Skip to content

Refactor BlackRock spec specific functions #1763

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 5 commits into from
Sep 8, 2025
Merged

Refactor BlackRock spec specific functions #1763

Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
4e56de8
small change
h-mayorquin Sep 5, 2025
e70355f
name refactoring
h-mayorquin Sep 5, 2025
f585105
Merge branch 'master' into fix_black_rock_1
h-mayorquin Sep 8, 2025
2c2285e
Merge branch 'master' into fix_black_rock_1
h-mayorquin Sep 8, 2025
8d20798
Merge branch 'master' into fix_black_rock_1
h-mayorquin Sep 8, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
138 changes: 70 additions & 68 deletions neo/rawio/blackrockrawio.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -188,67 +188,67 @@ def __init__(
# revision of the nsx and nev files to one of the reading routines
# NSX
self._nsx_header_reader = {
"2.1": self._read_nsx_header_variant_a,
"2.2": self._read_nsx_header_variant_b,
"2.3": self._read_nsx_header_variant_b,
"3.0": self._read_nsx_header_variant_b,
"2.1": self._read_nsx_header_spec_v21,
"2.2": self._read_nsx_header_spec_v22_30,
"2.3": self._read_nsx_header_spec_v22_30,
"3.0": self._read_nsx_header_spec_v22_30,
}
self._nsx_dataheader_reader = {
"2.1": self._read_nsx_dataheader_variant_a,
"2.2": self._read_nsx_dataheader_variant_b,
"2.3": self._read_nsx_dataheader_variant_b,
"3.0": self._read_nsx_dataheader_variant_b,
"3.0-ptp": self._read_nsx_dataheader_variant_c,
"2.1": self._read_nsx_dataheader_spec_v21,
"2.2": self._read_nsx_dataheader_spec_v22_30,
"2.3": self._read_nsx_dataheader_spec_v22_30,
"3.0": self._read_nsx_dataheader_spec_v22_30,
"3.0-ptp": self._read_nsx_dataheader_spec_v30_ptp,
}
self._nsx_data_reader = {
"2.1": self._read_nsx_data_variant_a,
"2.2": self._read_nsx_data_variant_b,
"2.3": self._read_nsx_data_variant_b,
"3.0": self._read_nsx_data_variant_b,
"3.0-ptp": self._read_nsx_data_variant_c,
"2.1": self._read_nsx_data_spec_v21,
"2.2": self._read_nsx_data_spec_v22_30,
"2.3": self._read_nsx_data_spec_v22_30,
"3.0": self._read_nsx_data_spec_v22_30,
"3.0-ptp": self._read_nsx_data_spec_v30_ptp,
}
self._nsx_params = {
"2.1": self._get_nsx_param_variant_a,
"2.2": self._get_nsx_param_variant_b,
"2.3": self._get_nsx_param_variant_b,
"3.0": self._get_nsx_param_variant_b,
"2.1": self._get_nsx_param_spec_v21,
"2.2": self._get_nsx_param_spec_v22_30,
"2.3": self._get_nsx_param_spec_v22_30,
"3.0": self._get_nsx_param_spec_v22_30,
}
# NEV
self._nev_header_reader = {
"2.1": self._read_nev_header_variant_a,
"2.2": self._read_nev_header_variant_b,
"2.3": self._read_nev_header_variant_c,
"3.0": self._read_nev_header_variant_c,
"2.1": self._read_nev_header_spec_v21,
"2.2": self._read_nev_header_spec_v22,
"2.3": self._read_nev_header_spec_v30_ptp,
"3.0": self._read_nev_header_spec_v30_ptp,
}
self._nev_data_reader = {
"2.1": self._read_nev_data_variant_a,
"2.2": self._read_nev_data_variant_a,
"2.3": self._read_nev_data_variant_b,
"3.0": self._read_nev_data_variant_c,
"2.1": self._read_nev_data_spec_v21_22,
"2.2": self._read_nev_data_spec_v21_22,
"2.3": self._read_nev_data_spec_v23,
"3.0": self._read_nev_data_spec_v30_ptp,
}
self._waveform_size = {
"2.1": self._get_waveform_size_variant_a,
"2.2": self._get_waveform_size_variant_a,
"2.3": self._get_waveform_size_variant_b,
"3.0": self._get_waveform_size_variant_b,
"2.1": self._get_waveform_size_spec_v21,
"2.2": self._get_waveform_size_spec_v21,
"2.3": self._get_waveform_size_spec_v22_30,
"3.0": self._get_waveform_size_spec_v22_30,
}
self._channel_labels = {
"2.1": self._get_channel_labels_variant_a,
"2.2": self._get_channel_labels_variant_b,
"2.3": self._get_channel_labels_variant_b,
"3.0": self._get_channel_labels_variant_b,
"2.1": self._get_channel_labels_spec_v21,
"2.2": self._get_channel_labels_spec_v22_30,
"2.3": self._get_channel_labels_spec_v22_30,
"3.0": self._get_channel_labels_spec_v22_30,
}
self._nonneural_evdicts = {
"2.1": self._get_nonneural_evdicts_variant_a,
"2.2": self._get_nonneural_evdicts_variant_a,
"2.3": self._get_nonneural_evdicts_variant_b,
"3.0": self._get_nonneural_evdicts_variant_b,
"2.1": self._get_nonneural_evdicts_spec_v21_22,
"2.2": self._get_nonneural_evdicts_spec_v21_22,
"2.3": self._get_nonneural_evdicts_spec_v23,
"3.0": self._get_nonneural_evdicts_spec_v23,
}
self._comment_evdict = {
"2.1": self._get_comment_evdict_variant_a,
"2.2": self._get_comment_evdict_variant_a,
"2.3": self._get_comment_evdict_variant_a,
"3.0": self._get_comment_evdict_variant_a,
"2.1": self._get_comment_evdict_spec_v21_22,
"2.2": self._get_comment_evdict_spec_v21_22,
"2.3": self._get_comment_evdict_spec_v21_22,
"3.0": self._get_comment_evdict_spec_v21_22,
}

def _parse_header(self):
Expand All @@ -267,9 +267,11 @@ def _parse_header(self):
self._nev_spec = self._extract_nev_file_spec()

# read nev headers
self._nev_basic_header, self._nev_ext_header = self._nev_header_reader[self._nev_spec]()
header_reader_function = self._nev_header_reader[self._nev_spec]
self._nev_basic_header, self._nev_ext_header = header_reader_function()

self.nev_data = self._nev_data_reader[self._nev_spec]()
nev_reader_function = self._nev_data_reader[self._nev_spec]
self.nev_data = nev_reader_function()
spikes, spike_segment_ids = self.nev_data["Spikes"]

# scan all channel to get number of Unit
Expand Down Expand Up @@ -850,7 +852,7 @@ def _extract_nev_file_spec(self):

return spec

def _read_nsx_header_variant_a(self, nsx_nb):
def _read_nsx_header_spec_v21(self, nsx_nb):
"""
Extract nsx header information from a 2.1 .nsx file
"""
Expand Down Expand Up @@ -883,7 +885,7 @@ def _read_nsx_header_variant_a(self, nsx_nb):

return nsx_basic_header, nsx_ext_header

def _read_nsx_header_variant_b(self, nsx_nb):
def _read_nsx_header_spec_v22_30(self, nsx_nb):
"""
Extract nsx header information from a 2.2 or 2.3 .nsx file
"""
Expand Down Expand Up @@ -964,15 +966,15 @@ def _read_nsx_dataheader(self, nsx_nb, offset):

return packet_header

def _read_nsx_dataheader_variant_a(self, nsx_nb, filesize=None, offset=None):
def _read_nsx_dataheader_spec_v21(self, nsx_nb, filesize=None, offset=None):
"""
Reads None for the nsx data header of file spec 2.1. Introduced to
facilitate compatibility with higher file spec.
"""

return None

def _read_nsx_dataheader_variant_b(
def _read_nsx_dataheader_spec_v22_30(
self,
nsx_nb,
filesize=None,
Expand Down Expand Up @@ -1025,7 +1027,7 @@ def _read_nsx_dataheader_variant_b(

return data_header

def _read_nsx_dataheader_variant_c(
def _read_nsx_dataheader_spec_v30_ptp(
self,
nsx_nb,
filesize=None,
Expand Down Expand Up @@ -1056,7 +1058,7 @@ def _read_nsx_dataheader_variant_c(

if not np.all(struct_arr["num_data_points"] == 1):
# some packets have more than 1 sample. Not actually ptp. Revert to non-ptp variant.
return self._read_nsx_dataheader_variant_b(nsx_nb, filesize=filesize, offset=offset)
return self._read_nsx_dataheader_spec_v22_30(nsx_nb, filesize=filesize, offset=offset)

# It is still possible there was a data break and the file has multiple segments.
# We can no longer rely on the presence of a header indicating a new segment,
Expand All @@ -1083,7 +1085,7 @@ def _read_nsx_dataheader_variant_c(
}
return data_header

def _read_nsx_data_variant_a(self, nsx_nb):
def _read_nsx_data_spec_v21(self, nsx_nb):
"""
Extract nsx data from a 2.1 .nsx file
"""
Expand All @@ -1102,7 +1104,7 @@ def _read_nsx_data_variant_a(self, nsx_nb):

return data

def _read_nsx_data_variant_b(self, nsx_nb):
def _read_nsx_data_spec_v22_30(self, nsx_nb):
"""
Extract nsx data (blocks) from a 2.2, 2.3, or 3.0 .nsx file.
Blocks can arise if the recording was paused by the user.
Expand All @@ -1124,7 +1126,7 @@ def _read_nsx_data_variant_b(self, nsx_nb):

return data

def _read_nsx_data_variant_c(self, nsx_nb):
def _read_nsx_data_spec_v30_ptp(self, nsx_nb):
"""
Extract nsx data (blocks) from a 3.0 .nsx file with PTP timestamps
yielding a timestamp per sample. Blocks can arise
Expand Down Expand Up @@ -1214,7 +1216,7 @@ def _read_nev_header(self, ext_header_variants):

return nev_basic_header, nev_ext_header

def _read_nev_header_variant_a(self):
def _read_nev_header_spec_v21(self):
"""
Extract nev header information from a 2.1 .nev file
"""
Expand All @@ -1230,7 +1232,7 @@ def _read_nev_header_variant_a(self):

return self._read_nev_header(ext_header_variants)

def _read_nev_header_variant_b(self):
def _read_nev_header_spec_v22(self):
"""
Extract nev header information from a 2.2 .nev file
"""
Expand All @@ -1249,7 +1251,7 @@ def _read_nev_header_variant_b(self):

return self._read_nev_header(ext_header_variants)

def _read_nev_header_variant_c(self):
def _read_nev_header_spec_v30_ptp(self):
"""
Extract nev header information from a 2.3 .nev file
"""
Expand Down Expand Up @@ -1478,7 +1480,7 @@ def _match_nsx_and_nev_segment_ids(self, nsx_nb):
if len(ev_ids):
ev_ids[:] = np.vectorize(new_nev_segment_id_mapping.__getitem__)(ev_ids)

def _read_nev_data_variant_a(self):
def _read_nev_data_spec_v21_22(self):
"""
Extract nev data from a 2.1 & 2.2 .nev file
"""
Expand All @@ -1488,7 +1490,7 @@ def _read_nev_data_variant_a(self):

return self._read_nev_data(nev_data_masks, nev_data_types)

def _read_nev_data_variant_b(self):
def _read_nev_data_spec_v23(self):
"""
Extract nev data from a 2.3 .nev file
"""
Expand All @@ -1514,7 +1516,7 @@ def _read_nev_data_variant_b(self):

return self._read_nev_data(nev_data_masks, nev_data_types)

def _read_nev_data_variant_c(self):
def _read_nev_data_spec_v30_ptp(self):
"""
Extract nev data from a 3.0 .nev file
"""
Expand Down Expand Up @@ -1943,7 +1945,7 @@ def _get_waveforms_dtype(self):

return dtype_waveforms

def _get_channel_labels_variant_a(self):
def _get_channel_labels_spec_v21(self):
"""
Returns labels for all channels for file spec 2.1
"""
Expand All @@ -1958,7 +1960,7 @@ def _get_channel_labels_variant_a(self):

return dict(zip(elids, labels))

def _get_channel_labels_variant_b(self):
def _get_channel_labels_spec_v22_30(self):
"""
Returns labels for all channels for file spec 2.2 and 2.3
"""
Expand All @@ -1967,7 +1969,7 @@ def _get_channel_labels_variant_b(self):

return dict(zip(elids, labels)) if len(labels) > 0 else None

def _get_waveform_size_variant_a(self):
def _get_waveform_size_spec_v21(self):
"""
Returns waveform sizes for all channels for file spec 2.1 and 2.2
"""
Expand All @@ -1978,7 +1980,7 @@ def _get_waveform_size_variant_a(self):

return wf_sizes

def _get_waveform_size_variant_b(self):
def _get_waveform_size_spec_v22_30(self):
"""
Returns waveform sizes for all channels for file spec 2.3
"""
Expand Down Expand Up @@ -2008,7 +2010,7 @@ def _get_left_sweep_waveforms(self):

return wf_left_sweep

def _get_nsx_param_variant_a(self, nsx_nb):
def _get_nsx_param_spec_v21(self, nsx_nb):
"""
Returns parameter (param_name) for a given nsx (nsx_nb) for file spec
2.1.
Expand Down Expand Up @@ -2074,7 +2076,7 @@ def _get_nsx_param_variant_a(self, nsx_nb):
# Returns complete dictionary because then it does not need to be called so often
return nsx_parameters

def _get_nsx_param_variant_b(self, param_name, nsx_nb):
def _get_nsx_param_spec_v22_30(self, param_name, nsx_nb):
"""
Returns parameter (param_name) for a given nsx (nsx_nb) for file spec
2.2 and 2.3.
Expand All @@ -2098,7 +2100,7 @@ def _get_nsx_param_variant_b(self, param_name, nsx_nb):

return nsx_parameters[param_name]

def _get_nonneural_evdicts_variant_a(self, data):
def _get_nonneural_evdicts_spec_v21_22(self, data):
"""
Defines event types and the necessary parameters to extract them from
a 2.1 and 2.2 nev file.
Expand Down Expand Up @@ -2190,7 +2192,7 @@ def _delete_empty_segments(self):

self._nb_segment -= 1

def _get_nonneural_evdicts_variant_b(self, data):
def _get_nonneural_evdicts_spec_v23(self, data):
"""
Defines event types and the necessary parameters to extract them from
a 2.3 nev file.
Expand Down Expand Up @@ -2218,7 +2220,7 @@ def _get_nonneural_evdicts_variant_b(self, data):

return event_types

def _get_comment_evdict_variant_a(self, data):
def _get_comment_evdict_spec_v21_22(self, data):
return {
"comments": {"name": "comments", "field": "comment", "mask": data["packet_id"] == 65535, "desc": "Comments"}
}
Expand Down
Loading