Some fixes to pairwise distances for cupy integration (#643)

Authors:
  - Corey J. Nolet (https://github.com/cjnolet)
  - Vinay Deshpande (https://github.com/vinaydes)

Approvers:
  - Divye Gala (https://github.com/divyegala)
  - Dante Gama Dessavre (https://github.com/dantegd)

URL: #643

python/pylibraft/pylibraft/distance/pairwise_distance.pyx

@@ -27,6 +27,13 @@ from libcpp cimport bool
 from .distance_type cimport DistanceType
 from pylibraft.common.handle cimport handle_t
 
+
+def is_c_cont(cai, dt):
+    return "strides" not in cai or \
+        cai["strides"] is None or \
+        cai["strides"][1] == dt.itemsize
+
+
 cdef extern from "raft_distance/pairwise_distance.hpp" \
         namespace "raft::distance::runtime":
 
@@ -54,12 +61,14 @@ cdef extern from "raft_distance/pairwise_distance.hpp" \
 
 DISTANCE_TYPES = {
     "l2": DistanceType.L2SqrtUnexpanded,
+    "sqeuclidean": DistanceType.L2Unexpanded,
     "euclidean": DistanceType.L2SqrtUnexpanded,
     "l1": DistanceType.L1,
     "cityblock": DistanceType.L1,
     "inner_product": DistanceType.InnerProduct,
     "chebyshev": DistanceType.Linf,
     "canberra": DistanceType.Canberra,
+    "cosine": DistanceType.CosineExpanded,
     "lp": DistanceType.LpUnexpanded,
     "correlation": DistanceType.CorrelationExpanded,
     "jaccard": DistanceType.JaccardExpanded,
@@ -68,21 +77,26 @@ DISTANCE_TYPES = {
     "jensenshannon": DistanceType.JensenShannon,
     "hamming": DistanceType.HammingUnexpanded,
     "kl_divergence": DistanceType.KLDivergence,
+    "minkowski": DistanceType.LpUnexpanded,
     "russellrao": DistanceType.RusselRaoExpanded,
     "dice": DistanceType.DiceExpanded
 }
 
-SUPPORTED_DISTANCES = list(DISTANCE_TYPES.keys())
+SUPPORTED_DISTANCES = ["euclidean", "l1", "cityblock", "l2", "inner_product",
+                       "chebyshev", "minkowski", "canberra", "kl_divergence",
+                       "correlation", "russellrao", "hellinger", "lp",
+                       "hamming", "jensenshannon", "cosine", "sqeuclidean"]
 
 
-def distance(X, Y, dists, metric="euclidean"):
+def distance(X, Y, dists, metric="euclidean", p=2.0):
     """
     Compute pairwise distances between X and Y
 
     Valid values for metric:
         ["euclidean", "l2", "l1", "cityblock", "inner_product",
          "chebyshev", "canberra", "lp", "hellinger", "jensenshannon",
-         "kl_divergence", "russellrao"]
+         "kl_divergence", "russellrao", "minkowski", "correlation",
+         "cosine"]
 
     Parameters
     ----------
@@ -91,6 +105,7 @@ def distance(X, Y, dists, metric="euclidean"):
     Y : CUDA array interface compliant matrix shape (n, k)
     dists : Writable CUDA array interface matrix shape (m, n)
     metric : string denoting the metric type (default="euclidean")
+    p : metric parameter (currently used only for "minkowski")
 
     Examples
     --------
@@ -113,14 +128,19 @@ def distance(X, Y, dists, metric="euclidean"):
         pairwise_distance(in1, in2, output, metric="euclidean")
    """
 
-    # TODO: Validate inputs, shapes, etc...
     x_cai = X.__cuda_array_interface__
     y_cai = Y.__cuda_array_interface__
     dists_cai = dists.__cuda_array_interface__
 
     m = x_cai["shape"][0]
     n = y_cai["shape"][0]
-    k = x_cai["shape"][1]
+
+    x_k = x_cai["shape"][1]
+    y_k = y_cai["shape"][1]
+
+    if x_k != y_k:
+        raise ValueError("Inputs must have same number of columns. "
+                         "a=%s, b=%s" % (x_k, y_k))
 
     x_ptr = <uintptr_t>x_cai["data"][0]
     y_ptr = <uintptr_t>y_cai["data"][0]
@@ -132,6 +152,12 @@ def distance(X, Y, dists, metric="euclidean"):
     y_dt = np.dtype(y_cai["typestr"])
     d_dt = np.dtype(dists_cai["typestr"])
 
+    x_c_contiguous = is_c_cont(x_cai, x_dt)
+    y_c_contiguous = is_c_cont(y_cai, y_dt)
+
+    if x_c_contiguous != y_c_contiguous:
+        raise ValueError("Inputs must have matching strides")
+
     if metric not in SUPPORTED_DISTANCES:
         raise ValueError("metric %s is not supported" % metric)
 
@@ -147,20 +173,20 @@ def distance(X, Y, dists, metric="euclidean"):
                           <float*> d_ptr,
                           <int>m,
                           <int>n,
-                          <int>k,
+                          <int>x_k,
                           <DistanceType>distance_type,
-                          <bool>True,
-                          <float>0.0)
+                          <bool>x_c_contiguous,
+                          <float>p)
     elif x_dt == np.float64:
         pairwise_distance(deref(h),
                           <double*> x_ptr,
                           <double*> y_ptr,
                           <double*> d_ptr,
                           <int>m,
                           <int>n,
-                          <int>k,
+                          <int>x_k,
                           <DistanceType>distance_type,
-                          <bool>True,
-                          <float>0.0)
+                          <bool>x_c_contiguous,
+                          <float>p)
     else:
         raise ValueError("dtype %s not supported" % x_dt)

python/pylibraft/pylibraft/test/test_distance.py

@@ -24,10 +24,10 @@
 
 class TestDeviceBuffer:
 
-    def __init__(self, ndarray):
+    def __init__(self, ndarray, order):
         self.ndarray_ = ndarray
         self.device_buffer_ = \
-            rmm.DeviceBuffer.to_device(ndarray.ravel(order="C").tobytes())
+            rmm.DeviceBuffer.to_device(ndarray.ravel(order=order).tobytes())
 
     @property
     def __cuda_array_interface__(self):
@@ -49,10 +49,13 @@ def copy_to_host(self):
 @pytest.mark.parametrize("n_cols", [100])
 @pytest.mark.parametrize("metric", ["euclidean", "cityblock", "chebyshev",
                                     "canberra", "correlation", "hamming",
-                                    "jensenshannon", "russellrao"])
+                                    "jensenshannon", "russellrao", "cosine",
+                                    "sqeuclidean"])
+@pytest.mark.parametrize("order", ["F", "C"])
 @pytest.mark.parametrize("dtype", [np.float32, np.float64])
-def test_distance(n_rows, n_cols, metric, dtype):
-    input1 = np.random.random_sample((n_rows, n_cols)).astype(dtype)
+def test_distance(n_rows, n_cols, metric, order, dtype):
+    input1 = np.random.random_sample((n_rows, n_cols))
+    input1 = np.asarray(input1, order=order).astype(dtype)
 
     # RussellRao expects boolean arrays
     if metric == "russellrao":
@@ -70,8 +73,8 @@ def test_distance(n_rows, n_cols, metric, dtype):
 
     expected[expected <= 1e-5] = 0.0
 
-    input1_device = TestDeviceBuffer(input1)
-    output_device = TestDeviceBuffer(output)
+    input1_device = TestDeviceBuffer(input1, order)
+    output_device = TestDeviceBuffer(output, order)
 
     pairwise_distance(input1_device, input1_device, output_device, metric)
     actual = output_device.copy_to_host()