def test_mask_out_artifacts():
# Create noisy array
samplerate = int(48e3)
duration = 30 # seconds
n_samples = samplerate*duration
noise_amplitude = 5
noise = noise_amplitude*np.random.normal(0,1,n_samples)
standard_dev = np.std(noise)
# add three artefacts
n_artifacts = 3
artifacts = np.zeros_like(noise)
artifact_duration = int(0.2*samplerate) # samples
artifact_signal = np.zeros((n_artifacts, artifact_duration))
for i in np.arange(n_artifacts):
artifact_signal[i, :] = noise_amplitude*np.random.normal(0,6,artifact_duration)
artifact_indices = np.tile(np.arange(artifact_duration), (3,1))
artifact_shift = np.array([int(n_samples*0.10), int(n_samples*0.20), int(n_samples*0.70)])
artifact_indices += artifact_shift.reshape((-1,1))
for i, indices in enumerate(artifact_indices):
artifacts[indices] = artifact_signal[i,:]
signal = noise + artifacts
timeseries = 'test_mask.mda'
timeseries_out = 'masked.mda'
# write as mda
mdaio.writemda32(signal.reshape((1,-1)), timeseries)
# run the mask artefacts
mask_out_artifacts(timeseries=timeseries, timeseries_out=timeseries_out, threshold=6, chunk_size=2000,
num_write_chunks=150)
# check that they are gone
read_data = mdaio.readmda(timeseries).reshape((-1,1))
masked_data = mdaio.readmda(timeseries_out).reshape((-1,1))
indices_masked = sum(masked_data[artifact_indices,0].flatten() == 0)
total_indices_to_mask = len(artifact_indices.flatten())
masked = indices_masked == total_indices_to_mask
os.remove(timeseries)
os.remove(timeseries_out)
if masked:
print('Artifacts 100% masked')
return True
else:
print('Artifacts %.2f%% masked' % (100*(indices_masked/total_indices_to_mask)))
return False
def compare_ground_truth(*, firings, firings_true, json_out, opts={}):
Ft = mdaio.readmda(mlp.realizeFile(firings_true))
F = mdaio.readmda(mlp.realizeFile(firings))
times1 = Ft[1, :]
labels1 = Ft[2, :]
times2 = F[1, :]
labels2 = F[2, :]
out = compare_ground_truth_helper(times1, labels1, times2, labels2)
with open(json_out, 'w') as outfile:
json.dump(out, outfile, indent=4)
def test_convert_array(dtype='int32', shape=[12, 3, 7]):
X = np.array(np.random.normal(0, 1, shape), dtype=dtype)
np.save('test_convert1.npy', X)
convert_array(input='test_convert1.npy',
output='test_convert2.mda') # npy -> mda
convert_array(input='test_convert2.mda',
output='test_convert3.npy') # mda -> npy
convert_array(input='test_convert3.npy',
output='test_convert4.dat') # npy -> dat
convert_array(input='test_convert4.dat',
output='test_convert5.npy',
dtype=dtype,
dimensions=','.join(str(entry)
for entry in X.shape)) # dat -> npy
convert_array(input='test_convert5.npy',
output='test_convert6.mda') # npy -> mda
convert_array(input='test_convert6.mda',
output='test_convert7.dat') # mda -> dat
convert_array(input='test_convert7.dat',
output='test_convert8.mda',
dtype=dtype,
dimensions=','.join(str(entry)
for entry in X.shape)) # dat -> mda
Y = mdaio.readmda('test_convert8.mda')
print(np.max(np.abs(X - Y)), Y.dtype)
def convert_firings(*, firings, params, res_fname, clu_fname, tetrode):
"""
Export firings (either .mda or .npy) to .res & .clu format.
Parameters
----------
firings : INPUT
Path of firings mda (or npy) file (RxL) where R>=3 and L is the number of events. Second row are timestamps, third row are integer labels.
params : INPUT
params_json including channel map for tetrode.
res_fname : OUTPUT
Path of output spike times .res file.
clu_fname : OUTPUT
Path of output spike ids .clu file.
tetrode : int
Which tetrode to write out firings for.
"""
F = mdaio.readmda(firings)
L = F.shape[1]
L = L
whch = F[0, :].ravel()[:]
times = F[1, :].ravel()[:]
labels = F[2, :].ravel().astype(int)[:]
K = np.max(labels)
with open(params, 'r') as fp:
params_obj = json.load(fp)
tetmap = []
pre = 1
for i, x in enumerate(params_obj['tetrodes']):
tetmap.append(list(range(pre, pre + len(x))))
pre += len(x)
which_tet = np.array([np.where(w == tetmap)[0][0] + 1 for w in whch])
inds_k = np.where(which_tet == int(tetrode))[0]
###### Write .res file ######
res = times[inds_k]
np.savetxt(res_fname, res, fmt='%d')
labels_tet = labels[inds_k]
u_labels_tet = np.unique(labels_tet)
K = len(u_labels_tet)
u_new_labels = np.argsort(u_labels_tet).argsort() + 2
new_labels = [
u_new_labels[(l == np.array(u_labels_tet)).argmax()]
for l in labels_tet
]
np.savetxt(clu_fname,
np.concatenate((np.array([K + 1]), new_labels)),
fmt='%d')
return True
def validate_sorting_results(*,dataset_dir,sorting_output_dir,output_dir):
if not os.path.exists(output_dir):
os.mkdir(output_dir)
compare_ground_truth(
firings=sorting_output_dir+'/firings.mda',
firings_true=dataset_dir+'/firings_true.mda',
json_out=output_dir+'/compare_ground_truth.json',
)
compute_templates(
timeseries=dataset_dir+'/raw.mda',
firings=dataset_dir+'/firings_true.mda',
templates_out=output_dir+'/templates_true.mda.prv'
)
mlp.runPipeline()
templates_true=mdaio.readmda(mlp.realizeFile(output_dir+'/templates_true.mda'))
amplitudes_true=np.max(np.max(np.abs(templates_true),axis=1),axis=0)
accuracies=get_accuracies(output_dir+'/compare_ground_truth.json')
return dict(
accuracies=accuracies,
amplitudes_true=amplitudes_true
)
def compute_templates_helper(*, timeseries, firings, clip_size=100):
X = mdaio.DiskReadMda(timeseries)
M, N = X.N1(), X.N2()
F = mdaio.readmda(firings)
L = F.shape[1]
L = L
T = clip_size
Tmid = int(np.floor((T + 1) / 2) - 1)
times = F[1, :].ravel()
labels = F[2, :].ravel().astype(int)
K = np.max(labels)
sums = np.zeros((M, T, K), dtype='float64')
counts = np.zeros(K)
for k in range(1, K + 1):
inds_k = np.where(labels == k)[0]
#TODO: subsample
for ind_k in inds_k:
t0 = int(times[ind_k])
if (clip_size <= t0) and (t0 < N - clip_size):
clip0 = X.readChunk(i1=0, N1=M, i2=t0 - Tmid, N2=T)
sums[:, :, k - 1] += clip0
counts[k - 1] += 1
templates = np.zeros((M, T, K))
for k in range(K):
templates[:, :, k] = sums[:, :, k] / counts[k]
return templates
def load_marks(marks_path, spikes_df):
marks = mdaio.readmda(marks_path)
if marks.shape[-1] == spikes_df.shape[0]:
ch_cols = [f'ch{c:>02d}' for c in np.arange(marks.shape[0])]
marks_df = pd.DataFrame(marks[:,0,:].squeeze().T, columns=ch_cols, \
index=spikes_df.index)
return marks_df
return
def test_synthesize_random_firings():
K = 10
synthesize_random_firings(K=K, firings_out='tmp.firings.mda')
firings = mdaio.readmda('tmp.firings.mda')
labels = firings[2, :]
assert (max(labels) == K)
assert (firings.shape[0] == 3)
return True
def __init__(self, firings_fname):
OutputExtractor.__init__(self)
print('Downloading file if needed: ' + firings_fname)
self._firings_path = mlp.realizeFile(firings_fname)
print('Done.')
self._firings = mdaio.readmda(self._firings_path)
self._times = self._firings[1, :]
self._labels = self._firings[2, :]
self._num_units = np.max(self._labels)
def apply_label_map(*, firings, label_map, firings_out):
"""
Apply a label map to a given firings, including masking and merging
Parameters
----------
firings : INPUT
Path of input firings mda file
label_map : INPUT
Path of input label map mda file [base 1, mapping to zero removes from firings]
firings_out : OUTPUT
...
"""
firings = mdaio.readmda(firings)
label_map = mdaio.readmda(label_map)
label_map = np.reshape(label_map, (-1, 2))
label_map = label_map[np.argsort(label_map[:,
0])] # Assure input is sorted
#Propagate merge pairs to lowest label number
for idx, label in enumerate(label_map[:, 1]):
# jfm changed on 12/8/17 because isin() is not isin() older versions of numpy. :)
#label_map[np.isin(label_map[:,0],label),0] = label_map[idx,0] # Input should be sorted
label_map[np.where(label_map[:, 0] == label)[0],
0] = label_map[idx, 0] # Input should be sorted
#Apply label map
for label_pair in range(label_map.shape[0]):
# jfm changed on 12/8/17 because isin() is not isin() older versions of numpy. :)
#firings[2, np.isin(firings[2, :], label_map[label_pair, 1])] = label_map[label_pair,0]
firings[2, np.where(
firings[2, :] == label_map[label_pair,
1])[0]] = label_map[label_pair, 0]
#Mask out all labels mapped to zero
firings = firings[:, firings[2, :] != 0]
#Write remapped firings
return mdaio.writemda64(firings, firings_out)
def load_clips(clips_path, spikes_df):
# load clips
clips = mdaio.readmda(clips_path)
if clips.shape[-1] == spikes_df.shape[0]:
clips_2d_list = [
clips[int(primary_chan - 1), :, i]
for i, primary_chan in enumerate(spikes_df.primary_chan.values)
]
clips_2d = np.array(clips_2d_list)
cl_cols = [f'{c:>03d}' for c in np.arange(clips_2d.shape[1])]
clips_df = pd.DataFrame(clips_2d, columns=cl_cols, \
index=spikes_df.index)
return clips_df
return
def initialize(self):
print('Downloading timeseries (if needed): {}'.format(
self._timeseries))
if self._timeseries is not None:
timeseries_path = mlp.realizeFile(self._timeseries)
print('Downloading firings (if needed): {}'.format(self._firings))
firings_path = mlp.realizeFile(self._firings)
if self._geom is not None:
print('Downloading geom (if needed): {}'.format(self._geom))
geom_path = mlp.realizeFile(self._geom)
self._G = np.genfromtxt(geom_path, delimiter=',').T
self._G = np.flip(self._G, axis=0)
else:
self._G = None
print('Reading arrays into memory...')
if self._timeseries is not None:
self._X = mdaio.readmda(timeseries_path)
else:
self._X = None
self._F = mdaio.readmda(firings_path)
self._times = self._F[1, :]
self._labels = self._F[2, :]
self._K = int(self._labels.max())
def get_result_from_folder(output_folder):
# overwrite the SorterBase.get_result
from mountainlab_pytools import mdaio
result_fname = Path(output_folder) / 'firings.mda'
assert result_fname.exists(), 'Result file does not exist: {}'.format(
str(result_fname))
firings = mdaio.readmda(str(result_fname))
sorting = se.NumpySortingExtractor()
sorting.set_times_labels(firings[1, :], firings[2, :])
return sorting
def test_compute_templates():
M, N, K, T, L = 5, 1000, 6, 50, 100
X = np.random.rand(M, N)
mdaio.writemda32(X, 'tmp.mda')
F = np.zeros((3, L))
F[1, :] = 1 + np.random.randint(N, size=(1, L))
F[2, :] = 1 + np.random.randint(K, size=(1, L))
mdaio.writemda64(F, 'tmp2.mda')
ret = compute_templates(timeseries='tmp.mda',
firings='tmp2.mda',
templates_out='tmp3.mda',
clip_size=T)
assert (ret)
templates0 = mdaio.readmda('tmp3.mda')
assert (templates0.shape == (M, T, K))
return True
def make_toes(fp):
d = mdaio.readmda(os.path.join(fp, 'mountainout/firings.curated.mda'))
alignfile = glob.glob(os.path.join(fp, '*.align'))
align = pd.read_csv(alignfile[0])
clusters = np.unique(d[2])
Fs = 30000
for cluster in clusters:
spikes = d[1, d[2] == cluster]
channel = channel_map(d[0, d[2] == cluster][0])
starts = np.asarray(align.total_start, dtype=int)
#starts = np.asarray(align.total_pulse, dtype = int)
stops = np.asarray(align.total_stop, dtype=int)
#stops = np.asarray(align.total_pulse+(1.5*Fs), dtype = int)
offsets = np.asarray(align.total_pulse, dtype=int)
indices = [(spikes >= start) & (spikes <= stop)
for start, stop in zip(starts, stops)]
spiketrains = [
spikes[ind] - offset for ind, offset in zip(indices, offsets)
]
dirname = os.path.join(fp, "ch%d_c%d" % (channel, cluster))
if not os.path.exists(dirname):
os.makedirs(dirname)
for stim in align['stim'].unique():
f = [spiketrains[rec] for rec in align[align['stim'] == stim].rec]
#put together an informative name for the file
song = list(align.song[align.stim == stim].unique())[0]
cond = list(align.condition[align.stim == stim].unique())[0]
name = "%s_%s" % (song, cond)
toefile = os.path.join(dirname, "%s.toe_lis" % name)
with open(toefile, "wt") as ftl:
tl.write(ftl, np.asarray(f) / Fs * 1000)
# for song in align['song'].unique():
# f = [spiketrains[rec] for rec in align[align['song']==song][align['condition']=='no-scene'].rec]
# name = song+'_no-scene'
# toefile = os.path.join(dirname, "%s.toe_lis" % name)
# with open(toefile, "wt") as ftl:
# tl.write(ftl, np.asarray(f)/Fs*1000)
# f = [spiketrains[rec] for rec in align[align['song']==song][align['condition'].str.contains('scene63')].rec]
# name = song+'_scene63'
# toefile = os.path.join(dirname, "%s.toe_lis" % name)
# with open(toefile, "wt") as ftl:
# tl.write(ftl, np.asarray(f)/Fs*1000)
auditory_plot(dirname)
cluster_info(dirname, fp, cluster)
def compute_templates_helper(*, timeseries, firings, clip_size=100):
X = DiskReadMda(timeseries)
M, N = X.N1(), X.N2()
N = N
F = mdaio.readmda(firings)
L = F.shape[1]
L = L
T = clip_size
times = F[1, :]
labels = F[2, :].astype(int)
K = np.max(labels)
compute_templates._sums = np.zeros((M, T, K))
compute_templates._counts = np.zeros(K)
def _kernel(chunk, info):
inds = np.where((info.t1 <= times) & (times <= info.t2))[0]
times0 = (times[inds] - info.t1 + info.t1a).astype(np.int32)
labels0 = labels[inds]
clips0 = np.zeros((M, clip_size, len(inds)),
dtype=np.float32,
order='F')
cpp.extract_clips(clips0, chunk, times0, clip_size)
for k in range(1, K + 1):
inds_kk = np.where(labels0 == k)[0]
compute_templates._sums[:, :, k -
1] = compute_templates._sums[:, :, k -
1] + np.sum(
clips0[:, :,
inds_kk],
axis=2)
compute_templates._counts[
k - 1] = compute_templates._counts[k - 1] + len(inds_kk)
return True
TCR = TimeseriesChunkReader(chunk_size_mb=40, overlap_size=clip_size * 2)
if not TCR.run(timeseries, _kernel):
return None
templates = np.zeros((M, T, K))
for k in range(1, K + 1):
if compute_templates._counts[k - 1]:
templates[:, :, k -
1] = compute_templates._sums[:, :, k -
1] / compute_templates._counts[
k - 1]
return templates
def loadSpikeTimestamps(data_file=None):
"""
Load spike timestamps, extracted from the rec file with exportmda
returns: Timestamps for spike data
"""
if data_file is None:
ts_file = QtHelperUtils.get_open_file_name(\
message="Select Timestamp MDA Files", file_format="LFP Data (.dat)")
# Now that we have the timestamp file, we have to read it
try:
timestamps = mdaio.readmda(ts_file)
except (FileNotFoundError, IOError) as err:
print(err)
print('Unable to read TIMESTAMPS file.')
timestamps = None
finally:
return timestamps
def load_firings(firings_path,
samples_offset,
ep_samp_start_offset,
animal,
date,
ntrode,
config_path,
fs=30000):
# load firings
firings = mdaio.readmda(firings_path)
#create spikes_df with firing times with inter-epoch gap
spike_cols = ['animal', 'day', 'epoch', 'ntrode', 'cluster', \
'timedelta', 'sampleindex']
spikes_df = pd.DataFrame(columns=spike_cols)
spikes_sampleindex = samples_offset[firings[1, :].astype(int)]
spikes_timedelta = pd.TimedeltaIndex(spikes_sampleindex / fs,
unit='s',
name='time')
spikes_df['sampleindex'] = spikes_sampleindex
spikes_df['timedelta'] = spikes_timedelta
spikes_df['cluster'] = firings[2, :].astype(int)
spikes_df['primary_chan'] = firings[0, :].astype(int)
#add animal, day, epoch cols:
spikes_df['animal'] = animal
spikes_df['day'] = core.convert_dates_to_days(animal, date, config_path)
spikes_df['ntrode'] = ntrode
spikes_df['epoch'] = 0
ep_samp_start_timedelta = pd.TimedeltaIndex([ep_s/fs for ep_s in \
ep_samp_start_offset], \
unit='s', name='time')
for epn, ep_samp_td in enumerate(ep_samp_start_timedelta):
spikes_df.loc[spikes_df['timedelta'] >= \
ep_samp_td, 'epoch'] = epn+1
spikes_df.set_index(['animal', 'day', 'epoch', 'timedelta', \
'ntrode', 'cluster'], inplace=True)
return spikes_df
def ironclust(*,
recording, # Recording object
tmpdir, # Temporary working directory
detect_sign=-1, # Polarity of the spikes, -1, 0, or 1
adjacency_radius=-1, # Channel neighborhood adjacency radius corresponding to geom file
detect_threshold=5, # Threshold for detection
merge_thresh=.98, # Cluster merging threhold 0..1
freq_min=300, # Lower frequency limit for band-pass filter
freq_max=6000, # Upper frequency limit for band-pass filter
pc_per_chan=3, # Number of pc per channel
prm_template_name, # Name of the template file
ironclust_src=None
):
if ironclust_src is None:
ironclust_src=os.getenv('IRONCLUST_SRC',None)
if not ironclust_src:
raise Exception('You must either set the IRONCLUST_SRC environment variable, or pass the ironclust_src parameter')
source_dir=os.path.dirname(os.path.realpath(__file__))
dataset_dir=tmpdir+'/ironclust_dataset'
# Generate three files in the dataset directory: raw.mda, geom.csv, params.json
si.MdaRecordingExtractor.writeRecording(recording=recording,save_path=dataset_dir)
samplerate=recording.getSamplingFrequency()
print('Reading timeseries header...')
HH=mdaio.readmda_header(dataset_dir+'/raw.mda')
num_channels=HH.dims[0]
num_timepoints=HH.dims[1]
duration_minutes=num_timepoints/samplerate/60
print('Num. channels = {}, Num. timepoints = {}, duration = {} minutes'.format(num_channels,num_timepoints,duration_minutes))
print('Creating .params file...')
txt=''
txt+='samplerate={}\n'.format(samplerate)
txt+='detect_sign={}\n'.format(detect_sign)
txt+='adjacency_radius={}\n'.format(adjacency_radius)
txt+='detect_threshold={}\n'.format(detect_threshold)
txt+='merge_thresh={}\n'.format(merge_thresh)
txt+='freq_min={}\n'.format(freq_min)
txt+='freq_max={}\n'.format(freq_max)
txt+='pc_per_chan={}\n'.format(pc_per_chan)
txt+='prm_template_name={}\n'.format(prm_template_name)
_write_text_file(dataset_dir+'/argfile.txt',txt)
print('Running IronClust...')
cmd_path = "addpath('{}', '{}/matlab', '{}/mdaio');".format(ironclust_src, ironclust_src, ironclust_src)
#"p_ironclust('$(tempdir)','$timeseries$','$geom$','$prm$','$firings_true$','$firings_out$','$(argfile)');"
cmd_call = "p_ironclust('{}', '{}', '{}', '', '', '{}', '{}');"\
.format(tmpdir, dataset_dir+'/raw.mda', dataset_dir+'/geom.csv', tmpdir+'/firings.mda', dataset_dir+'/argfile.txt')
cmd='matlab -nosplash -nodisplay -r "{} {} quit;"'.format(cmd_path, cmd_call)
print(cmd)
retcode=_run_command_and_print_output(cmd)
if retcode != 0:
raise Exception('IronClust returned a non-zero exit code')
# parse output
result_fname=tmpdir+'/firings.mda'
if not os.path.exists(result_fname):
raise Exception('Result file does not exist: '+ result_fname)
firings=mdaio.readmda(result_fname)
sorting=si.NumpySortingExtractor()
sorting.setTimesLabels(firings[1,:],firings[2,:])
return sorting
def read_data(self, dataset_id, file_id):
return readmda(self.directories[dataset_id][file_id])
def export_mountain_cells():
print('expecting call from channel level')
init_path = os.getcwd()
current_path = os.getcwd()
path_split = str.split(current_path,'/')
if path_split[-2] == 'mountains':
channel_path = path_split[-1]
os.chdir('output')
else:
os.chdir('../../../mountains/')
os.chdir(path_split[-1])
channel_path = path_split[-1]
os.chdir('output')
original = mdaio.readmda('firings.mda')
os.chdir('..')
start_time = {}
with open('start_indices.csv') as csvfile:
csvreader = csv.reader(csvfile,delimiter = ',')
linecount = 0
for line in csvreader:
if linecount == 0:
temp = []
for term in line[1:]:
temp.append(int(term.strip(" '][")))
else:
temp = []
for term in line[1:]:
temp.append(term.strip(" ']["))
start_time[line[0]] = temp
linecount += 1
current_path = os.getcwd()
ch = current_path.partition('channel')[1] + current_path.partition('channel')[2]
total_ind = len(original[1])
marker = 0
count = 0
for i in range(total_ind):
if count == len(start_time.get('2'))-1:
exporting_arr = [original[1][marker:total_ind],original[2][marker:total_ind]]
location = os.getcwd()
temp = location.split('/')
upper_folder1 = location[0:len(location)-len(temp[len(temp)-1])-1]
os.chdir(upper_folder1)
temp1 = upper_folder1.split('/')
upper_folder2 = upper_folder1[0:len(upper_folder1)-len(temp1[len(temp1)-1])-1]
os.chdir(upper_folder2)
session_path = upper_folder2 + '/' + start_time.get('2')[count]
os.chdir(session_path)
full_list = []
for name in os.listdir("."):
if os.path.isdir(name):
full_list.append(name)
for folder in full_list:
array_path = session_path + '/' + folder
os.chdir(array_path)
if os.path.isdir(channel_path):
os.chdir(array_path)
split_into_cells_intra_session(ch, exporting_arr, start_time.get('1')[count]);
os.chdir(location)
break
if original[1][i] >= start_time.get('1')[count+1]:
exporting_arr = [original[1][marker:i-1],original[2][marker:i-1]]
location = os.getcwd()
temp = location.split('/')
upper_folder1 = location[0:len(location)-len(temp[len(temp)-1])-1]
os.chdir(upper_folder1)
temp1 = upper_folder1.split('/')
upper_folder2 = upper_folder1[0:len(upper_folder1)-len(temp1[len(temp1)-1])-1]
os.chdir(upper_folder2)
session_path = upper_folder2 + '/' + start_time.get('2')[count]
os.chdir(session_path)
full_list = []
for name in os.listdir("."):
if os.path.isdir(name):
full_list.append(name)
for folder in full_list:
array_path = session_path + '/' + folder
os.chdir(array_path)
if os.path.isdir(channel_path):
os.chdir(array_path)
split_into_cells_intra_session(ch, exporting_arr, start_time.get('1')[count])
marker = i
count += 1
os.chdir(location)
os.chdir(init_path)
def convert_array(*,
input,
output,
format='',
format_out='',
dimensions='',
dtype='',
dtype_out='',
channels=''):
"""
Convert a multi-dimensional array between various formats ('.mda', '.npy', '.dat') based on the file extensions of the input/output files
Parameters
----------
input : INPUT
Path of input array file (can be repeated for concatenation).
output : OUTPUT
Path of the output array file.
format : string
The format for the input array (mda, npy, dat), or determined from the file extension if empty
format_out : string
The format for the output input array (mda, npy, dat), or determined from the file extension if empty
dimensions : string
Comma-separated list of dimensions (shape). If empty, it is auto-determined, if possible, by the input array. If second dim is -1 then it will be extrapolated from file size / first dim.
dtype : string
The data format for the input array. Choices: int8, int16, int32, uint16, uint32, float32, float64 (possibly float16 in the future).
dtype_out : string
The data format for the output array. If empty, the dtype for the input array is used.
channels : string
Comma-seperated list of channels to keep in output. Zero-based indexing. Only works for .dat to .mda conversions.
"""
if isinstance(input, (list, )):
multifile = True
inputs = input
input = inputs[0]
else:
multifile = False
format_in = format
if not format_in:
format_in = determine_file_format(file_extension(input), dimensions)
if not format_out:
format_out = determine_file_format(file_extension(output), dimensions)
print('Input/output formats: {}/{}'.format(format_in, format_out))
ext_in = file_extension(input)
dims = None
if (format_in == 'mda') and (dtype == ''):
header = mdaio.readmda_header(input)
dtype = header.dt
dims = header.dims
if (format_in == 'npy') and (dtype == ''):
A = np.load(input, mmap_mode='r')
dtype = npy_dtype_to_string(A.dtype)
dims = A.shape
A = 0
if dimensions:
dims2 = [int(entry) for entry in dimensions.split(',')]
if dims:
if len(dims) != len(dims2):
raise Exception(
'Inconsistent number of dimensions for input array')
if not np.all(np.array(dims) == np.array(dims2)):
raise Exception('Inconsistent dimensions for input array')
dims = dims2
if not dtype_out:
dtype_out = dtype
if not dtype:
raise Exception('Unable to determine datatype for input array')
if not dtype_out:
raise Exception('Unable to determine datatype for output array')
if (dims[1] == -1) and (dims[0] > 0):
if ((dtype) and (format_in == 'dat')):
bits = int(
dtype[-2:]
) # number of bits per entry of dtype, TODO: make this smarter
if not multifile:
filebytes = os.stat(input).st_size # bytes in input file
else:
dims1 = np.copy(dims)
filebytes1 = os.stat(input).st_size # bytes in input file
entries1 = int(filebytes1 / (int(bits / 8)))
dims1[1] = int(entries1 / dims1[0])
filebytes = sum([os.stat(inp).st_size for inp in inputs])
entries = int(filebytes / (int(bits / 8))) # entries in input file
dims[1] = int(entries / dims[0]) # caclulated second dimension
if DEBUG:
print(bits)
print(filebytes)
print(int(filebytes / (int(bits / 8))))
print(dims)
else:
raise Exception('Could not infer dimensions')
if not dims:
raise Exception('Unable to determine dimensions for input array')
if not channels:
channels = range(0, dims[0])
else:
channels = np.array([int(entry) for entry in channels.split(',')])
if DEBUG:
print(channels)
print('Using dtype={}, dtype_out={}, dimensions={}'.format(
dtype, dtype_out, ','.join(str(item) for item in dims)))
if (format_in == format_out) and ((dtype == dtype_out) or
(dtype_out == '')):
if multifile and (format_in == 'dat'):
print('Concatenating Files')
with open(output, "wb") as outfile:
for input_file in inputs:
with open(input_file, "rb") as inpt:
outfile.write(inpt.read())
elif not multifile:
print('Simply copying file...')
shutil.copyfile(input, output)
print('Done.')
return True
if format_out == 'dat' and not multifile:
if format_in == 'mda':
H = mdaio.readmda_header(input)
copy_raw_file_data(input,
output,
start_byte=H.header_size,
num_entries=np.product(dims),
dtype=dtype,
dtype_out=dtype_out)
return True
elif format_in == 'npy':
print(
'Warning: loading entire array into memory. This should be avoided in the future.'
)
A = np.load(input, mmap_mode='r').astype(dtype=dtype_out,
order='F',
copy=False)
A = A.ravel(order='F')
A.tofile(output)
# The following was problematic because of row-major ordering, i think
#header_size=determine_npy_header_size(input)
#copy_raw_file_data(input,output,start_byte=header_size,num_entries=np.product(dims),dtype=dtype,dtype_out=dtype_out)
return True
elif format_in == 'dat':
raise Exception('This case not yet implemented.')
else:
raise Exception('Unexpected case.')
elif (format_out == 'mda') or (format_out == 'npy'):
if format_in == 'dat' and multifile:
print(
'Warning: loading entire array into memory. This should be avoided in the future.'
)
print(channels) #DEBUG
A = np.fromfile(inputs[0], dtype=dtype, count=np.product(dims))
A = A.reshape(tuple(dims1), order='F')
A = A[channels, :]
for inputn in inputs[1:]:
An = np.fromfile(inputn, dtype=dtype, count=np.product(dims))
dimsN = np.copy(dims1)
dimsN[1] = An.size / dims1[0]
An = An.reshape(tuple(dimsN), order='F')
An = An[channels, :]
print(A.shape)
print(An.shape)
A = np.concatenate((A, An), axis=1)
print(A.shape) #DEBUG
if format_out == 'mda':
mdaio.writemda(A, output, dtype=dtype_out)
else:
mdaio.writenpy(A, output, dtype=dtype_out)
return True
elif format_in == 'dat' and not multifile:
print(
'Warning: loading entire array into memory. This should be avoided in the future.'
)
A = np.fromfile(input, dtype=dtype, count=np.product(dims))
A = A.reshape(tuple(dims), order='F')
A = A[channels, :]
if format_out == 'mda':
mdaio.writemda(A, output, dtype=dtype_out)
else:
mdaio.writenpy(A, output, dtype=dtype_out)
return True
elif format_in == 'mda' and not multifile:
print(
'Warning: loading entire array into memory. This should be avoided in the future.'
)
A = mdaio.readmda(input)
if format_out == 'mda':
mdaio.writemda(A, output, dtype=dtype_out)
else:
mdaio.writenpy(A, output, dtype=dtype_out)
return True
elif format_in == 'mda' and multifile:
print(
'Warning: loading entire array into memory. This should be avoided in the future.'
)
A = mdaio.readmda(inputs[0])
A = A[channels, :]
for inputn in inputs[1:]:
An = mdaio.readmda(inputn)
An = An[channels, :]
A = np.concatenate((A, An), axis=0)
if format_out == 'mda':
mdaio.writemda(A, output, dtype=dtype_out)
else:
mdaio.writenpy(A, output, dtype=dtype_out)
return True
elif format_in == 'npy' and not multifile:
print(
'Warning: loading entire array into memory. This should be avoided in the future.'
)
A = np.load(input, mmap_mode='r').astype(dtype=dtype,
order='F',
copy=False)
if format_out == 'mda':
mdaio.writemda(A, output, dtype=dtype_out)
else:
mdaio.writenpy(A, output, dtype=dtype_out)
return True
elif format_in == 'npy' and multifile:
print(
'Warning: loading entire array into memory. This should be avoided in the future.'
)
A = np.load(inputs[0], mmap_mode='r').astype(dtype=dtype,
order='F',
copy=False)
A = A[channels, :]
for inputn in inputs[1:]:
An = np.load(inputn, mmap_mode='r').astype(dtype=dtype,
order='F',
copy=False)
An = An[channels, :]
A = np.concatenate((A, An), axis=0)
if format_out == 'mda':
mdaio.writemda(A, output, dtype=dtype_out)
else:
mdaio.writenpy(A, output, dtype=dtype_out)
return True
else:
raise Exception('Unexpected case.')
else:
raise Exception('Unexpected output format: {}'.format(format_out))
raise Exception('Unexpected error.')
def separateSpikesInEpochs(data_dir=None,
firings_file='firings.curated.mda',
timestamp_files=None,
write_separated_spikes=True):
"""
Takes curated spikes from MountainSort and combines this information with spike timestamps to create separate curated spikes for each epoch
:firings_file: Curated firings file
:timestamp_files: Spike timestamps file list
:write_separated_spikes: If the separated spikes should be written back to the data directory.
:returns: List of spikes for each epoch
"""
if data_dir is None:
# Get the firings file
data_dir = QtHelperUtils.get_directory(
message="Select Curated firings location")
separated_tetrodes = []
curated_firings = []
merged_curated_firings = []
tetrode_list = os.listdir(data_dir)
for tt_dir in tetrode_list:
try:
if firings_file in os.listdir(data_dir + '/' + tt_dir):
curated_firings.append([])
separated_tetrodes.append(tt_dir)
firings_file_location = '/'.join(
[data_dir, tt_dir, firings_file])
merged_curated_firings.append(
mdaio.readmda(firings_file_location))
print(MODULE_IDENTIFIER +
'Read merged firings file for tetrode %s!' % tt_dir)
else:
print(MODULE_IDENTIFIER +
'Merged firings %s not found for tetrode %s!' %
(firings_file, tt_dir))
except (FileNotFoundError, IOError) as err:
print(MODULE_IDENTIFIER +
'Unable to read merged firings file for tetrode %s!' %
tt_dir)
print(err)
gui_root = Tk()
gui_root.withdraw()
timestamp_headers = []
if timestamp_files is None:
# Read all the timestamp files
timestamp_files = filedialog.askopenfilenames(initialdir=DEFAULT_SEARCH_PATH, \
title="Select all timestamp files", \
filetypes=(("Timestamps", ".mda"), ("All Files", "*.*")))
gui_root.destroy()
for ts_file in timestamp_files:
timestamp_headers.append(mdaio.readmda_header(ts_file))
# Now that we have both the timestamp headers and the timestamp files, we
# can separate spikes out. It is important here for the timestamp files to
# be in the same order as the curated firings as that is the only way for
# us to tell that the firings are being split up correctly.
print(MODULE_IDENTIFIER + 'Looking at spike timestamps in order')
print(timestamp_files)
# First splice up curated spikes into indiviual epochs
for tt_idx, tt_firings in enumerate(merged_curated_firings):
for ep_idx, ts_header in enumerate(timestamp_headers):
if tt_firings is None:
curated_firings[tt_idx].append(None)
continue
n_data_points = ts_header.dims[0]
print(MODULE_IDENTIFIER + 'Epoch ' + str(ep_idx) + ': ' +
str(n_data_points) + ' samples.')
last_spike_from_epoch = np.searchsorted(
tt_firings[1], n_data_points, side='left') - 1
# If there are no spikes in this epoch, there might still be some in future epochs!
if last_spike_from_epoch < 0:
tt_firings[1] = tt_firings[1] - float(n_data_points)
curated_firings[tt_idx].append(None)
continue
last_spike_sample_number = tt_firings[1][last_spike_from_epoch]
print(MODULE_IDENTIFIER + separated_tetrodes[tt_idx] + ': First spike ' + str(tt_firings[1][0])\
+ ', Last spike ' + str(last_spike_sample_number))
epoch_spikes = tt_firings[:, :last_spike_from_epoch]
curated_firings[tt_idx].append(epoch_spikes)
if last_spike_from_epoch < (len(tt_firings[1]) - 1):
# Slice the merged curated firing to only have the remaining spikes
tt_firings = tt_firings[:, last_spike_from_epoch + 1:]
print(MODULE_IDENTIFIER +
'Trimming curated spikes. Aggregate sample start ' +
str(tt_firings[1][0]))
tt_firings[1] = tt_firings[1] - float(n_data_points)
print(MODULE_IDENTIFIER + 'Sample number trimmed to ' +
str(tt_firings[1][0]))
else:
print(MODULE_IDENTIFIER + separated_tetrodes[tt_idx] +
', Reached end of curated firings at Epoch ' +
str(ep_idx))
tt_firings = None
print(MODULE_IDENTIFIER +
'Spikes separated in epochs. Substituting timestamps!')
# For each epoch replace the sample numbers with the corresponding
# timestamps. We are going through multiple revisions for this so that we
# only have to load one timestamp file at a time
for ep_idx, ts_file in enumerate(timestamp_files):
epoch_timestamps = mdaio.readmda(ts_file)
print(MODULE_IDENTIFIER + 'Epoch ' + str(ep_idx))
for tt_idx, tt_curated_firings in enumerate(curated_firings):
if tt_curated_firings[ep_idx] is None:
continue
# Need to use the original array because changes to tt_curated_firings do not get copied back
curated_firings[tt_idx][ep_idx][1] = epoch_timestamps[np.array(
tt_curated_firings[ep_idx][1], dtype=int)]
print(MODULE_IDENTIFIER + separated_tetrodes[tt_idx] + ': Samples (' + \
str(tt_curated_firings[ep_idx][1][0]) + ', ' + str(tt_curated_firings[ep_idx][1][-1]), ')')
if write_separated_spikes:
try:
for tt_idx, tet in enumerate(separated_tetrodes):
for ep_idx in range(len(timestamp_files)):
if curated_firings[tt_idx][ep_idx] is not None:
ep_firings_file_name = data_dir + '/' + tet + '/firings-' + \
str(ep_idx+1) + '.curated.mda'
mdaio.writemda64(curated_firings[tt_idx][ep_idx],
ep_firings_file_name)
except OSError as exception:
if exception.errno != errno.EEXIST:
print(MODULE_IDENTIFIER +
'Unable to write timestamped firings!')
print(exception)
return curated_firings
def compare_ground_truth(*, firings_true, firings, json_out, max_dt=20):
"""
compare a sorting (firings) with ground truth (firings_true)
Parameters
----------
firings_true : INPUT
Path of true firings file (RxL) R>=3, L=#evts
firings : INPUT
Path of sorted firings file (RxL) R>=3, L=#evts
json_out : OUTPUT
Path of the output file containing the results of the comparison
max_dt : int
Tolerance for matching events (in timepoints)
"""
print('Reading arrays...')
F = mdaio.readmda(firings)
Ft = mdaio.readmda(firings_true)
print('Initializing data...')
L = F.shape[1]
Lt = Ft.shape[1]
times = F[1, :]
times_true = Ft[1, :]
labels = F[2, :].astype(np.int32)
labels_true = Ft[2, :].astype(np.int32)
F = 0 # free memory? Alex: depends if python decides to call garbage collection
Ft = 0 # free memory?
N = np.maximum(np.max(times), np.max(times_true))
K = np.max(labels)
Kt = np.max(labels_true)
# todo: subsample in first pass to get the best
# First we split into segments
print('Splitting into segments')
segment_size = max_dt
num_segments = int(np.ceil(N / segment_size))
N = num_segments * segment_size
segments = []
# occupancy: K x num_segments
occupancy, counts = create_occupancy_array(times,
labels,
segment_size,
num_segments,
K,
spread=False,
multiplicity=True)
# occupancy_true: Kt x num_segments
occupancy_true, counts_true = create_occupancy_array(times_true,
labels_true,
segment_size,
num_segments,
Kt,
spread=True,
multiplicity=False)
# Note: we spread the occupancy_true but not the occupancy
# Note: we count the occupancy with multiplicity but not occupancy_true
print('Computing pairwise counts and accuracies...')
pairwise_counts = occupancy_true @ occupancy.transpose() # Kt x K
pairwise_accuracies = np.zeros((Kt, K))
for k1 in range(1, Kt + 1):
for k2 in range(1, K + 1): # jfm fixed +1 bug on 8/29/18
numer = pairwise_counts[k1 - 1, k2 - 1]
denom = counts_true[k1 - 1] + counts[k2 - 1] - numer
if denom > 0:
pairwise_accuracies[k1 - 1, k2 - 1] = numer / denom
print('Preparing output...')
ret = {"true_units": {}}
for k1 in range(1, Kt + 1):
k2_match = int(1 + np.argmax(pairwise_accuracies[k1 - 1, :].ravel()))
# todo: compute accuracy more precisely here
num_matches = int(pairwise_counts[k1 - 1, k2_match - 1])
num_false_positives = int(counts[k2_match - 1] - num_matches)
num_false_negatives = int(counts_true[k1 - 1] - num_matches)
unit = {
"best_match": k2_match,
"accuracy": pairwise_accuracies[k1 - 1, k2_match - 1],
"num_matches": num_matches,
"num_false_positives": num_false_positives,
"num_false_negatives": num_false_negatives
}
ret['true_units'][k1] = unit
print('Writing output...')
str = json.dumps(ret, indent=4)
with open(json_out, 'w') as out:
out.write(str)
print('Done.')
return True
from mountainlab_pytools import mdaio
import sys
from scipy.interpolate import interp1d
if len(sys.argv)<2:
print('Not enough input. I need the tetrode number #t (folder tet+#t where to find the files firings.mda and raw_filt.mda')
exit()
tet= sys.argv[1]
fold='tet'+tet
fpar = open(fold + '/' + 'tet' + tet + '.par.' + tet)
nchan = int(fpar.readline().split()[1])
print('Number of channels:',nchan)
a = mdaio.readmda(fold+'/raw_filt.mda')
b = mdaio.readmda(fold+'/firings.mda')
nC, L = a.shape # number of channels, length of recording
res = b[1,:].astype(int)
clu = b[2,:].astype(int)
print(res[-1])
c = np.zeros([len(res),nchan,32]) # was 32
ce = np.zeros([len(res),nchan,33])
for ir, r in enumerate(res):
if r > 15 and r < L-18:
c[ir,:,:] = a[:,r-15:r+17] # was 17
def __init__(self, path):
self._timeseries_path = path
self._timeseries = mdaio.readmda(path)
def compute_cluster_metrics(*,timeseries='',firings,metrics_out,clip_size=100,samplerate=0,
refrac_msec=1):
"""
Compute cluster metrics for a spike sorting output
Parameters
----------
firings : INPUT
Path of firings mda file (RxL) where R>=3 and L is the number of events. Second row are timestamps, third row are integer cluster labels.
timeseries : INPUT
Optional path of timeseries mda file (MxN) which could be raw or preprocessed
metrics_out : OUTPUT
Path of output json file containing the metrics.
clip_size : int
(Optional) clip size, aka snippet size (used when computing the templates, or average waveforms)
samplerate : float
Optional sample rate in Hz
refrac_msec : float
(Optional) Define interval (in ms) as refractory period. If 0 then don't compute the refractory period metric.
"""
print('Reading firings...')
F=mdaio.readmda(firings)
print('Initializing...')
R=F.shape[0]
L=F.shape[1]
assert(R>=3)
times=F[1,:]
labels=F[2,:].astype(np.int)
K=np.max(labels)
N=0
if timeseries:
X=mdaio.DiskReadMda(timeseries)
N=X.N2()
if (samplerate>0) and (N>0):
duration_sec=N/samplerate
else:
duration_sec=0
clusters=[]
for k in range(1,K+1):
inds_k=np.where(labels==k)[0]
metrics_k={
"num_events":len(inds_k)
}
if duration_sec:
metrics_k['firing_rate']=len(inds_k)/duration_sec
cluster={
"label":k,
"metrics":metrics_k
}
clusters.append(cluster)
if timeseries:
print('Computing templates...')
templates=compute_templates_helper(timeseries=timeseries,firings=firings,clip_size=clip_size)
for k in range(1,K+1):
template_k=templates[:,:,k-1]
# subtract mean on each channel (todo: vectorize this operation)
# Alex: like this?
# template_k[m,:] -= np.mean(template_k[m,:])
for m in range(templates.shape[0]):
template_k[m,:]=template_k[m,:]-np.mean(template_k[m,:])
peak_amplitude=np.max(np.abs(template_k))
clusters[k-1]['metrics']['peak_amplitude']=peak_amplitude
## todo: subtract template means, compute peak amplitudes
if refrac_msec > 0:
print('Computing Refractory Period Violations')
msec_string = '{0:.5f}'.format(refrac_msec).rstrip('0').rstrip('.')
rr_string = 'refractory_violation_{}msec'.format(msec_string)
max_dt_msec=50
bin_size_msec=refrac_msec
auto_cors = compute_cross_correlograms_helper(firings=firings,mode='autocorrelograms',samplerate=samplerate,max_dt_msec=max_dt_msec,bin_size_msec=bin_size_msec)
mid_ind = np.floor(max_dt_msec/bin_size_msec).astype(int)
mid_inds = np.arange(mid_ind-2,mid_ind+2)
for k0,auto_cor_obj in enumerate(auto_cors['correlograms']):
auto = auto_cor_obj['bin_counts']
k = auto_cor_obj['k']
peak = np.percentile(auto, 75)
mid = np.mean(auto[mid_inds])
rr = safe_div(mid,peak)
clusters[k-1]['metrics'][rr_string] = rr
ret={
"clusters":clusters
}
print('Writing output...')
str=json.dumps(ret,indent=4)
with open(metrics_out, 'w') as out:
out.write(str)
print('Done.')
return True
bandpass_filter.version = '0.1'
if __name__ == "__main__":
samplerate = int(3e4)
freq_min = 250
freq_max = 6000
data_dir = '../ephys_preprocessing/'
raw_data_ch1 = np.asarray(
sio.loadmat(os.path.join(data_dir, 'raw_data_ch1.mat'))['data'])
mdaio.writemda32(raw_data_ch1, os.path.join(data_dir, 'raw_data_ch1.mda'))
timeseries = os.path.join(data_dir, 'raw_data_ch1.mda')
timeseries_out = os.path.join(data_dir, 'filtered_raw_data_ch1.mda')
bandpass_filter(timeseries, timeseries_out, samplerate, freq_min, freq_max)
filtered_data = mdaio.readmda(
os.path.join(data_dir, 'filtered_raw_data_ch1.mda'))
detrended_data_ch1 = np.asarray(
sio.loadmat(os.path.join(data_dir, 'detrended_data_ch1.mat'))['copy'])
mdaio.writemda32(detrended_data_ch1,
os.path.join(data_dir, 'detrended_data_ch1.mda'))
timeseries = os.path.join(data_dir, 'detrended_data_ch1.mda')
timeseries_out = os.path.join(data_dir, 'filtered_detrended_data_ch1.mda')
bandpass_filter(timeseries, timeseries_out, samplerate, freq_min, freq_max)
filtered_data_detrended = mdaio.readmda(
os.path.join(data_dir, 'filtered_detrended_data_ch1.mda'))
plt.plot(raw_data_ch1[0, :], label='raw')
plt.plot(filtered_data_detrended[0, :], label='filtered_detrended')
# plt.plot(detrended_data_ch1[0, :], label='raw_detrended')
def read_mda_timestamps(file):
return readmda(file)
def loadClusteredData(data_location=None,
firings_file='firings.curated.mda',
helper_file='hand_curated.mv2',
time_limits=None):
"""
Load up clustered data and pool it.
:data_location: Directory which has clustered data from all the tetrodes.
:time_limits: (Floating Point) Real time limits within which the data should be extracted.
:returns: Spike data, separated into containers for individual units.
"""
if data_location is None:
# Get the location using a file dialog
data_location = QtHelperUtils.get_directory("Select data location.")
clustered_spikes = []
tt_cl_to_unique_cluster_id = {}
unique_cluster_id = 0
tetrode_list = os.listdir(data_location)
for tt_dir in tetrode_list:
tt_dir_path = os.path.join(data_location, tt_dir)
if not os.path.isdir(tt_dir_path):
continue
if firings_file in os.listdir(tt_dir_path):
tt_idx = tt_dir.split('nt')[1]
firings_file_path = os.path.join(tt_dir_path, firings_file)
curation_file_path = os.path.join(tt_dir_path, helper_file)
try:
# Read the firings file
firing_data = mdaio.readmda(firings_file_path)
except Exception as err:
print('Tetrode ' + tt_dir + 'Unable to read firings file!')
print(err)
continue
try:
# Read the curation file for info on spike clusters
with open(curation_file_path, 'r') as f:
curation_file = json.load(f)
# Get all cluster IDs. This includes noise, mua, everything!
cluster_ids = [
int(cl)
for cl in curation_file['cluster_attributes'].keys()
]
except (FileNotFoundError, IOError) as err:
print('Tetrode ' + tt_dir + 'Unable to read curation file.')
continue
# Read off spikes for individual clusters and assign unique cluster IDs to them
if time_limits is not None:
firing_times = (firing_data[1] -
firing_data[1][0]) / SPIKE_SAMPLING_RATE
time_limit_start_idx = np.searchsorted(firing_times,
time_limits[0],
side='left')
time_limit_finish_idx = np.searchsorted(firing_times,
time_limits[1],
side='right')
firing_data = firing_data[:, time_limit_start_idx:
time_limit_finish_idx]
firing_clusters = firing_data[2]
n_clusters = 0
for unit_id in cluster_ids:
unit_spikes = firing_data[1][firing_clusters == unit_id]
if len(unit_spikes > 0):
tt_cl_to_unique_cluster_id[(tt_idx,
unit_id)] = unique_cluster_id
n_clusters += 1
unique_cluster_id += 1
clustered_spikes.append(unit_spikes)
else:
clustered_spikes.append(None)
n_spikes = len(firing_data[1])
print('Tetrode %s loaded %d spikes from %d clusters.' %
(tt_dir, n_spikes, n_clusters))
else:
print('Tetrode ' + tt_dir + ': Firings file not found!')
return clustered_spikes
