Skip to content
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

update load_gpio_maxwell #53

Merged
merged 3 commits into from
Dec 6, 2023
Merged

update load_gpio_maxwell #53

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
c98785e
update load_gpio_maxwell
surygeng Nov 7, 2023
ef44afc
Merge branch 'master' of https://github.com/braingeneers/braingeneers…
DailyDreaming Dec 6, 2023
73e52e7
Print warnings to stderr.
DailyDreaming Dec 6, 2023
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
20 changes: 11 additions & 9 deletions src/braingeneers/data/datasets_electrophysiology.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -287,11 +287,11 @@ def load_windows(metadata, exp, window_centers, window_sz, dtype=np.float16,

# Check if window is out of bounds
if window[0] < 0 or window[1] > dataset_length:
print("Window out of bounds, inserting zeros for window",window)
print("Window out of bounds, inserting zeros for window", window)
try:
data_temp = np.zeros((data_temp.shape[0],window_sz),dtype=dtype)
except Exception as e:
print(e)
print(e, file=sys.stderr)
data_temp = load_window(metadata, exp, window, dtype=dtype, channels=channels)
else:
data_temp = load_window(metadata, exp, window, dtype=dtype, channels=channels)
Expand Down Expand Up @@ -659,14 +659,14 @@ def load_stims_maxwell(uuid: str, metadata_ephys_exp: dict = None, experiment_st
return df

except FileNotFoundError:
print(f'\tThere seems to be no stim log file for this experiment! :(')
print(f'\tThere seems to be no stim log file for this experiment! :(', file=sys.stderr)
return None
except OSError:
print(f'\tThere seems to be no stim log file (on s3) for this experiment! :(')
print(f'\tThere seems to be no stim log file (on s3) for this experiment! :(', file=sys.stderr)
return None


def load_gpio_maxwell(dataset_path, fs=20000):
def load_gpio_maxwell(dataset_path, fs=20000.0):
"""
Loads the GPIO events for optogenetics stimulation.
:param dataset_path: a local or a s3 path
Expand All @@ -675,10 +675,12 @@ def load_gpio_maxwell(dataset_path, fs=20000):
"""
with smart_open.open(dataset_path, 'rb') as f:
with h5py.File(f, 'r') as dataset:
assert 'bits' in dataset.keys(), 'No GPIO event in the dataset!'
if 'bits' not in dataset.keys():
print('No GPIO event in the dataset!', file=sys.stderr)
return np.array([])
bits_dataset = list(dataset['bits'])
bits_dataframe = [bits_dataset[i][0] for i in range(len(bits_dataset))]
rec_startframe = dataset['raw'][-1, 0] << 16 | dataset['raw'][-2, 0]
bits_dataframe = [bits_dataset[i][0] for i in range(len(bits_dataset))]
rec_startframe = dataset['sig'][-1, 0] << 16 | dataset['sig'][-2, 0]
if len(bits_dataframe) % 2 == 0:
stim_pairs = (np.array(bits_dataframe) - rec_startframe).reshape(len(bits_dataframe) // 2, 2)
return stim_pairs / fs
Expand Down Expand Up @@ -1228,7 +1230,7 @@ def _axion_generate_per_block_metadata(filename: str):

fid.seek(start + int(obj.length.item()), 0)
if fid.tell() != start + obj.length:
print('Unexpected Channel array length')
print('Unexpected Channel array length', file=sys.stderr)

elif obj.type == 3:
continue
Expand Down
19 changes: 19 additions & 0 deletions src/braingeneers/data/datasets_electrophysiology_test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -124,6 +124,25 @@ def test_modify_maxwell_metadata(self):

assert modified_metadata == expected_metadata

@skip_unittest_if_offline
def test_load_gpio_maxwell(self):
""" Read gpio event for Maxwell V1 file"""
data_1 = "s3://braingeneers/ephys/" \
"2023-04-02-hc328_rec/original/data/" \
"2023_04_02_hc328_0.raw.h5"
data_2 = "s3://braingeneers/ephys/" \
"2023-04-04-e-hc328_hckcr1-2_040423_recs/original/data/" \
"hc3.28_hckcr1_chip8787_plated4.4_rec4.4.raw.h5"
data_3 = "s3://braingeneers/ephys/" \
"2023-04-04-e-hc328_hckcr1-2_040423_recs/original/data/" \
"2023_04_04_hc328_hckcr1-2_3.raw.h5"
gpio_1 = ephys.load_gpio_maxwell(data_1)
gpio_2 = ephys.load_gpio_maxwell(data_2)
gpio_3 = ephys.load_gpio_maxwell(data_3)
self.assertEqual(gpio_1.shape, (1, 2))
self.assertEqual(gpio_2.shape, (0,))
self.assertEqual(gpio_3.shape, (29,))


class MEArecReaderTests(unittest.TestCase):
"""The fake reader test."""
Expand Down