[1099] | 1 | %'extract_multitif': read image series from PCO cameras (tiff image series) and write .png images |
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[930] | 2 | %------------------------------------------------------------------------ |
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| 3 | |
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[1099] | 4 | % function ParamOut=extract_multitif(Param) |
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[930] | 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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[1107] | 43 | % Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France |
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[930] | 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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[1099] | 60 | function ParamOut=extract_multitif(Param) |
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[930] | 61 | |
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| 62 | %%%%%%%%%%%%%%%%% INPUT PREPARATION MODE (no RUN) %%%%%%%%%%%%%%%%% |
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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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[1002] | 66 | ParamOut.NbSlice='off'; % impose calculation in a single process (no parallel processing to avoid 'holes')) |
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[930] | 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.OutputDirExt='.png';%set the output dir extension |
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| 73 | 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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[1068] | 74 | ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1) |
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[1099] | 75 | ParamOut.CPUTime=10;% expected time for writting the output of one source image ( in minute) |
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[930] | 76 | %% root input file(s) and type |
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| 77 | % check the existence of the first file in the series |
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| 78 | first_j=[];% note that the function will propose to cover the whole range of indices |
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| 79 | if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end |
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| 80 | last_j=[]; |
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| 81 | if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end |
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| 82 | PairString=''; |
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| 83 | if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end |
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| 84 | [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString); |
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| 85 | FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},... |
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| 86 | Param.InputTable{1,5},Param.InputTable{1,4},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 | |
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| 91 | %% check the validity of input file types |
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| 92 | FileInfo=get_file_info(FirstFileName); |
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[939] | 93 | if ~strcmp(FileInfo.FileType,'multimage') |
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| 94 | msgbox_uvmat('ERROR',['invalid file type input: ' FileInfo.FileType ' not an image']) |
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[930] | 95 | return |
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| 96 | end |
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[1002] | 97 | ParamOut.ActionInput.XmlFile=uigetfile_uvmat('pick xml file for timing',fileparts(fileparts(FirstFileName)),'.xml'); |
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[930] | 98 | return |
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| 99 | end |
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| 100 | %%%%%%%%%%%%%%%%% STOP HERE FOR PAMETER INPUT MODE %%%%%%%%%%%%%%%%% |
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| 101 | |
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| 102 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 103 | checkrun=1; |
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| 104 | RUNHandle=[]; |
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| 105 | WaitbarHandle=[]; |
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| 106 | if ischar(Param) |
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| 107 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 108 | checkrun=0; |
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| 109 | else |
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[1002] | 110 | hseries=findobj(allchild(0),'Tag','series'); |
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| 111 | RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series |
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| 112 | WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series |
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[930] | 113 | end |
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| 114 | |
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[939] | 115 | %% output directory |
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[1002] | 116 | OutputDir=fullfile(Param.InputTable{1,1},[Param.OutputSubDir Param.OutputDirExt]); |
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[930] | 117 | |
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[1002] | 118 | %% Timing |
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| 119 | XmlInputFile=Param.ActionInput.XmlFile; |
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| 120 | [XmlInput,errormsg]=imadoc2struct(XmlInputFile,'Camera'); |
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| 121 | if ~isempty(errormsg) |
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| 122 | disp(['bad xml input file: ' errormsg]) |
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| 123 | return |
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| 124 | end |
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| 125 | ImagesPerLevel=size(XmlInput.Time,2)-1;%100;%use the xmlinformation to get the nbre of j indices |
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| 126 | |
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[1099] | 127 | %% create the xml file for timing if it does not exist : example to adapt |
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| 128 | TEST=0; |
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| 129 | if TEST |
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| 130 | count0=14; |
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| 131 | Dtj=0.05;% time interval between frames |
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| 132 | ImagesPerLevel=455;% total number of images per position, ImagesPerLevel-Nbj images skiiped during motion between two positions |
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| 133 | Nbj=390; %Nbre of images kept at a given position |
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| 134 | Dti=Dtj*ImagesPerLevel; |
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| 135 | NbLevel=11; |
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| 136 | NbScan=3; |
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| 137 | TimeReturn=268.5; %time needed to return back to the first position (in sec) |
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| 138 | NbReturn=round(TimeReturn/Dtj); |
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| 139 | NbSkipReturn=NbReturn+1-NbLevel*ImagesPerLevel; |
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| 140 | |
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| 141 | Newxml=fullfile(Param.InputTable{1,1},[Param.InputTable{1,2} '.xml']); |
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| 142 | if ~exist(Newxml,'file') |
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| 143 | XmlInput.Camera.CameraName='PCO'; |
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| 144 | XmlInput.Camera.TimeUnit='s'; |
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| 145 | XmlInput.Camera.BurstTiming.FrameFrequency=1; |
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| 146 | XmlInput.Camera.BurstTiming.Time=0;% for 200 |
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| 147 | XmlInput.Camera.BurstTiming.Dtj=Dtj; |
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| 148 | XmlInput.Camera.BurstTiming.NbDtj=Nbj-1; |
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| 149 | XmlInput.Camera.BurstTiming.Dti=Dti; |
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| 150 | XmlInput.Camera.BurstTiming.NbDti=NbLevel-1; |
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| 151 | XmlInput.Camera.BurstTiming.Dtk=TimeReturn; |
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| 152 | XmlInput.Camera.BurstTiming.NbDtk=NbScan-1; |
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| 153 | t=struct2xml(XmlInput); |
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| 154 | t=set(t,1,'name','ImaDoc'); |
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| 155 | save(t,Newxml); |
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| 156 | end |
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[1002] | 157 | end |
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| 158 | |
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| 159 | %% loop on the files |
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| 160 | % include the first tiff file with no index in the first iteration |
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| 161 | if Param.IndexRange.first_i==1% first slice of processing |
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| 162 | firstindex=0; |
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| 163 | count=0; |
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| 164 | else |
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| 165 | firstindex=Param.IndexRange.first_i; |
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| 166 | ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif'); |
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| 167 | NbFrames=numel(imfinfo(ImageName)); |
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| 168 | count=Param.IndexRange.first_i*NbFrames; |
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| 169 | end |
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| 170 | for ifile=firstindex:Param.IndexRange.last_i |
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[1068] | 171 | tic |
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[1002] | 172 | if firstindex==0 && ifile==0% first slice of processing |
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| 173 | ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},'im.tif') |
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| 174 | else |
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| 175 | ImageName=fullfile(Param.InputTable{1,1},Param.InputTable{1,2},['im@' num2str(ifile,'%04d') '.tif']) |
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[930] | 176 | end |
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| 177 | NbFrames=numel(imfinfo(ImageName)); |
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[1002] | 178 | for iframe=1:NbFrames |
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[972] | 179 | if isequal(ImagesPerLevel,1)% mode series |
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[931] | 180 | OutputFile=fullfile(OutputDir,['img_' num2str(count+1) '.png']); |
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[972] | 181 | else % indices i and j |
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[930] | 182 | i_index=fix(count/ImagesPerLevel)+1; |
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| 183 | j_index=mod(count,ImagesPerLevel)+1; |
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| 184 | OutputFile=fullfile(OutputDir,['img_' num2str(i_index) '_' num2str(j_index) '.png']); |
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| 185 | end |
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[972] | 186 | if Param.CheckOverwrite ||~exist(OutputFile,'file') |
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| 187 | A=imread(ImageName,iframe); |
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| 188 | imwrite(A,OutputFile,'BitDepth',16); |
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| 189 | disp([OutputFile ' written']) |
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| 190 | else |
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| 191 | disp([OutputFile ' already exists']) |
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| 192 | end |
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[931] | 193 | count=count+1; |
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[930] | 194 | end |
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[1068] | 195 | tt=toc; |
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| 196 | disp(['elapsed time (in min.) for the file im@' num2str(ifile,'%04d')]) |
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| 197 | disp(num2str(tt/60)) |
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[930] | 198 | end |
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| 199 | |
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[972] | 200 | |
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[930] | 201 | |
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