def gpv(vl, t_cells, label_l, K, bin_size, room):
''' Returns a matrix of feature vectors.
The feature vector is:
[fr cell 1, fr cell 2, ..., fr cell n, frac in bin1, frac in bin2,...]
The matrix dimension is [# of vectors, # cells + # bins]
With labels [mode context1, mode context2,...]
K is the length of the subvector that will be used to calculate firing rate
'''
# Check data integrity
assert len(label_l) == len(vl['xs'])
assert (room[0][1] - room[0][0]) % bin_size == 0
assert (room[1][1] - room[1][0]) % bin_size == 0
xbins = (room[0][1] - room[0][0]) / bin_size
ybins = (room[1][1] - room[1][0]) / bin_size
end = (len(label_l) / K) * K # Use integer roundoff to our advantage
logging.warning('Threw away %i/%i points.',
len(label_l) - end, len(label_l))
# Generate an indicator array for identity of spiking cell
spks = spk_indicators(t_cells, len(label_l))
spks = spks[:end].reshape([-1, K]).astype(int) # make the right size
label_l = label_l[:end].reshape([-1, K])
# Generate an indicator array for bin number
bins = bin_indicator(vl['xs'], vl['ys'], xbins, ybins, bin_size, room)
bins = bins[:end].reshape([-1, K]) # Make the right size
# The main data structures
Xs = np.zeros([end / K, len(t_cells) + xbins * ybins])
# Put in cell firing rates
for tetrode, cell in t_cells:
cur_cell_id = cell_id(tetrode, cell, t_cells)
debug_tmp = np.bitwise_and(
spks,
np.ones(spks.shape).astype(int) * 2**cur_cell_id)
assert np.sum(debug_tmp == 0) + np.sum(
debug_tmp == 2**cur_cell_id) == debug_tmp.size
cur_cell_spk = (debug_tmp > 0)
Xs[:, cur_cell_id] = np.mean(cur_cell_spk, axis=1)
# Make sure spikes don't disappear
assert np.sum(cur_cell_spk) == len(np.unique(t_cells[(tetrode, cell)]))
# Put bin fractions in
for xbin, ybin in product(range(xbins), range(ybins)):
cbin_id = bin_id(xbin, ybin, ybins)
cbin_index = bin_index(xbin, ybin, ybins)
Xs[:, len(t_cells) + cbin_index] = np.mean(bins == cbin_id, axis=1)
Ys = np.squeeze(mode(label_l, axis=1)[0])
# All Ys are still valid labels
labels = np.unique(label_l)
assert np.sum(label_l == labels[0]) + np.sum(
label_l == labels[1]) == label_l.size
# Fractions add up to 1
assert np.allclose(np.ones(end / K), np.sum(Xs[:, len(t_cells):], axis=1))
# Bin fractions are right
if logging.getLogger().level <= 10:
bins2 = bins.reshape([-1])
for i in range(0, len(label_l) / K):
curv = Xs[i, len(t_cells):]
curbins = bins2[i * K:i * K + K]
for curbin in range(xbins * ybins):
assert 1.0 * np.sum(curbins == (curbin +
1)) / K == curv[curbin]
# Everything is between 0 and 1
assert np.all(Xs >= 0) and np.all(Xs <= 1)
# Check that no spikes are missing
if logging.getLogger().level <= 10:
for tetrode, cell in t_cells:
actual_spks = len(np.unique(t_cells[(tetrode, cell)]))
iid = cell_id(tetrode, cell, t_cells)
Xs_spks = K * np.sum(Xs[:, iid])
assert np.allclose(Xs_spks, actual_spks)
return Xs, Ys
def gpv(vl, t_cells, label_l, K, bin_size, room):
''' Returns a matrix of feature vectors that is
firing rate.
The feature vector is:
[fr cell 1, fr cell 2, ..., fr cell n, mode X, mode Y]
With labels [mode context1, mode context2,...]
t_cells
'''
# Check data integrity
assert len(label_l) == len(vl['xs'])
assert (room[0][1] - room[0][0]) % bin_size == 0
assert (room[1][1] - room[1][0]) % bin_size == 0
#cache_key = (vl['xs'][::100],t_cells,label_l[::112],K,bin_size,room,'gpv by bin')
#cache = try_cache(cache_key)
#if cache is not None: return cache
xbins = (room[0][1] - room[0][0]) / bin_size
ybins = (room[1][1] - room[1][0]) / bin_size
# Generate an indicator array for identity of spiking cell
spks = spk_indicators(t_cells, len(label_l))
labels = np.unique(label_l)
lbl_is = {lbl: np.nonzero(label_l == lbl)[0] for lbl in labels}
# Generate an indicator array for bin number
bins = bin_indicator(vl['xs'], vl['ys'], xbins, ybins, bin_size, room)
bin_is = {(xbin, ybin): np.nonzero(bins == bin_id(xbin, ybin, ybins))[0]
for xbin, ybin in product(range(xbins), range(ybins))}
# The main data structures
Xs = []
Ys = []
# Debug structures
all_accounted_for = 0 # Keep track of the moments in time
thrown_away = 0
for xbin, ybin, lbl in product(range(xbins), range(ybins), labels):
cbin_id = bin_id(xbin, ybin, ybins)
bin_i = bin_is[(xbin, ybin)]
lbl_i = lbl_is[lbl]
cur_i = np.intersect1d(bin_i, lbl_i)
if len(cur_i) == 0: continue # Never in this bin with this context
# Debug code
all_accounted_for += len(cur_i)
# Set up problem to use find_runs
sgn2 = np.zeros([len(label_l), 1])
sgn2[cur_i] = 1
sgn, run_len = find_runs(sgn2)
run_start = np.intersect1d(sgn, cur_i)
assert len(run_start) > 0
for st in run_start:
run_l = run_len[sgn == st]
if run_l < K:
thrown_away += run_l
continue
delt = (run_l / K) * K # Use rounding error to our advantage
thrown_away += run_l - delt
assert delt % K == 0
X = np.zeros([delt / K, len(t_cells) + xbins * ybins
]) # Extra vector space for x and y
spks_tmp = spks[st:st + delt].reshape([K, -1])
for tetrode, cell in t_cells:
cur_cell_id = cell_id(tetrode, cell, t_cells)
tmp = np.bitwise_and(
spks_tmp.astype(int),
np.ones(spks_tmp.shape).astype(int) * 2**cur_cell_id) > 0
rt = np.sum(tmp, axis=0)
X[:, cur_cell_id] = rt
X[:, len(t_cells) + bin_index(xbin, ybin, ybins)] = 1
Xs.append(X)
Ys.append(np.ones([delt / K]) * lbl)
assert all_accounted_for == len(label_l)
Xs = np.concatenate(Xs)
Ys = np.concatenate(Ys)
# Make sure bins were assigned correctly
for xbin, ybin in product(range(xbins), range(ybins)):
cbin_id = bin_id(xbin, ybin, ybins)
cbin_index = bin_index(xbin, ybin, ybins)
if K == 1:
assert np.sum(bins == cbin_id) == np.sum(Xs[:,
len(t_cells) +
cbin_index])
logging.warning('Threw away %i/%i points when generating PV by bin',
thrown_away, len(label_l))
#out = (Xs,Ys)
#logging.warning('Storing ByBin gpv')
#store_in_cache(cache_key,out)
return Xs, Ys
def gpv(vl, t_cells, label_l, K,bin_size, room):
''' Returns a matrix of feature vectors that is
firing rate.
The feature vector is:
[fr cell 1, fr cell 2, ..., fr cell n, mode X, mode Y]
With labels [mode context1, mode context2,...]
t_cells
'''
# Check data integrity
assert len(label_l) == len(vl['xs'])
assert (room[0][1]-room[0][0]) % bin_size == 0
assert (room[1][1]-room[1][0]) % bin_size == 0
#cache_key = (vl['xs'][::100],t_cells,label_l[::112],K,bin_size,room,'gpv by bin')
#cache = try_cache(cache_key)
#if cache is not None: return cache
xbins = (room[0][1]-room[0][0]) / bin_size
ybins = (room[1][1]-room[1][0]) / bin_size
# Generate an indicator array for identity of spiking cell
spks = spk_indicators(t_cells, len(label_l))
labels = np.unique(label_l)
lbl_is = {lbl:np.nonzero(label_l==lbl)[0] for lbl in labels}
# Generate an indicator array for bin number
bins = bin_indicator(vl['xs'],vl['ys'],xbins,ybins,bin_size,room)
bin_is = {(xbin,ybin):np.nonzero(bins==bin_id(xbin,ybin,ybins))[0] for xbin,ybin in product(range(xbins),range(ybins))}
# The main data structures
Xs = []
Ys = []
# Debug structures
all_accounted_for = 0 # Keep track of the moments in time
thrown_away = 0
for xbin,ybin,lbl in product(range(xbins),range(ybins),labels):
cbin_id = bin_id(xbin,ybin,ybins)
bin_i = bin_is[(xbin,ybin)]
lbl_i = lbl_is[lbl]
cur_i = np.intersect1d(bin_i, lbl_i)
if len(cur_i)==0:continue # Never in this bin with this context
# Debug code
all_accounted_for += len(cur_i)
# Set up problem to use find_runs
sgn2 = np.zeros([len(label_l),1])
sgn2[cur_i] = 1
sgn, run_len = find_runs(sgn2)
run_start = np.intersect1d(sgn,cur_i)
assert len(run_start) > 0
for st in run_start:
run_l = run_len[sgn==st]
if run_l<K:
thrown_away += run_l
continue
delt = (run_l/K)*K # Use rounding error to our advantage
thrown_away += run_l-delt
assert delt%K == 0
X = np.zeros([delt/K,len(t_cells)+xbins*ybins]) # Extra vector space for x and y
spks_tmp = spks[st:st+delt].reshape([K,-1])
for tetrode,cell in t_cells:
cur_cell_id = cell_id(tetrode,cell,t_cells)
tmp = np.bitwise_and(spks_tmp.astype(int), np.ones(spks_tmp.shape).astype(int)*2**cur_cell_id)>0
rt = np.sum(tmp,axis=0)
X[:,cur_cell_id] = rt
X[:,len(t_cells)+bin_index(xbin,ybin,ybins)] = 1
Xs.append(X)
Ys.append(np.ones([delt/K])*lbl)
assert all_accounted_for == len(label_l)
Xs = np.concatenate(Xs)
Ys = np.concatenate(Ys)
# Make sure bins were assigned correctly
for xbin,ybin in product(range(xbins),range(ybins)):
cbin_id = bin_id(xbin,ybin,ybins)
cbin_index = bin_index(xbin,ybin,ybins)
if K == 1:
assert np.sum(bins==cbin_id)==np.sum(Xs[:,len(t_cells)+cbin_index])
logging.warning('Threw away %i/%i points when generating PV by bin',thrown_away,len(label_l))
#out = (Xs,Ys)
#logging.warning('Storing ByBin gpv')
#store_in_cache(cache_key,out)
return Xs,Ys
def gpv(vl, t_cells, label_l, K,bin_size, room):
''' Returns a matrix of feature vectors.
The feature vector is:
[fr cell 1, fr cell 2, ..., fr cell n, frac in bin1, frac in bin2,...]
The matrix dimension is [# of vectors, # cells + # bins]
With labels [mode context1, mode context2,...]
K is the length of the subvector that will be used to calculate firing rate
'''
# Check data integrity
assert len(label_l) == len(vl['xs'])
assert (room[0][1]-room[0][0]) % bin_size == 0
assert (room[1][1]-room[1][0]) % bin_size == 0
xbins = (room[0][1]-room[0][0]) / bin_size
ybins = (room[1][1]-room[1][0]) / bin_size
end = (len(label_l)/K)*K # Use integer roundoff to our advantage
logging.warning('Threw away %i/%i points.',len(label_l)-end, len(label_l))
# Generate an indicator array for identity of spiking cell
spks = spk_indicators(t_cells, len(label_l))
spks = spks[:end].reshape([-1,K]).astype(int) # make the right size
label_l = label_l[:end].reshape([-1,K])
# Generate an indicator array for bin number
bins = bin_indicator(vl['xs'],vl['ys'],xbins,ybins,bin_size,room)
bins = bins[:end].reshape([-1,K]) # Make the right size
# The main data structures
Xs = np.zeros([end/K,len(t_cells)+xbins*ybins])
# Put in cell firing rates
for tetrode,cell in t_cells:
cur_cell_id = cell_id(tetrode,cell,t_cells)
debug_tmp = np.bitwise_and(spks, np.ones(spks.shape).astype(int)*2**cur_cell_id)
assert np.sum(debug_tmp == 0)+np.sum(debug_tmp==2**cur_cell_id)==debug_tmp.size
cur_cell_spk = (debug_tmp>0)
Xs[:,cur_cell_id] = np.mean(cur_cell_spk,axis=1)
# Make sure spikes don't disappear
assert np.sum(cur_cell_spk)==len(np.unique(t_cells[(tetrode,cell)]))
# Put bin fractions in
for xbin, ybin in product(range(xbins),range(ybins)):
cbin_id = bin_id(xbin,ybin,ybins)
cbin_index = bin_index(xbin,ybin,ybins)
Xs[:,len(t_cells)+cbin_index] = np.mean(bins==cbin_id,axis=1)
Ys = np.squeeze(mode(label_l,axis=1)[0])
# All Ys are still valid labels
labels = np.unique(label_l)
assert np.sum(label_l==labels[0])+np.sum(label_l==labels[1]) == label_l.size
# Fractions add up to 1
assert np.allclose(np.ones(end/K),np.sum(Xs[:,len(t_cells):],axis=1))
# Bin fractions are right
if logging.getLogger().level <= 10:
bins2 = bins.reshape([-1])
for i in range(0,len(label_l)/K):
curv = Xs[i,len(t_cells):]
curbins = bins2[i*K:i*K+K]
for curbin in range(xbins*ybins):
assert 1.0*np.sum(curbins==(curbin+1))/K == curv[curbin]
# Everything is between 0 and 1
assert np.all(Xs>=0) and np.all(Xs<=1)
# Check that no spikes are missing
if logging.getLogger().level <= 10:
for tetrode,cell in t_cells:
actual_spks = len(np.unique(t_cells[(tetrode,cell)]))
iid = cell_id(tetrode,cell,t_cells)
Xs_spks = K*np.sum(Xs[:,iid])
assert np.allclose(Xs_spks,actual_spks)
return Xs,Ys