Merge pull request #7 from Hekstra-Lab/fused

Add fused types to non-parallel version

examples/test.py

@@ -13,7 +13,8 @@
 shape = (int(np.max(im1) + 1), int(np.max(im2) + 1))
 out = overlap_parallel(im1.astype(np.int32), im2.astype(np.int32), shape)
 print(out.sum())
-out_serial = overlap(im1.astype(np.int32), im2.astype(np.int32), shape)
+# out_serial = overlap(im1.astype(np.int32), im2.astype(np.int32), shape)
+out_serial = overlap(im1.astype(np.uint16), im2.astype(np.uint16), shape)
 
 # from IPython import embed
 # embed(colors="Linux")

fast_overlap/fast_overlap.pyx

@@ -25,16 +25,28 @@ cpdef overlap_parallel(int [:,::1] prev, int[:,::1] curr, shape):
     cdef np.ndarray[int, ndim=2, mode="c"] output = np.zeros(shape, dtype=np.dtype("i"))
     cdef Py_ssize_t ncols = shape[1]
 
-    print('about to nogil')
     with nogil:
         overlap_parallel_cpp(&prev[0,0], &curr[0,0], prev.shape, &output[0,0], ncols)
     return output
 
 
+
+from libc cimport stdint
+
+ctypedef fused ints:
+    stdint.uint8_t
+    stdint.uint16_t
+    stdint.uint32_t
+    stdint.uint64_t
+    stdint.int8_t
+    stdint.int16_t
+    stdint.int32_t
+    stdint.int64_t
+
 # @cython.boundscheck(False)
 @cython.wraparound(False)
 @cython.nonecheck(False)
-cpdef overlap(int[:, :] prev, int[:,:] curr, shape):
+cpdef overlap(ints[:, :] prev, ints[:,:] curr, shape):
     """
     Calculate the pairwise overlap the labels for two arrays.
 

tests/test_overlap.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 
 import numpy as np
+import pytest
 
 import fast_overlap
 
@@ -9,8 +10,10 @@
 shape = (int(np.max(ims[0]) + 1), int(np.max(ims[1]) + 1))
 
 
-def test_overlap():
-    out = fast_overlap.overlap(ims[0].astype(np.int32), ims[1].astype(np.int32), shape)
+# test a few different types but not all
+@pytest.mark.parametrize("type", [np.uint16, np.uint64, np.int32, np.int64])
+def test_overlap(type):
+    out = fast_overlap.overlap(ims[0].astype(type), ims[1].astype(type), shape)
     assert np.all(out == expected)