % .Coord_y: name of y coordinate variable |
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51 | % .Coord_x: name of x coordinate variable |
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52 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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53 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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54 | |
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55 | %======================================================================= |
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56 | % Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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57 | % http://www.legi.grenoble-inp.fr |
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58 | % Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr |
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59 | % |
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60 | % This file is part of the toolbox UVMAT. |
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61 | % |
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62 | % UVMAT is free software; you can redistribute it and/or modify |
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63 | % it under the terms of the GNU General Public License as published |
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64 | % by the Free Software Foundation; either version 2 of the license, |
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65 | % or (at your option) any later version. |
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66 | % |
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67 | % UVMAT is distributed in the hope that it will be useful, |
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68 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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69 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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70 | % GNU General Public License (see LICENSE.txt) for more details. |
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71 | %======================================================================= |
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72 | |
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73 | function ParamOut=extract_multitif(Param) |
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74 | |
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75 | %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% |
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76 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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77 | ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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78 | ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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79 | ParamOut.NbSlice='on'; % |
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80 | ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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81 | ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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82 | ParamOut.FieldTransform = 'off';%can use a transform function |
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83 | ParamOut.ProjObject='off';%can use projection object(option 'off'/'on', |
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84 | ParamOut.Mask='off';%can use mask option (option 'off'/'on', 'off' by default) |
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85 | ParamOut.OutputDirExt='.png';%set the output dir extension |
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86 | ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice |
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87 | ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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88 | ParamOut.CPUTime=10;% expected time for writting the output of one source image ( in minute) |
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89 | %% root input file(s) and type |
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90 | % check the existence of the first file in the series |
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91 | first_j=[];% note that the function will propose to cover the whole range of indices |
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92 | if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end |
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93 | % % last_j=[]; |
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94 | % % if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end |
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95 | PairString=''; |
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96 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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97 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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98 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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99 | Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2); |
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100 | if ~exist(FirstFileName,'file') |
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101 | msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist']) |
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102 | end |
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103 | ParamOut.NbSlice=Param.IndexRange.MaxIndex_i; |
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104 | %% check the validity of input file types |
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105 | FileInfo=get_file_info(FirstFileName); |
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106 | if ~strcmp(FileInfo.FileType,'multimage') |
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107 | msgbox_uvmat('ERROR',['invalid file type input: ' FileInfo.FileType ' not a tiff image series']) |
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108 | return |
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109 | end |
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110 | ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); |
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111 | return |
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112 | end |
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113 | %%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% |
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114 | |
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115 | %% read input parameters from an xml file if input is a file name (batch mode) |
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116 | checkrun=1; |
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117 | RUNHandle=[]; |
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118 | WaitbarHandle=[]; |
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119 | if ischar(Param) |
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120 | Param=xml2struct(Param);% read Param as input file (batch case) |
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121 | checkrun=0; |
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122 | else |
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123 | hseries=findobj(allchild(0),'Tag','series'); |
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124 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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125 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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126 | end |
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127 | |
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128 | %% output directory |
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129 | OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); |
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130 | |
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131 | %% Timing |
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132 | XmlInputFile=Param.ActionInput.XmlFile; |
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133 | [XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera'); |
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134 | if ~isempty(errormsg) |
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135 | disp(['bad xml input file: ' errormsg]) |
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136 | return |
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137 | end |
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138 | ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices |
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139 | |
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140 | %% create the xml file for timing if it does not exist : example to adapt |
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141 | TEST=0; |
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142 | if TEST |
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143 | count0=14; |
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144 | Dtj=0.05;% time interval between frames |
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145 | ImagesPerLevel=455;% total number of images per position, ImagesPerLevel-Nbj images skiiped during motion between two positions |
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146 | Nbj=390; %Nbre of images kept at a given position |
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147 | Dti=Dtj*ImagesPerLevel; |
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148 | NbLevel=11; |
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149 | NbScan=3; |
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150 | TimeReturn=268.5; %time needed to return back to the first position (in sec) |
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151 | NbReturn=round(TimeReturn/Dtj); |
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152 | NbSkipReturn=NbReturn+1-NbLevel*ImagesPerLevel; |
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153 | |
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154 | Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']); |
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155 | if ~exist(Newxml,'file') |
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156 | XmlInput.Camera.CameraName='PCO'; |
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157 | XmlInput.Camera.TimeUnit='s'; |
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158 | XmlInput.Camera.BurstTiming.FrameFrequency=1; |
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159 | XmlInput.Camera.BurstTiming.Time=0;% for 200 |
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160 | XmlInput.Camera.BurstTiming.Dtj=Dtj; |
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161 | XmlInput.Camera.BurstTiming.NbDtj=Nbj-1; |
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162 | XmlInput.Camera.BurstTiming.Dti=Dti; |
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163 | XmlInput.Camera.BurstTiming.NbDti=NbLevel-1; |
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164 | XmlInput.Camera.BurstTiming.Dtk=TimeReturn; |
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165 | XmlInput.Camera.BurstTiming.NbDtk=NbScan-1; |
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166 | t=struct2xml(XmlInput); |
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167 | t=set(t,1,'name','ImaDoc'); |
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168 | save(t,Newxml); |
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169 | end |
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170 | end |
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171 | |
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172 | %% loop on the files |
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173 | % include the first tiff file with no index in the first iteration |
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174 | if Param.IndexRange.first_i==1% first slice of processing |
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175 | firstindex=0; |
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176 | count=0; |
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177 | else |
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178 | firstindex=Param.IndexRange.first_i; |
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179 | ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif'); |
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180 | NbFrames=numel(imfinfo(ImageName)); |
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181 | count=Param.IndexRange.first_i*NbFrames; |
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182 | end |
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183 | for ifile=firstindex:Param.IndexRange.last_i |
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184 | tic |
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185 | if firstindex==0 && ifile==0% first slice of processing |
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186 | ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') |
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187 | else |
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188 | ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif']) |
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189 | end |
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190 | NbFrames=numel(imfinfo(ImageName)); |
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191 | for iframe=1:NbFrames |
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192 | if isequal(ImagesPerLevel,1)% mode series |
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193 | OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); |
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194 | else % indices i and j |
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195 | i_index=fix(count/ImagesPerLevel)+1; |
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196 | j_index=mod(count,ImagesPerLevel)+1; |
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197 | OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); |
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198 | end |
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199 | if Param.CheckOverwrite ||~exist(OutputFile,'file') |
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200 | A=imread(ImageName,iframe); |
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201 | imwrite(A,OutputFile,'BitDepth',16); |
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202 | disp([OutputFile ' written']) |
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203 | else |
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204 | disp([OutputFile ' already exists']) |
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205 | end |
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206 | count=count+1; |
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207 | end |
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208 | tt=toc; |
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209 | disp(['elapsed time (in min.) for the file im@' num2str(ifile,'%04d')]) |
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210 | disp(num2str(tt/60)) |
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211 | end |
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212 | |
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213 | |
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214 | |
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