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dataSourceDRF.m
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dataSourceDRF.m
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% Definition of the class dataSourceDRF. This class imports into MoBILAB files
% recorder by Datariver saved in drf format.
%
% Author: Alejandro Ojeda, SCCN, INC, UCSD, 05-Apr-2011
%%
classdef dataSourceDRF < dataSource
methods
%%
function obj = dataSourceDRF(varargin)
% Creates a dataSourceDRF object.
%
% Input arguments:
% file: drf file recorded by Datariver
% mobiDataDirectory: path to the directory where the collection
% of files will be stored
%
% Output arguments:
% obj: dataSource object (handle)
%
% Usage:
% % file: drf file recorded by Datariver
% % mobiDataDirectory: path to the directory where the collection of
% % files are or will be stored.
%
% obj = dataSourceDRF( file, mobiDataDirectory);
if nargin==1, varargin = varargin{1};end
if length(varargin) < 2, error('Not enough input arguments.');end
sourceFileName = varargin{1};
mobiDataDirectory = varargin{2};
if length(varargin) == 3
tmpDir = varargin{3};
if ~exist(tmpDir,'dir') && ~isempty(tmpDir), mkdir(tmpDir);end
else tmpDir = '';
end
[drfFolder,drfName,ext] = fileparts(sourceFileName);
if ~strcmp(ext,'.drf'), error('prog:input',['dataSourceDRF cannot read ''' ext ''' format.']);end
if ~exist([drfFolder filesep drfName '.xml'],'file'), error('prog:input','Unable to read the correspondent xml header.');end
if strcmp(drfFolder,mobiDataDirectory), error('Source and destiny folders must be different.');end
uuid = generateUUID;
obj@dataSource(mobiDataDirectory,uuid);
obj.checkThisFolder(mobiDataDirectory);
% Some internal parameters
buffer_size = 4*2*2048; % only 16 Mbyte at a time in RAM (2*2048 int32 elements)
buffer_counter = 1;
stream_count = 1;
streamsList = {'biosemi' 'phasespace' 'videostream' 'audiosend' 'wii' 'eventcodes' 'hotgazestream' 'scenestream'};
parentCommand.commandName = 'dataSourceDRF';
parentCommand.varargin{1} = sourceFileName;
parentCommand.varargin{2} = mobiDataDirectory;
eegCount = 0;
mocapCount = 0;
metadata.sessionUUID = obj.sessionUUID;
% Preparing for the show!!!
xDom = xmlread([drfFolder filesep drfName '.xml']);
fid = fopen(sourceFileName,'r');
cleanupHandle = onCleanup(@()fclose(fid));
if fid<0, error('prog:input',['Could not read from: ' sourceFileName]);end
% Parsing the xml header
allfilesamples = xDom.getElementsByTagName('filesample');
reservedItem = xDom.getElementsByTagName('reserved');
for it=0:allfilesamples.getLength-1
tmp = allfilesamples.item(it).getElementsByTagName('stream_count');
offset = str2double(tmp.item(0).getAttribute('bytes'));
fseek(fid,offset,'cof');
allsamples = allfilesamples.item(it).getElementsByTagName('sample');
for jt=0:allsamples.getLength-1
allstreams = allsamples.item(jt).getElementsByTagName('stream');
for k=0:allstreams.getLength-1
convert_to_uV{stream_count} = [];%#ok
labels{stream_count} = [];%#ok
name{stream_count} = lower(char(allstreams.item(k).getAttribute('name'))); %#ok %data_type
tmpInd = find(name{stream_count} == '\');
if ~isempty(tmpInd), name{stream_count} = name{stream_count}(tmpInd(end)+1:end);end %#ok
samplingRate = str2double(allstreams.item(k).getAttribute('sampling_rate'));
data_tag = allstreams.item(k).getElementsByTagName('data');
data_child = data_tag.item(0).getChildNodes;
data_items = str2double(data_tag.item(0).getAttribute('items'));
item_size_tag = allstreams.item(k).getElementsByTagName('item_size');
hardwareMetaDataObj = hardwareMetaData;
hardwareMetaDataObj.reserved_bytes = char(reservedItem.item(0).getAttribute('bytes'));
hardwareMetaDataObj.offset = offset;
hardwareMetaDataObj.data_items = data_items;
hardwareMetaDataObj.item_size = str2double(item_size_tag.item(0).getAttribute('value'));
hardwareMetaDataObj.sampling_rate = samplingRate;
hardwareMetaDataObj.bytesHeader = str2double(allstreams.item(k).getAttribute('bytes'));
add_label = 1;
for kk=0:data_child.getLength-1
try%#ok
rep_lb = str2double(data_child.item(kk).getAttribute('count'));
uV = 1./str2double(data_child.item(kk).getAttribute('uV'));
if isempty(uV) || isnan(uV), uV = 1;end
if isempty(rep_lb), hardwareMetaDataObj.count(end+1) = 1;
else hardwareMetaDataObj.count(end+1) = rep_lb;
end
hardwareMetaDataObj.uV(end+1) = 1/uV;
tmplabels = [];
for kkk=0:data_child.item(kk).getLength-1
try %#ok
rd_label = char(data_child.item(kk).item(kkk).getAttribute('label'));
if ~isempty(rd_label), rd_label = strtrim(rd_label);end
hardwareMetaDataObj.label{end+1} = rd_label;
ind = strfind(rd_label,'%');
if ~isempty(ind), rd_label = rd_label(1:ind-1);end
tmplabels = cat(1,tmplabels,{rd_label});
add_label = add_label + 1;
end
end
repLabels = [];
if isempty(rep_lb)
repLabels = char(data_child.item(kk).getNodeName);
atrib = data_child.item(kk).getAttributes;
for atrib_iter=0:atrib.getLength-1, if ~isempty(atrib.item(atrib_iter).toString), repLabels = [repLabels '_' char(atrib.item(atrib_iter).toString)];end;end %#ok
if ~isempty(repLabels), repLabels = {repLabels};end
else for k4=1:rep_lb, for k5=1:length(tmplabels), repLabels{end+1,1} = [tmplabels{k5} num2str(k4)];end;end %#ok
end
labels{stream_count} = cat(1,labels{stream_count},repLabels); %#ok
convert_to_uV{stream_count} = cat(1,convert_to_uV{stream_count},repmat(uV,length(repLabels),1));%#ok
end
end
% creating the dataSource.item with the first samples
[samples,timeStamp,event,numberOfChannels] = read_stream(fid);
if numberOfChannels > 1
if numberOfChannels ~= str2double(data_child.getAttribute('items')) % length(labels{stream_count})
error('Cannot read the file, there is a mismatch between the header and the content of the drf file.');
end
end
if isempty(convert_to_uV{stream_count}),
if numberOfChannels > 0, convert_to_uV{stream_count} = ones(numberOfChannels,1);%#ok
else convert_to_uV{stream_count} = 1;%#ok
end
end
binFile = [tempname '.bin'];
if ~isempty(tmpDir)
[~,tmpName] = fileparts(binFile);
binFile = fullfile(tmpDir,tmpName);
end
if ~exist(binFile,'file'), fid2 = fopen(binFile,'w');fclose(fid2);end
[filepath,filename] = fileparts(binFile);
header = fullfile(filepath,[filename '.hdr']);
streamClass = '';
for sList=1:length(streamsList)
if ~isempty(strfind(lower(name{stream_count}),streamsList{sList})), streamClass = streamsList{sList};end
end
hardwareMetaDataObj.name = streamClass;
metadata.binFile = binFile;
metadata.header = header;
metadata.dob = now;
metadata.name = name{stream_count};
metadata.timeStamp = [];
if stream_count==1, metadata.samplingRate = samplingRate;end
metadata.numberOfChannels = numberOfChannels;
metadata.label = labels{stream_count};
metadata.writable = false;
metadata.parentCommand = parentCommand;
metadata.hardwareMetaData = hardwareMetaData;
metadata.precision = 'double';
metadata.event.label = cell(0,1);
metadata.event.hedTag = cell(0,1);
metadata.event.latencyInFrame = [];
uuid = generateUUID;
metadata.uuid = uuid;
metadata.unit = 'none';
switch streamClass
case 'biosemi'
if eegCount==0, eegName = 'eeg'; else eegName = ['eeg' num2str(eegCount)];end
metadata.name = eegName;
metadata.unit = 'microvolts';
metadata.class = 'eeg';
metadata.auxChannel.label = {};
metadata.auxChannel.data = [];
header = metadata2headerFile(metadata);
metadata = rmfield(metadata,'auxChannel');
eegCount = eegCount+1;
case 'phasespace'
if mocapCount==0, mocapName = 'mocap'; else mocapName = ['mocap' num2str(mocapCount)];end
metadata.name = mocapName;
metadata.animationParameters = struct('limits',[],'conn',[],'bodymodel',[]);
metadata.class = 'mocap';
header = metadata2headerFile(metadata);
metadata = rmfield(metadata,'animationParameters');
mocapCount = mocapCount+1;
case 'wii'
metadata.animationParameters = struct('limits',[],'conn',[],'bodymodel',[]);
metadata.class = 'wii';
header = metadata2headerFile(metadata);
metadata = rmfield(metadata,'animationParameters');
case 'videostream'
metadata.numberOfChannels = 1;
metadata.label = {'video frame'};
metadata.class = 'videoStream';
header = metadata2headerFile(metadata);
case 'scenestream'
metadata.numberOfChannels = 1;
metadata.label = {'video frame'};
metadata.class = 'videoStream';
header = metadata2headerFile(metadata);
case 'hotgazestream'
metadata.class = 'gazeStream';
header = metadata2headerFile(metadata);
case 'eventcodes'
metadata.class = 'markerStream';
header = metadata2headerFile(metadata);
otherwise
metadata.class = 'dataStream';
header = metadata2headerFile(metadata);
end
obj.addItem(header);
obj.item{stream_count}.addSamples(convert_to_uV{stream_count}.*samples,timeStamp,event);
stream_count = stream_count + 1;
end
end
end
% Reading from the binary file until the end
N = stream_count-1;
samples = cell(N,1);
timeStamp = cell(N,1);
event = cell(N,1);
oneTimeWarning = 1;
obj.container.lockGui('Reading...');
while ~feof(fid)
try fseek(fid,offset,'cof');
for stream_count=1:N
[tmpSamples,timeStamp{stream_count}(buffer_counter),event{stream_count}(buffer_counter)] = read_stream(fid);
try samples{stream_count}(:,buffer_counter) = tmpSamples;
catch ME
if strcmp(ME.identifier,'MATLAB:subsassigndimmismatch') && obj.item{stream_count}.numberOfChannels > 0
samples{stream_count}(:,buffer_counter) = nan;
if oneTimeWarning
warning('MoBILAB:corruptedFile',['From sample ' num2str(length(obj.item{stream_count}.timeStamp))...
' there are no more data in stream ' obj.item{stream_count}.name '.']);
oneTimeWarning = 0;
end
elseif obj.item{stream_count}.numberOfChannels ~= 0
error('MoBILAB:corruptedFile','The file is corrupted.');
end
end
end
buffer_counter = buffer_counter+1;
if buffer_counter > buffer_size
for stream_count=1:N
if ~isempty(samples{stream_count})
obj.item{stream_count}.addSamples(repmat(convert_to_uV{stream_count},...
buffer_size,1).*samples{stream_count}(:),timeStamp{stream_count}(:),...
event{stream_count}(:));
else obj.item{stream_count}.addSamples([],timeStamp{stream_count}(:),event{stream_count}(:));
end
end
buffer_counter = 1;
end
catch ME
if strcmpi(ME.identifier,'MoBILAB:corruptedFile') || strcmpi(ME.identifier,'MATLAB:badprecision_mx')
sampleNumber = length(obj.item{stream_count}.timeStamp) + buffer_counter;
warning('MoBILAB:corruptedFile',['File ''' drfName ''' is corrupted from sample ' num2str(sampleNumber)]);
end
for stream_count=1:N
try %#ok
% buffer_counter = length(timeStamp{stream_count});
timeStamp{stream_count} = timeStamp{stream_count}(1:buffer_counter-1);
event{stream_count} = event{stream_count}(1:buffer_counter-1);
if ~isempty(samples{stream_count})
samples{stream_count} = samples{stream_count}(:,1:buffer_counter-1);
obj.item{stream_count}.addSamples(repmat(convert_to_uV{stream_count},...
buffer_counter-1,1).*samples{stream_count}(:),timeStamp{stream_count},...
event{stream_count});
else obj.item{stream_count}.addSamples([],timeStamp{stream_count}(:),event{stream_count}(:));
end
end
end
end
end
% transpose the file to get the time dimension as the first
obj.disconnect;
for stream_count=1:N
binFile = [obj.mobiDataDirectory filesep name{stream_count} '_' obj.item{stream_count}.uuid '_' obj.sessionUUID '.bin'];
fid2 = fopen(binFile,'w');
cleanupHandle2 = onCleanup(@()fclose(fid2));
if obj.item{stream_count}.numberOfChannels > 0
tmp_mmfObj = memmapfile(obj.item{stream_count}.binFile,'Format',...
{obj.item{stream_count}.precision [obj.item{stream_count}.numberOfChannels length(obj.item{stream_count}.timeStamp)] 'x'},...
'Writable',obj.item{stream_count}.writable);
try data = tmp_mmfObj.Data.x; %#ok
catch ME
msg = sprintf('A subscripting operation on the Data field attempted to create a\ncomma-separated list. The memmapfile class does not support the use of\ncomma-separated lists when subscripting.');
if strcmp(ME.message,msg) && obj.item{stream_count}.numberOfChannels == 1
data = zeros(1,length(obj.item{stream_count}.timeStamp));
data(obj.item{stream_count}.event.latencyInFrame) = str2double(obj.item{stream_count}.event.label); %#ok
else
ME.rethrow;
end
end
for jt=1:obj.item{stream_count}.numberOfChannels
sample = eval([obj.item{stream_count}.precision '(data(jt,:));']);
fwrite(fid2,sample,obj.item{stream_count}.precision);
end
elseif obj.item{stream_count}.numberOfChannels == 0 && ~isempty(obj.item{stream_count}.event.latencyInFrame) && ~obj.item{end}.isMemoryMappingActive
data = zeros(1,length(obj.item{stream_count}.timeStamp));%#ok
sample = eval([obj.item{stream_count}.precision '(data(:));']);
fwrite(fid2,sample,obj.item{stream_count}.precision);
clear event
event.hedTag = obj.item{stream_count}.event.hedTag;
event.label = obj.item{stream_count}.event.label;
event.latencyInFrame = obj.item{stream_count}.event.latencyInFrame;
timeStamp = obj.item{stream_count}.timeStamp; %#ok
numberOfChannels = 1; %#ok
save(obj.item{stream_count}.header,'-mat','-append','event','timeStamp','numberOfChannels');
tmp_header = obj.item{stream_count}.header;
constructorHandle = eval(['@' class(obj.item{stream_count})]);
delete(obj.item{stream_count});
obj.item{stream_count} = constructorHandle(tmp_header);
else
obj.item{stream_count}.mmfObj = [];
end
java.io.File(obj.item{stream_count}.binFile).delete();
obj.item{stream_count}.binFile = binFile;
[path,filename] = fileparts(obj.item{stream_count}.binFile);
copyfile(obj.item{stream_count}.header,fullfile(path,[filename '.hdr']));
java.io.File(obj.item{stream_count}.header).delete();
obj.item{stream_count}.header = fullfile(path,[filename '.hdr']);
header = obj.item{stream_count}.header; %#ok
binFile = obj.item{stream_count}.binFile;%#ok
clear event
event.hedTag = obj.item{stream_count}.event.hedTag;
event.label = obj.item{stream_count}.event.label;
event.latencyInFrame = obj.item{stream_count}.event.latencyInFrame;
timeStamp = obj.item{stream_count}.timeStamp; %#ok
save(obj.item{stream_count}.header,'-mat','-append','event','timeStamp','header','binFile');
obj.item{stream_count}.container = obj;
end
obj.connect;
obj.checkTimeStamps;
obj.findSpaceBoundary;
obj.updateLogicalStructure;
obj.save(obj.mobiDataDirectory);
obj.container.lockGui;
end
%%
function checkTimeStamps(obj)
if obj.item{1}.timeStamp == 0, return;end
N = length(obj.item);
if N < 1, return;end
disp('Correcting time stamps if needed...')
t0 = double(obj.item{1}.timeStamp);
ind = find(abs(diff(t0)) > 2); % find discontinuities in time longer than 2 sec
t0 = (t0-t0(1))*1e-3; % from mili-sec to sec
sf = 1./(diff(t0)+eps);
tnew = (0:length(t0)-1)/obj.item{1}.samplingRate;
t = ttest(zscore(sf-obj.item{1}.samplingRate));
t(isnan(t)) = 0;
if t, warning(['There is an inconsistency between the sampling rate in the .xml file (' num2str(obj.item{1}.samplingRate) ' Hz), and the actual sampling rate (' num2str(mean(sf)) ' Hz).']);end
for it=1:N, obj.item{it}.correctTimeStampDefects(tnew,obj.item{1}.samplingRate);end
if ~isempty(ind), for it=1:N, obj.item{it}.event.addEvent(ind,'boundary');end;end
end
end
methods(Static)
function obj = merge(obj,dsourceObjs)
parentCommand.commandName = 'dataSourceFromFolder';
parentCommand.varargin = {fileparts(dsourceObjs{1}.item{1}.parentCommand.varargin{1}),obj.mobiDataDirectory};
Nf = length(dsourceObjs);
Nstreams = length(dsourceObjs{1}.item);
offset = zeros(Nstreams,Nf);
for it=1:Nstreams
for folder=1:Nf
offset(it,folder) = dsourceObjs{folder}.item{it}.timeStamp(end);
if dsourceObjs{1}.item{it}.numberOfChannels ~= dsourceObjs{folder}.item{it}.numberOfChannels
error('MoBILAB:merging','Cannot merge streams with different number of channels!!!');
end
end
end
offset = cumsum(max(offset));
for it=1:Nstreams
uuid = generateUUID;
binFile = fullfile(obj.mobiDataDirectory, [dsourceObjs{1}.item{it}.name '_' uuid '_' obj.sessionUUID '.bin']);
fid = fopen(binFile,'w');
for ch=1:dsourceObjs{1}.item{it}.numberOfChannels
for folder=1:Nf, fwrite(fid,dsourceObjs{folder}.item{it}.data(:,ch),dsourceObjs{1}.item{it}.precision);end
end
fclose(fid);
cumSize = zeros(Nf,1);
time = dsourceObjs{1}.item{it}.timeStamp;
for folder=2:Nf, time = [time offset(folder-1)+1/dsourceObjs{folder}.item{it}.samplingRate+dsourceObjs{folder}.item{it}.timeStamp];end%#ok
eventObj = event;
offsetEvents = [0;cumsum(cumSize)];
for folder=1:Nf
latency = offsetEvents(folder) + dsourceObjs{folder}.item{it}.event.latencyInFrame;
hedTag = dsourceObjs{folder}.item{it}.event.hedTag;
eventObj = eventObj.addEvent(latency,hedTag);
if folder+1 <= Nf, eventObj = eventObj.addEvent(offsetEvents(folder+1),'boundary');end
end
metadata = saveobj(dsourceObjs{1}.item{it});
metadata.binFile = binFile;
metadata.sessionUUID = obj.sessionUUID;
metadata.parentCommand = parentCommand;
metadata.timeStamp = time;
metadata.event = eventObj.saveobj;
header = metadata2headerFile(metadata);
obj.addItem(header);
end
end
end
end
%%
function [data,timestamp,event,number_of_channels,precision] = read_stream(fid)
timestamp = fread(fid,1,'int32');
event = fread(fid,1,'int32');
number_of_channels = fread(fid,1,'int32');
item_size = fread(fid,1,'int32');
precision = sprintf('int%i',8*item_size);
try
data = fread(fid,number_of_channels,precision);
catch ME
ME.rethrow;
end
end