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numba for scipy, specifically cdist

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0

I'm trying to speed up a comparison between two pointclouds, I have some code which took up to an hour to complete. I've butchered it to this and tried to implement numba. The code works with the exception of the scipy cdist function. It's my first test of using numba, where am I going wrong?

from numba import jit

@jit(nopython=True)
def near_dist_top(T, B):
 xi = [i[0] for i in T]
 yi = [i[1] for i in T]
 zi = [i[2] for i in T]
 XB = B

 insert_params = []

 for i in range(len(T)):
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 insert_params.append((xi[i], yi[i], zi[i], disti))
 # print("Top: " + str(i) + " of " + str(len(T)))
 print(i)
 return insert_params
 print(XB)

@@@ Edits @@@

Both T and B are lists of coordinates

(580992.507, 4275268.8321, 192.4599), (580992.507, 4275268.8391, 192.4209), (580992.507, 4275268.8391, 192.4209)

hmmm, does numba handle lists, does it need to be a numpy array, would cdist handle a numpy array...?

The error

numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Untyped global name 'cdist': cannot determine Numba type of <class 'function'>

File "scratch_28.py", line 132:
def near_dist_top(T, B):
 <source elided>
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 ^

python-3.x scipy numba

share|improve this question

edited Mar 9 at 8:54

Gary Nobles

asked Mar 9 at 0:49

Gary NoblesGary Nobles

394317

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Can you please post the stack trace ? Also, what does the argument T and B contain ?
  
  – Gambit
  Mar 9 at 5:25
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  What sor t of error? LIke something about not being able to implement cdist? How, by the way, are you importing or defining cdist? It's not 'native' numpy.
  
  – hpaulj
  Mar 9 at 7:03
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  ok, I've updated the question
  
  – Gary Nobles
  Mar 9 at 8:54
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  cdist is brought in using from scipy.spatial.distance import cdist
  
  – Gary Nobles
  Mar 9 at 8:55
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Is cdist in the list of of functions that can be handled with 'nopython'?
  
  – hpaulj
  Mar 9 at 15:20
  

  
  
  
  

 | 
show 5 more comments

0

I'm trying to speed up a comparison between two pointclouds, I have some code which took up to an hour to complete. I've butchered it to this and tried to implement numba. The code works with the exception of the scipy cdist function. It's my first test of using numba, where am I going wrong?

from numba import jit

@jit(nopython=True)
def near_dist_top(T, B):
 xi = [i[0] for i in T]
 yi = [i[1] for i in T]
 zi = [i[2] for i in T]
 XB = B

 insert_params = []

 for i in range(len(T)):
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 insert_params.append((xi[i], yi[i], zi[i], disti))
 # print("Top: " + str(i) + " of " + str(len(T)))
 print(i)
 return insert_params
 print(XB)

@@@ Edits @@@

Both T and B are lists of coordinates

(580992.507, 4275268.8321, 192.4599), (580992.507, 4275268.8391, 192.4209), (580992.507, 4275268.8391, 192.4209)

hmmm, does numba handle lists, does it need to be a numpy array, would cdist handle a numpy array...?

The error

numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Untyped global name 'cdist': cannot determine Numba type of <class 'function'>

File "scratch_28.py", line 132:
def near_dist_top(T, B):
 <source elided>
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 ^

python-3.x scipy numba

share|improve this question

edited Mar 9 at 8:54

Gary Nobles

asked Mar 9 at 0:49

Gary NoblesGary Nobles

394317

• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Can you please post the stack trace ? Also, what does the argument T and B contain ?
  
  – Gambit
  Mar 9 at 5:25
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  What sor t of error? LIke something about not being able to implement cdist? How, by the way, are you importing or defining cdist? It's not 'native' numpy.
  
  – hpaulj
  Mar 9 at 7:03
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  ok, I've updated the question
  
  – Gary Nobles
  Mar 9 at 8:54
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  cdist is brought in using from scipy.spatial.distance import cdist
  
  – Gary Nobles
  Mar 9 at 8:55
  

  
  
  
  


• 
  
  
  

  
  

  
  
  
  
  
  

  
  
  Is cdist in the list of of functions that can be handled with 'nopython'?
  
  – hpaulj
  Mar 9 at 15:20
  

  
  
  
  

 | 
show 5 more comments

I'm trying to speed up a comparison between two pointclouds, I have some code which took up to an hour to complete. I've butchered it to this and tried to implement numba. The code works with the exception of the scipy cdist function. It's my first test of using numba, where am I going wrong?

from numba import jit

@jit(nopython=True)
def near_dist_top(T, B):
 xi = [i[0] for i in T]
 yi = [i[1] for i in T]
 zi = [i[2] for i in T]
 XB = B

 insert_params = []

 for i in range(len(T)):
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 insert_params.append((xi[i], yi[i], zi[i], disti))
 # print("Top: " + str(i) + " of " + str(len(T)))
 print(i)
 return insert_params
 print(XB)

@@@ Edits @@@

Both T and B are lists of coordinates

(580992.507, 4275268.8321, 192.4599), (580992.507, 4275268.8391, 192.4209), (580992.507, 4275268.8391, 192.4209)

hmmm, does numba handle lists, does it need to be a numpy array, would cdist handle a numpy array...?

The error

numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Untyped global name 'cdist': cannot determine Numba type of <class 'function'>

File "scratch_28.py", line 132:
def near_dist_top(T, B):
 <source elided>
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 ^

python-3.x scipy numba

share|improve this question

edited Mar 9 at 8:54

Gary Nobles

asked Mar 9 at 0:49

Gary NoblesGary Nobles

394317

from numba import jit

@jit(nopython=True)
def near_dist_top(T, B):
 xi = [i[0] for i in T]
 yi = [i[1] for i in T]
 zi = [i[2] for i in T]
 XB = B

 insert_params = []

 for i in range(len(T)):
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 insert_params.append((xi[i], yi[i], zi[i], disti))
 # print("Top: " + str(i) + " of " + str(len(T)))
 print(i)
 return insert_params
 print(XB)

(580992.507, 4275268.8321, 192.4599), (580992.507, 4275268.8391, 192.4209), (580992.507, 4275268.8391, 192.4209)

numba.errors.TypingError: Failed in nopython mode pipeline (step: nopython frontend)
Untyped global name 'cdist': cannot determine Numba type of <class 'function'>

File "scratch_28.py", line 132:
def near_dist_top(T, B):
 <source elided>
 XA = [T[i]]
 disti = cdist(XA, XB, metric='euclidean').min()
 ^

share|improve this question

edited Mar 9 at 8:54

Gary Nobles

asked Mar 9 at 0:49

Gary NoblesGary Nobles

394317

share|improve this question

edited Mar 9 at 8:54

Gary Nobles

asked Mar 9 at 0:49

Gary NoblesGary Nobles

394317

asked Mar 9 at 0:49

Gary NoblesGary Nobles

394317

asked Mar 9 at 0:49

Gary NoblesGary Nobles

394317