Fix Centers function

AUTHORS

@@ -19,3 +19,4 @@ Contributors:
 * Giacomo Fiorin <giacomofiorin>
 * Eloy Félix <eloyfelix>
 * René Hafner (Hamburger) <renehamburger1993>
+* Anthony Cruz-Balberdy <acruzpr>

CHANGELOG

@@ -13,13 +13,15 @@ The rules for this file:
   * accompany each entry with github issue/PR number (Issue #xyz)
 
 ------------------------------------------------------------------------------
-??/??/2019 eloyfelix, renehamburger1993
+??/??/2020 eloyfelix, renehamburger1993, acruzpr
 
   * 0.6.0
 
   Enhancements
 
   * Allow parsing/writing gzipped DX files
+  * Allow the generation of coordinates for the cell centers using the origin as defined by APBS DX file format
+   or as defined by the Original DX file format (#78)
 
 
   Fixes

gridData/core.py

@@ -112,7 +112,7 @@ def __init__(self, grid=None, edges=None, origin=None, delta=None,
 
 
         .. versionchanged:: 0.5.0
-           New *file_format* keyword argument.
+           New *file_format* keyword argument
 
         """
         # file formats are guess from extension == lower case key
@@ -573,11 +573,25 @@ def save(self, filename):
         """
         self.export(filename, file_format="pickle")
 
-    def centers(self):
+    def centers(self, origin_centered=False):
         """Returns the coordinates of the centers of all grid cells as an
-        iterator."""
+        iterator.
+
+        Parameters
+        ----------
+        origin_centered : bool
+            When is set to True the origin will be set to the lower-left corner of the grid following
+            the APBS DX format specifications.
+
+            When is set to False the origin will be set to the center of the first grid cell following
+            the official DX format specifications.
+
+            .. versionchanged:: 0.6.0
+             New *origin_centered* keyword argument
+        """
         for idx in numpy.ndindex(self.grid.shape):
-            yield self.delta * numpy.array(idx) + self.origin
+            offset = 0.5 * self.delta if not origin_centered else 0
+            yield self.delta * numpy.array(idx) + self.origin + offset
 
     def check_compatible(self, other):
         """Check if *other* can be used in an arithmetic operation.

gridData/tests/test_grid.py

@@ -151,12 +151,23 @@ def test_non_orthonormal_boxes(self, data):
         with pytest.raises(NotImplementedError):
             Grid(data['griddata'], origin=data['origin'], delta=delta)
 
-    def test_centers(self, data):
+    def test_centers_false(self, data):
         # this only checks the edges. If you know an alternative
         # algorithm that isn't an exact duplicate of the one in
         # g.centers to test this please implement it.
         g = Grid(data['griddata'], origin=np.ones(3), delta=data['delta'])
-        centers = np.array(list(g.centers()))
+        centers = np.array(list(g.centers(False)))
+        offset = g.delta * 0.5
+        assert_array_equal(centers[0], g.origin + offset)
+        assert_array_equal(centers[-1] - g.origin - offset,
+                           (np.array(g.grid.shape) - 1) * data['delta'])
+
+    def test_centers_true(self, data):
+        # this only checks the edges. If you know an alternative
+        # algorithm that isn't an exact duplicate of the one in
+        # g.centers to test this please implement it.
+        g = Grid(data['griddata'], origin=np.ones(3), delta=data['delta'])
+        centers = np.array(list(g.centers(True)))
         assert_array_equal(centers[0], g.origin)
         assert_array_equal(centers[-1] - g.origin,
                            (np.array(g.grid.shape) - 1) * data['delta'])