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Commit c79c476d authored by Alán Muñoz's avatar Alán Muñoz
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post(multisignal): optimise align using bottleneck

parent 496c2d40
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#!/usr/bin/env python3 #!/usr/bin/env python3
import bottleneck as bn
import numpy as np import numpy as np
import pandas as pd import pandas as pd
from agora.abc import ParametersABC
from agora.abc import ParametersABC
from postprocessor.core.abc import PostProcessABC from postprocessor.core.abc import PostProcessABC
...@@ -97,7 +98,7 @@ class align(PostProcessABC): ...@@ -97,7 +98,7 @@ class align(PostProcessABC):
# i.e. if events_at_least = 1, then cells that have no birth events are # i.e. if events_at_least = 1, then cells that have no birth events are
# deleted. # deleted.
event_mask = mask_df.apply( event_mask = mask_df.apply(
lambda x: np.sum(x) >= self.events_at_least, axis=1 lambda x: bn.nansum(x) >= self.events_at_least, axis=1
) )
mask_df = mask_df.iloc[event_mask.to_list()] mask_df = mask_df.iloc[event_mask.to_list()]
...@@ -132,7 +133,7 @@ class align(PostProcessABC): ...@@ -132,7 +133,7 @@ class align(PostProcessABC):
# Do not remove bits of traces before first event # Do not remove bits of traces before first event
else: else:
# Add columns to left, filled with NaNs # Add columns to left, filled with NaNs
max_shift = np.max(shift_list) max_shift = bn.nanmax(shift_list)
mask_aligned = df_extend_nan(mask_aligned, max_shift) mask_aligned = df_extend_nan(mask_aligned, max_shift)
trace_aligned = df_extend_nan(trace_aligned, max_shift) trace_aligned = df_extend_nan(trace_aligned, max_shift)
# shift each # shift each
......
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