def communityOrientationStats():
"""
Calculate the orientation of all bacilli as the dot product from each of the Euclidean
basis vectors in R^3.
:@rtype: tuple
:@return:
"""
bdots = [[],[],[]]
fdots = [[],[],[]]
sRes = []
bacilli = []
filaments = []
#lengths = []
xbasis = Vec3f(1,0,0)
ybasis = Vec3f(0,1,0)
zbasis = Vec3f(0,0,1)
for i, bact in enumerate(DataStore.Bacteria()):
blen = len(bact.Markers)
if blen == 2:
bacilli.append(DataStore.BacteriaActors()[i])
v = bact.Markers[0] - bact.Markers[1]
#lengths.append(v.length())
v.normalize()
bdots[0].append(xbasis.dot(v))
bdots[1].append(ybasis.dot(v))
bdots[2].append(zbasis.dot(v))
# calculate filament orientations b/t each two markers
if blen > 2:
filaments.append(i)
_, _, _, splinePoints = generateSpline(bact.Markers)
sRes.append(len(splinePoints) - 1) # -1 b/c we're using every pair, not every point
sMarkers = [Vec3f(point) for point in splinePoints]
for j in range(len(sMarkers)-1):
v = sMarkers[j] - sMarkers[j+1]
v.normalize()
fdots[0].append(xbasis.dot(v))
fdots[1].append(ybasis.dot(v))
fdots[2].append(zbasis.dot(v))
# data = np.hstack((np.array(angles).T, np.array(lengths)[:,np.newaxis]))
# writeCSV(data, ['x','y','z','len'], 'olen.csv')
return bacilli, filaments, bdots, fdots, sRes
def _createFilamentSpline(self, markers):
profileData = vtk.vtkPolyData()
points, scalars, t, sList = generateSpline(markers)
fradius = self.actor_radius * 1.5
# Create the polyline.
lines = vtk.vtkCellArray()
lines.InsertNextCell(len(sList))
for i in range(len(sList)):
lines.InsertCellPoint(i)
profileData.SetPoints(points)
profileData.SetLines(lines)
profileData.GetPointData().SetScalars(scalars)
# Add thickness to the resulting line.
profileTubes = vtk.vtkTubeFilter()
profileTubes.SetNumberOfSides(20)
profileTubes.SetInput(profileData)
profileTubes.SetRadius(fradius)
profileMapper = vtk.vtkPolyDataMapper()
profileMapper.SetInput(profileTubes.GetOutput())
profileMapper.SetScalarRange(0,t)
profileMapper.ScalarVisibilityOff()
profile = vtk.vtkActor()
profile.SetMapper(profileMapper)
profile.GetProperty().SetDiffuseColor(self.color.r, self.color.g, self.color.b)
# profile.GetProperty().SetSpecular(.3)
# profile.GetProperty().SetSpecularPower(30)
markers[0].GetProperty().SetDiffuseColor(self.color.r, self.color.g, self.color.b)
markers[-1].GetProperty().SetDiffuseColor(self.color.r, self.color.g, self.color.b)
# Add capping spheres
filament = vtk.vtkAssembly()
filament.AddPart(self.CreateMarker(Vec3f(markers[0].GetCenter()), fradius))
filament.AddPart(profile)
filament.AddPart(self.CreateMarker(Vec3f(markers[-1].GetCenter()), fradius))
return filament