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fix bug in get_frame_indices #389

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merged 3 commits into from
Nov 28, 2024
Merged

fix bug in get_frame_indices #389

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cf2b0e2
fix bug in get_frame_indices
mschwoer Nov 27, 2024
2bfbfbb
adapt tests
mschwoer Nov 27, 2024
a83a958
upgrade alphabase to 1.4.2
mschwoer Nov 27, 2024
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2 changes: 1 addition & 1 deletion alphadia/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -745,7 +745,7 @@ def get_frame_indices(
optimal_cycle_limits[0] = precursor_cycle_max_index - optimal_len

if optimal_cycle_limits[0] < 0:
optimal_cycle_limits[0] = 0
optimal_cycle_limits[0] = 0 if precursor_cycle_max_index % 2 == 0 else 1

# Convert back to frame indices
frame_limits = optimal_cycle_limits * cycle_len + zeroth_frame
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2 changes: 1 addition & 1 deletion requirements/requirements.txt
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Expand Up @@ -5,7 +5,7 @@ numba==0.59.1
argparse==1.4.0
alpharaw==0.4.5
alphatims==1.0.8
alphabase==1.4.0 # test: tolerate_version
alphabase==1.4.2 # test: tolerate_version
peptdeep==1.3.0 # test: tolerate_version
progressbar==2.5
neptune==1.10.4
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2 changes: 1 addition & 1 deletion tests/unit_tests/test_data.py
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Expand Up @@ -367,7 +367,7 @@ def test_get_frame_indices_optimization_left_min_size_overflow(mock_alpha_raw_ji
optimize_size = 4
min_size = 1000
rt_values = np.array([90.0, 95.0], dtype=np.float32)
expected_indices = np.array([[0, 95, 1]], dtype=np.int64)
expected_indices = np.array([[5, 95, 1]], dtype=np.int64)

# when
frame_indices = mock_alpha_raw_jit.get_frame_indices(
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