BUG: lib: Fix histogram problem with signed integer arrays.

WarrenWeckesser · charris · commit 159507a9d212 · 2019-11-07T20:22:10.000-07:00
An input such as np.histogram(np.array([-2, 0, 127], dtype=np.int8), bins="auto") would raise the exception ValueError: Number of samples, -1, must be non-negative. The problem was that the peak-to-peak value for the input array was computed with the `ptp` method, which returned negative values for signed integer arrays when the actual value was more than the maximum signed value of the array's data type. The fix is to use a peak-to-peak function that returns an unsigned value for signed integer arrays. Closes numpygh-14379.
diff --git a/numpy/lib/histograms.py b/numpy/lib/histograms.py
@@ -22,6 +22,16 @@
 _range = range
 
 
+def _ptp(x):
+    """Peak-to-peak value of x.
+
+    This implementation avoids the problem of signed integer arrays having a
+    peak-to-peak value that cannot be represented with the array's data type.
+    This function returns an unsigned value for signed integer arrays.
+    """
+    return _unsigned_subtract(x.max(), x.min())
+
+
 def _hist_bin_sqrt(x, range):
     """
     Square root histogram bin estimator.
@@ -40,7 +50,7 @@ def _hist_bin_sqrt(x, range):
     h : An estimate of the optimal bin width for the given data.
     """
     del range  # unused
-    return x.ptp() / np.sqrt(x.size)
+    return _ptp(x) / np.sqrt(x.size)
 
 
 def _hist_bin_sturges(x, range):
@@ -63,7 +73,7 @@ def _hist_bin_sturges(x, range):
     h : An estimate of the optimal bin width for the given data.
     """
     del range  # unused
-    return x.ptp() / (np.log2(x.size) + 1.0)
+    return _ptp(x) / (np.log2(x.size) + 1.0)
 
 
 def _hist_bin_rice(x, range):
@@ -87,7 +97,7 @@ def _hist_bin_rice(x, range):
     h : An estimate of the optimal bin width for the given data.
     """
     del range  # unused
-    return x.ptp() / (2.0 * x.size ** (1.0 / 3))
+    return _ptp(x) / (2.0 * x.size ** (1.0 / 3))
 
 
 def _hist_bin_scott(x, range):
@@ -137,7 +147,7 @@ def _hist_bin_stone(x, range):
     """
 
     n = x.size
-    ptp_x = np.ptp(x)
+    ptp_x = _ptp(x)
     if n <= 1 or ptp_x == 0:
         return 0
 
@@ -184,7 +194,7 @@ def _hist_bin_doane(x, range):
             np.true_divide(temp, sigma, temp)
             np.power(temp, 3, temp)
             g1 = np.mean(temp)
-            return x.ptp() / (1.0 + np.log2(x.size) +
+            return _ptp(x) / (1.0 + np.log2(x.size) +
                                     np.log2(1.0 + np.absolute(g1) / sg1))
     return 0.0
 
diff --git a/numpy/lib/tests/test_histograms.py b/numpy/lib/tests/test_histograms.py
@@ -8,6 +8,7 @@
     assert_array_almost_equal, assert_raises, assert_allclose,
     assert_array_max_ulp, assert_raises_regex, suppress_warnings,
     )
+import pytest
 
 
 class TestHistogram(object):
@@ -591,6 +592,16 @@ def test_simple_range(self):
                 msg += " with datasize of {0}".format(testlen)
                 assert_equal(len(a), numbins, err_msg=msg)
 
+    @pytest.mark.parametrize("bins", ['auto', 'fd', 'doane', 'scott',
+                                      'stone', 'rice', 'sturges'])
+    def test_signed_integer_data(self, bins):
+        # Regression test for gh-14379.
+        a = np.array([-2, 0, 127], dtype=np.int8)
+        hist, edges = np.histogram(a, bins=bins)
+        hist32, edges32 = np.histogram(a.astype(np.int32), bins=bins)
+        assert_array_equal(hist, hist32)
+        assert_array_equal(edges, edges32)
+
     def test_simple_weighted(self):
         """
         Check that weighted data raises a TypeError
