def read_nbm(filename):
"""Reads NBF metadata, which is usually saved in an 'nbm' file. This
file contains basic information about the recording."""
attrs = {}
iprint('Reading nbm file {}.'.format(filename))
with open(filename) as f:
for line in f:
x = line[0:-1].split('=') # No spaces allowed please!!
if len(x) == 2:
attrs[x[0]] = x[1]
iprint('Attribute: {} = {}'.format(x[0], x[1]))
else:
wprint("Don't know what to do with this line: {}".format(line))
try:
date = attrs['date']
except:
date = None
if attrs['dirname'][0] == '.':
new_dirname = os.path.dirname(os.path.abspath(filename))
attrs['dirname'] = new_dirname
metadata = nb_metadata(attrs['dirname'],
sample_rate=float(attrs['sample_rate']),
nchannels=int(attrs['nchannels']),
start=int(attrs['start']),
end=int(attrs['end']),
date=date,
attributes=attrs)
return metadata
def parse_uri(uri, filename=None):
true_uri, rel = resolve_relative_paths(uri, filename)
if rel and filename is None:
wprint('URI path is relative, but no base filename is specified.')
else:
uri = true_uri
iprint('URI: {}'.format(uri))
desc = urisplit(uri)
return desc, rel
def create_table(self, es, name):
es.execute('pragma foreign_key=ON;')
try:
es.execute(self.defs[name])
if self.verbose:
iprint('Created table {}.'.format(name))
except Exception as e:
if self.verbose:
wprint('Could not create table {}. Error: {}'.format(name,e))
def maybe_fix_filenames(self, dirname):
old = os.path.dirname(self.filename)
iprint('maybe_fix_filenames: dirname={}'.format(dirname))
iprint('maybe_fix_filenames: old dirname={}'.format(old))
if dirname != old:
wprint('Directory was moved. Resetting...')
name = os.path.basename(dirname)
self.filename = os.path.join(dirname, '{}.nbm'.format(name))
self.rawfile = os.path.join(dirname, '{}.raw'.format(name))
self.meanfile = os.path.join(dirname, '{}-mean.pyr'.format(name))
self.minfile = os.path.join(dirname, '{}-min.pyr'.format(name))
self.maxfile = os.path.join(dirname, '{}-max.pyr'.format(name))
def set_functions(self, basis_id, fn_list):
n = len(fn_list[0])
for vec in fn_list:
if len(vec) != n:
wprint(
'db3.set_functions: All elements of fn_list must have equal length. Not adding this basis set!'
)
return False
for i in range(len(fn_list)):
vec = fn_list[i]
for k in range(n):
self.cur.execute(
'insert or replace into functions values({}, {}, {}, {});'.
format(basis_id, i, k, vec[k]))
self.commit()
return True
def cue(es):
"""Return a vector of length N (N = number of spike events) that is 0 up until a desired cue event (e.g., injection or behavioral event) and k (the event label) after that point."""
nev = es.event_count()
event_info = es.get_events()
if nev < 1:
wprint(
"Error: this file should have exactly 1 event. It contains {}!".
format(nev))
else:
event_time = event_info[0][0]
event_code = event_info[1][0]
n = es.get_spike_count()
vec = np.zeros(n)
state = 0
for i in range(0, n):
curr_time = es.get_spike_timestamp(i)
if curr_time > event_time:
vec[i] = event_code
return vec
def add_basis(self,
basis_id,
sigma,
width,
nfuncs=5,
offset=0,
name="gaussian_basis"):
"""Adds a Gaussian basis with the specified sigma and width in
SAMPLES to the database, with the desired ID."""
ret = True
self.cur.execute(
'SELECT * from basis where basisID == {};'.format(basis_id))
result = self.cur.fetchall()
iprint("{}".format(result))
if result is None or len(result) == 0:
self.cur.execute(
'INSERT INTO basis values ({}, {}, {}, {}, {}, "{}");'.format(
basis_id, offset, sigma, width, nfuncs, name))
self.conn.commit()
else:
result = result[0]
if math.fabs(result[1] - sigma) > 1.0e-06 or result[
2] != width or result[3] != nfuncs:
wprint(
"Basis ID {} is already in use with these parameters: sigma={}, window width={}, n={}"
.format(result[0], result[1], result[2], result[3]))
iprint("Here are the basis ID's in use in this file:")
self.cur.execute('SELECT * from basis;')
result = self.cur.fetchall()
iprint("BasisID offset sigma window nfuncs name")
for tuple in result:
iprint("{} {} {} {} {} {}".format(
tuple[0], tuple[1], tuple[2], tuple[3], tuple[4],
tuple[5]))
ret = False
else:
iprint(
"Your basis set is already available in {}.".format(self))
ret = True
return ret
def open(uri, filename=None):
"""Given a URI for a data source, open it and return the appropriate data source object."""
if True:
desc, rel = parse_uri(uri, filename)
else:
new_uri, rel = resolve_relative_paths(uri, filename)
if rel and filename is None:
wprint('Data store path is relative, but no event store is specified.')
else:
uri = new_uri
desc = urisplit(uri)
iprint('Opening data store at {}'.format(uriunsplit(desc)))
s = desc.scheme
if s is None:
return ndk.ds.neo_in.spike2(desc)
elif s == 'pre':
return ndk.ds.pre.pre_ds(desc)
elif s == 'smr':
return ndk.ds.neo_in.spike2(desc)
# elif s == 'file':
# return ndk.ds.neo.neo_in(desc)
elif s == 'cass':
return ndk.ds.cass.cdb(desc)
elif s == 'wav':
return ndk.ds.wav.wav_ds(desc.path)
elif s == 'ds':
return ndk.ds.mmap.mmap_ds(desc.path)
elif s == 'edf':
return ndk.ds.edf_ds(desc)
elif s == 'nbm':
iprint('NBF path: {}'.format(desc.path))
if rel and desc.path[0] == '/' and desc.path[1] == '.':
return ndk.ds.nbf(desc.path[1:]) # Hack!
else:
return ndk.ds.nbf(desc.path)
else:
print("Don't know what do with this URI scheme: {} (in {})".format(s, uri))