support py3.6+linux

README.md

@@ -8,7 +8,7 @@ Reference implementation of a two-level RCN model on MNIST classification. See t
 
 ## Setup
 
-Note: Python 2.7 is supported. The code was tested on OSX 10.11. It may work on other system platforms but not guaranteed.
+Note: Python 2.7 and python 3.6 is supported. The code was tested on OSX 10.11. It may work on other system platforms but not guaranteed.
 
 Before starting please make sure gcc is installed (`brew install gcc`) and up to date in order to compile the various dependencies (particularly numpy).
 

requirements.txt

@@ -1,7 +1,6 @@
-decorator==4.1.2
+decorator>=4.1.2
 networkx==1.11
-numpy==1.13.3
-olefile==0.44
-Pillow==4.1.1
-rcn-ref==1.0.0
-scipy==0.19.1
+numpy>=1.13.3
+olefile>=0.44
+Pillow>=4.1.1
+scipy>=0.19.1

science_rcn/dilation/dilation.cc

@@ -17,20 +17,39 @@ using namespace std;
 
 /* ==== Set up the methods table ====================== */
 static PyMethodDef dilationmethods[] = {
-    {"max_filter1d", py_max_filter1d, METH_VARARGS},
-    {"brute_max_filter1d", py_brute_max_filter1d, METH_VARARGS},
-    {NULL, NULL}   /* Sentinel - marks the end of this structure */
+    {"max_filter1d", py_max_filter1d, METH_VARARGS, "max filter1d"},
+    {"brute_max_filter1d", py_brute_max_filter1d, METH_VARARGS, "brute max filter1d"},
+    {NULL, NULL, 0, NULL}
 };
 
 
 /* ==== Initialize the C_test functions ====================== */
-extern "C" {
-void init_dilation()
+/* This initiates the module using the above definitions. */
+#if PY_VERSION_HEX >= 0x03000000
+static struct PyModuleDef moduledef = {
+    PyModuleDef_HEAD_INIT,
+    "_dilation",
+    NULL,
+    -1,
+    dilationmethods,
+    NULL,
+    NULL,
+    NULL,
+    NULL
+};
+
+PyMODINIT_FUNC PyInit__dilation(void)
 {
-    (void) Py_InitModule("_dilation", dilationmethods);
-    import_array(); // Must be present for NumPy.  Called first after above line.
+    import_array();
+    return PyModule_Create(&moduledef);
 }
+#else
+PyMODINIT_FUNC init_dilation(void)
+{
+    (void) Py_InitModule("_dilation", dilationmethods);
+    import_array();
 }
+#endif
 
 /// Check condition and return NULL (which will cause a python exception) if
 /// it's false, and include an arbitrary format string as the error message

science_rcn/inference.py

@@ -6,7 +6,6 @@
 Note that we use a faster implementation of 2D dilation, instead of the slower
 scipy.ndimage.morphology.grey_dilation.
 """
-from itertools import izip
 import logging
 import numpy as np
 import networkx as nx
@@ -56,7 +55,7 @@ def test_image(img, model_factors,
 
     # Forward pass inference
     fp_scores = np.zeros(len(model_factors[0]))
-    for i, (frcs, _, graph) in enumerate(izip(*model_factors)):
+    for i, (frcs, _, graph) in enumerate(list(zip(*model_factors))):
         fp_scores[i] = forward_pass(frcs,
                                     bu_msg,
                                     graph,
@@ -315,7 +314,7 @@ def infer_pbp(self):
         """Parallel loopy BP message passing, modifying state of `lat_messages`.
         See bwd_pass() for parameters.
         """
-        for it in xrange(self.n_iters):
+        for it in range(self.n_iters):
             new_lat_messages = self.new_messages()
             delta = new_lat_messages - self.lat_messages
             self.lat_messages += self.damping * delta

science_rcn/preproc.py

@@ -131,7 +131,7 @@ def generate_suppression_masks(filter_scale=4., num_orients=16):
     # Compute for orientations [0, pi), then flip for [pi, 2*pi)
     for i, angle in enumerate(np.linspace(0., np.pi, num_orients // 2, endpoint=False)):
         x, y = np.cos(angle), np.sin(angle)
-        for r in xrange(1, int(np.sqrt(2) * size / 2)):
+        for r in range(1, int(np.sqrt(2) * size / 2)):
             dx, dy = round(r * x), round(r * y)
             if abs(dx) > cx or abs(dy) > cy:
                 continue
@@ -160,7 +160,7 @@ def local_nonmax_suppression(filtered, suppression_masks, num_orients=16):
     localized = np.zeros_like(filtered)
     cross_orient_max = filtered.max(0)
     filtered[filtered < 0] = 0
-    for i, (layer, suppress_mask) in enumerate(zip(filtered, suppression_masks)):
+    for i, (layer, suppress_mask) in enumerate(list(zip(filtered, suppression_masks))):
         competitor_maxs = maximum_filter(layer, footprint=suppress_mask, mode='nearest')
         localized[i] = competitor_maxs <= layer
     localized[cross_orient_max > filtered] = 0

science_rcn/run.py

@@ -81,7 +81,7 @@ def run_experiment(data_dir='data/MNIST',
     train_partial = partial(train_image,
                             perturb_factor=perturb_factor)
     train_results = pool.map_async(train_partial, [d[0] for d in train_data]).get(9999999)
-    all_model_factors = zip(*train_results)
+    all_model_factors = list(zip(*train_results))
 
     LOG.info("Testing on {} images...".format(len(test_data)))
     test_partial = partial(test_image, model_factors=all_model_factors,
@@ -92,7 +92,7 @@ def run_experiment(data_dir='data/MNIST',
     correct = 0
     for test_idx, (winner_idx, _) in enumerate(test_results):
         correct += int(test_data[test_idx][1]) == winner_idx // (train_size // 10)
-    print "Total test accuracy = {}".format(float(correct) / len(test_results))
+    print("Total test accuracy = {}".format(float(correct) / len(test_results)))
 
     return all_model_factors, test_results
 

setup.py

@@ -24,7 +24,7 @@ def _findRequirements():
 # Check for MNIST data dir
 if not os.path.isdir('./data/MNIST'):
     if os.path.exists('./data/MNIST.zip'):
-        print "Extracting MNIST data..."
+        print("Extracting MNIST data...")
         with zipfile.ZipFile('./data/MNIST.zip', 'r') as z:
             z.extractall('./data/')
     else:
@@ -62,9 +62,9 @@ def finalize_options(self):
     setup_requires=['numpy>=1.13.3'],
     install_requires=[
         'networkx>=1.11,<1.12',
-        'numpy==1.13.3',
-        'pillow>=4.1.0,<4.2',
-        'scipy>=0.19.0,<0.20',
+        'numpy>=1.13.3',
+        'pillow>=4.1.0',
+        'scipy>=0.19.0',
         'setuptools>=36.5.0'
     ],
     ext_modules=[dilation_module],
@@ -73,6 +73,7 @@ def finalize_options(self):
         'Natural Language :: English',
         'Operating System :: MacOS :: MacOS X',
         'Programming Language :: Python :: 2.7',
+        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: Implementation :: CPython',
         'Programming Language :: C'],
     keywords='rcn',