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‎2pAnalysis/LoadSyncEpisodeFunction.m

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%% Load ThorSync Episode HDF5 file:
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% - all will be exported to base workspace with unique names.
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% - Attributes can be any combination of the following:
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% [syncDataOut=LoadSyncEpisode(fnam) -- Load the data from the h5 file at the fully qualified path 'fnam'
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% -- syncDataOut - Structure containing all of the data sets in the Thorsync dataset
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% Note: This version does not allow opening of only part of the sync episode. Any other arguments besides the file name are ignored.
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% This is modified for use as a function from LoadSyncFunction.m (c) 2014
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% --- Copyright (c) 2018, Thorlabs, Inc. All rights reserved. ---
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%% Copyright (c) 2018, Thorlabs, Inc. All rights reserved.
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%
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% Redistribution and use in source and binary forms, with or without
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% modification, are permitted provided that the following conditions are
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% met:
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%
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% * Redistributions of source code must retain the above copyright
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% notice, this list of conditions and the following disclaimer.
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% * Redistributions in binary form must reproduce the above copyright
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% notice, this list of conditions and the following disclaimer in the
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% documentation and/or other materials provided with the distribution
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%
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% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
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% IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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% THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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% PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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% EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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% PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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% PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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% LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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function [syncDataOut]=LoadSyncEpisodeFunction(fnam, lineNames)
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%[syncDataOut]=LoadSyncEpisodeFunction(fnam)
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% loads all Thorsync data in a .h5 file specified as fnam
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%
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% [syncDataOut]=LoadSyncEpisodeFunction(fnam, lineNames)
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% loads a subset of Thorsync data specified in lineNames
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%
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%
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% 17/7/20 DS added 2nd input
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%% Select one h5 file:
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% [filename, pathname] = uigetfile('*.h5', 'Pick a Sync Episode file');
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% if isequal(filename,0) || isequal(pathname,0)
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% disp('User pressed cancel')
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% return
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% else
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% disp(['User selected ', fullfile(pathname, filename)])
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% end
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if nargin < 2
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lineNames = [];
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end
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[pathname,name,ext]=fileparts(fnam);
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filename=[name ext];
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pathname=[pathname filesep];
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%% Load params from XML:
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clockRate = 20000000;
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sampleRate = LoadSyncXML(pathname);
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%% Start loading HDF5:
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pathandfilename = strcat(pathname,filename);
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info = h5info(pathandfilename);
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%% Parse input:
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props = {'start','length','interval'};
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data = {[1,1],[1 Inf],[1 1]};
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% if(~isempty(varargin))
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% assert(rem(length(varargin),2)==0 && iscellstr(varargin(1:2:end)), 'Inputs failed to conform to expected string-value pair format, eg> ''start'',1');
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% %foundProps = intersect(varargin(1:2:end), props);
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% IdxCell = cellfun(@(x) strcmpi(x,props),varargin(1:2:end),'UniformOutput',false);
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% val = double(cell2mat(varargin(2:2:end)))*sampleRate;
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% for i=1:length(val)
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% data{cell2mat(IdxCell(i))>0} = [1 val(i)];
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% end
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% end
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%% Read HDF5:
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for j=1:length(info.Groups)
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for k = 1:length(info.Groups(j).Datasets)
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datasetPath = strcat(info.Groups(j).Name,'/',info.Groups(j).Datasets(k).Name);
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datasetName = info.Groups(j).Datasets(k).Name;
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if ~(strcmp(info.Groups(j).Name,'/Global')) && ~isempty(lineNames) ...
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&& ~ismember(info.Groups(j).Datasets(k).Name, lineNames)
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continue;
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end
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datasetName(isspace(datasetName))='_';
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datasetValue = h5read(pathandfilename,datasetPath,data{1},data{2},data{3})';
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%h5read is inherently slow...particularly when reading over network
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% load digital line in binary:
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if(strcmp(info.Groups(j).Name,'/DI'))
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datasetValue(datasetValue>0) = 1;
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end
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% create time variable out of gCtr,
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% account for 20MHz sample rate:
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if(strcmp(info.Groups(j).Name,'/Global'))
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datasetValue = double(datasetValue)./clockRate;
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datasetName = 'time';
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end
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assignStr = UniqueName(datasetName);
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syncDataOut.(assignStr)=datasetValue;
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% assignin('base',assignStr,datasetValue);
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end
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end
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end
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function outStr = UniqueName(str)
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%% Generate unique name for variable to be exported.
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cellfind = @(string)(@(cell_contents)(strcmp(string,cell_contents)));
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vars = evalin('base','who');
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index = 1;
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unique = false;
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cmpStr = str;
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while (~unique)
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ret = cellfun(cellfind(cmpStr),vars);
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if(~any(ret))
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outStr = cmpStr;
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unique = true;
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else
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cmpStr = strcat(str,num2str(index,'%03d'));
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index=index+1;
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end
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end
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end
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%% Load ThorSync XML file:
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% - input file path, output sample rate.
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% --- Copyright (c) 2014, Thorlabs, Inc. All rights reserved. ---
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%% Copyright (c) 2014, Thorlabs, Inc. All rights reserved.
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%
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% Redistribution and use in source and binary forms, with or without
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% modification, are permitted provided that the following conditions are
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% met:
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%
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% * Redistributions of source code must retain the above copyright
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% notice, this list of conditions and the following disclaimer.
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% * Redistributions in binary form must reproduce the above copyright
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% notice, this list of conditions and the following disclaimer in the
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% documentation and/or other materials provided with the distribution
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%
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% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
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% IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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% THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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% PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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% EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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% PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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% PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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% LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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function sampleRate = LoadSyncXML(varargin)
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%% Load dll:
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xmlFile = strcat(varargin{1}, 'ThorRealTimeDataSettings.xml');
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assert(exist(xmlFile,'file')>0,'ThorRealTimeDataSettings.xml was not found. ');
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dataStruct = xml2struct(xmlFile);
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if(~isempty(dataStruct))
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BrdID = cellfun(@(x) strcmpi(x.Attributes.active,'1'),dataStruct.RealTimeDataSettings.DaqDevices.AcquireBoard);
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sampleID = cellfun(@(x) strcmpi(x.Attributes.enable,'1'),dataStruct.RealTimeDataSettings.DaqDevices.AcquireBoard{BrdID}.SampleRate);
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sampleRate = dataStruct.RealTimeDataSettings.DaqDevices.AcquireBoard{BrdID}.SampleRate{sampleID>0}.Attributes.rate;
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end
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end
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%% Convert xml file into a MATLAB structure
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% [ s ] = xml2struct( file )
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%
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% A file containing:
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% <XMLname attrib1="Some value">
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% <Element>Some text</Element>
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% <DifferentElement attrib2="2">Some more text</Element>
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% <DifferentElement attrib3="2" attrib4="1">Even more text</DifferentElement>
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% </XMLname>
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%
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% Will produce:
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% s.XMLname.Attributes.attrib1 = "Some value";
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% s.XMLname.Element.Text = "Some text";
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% s.XMLname.DifferentElement{1}.Attributes.attrib2 = "2";
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% s.XMLname.DifferentElement{1}.Text = "Some more text";
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% s.XMLname.DifferentElement{2}.Attributes.attrib3 = "2";
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% s.XMLname.DifferentElement{2}.Attributes.attrib4 = "1";
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% s.XMLname.DifferentElement{2}.Text = "Even more text";
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%
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% Please note that the following characters are substituted
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% '-' by '_dash_', ':' by '_colon_' and '.' by '_dot_'
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%
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% Written by W. Falkena, ASTI, TUDelft, 21-08-2010
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% Attribute parsing speed increased by 40% by A. Wanner, 14-6-2011
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% Added CDATA support by I. Smirnov, 20-3-2012
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%
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% Modified by X. Mo, University of Wisconsin, 12-5-2012
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%% Copyright (c) 2010, Wouter Falkena All rights reserved.
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%
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% Redistribution and use in source and binary forms, with or without
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% modification, are permitted provided that the following conditions are
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% met:
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%
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% * Redistributions of source code must retain the above copyright
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% notice, this list of conditions and the following disclaimer.
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% * Redistributions in binary form must reproduce the above copyright
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% notice, this list of conditions and the following disclaimer in the
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% documentation and/or other materials provided with the distribution
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%
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% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
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% IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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% THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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% PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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% CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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% EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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% PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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% PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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% LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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function [ s ] = xml2struct( file )
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%% Function:
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if (nargin < 1)
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clc;
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help xml2struct
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return
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end
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if isa(file, 'org.apache.xerces.dom.DeferredDocumentImpl') || isa(file, 'org.apache.xerces.dom.DeferredElementImpl')
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% input is a java xml object
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xDoc = file;
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else
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%check for existance
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if (exist(file,'file') == 0)
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%Perhaps the xml extension was omitted from the file name. Add the
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%extension and try again.
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if (isempty(strfind(file,'.xml')))
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file = [file '.xml'];
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end
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if (exist(file,'file') == 0)
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error(['The file ' file ' could not be found']);
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end
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end
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%read the xml file
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xDoc = xmlread(file);
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end
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%parse xDoc into a MATLAB structure
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s = parseChildNodes(xDoc);
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end
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% ----- Subfunction parseChildNodes -----
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function [children,ptext,textflag] = parseChildNodes(theNode)
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% Recurse over node children.
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children = struct;
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ptext = struct; textflag = 'Text';
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if hasChildNodes(theNode)
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childNodes = getChildNodes(theNode);
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numChildNodes = getLength(childNodes);
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for count = 1:numChildNodes
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theChild = item(childNodes,count-1);
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[text,name,attr,childs,textflag] = getNodeData(theChild);
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if (~strcmp(name,'#text') && ~strcmp(name,'#comment') && ~strcmp(name,'#cdata_dash_section'))
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%XML allows the same elements to be defined multiple times,
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%put each in a different cell
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if (isfield(children,name))
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if (~iscell(children.(name)))
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%put existsing element into cell format
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children.(name) = {children.(name)};
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end
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index = length(children.(name))+1;
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%add new element
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children.(name){index} = childs;
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if(~isempty(fieldnames(text)))
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children.(name){index} = text;
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end
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if(~isempty(attr))
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children.(name){index}.('Attributes') = attr;
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end
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else
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%add previously unknown (new) element to the structure
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children.(name) = childs;
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if(~isempty(text) && ~isempty(fieldnames(text)))
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children.(name) = text;
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end
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if(~isempty(attr))
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children.(name).('Attributes') = attr;
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end
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end
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else
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ptextflag = 'Text';
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if (strcmp(name, '#cdata_dash_section'))
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ptextflag = 'CDATA';
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elseif (strcmp(name, '#comment'))
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ptextflag = 'Comment';
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end
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%this is the text in an element (i.e., the parentNode)
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if (~isempty(regexprep(text.(textflag),'[\s]*','')))
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if (~isfield(ptext,ptextflag) || isempty(ptext.(ptextflag)))
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ptext.(ptextflag) = text.(textflag);
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else
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%what to do when element data is as follows:
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%<element>Text <!--Comment--> More text</element>
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%put the text in different cells:
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% if (~iscell(ptext)) ptext = {ptext}; end
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% ptext{length(ptext)+1} = text;
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%just append the text
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ptext.(ptextflag) = [ptext.(ptextflag) text.(textflag)];
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end
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end
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end
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end
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end
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end
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% ----- Subfunction getNodeData -----
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function [text,name,attr,childs,textflag] = getNodeData(theNode)
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% Create structure of node info.
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%make sure name is allowed as structure name
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name = toCharArray(getNodeName(theNode))';
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name = strrep(name, '-', '_dash_');
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name = strrep(name, ':', '_colon_');
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name = strrep(name, '.', '_dot_');
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attr = parseAttributes(theNode);
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if (isempty(fieldnames(attr)))
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attr = [];
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end
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%parse child nodes
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[childs,text,textflag] = parseChildNodes(theNode);
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if (isempty(fieldnames(childs)) && isempty(fieldnames(text)))
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%get the data of any childless nodes
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% faster than if any(strcmp(methods(theNode), 'getData'))
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% no need to try-catch (?)
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% faster than text = char(getData(theNode));
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text.(textflag) = toCharArray(getTextContent(theNode))';
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end
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end
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% ----- Subfunction parseAttributes -----
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function attributes = parseAttributes(theNode)
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% Create attributes structure.
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attributes = struct;
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if hasAttributes(theNode)
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theAttributes = getAttributes(theNode);
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numAttributes = getLength(theAttributes);
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for count = 1:numAttributes
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%attrib = item(theAttributes,count-1);
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%attr_name = regexprep(char(getName(attrib)),'[-:.]','_');
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%attributes.(attr_name) = char(getValue(attrib));
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%Suggestion of Adrian Wanner
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str = toCharArray(toString(item(theAttributes,count-1)))';
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k = strfind(str,'=');
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attr_name = str(1:(k(1)-1));
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attr_name = strrep(attr_name, '-', '_dash_');
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attr_name = strrep(attr_name, ':', '_colon_');
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attr_name = strrep(attr_name, '.', '_dot_');
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attributes.(attr_name) = str((k(1)+2):(end-1));
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end
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end
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end
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