Normalizing coordinates & neighborhoods

src/configuration.py

@@ -1,4 +1,143 @@
+import numpy as np
+
+from bitarray import bitarray
+from itertools import product
+from collections import namedtuple
+
+
+class Neighborhood:
     """
+    A neighborhood is a collection of cells around a given cell.
+
+    The neighborhood is closely related to a configuration, which
+    defines how a neighborhood is expected to look. One can think
+    of a neighborhood as an instantiation of a given configuration,
+    as it contains a focus cell and the cells that should be considered
+    when determing the focus cell's next state.
+
+
+    Offsets must be added separate from instantiation, since it isn't always necessary to
+    perform this computation in the first place (for example, if an ALWAYS_PASS flag is passed
+    as opposed to a MATCH flag).
+    """
+    def __init__(self, index):
+        """
+        Initializes the center cell.
+
+        Offsetted cells belonging in the given neighborhood must be added separately.
+        """
+        self.total = 0
+        self.index = index
+        self.neighbors = bitarray()
+
+    def populate(self, plane, offsets):
+        """
+        Given the plane and offsets, determines the cells in the given neighborhood.
+
+        Note this is a relatively expensive operation, especially if called on every cell
+        in a CAM every tick. Instead, consider using the provided class methods which
+        shift through the bitarray instead of recomputing offsets
+        """
+        self.neighbors = bitarray()
+        for offset in offsets:
+            f_index = plane.flatten(offset) + self.index
+            self.neighbors.append(plane[f_index % len(plane.bits)])
+
+        self.total = len(self.neighbors)
+
+    @classmethod
+    def get_neighborhoods(cls, plane, offsets):
+        """
+        Given the list of offsets, return a list of neighborhoods corresponding to every cell.
+
+        Since offsets should generally stay fixed for each cell in a plane, we first flatten
+        the coordinates (@offsets should be a list of tuples) relative to the first component
+        and cycle through all cells.
+
+        NOTE: If all you need are the total number of cells in each neighborhood, call the
+        get_totals method instead, which is significantly faster.
+        """
+        neighborhoods = []
+
+        if plane.N > 0:
+            f_offsets = list(map(plane.flatten, offsets))
+            for i in range(len(plane.bits)):
+                neighborhood = Neighborhood(plane.unflatten(i))
+                for j in range(len(f_offsets)):
+                    neighborhood.neighbors.append(plane.bits[j])
+                    plane.bits[j] += 1
+                neighborhood.total = len(neighborhood.neighbors)
+                neighborhoods.append(neighborhood)
+
+        return neighborhoods
+
+    @classmethod
+    def get_totals(cls, plane, offsets):
+        """
+        Returns the total number of neighbors for each cell in a plane.
+
+        After profiling with a previous version, I found that going through each index and totaling the number
+        of active states was taking much longer than I liked. Instead, we compute as many neighborhoods as possible
+        simultaneously, avoiding explicit summation via the "sum" function, at least for each state separately.
+
+        Because the states are now represented as binary values, we instead add the binary representations together.
+        And since offsets are generally consistent between each invocation of the "tick" function, we can add a row
+        at a time. For example, given a plane P of shape (3, 3) and the following setup:
+
+        [[0, 1, 1, 0, 1]
+        ,[1, 0, 0, 1, 1]    ALIGN    11010    SUM
+        ,[0, 1, 1, 0, 0]  =========> 11000 =========> 32111
+        ,[1, 0, 0, 1, 0]             10101
+        ,[0, 0, 0, 0, 1]
+        ]
+
+        with focus cell (1, 1) in the middle and offsets (-1, 0), (1, 0), (-1, 1), we can align the cells according to the above.
+        The resulting sum states there are 3 neighbors at (1, 1), 2 neighbors at (1, 2), and 1 neighbor at (1, 3), (1, 4), and (1, 0).
+
+        We do this in chunks of 9, depending on the number of offsets, so no overflowing of a single column can occur.
+        We can then find the total of the ith neighborhood by checking the sum of the ith index of the summation of every
+        9 chunks of numbers (this is done at the Nth-1 dimension).
+        """
+        n_counts = []
+
+        # In the first dimension, we have to simply loop through and count for each bit
+        if 0 < plane.N <= 1:
+            for i in range(len(plane.bits)):
+                n_counts.append(sum([plane.bits[i+j] for j in offsets]))
+        else:
+            for level in range(plane.shape[0]):
+
+                # Since working in N dimensional space, we calculate the totals at a
+                # rate of N-1. We do this by generalizing the above doc description, and
+                # limit our focus to the offsetted subplane adjacent to the current level,
+                # then slicing the returned set of bits accordingly
+                neighboring = []
+                for offset in offsets:
+                    adj_level = level + offset[0]
+                    sub_plane = plane[adj_level]
+                    sub_index = sub_plane.flatten(offset[1:])
+                    sequence = sub_plane.bits[sub_index:] + sub_plane.bits[:sub_index]
+                    neighboring.append(int(sequence.to01()))
+
+                # Collect our totals, breaking up each set of neighborhood totals into 9
+                # and then adding the resulting collection back up (note once chunks have
+                # been added, we add each digit separately (the total reduced by factor of 9))
+                totals = [0] * (plane.offsets[0])
+                chunks = map(sum, [neighboring[i:i+9] for i in range(0, len(neighboring), 9)])
+                for chunk in chunks:
+                    padded_chunk = map(int, str(chunk).zfill(len(totals)))
+                    totals = map(sum, zip(totals, padded_chunk))
+
+                # Neighboring totals now align with original grid
+                n_counts += list(totals)
+
+        return n_counts
+
+
+class Configuration:
+    """
+    Represents an expected neighborhood; to be compared to an actual neighborhood in a CAM.
+
     A configuration defines an expectation of a cell's neighborhood, and the cell's new state if is passes
     this expectation.
 
@@ -17,83 +156,8 @@ one. But how do we allow two possibilities to yield a 1? We add an additional co
 
     Often times, a single configuration is perfectly fine, and the exact bits are irrelevant. This
     is the case for all life-life automata for example. In this case, we create a configuration
-with the ALWAYS_PASS flag set in the given ruleset the configuration is bundled in.
+    with the always_pass flag set in the given ruleset the configuration is bundled in.
-
-@date: June 5th, 2015
     """
-import numpy as np
-from itertools import product
-from collections import namedtuple
-
-
-class Neighborhood:
-    """
-    Specifies the cells that should be considered when referencing a particular cell.
-
-    The neighborhood is a wrapper class that stores information regarding a particular cell.
-    Offsets must be added separate from instantiation, since it isn't always necessary to
-    perform this computation in the first place (for example, if an ALWAYS_PASS flag is passed
-    as opposed to a MATCH flag).
-
-    It may be helpful to consider a configuration as a template of a neighborhood, and a neighborhood
-    as an instantiation of a configuration (one with concrete values as opposed to templated ones).
-    """
-
-    def __init__(self, flat_index, bit_index, total):
-        """
-        Initializes the center cell.
-
-        Offsetted cells belonging in the given neighborhood must be added separately.
-        """
-        self.states = None
-        self.bit_indices = None
-        self.flat_indices = None
-
-        self.total = total
-        self.bit_index = bit_index
-        self.flat_index = flat_index
-
-
-    def process_offsets(self, plane, offsets):
-        """
-        Given the plane and offsets, determines the cells in the given neighborhood.
-
-        This is rather expensive to call on every cell in a grid, so should be used with caution.
-        Namely, this is useful when we need to determine matches within a threshold, since total cells
-        of a neighborhood are precomputed in the ruleset.
-
-        For example, if we need an exact match of a configuration, we have to first process all the
-        offsets of a neighborhood to determine that it indeed matches the configuration (if this was
-        not called, self.offsets would remain empty).
-        """
-        flat_indices, bit_indices, _ = zip(*offsets)
-
-        states = []
-        for i in range(len(flat_indices)):
-            bit_index = bit_indices[i]
-            flat_index = flat_indices[i]
-            states.append(plane.grid.flat[flat_index][bit_index])
-
-        self.states = np.array(states)
-        self.bit_indices = np.array(bit_indices)
-        self.flat_indices = np.array(flat_indices)
-
-
-class Configuration:
-    """
-    Represents an expected neighborhood; to be compared to an actual neighborhood in a CAM.
-
-    A configuration allows specification of a neighborhood, not the actual state of a neighborhood.
-    It is merely used for reference by a ruleset, which takes in a series of configurations and
-    returns the state referenced by the first configuration that passes.
-    """
-
-    # An offset contains the flat_offset, which refers to the bitarray of the plane.grid.flat that
-    # a given offset is pointing to. The bit_offset refers to the index of the bitarray at the
-    # given flat_offset. State describes the expected state at the given (flat_offset, bit_offset).
-
-    Offset = namedtuple('Offset', ['flat_offset', 'bit_offset', 'state'])
-
 
     @staticmethod
     def moore(plane, value=1):
@@ -113,7 +177,6 @@ class Configuration:
 
         return offsets
 
-
     @staticmethod
     def neumann(plane, value=1):
         """
@@ -125,7 +188,7 @@ class Configuration:
 
         Note the center cell is excluded, so the total number of offsets are 2N.
         """
-        offsets = []
+        offsets = {}
         variant = [0] * len(plane.shape)
         for i in range(len(variant)):
             for j in [-1, 1]:
@@ -135,7 +198,6 @@ class Configuration:
 
         return offsets
 
-
     def __init__(self, next_state, **kwargs):
         """
         @next_state: Represents the next state of a cell given a configuration passes.
@@ -145,12 +207,12 @@ class Configuration:
                      referring to the offsets checked in a given neighborhood) with an expected
                      state value and a 'plane' key, corresponding to the plane in question.
         """
-        self.offsets = []
+        self.offsets = bitarray()
+        self.sequence = bitarray()
         self.next_state = next_state
         if 'plane' in kwargs and 'offsets' in kwargs:
             self.extend_offsets(kwargs['plane'], kwargs['offsets'])
 
-
     def extend_offsets(self, plane, offsets):
         """
         Allow for customizing of configuration.
@@ -160,9 +222,9 @@ class Configuration:
         of the value at the first coordinate.
         """
         for coor, bit in offsets.items():
-            flat_index, bit_index = plane.flatten(coor)
+            f_index = plane.flatten(coor)
-            self.offsets.append(Configuration.Offset(flat_index, bit_index, bit))
+            self.offsets.append(f_index)
-
+            self.sequence.append(bit)
 
     def passes(self, plane, neighborhood, vfunc, *args):
         """
@@ -184,18 +246,14 @@ class Configuration:
         except TypeError:
             return (True, self.next_state)
 
-
     def matches(self, plane, neighborhood):
         """
         Determines that neighborhood matches expectation exactly.
 
         Note this behaves like the _tolerates method with a tolerance of 1.
         """
-        neighborhood.process_offsets(plane, self.offsets)
+        neighborhood.populate(plane, self.offsets)
-        bits = np.array([offset[2] for offset in self.offsets])
+        return not self.sequence ^ neighborhood.neighbors
-
-        return not np.count_nonzero(bits ^ neighborhood.states)
-
 
     def tolerates(self, plane, neighborhood, tolerance):
         """
@@ -204,12 +262,9 @@ class Configuration:
         We see that the percentage of actual matches are greater than or equal to the given tolerance level. If so, we
         consider this cell to be alive. Note tolerance must be a value 0 <= t <= 1.
         """
-        neighborhood.process_offsets(plane, self.offsets)
+        neighborhood.populate(plane, self.offsets)
-        bits = np.array([offset[2] for offset in self.offsets])
+        non_matches = self.sequence ^ neighborhood.neighbors
-        non_matches = np.count_nonzero(bits ^ neighborhood.states)
+        return (non_matches / len(self.sequence)) >= tolerance
-
-        return (non_matches / len(bits)) >= tolerance
-
 
     def satisfies(self, plane, neighborhood, valid_func, *args):
         """

src/neighborhood.py

@@ -1,127 +0,0 @@
-"""
-A neighborhood is a collection of cells around a given cell.
-
-The neighborhood is closely related to a configuration, which
-defines how a neighborhood is expected to look. One can think
-of a neighborhood as an instantiation of a given configuration,
-as it contains a focus cell and the cells that should be considered
-when determing the focus cell's next state.
-
-@date: June 18, 2015
-"""
-
-class Neighborhood:
-    """
-    The neighborhood is a wrapper class that stores information regarding a particular cell.
-    Offsets must be added separate from instantiation, since it isn't always necessary to
-    perform this computation in the first place (for example, if an ALWAYS_PASS flag is passed
-    as opposed to a MATCH flag).
-    """
-    def __init__(self, index):
-        """
-        Initializes the center cell.
-
-        Offsetted cells belonging in the given neighborhood must be added separately.
-        """
-        self.total = 0
-        self.index = index
-        self.neighbors = []
-
-    def populate(self, offsets, plane):
-        """
-        Given the plane and offsets, determines the cells in the given neighborhood.
-
-        Note this is a relatively expensive operation, especially if called on every cell
-        in a CAM every tick. Instead, consider using the provided class methods which
-        shift through the bitarray instead of recomputing offsets
-        """
-        self.neighbors = plane[offsets]
-        self.total = len(self.neighbors)
-
-    @classmethod
-    def get_neighborhoods(cls, plane, offsets):
-        """
-        Given the list of offsets, return a list of neighborhoods corresponding to every cell.
-
-        Since offsets should generally stay fixed for each cell in a plane, we first flatten
-        the coordinates (@offsets should be a list of tuples) relative to the first component
-        and cycle through all cells.
-
-        NOTE: If all you need are the total number of cells in each neighborhood, call the
-        get_totals method instead, which is significantly faster.
-        """
-        neighborhoods = []
-
-        if plane.N > 0:
-            f_offsets = list(map(plane.flatten, offsets))
-            for i in range(len(plane.bits)):
-                neighborhood = Neighborhood(plane.unflatten(i))
-                for j in range(len(f_offsets)):
-                    neighborhood.neighbors.append(plane.bits[j])
-                    plane.bits[j] += 1
-                neighborhood.total = len(neighborhood.neighbors)
-                neighborhoods.append(neighborhood)
-
-        return neighborhoods
-
-    @classmethod
-    def get_totals(cls, plane, offsets):
-        """
-        Returns the total number of neighbors for each cell in a plane.
-
-        After profiling with a previous version, I found that going through each index and totaling the number
-        of active states was taking much longer than I liked. Instead, we compute as many neighborhoods as possible
-        simultaneously, avoiding explicit summation via the "sum" function, at least for each state separately.
-
-        Because the states are now represented as binary values, we instead add the binary representations together.
-        And since offsets are generally consistent between each invocation of the "tick" function, we can add a row
-        at a time. For example, given a plane P of shape (3, 3) and the following setup:
-
-        [[0, 1, 1, 0, 1]
-        ,[1, 0, 0, 1, 1]    ALIGN    11010    SUM
-        ,[0, 1, 1, 0, 0]  =========> 11000 =========> 32111
-        ,[1, 0, 0, 1, 0]             10101
-        ,[0, 0, 0, 0, 1]
-        ]
-
-        with focus cell (1, 1) in the middle and offsets (-1, 0), (1, 0), (-1, 1), we can align the cells according to the above.
-        The resulting sum states there are 3 neighbors at (1, 1), 2 neighbors at (1, 2), and 1 neighbor at (1, 3), (1, 4), and (1, 0).
-
-        We do this in chunks of 9, depending on the number of offsets, so no overflowing of a single column can occur.
-        We can then find the total of the ith neighborhood by checking the sum of the ith index of the summation of every
-        9 chunks of numbers (this is done at the Nth-1 dimension).
-        """
-        n_counts = []
-
-        # In the first dimension, we have to simply loop through and count for each bit
-        if 0 < plane.N <= 1:
-            for i in range(len(plane.bits)):
-                n_counts.append(sum([plane.bits[i+j] for j in offsets]))
-        else:
-            for level in range(plane.shape[0]):
-
-                # Since working in N dimensional space, we calculate the totals at a
-                # rate of N-1. We do this by generalizing the above doc description, and
-                # limit our focus to the offsetted subplane adjacent to the current level,
-                # then slicing the returned set of bits accordingly
-                neighboring = []
-                for offset in offsets:
-                    adj_level = level + offset[0]
-                    sub_plane = plane[adj_level]
-                    sub_index = sub_plane.flatten(offset[1:])
-                    sequence = sub_plane.bits[sub_index:] + sub_plane.bits[:sub_index]
-                    neighboring.append(int(sequence.to01()))
-
-                # Collect our totals, breaking up each set of neighborhood totals into 9
-                # and then adding the resulting collection back up (note once chunks have
-                # been added, we add each digit separately (the total reduced by factor of 9))
-                totals = [0] * (plane.offsets[0])
-                chunks = map(sum, [neighboring[i:i+9] for i in range(0, len(neighboring), 9)])
-                for chunk in chunks:
-                    padded_chunk = map(int, str(chunk).zfill(len(totals)))
-                    totals = map(sum, zip(totals, padded_chunk))
-
-                # Neighboring totals now align with original grid
-                n_counts += list(totals)
-
-        return n_counts

src/plane.py

@@ -1,16 +1,3 @@
-"""
-Wrapper of a bitarray.
-
-For the sake of compactness, the use of numpy arrays have been completely abandoned as a representation
-of the data. This also allows for a bit more consistency throughout the library, where I've often used
-the flat iterator provided by numpy, and other times used the actual array.
-
-The use of just a bitarray also means it is significantly more compact, indexing of a plane should be
-more efficient, and the entire association between an N-1 dimensional grid with the current shape of
-the plane is no longer a concern.
-
-@date: June 05, 2015
-"""
 import random
 import operator
 import numpy as np
@@ -20,12 +7,37 @@ from bitarray import bitarray
 from collections import deque
 
 
+class Coordinate:
+    """
+    Allow normilization between flat indices and offsets.
+    """
+
+    def __init__(self, index, plane):
+        """
+
+        """
+        if type(index) is tuple:
+            self.index = index
+            self.flat = plane.flatten(index)
+        else:
+            self.flat = index
+            self.index = plane.unflatten(index)
+
+
 class Plane:
     """
     Represents a cell plane, with underlying usage of bitarrays.
 
     The following maintains the shape of a contiguous block of memory, allowing the user to interact
     with it as if it was a multidimensional array.
+
+    For the sake of compactness, the use of numpy arrays have been completely abandoned as a representation
+    of the data. This also allows for a bit more consistency throughout the library, where I've often used
+    the flat iterator provided by numpy, and other times used the actual array.
+
+    The use of just a bitarray also means it is significantly more compact, indexing of a plane should be
+    more efficient, and the entire association between an N-1 dimensional grid with the current shape of
+    the plane is no longer a concern.
     """
 
     def __init__(self, shape, bits = None):

src/ruleset.py

@@ -64,7 +64,19 @@ class Ruleset:
                arg should be a function returning a BOOL, which takes in a current cell's value, and the
                value of its neighbors.
         """
-        next_states = []
+
+        # These are the states of configurations that pass (note if all configurations
+        # fail for any state, the state remains the same)
+        next_states = plane.bits.copy()
+
+        # These are the states we attempt to apply a configuration to
+        # Since totals are computed simultaneously, we save which states do not pass
+        # for each configuration
+        current_states = enumerate(plane.bits)
+        for config in self.configurations:
+            totals = Neighborhood.get_totals(plane, config.offsets)
+
+
 
         for index, state in enumerate(plane.bits):
 

tests/configuration_test.py

@@ -0,0 +1,54 @@
+import os, sys
+sys.path.insert(0, os.path.join('..', 'src'))
+
+import plane
+import numpy as np
+from neighborhood import Neighborhood
+from configuration import Configuration
+
+
+class TestConfiguration:
+    """
+
+    """
+    def setUp(self):
+        self.neighborhood = Neighborhood(0)
+
+        self.plane2d = plane.Plane((100, 100))
+        self.config2d = Configuration(0, plane=self.plane2d, offsets={
+            (-1, -1): 1,
+            (-1, 0): 1,
+            (1, -1): 1,
+            (0, 0): 1
+        })
+
+        self.plane3d = plane.Plane((100, 100, 100))
+        self.config3d = Configuration(1, plane=self.plane3d, offsets={
+            (-1, 0, 1): 1,
+            (-2, 1, 1): 1,
+            (-1, 0, 0): 0
+        })
+
+    def test_mooreNeighborhoodOffsets(self):
+        """
+
+        """
+        assert len(Configuration.moore(self.plane2d)) == 8
+        assert len(Configuration.moore(self.plane3d)) == 26
+
+    def test_neumannNeighborhoodOffsets(self):
+        """
+
+        """
+        assert len(Configuration.neumann(self.plane2d)) == 4
+        assert len(Configuration.neumann(self.plane3d)) == 6
+
+    def test_matchNeighborhood(self):
+        """
+
+        """
+        assert not self.config2d.matches(self.plane2d, self.neighborhood)
+        self.plane2d[[(-1, -1), (-1, 0), (1, -1), (0, 0)]] = 1
+        assert self.config2d.matches(self.plane2d, self.neighborhood)
+
+

tests/neighborhood_test.py

@@ -8,7 +8,7 @@ import numpy as np
 from neighborhood import Neighborhood
 
 
-class TestProperties:
+class TestNeighborhood:
     """
 
     """
@@ -17,12 +17,12 @@ class TestProperties:
         self.neigh2d = Neighborhood(0)
         self.offsets2d = [(-1, 0), (1, 0)]
         self.plane2d = plane.Plane((100, 100))
-        self.neigh2d.populate(self.offsets2d, self.plane2d)
+        self.neigh2d.populate(self.plane2d, self.offsets2d)
 
         self.neigh3d = Neighborhood(0)
         self.offsets3d = [(-1, 0, 0), (1, 0, 1)]
         self.plane3d = plane.Plane((100, 100, 100))
-        self.neigh3d.populate(self.offsets3d, self.plane3d)
+        self.neigh3d.populate(self.plane3d, self.offsets3d)
 
     def test_neighborhoodLength(self):
         """
@@ -87,4 +87,3 @@ class TestProperties:
         assert np.count_nonzero(np.array(t1)) == 200
         assert np.count_nonzero(np.array(t2)) == 20000
 
-

tests/plane_test.py

@@ -5,7 +5,7 @@ import plane
 import numpy as np
 
 
-class TestProperties:
+class TestPlane:
     """
 
     """
@@ -41,15 +41,6 @@ class TestProperties:
         assert len(self.plane2d.bits) == 100 * 100
         assert len(self.plane3d.bits) == 100 * 100 * 100
 
-
-class TestIndexing:
-    """
-
-    """
-    def setUp(self):
-        self.plane2d = plane.Plane((100, 100))
-        self.plane3d = plane.Plane((100, 100, 100))
-
     def test_tupleAssignment(self):
         """
         Tuple Assignment.