def testAllSampleFilesLoadable(self):
filenames = [
("CablesIncluded.xml", {}),
("L23PyrFRB.morph.xml", { 'dendrite_group': 'dendrite', 'soma_group':'soma' }),
("Simple.morph.xml", {}),
("SimpleNeuroML.xml", {}),
]
for f, regions in filenames:
full = os.path.join(TestMorphMLLoading.dir, f)
m6 = MorphologyLoader.fromMorphML(open(full), regions=regions)
def testAllSampleFilesLoadable(self):
filenames = [
("CablesIncluded.xml", {}),
("L23PyrFRB.morph.xml", {
'dendrite_group': 'dendrite',
'soma_group': 'soma'
}),
("Simple.morph.xml", {}),
("SimpleNeuroML.xml", {}),
]
for f, regions in filenames:
full = os.path.join(TestMorphMLLoading.dir, f)
m6 = MorphologyLoader.fromMorphML(open(full), regions=regions)
def testBasicLoad(self):
f = StringIO.StringIO(TestSWC.swcSample)
m = MorphologyLoader.fromSWC(src=f, morphname=None, regionNames=None)
print m
self.assertEqual(len(m), 6)
self.assertEqual(len(m.get_regions()), 2)
root = m.get_root_section()
self.assertAlmostEqual(root.p_x, 1591.43)
self.assertAlmostEqual(root.p_y, 53.87 )
self.assertAlmostEqual(root.p_z, 20.48 )
self.assertAlmostEqual(root.p_r, 0.15 )
self.assertAlmostEqual(root.d_x, 1590.78)
self.assertAlmostEqual(root.d_y, 50.61 )
self.assertAlmostEqual(root.d_z, 20.48 )
self.assertAlmostEqual(root.d_r, 5.80 )
def testBasicLoad(self):
f = StringIO.StringIO(TestSWC.swcSample)
m = MorphologyLoader.fromSWC(src=f, morphname=None, regionNames=None)
print m
self.assertEqual(len(m), 6)
self.assertEqual(len(m.get_regions()), 2)
root = m.get_root_section()
self.assertAlmostEqual(root.p_x, 1591.43)
self.assertAlmostEqual(root.p_y, 53.87)
self.assertAlmostEqual(root.p_z, 20.48)
self.assertAlmostEqual(root.p_r, 0.15)
self.assertAlmostEqual(root.d_x, 1590.78)
self.assertAlmostEqual(root.d_y, 50.61)
self.assertAlmostEqual(root.d_z, 20.48)
self.assertAlmostEqual(root.d_r, 5.80)
def testCablesIncluded(self):
#print 'Testing MorphML'
full = os.path.join(TestMorphMLLoading.dir, "CablesIncluded.xml")
m = MorphologyLoader.fromMorphML(open(full))
# The morphology has 6 segments and 2 regions:
self.assertEqual(len(m), 6)
self.assertEqual(len(m.get_regions()), 2)
self.assertEqual(set([r.name for r in m.get_regions()]),
set(['somagroup', 'dendritegroup']))
s = list(m)
self.assertTrue(s[0].is_a_root_section())
self.assertFalse(s[1].is_a_root_section())
self.assertFalse(s[2].is_a_root_section())
self.assertFalse(s[3].is_a_root_section())
self.assertFalse(s[4].is_a_root_section())
self.assertFalse(s[5].is_a_root_section())
# Sections::
# SECTION ID=0
self.assertListAlmostEqual([s[0].p_x, s[0].p_y, s[0].p_z, s[0].p_r],
[0.0, 0.0, 0.0, 5.0])
self.assertListAlmostEqual([s[0].d_x, s[0].d_y, s[0].d_z, s[0].d_r],
[10.0, 0.0, 0.0, 5.0])
self.assertEqual(m.get_region('somagroup'), s[0].region)
self.assertEqual(s[0].idtag, 'SomaSeg')
root = s[0]
# SECTION ID=1
s1 = m.get_section(idtag='DendSeg1')
self.assertEqual(s1.parent, root)
self.assertEqual(m.get_region('dendritegroup'), s1.region)
self.assertListAlmostEqual([s1.d_x, s1.d_y, s1.d_z, s1.d_r],
[5.0, 10.0, 0.0, 2.5])
# SECTION ID=2
s2 = m.get_section(idtag='DendSeg2')
self.assertEqual(s2.parent, s1)
self.assertEqual(m.get_region('dendritegroup'), s2.region)
self.assertListAlmostEqual([s2.d_x, s2.d_y, s2.d_z, s2.d_r],
[5.0, 20.0, 0.0, 2.5])
# SECTION ID=3
s3 = m.get_section(idtag='DendSeg3')
self.assertEqual(s3.parent, s2)
self.assertEqual(m.get_region('dendritegroup'), s3.region)
self.assertListAlmostEqual([s3.d_x, s3.d_y, s3.d_z, s3.d_r],
[5.0, 30.0, 0.0, 2.5])
# SECTION ID=4
s4 = m.get_section(idtag='DendSeg4')
self.assertEqual(s4.parent, root)
self.assertEqual(m.get_region('dendritegroup'), s4.region)
self.assertListAlmostEqual([s4.d_x, s4.d_y, s4.d_z, s4.d_r],
[10.0, 0.0, 10.0, 1.5])
# SECTION ID=5
s5 = m.get_section(idtag='DendSeg5')
self.assertEqual(s5.parent, s4)
self.assertEqual(m.get_region('dendritegroup'), s5.region)
self.assertListAlmostEqual([s5.d_x, s5.d_y, s5.d_z, s5.d_r],
[10.0, 0.0, 20.0, 1.5])
def testCablesIncluded(self):
#print 'Testing MorphML'
full = os.path.join(TestMorphMLLoading.dir, "CablesIncluded.xml")
m = MorphologyLoader.fromMorphML(open(full))
# The morphology has 6 segments and 2 regions:
self.assertEqual(len(m), 6)
self.assertEqual(len(m.get_regions()), 2)
self.assertEqual(set([r.name for r in m.get_regions()]), set(['somagroup', 'dendritegroup']))
s = list(m)
self.assertTrue( s[0].is_a_root_section())
self.assertFalse(s[1].is_a_root_section())
self.assertFalse(s[2].is_a_root_section())
self.assertFalse(s[3].is_a_root_section())
self.assertFalse(s[4].is_a_root_section())
self.assertFalse(s[5].is_a_root_section())
# Sections::
# SECTION ID=0
self.assertListAlmostEqual(
[s[0].p_x, s[0].p_y, s[0].p_z, s[0].p_r],
[0.0, 0.0, 0.0, 5.0])
self.assertListAlmostEqual(
[s[0].d_x, s[0].d_y, s[0].d_z, s[0].d_r],
[10.0, 0.0, 0.0, 5.0])
self.assertEqual(m.get_region('somagroup'), s[0].region)
self.assertEqual(s[0].idtag, 'SomaSeg')
root = s[0]
# SECTION ID=1
s1 = m.get_section(idtag = 'DendSeg1')
self.assertEqual(s1.parent, root)
self.assertEqual(m.get_region('dendritegroup'), s1.region)
self.assertListAlmostEqual(
[s1.d_x, s1.d_y, s1.d_z, s1.d_r],
[5.0, 10.0, 0.0, 2.5])
# SECTION ID=2
s2 = m.get_section(idtag = 'DendSeg2')
self.assertEqual(s2.parent, s1)
self.assertEqual(m.get_region('dendritegroup'), s2.region)
self.assertListAlmostEqual(
[s2.d_x, s2.d_y, s2.d_z, s2.d_r],
[5.0, 20.0, 0.0, 2.5])
# SECTION ID=3
s3 = m.get_section(idtag = 'DendSeg3')
self.assertEqual(s3.parent, s2)
self.assertEqual(m.get_region('dendritegroup'), s3.region)
self.assertListAlmostEqual(
[s3.d_x, s3.d_y, s3.d_z, s3.d_r],
[5.0, 30.0, 0.0, 2.5])
# SECTION ID=4
s4 = m.get_section(idtag = 'DendSeg4')
self.assertEqual(s4.parent, root)
self.assertEqual(m.get_region('dendritegroup'), s4.region)
self.assertListAlmostEqual(
[s4.d_x, s4.d_y, s4.d_z, s4.d_r],
[10.0, 0.0, 10.0, 1.5])
# SECTION ID=5
s5 = m.get_section(idtag = 'DendSeg5')
self.assertEqual(s5.parent, s4)
self.assertEqual(m.get_region('dendritegroup'), s5.region)
self.assertListAlmostEqual(
[s5.d_x, s5.d_y, s5.d_z, s5.d_r],
[10.0, 0.0, 20.0, 1.5])
