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Edit NeuralynxIO to include all valid samples from NCS files (analog signals) #881

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emelon8 wants to merge 6 commits into from
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Edit NeuralynxIO to include all valid samples from NCS files (analog signals) #881

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df59b86
Edit NeuralynxIO to include all valid samples from NCS files (analog …
emelon8 Oct 10, 2020
48d9852
Fix PEP 8 issue
emelon8 Oct 10, 2020
d989756
Fix to recognize time and record loss gaps
emelon8 Oct 11, 2020
3c223c1
Fix PEP 8 issue
emelon8 Oct 11, 2020
ba695eb
Streamline code for gap_candidates
emelon8 Oct 13, 2020
9fa91f7
Fix PEP 8 issue
emelon8 Oct 13, 2020
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19 changes: 7 additions & 12 deletions neo/rawio/neuralynxrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -305,7 +305,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, chann

block_start = i_start // BLOCK_SIZE
block_stop = i_stop // BLOCK_SIZE + 1
sl0 = i_start % 512
sl0 = i_start % BLOCK_SIZE
sl1 = sl0 + (i_stop - i_start)

if channel_indexes is None:
Expand Down Expand Up @@ -483,18 +483,13 @@ def read_ncs_files(self, ncs_filenames):
if self.use_cache:
self.add_in_cache(lost_indexes=lost_indexes)

gap_candidates = np.unique([0]
+ [data0.size]
+ (gap_indexes + 1).tolist()
+ lost_indexes.tolist()) # linear
gap_candidates = np.unique(np.concatenate(([0],
gap_indexes + 1,
lost_indexes + 1,
[data0.size])))

gap_pairs = np.vstack([gap_candidates[:-1], gap_candidates[1:]]).T # 2D (n_segments, 2)

# construct proper gap ranges free of lost samples artifacts
minimal_segment_length = 1 # in blocks
goodpairs = np.diff(gap_pairs, 1).reshape(-1) > minimal_segment_length
gap_pairs = gap_pairs[goodpairs] # ensures a segment is at least a block wide

self._nb_segment = len(gap_pairs)
self._sigs_memmap = [{} for seg_index in range(self._nb_segment)]
self._sigs_t_start = []
Expand All @@ -521,13 +516,13 @@ def read_ncs_files(self, ncs_filenames):
if chan_uid == chan_uid0:
ts0 = subdata[0]['timestamp']
ts1 = subdata[-1]['timestamp'] \
+ np.uint64(BLOCK_SIZE / self._sigs_sampling_rate * 1e6)
+ np.uint64(subdata[-1]['nb_valid'] / self._sigs_sampling_rate * 1e6)
self._timestamp_limits.append((ts0, ts1))
t_start = ts0 / 1e6
self._sigs_t_start.append(t_start)
t_stop = ts1 / 1e6
self._sigs_t_stop.append(t_stop)
length = subdata.size * BLOCK_SIZE
length = (subdata[:-1].size * BLOCK_SIZE) + int(subdata[-1]['nb_valid'])
self._sigs_length.append(length)


Expand Down