def gate(self, fcm, chan=None, name=None, _full=False):
"""
return gated region
"""
if chan is None:
chan = self.chan
if name is None:
if self.name is not '':
name = self.name
else:
name = ''
if name is not "" and len(name) != 4:
raise ValueError(
'name must be empty or contain 4 items: name is %s' %
str(name))
# I (+,+), II (-,+), III (-,-), and IV (+,-)
x = fcm.view()[:, chan[0]]
y = fcm.view()[:, chan[1]]
quad = {}
quad[1] = (x > self.vert[0]) & (y > self.vert[1]) # (+,+)
quad[2] = (x < self.vert[0]) & (y > self.vert[1]) # (-,+)
quad[3] = (x < self.vert[0]) & (y < self.vert[1]) # (-,-)
quad[4] = (x > self.vert[0]) & (y < self.vert[1]) # (+,-)
root = fcm.get_cur_node()
cname = root.name
if name is "":
name = ["q%d" % i for i in quad.keys()]
if _full:
nodes = []
for i in quad.keys():
if not self.allow_empty:
if True in quad[i]:
fcm.tree.visit(cname)
node = GatingNode(name[i - 1], root, quad[i])
fcm.add_view(node)
if _full:
nodes.append(node)
else:
fcm.tree.visit(cname)
node = GatingNode(name[i - 1], root, quad[i])
fcm.add_view(node)
if _full:
nodes.append(node)
if _full:
return nodes
else:
return fcm
def gate(self, fcm, chan=None, op=None, name=None):
"""
return all events greater (or less) than a threshold
allowed op are 'g' (greater) or 'l' (less)
"""
if chan is None:
chan = self.chan
x = fcm.view()[:, chan]
if op is None:
op = self.op
if op == 'g':
idxs = numpy.greater(x, self.vert)
elif op == 'l':
idxs = numpy.less(x, self.vert)
else:
raise ValueError('op should be "g" or "l", received "%s"' %
str(op))
if name is None:
name = self.name
node = GatingNode(name, fcm.get_cur_node(), idxs)
fcm.add_view(node)
return fcm
def gate(self, fcm, chan=None, invert=False, name=None):
"""
return gated region of FCM data
"""
if chan is None:
chan = self.chan
if isinstance(chan, tuple):
chan = list(chan)
for i, j in enumerate(chan):
if isinstance(j, str):
chan[i] = fcm.name_to_index(j)[0]
if name is None:
name = self.name
idxs = points_in_poly(self.vert, fcm.view()[:, chan])
# matplotlib has points in poly routine in C
# no faster than our numpy version
# idxs = points_inside_poly(fcm.view()[:, chan], self.vert)
if invert:
idxs = numpy.invert(idxs)
node = GatingNode(name, fcm.get_cur_node(), idxs)
fcm.add_view(node)
return fcm
def gate(self, fcm, chan=None, name=None):
"""
return interval region.
"""
if chan is None:
chan = self.chan
if name is None:
name = self.name
assert (len(self.chan) == 1)
assert (len(self.vert) == 2)
assert (self.vert[1] >= self.vert[0])
x = fcm.view()[:, chan[0]]
idxs = numpy.logical_and(x > self.vert[0], x < self.vert[1])
node = GatingNode(name, fcm.get_cur_node(), idxs)
fcm.add_view(node)
return fcm