[245] | 1 | %'relabel_i_j': relabel an image series with two indices, and correct errors from the RDvision transfer program
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[457] | 2 | %------------------------------------------------------------------------
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| 3 | % function GUI_config=relabel_i_j(Param)
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| 4 | %------------------------------------------------------------------------
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[40] | 5 |
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[457] | 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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[214] | 47 |
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[457] | 48 | function GUI_config=relabel_i_j(Param)
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[40] | 49 |
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[457] | 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 | GUI_config={'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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[245] | 63 | return
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[216] | 64 | end
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[40] | 65 |
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[457] | 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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[245] | 73 | else
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[457] | 74 | hseries=guidata(Param.hseries);%handles of the GUI series
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[462] | 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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[245] | 80 | end
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[462] | 81 | ParamOut=Param; %default output
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[457] | 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 | % filecell{iview,fileindex}: cell array representing the list of file names
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| 94 | % iview: line in the table corresponding to a given file series
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| 95 | % fileindex: file index within the file series,
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| 96 | % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
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| 97 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
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| 98 | % set of frame indices used for movie or multimage input
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| 99 | % numbers of slices and file indices
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| 100 |
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| 101 | NbSlice=1;%default
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| 102 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
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| 103 | NbSlice=Param.IndexRange.NbSlice;
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[245] | 104 | end
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[457] | 105 | nbview=numel(i1_series);%number of input file series (lines in InputTable)
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| 106 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
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| 107 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index
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| 108 | nbfield=nbfield_j*nbfield_i; %total number of fields
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| 109 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices)
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| 110 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
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[214] | 111 |
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[457] | 112 | %determine the file type on each line from the first input file
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| 113 | ImageTypeOptions={'image','multimage','mmreader','video'};
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| 114 | NcTypeOptions={'netcdf','civx','civdata'};
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| 115 | for iview=1:nbview
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| 116 | if ~exist(filecell{iview,1}','file')
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| 117 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
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[249] | 118 | return
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[214] | 119 | end
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[457] | 120 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
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| 121 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
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| 122 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
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| 123 | if ~isempty(j1_series{iview})
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| 124 | frame_index{iview}=j1_series{iview};
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[40] | 125 | else
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[457] | 126 | frame_index{iview}=i1_series{iview};
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[214] | 127 | end
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[457] | 128 | end
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| 129 |
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| 130 | %% calibration data and timing: read the ImaDoc files
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| 131 | mode=''; %default
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| 132 | timecell={};
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| 133 | itime=0;
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| 134 | NbSlice_calib={};
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| 135 | XmlData=cell(1,nbview);%initiate the structures containing the data from the xml file (calibration and timing)
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| 136 | for iview=1:nbview%Loop on views
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| 137 | SubDirBase=regexprep(SubDir{iview},'\..*','');%take the root part of SubDir, before the first dot '.'
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| 138 | filexml=[fullfile(RootPath{iview},SubDirBase) '.xml'];%new convention: xml at the level of the image folder
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| 139 | if ~exist(filexml,'file')
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| 140 | filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.xml']; % old convention: xml inside the image folder
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| 141 | if ~exist(filexml,'file')
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| 142 | filexml=[fullfile(RootPath{iview},SubDir{iview},RootFile{iview}) '.civ']; % very old convention: .civ file
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| 143 | if ~exist(filexml,'file')
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| 144 | filexml='';
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| 145 | end
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[249] | 146 | end
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[223] | 147 | end
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[457] | 148 | if ~isempty(filexml)
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| 149 | [XmlData{iview},error]=imadoc2struct_special(filexml);
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| 150 | end
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| 151 | if isfield(XmlData{iview},'Time')
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| 152 | itime=itime+1;
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| 153 | timecell{itime}=XmlData{iview}.Time;
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| 154 | end
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| 155 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord')
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| 156 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform
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| 157 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1})
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| 158 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series');
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[249] | 159 | end
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[223] | 160 | end
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[457] | 161 | end
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| 162 |
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| 163 | %% check coincidence in time for several input file series
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| 164 | % not relevant
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| 165 |
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| 166 | %% coordinate transform or other user defined transform
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| 167 | %not relevant
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| 168 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%%
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| 169 | % EDIT FROM HERE
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| 170 |
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| 171 | %% check the validity of input file types
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| 172 | if CheckImage{1}
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| 173 | FileExtOut='.png'; % write result as .png images for image inputs
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| 174 | elseif CheckNc{1}
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| 175 | FileExtOut='.nc';% write result as .nc files for netcdf inputs
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| 176 | else
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| 177 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
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| 178 | return
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| 179 | end
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| 180 | if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
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| 181 | msgbox_uvmat('ERROR','input must be two image series or two netcdf file series')
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| 182 | return
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| 183 | end
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| 184 | NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
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| 185 | if NbSlice~=nbfield_j
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| 186 | 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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| 187 | if ~strcmp(answer,'Yes')
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| 188 | return
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[245] | 189 | end
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[40] | 190 | end
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| 191 |
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[457] | 192 | %% Set field names and velocity types
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| 193 | % not relevant here
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[245] | 194 |
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[457] | 195 | %% Initiate output fields
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| 196 | % not relevant here
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| 197 |
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| 198 | %% interactive input of specific parameters (for RDvision system)
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| 199 | display('RDvision system')
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| 200 | first_label=0; %image numbers start from 0
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| 201 | if ~strcmp(NomType{1},'_000001')
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| 202 | 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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| 203 | return
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| 204 | else
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| 205 | 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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| 206 | if ~strcmp(answer,'Yes')
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| 207 | return
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| 208 | end
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| 209 | end
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| 210 |
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| 211 | %% read imadoc
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| 212 | % RootPath=get(hseries.RootPath,'String');
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| 213 | % RootFile=get(hseries.RootFile,'String');
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| 214 | % if ~iscell(RootFile)
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| 215 | % msgbox_uvmat('ERROR','please enter an input image series from RDVision system')%error message for xml file reading
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| 216 | % return
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| 217 | % end
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| 218 | % basename=fullfile(RootPath{1},RootFile{1});
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| 219 | % [XmlData,warntext]=imadoc2struct_special([basename '.xml']);% read the xml file appended to the present function (containing bug corrections)
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| 220 | % if ~isempty(warntext)
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| 221 | % msgbox_uvmat('ERROR',warntext)%error message for xml file reading
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| 222 | % end
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| 223 | % nbfield1=size(XmlData.Time,1);
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| 224 | % nbfield2=size(XmlData.Time,2);
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| 225 | % set(hseries.first_i,'String',num2str(first_label))% display the first image in the process
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| 226 | % set(hseries.last_i,'String',num2str(nbfield1*nbfield2-1+first_label))% display the last image in the process
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| 227 | % set(hseries.nb_field,'String',{num2str(nbfield1*nbfield2-1+first_label)})% display the total nbre of images
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| 228 | % SeriesData=get(hGUI,'UserData');
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| 229 |
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| 230 |
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| 231 | %% stop program there when it is selected in the menu (no run action)
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| 232 | % if ~exist('num_i1','var')
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| 233 | % return
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| 234 | % end
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| 235 | % if nbfield2>=2
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| 236 | % answer=msgbox_uvmat('',[num2str(nbfield1) ' bursts containing ' num2str(nbfield2) ' images each']);%error message for directory creation
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| 237 | % nomtype='_i_j';
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| 238 | % else
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| 239 | % answer=msgbox_uvmat('',['image series with ' num2str(nbfield1) ' images']);%error message for directory creation
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| 240 | % nomtype='_i';
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| 241 | % end
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| 242 | % if ~strcmp(answer,'Yes')
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| 243 | % return
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| 244 | % end
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| 245 |
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| 246 | %% copy and adapt the xml file
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| 247 | if ~isempty(XmlData{1})
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| 248 |
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| 249 | % if exist([basename '.xml'],'file')
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| 250 | % try
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| 251 | % copyfile([basename '.xml'],[basename '.xml~']);% backup the xml file
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| 252 | % catch ME
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| 253 | % msgbox_uvmat('ERROR',ME.message);
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| 254 | % return
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| 255 | % end
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| 256 | % filexml=[filebase{1} '.xml']
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| 257 | t=xmltree(filexml);
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| 258 |
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| 259 | %update information on the first image name in the series
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| 260 | uid_Heading=find(t,'ImaDoc/Heading');
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| 261 | if isempty(uid_Heading)
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| 262 | [t,uid_Heading]=add(t,1,'element','Heading');
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| 263 | end
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| 264 | uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
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| 265 | j1=[];
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| 266 | if ~isempty(j1_series{1})
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| 267 | j1=j1_series{1};
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| 268 | end
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| 269 | ImageName=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1_series{1}(1),[],j);
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| 270 | % ImageName=name_generator(basename,1,1,'.png','_i_j');
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| 271 | [pth,ImageName]=fileparts(ImageName);
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| 272 | ImageName=[ImageName '.png'];
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| 273 | if isempty(uid_ImageName)
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| 274 | [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
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| 275 | end
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| 276 | uid_value=children(t,uid_ImageName);
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| 277 | if isempty(uid_value)
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| 278 | t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension
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| 279 | else
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| 280 | t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension
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| 281 | end
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| 282 |
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| 283 | %%%% correction RDvision %%%%
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| 284 | if isfield(XmlData,'NbDtj')
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| 285 | uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
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| 286 | uid_value=children(t,uid_NbDtj);
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| 287 | if ~isempty(uid_value)
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| 288 | t=set(t,uid_value(1),'value',num2str(XmlData.NbDtj));
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| 289 | end
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| 290 | end
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| 291 | if isfield(XmlData,'NbDtk')
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| 292 | uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
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| 293 | uid_value=children(t,uid_NbDtk);
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| 294 | if ~isempty(uid_value)
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| 295 | t=set(t,uid_value(1),'value',num2str(XmlData.NbDtk));
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| 296 | end
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| 297 | end
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| 298 | if isempty(j1_series{1}) && isfield(XmlData,'NbDti')
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| 299 | uid_Dti=find(t,'ImaDoc/Camera/BurstTiming/Dti');
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| 300 | t=add(t,uid_Dti,'chardata',num2str(XmlData.Dti));
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| 301 | uid_NbDti=find(t,'ImaDoc/Camera/BurstTiming/NbDti');
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| 302 | t=add(t,uid_NbDti,'chardata',num2str(XmlData.NbDti));
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| 303 | uid_NbDtj=find(t,'ImaDoc/Camera/BurstTiming/NbDtj');
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| 304 | uid_NbDtk=find(t,'ImaDoc/Camera/BurstTiming/NbDtk');
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| 305 | t=delete(t,uid_NbDtj);
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| 306 | t=delete(t,uid_NbDtk);
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| 307 | uid_Dtj=find(t,'ImaDoc/Camera/BurstTiming/Dtj');
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| 308 | uid_Dtk=find(t,'ImaDoc/Camera/BurstTiming/Dtk');
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| 309 | t=delete(t,uid_Dtj);
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| 310 | t=delete(t,uid_Dtk);
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| 311 | end
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| 312 | SubDirBase=regexprep(SubDir{1},'\..*','');%take the root part of SubDir, before the first dot '.'
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| 313 | filexml_new=[fullfile(RootPath{1},SubDirBase) '.xml'];
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| 314 | save(t,filexml_new)
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| 315 | % end
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| 316 | end
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| 317 |
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| 318 | %% main loop on images
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| 319 | %j1=[];%default
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| 320 | nbfield2=size(XmlData{1}.Time,2);
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| 321 | for ifile=1:nbfield
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| 322 | if checkrun
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[478] | 323 | update_waitbar(hseries.Waitbar,ifile/nbfield)
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[457] | 324 | stopstate=get(hseries.RUN,'BusyAction');
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| 325 | else
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| 326 | stopstate='queue';
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| 327 | end
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| 328 | if isequal(stopstate,'queue') % enable STOP command
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| 329 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile));
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| 330 | j1=mod(ifile-1+first_label,nbfield2)+1;
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| 331 | i1=floor((ifile-1+first_label)/nbfield2)+1;
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| 332 | % filename_new=name_generator(basename,num_i,num_j,'.png',nomtype);
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| 333 | filename_new=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},'_1_1',i1,[],j1);
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| 334 | try
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| 335 | movefile(filename,filename_new);
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| 336 | [s,errormsg] = fileattrib(filename_new,'-w','a'); %set images to read only '-w' for all users ('a')
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| 337 | if ~s
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| 338 | msgbox_uvmat('ERROR',errormsg);
|
---|
| 339 | return
|
---|
| 340 | end
|
---|
| 341 | catch ME
|
---|
| 342 | msgbox_uvmat('ERROR',ME.message);
|
---|
[214] | 343 | return
|
---|
| 344 | end
|
---|
| 345 | end
|
---|
[40] | 346 | end
|
---|
| 347 |
|
---|
[457] | 348 | %'imadoc2struct_special': reads the xml file for image documentation
|
---|
[214] | 349 | %------------------------------------------------------------------------
|
---|
[457] | 350 | % function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
|
---|
[214] | 351 | %
|
---|
| 352 | % OUTPUT:
|
---|
| 353 | % s: structure representing ImaDoc
|
---|
| 354 | % s.Heading: information about the data hierarchical structure
|
---|
| 355 | % s.Time: matrix of times
|
---|
| 356 | % s.TimeUnit
|
---|
| 357 | % s.GeometryCalib: substructure containing the parameters for geometric calibration
|
---|
| 358 | % errormsg: error message
|
---|
| 359 | %
|
---|
| 360 | % INPUT:
|
---|
| 361 | % ImaDoc: full name of the xml input file with head key ImaDoc
|
---|
| 362 | % option: ='GeometryCalib': read the data of GeometryCalib, including source point coordinates
|
---|
| 363 |
|
---|
[457] | 364 | function [s,errormsg]=imadoc2struct_special(ImaDoc,option)
|
---|
[223] | 365 |
|
---|
[214] | 366 | %% default input and output
|
---|
| 367 | if ~exist('option','var')
|
---|
| 368 | option='*';
|
---|
| 369 | end
|
---|
| 370 | errormsg=[];%default
|
---|
| 371 | s.Heading=[];%default
|
---|
| 372 | s.Time=[]; %default
|
---|
| 373 | s.TimeUnit=[]; %default
|
---|
| 374 | s.GeometryCalib=[];
|
---|
| 375 | tsai=[];%default
|
---|
| 376 |
|
---|
| 377 | %% opening the xml file
|
---|
| 378 | if exist(ImaDoc,'file')~=2, errormsg=[ ImaDoc ' does not exist']; return;end;%input file does not exist
|
---|
| 379 | try
|
---|
| 380 | t=xmltree(ImaDoc);
|
---|
| 381 | catch
|
---|
| 382 | errormsg={[ImaDoc ' is not a valid xml file']; lasterr};
|
---|
| 383 | display(errormsg);
|
---|
| 384 | return
|
---|
| 385 | end
|
---|
| 386 | uid_root=find(t,'/ImaDoc');
|
---|
| 387 | if isempty(uid_root), errormsg=[ImaDoc ' is not an image documentation file ImaDoc']; return; end;%not an ImaDoc .xml file
|
---|
| 388 |
|
---|
| 389 |
|
---|
| 390 | %% Heading
|
---|
| 391 | uid_Heading=find(t,'/ImaDoc/Heading');
|
---|
| 392 | if ~isempty(uid_Heading),
|
---|
| 393 | uid_Campaign=find(t,'/ImaDoc/Heading/Campaign');
|
---|
| 394 | uid_Exp=find(t,'/ImaDoc/Heading/Experiment');
|
---|
| 395 | uid_Device=find(t,'/ImaDoc/Heading/Device');
|
---|
| 396 | uid_Record=find(t,'/ImaDoc/Heading/Record');
|
---|
| 397 | uid_FirstImage=find(t,'/ImaDoc/Heading/ImageName');
|
---|
| 398 | s.Heading.Campaign=get(t,children(t,uid_Campaign),'value');
|
---|
| 399 | s.Heading.Experiment=get(t,children(t,uid_Exp),'value');
|
---|
| 400 | s.Heading.Device=get(t,children(t,uid_Device),'value');
|
---|
| 401 | if ~isempty(uid_Record)
|
---|
| 402 | s.Heading.Record=get(t,children(t,uid_Record),'value');
|
---|
| 403 | end
|
---|
| 404 | s.Heading.ImageName=get(t,children(t,uid_FirstImage),'value');
|
---|
| 405 | end
|
---|
| 406 |
|
---|
| 407 | %% Camera and timing
|
---|
| 408 | if strcmp(option,'*') || strcmp(option,'Camera')
|
---|
| 409 | uid_Camera=find(t,'/ImaDoc/Camera');
|
---|
| 410 | if ~isempty(uid_Camera)
|
---|
| 411 | uid_ImageSize=find(t,'/ImaDoc/Camera/ImageSize');
|
---|
| 412 | if ~isempty(uid_ImageSize);
|
---|
| 413 | ImageSize=get(t,children(t,uid_ImageSize),'value');
|
---|
| 414 | xindex=findstr(ImageSize,'x');
|
---|
| 415 | if length(xindex)>=2
|
---|
| 416 | s.Npx=str2double(ImageSize(1:xindex(1)-1));
|
---|
| 417 | s.Npy=str2double(ImageSize(xindex(1)+1:xindex(2)-1));
|
---|
| 418 | end
|
---|
| 419 | end
|
---|
| 420 | uid_TimeUnit=find(t,'/ImaDoc/Camera/TimeUnit');
|
---|
| 421 | if ~isempty(uid_TimeUnit)
|
---|
| 422 | s.TimeUnit=get(t,children(t,uid_TimeUnit),'value');
|
---|
| 423 | end
|
---|
| 424 | uid_BurstTiming=find(t,'/ImaDoc/Camera/BurstTiming');
|
---|
| 425 | if ~isempty(uid_BurstTiming)
|
---|
| 426 | for k=1:length(uid_BurstTiming)
|
---|
| 427 | subt=branch(t,uid_BurstTiming(k));%subtree under BurstTiming
|
---|
| 428 | % reading Dtk
|
---|
| 429 | Frequency=get_value(subt,'/BurstTiming/FrameFrequency',1);
|
---|
| 430 | Dtj=get_value(subt,'/BurstTiming/Dtj',[]);
|
---|
| 431 | Dtj=Dtj/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
|
---|
| 432 | NbDtj=get_value(subt,'/BurstTiming/NbDtj',1);
|
---|
| 433 | %%%% correction RDvision %%%%
|
---|
[245] | 434 | % NbDtj=NbDtj/numel(Dtj);
|
---|
| 435 | % s.NbDtj=NbDtj;
|
---|
| 436 | % %%%%
|
---|
[249] | 437 | Dti=get_value(subt,'/BurstTiming/Dti',[]);
|
---|
| 438 | NbDti=get_value(subt,'/BurstTiming/NbDti',1);
|
---|
[245] | 439 | %%%% correction RDvision %%%%
|
---|
| 440 | if isempty(Dti)% series
|
---|
[249] | 441 | Dti=Dtj;
|
---|
| 442 | NbDti=NbDtj;
|
---|
[245] | 443 | Dtj=[];
|
---|
| 444 | s.Dti=Dti;
|
---|
| 445 | else
|
---|
[457] | 446 | % NbDtj=NbDtj/numel(Dtj);%bursts
|
---|
[245] | 447 | s.NbDtj=NbDtj;
|
---|
| 448 | end
|
---|
| 449 | %%%% %%%%
|
---|
[214] | 450 | Dti=Dti/Frequency;%Dtj converted from frame unit to TimeUnit (e.g. 's')
|
---|
[245] | 451 |
|
---|
[214] | 452 | Time_val=get_value(subt,'/BurstTiming/Time',0);%time in TimeUnit
|
---|
| 453 | if ~isempty(Dti)
|
---|
| 454 | Dti=reshape(Dti'*ones(1,NbDti),NbDti*numel(Dti),1); %concatene Dti vector NbDti times
|
---|
| 455 | Time_val=[Time_val;Time_val(end)+cumsum(Dti)];%append the times defined by the intervals Dti
|
---|
| 456 | end
|
---|
| 457 | if ~isempty(Dtj)
|
---|
| 458 | Dtj=reshape(Dtj'*ones(1,NbDtj),1,NbDtj*numel(Dtj)); %concatene Dtj vector NbDtj times
|
---|
| 459 | Dtj=[0 Dtj];
|
---|
| 460 | Time_val=Time_val*ones(1,numel(Dtj))+ones(numel(Time_val),1)*cumsum(Dtj);% produce a time matrix with Dtj
|
---|
| 461 | end
|
---|
| 462 | % reading Dtk
|
---|
| 463 | Dtk=get_value(subt,'/BurstTiming/Dtk',[]);
|
---|
| 464 | NbDtk=get_value(subt,'/BurstTiming/NbDtk',1);
|
---|
| 465 | %%%% correction RDvision %%%%
|
---|
[223] | 466 | if ~isequal(NbDtk,1)
|
---|
| 467 | NbDtk=-1+(NbDtk+1)/(NbDti+1);
|
---|
| 468 | end
|
---|
[214] | 469 | s.NbDtk=NbDtk;
|
---|
| 470 | %%%%%
|
---|
| 471 | if isempty(Dtk)
|
---|
| 472 | s.Time=[s.Time;Time_val];
|
---|
| 473 | else
|
---|
| 474 | for kblock=1:NbDtk+1
|
---|
| 475 | Time_val_k=Time_val+(kblock-1)*Dtk;
|
---|
| 476 | s.Time=[s.Time;Time_val_k];
|
---|
| 477 | end
|
---|
| 478 | end
|
---|
| 479 | end
|
---|
| 480 | end
|
---|
| 481 | end
|
---|
| 482 | end
|
---|
| 483 |
|
---|
| 484 | %% motor
|
---|
| 485 | if strcmp(option,'*') || strcmp(option,'GeometryCalib')
|
---|
| 486 | uid_subtree=find(t,'/ImaDoc/TranslationMotor');
|
---|
| 487 | if length(uid_subtree)==1
|
---|
| 488 | subt=branch(t,uid_subtree);%subtree under GeometryCalib
|
---|
| 489 | [s.TranslationMotor,errormsg]=read_subtree(subt,{'Nbslice','ZStart','ZEnd'},[1 1 1],[1 1 1]);
|
---|
| 490 | end
|
---|
| 491 | end
|
---|
| 492 | %% geometric calibration
|
---|
| 493 | if strcmp(option,'*') || strcmp(option,'GeometryCalib')
|
---|
| 494 | uid_GeometryCalib=find(t,'/ImaDoc/GeometryCalib');
|
---|
| 495 | if ~isempty(uid_GeometryCalib)
|
---|
| 496 | if length(uid_GeometryCalib)>1
|
---|
| 497 | errormsg=['More than one GeometryCalib in ' filecivxml];
|
---|
| 498 | return
|
---|
| 499 | end
|
---|
| 500 | subt=branch(t,uid_GeometryCalib);%subtree under GeometryCalib
|
---|
| 501 | cont=get(subt,1,'contents');
|
---|
| 502 | if ~isempty(cont)
|
---|
| 503 | uid_CalibrationType=find(subt,'/GeometryCalib/CalibrationType');
|
---|
| 504 | if isequal(length(uid_CalibrationType),1)
|
---|
| 505 | tsai.CalibrationType=get(subt,children(subt,uid_CalibrationType),'value');
|
---|
| 506 | end
|
---|
| 507 | uid_CoordUnit=find(subt,'/GeometryCalib/CoordUnit');
|
---|
| 508 | if isequal(length(uid_CoordUnit),1)
|
---|
| 509 | tsai.CoordUnit=get(subt,children(subt,uid_CoordUnit),'value');
|
---|
| 510 | end
|
---|
| 511 | uid_fx_fy=find(subt,'/GeometryCalib/fx_fy');
|
---|
| 512 | focal=[];%default fro old convention (Reg Wilson)
|
---|
| 513 | if isequal(length(uid_fx_fy),1)
|
---|
| 514 | tsai.fx_fy=str2num(get(subt,children(subt,uid_fx_fy),'value'));
|
---|
| 515 | else %old convention (Reg Wilson)
|
---|
| 516 | uid_focal=find(subt,'/GeometryCalib/focal');
|
---|
| 517 | uid_dpx_dpy=find(subt,'/GeometryCalib/dpx_dpy');
|
---|
| 518 | uid_sx=find(subt,'/GeometryCalib/sx');
|
---|
| 519 | if ~isempty(uid_focal) && ~isempty(uid_dpx_dpy) && ~isempty(uid_sx)
|
---|
| 520 | dpx_dpy=str2num(get(subt,children(subt,uid_dpx_dpy),'value'));
|
---|
| 521 | sx=str2num(get(subt,children(subt,uid_sx),'value'));
|
---|
| 522 | focal=str2num(get(subt,children(subt,uid_focal),'value'));
|
---|
| 523 | tsai.fx_fy(1)=sx*focal/dpx_dpy(1);
|
---|
| 524 | tsai.fx_fy(2)=focal/dpx_dpy(2);
|
---|
| 525 | end
|
---|
| 526 | end
|
---|
| 527 | uid_Cx_Cy=find(subt,'/GeometryCalib/Cx_Cy');
|
---|
| 528 | if ~isempty(uid_Cx_Cy)
|
---|
| 529 | tsai.Cx_Cy=str2num(get(subt,children(subt,uid_Cx_Cy),'value'));
|
---|
| 530 | end
|
---|
| 531 | uid_kc=find(subt,'/GeometryCalib/kc');
|
---|
| 532 | if ~isempty(uid_kc)
|
---|
| 533 | tsai.kc=str2double(get(subt,children(subt,uid_kc),'value'));
|
---|
| 534 | else %old convention (Reg Wilson)
|
---|
| 535 | uid_kappa1=find(subt,'/GeometryCalib/kappa1');
|
---|
| 536 | if ~isempty(uid_kappa1)&& ~isempty(focal)
|
---|
| 537 | kappa1=str2double(get(subt,children(subt,uid_kappa1),'value'));
|
---|
| 538 | tsai.kc=-kappa1*focal*focal;
|
---|
| 539 | end
|
---|
| 540 | end
|
---|
| 541 | uid_Tx_Ty_Tz=find(subt,'/GeometryCalib/Tx_Ty_Tz');
|
---|
| 542 | if ~isempty(uid_Tx_Ty_Tz)
|
---|
| 543 | tsai.Tx_Ty_Tz=str2num(get(subt,children(subt,uid_Tx_Ty_Tz),'value'));
|
---|
| 544 | end
|
---|
| 545 | uid_R=find(subt,'/GeometryCalib/R');
|
---|
| 546 | if ~isempty(uid_R)
|
---|
| 547 | RR=get(subt,children(subt,uid_R),'value');
|
---|
| 548 | if length(RR)==3
|
---|
| 549 | tsai.R=[str2num(RR{1});str2num(RR{2});str2num(RR{3})];
|
---|
| 550 | end
|
---|
| 551 | end
|
---|
| 552 |
|
---|
| 553 | %look for laser plane definitions
|
---|
| 554 | uid_Angle=find(subt,'/GeometryCalib/PlaneAngle');
|
---|
| 555 | uid_Pos=find(subt,'/GeometryCalib/SliceCoord');
|
---|
| 556 | if isempty(uid_Pos)
|
---|
| 557 | uid_Pos=find(subt,'/GeometryCalib/PlanePos');%old convention
|
---|
| 558 | end
|
---|
| 559 | if ~isempty(uid_Angle)
|
---|
| 560 | tsai.PlaneAngle=str2num(get(subt,children(subt,uid_Angle),'value'));
|
---|
| 561 | end
|
---|
| 562 | if ~isempty(uid_Pos)
|
---|
| 563 | for j=1:length(uid_Pos)
|
---|
| 564 | tsai.SliceCoord(j,:)=str2num(get(subt,children(subt,uid_Pos(j)),'value'));
|
---|
| 565 | end
|
---|
| 566 | uid_DZ=find(subt,'/GeometryCalib/SliceDZ');
|
---|
| 567 | uid_NbSlice=find(subt,'/GeometryCalib/NbSlice');
|
---|
| 568 | if ~isempty(uid_DZ) && ~isempty(uid_NbSlice)
|
---|
| 569 | DZ=str2double(get(subt,children(subt,uid_DZ),'value'));
|
---|
| 570 | NbSlice=get(subt,children(subt,uid_NbSlice),'value');
|
---|
| 571 | if isequal(NbSlice,'volume')
|
---|
| 572 | tsai.NbSlice='volume';
|
---|
| 573 | NbSlice=NbDtj+1;
|
---|
| 574 | else
|
---|
| 575 | tsai.NbSlice=str2double(NbSlice);
|
---|
| 576 | end
|
---|
| 577 | tsai.SliceCoord=ones(NbSlice,1)*tsai.SliceCoord+DZ*(0:NbSlice-1)'*[0 0 1];
|
---|
| 578 | end
|
---|
| 579 | end
|
---|
| 580 | tsai.SliceAngle=get_value(subt,'/GeometryCalib/SliceAngle',[0 0 0]);
|
---|
| 581 | tsai.VolumeScan=get_value(subt,'/GeometryCalib/VolumeScan','n');
|
---|
| 582 | tsai.InterfaceCoord=get_value(subt,'/GeometryCalib/InterfaceCoord',[0 0 0]);
|
---|
| 583 | tsai.RefractionIndex=get_value(subt,'/GeometryCalib/RefractionIndex',1);
|
---|
| 584 |
|
---|
| 585 | if strcmp(option,'GeometryCalib')
|
---|
| 586 | tsai.PointCoord=get_value(subt,'/GeometryCalib/SourceCalib/PointCoord',[0 0 0 0 0]);
|
---|
| 587 | end
|
---|
| 588 | s.GeometryCalib=tsai;
|
---|
| 589 | end
|
---|
| 590 | end
|
---|
| 591 | end
|
---|
| 592 |
|
---|
| 593 | %--------------------------------------------------
|
---|
| 594 | % read a subtree
|
---|
| 595 | % INPUT:
|
---|
| 596 | % t: xltree
|
---|
| 597 | % head_element: head elelemnt of the subtree
|
---|
| 598 | % Data, structure containing
|
---|
| 599 | % .Key: element name
|
---|
| 600 | % .Type: type of element ('charg', 'float'....)
|
---|
| 601 | % .NbOccur: nbre of occurrence, NaN for un specified number
|
---|
| 602 | function [s,errormsg]=read_subtree(subt,Data,NbOccur,NumTest)
|
---|
| 603 | %--------------------------------------------------
|
---|
| 604 | s=[];%default
|
---|
| 605 | errormsg='';
|
---|
| 606 | head_element=get(subt,1,'name');
|
---|
| 607 | cont=get(subt,1,'contents');
|
---|
| 608 | if ~isempty(cont)
|
---|
| 609 | for ilist=1:length(Data)
|
---|
| 610 | uid_key=find(subt,[head_element '/' Data{ilist}]);
|
---|
| 611 | if ~isequal(length(uid_key),NbOccur(ilist))
|
---|
| 612 | errormsg=['wrong number of occurence for ' Data{ilist}];
|
---|
| 613 | return
|
---|
| 614 | end
|
---|
| 615 | for ival=1:length(uid_key)
|
---|
| 616 | val=get(subt,children(subt,uid_key(ival)),'value');
|
---|
| 617 | if ~NumTest(ilist)
|
---|
| 618 | eval(['s.' Data{ilist} '=val;']);
|
---|
| 619 | else
|
---|
| 620 | eval(['s.' Data{ilist} '=str2double(val);'])
|
---|
| 621 | end
|
---|
| 622 | end
|
---|
| 623 | end
|
---|
| 624 | end
|
---|
| 625 |
|
---|
| 626 |
|
---|
| 627 | %--------------------------------------------------
|
---|
| 628 | % read an xml element
|
---|
| 629 | function val=get_value(t,label,default)
|
---|
| 630 | %--------------------------------------------------
|
---|
| 631 | val=default;
|
---|
| 632 | uid=find(t,label);%find the element iud(s)
|
---|
| 633 | if ~isempty(uid) %if the element named label exists
|
---|
| 634 | uid_child=children(t,uid);%find the children
|
---|
| 635 | if ~isempty(uid_child)
|
---|
| 636 | data=get(t,uid_child,'type');%get the type of child
|
---|
| 637 | if iscell(data)% case of multiple element
|
---|
| 638 | for icell=1:numel(data)
|
---|
| 639 | val_read=str2num(get(t,uid_child(icell),'value'));
|
---|
| 640 | if ~isempty(val_read)
|
---|
| 641 | val(icell,:)=val_read;
|
---|
| 642 | end
|
---|
| 643 | end
|
---|
| 644 | % val=val';
|
---|
| 645 | else % case of unique element value
|
---|
| 646 | val_read=str2num(get(t,uid_child,'value'));
|
---|
| 647 | if ~isempty(val_read)
|
---|
| 648 | val=val_read;
|
---|
| 649 | else
|
---|
| 650 | val=get(t,uid_child,'value');%char string data
|
---|
| 651 | end
|
---|
| 652 | end
|
---|
| 653 | end
|
---|
| 654 | end
|
---|