def add_shape_to_detector(
builder: NexusBuilder,
detector_group: h5py.Group,
detector_ids: np.ndarray,
voxels: np.ndarray,
vertices: np.ndarray,
offsets: Tuple[np.ndarray, np.ndarray, np.ndarray],
):
builder.add_dataset(detector_group, "x_pixel_offset", offsets[0],
{"units": "m"})
builder.add_dataset(detector_group, "y_pixel_offset", offsets[1],
{"units": "m"})
builder.add_dataset(detector_group, "z_pixel_offset", offsets[2],
{"units": "m"})
winding_order = voxels.flatten().astype(np.int32)
vertices_in_face = 4
faces = np.arange(0, winding_order.size, vertices_in_face)
shape_group = builder.add_nx_group(detector_group, "detector_shape",
"NXoff_geometry")
builder.add_dataset(shape_group, "vertices", vertices.astype(np.float64))
builder.add_dataset(shape_group, "winding_order", winding_order)
builder.add_dataset(shape_group, "faces", faces.astype(np.int32))
builder.add_dataset(shape_group, "detector_faces",
detector_ids.astype(np.int32))
builder.add_dataset(
detector_group,
"detector_number",
np.unique(detector_ids[:, 1]).astype(np.int32),
)
transforms_group = builder.add_nx_group(detector_group, "transformations",
"NXtransformations")
builder.add_transformation(
transforms_group,
"translation",
-4.1,
"m",
[0.0, 0.0, 1.0],
name="translation",
)
return transforms_group
def add_voxel_detector(nexus_builder: NexusBuilder, n_voxels: int = 3):
detector_group = nexus_builder.add_detector_minimal(
"voxel geometry detector", 1)
vertices = np.array([[0.0, 0.0, 0.0]])
off_faces = np.empty((0, 4), dtype=int)
detector_numbers = np.arange(n_voxels)
detector_faces = np.empty((0, 2), dtype=int)
for voxel_number in range(n_voxels):
# Each voxel is a regular octahedron
new_vertices = np.array([
[0.0, 0.0, 1.0 - 2 * voxel_number],
[1.0, 0.0, 0.0 - 2 * voxel_number],
[0.0, 1.0, 0.0 - 2 * voxel_number],
[-1.0, 0.0, 0.0 - 2 * voxel_number],
[0.0, -1.0, 0.0 - 2 * voxel_number],
[0.0, 0.0, -1.0 - 2 * voxel_number],
])
vertices = np.append(vertices[:-1, :], new_vertices, axis=0)
# Number of vertices followed by vertex indices for each face
# the first column doesn't end up in the NeXus file dataset
new_off_faces = np.array([
[3, 1 + 5 * voxel_number, 5 * voxel_number, 4 + 5 * voxel_number],
[3, 4 + 5 * voxel_number, 5 * voxel_number, 3 + 5 * voxel_number],
[3, 3 + 5 * voxel_number, 5 * voxel_number, 2 + 5 * voxel_number],
[3, 2 + 5 * voxel_number, 5 * voxel_number, 1 + 5 * voxel_number],
[
3, 1 + 5 * voxel_number, 5 + 5 * voxel_number,
2 + 5 * voxel_number
],
[
3, 2 + 5 * voxel_number, 5 + 5 * voxel_number,
3 + 5 * voxel_number
],
[
3, 3 + 5 * voxel_number, 5 + 5 * voxel_number,
4 + 5 * voxel_number
],
[
3, 4 + 5 * voxel_number, 5 + 5 * voxel_number,
1 + 5 * voxel_number
],
])
off_faces = np.append(off_faces, new_off_faces, axis=0)
detector_number = detector_numbers[voxel_number]
# Map 8 faces to each detector number
new_detector_faces = np.array([
[detector_number * 8, detector_number],
[1 + detector_number * 8, detector_number],
[2 + detector_number * 8, detector_number],
[3 + detector_number * 8, detector_number],
[4 + detector_number * 8, detector_number],
[5 + detector_number * 8, detector_number],
[6 + detector_number * 8, detector_number],
[7 + detector_number * 8, detector_number],
])
detector_faces = np.append(detector_faces, new_detector_faces, axis=0)
nexus_builder.add_shape(detector_group, "detector_shape", vertices,
off_faces, detector_faces)
nexus_builder.add_dataset(detector_group, "detector_number",
detector_numbers)
transform_group = nexus_builder.add_nx_group(detector_group,
"transformations",
"NXtransformation")
position = nexus_builder.add_transformation(
transform_group,
"translation",
np.array([2.0]),
units="m",
vector=[1.0, 0.0, 1.0],
name="position",
)
nexus_builder.add_dataset(detector_group, "depends_on", position.name)
# Record the voxel positions
x_offsets = 1.1 * np.ones(n_voxels, dtype=float)
y_offsets = 2.2 * np.ones(n_voxels, dtype=float)
z_offsets = np.arange(-n_voxels, n_voxels, 2.0, dtype=float)
nexus_builder.add_dataset(detector_group, "x_pixel_offset", x_offsets)
nexus_builder.add_dataset(detector_group, "y_pixel_offset", y_offsets)
nexus_builder.add_dataset(detector_group, "z_pixel_offset", z_offsets)
write_to_off_file(f"{n_voxels}_voxels.off", vertices.shape[0],
off_faces.shape[0], vertices, off_faces)