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Merged
Paschas merged 3 commits into from
May 17, 2024
Merged

updates #1

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a96daa8
Updated np.int (deprecated) to int
azmaite Apr 10, 2024
22bf1af
Merge pull request #15 from NeLy-EPFL/integer_fix
Apr 10, 2024
0bad20e
bump version
azmaite Apr 10, 2024
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2 changes: 1 addition & 1 deletion setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@

setup(
name="utils2p",
version="1.0.0",
version="1.0.1",
packages=["utils2p", "utils2p.external", "utils2p.external.tifffile"],
author="Florian Aymanns",
author_email="florian.aymanns@epfl.ch",
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4 changes: 2 additions & 2 deletions tests/test_main.py
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Expand Up @@ -567,8 +567,8 @@ def test_find_raw_file(default_exp_dir):

def test_load_optical_flow(tmpdir):
n_timepoints = 10
opt_flow_data = np.zeros((n_timepoints, 5), dtype=np.int)
opt_flow_data[:, 4] = np.arange(n_timepoints, dtype=np.int)
opt_flow_data = np.zeros((n_timepoints, 5), dtype=int)
opt_flow_data[:, 4] = np.arange(n_timepoints, dtype=int)
opt_flow_data[1, 0] = -1
opt_flow_data[3, 1] = 1
opt_flow_data[6, 2] = 2
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14 changes: 7 additions & 7 deletions utils2p/synchronization.py
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Expand Up @@ -421,7 +421,7 @@ def process_cam_line(line, seven_camera_metadata):
1)] <= i:
current_frame += 1
processed_line[start:stop] = current_frame
return processed_line.astype(np.int)
return processed_line.astype(int)


def process_frame_counter(line, metadata=None, steps_per_frame=None):
Expand Down Expand Up @@ -514,7 +514,7 @@ def process_frame_counter(line, metadata=None, steps_per_frame=None):
# Case of one frame/volume only
if len(rising_edges) <= steps_per_frame:
processed_frame_counter[rising_edges[0]:] = 0
return processed_frame_counter.astype(np.int)
return processed_frame_counter.astype(int)

for i, index in enumerate(
range(0,
Expand All @@ -523,7 +523,7 @@ def process_frame_counter(line, metadata=None, steps_per_frame=None):
rising_edges[index]:rising_edges[index + steps_per_frame]] = i
processed_frame_counter[rising_edges[-1 * steps_per_frame]:] = (
processed_frame_counter[rising_edges[-1 * steps_per_frame] - 1] + 1)
return processed_frame_counter.astype(np.int)
return processed_frame_counter.astype(int)


def process_stimulus_line(line):
Expand Down Expand Up @@ -559,7 +559,7 @@ def process_stimulus_line(line):
processed_stimulus_line = np.zeros_like(line)
indices = np.where(line > 0)
processed_stimulus_line[indices] = 1
return processed_stimulus_line.astype(np.int)
return processed_stimulus_line.astype(int)


def process_optical_flow_line(line):
Expand Down Expand Up @@ -610,7 +610,7 @@ def process_optical_flow_line(line):
processed_optical_flow_line[rising_edges[i]:rising_edges[i + 1]] = i
processed_optical_flow_line[rising_edges[-1]:] = (
processed_optical_flow_line[rising_edges[-1] - 1] + 1)
return processed_optical_flow_line.astype(np.int)
return processed_optical_flow_line.astype(int)


def crop_lines(mask, lines):
Expand Down Expand Up @@ -714,7 +714,7 @@ def beh_idx_to_2p_idx(beh_indices, cam_line, frame_counter):
if not cam_line[0] < 0:
thor_sync_indices = np.append(np.array([0]), thor_sync_indices)

indices_2p = np.ones(len(beh_indices), dtype=np.int) * np.nan
indices_2p = np.ones(len(beh_indices), dtype=int) * np.nan

first_frame_of_cam_line = np.min(cam_line[np.where(cam_line >= 0)])

Expand All @@ -728,7 +728,7 @@ def beh_idx_to_2p_idx(beh_indices, cam_line, frame_counter):
thor_sync_index = thor_sync_indices[frame_num]
indices_2p[i] = frame_counter[thor_sync_index]

return indices_2p.astype(np.int)
return indices_2p.astype(int)


def reduce_during_2p_frame(frame_counter, values, function):
Expand Down