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convert_open_ephys_to_kwik.m
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convert_open_ephys_to_kwik.m
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function info = convert_open_ephys_to_kwik(varargin)
%
% Converts Open Ephys data to KWIK format
%
% by Josh Siegle, November 2013
%
% info = convert_open_ephys_to_kwik(input_directory, output_directory)
%
% input_directory: folder with Open Ephys data
% output_directory (optional): folder to save the KWIK files
% - defaults to using the input_directory
%
% KWIK file contains:
% - metadata
% - spikes times
% - clusters
% - recording for each spike time
% - probe-related information
% - information about channels
% - information about cluster groups
% - events, event types
% - aesthetic information, user data, application data
%
% KWX file contains:
% - spike features, masks, waveforms
%
% KWD file contains:
% - raw/filtered recordings
%
% all files contain a kwik_version attribute (currently equal to 2)
%
% PRM = processing parameters
% PRB = probe parameters
input_directory = varargin{1};
if (nargin == 1)
output_directory = input_directory;
else
output_directory = varargin{2};
end
info = get_session_info(input_directory);
% loop over experiments
for kE = 1:length(info)
experiment_prefix = ['experiment' num2str(kE)];
%%
% 1. create the KWIK file
kwikfile = [get_full_path(output_directory) filesep ...
experiment_prefix '_session_info.kwik'];
disp(['Writing ' kwikfile '...'])
info(kE).kwikfile = kwikfile;
if numel(dir(kwikfile))
delete(kwikfile)
end
H5F.create(kwikfile);
h5writeatt(kwikfile, '/', 'kwik_version', '2')
%%
% 2. create the KWD files
processor_index = 0;
for processor = 1:size(info(kE).processors,1)
recorded_channels_per_block = info(kE).processors{processor, 3};
num_blocks = length(recorded_channels_per_block);
recorded_channels = unique([recorded_channels_per_block{:}]);
% check for missing files and filter
files_exist = cellfun(@(name) exist(name, 'file'), recorded_channels) == 2;
if ~all(files_exist)
warning('Some data files for %s (node %d) are missing.', ...
info(kE).processors{processor, 2}, info(kE).processors{processor, 1});
% remove each missing file from per-recording lists
for missing_file_ind = find(~files_exist(:)')
missing_file = recorded_channels{missing_file_ind};
for block = 1:num_blocks
files = recorded_channels_per_block{block};
recorded_channels_per_block{block} = files(~strcmp(missing_file, files));
end
end
% remove missing files from merged list
recorded_channels = recorded_channels(files_exist);
end
num_channels = length(recorded_channels);
if num_channels == 0
continue;
end
processor_index = processor_index + 1;
if processor_index == 1
kwik_blocks_written = false(num_blocks, 1);
end
% initialize this processor's kwd file
kwdfile = [get_full_path(output_directory) filesep ...
experiment_prefix '_' ...
int2str(info(kE).processors{processor,1}) '_raw.kwd'];
info(kE).kwdfiles{processor_index} = kwdfile;
if numel(dir(kwdfile))
delete(kwdfile);
end
disp(['Writing ' kwdfile '...']);
H5F.create(kwdfile);
h5writeatt(kwdfile, '/', 'kwik_version', uint16(2));
blocks_to_write = find(cellfun(@length, recorded_channels_per_block) ~= 0)';
% initialize data fields
for block = blocks_to_write
this_block_num_channels = length(recorded_channels_per_block{block});
internal_path = ['/recordings/' int2str(block-1)];
h5create(kwdfile, [internal_path '/application_data/channel_bit_volts'], ...
this_block_num_channels, 'DataType', 'single');
h5create(kwdfile, [internal_path '/application_data/channel_sample_rates'], ...
this_block_num_channels, 'DataType', 'single');
h5create(kwdfile, [internal_path '/application_data/timestamps'], ...
[this_block_num_channels Inf], ...
'Datatype', 'int64', 'ChunkSize', [this_block_num_channels 16]);
h5create(kwdfile, [internal_path '/data'], ...
[this_block_num_channels Inf], ...
'Datatype', 'int16', 'ChunkSize', [this_block_num_channels 2048]);
end
% keep track of whether each block is multi-sample-rate
first_sample_rate = zeros(num_blocks, 1);
is_multi_sample_rate = false(num_blocks, 1);
% add data from each channel
for ch = 1:num_channels
filename_in = recorded_channels{ch};
[data, timestamps, info_continuous] = load_open_ephys_data_faster(filename_in, 'unscaledInt16');
this_channel_blocks = unique(info_continuous.recNum);
block_size = info_continuous.header.blockLength;
for block = this_channel_blocks' + 1 % make sure it's one-based so they can be used for indexing
in_block = find(info_continuous.recNum == block - 1);
start_sample = (in_block(1)-1)*block_size+1;
end_sample = (in_block(end)-1)*block_size+block_size;
this_block_data = int16(data(start_sample:end_sample));
this_block_ts = int64(info_continuous.ts(in_block));
internal_path = ['/recordings/' int2str(block-1)];
chan_ind_in_block = find(strcmp(filename_in, recorded_channels_per_block{block}));
chan_sample_rate = info_continuous.header.sampleRate;
if chan_ind_in_block == 1
% only write attributes for first channel
if block > length(kwik_blocks_written) || ~kwik_blocks_written(block)
% only write to the kwik file once per block, over all processors
kwik_blocks_written(block) = true;
h5create(kwikfile, [internal_path '/start_sample'], [1 1],...
'Datatype', 'int64');
h5write(kwikfile, [internal_path '/start_sample'], int64(timestamps(start_sample)));
h5create(kwikfile, [internal_path '/sample_rate'], [1 1],...
'Datatype', 'int16');
h5write(kwikfile, [internal_path '/sample_rate'], int16(chan_sample_rate));
end
% attributes
h5writeatt(kwdfile, internal_path, 'start_sample', uint32(0));
h5writeatt(kwdfile, internal_path, 'sample_rate', single(info_continuous.header.sampleRate));
h5writeatt(kwdfile, internal_path, 'bit_depth', uint32(16));
h5writeatt(kwdfile, internal_path, 'name', sprintf('Open Ephys Recording #%d', block - 1));
h5writeatt(kwdfile, internal_path, 'start_time', uint64(this_block_ts(1)));
end
% keep track of whether this block is multi-sample-rate
if first_sample_rate(block) == 0
first_sample_rate(block) = chan_sample_rate;
else
is_multi_sample_rate(block) = is_multi_sample_rate(block) | chan_sample_rate ~= first_sample_rate(block);
end
% write data
h5write(kwdfile, [internal_path '/application_data/channel_bit_volts'], ...
single(info_continuous.header.bitVolts), chan_ind_in_block, 1);
h5write(kwdfile, [internal_path '/application_data/channel_sample_rates'], ...
single(chan_sample_rate), chan_ind_in_block, 1);
h5write(kwdfile, [internal_path '/application_data/timestamps'], ...
this_block_ts', [chan_ind_in_block 1], [1 length(this_block_ts)]);
h5write(kwdfile, [internal_path '/data'], ...
(this_block_data(1:end))', [chan_ind_in_block 1], [1 numel(this_block_data)]);
end
end
for block = blocks_to_write
internal_path = ['/recordings/' int2str(block - 1)];
h5writeatt(kwdfile, [internal_path '/application_data'], 'is_multiSampleRate_data', uint8(is_multi_sample_rate(block)));
end
end
%%
% 3. create the KWX file
kwxfile = [get_full_path(output_directory) filesep ...
experiment_prefix '.kwx'];
info(kE).kwxfile = kwxfile;
if numel(dir(kwxfile))
delete(kwxfile)
end
for block = 1:size(info(kE).electrodes,1)
filename_string = info(kE).electrodes{block, 1};
channels = info(kE).electrodes{block, 2};
internal_path = ['/channel_groups/' int2str(block-1)];
for ch = 1:length(channels)
h5create(kwikfile, [internal_path '/' int2str(ch-1) '/kwd_index'], [1 1], 'Datatype', 'int16');
h5write(kwikfile, [internal_path '/' int2str(ch-1) '/kwd_index'], int16(channels(ch)));
end
h5writeatt(kwikfile, internal_path, 'name', filename_string);
filename_string(filename_string == ' ') = [ ];
filename_in = [input_directory filesep ...
filename_string '.spikes'];
[data, ~, info_spikes] = load_open_ephys_data(filename_in);
h5create(kwxfile, [internal_path '/waveforms_filtered'], ...
size(data), ...
'Datatype', 'int16', ...
'ChunkSize',[1 size(data,2) size(data,3)]);
rescaled_waveforms = data.*repmat(reshape(info_spikes.gain, ...
[size(info_spikes.gain,1) 1 size(info_spikes.gain,2)]), ...
[1 size(data,2) 1])./1000;
h5write(kwxfile,[internal_path '/waveforms_filtered'], ...
int16(rescaled_waveforms));
end
end