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)
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 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 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 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 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 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 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)
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # ---------------------------------------------------------------------- """Load SWC data from a string directly into a MorphologyArray. We can load .swc from any file-like object, so we can use StringIO to load directly from strings. """ from morphforge.morphology.core import MorphologyArray from StringIO import StringIO swcSrc = """ 1 0 1.0 2.0 3.0 4.0 -1 2 0 5.0 6.0 7.0 8.0 1 """ m = MorphologyArray.fromSWC(StringIO(swcSrc)) print 'Morphology Vertices:' print m._vertices print 'Morphology Connectivity:' print m._connectivity
from morphforge.morphology.core import MorphologyArray from StringIO import StringIO swcSrc = """ 1 0 1.0 2.0 3.0 4.0 -1 2 0 5.0 6.0 7.0 8.0 1 """ m = MorphologyArray.fromSWC(StringIO(swcSrc)) print 'Morphology Vertices:' print m._vertices print 'Morphology Connectivity:' print m._connectivity
