BUG Wrong output for very large input arrays.

Closes #35.
pydata · Mar 17, 2012 · 7147ad8 · 7147ad8
1 parent 6de1216
commit 7147ad8
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Showing 16 changed files with 27 additions and 26 deletions.
diff --git a/RELEASE.rst b/RELEASE.rst
@@ -23,6 +23,7 @@ Bottleneck 0.6.0
 
 - #31 Confusing error message in partsort and argpartsort
 - #32 Update path in MANIFEST.in
+- #35 Wrong output for very large (2**31) input arrays
 
 Older versions
 ==============

diff --git a/bottleneck/src/template/func/nanmean.py b/bottleneck/src/template/func/nanmean.py
@@ -21,7 +21,7 @@
 @cython.wraparound(False)
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a):
     "Mean of NDIMd array with dtype=DTYPE along axis=AXIS ignoring NaNs."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef np.DTYPE_t asum = 0, ai
 """
 
@@ -141,7 +141,7 @@ def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a):
 # Int dtypes (axis=None) ----------------------------------------------------
 
 ints_None = deepcopy(ints) 
-ints_None['top'] = ints['top'] + "    cdef int size\n"
+ints_None['top'] = ints['top'] + "    cdef Py_ssize_t size\n"
 ints_None['axisNone'] = True
 
 loop = {}

diff --git a/bottleneck/src/template/func/nanstd.py b/bottleneck/src/template/func/nanstd.py
@@ -21,7 +21,7 @@
 @cython.wraparound(False)
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int ddof):
     "Variance of NDIMd array with dtype=DTYPE along axis=AXIS ignoring NaNs."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef np.DTYPE_t asum = 0, amean, ai
 """
 
@@ -193,7 +193,7 @@ def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int ddof):
 # Int dtypes (axis=None) ----------------------------------------------------
 
 ints_None = deepcopy(ints) 
-ints_None['top'] = ints['top'] + "    cdef int size\n"
+ints_None['top'] = ints['top'] + "    cdef Py_ssize_t size\n"
 ints_None['axisNone'] = True
 
 loop = {}

diff --git a/bottleneck/src/template/func/nansum.py b/bottleneck/src/template/func/nansum.py
@@ -135,7 +135,7 @@ def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a):
 # Int dtypes (axis=None) ----------------------------------------------------
 
 ints_None = deepcopy(ints) 
-ints_None['top'] = ints['top'] + "    cdef int size\n"
+ints_None['top'] = ints['top'] + "    cdef Py_ssize_t size\n"
 ints_None['axisNone'] = True
 
 loop = {}

diff --git a/bottleneck/src/template/func/nanvar.py b/bottleneck/src/template/func/nanvar.py
@@ -21,7 +21,7 @@
 @cython.wraparound(False)
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int ddof):
     "Variance of NDIMd array with dtype=DTYPE along axis=AXIS ignoring NaNs."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef np.DTYPE_t asum = 0, amean, ai
 """
 
@@ -193,7 +193,7 @@ def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int ddof):
 # Int dtypes (axis=None) ----------------------------------------------------
 
 ints_None = deepcopy(ints) 
-ints_None['top'] = ints['top'] + "    cdef int size\n"
+ints_None['top'] = ints['top'] + "    cdef Py_ssize_t size\n"
 ints_None['axisNone'] = True
 
 loop = {}

diff --git a/bottleneck/src/template/move/move_max.py b/bottleneck/src/template/move/move_max.py
@@ -197,7 +197,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int window):
     "Moving max of NDIMd array of dtype=DTYPE along axis=AXIS."
     cdef np.float64_t ai, aold
-    cdef int count
+    cdef Py_ssize_t count
     cdef pairs* ring
     cdef pairs* minpair
     cdef pairs* end

diff --git a/bottleneck/src/template/move/move_mean.py b/bottleneck/src/template/move/move_mean.py
@@ -23,7 +23,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a,
                                   int window):
     "Moving mean of NDIMd array of dtype=DTYPE along axis=AXIS."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef double asum = 0, ai, aold
 """
 

diff --git a/bottleneck/src/template/move/move_min.py b/bottleneck/src/template/move/move_min.py
@@ -197,7 +197,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int window):
     "Moving min of NDIMd array of dtype=DTYPE along axis=AXIS."
     cdef np.float64_t ai, aold
-    cdef int count
+    cdef Py_ssize_t count
     cdef pairs* ring
     cdef pairs* minpair
     cdef pairs* end

diff --git a/bottleneck/src/template/move/move_nanmax.py b/bottleneck/src/template/move/move_nanmax.py
@@ -197,7 +197,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int window):
     "Moving max of NDIMd array of dtype=DTYPE along axis=AXIS ignoring NaNs."
     cdef np.float64_t ai, aold
-    cdef int count
+    cdef Py_ssize_t count
     cdef pairs* ring
     cdef pairs* minpair
     cdef pairs* end

diff --git a/bottleneck/src/template/move/move_nanmean.py b/bottleneck/src/template/move/move_nanmean.py
@@ -23,7 +23,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a,
                                   int window):
     "Moving mean of NDIMd array of dtype=DTYPE along axis=AXIS ignoring NaNs."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef double asum = 0, aold, ai
 """
 

diff --git a/bottleneck/src/template/move/move_nanmin.py b/bottleneck/src/template/move/move_nanmin.py
@@ -197,7 +197,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a, int window):
     "Moving min of NDIMd array of dtype=DTYPE along axis=AXIS ignoring NaNs."
     cdef np.float64_t ai, aold
-    cdef int count
+    cdef Py_ssize_t count
     cdef pairs* ring
     cdef pairs* minpair
     cdef pairs* end

diff --git a/bottleneck/src/template/move/move_nanstd.py b/bottleneck/src/template/move/move_nanstd.py
@@ -23,7 +23,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a,
                                   int window, int ddof):
     "Moving std of NDIMd array of dtype=DTYPE along axis=AXIS, ignoring NaNs."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef double asum = 0, a2sum = 0, ai
 """
 

diff --git a/bottleneck/src/template/move/move_nansum.py b/bottleneck/src/template/move/move_nansum.py
@@ -23,7 +23,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a,
                                   int window):
     "Moving sum of NDIMd array of dtype=DTYPE along axis=AXIS, ignoring NaNs."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef double asum = 0, ai, aold
 """
 

diff --git a/bottleneck/src/template/move/move_std.py b/bottleneck/src/template/move/move_std.py
@@ -23,7 +23,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a,
                                   int window, int ddof):
     "Moving std of NDIMd array of dtype=DTYPE along axis=AXIS."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef double asum = 0, a2sum = 0, ai
 """
 

diff --git a/bottleneck/src/template/move/move_sum.py b/bottleneck/src/template/move/move_sum.py
@@ -23,7 +23,7 @@
 def NAME_NDIMd_DTYPE_axisAXIS(np.ndarray[np.DTYPE_t, ndim=NDIM] a,
                                   int window):
     "Moving sum of NDIMd array of dtype=DTYPE along axis=AXIS."
-    cdef int count = 0
+    cdef Py_ssize_t count = 0
     cdef double asum = 0, ai, aold
 """
 

diff --git a/bottleneck/src/template/template.py b/bottleneck/src/template/template.py
@@ -234,8 +234,8 @@ def loop_cdef(ndim, dtype, axis, is_reducing_function, cdef_output=True):
 
     The output string contains code for: index array counters, one for each
     dimension (cdef Py_size_t i0, i1, i2, ....); the length along each
-    dimension of the input array, `a` (cdef int n0 = a.shape[0],...); the
-    initialized, empty output array, `y`.
+    dimension of the input array, `a` (cdef Py_ssize_t n0 = a.shape[0],...);
+    the initialized, empty output array, `y`.
 
     Parameters
     ----------
@@ -275,9 +275,9 @@ def loop_cdef(ndim, dtype, axis, is_reducing_function, cdef_output=True):
         cdef Py_ssize_t i0, i1, i2
         cdef np.npy_intp *dim
         dim = PyArray_DIMS(a)
-        cdef int n0 = dim[0]
-        cdef int n1 = dim[1]
-        cdef int n2 = dim[2]
+        Py_ssize_t n0 = dim[0]
+        Py_ssize_t n1 = dim[1]
+        Py_ssize_t n2 = dim[2]
         cdef np.npy_intp *dims = [n0, n2]
         cdef np.ndarray[np.float64_t, ndim=2] y = PyArray_EMPTY(2, dims,
                                                   NPY_float64, 0)
@@ -289,9 +289,9 @@ def loop_cdef(ndim, dtype, axis, is_reducing_function, cdef_output=True):
         cdef Py_ssize_t i0, i1, i2
         cdef np.npy_intp *dim
         dim = PyArray_DIMS(a)
-        cdef int n0 = dim[0]
-        cdef int n1 = dim[1]
-        cdef int n2 = dim[2]
+        Py_ssize_t n0 = dim[0]
+        Py_ssize_t n1 = dim[1]
+        Py_ssize_t n2 = dim[2]
         cdef np.npy_intp *dims = [n0, n1, n2]
         cdef np.ndarray[np.float64_t, ndim=3] y = PyArray_EMPTY(3, dims,
                                                   NPY_float64, 0)
@@ -316,7 +316,7 @@ def loop_cdef(ndim, dtype, axis, is_reducing_function, cdef_output=True):
     cdefs.append(tab + "cdef np.npy_intp *dim")
     cdefs.append(tab + "dim = PyArray_DIMS(a)")
     for dim in range(ndim):
-        cdefs.append(tab + "cdef int n%d = dim[%d]" % (dim, dim))
+        cdefs.append(tab + "cdef Py_ssize_t n%d = dim[%d]" % (dim, dim))
 
     if not cdef_output:
         return '\n'.join(cdefs) + '\n'