Add basic tests

Author: thodson-usgs

docs/bitinfo.rst

@@ -0,0 +1,10 @@
+PCodec
+======
+
+.. automodule:: numcodecs.bitinfo
+
+.. autoclass:: BitInfo
+
+    .. autoattribute:: codec_id
+    .. automethod:: encode
+    .. automethod:: decode

docs/index.rst

@@ -77,6 +77,7 @@ Contents
     delta
     fixedscaleoffset
     quantize
+    bitinfo
     bitround
     packbits
     categorize

docs/release.rst

@@ -14,6 +14,8 @@ Unreleased
 Enhancements
 ~~~~~~~~~~~~
 
+* Add BitInfo codec
+  By :user:`Tim Hodson <thodson-usgs>`.
 * Use PyData theme for docs
   By :user:`John Kirkham <jakirkham>`, :issue:`485`.
 

numcodecs/bitinfo.py

@@ -115,6 +115,8 @@ def exponent_mask(dtype):
         mask = 0x7F80_0000
     elif dtype == np.float64:
         mask = 0x7FF0_0000_0000_0000
+    else:
+        raise ValueError(f"Unsupported dtype {dtype}")
     return mask
 
 
@@ -175,6 +177,7 @@ def signed_exponent(A):
 def bitpaircount_u1(a, b):
     assert a.dtype == "u1"
     assert b.dtype == "u1"
+
     unpack_a = np.unpackbits(a.flatten()).astype("u1")
     unpack_b = np.unpackbits(b.flatten()).astype("u1")
 
@@ -188,6 +191,7 @@ def bitpaircount_u1(a, b):
 def bitpaircount(a, b):
     assert a.dtype.kind == "u"
     assert b.dtype.kind == "u"
+
     nbytes = max(a.dtype.itemsize, b.dtype.itemsize)
 
     a, b = np.broadcast_arrays(a, b)
@@ -203,6 +207,9 @@ def bitpaircount(a, b):
 def mutual_information(a, b, base=2):
     """Calculate the mutual information between two arrays.
     """
+    assert a.dtype == b.dtype
+    assert a.dtype.kind == "u"
+
     size = np.prod(np.broadcast_shapes(a.shape, b.shape))
     counts = bitpaircount(a, b)
 
@@ -228,6 +235,8 @@ def bitinformation(a, axis=0):
     -------
     info_per_bit : array
     """
+    assert a.dtype.kind == "u"
+
     sa = tuple(slice(0, -1) if i == axis else slice(None) for i in range(len(a.shape)))
     sb = tuple(
         slice(1, None) if i == axis else slice(None) for i in range(len(a.shape))

numcodecs/bitround.py

@@ -73,7 +73,23 @@ def decode(self, buf, out=None):
         return ndarray_copy(data, out)
 
     @staticmethod
-    def bitround(buf, keepbits, dtype):
+    def bitround(buf, keepbits: int, dtype):
+        """Drop bits from the mantissa of a floating point array
+
+        Parameters
+        ----------
+        buf: ndarray
+            The input array
+        keepbits: int
+            The number of bits to keep
+        dtype: dtype
+            The dtype of the input array
+
+        Returns
+        -------
+        ndarray
+            The bitrounded array transformed to an integer type
+        """
         bits = max_bits[str(dtype)]
         a_int_dtype = np.dtype(buf.dtype.str.replace("f", "i"))
         all_set = np.array(-1, dtype=a_int_dtype)

numcodecs/tests/test_bitinfo.py

@@ -0,0 +1,73 @@
+import numpy as np
+
+import pytest
+
+from numcodecs.bitinfo import BitInfo, exponent_bias, mutual_information
+
+def test_bitinfo_initialization():
+    bitinfo = BitInfo(0.5)
+    assert bitinfo.info_level == 0.5
+    assert bitinfo.axes is None
+
+    bitinfo = BitInfo(0.5, axes=1)
+    assert bitinfo.axes == [1]
+
+    bitinfo = BitInfo(0.5, axes=[1, 2])
+    assert bitinfo.axes == [1, 2]
+
+    with pytest.raises(ValueError):
+        BitInfo(-0.1)
+
+    with pytest.raises(ValueError):
+        BitInfo(1.1)
+
+    with pytest.raises(ValueError):
+        BitInfo(0.5, axes=1.5)
+
+    with pytest.raises(ValueError):
+        BitInfo(0.5, axes=[1, 1.5])
+
+
+def test_bitinfo_encode():
+    bitinfo = BitInfo(info_level=0.5)
+    a = np.array([1.0, 2.0, 3.0], dtype="float32")
+    encoded = bitinfo.encode(a)
+    decoded = bitinfo.decode(encoded)
+    assert decoded.dtype == a.dtype
+
+
+def test_bitinfo_encode_errors():
+    bitinfo = BitInfo(0.5)
+    a = np.array([1, 2, 3], dtype="int32")
+    with pytest.raises(TypeError):
+        bitinfo.encode(a)
+
+    a = np.array([1.0, 2.0, 3.0], dtype="float128")
+    with pytest.raises(TypeError):
+        bitinfo.encode(a)
+
+
+def test_exponent_bias():
+    assert exponent_bias("f2") == 15
+    assert exponent_bias("f4") == 127
+    assert exponent_bias("f8") == 1023
+
+    with pytest.raises(ValueError):
+        exponent_bias("int32")
+
+
+def test_mutual_information():
+    """ Test mutual information calculation
+
+    Tests for changes to the mutual_information
+    but not the correcteness of the original.
+    """
+    a = np.arange(10.0, dtype='float32')
+    b = a + 1000
+    c = a[::-1].copy()
+    dt = np.dtype('uint32')
+    a,b,c = map(lambda x: x.view(dt), [a,b,c])
+
+    assert mutual_information(a, a).sum() == 7.020411549771797
+    assert mutual_information(a, b).sum() == 0.0
+    assert mutual_information(a, c).sum() == 0.6545015579460758