def testChainOp(self):
verts = array([[-.1, -.1], [-.1, 1.1], [1.1, 1.1], [1.1, -.1]])
cols = [0, 1]
g = PolyGate(verts, cols)
self.fcm.gate(g).gate(g)
self.assertTrue(all(self.fcm.view() == array([[0, 1, 2]])),
'gate excluded wrong points')
def build_Polygon(rect, prefix=None, suffix=None, name_prefix=None):
if isinstance(name_prefix, str):
name = name_prefix + "::" + rect.attrib['name']
else:
name = rect.attrib['name']
verts = []
axis = [rect.attrib['xAxisName'], rect.attrib['yAxisName']]
if prefix is not None and prefix is not '':
for i,j in enumerate(axis):
if j.startswith(prefix):
axis[i] = j.replace(prefix,'')
if suffix is not None and suffix is not '':
for i,j in enumerate(axis):
if j.endswith(suffix):
axis[i] = j[:-(len(suffix))]
#replaced[i] = True
axis = tuple(axis)
for vert in rect.iter('Vertex'):
x = float(vert.attrib['x'])
y = float(vert.attrib['y'])
verts.append((x,y))
return PolyGate(verts, axis, name)
def testGate(self):
verts = array([[-.1, -.1], [-.1, 1.1], [1.1, 1.1], [1.1, -.1]])
cols = [0, 1]
g = PolyGate(verts, cols)
self.fcms.gate(g)
assert_array_equal(self.fcms['test_fcm1'].view(), array([[1, 1, 1]]),
'Gating failed')
assert_array_equal(self.fcms['test_fcm2'].view(), array([[1, 1, 1]]),
'Gating failed')
def testPolyGate(self):
verts = array([[-.1, -.1], [-.1, 1.1], [1.1, 1.1], [1.1, -.1]])
cols = [0, 1]
g = PolyGate(verts, cols)
self.fcm.gate(g)
assert all(self.fcm.view() == array([[0, 1, 2]
])), 'gate excluded wrong points'
self.fcm.visit('root')
self.fcm.gate(g)
nodes = self.fcm.tree.nodes.keys()
assert 'g2' in nodes, 'gating name mangled'
assert 'g1' in nodes, 'gating name mangled'
def testEmptyPolyGate(self):
verts = array([[10, 10], [10, 11], [11, 11], [11, 10]])
cols = [0, 1]
g = PolyGate(verts, cols)
self.fcm.gate(g)
assert_array_equal(self.fcm.view(),
array([]).reshape((0, 3)), 'gated region not empty')
self.fcm.gate(g)
assert_array_equal(self.fcm.view(),
array([]).reshape((0, 3)), 'gated region not empty')
nodes = self.fcm.tree.nodes.keys()
assert 'g2' in nodes, 'gating name mangled'
assert 'g1' in nodes, 'gating name mangled'
def testCopy(self):
cpy = self.fcm.copy()
self.assertFalse(cpy is self.fcm,
"copy reproduced the exact same object")
self.assertTrue(cpy.tree.pprint() == self.fcm.tree.pprint(),
"copy failed to reproduce the view tree")
# make sure changes to object self.fcm don't show up on cpy
verts = array([[-.1, -.1], [-.1, 1.1], [1.1, 1.1], [1.1, -.1]])
cols = [0, 1]
g = PolyGate(verts, cols)
self.fcm.gate(g)
self.assertFalse(cpy.tree.pprint() == self.fcm.tree.pprint(),
"copy failed to reproduce the view tree")
#make sure tree is actually copied
cpy = self.fcm.copy()
self.assertTrue(cpy.tree.pprint() == self.fcm.tree.pprint(),
"copy failed to reproduce the view tree")
alpha=alpha,
**kwargs)
ax.fill(gate.vert.T[0],
gate.vert.T[1],
edgecolor='black',
facecolor='none')
if __name__ == '__main__':
import fcm
import numpy
import matplotlib
import matplotlib.pyplot as plt
x = fcm.loadFCS('../../sample_data/3FITC_4PE_004.fcs')
g = PolyGate(numpy.array([[0, 0], [500, 0], [500, 500], [0, 500]]), [0, 1])
g3 = QuadGate([250, 300], (2, 3))
fig = plt.figure()
ax = fig.add_subplot(2, 2, 1)
plot_gate(x, g, ax, name="firstgate", alpha=.5, bgalpha=.5)
ax = fig.add_subplot(2, 2, 2)
mx = x[:, 2].max()
print mx
g2 = ThresholdGate(mx - 1, 2)
plot_gate(x, g2, ax, name="secondgate", chan=(2, 3),
alpha=.5) # , bgc='red', c='green')
print x.shape
print x[:]
x.visit('root')
ax = fig.add_subplot(2, 2, 3)
