def copy(kfile, afile, datatypes=0):
"""
copies the contents of .kwd hdf5 file to a .arf hdf5 file
"""
# copy top level attributes
for k,v in kfile.attrs.items():
afile.attrs[k] = v
# descend into /recordings
recordings = kfile["recordings"]
# recordings holds the "entries", which have names "0", "1", "2", etc
for kname, kentry in recordings.items():
timestamp = 0 # TODO determine correct timestamp
e = arf.create_entry(afile, kname, timestamp)
for k,v in kentry.attrs.items():
e.attrs[k] = v
kdata = kentry["data"]
if len(datatypes) == 1:
datatypes = datatypes * kdata.shape[1]
else:
assert len(datatypes) == kdata.shape[1]
channel_bit_volts = kentry["application_data"].attrs["channel_bit_volts"]
channel_sample_rates = kentry["application_data"].attrs["channel_sample_rates"]
# kwik files are SxN datasets, while in arf it's N datasets of length S
for i in range(kdata.shape[1]):
dset = arf.create_dataset(e, name=str(i), data=np.array([],dtype=np.int16),
maxshape=(kdata.shape[0],),
sampling_rate=channel_sample_rates[i],
units='samples', datatype=datatypes[i],
compression=6)
dset.attrs["bit_volts"] = channel_bit_volts[i]
for j in range(int(kdata.shape[0]/BUFFERSIZE) + 1):
index = j*BUFFERSIZE
arf.append_data(dset, kdata[index:index + BUFFERSIZE, i])
def test07_append_to_table():
fp = arf.open_file("test07", mode="a", driver="core", backing_store=False)
dtype = nx.dtype({'names': ("f1","f2"), 'formats': [nx.uint, nx.int32]})
dset = arf.create_table(fp, 'test', dtype=dtype)
assert_equal(dset.shape[0], 0)
arf.append_data(dset, (5, 10))
assert_equal(dset.shape[0], 1)
def add_label(self, name, start, stop):
"""adds label to plot if possible. Returns the index of the new label in the sorted dataset"""
if self.lbl.maxshape != (None,): #if dataset is extensible
win = self.parentWidget().getViewWidget()
reply = QMessageBox.question(win,"", "Label cannot be added because dataset is not extensible. Replace with extensible dataset?", QMessageBox.No | QMessageBox.Yes, QMessageBox.No)
self.key = None #because keyReleaseEvent may be ignored during message box display
if reply == QMessageBox.Yes:
lbl = self.file[self.path]
self.lbl = replace_dataset(lbl, lbl.parent, data=lbl[:], maxshape=(None,))
else:
return
elif self.file.mode == 'r':
win = self.parentWidget().getViewWidget()
QMessageBox.critical(win,"", "Cannot add label. Make sure you have write permission for this file.", QMessageBox.Ok)
self.key = None
return
arf.append_data(self.lbl,(name,start,stop))
self.double_clicked = np.append(self.double_clicked,False)
sort_idx = self.sort_lbl()
new_idx = np.argmax(sort_idx==(len(self.lbl)-1))
self.plot_all_events()
return new_idx
def test07_append_to_table():
fp = arf.open_file("test07", mode="a", driver="core", backing_store=False)
dtype = nx.dtype({'names': ("f1","f2"), 'formats': [nx.uint, nx.int32]})
dset = arf.create_table(fp, 'test', dtype=dtype)
assert_equal(dset.shape[0], 0)
arf.append_data(dset, (5, 10))
assert_equal(dset.shape[0], 1)
def save(stream, filename, path, sampling_rate=None, chunk_size=None):
""" Saves a Stream object to an .arf file.
Can't be called by an instance of ArfStreamer.
"""
if chunk_size == None:
chunk_size = stream.chunk_size
if sampling_rate == None:
raise Exception("You must specify the sampling rate in ArfStreamer.save")
with arf.open_file(filename, 'a') as file:
path = path.split("/")
dst_name = path[-1]
grp_path = "/".join(path[:-1])
grp = file.require_group(grp_path)
#Get first batch of data
data = stream.read(chunk_size)
try:
dst = arf.create_dataset(grp, dst_name, data,
maxshape=(None,), sampling_rate=sampling_rate)
except:
raise ValueError('Error, maybe dataset with that name already exists')
while True:
data = stream.read(chunk_size)
if len(data) == 0:
break
arf.append_data(dst, data)
file.flush()
def match_stimuli(stimuli, entries, sampling_rate, table_name='stimuli'):
"""
Create labels in arf entries that indicate stimulus onset and
offset. As the explog (or equivalent logfile) is parsed, the
onset times of the entries and stimuli are collected. Based on
these times, this function matches each item in the list of
stimuli to an entry.
stimuli: dictionary of onset, stimulus_name pairs
entries: dictionary of onset, arf entry pairs
sampling_rate: the sampling rate of the onset times
table_name: the name of the node to store the label data in
"""
log.debug("Matching stimuli to entries:")
entry_times = nx.sort(list(entries.keys()))
# slow, but simple
for onset in sorted(stimuli.keys()):
stim = stimuli[onset]
idx = entry_times.searchsorted(onset, side='right') - 1
if idx < 0 or idx > entry_times.size:
log.debug("%s (onset=%d) -> no match!", stim, onset)
continue
eonset = entry_times[idx]
entry = entries[eonset]
units = 'samples'
t_onset = onset - eonset
# check that stim isn't occuring after the end of the recording
max_length = max(dset.size for dset in entry.values())
if t_onset >= max_length:
log.debug("%s (onset=%d) -> after end of last entry", stim, onset)
continue
log.debug("%s (onset=%d) -> %s @ %d samples",
stim, onset, entry.name, t_onset)
# add to list of intervals. this is trickier in h5py
if table_name not in entry:
stimtable = arf.create_table(
entry, table_name, event_dtype,
sampling_rate=sampling_rate,
units=units, datatype=arf.DataTypes.EVENT)
arf.set_uuid(
stimtable, get_uuid(entry.attrs['pen'], entry.attrs['site'], table_name))
else:
stimtable = entry[table_name]
arf.append_data(stimtable, (t_onset, 0x00, stim))
entry.attrs['protocol'] = stim
def mouseClickEvent(self, event):
if event.button() == Qt.LeftButton:
pos=self.getViewBox().mapSceneToView(event.scenePos())
t = pos.x() * self.scaling_factor
if self.key and not self.activeLabel:
arf.append_data(self.lbl, (self.key, t, t))
self.activeLabel = self.plot_complex_event(self.lbl[-1])
if event.modifiers() != Qt.ShiftModifier:
self.sort_lbl()
self.activeLabel = None
elif self.activeLabel:
if t >= self.lbl[-1]['start']:
self.lbl[-1] = (self.lbl[-1]['name'], self.lbl[-1]['start'], t)
else:
self.lbl[-1] = (self.lbl[-1]['name'], t, self.lbl[-1]['stop'])
new_region = (np.array([self.lbl[-1]['start'], self.lbl[-1]['stop']])/
self.scaling_factor)
self.activeLabel.setRegion(new_region)
self.activeLabel = None
self.sort_lbl()
def test07_append_to_table():
fp = arf.open_file("test07", mode="a", driver="core", backing_store=False)
dset = arf.create_table(fp, 'test', dtype=nx.dtype([('f1', nx.uint), ('f2', nx.int32)]))
assert_equal(dset.shape[0], 0)
arf.append_data(dset, (5, 10))
assert_equal(dset.shape[0], 1)
