[563] | 1 | %'relabel_i_j': 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=relabel_i_j(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 | % This function is used in four modes by the GUI series: |
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| 9 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 10 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 11 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 12 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 13 | % |
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| 14 | % This function is used in four modes by the GUI series: |
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| 15 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 16 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 17 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 18 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 19 | % |
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| 20 | %OUTPUT |
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| 21 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 22 | % |
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| 23 | %INPUT: |
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| 24 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 25 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 26 | % In the absence of input (as activated when the current Action is selected |
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| 27 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
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| 28 | % |
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| 29 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 30 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 31 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 32 | % .OutputSubDir: name of the subdirectory for data outputs |
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| 33 | % .OutputDir: directory for data outputs, including path |
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| 34 | % .Action: .ActionName: name of the current activated function |
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| 35 | % .ActionPath: path of the current activated function |
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| 36 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 37 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 38 | % .TransformPath: path of the selected transform function |
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| 39 | % .TransformHandle: corresponding function handle |
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| 40 | % .InputFields: sub structure describing the input fields withfields |
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| 41 | % .FieldName: name of the field |
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| 42 | % .VelType: velocity type |
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| 43 | % .FieldName_1: name of the second field in case of two input series |
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| 44 | % .VelType_1: velocity type of the second field in case of two input series |
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| 45 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 46 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 47 | |
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| 48 | function ParamOut=relabel_i_j(Param) %default output=relabel_i_j(Param) |
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| 49 | |
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| 50 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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| 51 | if ~exist('Param','var') % case with no input parameter |
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| 52 | ParamOut={'NbViewMax';1;...% max nbre of input file series (default='' , no limitation) |
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| 53 | 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) |
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| 54 | 'WholeIndexRange';'on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 55 | 'NbSlice';'off'; ...%nbre of slices ('off' by default) |
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| 56 | 'VelType';'off';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 57 | 'FieldName';'off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 58 | 'FieldTransform'; 'off';...%can use a transform function |
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| 59 | 'ProjObject';'off';...%can use projection object(option 'off'/'on', |
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| 60 | 'Mask';'off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 61 | 'OutputDirExt';'';...%set the output dir extension |
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| 62 | ''}; |
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| 63 | return |
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| 64 | end |
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| 65 | |
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| 66 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 67 | %% select different modes, RUN, parameter input, BATCH |
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| 68 | % BATCH case: read the xml file for batch case |
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| 69 | if ischar(Param) |
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| 70 | Param=xml2struct(Param); |
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| 71 | checkrun=0; |
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| 72 | % RUN case: parameters introduced as the input structure Param |
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| 73 | else |
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| 74 | hseries=guidata(Param.hseries);%handles of the GUI series |
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| 75 | if isfield(Param,'Specific')&& strcmp(Param.Specific,'?') |
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| 76 | checkrun=1;% will only search interactive input parameters (preparation of BATCH mode) |
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| 77 | else |
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| 78 | checkrun=2; % indicate the RUN option is used |
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| 79 | end |
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| 80 | end |
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| 81 | ParamOut=Param; %default output |
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| 82 | |
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| 83 | %% root input file(s) and type |
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| 84 | RootPath=Param.InputTable(:,1); |
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| 85 | RootFile=Param.InputTable(:,3); |
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| 86 | SubDir=Param.InputTable(:,2); |
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| 87 | NomType=Param.InputTable(:,4); |
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| 88 | FileExt=Param.InputTable(:,5); |
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| 89 | |
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| 90 | % get the set of input file names (cell array filecell), and the lists of |
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| 91 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
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| 92 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 93 | |
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| 94 | % numbers of slices and file indices |
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| 95 | |
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| 96 | NbSlice=1;%default |
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| 97 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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| 98 | NbSlice=Param.IndexRange.NbSlice; |
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| 99 | end |
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| 100 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 101 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 102 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 103 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 104 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 105 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 106 | |
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| 107 | %determine the file type on each line from the first input file |
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| 108 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 109 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 110 | for iview=1:nbview |
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| 111 | if ~exist(filecell{iview,1}','file') |
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| 112 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
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| 113 | return |
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| 114 | end |
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| 115 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); |
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| 116 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 117 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 118 | if ~isempty(j1_series{iview}) |
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| 119 | frame_index{iview}=j1_series{iview}; |
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| 120 | else |
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| 121 | frame_index{iview}=i1_series{iview}; |
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| 122 | end |
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| 123 | end |
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| 124 | |
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| 125 | %% calibration data and timing: read the ImaDoc files |
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| 126 | mode=''; %default |
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| 127 | timecell={}; |
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| 128 | itime=0; |
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| 129 | NbSlice_calib={}; |
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| 130 | XmlData=cell(1,nbview);%initiate the structures containing the data from the xml file (calibration and timing) |
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| 131 | for iview=1:nbview%Loop on views |
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| 132 | SubDirBase=regexprep(SubDir{iview},'\..*','');%take the root part of SubDir, before the first dot '.' |
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| 133 | filexml=[fullfile(RootPath{iview},SubDirBase) '.xml'];%new convention: xml at the level of the image folder |
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| 134 | if ~exist(filexml,'file') |
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| 135 | filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.xml']; % old convention: xml inside the image folder |
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| 136 | if ~exist(filexml,'file') |
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| 137 | filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.civ']; % very old convention: .civ file |
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| 138 | if ~exist(filexml,'file') |
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| 139 | filexml=''; |
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| 140 | end |
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| 141 | end |
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| 142 | end |
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| 143 | if ~isempty(filexml) |
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| 144 | [XmlData{iview},error]=imadoc2struct_special(filexml); |
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| 145 | end |
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| 146 | if isfield(XmlData{iview},'Time') |
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| 147 | itime=itime+1; |
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| 148 | timecell{itime}=XmlData{iview}.Time; |
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| 149 | end |
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| 150 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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| 151 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
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| 152 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 153 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 154 | end |
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| 155 | end |
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| 156 | end |
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| 157 | |
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| 158 | %% check coincidence in time for several input file series |
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| 159 | % not relevant |
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| 160 | |
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| 161 | %% coordinate transform or other user defined transform |
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| 162 | %not relevant |
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| 163 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 164 | % EDIT FROM HERE |
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| 165 | |
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| 166 | %% check the validity of input file types |
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| 167 | if CheckImage{1} |
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| 168 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 169 | elseif CheckNc{1} |
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| 170 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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| 171 | else |
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| 172 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
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| 173 | return |
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| 174 | end |
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| 175 | if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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| 176 | msgbox_uvmat('ERROR','input must be two image series or two netcdf file series') |
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| 177 | return |
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| 178 | end |
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| 179 | % NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series |
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| 180 | % if NbSlice~=nbfield_j |
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| 181 | % answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); |
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| 182 | % if ~strcmp(answer,'Yes') |
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| 183 | % return |
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| 184 | % end |
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| 185 | % end |
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| 186 | |
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| 187 | %% Set field names and velocity types |
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| 188 | % not relevant here |
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| 189 | |
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| 190 | %% Initiate output fields |
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| 191 | % not relevant here |
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| 192 | |
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| 193 | %% interactive input of specific parameters (for RDvision system) |
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| 194 | display('RDvision system') |
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| 195 | first_label=0; %image numbers start from 0 |
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| 196 | if ~strcmp(NomType{1},'_000001') |
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| 197 | msgbox_uvmat('WARNING','the input is not a file from RDvision: this function relabel_i_j has no action');%error message for directory creation |
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| 198 | return |
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| 199 | else |
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| 200 | answer=msgbox_uvmat('','this function will relabel the file series from RDvision from and correct the xml file');%error message for directory creation |
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| 201 | if ~strcmp(answer,'Yes') |
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| 202 | return |
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| 203 | end |
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| 204 | end |
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| 205 | |
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| 206 | %% copy and adapt the xml file |
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| 207 | NomTypeNew='_1_1'; |
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| 208 | if ~isempty(XmlData{1}) |
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| 209 | t=xmltree(filexml); |
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| 210 | |
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| 211 | %update information on the first image name in the series |
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| 212 | uid_Heading=find(t,'ImaDoc/Heading'); |
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| 213 | if isempty(uid_Heading) |
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| 214 | [t,uid_Heading]=add(t,1,'element','Heading'); |
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| 215 | end |
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| 216 | uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); |
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| 217 | j1=[]; |
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| 218 | if ~isempty(j1_series{1}) |
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| 219 | j1=j1_series{1}; |
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| 220 | end |
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| 221 | ImageName=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1_series{1}(1),[],j1); |
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| 222 | [pth,ImageName]=fileparts(ImageName); |
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| 223 | ImageName=[ImageName '.png']; |
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| 224 | if isempty(uid_ImageName) |
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| 225 | [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); |
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| 226 | end |
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| 227 | uid_value=children(t,uid_ImageName); |
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| 228 | if isempty(uid_value) |
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| 229 | t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension |
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| 230 | else |
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| 231 | t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension |
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| 232 | end |
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| 233 | |
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| 234 | %%%% correction RDvision %%%% |
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| 235 | if isfield(XmlData{1},'NbDtj') |
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| 236 | uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); |
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| 237 | uid_value=children(t,uid_NbDtj); |
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| 238 | if ~isempty(uid_value) |
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| 239 | t=set(t,uid_value(1),'value',num2str(XmlData{1}.NbDtj)); |
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| 240 | end |
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| 241 | end |
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| 242 | if isfield(XmlData{1},'NbDtk') |
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| 243 | uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); |
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| 244 | uid_value=children(t,uid_NbDtk); |
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| 245 | if ~isempty(uid_value) |
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| 246 | t=set(t,uid_value(1),'value',num2str(XmlData{1}.NbDtk)); |
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| 247 | end |
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| 248 | end |
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| 249 | if isempty(j1_series{1}) && isfield(XmlData{1},'NbDti') |
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| 250 | uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti'); |
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| 251 | t=add(t,uid_Dti,'chardata',num2str(XmlData{1}.Dti)); |
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| 252 | uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti'); |
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| 253 | t=add(t,uid_NbDti,'chardata',num2str(XmlData{1}.NbDti)); |
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| 254 | uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj'); |
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| 255 | uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk'); |
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| 256 | t=delete(t,uid_NbDtj); |
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| 257 | t=delete(t,uid_NbDtk); |
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| 258 | uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj'); |
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| 259 | uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk'); |
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| 260 | t=delete(t,uid_Dtj); |
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| 261 | t=delete(t,uid_Dtk); |
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| 262 | NomTypeNew='_1'; |
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| 263 | end |
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| 264 | SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.' |
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| 265 | filexml_new=[fullfile(RootPath{1},SubDirBase) '.xml']; |
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| 266 | save(t,filexml_new) |
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| 267 | end |
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| 268 | |
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| 269 | %% main loop on images |
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| 270 | %j1=[];%default |
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| 271 | nbfield2=size(XmlData{1}.Time,2); |
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| 272 | for ifile=1:nbfield |
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| 273 | if checkrun |
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| 274 | update_waitbar(hseries.Waitbar,ifile/nbfield) |
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| 275 | drawnow |
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| 276 | stopstate=get(hseries.RUN,'BusyAction'); |
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| 277 | else |
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| 278 | stopstate='queue'; |
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| 279 | end |
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| 280 | if isequal(stopstate,'queue') % enable STOP command |
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| 281 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile)); |
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| 282 | j1=mod(ifile-1+first_label,nbfield2)+1; |
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| 283 | i1=floor((ifile-1+first_label)/nbfield2)+1; |
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| 284 | filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomTypeNew,i1,[],j1); |
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| 285 | try |
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| 286 | movefile(filename,filename_new); |
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| 287 | [s,errormsg] = fileattrib(filename_new,'-w','a'); %set images to read only '-w' for all users ('a') |
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| 288 | if ~s |
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| 289 | msgbox_uvmat('ERROR',errormsg); |
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| 290 | return |
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| 291 | end |
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| 292 | catch ME |
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| 293 | msgbox_uvmat('ERROR',ME.message); |
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| 294 | return |
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| 295 | end |
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| 296 | end |
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| 297 | end |
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| 298 | |
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| 299 | %'imadoc2struct_special': reads the xml file for image documentation |
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| 300 | %------------------------------------------------------------------------ |
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| 301 | % function [s,errormsg]=imadoc2struct_special(ImaDoc,option) |
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| 302 | % |
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| 303 | % OUTPUT: |
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| 304 | % s: structure representing ImaDoc |
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| 305 | % s.Heading: information about the data hierarchical structure |
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| 306 | % s.Time: matrix of times |
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| 307 | % s.TimeUnit |
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| 308 | % s.GeometryCalib: substructure containing the parameters for geometric calibration |
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| 309 | % errormsg: error message |
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| 310 | % |
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| 311 | % INPUT: |
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| 312 | % ImaDoc: full name of the xml input file with head key ImaDoc |
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| 313 | % option: ='GeometryCalib': read the data of GeometryCalib, including source point coordinates |
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| 314 | |
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| 315 | function [s,errormsg]=imadoc2struct_special(ImaDoc,option) |
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| 316 | |
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| 317 | %% default input and output |
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| 318 | if ~exist('option','var') |
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| 319 | option='*'; |
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| 320 | end |
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| 321 | errormsg=[];%default |
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| 322 | s.Heading=[];%default |
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| 323 | s.Time=[]; %default |
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| 324 | s.TimeUnit=[]; %default |
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| 325 | s.GeometryCalib=[]; |
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| 326 | tsai=[];%default |
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| 327 | |
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| 328 | %% opening the xml file |
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| 329 | if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist |
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| 330 | try |
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| 331 | t=xmltree(ImaDoc); |
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| 332 | catch |
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| 333 | errormsg={[ImaDoc ' is not a valid xml file']; lasterr}; |
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| 334 | display(errormsg); |
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| 335 | return |
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| 336 | end |
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| 337 | uid_root=find(t,'/ImaDoc'); |
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| 338 | if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file |
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| 339 | |
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| 340 | |
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| 341 | %% Heading |
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| 342 | uid_Heading=find(t,'/ImaDoc/Heading'); |
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| 343 | if ~isempty(uid_Heading), |
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| 344 | uid_Campaign=find(t,'/ImaDoc/Heading/Campaign'); |
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| 345 | uid_Exp=find(t,'/ImaDoc/Heading/Experiment'); |
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| 346 | uid_Device=find(t,'/ImaDoc/Heading/Device'); |
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| 347 | uid_Record=find(t,'/ImaDoc/Heading/Record'); |
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| 348 | uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName'); |
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| 349 | s.Heading.Campaign=get(t,children(t,uid_Campaign),'value'); |
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| 350 | s.Heading.Experiment=get(t,children(t,uid_Exp),'value'); |
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| 351 | s.Heading.Device=get(t,children(t,uid_Device),'value'); |
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| 352 | if ~isempty(uid_Record) |
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| 353 | s.Heading.Record=get(t,children(t,uid_Record),'value'); |
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| 354 | end |
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| 355 | s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value'); |
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| 356 | end |
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| 357 | |
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| 358 | %% Camera and timing |
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| 359 | if strcmp(option,'*') || strcmp(option,'Camera') |
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| 360 | uid_Camera=find(t,'/ImaDoc/Camera'); |
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| 361 | if ~isempty(uid_Camera) |
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| 362 | uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize'); |
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| 363 | if ~isempty(uid_ImageSize); |
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| 364 | ImageSize=get(t,children(t,uid_ImageSize),'value'); |
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| 365 | xindex=findstr(ImageSize,'x'); |
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| 366 | if length(xindex)>=2 |
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| 367 | s.Npx=str2double(ImageSize(1:xindex(1)-1)); |
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| 368 | s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1)); |
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| 369 | end |
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| 370 | end |
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| 371 | uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit'); |
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| 372 | if ~isempty(uid_TimeUnit) |
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| 373 | s.TimeUnit=get(t,children(t,uid_TimeUnit),'value'); |
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| 374 | end |
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| 375 | uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming'); |
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| 376 | if ~isempty(uid_BurstTiming) |
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| 377 | for k=1:length(uid_BurstTiming) |
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| 378 | subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming |
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| 379 | % reading Dtk |
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| 380 | Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1); |
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| 381 | Dtj=get_value(subt,'/BurstTiming/Dtj',[]); |
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| 382 | Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') |
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| 383 | NbDtj=get_value(subt,'/BurstTiming/NbDtj',[]); |
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| 384 | %%%% correction RDvision %%%% |
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| 385 | % NbDtj=NbDtj/numel(Dtj); |
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| 386 | % s.NbDtj=NbDtj; |
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| 387 | % %%%% |
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| 388 | Dti=get_value(subt,'/BurstTiming/Dti',[]); |
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| 389 | NbDti=get_value(subt,'/BurstTiming/NbDti',1); |
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| 390 | %%%% correction RDvision %%%% |
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| 391 | if isempty(Dti)% series |
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| 392 | Dti=Dtj; |
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| 393 | NbDti=NbDtj; |
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| 394 | Dtj=[]; |
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| 395 | s.Dti=Dti; |
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| 396 | s.NbDti=NbDti; |
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| 397 | else |
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| 398 | % NbDtj=NbDtj/numel(Dtj);%bursts |
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| 399 | if ~isempty(NbDtj) |
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| 400 | s.NbDtj=NbDtj/numel(Dtj);%bursts; |
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| 401 | else |
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| 402 | s.NbDtj=1; |
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| 403 | end |
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| 404 | end |
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| 405 | %%%% %%%% |
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| 406 | Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's') |
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| 407 | |
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| 408 | Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit |
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| 409 | if ~isempty(Dti) |
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| 410 | Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times |
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| 411 | Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti |
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| 412 | end |
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| 413 | if ~isempty(Dtj) |
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| 414 | Dtj=reshape(Dtj'*ones(1,s.NbDtj),1,s.NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times |
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| 415 | Dtj=[0 Dtj]; |
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| 416 | Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj |
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| 417 | end |
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| 418 | % reading Dtk |
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| 419 | Dtk=get_value(subt,'/BurstTiming/Dtk',[]); |
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| 420 | NbDtk=get_value(subt,'/BurstTiming/NbDtk',1); |
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| 421 | %%%% correction RDvision %%%% |
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| 422 | if ~isequal(NbDtk,1) |
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| 423 | NbDtk=-1+(NbDtk+1)/(NbDti+1); |
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| 424 | end |
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| 425 | s.NbDtk=NbDtk; |
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| 426 | %%%%% |
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| 427 | if isempty(Dtk) |
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| 428 | s.Time=[s.Time;Time_val]; |
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| 429 | else |
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| 430 | for kblock=1:NbDtk+1 |
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| 431 | Time_val_k=Time_val+(kblock-1)*Dtk; |
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| 432 | s.Time=[s.Time;Time_val_k]; |
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| 433 | end |
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| 434 | end |
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| 435 | end |
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| 436 | end |
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| 437 | end |
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| 438 | end |
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| 439 | |
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| 440 | %% motor |
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| 441 | if strcmp(option,'*') || strcmp(option,'GeometryCalib') |
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| 442 | uid_subtree=find(t,'/ImaDoc/TranslationMotor'); |
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| 443 | if length(uid_subtree)==1 |
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| 444 | subt=branch(t,uid_subtree);%subtree under GeometryCalib |
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| 445 | [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]); |
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| 446 | end |
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| 447 | end |
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| 448 | %% geometric calibration |
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| 449 | if strcmp(option,'*') || strcmp(option,'GeometryCalib') |
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| 450 | uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib'); |
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| 451 | if ~isempty(uid_GeometryCalib) |
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| 452 | if length(uid_GeometryCalib)>1 |
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| 453 | errormsg=['More than one GeometryCalib in ' filecivxml]; |
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| 454 | return |
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| 455 | end |
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| 456 | subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib |
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| 457 | cont=get(subt,1,'contents'); |
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| 458 | if ~isempty(cont) |
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| 459 | uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType'); |
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| 460 | if isequal(length(uid_CalibrationType),1) |
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| 461 | tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value'); |
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| 462 | end |
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| 463 | uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit'); |
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| 464 | if isequal(length(uid_CoordUnit),1) |
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| 465 | tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value'); |
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| 466 | end |
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| 467 | uid_fx_fy=find(subt,'/GeometryCalib/fx_fy'); |
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| 468 | focal=[];%default fro old convention (Reg Wilson) |
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| 469 | if isequal(length(uid_fx_fy),1) |
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| 470 | tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value')); |
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| 471 | else %old convention (Reg Wilson) |
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| 472 | uid_focal=find(subt,'/GeometryCalib/focal'); |
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| 473 | uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy'); |
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| 474 | uid_sx=find(subt,'/GeometryCalib/sx'); |
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| 475 | if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx) |
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| 476 | dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value')); |
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| 477 | sx=str2num(get(subt,children(subt,uid_sx),'value')); |
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| 478 | focal=str2num(get(subt,children(subt,uid_focal),'value')); |
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| 479 | tsai.fx_fy(1)=sx*focal/dpx_dpy(1); |
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| 480 | tsai.fx_fy(2)=focal/dpx_dpy(2); |
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| 481 | end |
---|
| 482 | end |
---|
| 483 | uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy'); |
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| 484 | if ~isempty(uid_Cx_Cy) |
---|
| 485 | tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value')); |
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| 486 | end |
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| 487 | uid_kc=find(subt,'/GeometryCalib/kc'); |
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| 488 | if ~isempty(uid_kc) |
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| 489 | tsai.kc=str2double(get(subt,children(subt,uid_kc),'value')); |
---|
| 490 | else %old convention (Reg Wilson) |
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| 491 | uid_kappa1=find(subt,'/GeometryCalib/kappa1'); |
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| 492 | if ~isempty(uid_kappa1)&& ~isempty(focal) |
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| 493 | kappa1=str2double(get(subt,children(subt,uid_kappa1),'value')); |
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| 494 | tsai.kc=-kappa1*focal*focal; |
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| 495 | end |
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| 496 | end |
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| 497 | uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz'); |
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| 498 | if ~isempty(uid_Tx_Ty_Tz) |
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| 499 | tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value')); |
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| 500 | end |
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| 501 | uid_R=find(subt,'/GeometryCalib/R'); |
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| 502 | if ~isempty(uid_R) |
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| 503 | RR=get(subt,children(subt,uid_R),'value'); |
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| 504 | if length(RR)==3 |
---|
| 505 | tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})]; |
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| 506 | end |
---|
| 507 | end |
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| 508 | |
---|
| 509 | %look for laser plane definitions |
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| 510 | uid_Angle=find(subt,'/GeometryCalib/PlaneAngle'); |
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| 511 | uid_Pos=find(subt,'/GeometryCalib/SliceCoord'); |
---|
| 512 | if isempty(uid_Pos) |
---|
| 513 | uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention |
---|
| 514 | end |
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| 515 | if ~isempty(uid_Angle) |
---|
| 516 | tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value')); |
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| 517 | end |
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| 518 | if ~isempty(uid_Pos) |
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| 519 | for j=1:length(uid_Pos) |
---|
| 520 | tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value')); |
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| 521 | end |
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| 522 | uid_DZ=find(subt,'/GeometryCalib/SliceDZ'); |
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| 523 | uid_NbSlice=find(subt,'/GeometryCalib/NbSlice'); |
---|
| 524 | if ~isempty(uid_DZ) && ~isempty(uid_NbSlice) |
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| 525 | DZ=str2double(get(subt,children(subt,uid_DZ),'value')); |
---|
| 526 | NbSlice=get(subt,children(subt,uid_NbSlice),'value'); |
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| 527 | if isequal(NbSlice,'volume') |
---|
| 528 | tsai.NbSlice='volume'; |
---|
| 529 | NbSlice=NbDtj+1; |
---|
| 530 | else |
---|
| 531 | tsai.NbSlice=str2double(NbSlice); |
---|
| 532 | end |
---|
| 533 | tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1]; |
---|
| 534 | end |
---|
| 535 | end |
---|
| 536 | tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]); |
---|
| 537 | tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n'); |
---|
| 538 | tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]); |
---|
| 539 | tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1); |
---|
| 540 | |
---|
| 541 | if strcmp(option,'GeometryCalib') |
---|
| 542 | tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]); |
---|
| 543 | end |
---|
| 544 | s.GeometryCalib=tsai; |
---|
| 545 | end |
---|
| 546 | end |
---|
| 547 | end |
---|
| 548 | |
---|
| 549 | %-------------------------------------------------- |
---|
| 550 | % read a subtree |
---|
| 551 | % INPUT: |
---|
| 552 | % t: xltree |
---|
| 553 | % head_element: head elelemnt of the subtree |
---|
| 554 | % Data, structure containing |
---|
| 555 | % .Key: element name |
---|
| 556 | % .Type: type of element ('charg', 'float'....) |
---|
| 557 | % .NbOccur: nbre of occurrence, NaN for un specified number |
---|
| 558 | function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest) |
---|
| 559 | %-------------------------------------------------- |
---|
| 560 | s=[];%default |
---|
| 561 | errormsg=''; |
---|
| 562 | head_element=get(subt,1,'name'); |
---|
| 563 | cont=get(subt,1,'contents'); |
---|
| 564 | if ~isempty(cont) |
---|
| 565 | for ilist=1:length(Data) |
---|
| 566 | uid_key=find(subt,[head_element '/' Data{ilist}]); |
---|
| 567 | if ~isequal(length(uid_key),NbOccur(ilist)) |
---|
| 568 | errormsg=['wrong number of occurence for ' Data{ilist}]; |
---|
| 569 | return |
---|
| 570 | end |
---|
| 571 | for ival=1:length(uid_key) |
---|
| 572 | val=get(subt,children(subt,uid_key(ival)),'value'); |
---|
| 573 | if ~NumTest(ilist) |
---|
| 574 | eval(['s.' Data{ilist} '=val;']); |
---|
| 575 | else |
---|
| 576 | eval(['s.' Data{ilist} '=str2double(val);']) |
---|
| 577 | end |
---|
| 578 | end |
---|
| 579 | end |
---|
| 580 | end |
---|
| 581 | |
---|
| 582 | |
---|
| 583 | %-------------------------------------------------- |
---|
| 584 | % read an xml element |
---|
| 585 | function val=get_value(t,label,default) |
---|
| 586 | %-------------------------------------------------- |
---|
| 587 | val=default; |
---|
| 588 | uid=find(t,label);%find the element iud(s) |
---|
| 589 | if ~isempty(uid) %if the element named label exists |
---|
| 590 | uid_child=children(t,uid);%find the children |
---|
| 591 | if ~isempty(uid_child) |
---|
| 592 | data=get(t,uid_child,'type');%get the type of child |
---|
| 593 | if iscell(data)% case of multiple element |
---|
| 594 | for icell=1:numel(data) |
---|
| 595 | val_read=str2num(get(t,uid_child(icell),'value')); |
---|
| 596 | if ~isempty(val_read) |
---|
| 597 | val(icell,:)=val_read; |
---|
| 598 | end |
---|
| 599 | end |
---|
| 600 | % val=val'; |
---|
| 601 | else % case of unique element value |
---|
| 602 | val_read=str2num(get(t,uid_child,'value')); |
---|
| 603 | if ~isempty(val_read) |
---|
| 604 | val=val_read; |
---|
| 605 | else |
---|
| 606 | val=get(t,uid_child,'value');%char string data |
---|
| 607 | end |
---|
| 608 | end |
---|
| 609 | end |
---|
| 610 | end |
---|