def readSkelFromFile(fname, iz, iy, ix, bsize, anisotropy):
print("Reading from file: " + fname)
with open(fname, 'r') as f:
inp_swc = f.read()
skel_read = PrecomputedSkeleton.from_swc(inp_swc)
# revert order from x y z to z y x
vertices_copy = skel_read.vertices.copy()
skel_read.vertices[:, 0] = vertices_copy[:, 2]
skel_read.vertices[:, 2] = vertices_copy[:, 0]
x_offset = ix * bsize[OR_X] * anisotropy[OR_X]
y_offset = iy * bsize[OR_Y] * anisotropy[OR_Y]
z_offset = iz * bsize[OR_Z] * anisotropy[OR_Z]
transform_ = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0]])
transform_[0, 3] = z_offset
transform_[1, 3] = y_offset
transform_[2, 3] = x_offset
skel_read.transform = transform_
skel_read.apply_transform()
skel_read.transform = np.array([[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0]])
return skel_read
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 = PrecomputedSkeleton.from_swc(test_file)
assert skel.vertices.shape[0] == 8
assert skel.edges.shape[0] == 7
skel_gt = PrecomputedSkeleton(
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 PrecomputedSkeleton.equivalent(skel, skel_gt)
def readSkelFromFile(fname, bz, by, bx, bsize, anisotropy):
print("Reading from file: " + fname)
with open(fname, 'r') as f:
inp_swc = f.read()
skel_read = PrecomputedSkeleton.from_swc(inp_swc)
x_offset = bx*bsize[0]*anisotropy[0]
y_offset = by*bsize[1]*anisotropy[1]
z_offset = bz*bsize[2]*anisotropy[2]
print("Block: " + str((bx,by,bz)))
print("Offset: "+ str((x_offset,y_offset,z_offset)))
skel_read.transform = np.array([[1,0,0,x_offset],
[0,1,0,y_offset],
[0,0,1,z_offset]])
print("transform: " + str(skel_read.transform))
# print("xmin, xmax: " + str(np.min(skel_read.vertices[:,0])) + ", " + str(np.max(skel_read.vertices[:,0])))
# print("ymin, ymax: " + str(np.min(skel_read.vertices[:,1])) + ", " + str(np.max(skel_read.vertices[:,1])))
# print("zmin, zmax: " + str(np.min(skel_read.vertices[:,2])) + ", " + str(np.max(skel_read.vertices[:,2])))
# print("----------------------------")
#
skel_read.apply_transform()
#
# print("xmin, xmax: " + str(np.min(skel_read.vertices[:,0])) + ", " + str(np.max(skel_read.vertices[:,0])))
# print("ymin, ymax: " + str(np.min(skel_read.vertices[:,1])) + ", " + str(np.max(skel_read.vertices[:,1])))
# print("zmin, zmax: " + str(np.min(skel_read.vertices[:,2])) + ", " + str(np.max(skel_read.vertices[:,2])))
skel_read.transform = np.array([[1,0,0,0],
[0,1,0,0],
[0,0,1,0]])
return skel_read