pythran

utils/__init__.py → pylandstats/compute.py

@@ -1,26 +1,27 @@
 import numpy as np
-from numba import pycc
 
-cc = pycc.CC('pylandstats_compute')
 
-
-@cc.export('compute_adjacency_arr', 'uint32[:,:,:](uint32[:,:], int32)')
 def compute_adjacency_arr(padded_arr, num_classes):
     # flat-array approach to pixel adjacency from link below:
     # https://ilovesymposia.com/2016/12/20/numba-in-the-real-world/
     # the first axis of `adjacency_arr` is of fixed size of 2 and serves to
     # distinguish between vertical and horizontal adjacencies (we could also
     # use a tuple of two 2-D arrays)
-    adjacency_arr = np.zeros((2, num_classes + 1, num_classes + 1),
-                             dtype=np.uint32)
-    num_cols = padded_arr.shape[1]
+    # adjacency_arr = np.zeros((2, num_classes + 1, num_classes + 1),
+    #                          dtype=np.uint32)
+    num_cols_adjacency = num_classes + 1
+    horizontal_adjacency_arr = np.zeros(
+        num_cols_adjacency * num_cols_adjacency, dtype=np.uint32)
+    vertical_adjacency_arr = np.zeros(num_cols_adjacency * num_cols_adjacency,
+                                      dtype=np.uint32)
+    num_cols_pixel = padded_arr.shape[1]
     flat_arr = padded_arr.ravel()
     # steps_to_neighbours as argument to distinguish between vertical/
     # horizontal adjacencies
     # steps_to_neighbours = [1, num_cols, -1, -num_cols]
     horizontal_neighbours = [1, -1]
-    vertical_neighbours = [num_cols, -num_cols]
-    start = num_cols + 1
+    vertical_neighbours = [num_cols_pixel, -num_cols_pixel]
+    start = num_cols_pixel + 1
     end = len(flat_arr) - start
     for i in range(start, end):
         class_i = flat_arr[i]
@@ -33,12 +34,14 @@ def compute_adjacency_arr(padded_arr, num_classes):
         # adjacency_arr[1, class_i, class_above] += 1
         # adjacency_arr[1, class_i, class_below] += 1
         for neighbour in horizontal_neighbours:
-            adjacency_arr[0, class_i, flat_arr[i + neighbour]] += 1
+            # adjacency_arr[0, class_i, flat_arr[i + neighbour]] += 1
+            horizontal_adjacency_arr[class_i + num_cols_adjacency *
+                                     flat_arr[i + neighbour]] += 1
         for neighbour in vertical_neighbours:
-            adjacency_arr[1, class_i, flat_arr[i + neighbour]] += 1
-
-    return adjacency_arr
-
+            # adjacency_arr[1, class_i, flat_arr[i + neighbour]] += 1
+            vertical_adjacency_arr[class_i + num_cols_adjacency *
+                                   flat_arr[i + neighbour]] += 1
 
-if __name__ == '__main__':
-    cc.compile()
+    return np.stack(
+        (horizontal_adjacency_arr, vertical_adjacency_arr)).reshape(
+            (2, num_cols_adjacency, num_cols_adjacency))

pylandstats/compute.pythran

@@ -0,0 +1 @@
+export compute_adjacency_arr(uint32[:,:], int)

pyproject.toml

@@ -1,2 +1,2 @@
 [build-system]
-requires = ['setuptools>=40.8.0', 'wheel', 'numba', 'numpy']
+requires = ['setuptools>=40.8.0', 'wheel', 'pythran', 'numpy']

setup.py

@@ -1,12 +1,10 @@
 # coding=utf-8
 
-from distutils.command.build_ext import build_ext
-from distutils.sysconfig import customize_compiler
 from io import open  # compatible enconding parameter
 from os import path
 
-from setuptools import find_packages, setup
-from utils import cc
+from pythran.dist import PythranBuildExt, PythranExtension
+from setuptools import dist, find_packages, setup
 
 __version__ = '0.5.0'
 
@@ -39,21 +37,8 @@
     x.strip().replace('git+', '') for x in all_reqs if x.startswith('git+')
 ]
 
-
-# Avoid a gcc warning (see https://stackoverflow.com/questions/8106258/cc1plus-
-# warning-command-line-option-wstrict-prototypes-is-valid-for-ada-c-o):
-# cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid
-# for C/ObjC but not for C++
-# See also: https://github.com/numba/numba/issues/3361
-class BuildExt(build_ext):
-    def build_extensions(self):
-        customize_compiler(self.compiler)
-        try:
-            self.compiler.compiler_so.remove("-Wstrict-prototypes")
-        except (AttributeError, ValueError):
-            pass
-        build_ext.build_extensions(self)
-
+# This is required to be able to use pythran in setup.py
+dist.Distribution(dict(setup_requires='pythran'))
 
 setup(
     name='pylandstats',
@@ -71,6 +56,8 @@ def build_extensions(self):
     install_requires=install_requires,
     extras_require={'geo': geo},
     dependency_links=dependency_links,
-    cmdclass={'build_ext': BuildExt},
-    ext_modules=[cc.distutils_extension()],
+    ext_modules=[
+        PythranExtension('pylandstats_compute', ['pylandstats/compute.py'])
+    ],
+    cmdclass={'build_ext': PythranBuildExt},
 )

tests/test_pylandstats.py

@@ -405,9 +405,12 @@ def test_multilandscape_metric_kws(self):
                 else:
                     self.assertLess(class_metrics['total_area'],
                                     class_metrics_kws['total_area'])
+                    # we need quite some tolerance because pixel resolutions in
+                    # raster files might be wierd float values, e.g., 99.13213
+                    # instead of 100 (meters)
                     self.assertLessEqual(
                         class_metrics['total_edge'],
-                        class_metrics_kws['total_edge'] + .0004)
+                        1.01 * class_metrics_kws['total_edge'])
 
     def test_multilandscape_plot_metrics(self):
         ml = self.InstantiableMultiLandscape(self.landscape_fps,