From e6ee2c0db607c09454f630d6f10372b4e12e81db Mon Sep 17 00:00:00 2001
From: "Thouis (Ray) Jones" <thouis@seas.harvard.edu>
Date: Tue, 5 Mar 2013 10:37:56 -0500
Subject: [PATCH] BUG: not all histogram memory was aligned correctly

---
 skimage/filter/_ctmf.pyx | 24 +++++++++++-------------
 skimage/filter/setup.py  |  3 ++-
 2 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/skimage/filter/_ctmf.pyx b/skimage/filter/_ctmf.pyx
index 1a03ff5a..7cb5251f 100644
--- a/skimage/filter/_ctmf.pyx
+++ b/skimage/filter/_ctmf.pyx
@@ -20,7 +20,7 @@ from libc.stdlib cimport malloc, free
 from libc.string cimport memset
 
 
-cdef extern from "../_shared/vectorized_ops.h":
+cdef extern from "vectorized_ops.h":
     void add16(cnp.uint16_t *dest, cnp.uint16_t *src)
     void sub16(cnp.uint16_t *dest, cnp.uint16_t *src)
 
@@ -91,8 +91,9 @@ cdef struct SCoord:
     Py_ssize_t y
 
 cdef struct Histograms:
-    void *memory                # pointer to the allocated memory
-    Histogram *histogram        # pointer to the histogram memory
+    HistogramPiece accumulator  # running histogram (32-byte aligned)
+    void *memory                # pointer to the unaligned allocated memory
+    Histogram *histogram        # pointer to the histogram memory (aligned)
     PixelCount *pixel_count     # pointer to the pixel count memory
     cnp.uint8_t *data           # pointer to the image data
     cnp.uint8_t *mask           # pointer to the image mask
@@ -142,9 +143,6 @@ cdef struct Histograms:
 
     Py_ssize_t row_stride          # stride between one row and the next
     Py_ssize_t col_stride          # stride between one column and the next
-    # The accumulator holds the running histogram
-    #
-    HistogramPiece accumulator
     #
     # The running count of pixels in the accumulator
     #
@@ -188,10 +186,12 @@ cdef Histograms *allocate_histograms(Py_ssize_t rows,
 
     memory_size = (adjusted_stripe_length *
                    (sizeof(Histogram) + sizeof(PixelCount)) +
-                   sizeof(Histograms) + 32)
+                   sizeof(Histograms) + 64)
     ptr = malloc(memory_size)
     memset(ptr, 0, memory_size)
-    ph = <Histograms *> ptr
+    # align ph.accumulator to 32-byte boundary
+    roundoff = (<Py_ssize_t> ptr + 31) % 32
+    ph = <Histograms *> (ptr + 31 - roundoff)
     if not ptr:
         return ph
     ph.memory = ptr
@@ -201,10 +201,8 @@ cdef Histograms *allocate_histograms(Py_ssize_t rows,
     #
     # Align histogram memory to a 32-byte boundary
     #
-    roundoff = <Py_ssize_t>ptr
-    roundoff += 31
-    roundoff -= roundoff % 32
-    ptr = <void *> roundoff
+    roundoff = (<Py_ssize_t> ptr + 31) % 32
+    ptr += 31 - roundoff
     ph.histogram = <Histogram *> ptr
     #
     # Fill in the statistical things we keep around
@@ -696,7 +694,7 @@ cdef int c_median_filter(Py_ssize_t rows,
         #
         # Initialize the accumulator (octagon histogram) to zero
         #
-        memset(&ph.accumulator, 0, sizeof(ph.accumulator))
+        memset(&(ph.accumulator), 0, sizeof(ph.accumulator))
         ph.accumulator_count = 0
         for i in range(16):
             ph.last_update_column[i] = -radius-1
diff --git a/skimage/filter/setup.py b/skimage/filter/setup.py
index 934d3f2e..dba8172c 100644
--- a/skimage/filter/setup.py
+++ b/skimage/filter/setup.py
@@ -26,7 +26,8 @@ def configuration(parent_package='', top_path=None):
     cython(['rank/bilateral_rank.pyx'], working_path=base_path)
 
     config.add_extension('_ctmf', sources=['_ctmf.c'],
-        include_dirs=[get_numpy_include_dirs()])
+                         depends=['../_shared/vectorized_ops.h'],
+                         include_dirs=[get_numpy_include_dirs(), '../_shared'])
     config.add_extension('_denoise_cy', sources=['_denoise_cy.c'],
         include_dirs=[get_numpy_include_dirs(), '../_shared'])
     config.add_extension('rank._core8', sources=['rank/_core8.c'],