From db65e15345734aa81f83de7acffcfae2ae57029f Mon Sep 17 00:00:00 2001
From: Thiago Franco de Moraes <totonixsame@gmail.com>
Date: Tue, 24 Feb 2015 13:49:16 -0300
Subject: [PATCH] Added a cython version to threshold

---
 invesalius/data/slice_.py     | 16 ++++++++++------
 invesalius/data/threshold.pyx | 32 ++++++++++++++++++++++++++++++++
 setup.py                      |  7 ++++++-
 3 files changed, 48 insertions(+), 7 deletions(-)
 create mode 100644 invesalius/data/threshold.pyx

diff --git a/invesalius/data/slice_.py b/invesalius/data/slice_.py
index 7fb0a24..49ee223 100644
--- a/invesalius/data/slice_.py
+++ b/invesalius/data/slice_.py
@@ -35,6 +35,8 @@ from mask import Mask
 from project import Project
 from data import mips
 
+from data import threshold
+
 OTHER=0
 PLIST=1
 WIDGET=2
@@ -1206,12 +1208,14 @@ class Slice(object):
         given slice_matrix.
         """
         thresh_min, thresh_max = self.current_mask.threshold_range
-        m = (((slice_matrix >= thresh_min) & (slice_matrix <= thresh_max)) * 255)
-        m[mask == 1] = 1
-        m[mask == 2] = 2
-        m[mask == 253] = 253
-        m[mask == 254] = 254
-        return m.astype('uint8')
+        #m = (((slice_matrix >= thresh_min) & (slice_matrix <= thresh_max)) * 255)
+        #m[mask == 1] = 1
+        #m[mask == 2] = 2
+        #m[mask == 253] = 253
+        #m[mask == 254] = 254
+        m = numpy.zeros_like(mask, dtype='uint8')
+        threshold.threshold(slice_matrix, m, thresh_min, thresh_max)
+        return m
 
     def do_threshold_to_all_slices(self):
         mask = self.current_mask
diff --git a/invesalius/data/threshold.pyx b/invesalius/data/threshold.pyx
new file mode 100644
index 0000000..e375f7b
--- /dev/null
+++ b/invesalius/data/threshold.pyx
@@ -0,0 +1,32 @@
+import numpy as np
+cimport numpy as np
+cimport cython
+
+from libc.math cimport floor, ceil, sqrt, fabs
+from cython.parallel import prange
+
+DTYPE8 = np.uint8
+ctypedef np.uint8_t DTYPE8_t
+
+DTYPE16 = np.int16
+ctypedef np.int16_t DTYPE16_t
+
+DTYPEF32 = np.float32
+ctypedef np.float32_t DTYPEF32_t
+
+@cython.boundscheck(False) # turn of bounds-checking for entire function
+@cython.cdivision(True)
+@cython.wraparound(False)
+def threshold(DTYPE16_t[:, :] image, DTYPE8_t[:, :] mask, DTYPE16_t low, DTYPE16_t high):
+    cdef int sy = image.shape[0]
+    cdef int sx = image.shape[1]
+    cdef int x, y
+    cdef DTYPE16_t v
+    for y in prange(sy, nogil=True):
+        for x in xrange(sx):
+            v = mask[y, x]
+            if not v:
+                if v >= low and v <= high:
+                    mask[y, x] = 255
+                else:
+                    mask[y, x] = 0
diff --git a/setup.py b/setup.py
index 794452e..f601e2d 100644
--- a/setup.py
+++ b/setup.py
@@ -12,7 +12,12 @@ if sys.platform == 'linux2':
         ext_modules = [ Extension("invesalius.data.mips", ["invesalius/data/mips.pyx"],
                                   include_dirs =  [numpy.get_include()],
                                   extra_compile_args=['-fopenmp'],
-                                  extra_link_args=['-fopenmp'],)]
+                                  extra_link_args=['-fopenmp'],),
+                       Extension("invesalius.data.threshold", ["invesalius/data/threshold.pyx"],
+                                  include_dirs =  [numpy.get_include()],
+                                  extra_compile_args=['-fopenmp'],
+                                  extra_link_args=['-fopenmp'],),
+                      ]
          )
 
 elif sys.platform == 'win32':
--
libgit2 0.21.2