def getBoundingCEllipsoidVol(self, transformedCP, ET=None, retA=False):
"""Return the volume of the minimum bounding coverage ellipsoid"""
if ET is None:
ET = EllipsoidTool()
(A, center, radii, _rotation) = self.getBoundingEllipsoid(transformedCP, ET=ET, retA=True)
if retA:
return ((A, center), ET.getEllipsoidVolume(radii))
else:
return ET.getEllipsoidVolume(radii)
def getBoundingCEllipsoidVol(self, transformedCP, ET=None, retA=False):
"""Return the volume of the minimum bounding coverage ellipsoid"""
if ET is None:
ET = EllipsoidTool()
(A, center, radii,
_rotation) = self.getBoundingEllipsoid(transformedCP,
ET=ET,
retA=True)
if retA:
return ((A, center), ET.getEllipsoidVolume(radii))
else:
return ET.getEllipsoidVolume(radii)
def getBoundingKEllipseArea(self, KPCAs, ET=None, retA=False):
"""Return the area of the minimum bounding kmer PCA ellipse"""
if len(KPCAs) > 1:
if ET is None:
ET = EllipsoidTool()
(A, center, radii, _rotation) = ET.getMinVolEllipse(KPCAs, retA=True)
if retA:
return ((A, center), ET.getEllipsoidVolume(radii))
else:
return ET.getEllipsoidVolume(radii)
else: # minimum bounding ellipse of a point is 0
if retA:
return ((np.zeros((2,2)), KPCAs[0]), 0)
else:
return 0
def getBoundingKEllipseArea(self, KPCAs, ET=None, retA=False):
"""Return the area of the minimum bounding kmer PCA ellipse"""
if len(KPCAs) > 1:
if ET is None:
ET = EllipsoidTool()
(A, center, radii, _rotation) = ET.getMinVolEllipse(KPCAs,
retA=True)
if retA:
return ((A, center), ET.getEllipsoidVolume(radii))
else:
return ET.getEllipsoidVolume(radii)
else: # minimum bounding ellipse of a point is 0
if retA:
return ((np.zeros((2, 2)), KPCAs[0]), 0)
else:
return 0
def getBoundingEllipsoid(self, transformedCP, ET=None, retA=False):
"""Return the minimum bounding ellipsoid
returns (center, radii, rotation) or (A, center, radii, rotation)
"""
bin_points = np.array([transformedCP[i] for i in self.rowIndices])
if len(bin_points) > 1:
if ET is None:
ET = EllipsoidTool()
try:
return ET.getMinVolEllipse(bin_points, retA=retA)
except:
print bin_points
raise
else: # minimum bounding ellipse of a point is 0
if retA:
return (np.zeros((3,3)), transformedCP[self.rowIndices[0]], np.zeros((3)), np.eye(3))
else:
return (transformedCP[self.rowIndices[0]], np.zeros((3)), np.eye(3))
def getBoundingEllipsoid(self, transformedCP, ET=None, retA=False):
"""Return the minimum bounding ellipsoid
returns (center, radii, rotation) or (A, center, radii, rotation)
"""
bin_points = np.array([transformedCP[i] for i in self.rowIndices])
if len(bin_points) > 1:
if ET is None:
ET = EllipsoidTool()
try:
return ET.getMinVolEllipse(bin_points, retA=retA)
except:
print(bin_points)
raise
else: # minimum bounding ellipse of a point is 0
if retA:
return (np.zeros(
(3, 3)), transformedCP[self.rowIndices[0]], np.zeros(
(3)), np.eye(3))
else:
return (transformedCP[self.rowIndices[0]], np.zeros(
(3)), np.eye(3))
