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Original channel idx #133

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merged 1 commit into from
Jan 21, 2025
Merged

Original channel idx #133

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11 changes: 8 additions & 3 deletions atlaselectrophysiology/load_data_local.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@

class LoadDataLocal:
def __init__(self):
ONE(silent=True, password='international')
ONE(base_url='https://openalyx.internationalbrainlab.org', silent=True, password='international')
self.brain_atlas = atlas.AllenAtlas(25)
self.franklin_atlas = None
self.folder_path = None
Expand Down Expand Up @@ -99,8 +99,11 @@ def get_data(self):

shank_chns = np.bitwise_and(self.chn_coords_all[:, 0] >= shanks[self.shank_idx][0],
self.chn_coords_all[:, 0] <= shanks[self.shank_idx][1])
self.orig_idx = np.where(shank_chns)[0]
self.chn_coords = self.chn_coords_all[shank_chns, :]

else:
self.orig_idx = None
self.chn_coords = self.chn_coords_all

chn_depths = self.chn_coords[:, 1]
Expand Down Expand Up @@ -261,8 +264,7 @@ def upload_data(self, feature, track, xyz_channels):
with open(self.folder_path.joinpath(prev_align_filename), "w") as f:
json.dump(original_json, f, indent=2, separators=(',', ': '))

@staticmethod
def create_channel_dict(brain_regions):
def create_channel_dict(self, brain_regions):
"""
Create channel dictionary in form to write to json file
:param brain_regions: information about location of electrode channels in brain atlas
Expand All @@ -281,6 +283,9 @@ def create_channel_dict(brain_regions):
'brain_region_id': int(brain_regions.id[i]),
'brain_region': brain_regions.acronym[i]
}
if self.orig_idx is not None:
channel['original_channel_idx'] = int(self.orig_idx[i])

data = {'channel_' + str(i): channel}
channel_dict.update(data)

Expand Down
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