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multiple minor changes #1

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19 changes: 16 additions & 3 deletions xds_python/xds.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,6 +175,8 @@ def clean_up_trials(self):
For some trials the timings for trial_start, trial_end or trial_gocue are nans.
This function will get rid of these trials.

Trials with invalid timings will also be removed.

Returns
-------
None.
Expand All @@ -189,6 +191,13 @@ def clean_up_trials(self):
end_nan_idx = np.argwhere(np.isnan(trial_end_time))[:,0]
union_nan_idx = np.asarray(sorted(list(set(gocue_nan_idx).union(set(start_nan_idx)).union(set(end_nan_idx))),
reverse = True))
start_early_idx = np.argwhere(trial_start_time < self.time_frame[0])[:,0]
end_late_idx = np.argwhere(trial_end_time > self.time_frame[-1])[:,0]
union_invalid_idx = np.asarray(sorted(list(set(start_early_idx).union(set(end_late_idx))),
reverse = True))

union_nan_idx = np.asarray(sorted(list(set(union_nan_idx).union(set(union_invalid_idx))),
reverse = True))
if len(union_nan_idx)>0:
self.trial_gocue_time = np.delete(self.trial_gocue_time, union_nan_idx, axis = 0)
self.trial_start_time = np.delete(self.trial_start_time, union_nan_idx)
Expand Down Expand Up @@ -239,15 +248,16 @@ def compute_movement_onset_time(self, channel = 0, thr = 0.4):
"""
if (hasattr(self, 'curs_p')|hasattr(self, 'kin_p')):
idx = [np.where((self.time_frame > t[0]) & (self.time_frame < t[1]) )[0]
for t in zip(self.trial_start_time, self.trial_end_time)]
# for t in zip(self.trial_start_time, self.trial_end_time)]
for t in zip(self.trial_gocue_time, self.trial_end_time)]
trial_time_frame = [self.time_frame[n] for n in idx]
trial_curs_p = [self.curs_p[n] for n in idx]
idx_onset = find_movement_onset(trial_curs_p, channel, thr)
time_onset = [trial_time_frame[i][idx_onset[i]] for i in range(len(trial_time_frame))]
print('Get the movement onset time!')
self.trial_movement_onset_time = np.array(time_onset).reshape((-1,))
else:
print('There is no force data in this file')
print('There is no movement data in this file')

def get_trials_idx(self, my_type, start_event, time_before_start, end_event = 'end_time', time_after_end = 0, raw_flag = 0, gadget_number = -1):
"""
Expand Down Expand Up @@ -543,7 +553,10 @@ def bin_spikes(self, bin_size, mode = 'center'):
out, _ = np.histogram(bb, bins)
spike_counts.append(out)
bins = bins.reshape((len(bins),1))
return bins[1:], np.asarray(spike_counts).T
bins = bins[1:] - bin_size / 2
bins = bins[1:-1]; spike_counts = np.asarray(spike_counts).T[1:-1, ...]
return bins, spike_counts
# return bins[1:], np.asarray(spike_counts).T

def resample_EMG(self, new_bin_size):
"""
Expand Down
11 changes: 9 additions & 2 deletions xds_python/xds_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,10 @@ def parse_meta(raw_meta):
meta['array'] = ''.join([chr(int(each)) for each in np.asarray(raw_meta['array'])])
meta['dateTime'] = ''.join([chr(int(each)) for each in np.asarray(raw_meta['dateTime'])])
meta['processedTime'] = ''.join([chr(int(each)) for each in np.asarray(raw_meta['processedTime'])])
meta['rawFileName'] = ''.join([chr(int(each)) for each in np.asarray(raw_meta['rawFileName'])])
try:
meta['rawFileName'] = ''.join([chr(int(each)) for each in np.asarray(raw_meta['rawFileName'])])
except Exception:
meta['rawFileName'] = ''
meta['task'] = ''.join([chr(int(each)) for each in np.asarray(raw_meta['task'])])
meta['duration'] = np.asarray(raw_meta['duration'])[0][0]
meta['lab'] = np.asarray(raw_meta['lab'])[0][0]
Expand Down Expand Up @@ -127,7 +130,11 @@ def parse_scipy(path, file_name):
parsed = {}
if path[-1] != '/':
path = path + '/'
read_data = sio.loadmat(path + file_name)
try:
read_data = sio.loadmat(path + file_name)
except:
import mat73
read_data = mat73.loadmat(path + file_name)
xds = read_data['xds']

# -------- meta information -------- #
Expand Down