Skip to content

Commit

Permalink
tests for different segment length added (also fail as of v0.9.0); co…
Browse files Browse the repository at this point in the history 
…de readability improved
  • Loading branch information
@jlubo
jlubo committed Sep 27, 2023
1 parent 7f77d60 commit 0bcc339
Showing 1 changed file with 58 additions and 35 deletions.
93 changes: 58 additions & 35 deletions python/test/unit/test_diffusion.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -97,23 +97,25 @@ def __init__(self, args):

# get_morph_and_decor
# Method that sets up and returns a morphology and decoration for given parameters
# - num_segs: number of segments
# - num_segs: number of segments (1, 2, or 3; in the case of 1 or 2, there'll be one branch, in the case of 3, there'll be three branches)
# - num_cvs_per_seg: number of CVs per segment
# - length: length of the whole setup (in case of 1 or 2 segments, one branch) in µm
# - l_1: axial length of the first segment in µm
# - l_2: axial length of the second segment in µm
# - l_3: axial length of the third segment in µm
# - radius_1: radius of the first segment in µm
# - radius_2: radius of the second segment in µm
# - radius_3: radius of the third segment in µm
def get_morph_and_decor(
self, num_segs, num_cvs_per_seg, length, radius_1, radius_2, radius_3
self, num_segs, num_cvs_per_seg, l_1, l_2, l_3, radius_1, radius_2, radius_3
):
# ---------------------------------------------------------------------------------------
# set up the morphology
tree = A.segment_tree()
if num_segs == 1:
_ = tree.append(
A.mnpos,
A.mpoint(-length / 2, 0, 0, radius_1),
A.mpoint(+length / 2, 0, 0, radius_1),
A.mpoint(-l_1, 0, 0, radius_1),
A.mpoint(0, 0, 0, radius_1),
tag=0,
)

Expand All @@ -127,14 +129,14 @@ def get_morph_and_decor(
elif num_segs == 2:
s = tree.append(
A.mnpos,
A.mpoint(-length / 2, 0, 0, radius_1),
A.mpoint(-l_1, 0, 0, radius_1),
A.mpoint(0, 0, 0, radius_1),
tag=0,
)
_ = tree.append(
s,
A.mpoint(0, 0, 0, radius_2),
A.mpoint(+length / 2, 0, 0, radius_2),
A.mpoint(+l_2, 0, 0, radius_2),
tag=1,
)

Expand All @@ -150,20 +152,20 @@ def get_morph_and_decor(
elif num_segs == 3:
s = tree.append(
A.mnpos,
A.mpoint(-1 / 3 * length, 0, 0, radius_1),
A.mpoint(-l_1, 0, 0, radius_1),
A.mpoint(0, 0, 0, radius_1),
tag=0,
)
_ = tree.append(
s,
A.mpoint(0, 0, 0, radius_2),
A.mpoint(+1 / 3 * length, 0, 0, radius_2),
A.mpoint(+l_2, 0, 0, radius_2),
tag=1,
)
_ = tree.append(
s,
A.mpoint(-1 / 3 * length, 0, 0, radius_3),
A.mpoint(-2 / 3 * length, 0, 0, radius_3),
A.mpoint(0, 0, 0, radius_3),
A.mpoint(+l_3, 0, 0, radius_3),
tag=2,
)

Expand Down Expand Up @@ -219,30 +221,36 @@ def get_morph_and_decor(
# Method that runs an Arbor simulation with diffusion across different segments and subsequently
# performs tests on the results
# - cat: catalogue of custom mechanisms
# - num_segs: number of segments
# - num_segs: number of segments (1, 2, or 3)
# - num_cvs_per_seg: number of CVs per segment
# - length: length of the whole setup (in case of 1 or 2 segments, one branch) in µm
# - l_1 [optional]: axial length of the first segment in µm
# - l_2 [optional]: axial length of the second segment in µm
# - l_3 [optional]: axial length of the third segment in µm
# - r_1 [optional]: radius of the first segment in µm
# - r_2 [optional]: radius of the second segment in µm
# - r_3 [optional]: radius of the third segment in µm
def simulate_and_test_diffusion(
self, cat, num_segs, num_cvs_per_seg, length, r_1, r_2=0.0, r_3=0.0
self,
cat,
num_segs,
num_cvs_per_seg,
l_1=5.0,
l_2=5.0,
l_3=5.0,
r_1=4.0,
r_2=4.0,
r_3=4.0,
):
# ---------------------------------------------------------------------------------------
# set parameters and calculate geometrical measures
radius_1 = r_1
if num_segs > 1:
radius_2 = r_2
else:
radius_2 = 0
if num_segs > 2:
radius_3 = r_3
else:
radius_3 = 0

length_per_seg = length / num_segs # axial length of a segment in µm
volume_tot = (
np.pi * (radius_1**2 + radius_2**2 + radius_3**2) * length_per_seg
if num_segs < 2:
r_2 = l_2 = 0
r_3 = l_3 = 0
elif num_segs < 3:
r_3 = l_3 = 0

volume_tot = np.pi * (
r_1**2 * l_1 + r_2**2 * l_2 + r_3**2 * l_3
) # volume of the whole setup in µm^3
volume_per_cv = volume_tot / (
num_segs * num_cvs_per_seg
Expand All @@ -258,7 +266,7 @@ def simulate_and_test_diffusion(
# ---------------------------------------------------------------------------------------
# get morphology, decoration, and labels, and add the diffusive particle species 's'
morph, dec, labels = self.get_morph_and_decor(
num_segs, num_cvs_per_seg, length, radius_1, radius_2, radius_3
num_segs, num_cvs_per_seg, l_1, l_2, l_3, r_1, r_2, r_3
)
dec.set_ion("s", int_con=0.0, diff=diffusivity)

Expand Down Expand Up @@ -352,30 +360,45 @@ def simulate_and_test_diffusion(
) # max_{t}(s⋅V) [direct]

# test_diffusion_equal_radii
# Test: simulations with segments of equal radius
# Test: simulations with segments of equal length and equal radius
# - diffusion_catalogue: catalogue of diffusion mechanisms
@fixtures.diffusion_catalogue()
def test_diffusion_equal_radii(self, diffusion_catalogue):
self.simulate_and_test_diffusion(
diffusion_catalogue, 1, 600, 10, 4
diffusion_catalogue, 1, 600, l_1=5, r_1=4
) # 1 segment with radius 4 µm
self.simulate_and_test_diffusion(
diffusion_catalogue, 2, 300, 10, 4, 4
diffusion_catalogue, 2, 300, l_1=5, l_2=5, r_1=4, r_2=4
) # 2 segments with radius 4 µm
self.simulate_and_test_diffusion(
diffusion_catalogue, 3, 200, 10, 4, 4, 4
diffusion_catalogue, 3, 200, l_1=5, l_2=5, l_3=5, r_1=4, r_2=4, r_3=4
) # 3 segments with radius 4 µm

""" TODO: not succeeding as of Arbor v0.9.0:
# test_diffusion_different_length
# Test: simulations with segments of different length but equal radius
# - diffusion_catalogue: catalogue of diffusion mechanisms
@fixtures.diffusion_catalogue()
def test_diffusion_different_length(self, diffusion_catalogue):
self.simulate_and_test_diffusion(
diffusion_catalogue, 1, 600, l_1=5, r_1=4
) # 1 segment with radius 4 µm
self.simulate_and_test_diffusion(
diffusion_catalogue, 2, 300, l_1=5, l_2=3, r_1=4, r_2=4
) # 2 segments with radius 4 µm
self.simulate_and_test_diffusion(
diffusion_catalogue, 3, 200, l_1=5, l_2=3, l_3=3, r_1=4, r_2=4, r_3=4
) # 3 segments with radius 4 µm
# test_diffusion_different_radii
# Test: simulations with segments of different radius
# Test: simulations with segments of equal length but different radius
# - diffusion_catalogue: catalogue of diffusion mechanisms
@fixtures.diffusion_catalogue()
def test_diffusion_different_radii(self, diffusion_catalogue):
self.simulate_and_test_diffusion(
diffusion_catalogue, 2, 300, 10, 4, 6
diffusion_catalogue, 2, 300, l_1=5, l_2=5, r_1=4, r_2=6
) # 2 segments with radius 4 µm and 6 µm
self.simulate_and_test_diffusion(
diffusion_catalogue, 3, 200, 10, 4, 6, 6
diffusion_catalogue, 3, 200, l_1=5, l_2=5, l_3=5, r_1=4, r_2=6, r_3=6
) # 3 segments with radius 4 µm and 6 µm
"""

0 comments on commit 0bcc339

Please sign in to comment.