def test_1(self):
a = np.arange(10)
b = np.arange(10)
res = np.zeros((a.shape[0] * b.shape[0], 2), dtype=np.int)
cgmath.inter_index_array(a, b, res)
ref = self._manual(a, b)
assert_array_almost_equal(ref, res)
def test_1(self):
a = np.arange(10)
b = np.arange(10)
res = np.zeros((a.shape[0] * b.shape[0], 2), dtype=np.int)
cgmath.inter_index_array(a, b, res)
ref = self._manual(a, b)
assert_array_almost_equal(ref, res)
def cellgrid_self_distance_array(cg1):
"""Calculate all pairwise distances within a certain CellGrid
:Returns:
indices, distances
indices - (n, 2)
distances (n)
"""
box = cg1.box
Nreq = _calculate_self_distance_array_size(cg1)
indices = np.empty((Nreq, 2), dtype=np.int)
dist = np.empty(Nreq, dtype=np.float32)
pos = 0
for cell in cg1:
n = len(cell)
if n > 1:
# Do own cell as a self distance comparison
cgmath.intra_distance_array_withpbc(
cell.coordinates,
box,
dist[pos:]
)
cgmath.intra_index_array(
cell.indices,
indices[pos:]
)
pos += n * (n - 1) // 2
# Then all half neighbours as a full comparison
for addr in cell.half_neighbours:
other = cg1[addr]
if not other:
continue
cgmath.inter_distance_array_withpbc(
cell.coordinates,
other.coordinates,
box,
dist[pos:]
)
cgmath.inter_index_array(
cell.indices,
other.indices,
indices[pos:]
)
pos += n * len(other)
return indices, dist
def cellgrid_distance_array(cg1, cg2):
"""Calculate all pairwise distances between pairs in cg1 and cg2
:Returns:
indices, distances
indices - (n, 2) array of indices
The first index refers to coordinates within cg1
The second index from cg2
distances - (n) Array of distances
"""
if not cg1 == cg2:
raise ValueError("CellGrids are not compatible")
# calculate required size of array
Nreq = _calculate_distance_array_size(cg1, cg2)
dist = np.empty(Nreq, dtype=np.float32)
indices = np.empty((Nreq, 2), dtype=np.int)
box = cg1.box
# Calculate distances cell by cell
pos = 0
# For each cell in cg1
for cell in cg1:
# Iterate over all neighbours in other cellgrid
for addr in itertools.chain([cell.address], cell.all_neighbours):
other = cg2[addr]
cgmath.inter_distance_array_withpbc(
cell.coordinates,
other.coordinates,
box,
dist[pos:]
)
cgmath.inter_index_array(
cell.indices,
other.indices,
indices[pos:]
)
pos += len(cell) * len(other)
return indices, dist
def cellgrid_self_distance_array(cg1):
"""Calculate all pairwise distances within a certain CellGrid
:Returns:
indices, distances
indices - (n, 2)
distances (n)
"""
box = cg1.box
Nreq = _calculate_self_distance_array_size(cg1)
indices = np.empty((Nreq, 2), dtype=np.int)
dist = np.empty(Nreq, dtype=cg1.datatype)
pos = 0
for cell in cg1:
n = len(cell)
if n > 1:
# Do own cell as a self distance comparison
cgmath.intra_distance_array_withpbc(cell.coordinates, box,
dist[pos:])
cgmath.intra_index_array(cell.indices, indices[pos:])
pos += n * (n - 1) // 2
# Then all half neighbours as a full comparison
for addr in cell.half_neighbours:
other = cg1[addr]
if not other:
continue
cgmath.inter_distance_array_withpbc(cell.coordinates,
other.coordinates, box,
dist[pos:])
cgmath.inter_index_array(cell.indices, other.indices,
indices[pos:])
pos += n * len(other)
return indices, dist
def cellgrid_distance_array(cg1, cg2):
"""Calculate all pairwise distances between pairs in cg1 and cg2
:Returns:
indices, distances
indices - (n, 2) array of indices
The first index refers to coordinates within cg1
The second index from cg2
distances - (n) Array of distances
"""
if not cg1 == cg2:
raise ValueError("CellGrids are not compatible")
# calculate required size of array
Nreq = _calculate_distance_array_size(cg1, cg2)
dist = np.empty(Nreq, dtype=cg1.datatype)
indices = np.empty((Nreq, 2), dtype=np.int)
box = cg1.box
# Calculate distances cell by cell
pos = 0
# For each cell in cg1
for cell in cg1:
# Iterate over all neighbours in other cellgrid
for addr in itertools.chain([cell.address], cell.all_neighbours):
other = cg2[addr]
cgmath.inter_distance_array_withpbc(cell.coordinates,
other.coordinates, box,
dist[pos:])
cgmath.inter_index_array(cell.indices, other.indices,
indices[pos:])
pos += len(cell) * len(other)
return indices, dist