Int replaced by floor to accept negative coordinates. (#3264)

---------

Co-authored-by: Robert A McDougal <robert.mcdougal@yale.edu>

Author: ceciliaromaro

share/lib/python/neuron/rxd/node.py

@@ -35,6 +35,8 @@
 _concentration_node = 0
 _molecule_node = 1
 
+_floor = numpy.floor
+
 
 def _get_data():
     return (_volumes, _surface_area, _diffs)
@@ -650,9 +652,9 @@ def satisfies(self, condition):
             x, y, z = condition
             mesh = self._r._mesh_grid
             return (
-                int((x - mesh["xlo"]) / mesh["dx"]) == self._i
-                and int((y - mesh["ylo"]) / mesh["dy"]) == self._j
-                and int((z - mesh["zlo"]) / mesh["dz"]) == self._k
+                _floor((x - mesh["xlo"]) / mesh["dx"]) == self._i
+                and _floor((y - mesh["ylo"]) / mesh["dy"]) == self._j
+                and _floor((z - mesh["zlo"]) / mesh["dz"]) == self._k
             )
         # check for a position condition so as to provide a more useful error
         checked_for_normalized_position = False
@@ -885,8 +887,8 @@ def satisfies(self, condition):
             x, y, z = condition
             r = self._regionref()
             return (
-                int((x - r._xlo) / r._dx[0]) == self._i
-                and int((y - r._ylo) / r._dx[1]) == self._j
-                and int((z - r._zlo) / r._dx[2]) == self._k
+                _floor((x - r._xlo) / r._dx[0]) == self._i
+                and _floor((y - r._ylo) / r._dx[1]) == self._j
+                and _floor((z - r._zlo) / r._dx[2]) == self._k
             )
         raise RxDException(f"unrecognized node condition: {condition}")

test/rxd/3d/test_node_selection.py

@@ -1,3 +1,6 @@
+import weakref
+
+
 def test_node_selection(neuron_instance):
     """Test selection of 3D nodes"""
 
@@ -16,4 +19,8 @@ def test_node_selection(neuron_instance):
     assert nodes((5.2, 0.1, 0.3))[0].x3d == 5.125
     assert nodes((5.2, 0.1, 0.3))[0].y3d == 0.125
     assert nodes((5.2, 0.1, 0.3))[0].z3d == 0.375
+
+    nodes.append(rxd.node.Node3D(0, -1, 0, 0, cyt, 0, dend(0.5), weakref.ref(c)))
+
     assert len(nodes((5, 0, 0))) == 1
+    assert nodes[-1] in nodes((nodes[-1].x3d, nodes[-1].y3d, nodes[-1].z3d))