def CalculateOrientations(self):
if NoBacteria(): return
ds = communityOrientationStats()
for s in ds:
self.ao(str(s))
def exportOrientations(path):
from calc.stat import communityOrientationStats
_, _, bdots, _, _ = communityOrientationStats()
# move data into [0...1] range
bdots = [map(abs, bdots[i]) for i in range(3)]
# bdots is 3 x n with X,Y,Z for each bacillus in one column, we want them as one row
data = np.array(bdots).T
writeCSV(data, ['x','y','z'], path)
def ColorByOrientation(self, colorScheme=None):
if NoBacteria(): return
bacilli, filaments, bdots, fdots, sRes = communityOrientationStats()
bdots = [map(abs, bdots[i]) for i in range(3)]
fdots = [map(abs, fdots[i]) for i in range(3)]
if colorScheme is None:
colorScheme = Vec3f(2,1,0)
for i, a in enumerate(bacilli):
aColl = vtk.vtkPropCollection()
a.GetActors(aColl)
aColl.InitTraversal()
actors = [aColl.GetNextProp() for _ in range(aColl.GetNumberOfItems())]
for actor in actors:
actor.GetProperty().SetDiffuseColor(bdots[colorScheme.x][i],
bdots[colorScheme.y][i],
bdots[colorScheme.z][i])
for j, fID in enumerate(filaments):
fColl = vtk.vtkPropCollection()
DataStore.BacteriaActors()[fID].GetActors(fColl)
fColl.InitTraversal()
factors = [fColl.GetNextProp() for _ in range(fColl.GetNumberOfItems())]
# Set color LUT for filament spline based on marker positions
colorTransferFunction = vtk.vtkColorTransferFunction()
fdotIdx = sum(sRes[:j])
for k in range(0, sRes[j]):
colorTransferFunction.AddRGBPoint(k,fdots[colorScheme.x][fdotIdx+k],
fdots[colorScheme.y][fdotIdx+k],
fdots[colorScheme.z][fdotIdx+k])
# print 'RGB:',fdots[colorScheme.x][fdotIdx+k],fdots[colorScheme.y][fdotIdx+k],fdots[colorScheme.z][fdotIdx+k]
# filament spline
factors[1].GetMapper().SetLookupTable(colorTransferFunction)
factors[1].GetMapper().ScalarVisibilityOn()
factors[1].GetMapper().SetColorModeToMapScalars()
factors[1].GetMapper().InterpolateScalarsBeforeMappingOff()
# sphere caps
self.setColor(factors[0], fdotIdx, fdots, colorScheme)
self.setColor(factors[-1], fdotIdx+k, fdots, colorScheme)
self.iren.Render()