naive jit implementation for cooling (#1408)

Co-authored-by: Andy Maloney <[email protected]>

datashader/layout.py

@@ -3,11 +3,11 @@
 
 from __future__ import annotations
 
+import numba as nb
 import numpy as np
 import param
 import scipy.sparse
 
-
 class LayoutAlgorithm(param.ParameterizedFunction):
     """
     Baseclass for all graph layout algorithms.
@@ -172,13 +172,25 @@ def _merge_points_with_nodes(nodes, points, params):
     n[params.y] = points[:, 1]
     return n
 
-
 def cooling(matrix, points, temperature, params):
-    dt = temperature / float(params.iterations + 1)
-    displacement = np.zeros((params.dim, len(points)))
-    for iteration in range(params.iterations):
+    matrix = matrix.toarray()
+    c_params = {
+        'iterations': params.iterations,
+        'dim': params.dim,
+        'k': params.k,
+        'nohubs': params.nohubs,
+        'linlog': params.linlog
+    }
+    _cooling(matrix, points, temperature, **c_params)
+
+
+@nb.jit(nopython=True, nogil=True, parallel=True)
+def _cooling(matrix, points, temperature, iterations, dim, k, nohubs, linlog):
+    dt = temperature / float(iterations + 1)
+    displacement = np.zeros((dim, len(points)))
+    for iteration in range(iterations):
         displacement *= 0
-        for i in range(matrix.shape[0]):
+        for i in nb.prange(matrix.shape[0]):
             # difference between this row's node position and all others
             delta = (points[i] - points).T
 
@@ -189,16 +201,16 @@ def cooling(matrix, points, temperature, params):
             distance = np.where(distance < 0.01, 0.01, distance)
 
             # the adjacency matrix row
-            ai = matrix[i].toarray()
+            ai = matrix[i]
 
             # displacement "force"
-            dist = params.k * params.k / distance ** 2
+            dist = k * k / distance ** 2
 
-            if params.nohubs:
+            if nohubs:
                 dist = dist / float(ai.sum(axis=1) + 1)
-            if params.linlog:
+            if linlog:
                 dist = np.log(dist + 1)
-            displacement[:, i] += (delta * (dist - ai * distance / params.k)).sum(axis=1)
+            displacement[:, i] += (delta * (dist - ai * distance / k)).sum(axis=1)
 
         # update points
         length = np.sqrt((displacement ** 2).sum(axis=0))