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Fix: handle edge case in synapse location calculation with syn_description #184

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merged 3 commits into from
May 24, 2024
Merged

Fix: handle edge case in synapse location calculation with syn_description #184

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80a34e9
Handle edge case in synapse location when using syn_description
ilkilic May 24, 2024
f738680
fix: replace deprecated get_cmap with colormaps
ilkilic May 24, 2024
45ac1d9
fix unit tests
ilkilic May 24, 2024
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4 changes: 2 additions & 2 deletions bluecellulab/psegment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ class PSegment:

def __init__(self, hsegment, parentsection):
# import matplotlib as plt
from matplotlib import cm
from matplotlib import colormaps

self.hsegment = hsegment
self.parentsection = parentsection
Expand All @@ -35,7 +35,7 @@ def __init__(self, hsegment, parentsection):
self.figure = None
self.figX = None
self.figY = None
self.color_map = cm.get_cmap("hot")
self.color_map = colormaps["hot"]
self.ax = None
self.patch = None
self.plotvariable = None
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4 changes: 4 additions & 0 deletions bluecellulab/synapse/synapse_factory.py
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Expand Up @@ -118,6 +118,10 @@ def determine_synapse_location(cls, syn_description: pd.Series, cell: bluecellul
not np.isnan(syn_description[SynapseProperty.AFFERENT_SECTION_POS])):
# position is pre computed in SONATA
location = syn_description[SynapseProperty.AFFERENT_SECTION_POS]
if location == 0.0:
location = 0.0000001
elif location >= 1.0:
location = 0.9999999
else:
ipt = syn_description[SynapseProperty.POST_SEGMENT_ID]
syn_offset = syn_description[SynapseProperty.POST_SEGMENT_OFFSET]
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5 changes: 4 additions & 1 deletion tests/test_synapse/test_synapse_factory.py
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Expand Up @@ -60,8 +60,11 @@ def test_determine_synapse_location(self):
# set afferent_section_pos
self.syn_description[SynapseProperty.AFFERENT_SECTION_POS] = 1.2
res = SynapseFactory.determine_synapse_location(self.syn_description, self.cell)
assert res.location == 1.2
assert res.location == 0.9999999
assert res.section.L == pytest.approx(9.530376893488256)
self.syn_description[SynapseProperty.AFFERENT_SECTION_POS] = 0
res = SynapseFactory.determine_synapse_location(self.syn_description, self.cell)
assert res.location == 0.0000001

def test_synlocation_to_segx(self):
ipt = 13
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