1 | %'read_multimadoc': read a set of Imadoc files for different file series and compare their timing |
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2 | %------------------------------------------------------------------------ |
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3 | % [XmlData,NbSlice_calib,time,warnmsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series) |
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4 | % |
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5 | % OUTPUT: |
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6 | % XmlData(iview): cell array of structures representing the contents of the xml files, iview =index of the input file series |
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7 | % NbSlice_calib: nbre of slices detected in the geometric calibration data |
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8 | % Time(iview,i,j): matrix of times, iview =index of the series, i,j=file indices within the series |
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9 | % if the time is not consistent in all series, the time from the first series is chosen |
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10 | % warnmsg: warning message, ='' if OK |
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11 | % |
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12 | % INPUT: |
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13 | % RootPath,SubDir,RootFile,FileExt: cell arrays characterizing the input file series |
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14 | % i1_series,i2_series,j1_series,j2_series: cell arrays of file index arrays, as given by the fct uvmat/get_file_series |
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15 | |
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16 | %======================================================================= |
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17 | % Copyright 2008-2015, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France |
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18 | % http://www.legi.grenoble-inp.fr |
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19 | % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr |
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20 | % |
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21 | % This file is part of the toolbox UVMAT. |
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22 | % |
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23 | % UVMAT is free software; you can redistribute it and/or modify |
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24 | % it under the terms of the GNU General Public License as published |
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25 | % by the Free Software Foundation; either version 2 of the license, |
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26 | % or (at your option) any later version. |
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27 | % |
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28 | % UVMAT is distributed in the hope that it will be useful, |
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29 | % but WITHOUT ANY WARRANTY; without even the implied warranty of |
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30 | % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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31 | % GNU General Public License (see LICENSE.txt) for more details. |
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32 | %======================================================================= |
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33 | |
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34 | function [XmlData,NbSlice_calib,Time,warnmsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series) |
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35 | warnmsg=''; |
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36 | if ischar(RootPath) |
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37 | RootPath={RootPath};SubDir={SubDir};RootFile={RootFile};FileExt={FileExt}; |
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38 | end |
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39 | nbview=numel(RootPath); |
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40 | XmlData=cell(1,nbview);%initiate the structures containing the data from the xml file (calibration and timing) |
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41 | NbSlice_calib=cell(1,nbview); |
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42 | timecell=cell(1,nbview); |
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43 | for iview=1:nbview%Loop on views |
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44 | XmlFileName=find_imadoc(RootPath{iview},SubDir{iview},RootFile{iview},FileExt{iview}); |
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45 | if ~isempty(XmlFileName) |
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46 | [XmlData{iview},warnmsg]=imadoc2struct(XmlFileName);% read the ImaDoc xml file |
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47 | end |
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48 | if isfield(XmlData{iview},'Time') |
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49 | timecell{iview}=XmlData{iview}.Time; |
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50 | end |
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51 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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52 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
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53 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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54 | warnmsg='inconsistent number of Z indices in field series'; |
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55 | end |
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56 | end |
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57 | end |
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58 | |
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59 | %% check coincidence in time for several input file series |
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60 | if isempty(timecell) |
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61 | Time=[]; |
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62 | else |
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63 | Time=get_time(timecell{1},i1_series{1},i2_series{1},j1_series{1},j2_series{1}); |
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64 | end |
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65 | if nbview>1 |
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66 | Time=shiftdim(Time,-1); % add a singleton dimension for nbview |
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67 | for icell=2:nbview |
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68 | if isequal(size(timecell{icell}),size(timecell{1})) |
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69 | time_line=get_time(timecell{icell},i1_series{icell},i2_series{icell},j1_series{icell},j2_series{icell}); |
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70 | Time=cat(1,Time,shiftdim(time_line,-1)); |
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71 | else |
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72 | warnmsg='inconsistent time array dimensions in ImaDoc fields, the time for the first series is used'; |
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73 | Time=cat(1,Time,Time(1,:,:));% copy times of the first line |
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74 | break |
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75 | end |
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76 | end |
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77 | end |
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78 | |
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79 | function time=get_time(timeimadoc,i1_series,i2_series,j1_series,j2_series) |
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80 | time=[]; |
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81 | if ~ (isempty(i2_series)||size(timeimadoc,1) < i2_series(end) ||( ~isempty(j2_series) && size(timeimadoc,2) < j2_series(end)))% time array absent or too short in ImaDoc xml file' |
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82 | if isempty(j1_series) |
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83 | j1_series=1; |
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84 | end |
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85 | time=timeimadoc(i1_series+1,j1_series+1); |
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86 | if ~isempty(j2_series) |
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87 | time=[time timeimadoc(i1_series+1,j2_series+1)]; |
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88 | end |
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89 | if ~isempty(i2_series) |
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90 | time=[time timeimadoc(i2_series+1,j1_series+1)]; |
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91 | if ~isempty(j2_series) |
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92 | time=[time timeimadoc(i2_series+1,j2_series+1)]; |
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93 | end |
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94 | end |
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95 | time=mean(time,2); |
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96 | time=time'; |
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97 | end |
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