From 6f771cda95fee80991f648a69a934d38ee265872 Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Thu, 27 Apr 2017 09:29:03 -0700
Subject: [PATCH 01/14] added shapes and changed border treatment

---
 brainiak/searchlight/searchlight.py         | 27 +++++++++++++++++++--
 examples/searchlight/example_searchlight.py |  3 ++-
 2 files changed, 27 insertions(+), 3 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index e5f7fdf9d..e58c1ac43 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -15,6 +15,7 @@
 import numpy as np
 from mpi4py import MPI
 import sys
+from scipy.spatial.distance import cityblock
 
 """Distributed Searchlight
 """
@@ -23,6 +24,21 @@
         "Searchlight",
 ]
 
+class Cube:
+    def __init__(self, rad):
+        self.rad = rad
+        self.data = np.ones((2*rad+1,2*rad+1,2*rad+1), dtype=np.bool)
+
+class Diamond:
+    def __init__(self, rad):
+        self.rad = rad
+        self.data = np.zeros((2*rad+1,2*rad+1,2*rad+1), dtype=np.bool)
+        for r1 in range(2*self.rad+1):
+            for r2 in range(2*self.rad+1):
+                for r3 in range(2*self.rad+1):
+                   if(cityblock( (r1,r2,r3) , (self.rad, self.rad, self.rad) ) <= self.rad):
+                       self.data[r1,r2,r3] = True
+        print(self.data)
 
 class Searchlight:
     """Distributed Searchlight
@@ -33,7 +49,7 @@ class Searchlight:
     Optionally, users can define a block function which runs over
     larger portions of the volume called blocks.
     """
-    def __init__(self, sl_rad=1, max_blk_edge=10):
+    def __init__(self, sl_rad=1, max_blk_edge=10, shape=Cube):
         """Constructor
 
         Parameters
@@ -48,6 +64,7 @@ def __init__(self, sl_rad=1, max_blk_edge=10):
         self.sl_rad = sl_rad
         self.max_blk_edge = max_blk_edge
         self.comm = MPI.COMM_WORLD
+        self.shape = shape(sl_rad).data
 
     def _get_ownership(self, data):
         """Determine on which rank each subject currently resides
@@ -345,6 +362,10 @@ def _singlenode_searchlight(l, msk, mysl_rad, bcast_var):
                                                           mysl_rad:-mysl_rad,
                                                           mysl_rad:-mysl_rad]
 
+            def check_mask(mask_cube):
+                res = mask_cube[self.shape]
+                return np.any(res) and np.all(res)
+
             import pathos.multiprocessing
             inlist = [([ll[i:i+2*mysl_rad+1,
                            j:j+2*mysl_rad+1,
@@ -356,7 +377,9 @@ def _singlenode_searchlight(l, msk, mysl_rad, bcast_var):
                            k:k+2*mysl_rad+1],
                        mysl_rad,
                        bcast_var)
-                      if msk[i+mysl_rad, j+mysl_rad, k+mysl_rad] else None
+                      if check_mask(msk[i:i+2*mysl_rad+1,
+                                        j:j+2*mysl_rad+1,
+                                        k:k+2*mysl_rad+1]) else None
                       for i in range(0, outmat.shape[0])
                       for j in range(0, outmat.shape[1])
                       for k in range(0, outmat.shape[2])]
diff --git a/examples/searchlight/example_searchlight.py b/examples/searchlight/example_searchlight.py
index 2da316b4f..ca29435f5 100644
--- a/examples/searchlight/example_searchlight.py
+++ b/examples/searchlight/example_searchlight.py
@@ -17,6 +17,7 @@
 import sys
 
 from brainiak.searchlight.searchlight import Searchlight
+from brainiak.searchlight.searchlight import Diamond
 
 """Distributed Searchlight Example
 example usage: mpirun -n 4 python3 example_searchlight.py
@@ -66,7 +67,7 @@
       data[pt[0]:pt[0]+kernel_dim,pt[1]:pt[1]+kernel_dim,pt[2]:pt[2]+kernel_dim,idx] -= kernel * weight
 
 # Create searchlight object
-sl = Searchlight(sl_rad=1, max_blk_edge=5)
+sl = Searchlight(sl_rad=1, max_blk_edge=5, shape=Diamond)
 
 # Distribute data to processes
 sl.distribute([data], mask)

From 1350f1161a7af37b7b4659348ebf091f7861cfba Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Thu, 27 Apr 2017 10:23:00 -0700
Subject: [PATCH 02/14] fixed for pr-check

---
 brainiak/searchlight/searchlight.py   | 39 +++++++++++++++++++++++----
 tests/searchlight/test_searchlight.py |  3 ++-
 2 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index e58c1ac43..a5feba853 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -24,21 +24,50 @@
         "Searchlight",
 ]
 
+
 class Cube:
+    """Cube
+
+    Searchlight shape which is a (2*rad+1)^3 cube
+    """
     def __init__(self, rad):
+        """Constructor
+
+        Parameters
+        ----------
+
+        rad: radius, in voxels, of the sphere inscribed in the
+             searchlight cube, not counting the center voxel
+
+        """
         self.rad = rad
-        self.data = np.ones((2*rad+1,2*rad+1,2*rad+1), dtype=np.bool)
+        self.data = np.ones((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
+
 
 class Diamond:
+    """Diamond
+
+    Searchlight shape which is a (2*rad+1)^3 diamond
+    """
     def __init__(self, rad):
+        """Constructor
+
+        Parameters
+        ----------
+
+        rad: radius, in voxels, of the sphere inscribed in the
+             searchlight cube, not counting the center voxel
+
+        """
         self.rad = rad
-        self.data = np.zeros((2*rad+1,2*rad+1,2*rad+1), dtype=np.bool)
+        self.data = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
         for r1 in range(2*self.rad+1):
             for r2 in range(2*self.rad+1):
                 for r3 in range(2*self.rad+1):
-                   if(cityblock( (r1,r2,r3) , (self.rad, self.rad, self.rad) ) <= self.rad):
-                       self.data[r1,r2,r3] = True
-        print(self.data)
+                    if(cityblock((r1, r2, r3),
+                                 (self.rad, self.rad, self.rad)) <= self.rad):
+                        self.data[r1, r2, r3] = True
+
 
 class Searchlight:
     """Distributed Searchlight
diff --git a/tests/searchlight/test_searchlight.py b/tests/searchlight/test_searchlight.py
index 85a6e26ae..250a1176b 100644
--- a/tests/searchlight/test_searchlight.py
+++ b/tests/searchlight/test_searchlight.py
@@ -78,7 +78,8 @@ def sfn(l,msk,myrad,bcast_var):
       for d0 in range(rad, global_outputs.shape[0]-rad):
         for d1 in range(rad, global_outputs.shape[1]-rad):
           for d2 in range(rad, global_outputs.shape[2]-rad):
-            if mask[d0, d1, d2]:
+            msk_blk = mask[d0:d0+2*rad+1, d1:d1+2*rad+1, d2:d2+2*rad+1]
+            if np.all(msk_blk) and np.any(msk_blk):
               assert np.array_equal(np.array(global_outputs[d0,d1,d2]), np.array([d0,d1,d2]))
   
   

From 160914926505c71434967cfe749d34b70ebdd1ac Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Fri, 28 Apr 2017 06:52:40 -0700
Subject: [PATCH 03/14] Added test for shapes

---
 brainiak/searchlight/searchlight.py   |  8 ++-
 tests/searchlight/test_searchlight.py |  1 -
 tests/searchlight/test_shapes.py      | 80 +++++++++++++++++++++++++++
 3 files changed, 86 insertions(+), 3 deletions(-)
 create mode 100644 tests/searchlight/test_shapes.py

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index a5feba853..26b1f2eac 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -78,7 +78,7 @@ class Searchlight:
     Optionally, users can define a block function which runs over
     larger portions of the volume called blocks.
     """
-    def __init__(self, sl_rad=1, max_blk_edge=10, shape=Cube):
+    def __init__(self, sl_rad=1, max_blk_edge=-1, shape=Cube):
         """Constructor
 
         Parameters
@@ -91,9 +91,13 @@ def __init__(self, sl_rad=1, max_blk_edge=10, shape=Cube):
 
         """
         self.sl_rad = sl_rad
-        self.max_blk_edge = max_blk_edge
+        if max_blk_edge == -1:
+            self.max_blk_edge = 3 * sl_rad
+        else:
+            self.max_blk_edge = max_blk_edge
         self.comm = MPI.COMM_WORLD
         self.shape = shape(sl_rad).data
+        self.bcast_var = None
 
     def _get_ownership(self, data):
         """Determine on which rank each subject currently resides
diff --git a/tests/searchlight/test_searchlight.py b/tests/searchlight/test_searchlight.py
index 250a1176b..6c4c8275c 100644
--- a/tests/searchlight/test_searchlight.py
+++ b/tests/searchlight/test_searchlight.py
@@ -136,4 +136,3 @@ def do_test(dim0, dim1, dim2, ntr, nsubj, max_blk_edge, rad):
   do_test(dim0=7, dim1=5, dim2=9, ntr=5, nsubj=1, max_blk_edge=4, rad=2)
   do_test(dim0=7, dim1=5, dim2=9, ntr=5, nsubj=1, max_blk_edge=4, rad=3)
 
-test_correctness()
diff --git a/tests/searchlight/test_shapes.py b/tests/searchlight/test_shapes.py
new file mode 100644
index 000000000..90833d742
--- /dev/null
+++ b/tests/searchlight/test_shapes.py
@@ -0,0 +1,80 @@
+#  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.
+
+import numpy as np
+from mpi4py import MPI
+import sys
+
+from brainiak.searchlight.searchlight import Searchlight
+from brainiak.searchlight.searchlight import Diamond
+
+def test_cube():
+    sl = Searchlight(sl_rad=3)
+    comm = MPI.COMM_WORLD
+    rank = comm.rank
+    size = comm.size
+    dim0, dim1, dim2 = (50,50,50)
+    ntr = 30
+    nsubj = 3
+    mask = np.zeros((dim0,dim1,dim2), dtype=np.bool)
+    data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
+
+    # Put a spot in the mask
+    mask[10:17,10:17,10:17] = True
+
+    def sfn(l, msk, myrad, bcast_var):
+        return 1.0
+
+    sl.distribute(data, mask)
+    global_outputs = sl.run_searchlight(sfn)
+
+    if rank == 0:
+        assert global_outputs[13,13,13] == 1.0
+        global_outputs[13,13,13] = None
+
+        for i in range(global_outputs.shape[0]):
+            for j in range(global_outputs.shape[1]):
+                for k in range(global_outputs.shape[2]):
+                    assert global_outputs[i,j,k] == None
+
+def test_diamond():
+    sl = Searchlight(sl_rad=3)
+    comm = MPI.COMM_WORLD
+    rank = comm.rank
+    size = comm.size
+    dim0, dim1, dim2 = (50,50,50)
+    ntr = 30
+    nsubj = 3
+    mask = np.zeros((dim0,dim1,dim2), dtype=np.bool)
+    data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
+
+    # Put a spot in the mask
+    mask[10:17,10:17,10:17] = Diamond(3)
+
+    def sfn(l, msk, myrad, bcast_var):
+        return 1.0
+
+    sl.distribute(data, mask)
+    global_outputs = sl.run_searchlight(sfn)
+
+    if rank == 0:
+        assert global_outputs[13,13,13] == 1.0
+        global_outputs[13,13,13] = None
+
+        for i in range(global_outputs.shape[0]):
+            for j in range(global_outputs.shape[1]):
+                for k in range(global_outputs.shape[2]):
+                    assert global_outputs[i,j,k] == None
+
+

From 8879b0eec7df03fb6339d338d533e2a01412146e Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Fri, 28 Apr 2017 07:38:22 -0700
Subject: [PATCH 04/14] pr changes

---
 brainiak/searchlight/searchlight.py   | 41 ++++++++++++++----
 tests/searchlight/test_searchlight.py | 62 +++++++++++++++++++++++++++
 2 files changed, 94 insertions(+), 9 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 26b1f2eac..3cf305a44 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -25,7 +25,25 @@
 ]
 
 
-class Cube:
+class Shape:
+    """Shape
+
+    Searchlight shape which is contained in a (2*rad+1)^3 cube
+    """
+    def __init__(self, rad):
+        """Constructor
+
+        Parameters
+        ----------
+
+        rad: radius, in voxels, of the sphere inscribed in the
+             searchlight cube, not counting the center voxel
+
+        """
+        self.rad = rad
+
+
+class Cube(Shape):
     """Cube
 
     Searchlight shape which is a (2*rad+1)^3 cube
@@ -40,14 +58,19 @@ def __init__(self, rad):
              searchlight cube, not counting the center voxel
 
         """
+        super(Cube, self).__init__(rad)
         self.rad = rad
         self.data = np.ones((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
 
 
-class Diamond:
+class Diamond(Shape):
     """Diamond
 
-    Searchlight shape which is a (2*rad+1)^3 diamond
+    Searchlight shape which is a (2*rad+1)^3 diamond. A diamond
+    is inscribed in the (2*rad+1)^3 cube. Any location in the cube
+    which has a Manhattan distance of less than rad from the center
+    point is set to True.
+
     """
     def __init__(self, rad):
         """Constructor
@@ -59,7 +82,7 @@ def __init__(self, rad):
              searchlight cube, not counting the center voxel
 
         """
-        self.rad = rad
+        super(Diamond, self).__init__(rad)
         self.data = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
         for r1 in range(2*self.rad+1):
             for r2 in range(2*self.rad+1):
@@ -78,7 +101,7 @@ class Searchlight:
     Optionally, users can define a block function which runs over
     larger portions of the volume called blocks.
     """
-    def __init__(self, sl_rad=1, max_blk_edge=-1, shape=Cube):
+    def __init__(self, sl_rad=1, max_blk_edge=10, shape=Cube):
         """Constructor
 
         Parameters
@@ -89,12 +112,12 @@ def __init__(self, sl_rad=1, max_blk_edge=-1, shape=Cube):
 
         max_blk_edge: max edge length, in voxels, of the 3D block
 
+        shape: brainiak.searchlight.searchlight.Shape indicating the
+        shape in voxels of the searchlight region
+
         """
         self.sl_rad = sl_rad
-        if max_blk_edge == -1:
-            self.max_blk_edge = 3 * sl_rad
-        else:
-            self.max_blk_edge = max_blk_edge
+        self.max_blk_edge = max_blk_edge
         self.comm = MPI.COMM_WORLD
         self.shape = shape(sl_rad).data
         self.bcast_var = None
diff --git a/tests/searchlight/test_searchlight.py b/tests/searchlight/test_searchlight.py
index 6c4c8275c..3a0b6fb64 100644
--- a/tests/searchlight/test_searchlight.py
+++ b/tests/searchlight/test_searchlight.py
@@ -17,10 +17,72 @@
 import sys
 
 from brainiak.searchlight.searchlight import Searchlight
+from brainiak.searchlight.searchlight import Diamond
 
 """Distributed Searchlight Test
 """
 
+
+def test_cube():
+    sl = Searchlight(sl_rad=3)
+    comm = MPI.COMM_WORLD
+    rank = comm.rank
+    size = comm.size
+    dim0, dim1, dim2 = (50,50,50)
+    ntr = 30
+    nsubj = 3
+    mask = np.zeros((dim0,dim1,dim2), dtype=np.bool)
+    data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
+
+    # Put a spot in the mask
+    mask[10:17,10:17,10:17] = True
+
+    def sfn(l, msk, myrad, bcast_var):
+        return 1.0
+
+    sl.distribute(data, mask)
+    global_outputs = sl.run_searchlight(sfn)
+
+    if rank == 0:
+        assert global_outputs[13,13,13] == 1.0
+        global_outputs[13,13,13] = None
+
+        for i in range(global_outputs.shape[0]):
+            for j in range(global_outputs.shape[1]):
+                for k in range(global_outputs.shape[2]):
+                    assert global_outputs[i,j,k] == None
+
+def test_diamond():
+    sl = Searchlight(sl_rad=3)
+    comm = MPI.COMM_WORLD
+    rank = comm.rank
+    size = comm.size
+    dim0, dim1, dim2 = (50,50,50)
+    ntr = 30
+    nsubj = 3
+    mask = np.zeros((dim0,dim1,dim2), dtype=np.bool)
+    data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
+
+    # Put a spot in the mask
+    mask[10:17,10:17,10:17] = Diamond(3)
+
+    def sfn(l, msk, myrad, bcast_var):
+        return 1.0
+
+    sl.distribute(data, mask)
+    global_outputs = sl.run_searchlight(sfn)
+
+    if rank == 0:
+        assert global_outputs[13,13,13] == 1.0
+        global_outputs[13,13,13] = None
+
+        for i in range(global_outputs.shape[0]):
+            for j in range(global_outputs.shape[1]):
+                for k in range(global_outputs.shape[2]):
+                    assert global_outputs[i,j,k] == None
+
+
+
 def test_instantiate():
   sl = Searchlight(sl_rad=5, max_blk_edge=10)
   assert sl

From f017d9275196483f33c3fee47b766de2ec72f570 Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Fri, 28 Apr 2017 07:39:18 -0700
Subject: [PATCH 05/14] Removed test shapes

---
 tests/searchlight/test_shapes.py | 80 --------------------------------
 1 file changed, 80 deletions(-)
 delete mode 100644 tests/searchlight/test_shapes.py

diff --git a/tests/searchlight/test_shapes.py b/tests/searchlight/test_shapes.py
deleted file mode 100644
index 90833d742..000000000
--- a/tests/searchlight/test_shapes.py
+++ /dev/null
@@ -1,80 +0,0 @@
-#  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.
-
-import numpy as np
-from mpi4py import MPI
-import sys
-
-from brainiak.searchlight.searchlight import Searchlight
-from brainiak.searchlight.searchlight import Diamond
-
-def test_cube():
-    sl = Searchlight(sl_rad=3)
-    comm = MPI.COMM_WORLD
-    rank = comm.rank
-    size = comm.size
-    dim0, dim1, dim2 = (50,50,50)
-    ntr = 30
-    nsubj = 3
-    mask = np.zeros((dim0,dim1,dim2), dtype=np.bool)
-    data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
-
-    # Put a spot in the mask
-    mask[10:17,10:17,10:17] = True
-
-    def sfn(l, msk, myrad, bcast_var):
-        return 1.0
-
-    sl.distribute(data, mask)
-    global_outputs = sl.run_searchlight(sfn)
-
-    if rank == 0:
-        assert global_outputs[13,13,13] == 1.0
-        global_outputs[13,13,13] = None
-
-        for i in range(global_outputs.shape[0]):
-            for j in range(global_outputs.shape[1]):
-                for k in range(global_outputs.shape[2]):
-                    assert global_outputs[i,j,k] == None
-
-def test_diamond():
-    sl = Searchlight(sl_rad=3)
-    comm = MPI.COMM_WORLD
-    rank = comm.rank
-    size = comm.size
-    dim0, dim1, dim2 = (50,50,50)
-    ntr = 30
-    nsubj = 3
-    mask = np.zeros((dim0,dim1,dim2), dtype=np.bool)
-    data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
-
-    # Put a spot in the mask
-    mask[10:17,10:17,10:17] = Diamond(3)
-
-    def sfn(l, msk, myrad, bcast_var):
-        return 1.0
-
-    sl.distribute(data, mask)
-    global_outputs = sl.run_searchlight(sfn)
-
-    if rank == 0:
-        assert global_outputs[13,13,13] == 1.0
-        global_outputs[13,13,13] = None
-
-        for i in range(global_outputs.shape[0]):
-            for j in range(global_outputs.shape[1]):
-                for k in range(global_outputs.shape[2]):
-                    assert global_outputs[i,j,k] == None
-
-

From 3c367ecbd7573eb75cc0745c7e29a58092259885 Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Sat, 29 Apr 2017 07:05:59 -0700
Subject: [PATCH 06/14] documenting data_ attribute

---
 brainiak/searchlight/searchlight.py | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 3cf305a44..19c0436bf 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -29,7 +29,14 @@ class Shape:
     """Shape
 
     Searchlight shape which is contained in a (2*rad+1)^3 cube
+
+    Attributes
+    ----------
+
+    data_ : a 3D boolean numpy array of size (2*rad+1)^3 which is set
+            to True within the boundaries of the desired shape
     """
+
     def __init__(self, rad):
         """Constructor
 
@@ -58,9 +65,9 @@ def __init__(self, rad):
              searchlight cube, not counting the center voxel
 
         """
-        super(Cube, self).__init__(rad)
+        super().__init__(rad)
         self.rad = rad
-        self.data = np.ones((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
+        self.data_ = np.ones((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
 
 
 class Diamond(Shape):
@@ -82,14 +89,14 @@ def __init__(self, rad):
              searchlight cube, not counting the center voxel
 
         """
-        super(Diamond, self).__init__(rad)
-        self.data = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
+        super().__init__(rad)
+        self.data_ = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
         for r1 in range(2*self.rad+1):
             for r2 in range(2*self.rad+1):
                 for r3 in range(2*self.rad+1):
                     if(cityblock((r1, r2, r3),
                                  (self.rad, self.rad, self.rad)) <= self.rad):
-                        self.data[r1, r2, r3] = True
+                        self.data_[r1, r2, r3] = True
 
 
 class Searchlight:
@@ -119,7 +126,7 @@ def __init__(self, sl_rad=1, max_blk_edge=10, shape=Cube):
         self.sl_rad = sl_rad
         self.max_blk_edge = max_blk_edge
         self.comm = MPI.COMM_WORLD
-        self.shape = shape(sl_rad).data
+        self.shape = shape(sl_rad).data_
         self.bcast_var = None
 
     def _get_ownership(self, data):

From 8bea46135b7b2d29a3448a715aef747be2e3e938 Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Mon, 1 May 2017 03:44:53 -0700
Subject: [PATCH 07/14] fixed shape test

---
 brainiak/searchlight/searchlight.py   |  6 ++----
 tests/searchlight/test_searchlight.py | 11 +++++++----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 19c0436bf..6e4282012 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -428,16 +428,14 @@ def _singlenode_searchlight(l, msk, mysl_rad, bcast_var):
             def check_mask(mask_cube):
                 res = mask_cube[self.shape]
                 return np.any(res) and np.all(res)
-
+            
             import pathos.multiprocessing
             inlist = [([ll[i:i+2*mysl_rad+1,
                            j:j+2*mysl_rad+1,
                            k:k+2*mysl_rad+1,
                            :]
                         for ll in l],
-                       msk[i:i+2*mysl_rad+1,
-                           j:j+2*mysl_rad+1,
-                           k:k+2*mysl_rad+1],
+                        self.shape,
                        mysl_rad,
                        bcast_var)
                       if check_mask(msk[i:i+2*mysl_rad+1,
diff --git a/tests/searchlight/test_searchlight.py b/tests/searchlight/test_searchlight.py
index 3a0b6fb64..df458bc09 100644
--- a/tests/searchlight/test_searchlight.py
+++ b/tests/searchlight/test_searchlight.py
@@ -23,7 +23,7 @@
 """
 
 
-def test_cube():
+def test_searchlight_with_cube():
     sl = Searchlight(sl_rad=3)
     comm = MPI.COMM_WORLD
     rank = comm.rank
@@ -38,6 +38,7 @@ def test_cube():
     mask[10:17,10:17,10:17] = True
 
     def sfn(l, msk, myrad, bcast_var):
+        assert np.all(msk)
         return 1.0
 
     sl.distribute(data, mask)
@@ -52,8 +53,8 @@ def sfn(l, msk, myrad, bcast_var):
                 for k in range(global_outputs.shape[2]):
                     assert global_outputs[i,j,k] == None
 
-def test_diamond():
-    sl = Searchlight(sl_rad=3)
+def test_searchlight_with_diamond():
+    sl = Searchlight(sl_rad=3, shape=Diamond)
     comm = MPI.COMM_WORLD
     rank = comm.rank
     size = comm.size
@@ -64,9 +65,11 @@ def test_diamond():
     data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
 
     # Put a spot in the mask
-    mask[10:17,10:17,10:17] = Diamond(3)
+    mask[10:17,10:17,10:17] = Diamond(3).data_
 
     def sfn(l, msk, myrad, bcast_var):
+        assert np.all(msk[Diamond(3).data_])
+        assert not np.any(msk[~Diamond(3).data_])
         return 1.0
 
     sl.distribute(data, mask)

From 08cd4c8352c0a983b68e5a2651dce1a0ffded3a5 Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Mon, 1 May 2017 03:54:17 -0700
Subject: [PATCH 08/14] style fixes

---
 brainiak/searchlight/searchlight.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 6e4282012..eb3e1fe62 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -428,14 +428,14 @@ def _singlenode_searchlight(l, msk, mysl_rad, bcast_var):
             def check_mask(mask_cube):
                 res = mask_cube[self.shape]
                 return np.any(res) and np.all(res)
-            
+
             import pathos.multiprocessing
             inlist = [([ll[i:i+2*mysl_rad+1,
                            j:j+2*mysl_rad+1,
                            k:k+2*mysl_rad+1,
                            :]
                         for ll in l],
-                        self.shape,
+                       self.shape,
                        mysl_rad,
                        bcast_var)
                       if check_mask(msk[i:i+2*mysl_rad+1,

From 2678f6aeb7034f3483a7283bc74850f9f1eadb7f Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Mon, 1 May 2017 03:55:58 -0700
Subject: [PATCH 09/14] Fixed description of Diamond

---
 brainiak/searchlight/searchlight.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index eb3e1fe62..5a332d703 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -73,8 +73,8 @@ def __init__(self, rad):
 class Diamond(Shape):
     """Diamond
 
-    Searchlight shape which is a (2*rad+1)^3 diamond. A diamond
-    is inscribed in the (2*rad+1)^3 cube. Any location in the cube
+    Searchlight shape which is a diamond 
+    inscribed in a (2*rad+1)^3 cube. Any location in the cube
     which has a Manhattan distance of less than rad from the center
     point is set to True.
 

From 32358d40a69bf258a70e2f5bb5d1f6c09384dadd Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Mon, 1 May 2017 06:31:39 -0700
Subject: [PATCH 10/14] removed trailing whitespace

---
 brainiak/searchlight/searchlight.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 5a332d703..9d691d4aa 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -73,7 +73,7 @@ def __init__(self, rad):
 class Diamond(Shape):
     """Diamond
 
-    Searchlight shape which is a diamond 
+    Searchlight shape which is a diamond
     inscribed in a (2*rad+1)^3 cube. Any location in the cube
     which has a Manhattan distance of less than rad from the center
     point is set to True.

From 9550b946b2fe79f8e5e58c488d7e5820d21afcf5 Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Mon, 1 May 2017 06:56:58 -0700
Subject: [PATCH 11/14] added check_mask_ function

---
 brainiak/searchlight/searchlight.py   | 53 +++++++++++++++++----------
 tests/searchlight/test_searchlight.py |  6 +--
 2 files changed, 37 insertions(+), 22 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 9d691d4aa..299cacf73 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -28,13 +28,14 @@
 class Shape:
     """Shape
 
-    Searchlight shape which is contained in a (2*rad+1)^3 cube
+    Searchlight shape which is contained in a cube sized
+    (2*rad+1,2*rad+1,2*rad+1)
 
     Attributes
     ----------
 
-    data_ : a 3D boolean numpy array of size (2*rad+1)^3 which is set
-            to True within the boundaries of the desired shape
+    mask_ : a 3D boolean numpy array of size (2*rad+1,2*rad+1,2*rad+1)
+            which is set to True within the boundaries of the desired shape
     """
 
     def __init__(self, rad):
@@ -53,7 +54,7 @@ def __init__(self, rad):
 class Cube(Shape):
     """Cube
 
-    Searchlight shape which is a (2*rad+1)^3 cube
+    Searchlight shape which is a cube of size (2*rad+1,2*rad+1,2*rad+1)
     """
     def __init__(self, rad):
         """Constructor
@@ -67,17 +68,16 @@ def __init__(self, rad):
         """
         super().__init__(rad)
         self.rad = rad
-        self.data_ = np.ones((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
+        self.mask_ = np.ones((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
 
 
 class Diamond(Shape):
     """Diamond
 
     Searchlight shape which is a diamond
-    inscribed in a (2*rad+1)^3 cube. Any location in the cube
-    which has a Manhattan distance of less than rad from the center
-    point is set to True.
-
+    inscribed in a cube of size (2*rad+1,2*rad+1,2*rad+1).
+    Any location in the cube which has a Manhattan distance of less than rad
+    from the center point is set to True.
     """
     def __init__(self, rad):
         """Constructor
@@ -90,13 +90,13 @@ def __init__(self, rad):
 
         """
         super().__init__(rad)
-        self.data_ = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
+        self.mask_ = np.zeros((2*rad+1, 2*rad+1, 2*rad+1), dtype=np.bool)
         for r1 in range(2*self.rad+1):
             for r2 in range(2*self.rad+1):
                 for r3 in range(2*self.rad+1):
                     if(cityblock((r1, r2, r3),
                                  (self.rad, self.rad, self.rad)) <= self.rad):
-                        self.data_[r1, r2, r3] = True
+                        self.mask_[r1, r2, r3] = True
 
 
 class Searchlight:
@@ -126,7 +126,7 @@ def __init__(self, sl_rad=1, max_blk_edge=10, shape=Cube):
         self.sl_rad = sl_rad
         self.max_blk_edge = max_blk_edge
         self.comm = MPI.COMM_WORLD
-        self.shape = shape(sl_rad).data_
+        self.shape = shape(sl_rad).mask_
         self.bcast_var = None
 
     def _get_ownership(self, data):
@@ -390,6 +390,25 @@ def run_block_function(self, block_fn):
 
         return outmat
 
+    def _check_mask(self, mask_cube):
+        """Check if a mask region overlaps with the searchlight shape
+
+        Parameters
+        ----------
+
+        mask_cube:  Boolean numpy array of size (2*rad+1,2*rad+1,2*rad+1),
+                    which is to be matched against the searchlight shape
+
+        Returns
+        -------
+
+        True if every true location in the searchlight shape is also set to
+        True in the corresponding mask_cube location.
+        """
+
+        res = mask_cube[self.shape]
+        return np.any(res) and np.all(res)
+
     def run_searchlight(self, voxel_fn, pool_size=None):
         """Perform a function at each active voxel
 
@@ -425,10 +444,6 @@ def _singlenode_searchlight(l, msk, mysl_rad, bcast_var):
                                                           mysl_rad:-mysl_rad,
                                                           mysl_rad:-mysl_rad]
 
-            def check_mask(mask_cube):
-                res = mask_cube[self.shape]
-                return np.any(res) and np.all(res)
-
             import pathos.multiprocessing
             inlist = [([ll[i:i+2*mysl_rad+1,
                            j:j+2*mysl_rad+1,
@@ -438,9 +453,9 @@ def check_mask(mask_cube):
                        self.shape,
                        mysl_rad,
                        bcast_var)
-                      if check_mask(msk[i:i+2*mysl_rad+1,
-                                        j:j+2*mysl_rad+1,
-                                        k:k+2*mysl_rad+1]) else None
+                      if self._check_mask(msk[i:i+2*mysl_rad+1,
+                                              j:j+2*mysl_rad+1,
+                                              k:k+2*mysl_rad+1]) else None
                       for i in range(0, outmat.shape[0])
                       for j in range(0, outmat.shape[1])
                       for k in range(0, outmat.shape[2])]
diff --git a/tests/searchlight/test_searchlight.py b/tests/searchlight/test_searchlight.py
index df458bc09..9b3568094 100644
--- a/tests/searchlight/test_searchlight.py
+++ b/tests/searchlight/test_searchlight.py
@@ -65,11 +65,11 @@ def test_searchlight_with_diamond():
     data = [np.empty((dim0,dim1,dim2,ntr), dtype=np.object) if i % size == rank else None for i in range(0, nsubj)]
 
     # Put a spot in the mask
-    mask[10:17,10:17,10:17] = Diamond(3).data_
+    mask[10:17,10:17,10:17] = Diamond(3).mask_
 
     def sfn(l, msk, myrad, bcast_var):
-        assert np.all(msk[Diamond(3).data_])
-        assert not np.any(msk[~Diamond(3).data_])
+        assert np.all(msk[Diamond(3).mask_])
+        assert not np.any(msk[~Diamond(3).mask_])
         return 1.0
 
     sl.distribute(data, mask)

From 73bcad3d00777f0c9cdfe507f543b474064b98de Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Wed, 3 May 2017 06:46:10 -0700
Subject: [PATCH 12/14] Added documentation to clarify border regions

---
 brainiak/searchlight/searchlight.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 299cacf73..7d8648ca0 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -410,7 +410,10 @@ def _check_mask(self, mask_cube):
         return np.any(res) and np.all(res)
 
     def run_searchlight(self, voxel_fn, pool_size=None):
-        """Perform a function at each active voxel
+        """Perform a function at each voxel which is valid for the
+        user-provided shape. This means, the user-provided mask, centered at
+        the active voxel, must be True at each location in which the shape is
+        True. 
 
         Parameters
         ----------

From 0de82937e9eaaee1f1b3fcf0f19f5377ffc54d34 Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Wed, 10 May 2017 04:54:21 -0700
Subject: [PATCH 13/14] Added documentation

---
 brainiak/searchlight/searchlight.py   | 43 ++++++++++-----------------
 tests/searchlight/test_searchlight.py | 13 ++++----
 2 files changed, 23 insertions(+), 33 deletions(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index 7d8648ca0..dc44f540a 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -390,30 +390,10 @@ def run_block_function(self, block_fn):
 
         return outmat
 
-    def _check_mask(self, mask_cube):
-        """Check if a mask region overlaps with the searchlight shape
-
-        Parameters
-        ----------
-
-        mask_cube:  Boolean numpy array of size (2*rad+1,2*rad+1,2*rad+1),
-                    which is to be matched against the searchlight shape
-
-        Returns
-        -------
-
-        True if every true location in the searchlight shape is also set to
-        True in the corresponding mask_cube location.
-        """
-
-        res = mask_cube[self.shape]
-        return np.any(res) and np.all(res)
-
     def run_searchlight(self, voxel_fn, pool_size=None):
-        """Perform a function at each voxel which is valid for the
-        user-provided shape. This means, the user-provided mask, centered at
-        the active voxel, must be True at each location in which the shape is
-        True. 
+        """Perform a function at each voxel which is set to True in the
+        user-provided mask. The mask passed to the searchlight function will be
+        further masked by the user-provided searchlight shape. 
 
         Parameters
         ----------
@@ -439,6 +419,15 @@ def run_searchlight(self, voxel_fn, pool_size=None):
         pool_size:    Number of parallel processes in shared memory
                       process pool
 
+        Returns
+        -------
+
+        A volume which is the same size as the mask, however a number of voxels
+        equal to the searchlight radius has been removed from each border of
+        the volume. This volume contains the values returned from the
+        searchlight function at each voxel which was set to True in the mask,
+        and None elsewhere.
+
         """
 
         def _singlenode_searchlight(l, msk, mysl_rad, bcast_var):
@@ -453,12 +442,12 @@ def _singlenode_searchlight(l, msk, mysl_rad, bcast_var):
                            k:k+2*mysl_rad+1,
                            :]
                         for ll in l],
-                       self.shape,
+                       msk[i:i+2*mysl_rad+1,
+                           j:j+2*mysl_rad+1,
+                           k:k+2*mysl_rad+1] * self.shape,
                        mysl_rad,
                        bcast_var)
-                      if self._check_mask(msk[i:i+2*mysl_rad+1,
-                                              j:j+2*mysl_rad+1,
-                                              k:k+2*mysl_rad+1]) else None
+                      if msk[i+mysl_rad, j+mysl_rad, k+mysl_rad] else None
                       for i in range(0, outmat.shape[0])
                       for j in range(0, outmat.shape[1])
                       for k in range(0, outmat.shape[2])]
diff --git a/tests/searchlight/test_searchlight.py b/tests/searchlight/test_searchlight.py
index 9b3568094..8d673edc4 100644
--- a/tests/searchlight/test_searchlight.py
+++ b/tests/searchlight/test_searchlight.py
@@ -38,8 +38,9 @@ def test_searchlight_with_cube():
     mask[10:17,10:17,10:17] = True
 
     def sfn(l, msk, myrad, bcast_var):
-        assert np.all(msk)
+      if np.all(msk) and np.any(msk):
         return 1.0
+      return None
 
     sl.distribute(data, mask)
     global_outputs = sl.run_searchlight(sfn)
@@ -68,9 +69,10 @@ def test_searchlight_with_diamond():
     mask[10:17,10:17,10:17] = Diamond(3).mask_
 
     def sfn(l, msk, myrad, bcast_var):
-        assert np.all(msk[Diamond(3).mask_])
         assert not np.any(msk[~Diamond(3).mask_])
-        return 1.0
+        if np.all(msk[Diamond(3).mask_]):
+            return 1.0
+        return None
 
     sl.distribute(data, mask)
     global_outputs = sl.run_searchlight(sfn)
@@ -143,9 +145,8 @@ def sfn(l,msk,myrad,bcast_var):
       for d0 in range(rad, global_outputs.shape[0]-rad):
         for d1 in range(rad, global_outputs.shape[1]-rad):
           for d2 in range(rad, global_outputs.shape[2]-rad):
-            msk_blk = mask[d0:d0+2*rad+1, d1:d1+2*rad+1, d2:d2+2*rad+1]
-            if np.all(msk_blk) and np.any(msk_blk):
-              assert np.array_equal(np.array(global_outputs[d0,d1,d2]), np.array([d0,d1,d2]))
+              if mask[d0, d1, d2]:
+                  assert np.array_equal(np.array(global_outputs[d0,d1,d2]), np.array([d0,d1,d2]))
   
   
   def block_test(data, mask, max_blk_edge, rad):

From e564dce497c3bd9fa19101480bcca50b448595bd Mon Sep 17 00:00:00 2001
From: Michael Anderson <michael.j.anderson@intel.com>
Date: Wed, 10 May 2017 04:55:47 -0700
Subject: [PATCH 14/14] removed trailing whitespace

---
 brainiak/searchlight/searchlight.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/brainiak/searchlight/searchlight.py b/brainiak/searchlight/searchlight.py
index dc44f540a..0f009da44 100644
--- a/brainiak/searchlight/searchlight.py
+++ b/brainiak/searchlight/searchlight.py
@@ -393,7 +393,7 @@ def run_block_function(self, block_fn):
     def run_searchlight(self, voxel_fn, pool_size=None):
         """Perform a function at each voxel which is set to True in the
         user-provided mask. The mask passed to the searchlight function will be
-        further masked by the user-provided searchlight shape. 
+        further masked by the user-provided searchlight shape.
 
         Parameters
         ----------