def testComparisonFailureAddingEpsilon2(self):
"""Load and complex .swc file, and
change each [x, y, z, r] value in the vertices matrix
individually, to check that it is not the same.
"""
testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc")
m = MorphologyArray.fromSWC(srcSWCFile)
MFRandom.seed(0)
for i in range(len(m)):
print i, len(m)
for j in range(4):
# Only test 2% of cases:
if not np.random.rand() < 0.02:
continue
m1 = MorphologyArray.fromSWC(srcSWCFile)
m1._vertices[i, j] = m1._vertices[i, j] + 0.01
assert MorphArrayComparison.are_same(m,
m1,
max_node_distance=0.02)
assert not MorphArrayComparison.are_same(
m, m1, max_node_distance=0.005)
def testComparisonFailureDifferentMorphologies(self):
"""Verify simple .swc snippets are different to each other"""
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['A']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['B']))
m3 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
assert not MorphArrayComparison.are_same(m1, m2, max_node_distance= 0.00001)
assert not MorphArrayComparison.are_same(m1, m3, max_node_distance= 0.00001)
assert not MorphArrayComparison.are_same(m2, m3, max_node_distance= 0.00001)
def testComparisonFailureDifferentMorphologies(self):
"""Verify simple .swc snippets are different to each other"""
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['A']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['B']))
m3 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
assert not MorphArrayComparison.are_same(
m1, m2, max_node_distance=0.00001)
assert not MorphArrayComparison.are_same(
m1, m3, max_node_distance=0.00001)
assert not MorphArrayComparison.are_same(
m2, m3, max_node_distance=0.00001)
def testComparisonFailureAddingEpsilon1(self):
"""Load simple .swc snippets, and change each [x, y, z, r] value in the vertices matrix
individually, to check that it is not the same. """
m = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
for i in range(len(m)):
for j in range(4):
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
m1._vertices[i, j] = m1._vertices[i, j] + 0.01
assert MorphArrayComparison.are_same(m, m1, max_node_distance= 0.02)
assert not MorphArrayComparison.are_same(m, m1, max_node_distance= 0.005)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
m1._vertices[i, j] = m1._vertices[i, j] - 0.001
assert MorphArrayComparison.are_same(m, m1, max_node_distance= 0.002)
assert not MorphArrayComparison.are_same(m, m1, max_node_distance= 0.0005)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Cii']))
m1._vertices[i, j] = m1._vertices[i, j] + 0.01
assert MorphArrayComparison.are_same(m, m1, max_node_distance= 0.02)
assert not MorphArrayComparison.are_same(m, m1, max_node_distance= 0.005)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Cii']))
m1._vertices[i, j] = m1._vertices[i, j] - 0.001
assert MorphArrayComparison.are_same(m, m1, max_node_distance= 0.002)
assert not MorphArrayComparison.are_same(m, m1, max_node_distance= 0.0005)
def testComparisonSucessful(self):
"""Verify simple .swc snippets are the same"""
# Loading
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['A']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['A']))
assert MorphArrayComparison.are_same(m1, m2, max_node_distance=0.00001)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['B']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['B']))
assert MorphArrayComparison.are_same(m1, m2, max_node_distance=0.00001)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['Cii']))
assert MorphArrayComparison.are_same(m1, m2, max_node_distance=0.00001)
def testComparisonFailureTransplantingALeafNode(self):
"""Remap each leaf node in a complex swc file, onto
different internal nodes of the morphology,
and check that the morphology is considered different
"""
testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc")
m = MorphologyArray.fromSWC(srcSWCFile)
# Find the leaf nodes:
leaf_nodes = m.get_leaf_vertices_indices()
for new_parent in [0, 10, 20, leaf_nodes[-1]]:
for l in leaf_nodes[:-1]:
v = m._vertices.copy()
c = m._connectivity.copy()
# Rewrite the connectivity matrix, mapping the
# leaf to a new_parent:
c[c == l] = new_parent
mNew = MorphologyArray(vertices=v, connectivity=c)
assert not MorphArrayComparison.are_same(
m, mNew, max_node_distance=0.00001)
def testComparisonSucessful(self):
"""Verify simple .swc snippets are the same"""
# Loading
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['A']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['A']))
assert MorphArrayComparison.are_same(m1, m2, max_node_distance= 0.00001)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['B']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['B']))
assert MorphArrayComparison.are_same(m1, m2, max_node_distance= 0.00001)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
m2 = MorphologyArray.fromSWC(StringIO(swc_srcs['Cii']))
assert MorphArrayComparison.are_same(m1, m2, max_node_distance= 0.00001)
def testComparisonFailureTransplantingALeafNode(self):
"""Remap each leaf node in a complex swc file, onto
different internal nodes of the morphology,
and check that the morphology is considered different
"""
testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc")
m = MorphologyArray.fromSWC(srcSWCFile)
# Find the leaf nodes:
leaf_nodes = m.get_leaf_vertices_indices()
for new_parent in [0, 10, 20, leaf_nodes[-1]]:
for l in leaf_nodes[:-1]:
v = m._vertices.copy()
c = m._connectivity.copy()
# Rewrite the connectivity matrix, mapping the
# leaf to a new_parent:
c[c==l]=new_parent
mNew = MorphologyArray(vertices=v, connectivity=c)
assert not MorphArrayComparison.are_same(m, mNew, max_node_distance= 0.00001)
def testComparisonFailureAddingEpsilon2(self):
"""Load and complex .swc file, and
change each [x, y, z, r] value in the vertices matrix
individually, to check that it is not the same.
"""
testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc")
m = MorphologyArray.fromSWC(srcSWCFile)
MFRandom.seed(0)
for i in range(len(m)):
print i, len(m)
for j in range(4):
# Only test 2% of cases:
if not np.random.rand() < 0.02:
continue
m1 = MorphologyArray.fromSWC(srcSWCFile)
m1._vertices[i, j] = m1._vertices[i, j] + 0.01
assert MorphArrayComparison.are_same(m, m1, max_node_distance= 0.02)
assert not MorphArrayComparison.are_same(m, m1, max_node_distance= 0.005)
def testComparisonFailureAddingEpsilon1(self):
"""Load simple .swc snippets, and change each [x, y, z, r] value in the vertices matrix
individually, to check that it is not the same. """
m = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
for i in range(len(m)):
for j in range(4):
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
m1._vertices[i, j] = m1._vertices[i, j] + 0.01
assert MorphArrayComparison.are_same(m,
m1,
max_node_distance=0.02)
assert not MorphArrayComparison.are_same(
m, m1, max_node_distance=0.005)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Ci']))
m1._vertices[i, j] = m1._vertices[i, j] - 0.001
assert MorphArrayComparison.are_same(m,
m1,
max_node_distance=0.002)
assert not MorphArrayComparison.are_same(
m, m1, max_node_distance=0.0005)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Cii']))
m1._vertices[i, j] = m1._vertices[i, j] + 0.01
assert MorphArrayComparison.are_same(m,
m1,
max_node_distance=0.02)
assert not MorphArrayComparison.are_same(
m, m1, max_node_distance=0.005)
m1 = MorphologyArray.fromSWC(StringIO(swc_srcs['Cii']))
m1._vertices[i, j] = m1._vertices[i, j] - 0.001
assert MorphArrayComparison.are_same(m,
m1,
max_node_distance=0.002)
assert not MorphArrayComparison.are_same(
m, m1, max_node_distance=0.0005)
m = MorphologyImporter.fromSWCFile(filename="/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc", astype=MorphologyTree)
MorphologyExporter.toSWCFile(morphology = m, filename="/home/michael/Desktop/test1.swc")
m2 = MorphologyImporter.fromSWCFile(filename="/home/michael/Desktop/test1.swc", astype=MorphologyTree)
#m2 = MorphologyLoader.fromSWC(src=open("/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc"))
are_same = MorphArrayComparison.are_same(m, m2)
print are_same
#m = MorphologyLoader2.loadSWCFile(filename="/home/michael/workspace/morphforge/src/test_data/swc_srcs/05b_pyramidal9aACC.CNG_short.swc", astype=MorphologyTree)
#MayaViRenderer(morph=m).showSimpleCylinders().show()
#MorphologyLoader2.loadSWCFile(astype=MorphologyArray)
MatPlotLibViewer(m)
import pylab
pylab.show()
from morphforge.morphology.importer.morphologyimporter import MorphologyImporter
from morphforge.morphology.exporter.morphologyexporter import MorphologyExporter
from morphforge.morphology.comparison.comparearrays import MorphArrayComparison
from morphforge.morphology.builders.morphologyloader import MorphologyLoader
m = MorphologyImporter.fromSWCFile(
filename=
"/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc",
astype=MorphologyTree)
MorphologyExporter.toSWCFile(morphology=m,
filename="/home/michael/Desktop/test1.swc")
m2 = MorphologyImporter.fromSWCFile(filename="/home/michael/Desktop/test1.swc",
astype=MorphologyTree)
#m2 = MorphologyLoader.fromSWC(src=open("/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc"))
are_same = MorphArrayComparison.are_same(m, m2)
print are_same
#m = MorphologyLoader2.loadSWCFile(filename="/home/michael/workspace/morphforge/src/test_data/swc_srcs/05b_pyramidal9aACC.CNG_short.swc", astype=MorphologyTree)
#MayaViRenderer(morph=m).showSimpleCylinders().show()
#MorphologyLoader2.loadSWCFile(astype=MorphologyArray)
MatPlotLibViewer(m)
import pylab
pylab.show()