brainiak · mihaic · Oct 3, 2016 · Sep 23, 2016 · Sep 23, 2016 · Sep 23, 2016
diff --git a/.gitignore b/.gitignore
@@ -23,3 +23,4 @@ junit-*.xml
 __pycache__
 
 brainiak/fcma/cython_blas.c
+brainiak/eventseg/_utils.c
diff --git a/brainiak/eventseg/_utils.pyx b/brainiak/eventseg/_utils.pyx
@@ -0,0 +1,31 @@
+#  Copyright 2016 Intel Corporation
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+
+from libc.math cimport log
+import numpy as np
+cimport numpy as np
+
+def masked_log(x):
+    """x is a 1D numpy array"""
+    """returns -Inf for x <=0 and log(x) otherwise"""
+    y = np.empty(x.shape, dtype=x.dtype)
+    lim = x.shape[0]
+    for i in range(lim):
+      if x[i] <= 0:
+        y[i] = float('-inf')
+      else:
+        y[i] = log(x[i])
+    return y
+
diff --git a/brainiak/eventseg/event.py b/brainiak/eventseg/event.py
@@ -27,6 +27,7 @@
 import copy
 from sklearn.base import BaseEstimator
 from sklearn.utils.validation import check_is_fitted, check_array
+import brainiak.eventseg.utils as utils
 
 logger = logging.getLogger(__name__)
 
@@ -299,8 +300,11 @@ def _log(self, x):
         log_ma: ndarray of floats
             log of x, with x<=0 values replaced with -inf
         """
-        log_ma = np.ma.log(x).filled(float("-inf"))
-        return log_ma
+
+        xshape = x.shape
+        _x = x.flatten()
+        y = utils.masked_log(_x)
+        return y.reshape(xshape)
 
     def find_events(self, testing_data, var=None, scramble=False):
         """Applies learned event segmentation to new testing dataset

diff --git a/brainiak/hyperparamopt/__init__.py b/brainiak/hyperparamopt/__init__.py
@@ -1,4 +1 @@
 """ Hyper parameter optimization package """
-
-import pyximport
-pyximport.install()
diff --git a/setup.py b/setup.py
@@ -19,56 +19,23 @@
     long_description = f.read()
 
 
-class get_pybind_include(object):
-    """Helper class to determine the pybind11 include path
-
-    The purpose of this class is to postpone importing pybind11
-    until it is actually installed, so that the ``get_include()``
-    method can be invoked. """
-
-    def __init__(self, user=False):
-        self.user = user
-
-    # Required by Cython
-    def __add__(self, x):
-        import pybind11
-        return pybind11.get_include(self.user) + x
-
-    def __str__(self):
-        import pybind11
-        return pybind11.get_include(self.user)
-
-    def endswith(self, x):
-        import pybind11
-        return pybind11.get_include(self.user).endswith(x)
-
-    def startswith(self, x):
-        import pybind11
-        return pybind11.get_include(self.user).startswith(x)
-
 ext_modules = [
     Extension(
         'brainiak.factoranalysis.tfa_extension',
         ['brainiak/factoranalysis/tfa_extension.cpp'],
-        include_dirs=[
-            # Path to pybind11 headers
-            get_pybind_include(),
-            get_pybind_include(user=True)
-        ],
     ),
     Extension(
         'brainiak.fcma.fcma_extension',
         ['brainiak/fcma/src/fcma_extension.cc'],
-        include_dirs=[
-            # Path to pybind11 headers
-            get_pybind_include(),
-            get_pybind_include(user=True)
-        ],
     ),
     Extension(
         'brainiak.fcma.cython_blas',
         ['brainiak/fcma/cython_blas.pyx'],
     ),
+    Extension(
+        'brainiak.eventseg.utils',
+        ['brainiak/eventseg/_utils.pyx'],
+    ),
 ]
 
 
@@ -133,10 +100,24 @@ def build_extensions(self):
                 ext.extra_link_args.append(cpp_flag(self.compiler))
         build_ext.build_extensions(self)
 
+    def finalize_options(self):
+        super().finalize_options()
+        import numpy
+        import pybind11
+        self.include_dirs.extend([
+            numpy.get_include(),
+            pybind11.get_include(user=True),
+            pybind11.get_include(),
+        ])
+
+
 setup(
     name='brainiak',
     use_scm_version=True,
     setup_requires=[
+        'cython',
+        'numpy',
+        'pybind11>=1.7',
         'setuptools_scm',
     ],
     install_requires=[
Original file line number	Diff line number	Diff line change
Expand Up		@@ -23,3 +23,4 @@ junit-*.xml
		__pycache__

		brainiak/fcma/cython_blas.c
		brainiak/eventseg/_utils.c