def test_read_duplicate_vertex_swc():
test_file = """
1 0 -18.458370 23.227150 -84.035016 1.000000 -1
2 0 -18.159709 22.925778 -82.984344 1.000000 1
3 0 -17.861047 22.624407 -82.984344 1.000000 2
4 0 -17.562385 22.624407 -82.984344 1.000000 3
5 0 -16.965061 22.021663 -82.984344 1.000000 4
6 0 -16.965061 21.720292 -82.984344 1.000000 5
7 0 -16.069075 21.720292 -82.984344 1.000000 6
8 0 -16.069075 21.117548 -80.883000 1.000000 7
9 0 -15.770414 20.816176 -80.883000 1.000000 8
10 0 -15.770414 20.514805 -80.883000 1.000000 9
11 0 -15.770414 20.816176 -80.883000 1.000000 10
12 0 -16.069075 21.117548 -80.883000 1.000000 11
13 0 -16.069075 21.418920 -80.883000 1.000000 12
14 0 -16.069075 20.816176 -78.781655 1.000000 13
15 0 -15.471752 20.213433 -76.680311 1.000000 14
16 0 -15.471752 19.309318 -76.680311 1.000000 15
17 0 -15.471752 19.007946 -75.629639 1.000000 16
18 0 -15.173090 18.706574 -74.578966 1.000000 17
19 0 -14.874428 18.706574 -74.578966 1.000000 18
20 0 -14.575766 18.405202 -74.578966 1.000000 19
"""
skel = Skeleton.from_swc(test_file)
assert skel.vertices.shape[0] == 20
skel2 = Skeleton.from_swc(skel.to_swc())
assert skel2.vertices.shape[0] == 20
assert Skeleton.equivalent(skel, skel2)
def _swc2skeleton(self, swc_file, benchmarking=False, origin=None):
"""Converts swc file into Skeleton object
Arguments:
swc_file {str} -- path to SWC file
Keyword Arguments:
origin {numpy array with shape (3,1)} -- origin of coordinate frame in microns, (default: None assumes (0,0,0) origin)
Returns:
skel {cloudvolume.Skeleton} -- Skeleton object of given SWC file
"""
with open(swc_file, "r") as f:
contents = f.read()
# get every line that starts with a hashtag
comments = [
i.split(" ") for i in contents.split("\n") if i.startswith("#")
]
offset = np.array(
[float(j) for i in comments for j in i[2:] if "OFFSET" in i])
color = [
float(j) for i in comments for j in i[2].split(",") if "COLOR" in i
]
# set alpha to 0.0 so skeleton is opaque
color.append(0.0)
color = np.array(color, dtype="float32")
skel = Skeleton.from_swc(contents)
# physical units
# space can be 'physical' or 'voxel'
skel.space = "physical"
# hard coding parsing the id from the filename
idx = swc_file.find("G")
if benchmarking == True:
idx1 = swc_file.find("_",
swc_file.find("_") +
1) # finding second occurence of "_"
idx2 = swc_file.find(".")
skel.id = swc_file[idx1 + 1:idx2]
else:
skel.id = int(swc_file[idx + 2:idx + 5])
# hard coding changing data type of vertex_types
skel.extra_attributes[-1]["data_type"] = "float32"
skel.extra_attributes.append({
"id": "vertex_color",
"data_type": "float32",
"num_components": 4
})
# add offset to vertices
# and shift by origin
skel.vertices += offset
if origin is not None:
skel.vertices -= origin
# convert from microns to nanometers
skel.vertices *= 1000
skel.vertex_color = np.zeros((skel.vertices.shape[0], 4),
dtype="float32")
skel.vertex_color[:, :] = color
return skel
def view(filename):
"""Visualize a .swc or .npy file."""
basename, ext = os.path.splitext(filename)
if ext == ".swc":
with open(filename, "rt") as swc:
skel = Skeleton.from_swc(swc.read())
skel.viewer()
elif ext == ".npy":
labels = np.load(filename)
cloudvolume.view(labels, segmentation=True)
else:
print("kimimaro: {filename} was not a .swc or .npy file.")
def test_read_swc():
# From http://research.mssm.edu/cnic/swc.html
test_file = """# ORIGINAL_SOURCE NeuronStudio 0.8.80
# CREATURE
# REGION
# FIELD/LAYER
# TYPE
# CONTRIBUTOR
# REFERENCE
# RAW
# EXTRAS
# SOMA_AREA
# SHINKAGE_CORRECTION 1.0 1.0 1.0
# VERSION_NUMBER 1.0
# VERSION_DATE 2007-07-24
# SCALE 1.0 1.0 1.0
1 1 14.566132 34.873772 7.857000 0.717830 -1
2 0 16.022520 33.760513 7.047000 0.463378 1
3 5 17.542000 32.604973 6.885001 0.638007 2
4 0 19.163984 32.022469 5.913000 0.602284 3
5 0 20.448090 30.822802 4.860000 0.436025 4
6 6 21.897903 28.881084 3.402000 0.471886 5
7 0 18.461960 30.289471 8.586000 0.447463 3
8 6 19.420759 28.730757 9.558000 0.496217 7"""
skel = Skeleton.from_swc(test_file)
assert skel.vertices.shape[0] == 8
assert skel.edges.shape[0] == 7
skel_gt = Skeleton(
vertices=[[14.566132, 34.873772, 7.857000],
[16.022520, 33.760513, 7.047000],
[17.542000, 32.604973, 6.885001],
[19.163984, 32.022469, 5.913000],
[20.448090, 30.822802, 4.860000],
[21.897903, 28.881084, 3.402000],
[18.461960, 30.289471, 8.586000],
[19.420759, 28.730757, 9.558000]],
edges=[(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (2, 6), (7, 6)],
radii=[
0.717830, 0.463378, 0.638007, 0.602284, 0.436025, 0.471886,
0.447463, 0.496217
],
vertex_types=[1, 0, 5, 0, 0, 6, 0, 6],
)
assert Skeleton.equivalent(skel, skel_gt)
skel = Skeleton.from_swc(skel.to_swc())
assert np.all(np.abs(skel.vertices - skel_gt.vertices) < 0.00001)
# sorts edges
skel = skel.consolidate()
skel_gt = skel_gt.consolidate()
assert np.all(skel.edges == skel_gt.edges)
assert np.all(np.abs(skel.radii - skel_gt.radii) < 0.00001)
Nv = skel.vertices.shape[0]
Ne = skel.edges.shape[0]
for _ in range(10):
skel = Skeleton.from_swc(skel.to_swc())
assert skel.vertices.shape[0] == Nv
assert skel.edges.shape[0] == Ne
