Merge pull request #2 from MarekSuchanek/speedup

Speedup via Cython

Author: MarekSuchanek

.gitignore

@@ -90,3 +90,13 @@ ENV/
 
 # PyCharm
 .idea
+
+# MI-PYT tests
+tests2
+
+# Own
+maze.c
+maze.cpp
+maze.html
+generate.py
+random.csv

.travis.yml

@@ -5,4 +5,13 @@ install:
 - pip install -U pip
 - pip install -r requirements.txt
 script:
+- python setup.py develop
 - python -m pytest
+addons:
+  apt:
+    sources:
+    - ubuntu-toolchain-r-test
+    packages:
+    - gcc-4.8
+    - g++-4.8
+    - python3-dev

README.md

@@ -35,6 +35,19 @@ have this version of Python). Then you can install dependencies via:
 pip install -r requirements.txt
 ```
 
+For speedup is analysis written in Cython so you need to compile it with
+via:
+
+```
+python setup.py develop
+```
+
+or
+
+```
+python setup.py install
+```
+
 ## Usage
 
 ```
@@ -65,7 +78,7 @@ maze.NoPathExistsException
 
 ## Testing
 
-After installing dependencies you can run tests with `pytest`:
+After installing dependencies and compilation you can run tests with `pytest`:
 
 ```
 python -m pytest

generate.py

@@ -0,0 +1,14 @@
+from random import randint
+
+if __name__ == '__main__':
+    w = 1000
+    h = 1000
+    min_val = -1000
+    max_val = 2000
+    for i in range(h):
+        for j in range(w-1):
+            if randint(0,10) < 8:
+                print(randint(min_val, max_val), end=',')
+            else:
+                print(1, end=',')
+        print(randint(min_val, max_val))

maze.py

@@ -0,0 +1,107 @@
+# distutils: language=c++
+import numpy as np
+cimport numpy as np
+import cython
+from libcpp cimport bool
+from libcpp.queue cimport queue
+from libcpp.vector cimport vector
+from libcpp.pair cimport pair
+from libcpp.map cimport map
+
+cdef struct coords:
+    int x
+    int y
+
+cdef struct qitem:
+    int x
+    int y
+    int distance
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cdef bool directions2reachable(np.ndarray[np.int8_t, ndim=2] directions, int w, int h):
+    with cython.nogil:
+        for x in range(w):
+            for y in range(h):
+                with cython.gil:
+                    if directions[x, y] == ord(b' '):
+                        return False
+    return True
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cpdef flood(np.ndarray[np.int8_t, ndim=2] maze, int w, int h):
+    cdef int x, y, i
+    cdef queue[qitem] q
+    cdef np.ndarray[np.int32_t, ndim=2] distances
+    cdef np.ndarray[np.int8_t, ndim=2] directions
+    distances = np.full((w, h), -1, dtype='int32')
+    directions = np.full((w, h), b' ', dtype=('a', 1))
+
+    with cython.nogil:
+        for x in range(w):
+            for y in range(h):
+                with cython.gil:
+                    if maze[x, y] < 0:
+                        directions[x, y] = b'#'
+                    elif maze[x, y] == 1:
+                        q.push(qitem(x, y, 0))
+                        distances[x, y] = 0
+                        directions[x, y] = b'X'
+
+    cdef coords *dir_offsets = [coords(1, 0), coords(-1, 0), coords(0, 1), coords(0, -1)]
+    cdef np.int8_t *dir_chars = [b'^', b'v', b'<', b'>']
+    while not q.empty():
+        item = q.front()
+        q.pop()
+        for i in range(4):
+            offset = dir_offsets[i]
+            x = item.x + offset.x
+            y = item.y + offset.y
+            if 0 <= x < w and 0 <= y < h:
+                if maze[x, y] >= 0 and distances[x, y] == -1:
+                    distances[x, y] = item.distance+1
+                    directions[x, y] = dir_chars[i]
+                    q.push(qitem(x, y, item.distance+1))
+
+    return distances, directions, directions2reachable(directions, w, h)
+
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cpdef build_path(np.ndarray[np.int8_t, ndim=2] directions, int row, int column):
+    if directions[row, column] == b'#' or directions[row, column] == b' ':
+        raise NoPathExistsException
+    cdef vector[pair[int,int]] path
+    cdef map[char,coords] dirs
+    dirs.insert(pair[char,coords](b'v', coords(1, 0)))
+    dirs.insert(pair[char,coords](b'^', coords(-1, 0)))
+    dirs.insert(pair[char,coords](b'>', coords(0, 1)))
+    dirs.insert(pair[char,coords](b'<', coords(0, -1)))
+    path.push_back(pair[int,int](row, column))
+    while directions[row, column] != b'X':
+        d = dirs[directions[row, column]]
+        row += d.x
+        column += d.y
+        path.push_back(pair[int,int](row, column))
+    return path
+
+
+cdef class NoPathExistsException(Exception):
+    pass
+
+
+class MazeAnalysis:
+
+    def __init__(self, maze):
+        maze = np.atleast_2d(maze.astype('int8')) # fix matrix type & dims
+        self.distances, self.directions, self.is_reachable = flood(maze, *maze.shape)
+
+    def path(self, row, column):
+        return build_path(self.directions, row, column)
+
+
+cpdef analyze(maze):
+    return MazeAnalysis(maze)

maze.pyx

@@ -1,3 +1,4 @@
-numpy>==1.11.2
+numpy>=1.11.2
 py>=1.4.31
 pytest>=3.0.4
+Cython>=0.25.1

requirements.txt

@@ -0,0 +1,44 @@
+from setuptools import setup, find_packages
+from Cython.Build import cythonize
+import numpy
+
+with open('README.md') as f:
+    long_description = ''.join(f.readlines())
+
+setup(
+    name='maze',
+    version=0.2,
+    keywords='maze analysis matrix cython',
+    description='Simple python maze analyzer for finding shortest path',
+    long_description=long_description,
+    author='Marek Suchánek',
+    author_email='[email protected]',
+    license='MIT',
+    packages=find_packages(),
+    ext_modules=cythonize(
+        'maze.pyx',
+        language_level=3,
+        include_dirs=[numpy.get_include()],
+        language="c++"
+    ),
+    include_dirs=[numpy.get_include()],
+    install_requires=[
+        'Cython>=0.25.1',
+        'numpy>=1.11.2',
+        'py>=1.4.31',
+    ],
+    setup_requires=[
+        'pytest-runner'
+    ],
+    tests_require=[
+        'pytest',
+    ],
+    classifiers=[
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: Implementation :: CPython',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.5',
+        'Topic :: Scientific/Engineering :: Mathematics',
+    ],
+)

setup.py

@@ -15,7 +15,7 @@ def load_mazes(folder):
         path = os.path.join(folder, name)
         if os.path.isfile(path) and name.endswith('.csv'):
             maze_num = int(name[:-4])
-            result[maze_num] = np.loadtxt(path, delimiter=',')
+            result[maze_num] = np.loadtxt(path, delimiter=',', dtype='int8')
     return result