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Aplowman/develop #50

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d44285e
build: bump pyvista dep
aplowman Mar 28, 2024
769c000
fix: `CIPHERGeometry.to_zarr` when writing a zip file
aplowman Apr 2, 2024
4f02ecf
fix: add option to not close store in `CIPHEROutput.to_zarr`
aplowman Apr 2, 2024
03a2513
fix: add some exception handling in `CIPHEROutput.get_incremental_data`
aplowman Apr 4, 2024
4798a62
fix: add more exception handling in `CIPHEROutput.get_incremental_data`
aplowman Apr 5, 2024
bb19744
fix: remove trailing new lines from separate mapping files, which con…
aplowman Apr 15, 2024
b5323f2
feat: add `combine_phases` arg to `CIPHERGeometry`
aplowman Apr 15, 2024
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27 changes: 20 additions & 7 deletions cipher_parse/cipher_input.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -333,6 +333,7 @@ def from_voronoi(
num_phases=None,
random_seed=None,
is_periodic=False,
combine_phases=None,
):
geometry = CIPHERGeometry.from_voronoi(
num_phases=num_phases,
Expand All @@ -343,6 +344,7 @@ def from_voronoi(
size=size,
random_seed=random_seed,
is_periodic=is_periodic,
combine_phases=combine_phases,
)

inp = cls(
Expand All @@ -366,6 +368,7 @@ def from_seed_voronoi(
solution_parameters,
random_seed=None,
is_periodic=False,
combine_phases=None,
):
return cls.from_voronoi(
seeds=seeds,
Expand All @@ -378,6 +381,7 @@ def from_seed_voronoi(
solution_parameters=solution_parameters,
random_seed=random_seed,
is_periodic=is_periodic,
combine_phases=combine_phases,
)

@classmethod
Expand All @@ -393,6 +397,7 @@ def from_random_voronoi(
solution_parameters,
random_seed=None,
is_periodic=False,
combine_phases=None,
):
return cls.from_voronoi(
num_phases=num_phases,
Expand All @@ -405,6 +410,7 @@ def from_random_voronoi(
solution_parameters=solution_parameters,
random_seed=random_seed,
is_periodic=is_periodic,
combine_phases=combine_phases,
)

@classmethod
Expand All @@ -418,13 +424,15 @@ def from_voxel_phase_map(
outputs,
solution_parameters,
random_seed=None,
combine_phases=None,
):
geometry = CIPHERGeometry(
voxel_phase=voxel_phase,
materials=materials,
interfaces=interfaces,
size=size,
random_seed=random_seed,
combine_phases=combine_phases,
)
inp = cls(
geometry=geometry,
Expand All @@ -445,6 +453,7 @@ def from_dream3D(
solution_parameters,
container_labels=None,
phase_type_map=None,
combine_phases=None,
):
default_container_labels = {
"SyntheticVolumeDataContainer": "SyntheticVolumeDataContainer",
Expand Down Expand Up @@ -559,6 +568,7 @@ def from_dream3D(
components=components,
outputs=outputs,
solution_parameters=solution_parameters,
combine_phases=combine_phases,
)

@property
Expand Down Expand Up @@ -604,14 +614,17 @@ def write_yaml(self, path, separate_mappings=False):

self.geometry._validate_interface_map()

phase_mat_str = compress_1D_array_string(self.geometry.phase_material + 1) + "\n"
vox_phase_str = (
compress_1D_array_string(self.geometry.voxel_phase.flatten(order="F") + 1)
+ "\n"
)
int_str = (
compress_1D_array_string(self.geometry.interface_map_int.flatten() + 1) + "\n"
phase_mat_str = compress_1D_array_string(self.geometry.phase_material + 1)
vox_phase_str = compress_1D_array_string(
self.geometry.voxel_phase.flatten(order="F") + 1
)
int_str = compress_1D_array_string(self.geometry.interface_map_int.flatten() + 1)

if not separate_mappings:
# CIPHER does not like trailing new lines in the mapping text files:
phase_mat_str += "\n"
vox_phase_str += "\n"
int_str += "\n"

if separate_mappings:
phase_mat_map = "phase_material_mapping.txt"
Expand Down
75 changes: 60 additions & 15 deletions cipher_parse/cipher_output.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -246,15 +246,28 @@ def get_incremental_data(self):
incremental_data = []
for file_i_idx, file_i in enumerate(vtu_file_list):
print(f"Reading VTU file {file_i.name}...", flush=True)
mesh = pv.get_reader(file_i).read()
try:
mesh = pv.get_reader(file_i).read()
except Exception:
print(f"Failed to read VTU file {file_i.name}.", flush=True)
continue
vtu_file_name = file_i.name

img_data = pv.ImageData(dimensions=grid_size)

print(
f"Resampling VTU file {file_i.name} onto an image-data mesh...",
flush=True,
)
img_mesh = img_data.sample(mesh)
try:
img_mesh = img_data.sample(mesh)
except Exception:
print(
f"Failed to re-sample VTU file {file_i.name} onto an image "
f"data grid.",
flush=True,
)
continue

inc_data_i = {
"increment": int(re.search(r"\d+", vtu_file_name).group()),
Expand All @@ -267,7 +280,15 @@ def get_incremental_data(self):

standard_outputs = {}
for name in output_lookup:
arr_flat = img_mesh.get_array(output_lookup[name])
try:
arr_flat = img_mesh.get_array(output_lookup[name])
except KeyError:
print(
f"Failed to get array {output_lookup[name]} from file "
f"{file_i.name}",
flush=True,
)
continue
arr = arr_flat.reshape(img_mesh.dimensions, order="F")
if name in STANDARD_OUTPUTS_TYPES:
arr = arr.astype(STANDARD_OUTPUTS_TYPES[name])
Expand All @@ -278,19 +299,33 @@ def get_incremental_data(self):
name_i = derive_out_i["name"]
func = DERIVED_OUTPUTS_FUNCS[name_i]
func_args = {"input_data": inp_dat}
func_args.update(
{i: standard_outputs[i] for i in DERIVED_OUTPUTS_REQUIREMENTS[name_i]}
)
try:
func_args.update(
{
i: standard_outputs[i]
for i in DERIVED_OUTPUTS_REQUIREMENTS[name_i]
}
)
except KeyError:
print(
f"Failed to prepare arguments for derived output function "
f"{func.__name__!r}.",
flush=True,
)
continue
derived_outputs[name_i] = func(**func_args)

for out_name, keep_idx in outputs_keep_idx.items():
if file_i_idx in keep_idx:
if out_name in DERIVED_OUTPUTS_REQUIREMENTS:
# a derived output:
inc_data_i[out_name] = derived_outputs[out_name]
else:
# a standard output:
inc_data_i[out_name] = standard_outputs[out_name]
try:
if out_name in DERIVED_OUTPUTS_REQUIREMENTS:
# a derived output:
inc_data_i[out_name] = derived_outputs[out_name]
else:
# a standard output:
inc_data_i[out_name] = standard_outputs[out_name]
except KeyError:
continue

incremental_data.append(inc_data_i)

Expand Down Expand Up @@ -434,7 +469,7 @@ def from_JSON_file(cls, path):
data = json.load(fp)
return cls.from_JSON(data)

def to_zarr(self, path):
def to_zarr(self, path, overwrite=False, close_store=None):
"""Save to a persistent zarr store.

This does not yet save `geometries`.
Expand All @@ -455,18 +490,28 @@ def to_zarr(self, path):
out_group.create_dataset(
name="stdout_file_str",
data=self.stdout_file_str.splitlines(),
overwrite=overwrite,
)
out_group.create_dataset(
name="input_YAML_file_str",
data=self.input_YAML_file_str.splitlines(),
overwrite=overwrite,
)
inc_dat_group = out_group.create_group("incremental_data", overwrite=True)
for idx, inc_dat_i in enumerate(self.incremental_data):
inc_dat_i_group = inc_dat_group.create_group(f"{idx}")
inc_dat_i_group.attrs.put({k: inc_dat_i[k] for k in INC_DATA_NON_ARRAYS})
for k in inc_dat_i:
if k not in INC_DATA_NON_ARRAYS:
inc_dat_i_group.create_dataset(name=k, data=inc_dat_i[k])
inc_dat_i_group.create_dataset(
name=k, data=inc_dat_i[k], overwrite=overwrite
)

if path.endswith(".zip") and close_store is None:
close_store = True

if close_store:
out_group.store.close()

return out_group

Expand All @@ -477,7 +522,7 @@ def from_zarr(cls, path, cipher_input=None, quiet=True):
This does not yet load `geometries`.

"""
group = zarr.open_group(store=path)
group = zarr.open_group(store=path, mode="r")
attrs = group.attrs.asdict()
kwargs = {
"directory": attrs["directory"],
Expand Down
110 changes: 109 additions & 1 deletion cipher_parse/geometry.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
import random

from damask import Orientation
import pyvista as pv
import numpy as np
Expand Down Expand Up @@ -39,6 +41,7 @@ def __init__(
time=None,
increment=None,
incremental_data_idx=None,
combine_phases=None,
):
"""
Parameters
Expand Down Expand Up @@ -107,6 +110,22 @@ def __init__(

self._ensure_phase_assignment(random_seed)

if combine_phases:
# combine multiple phases into the same phase to reduce the computational cost
self.voxel_phase = self.combine_phases_per_phase_type(
voxel_map,
materials,
combine_phases,
)
self.voxel_map = VoxelMap(
region_ID=voxel_phase,
size=size,
is_periodic=is_periodic,
quiet=quiet,
)
all_phases = self.present_phases
self._num_phases = all_phases.size

self._phase_material = self._get_phase_material()
self._validate_interfaces()
self._check_interface_phase_pairs()
Expand All @@ -131,6 +150,93 @@ def __init__(
self._misorientation_matrix = None
self._misorientation_matrix_is_degrees = None

@staticmethod
def combine_phases_per_phase_type(voxel_map, materials, combine_phases):

print(f"combining phases according to {combine_phases}")

voxel_phase_new = voxel_map.region_ID
neighbours = voxel_map.neighbour_list

for mat in materials:
for pt_i in mat.phase_types:
print(f"{pt_i.name=}")
max_phases_i = combine_phases.get(pt_i.name)
if max_phases_i:

n_phases = pt_i.phases.size
group_size = int(np.ceil(n_phases / max_phases_i))

print(f" n_phases: {n_phases}")
print(f" max_phases_i: {max_phases_i}")
print(f" group_size: {group_size}")

voxel_phase_new = np.copy(voxel_phase_new)

reassignment = {}
reassignment_inv = {}
possible_IDs_idx = set(range(max_phases_i, n_phases))
possible_IDs = set(pt_i.phases[list(possible_IDs_idx)])
count = 0
kept_IDs = []
for root_ID_idx in range(int(np.ceil(n_phases / group_size))):

root_ID = pt_i.phases[root_ID_idx]
kept_IDs.append(root_ID)

neighbours_i = set(neighbours[:, neighbours[0] == root_ID][1])
possible_IDs -= {root_ID}
possible_IDs_i = possible_IDs - neighbours_i
shared_IDs = [root_ID]
count += 1

for _ in range(1, group_size):
if count >= n_phases:
break
try:
sampled_ID = random.sample(possible_IDs_i, 1)[0]
except ValueError:
print(
f"No non-neighbouring samples left for root_ID: {root_ID}."
)
# allow touching phase IDs within this group:
possible_IDs_i = possible_IDs - set(shared_IDs)

if possible_IDs_i:
sampled_ID = random.sample(possible_IDs_i, 1)[0]
else:
raise ValueError(
f"Cannot find non-neighbouring root IDs"
) from None

neighbours_sampled = set(
neighbours[:, neighbours[0] == sampled_ID][1]
)
possible_IDs_i -= neighbours_sampled
possible_IDs_i -= {sampled_ID}
possible_IDs -= {sampled_ID}
shared_IDs.append(sampled_ID)
count += 1

for i in shared_IDs:
reassignment[i] = root_ID
voxel_phase_new[voxel_phase_new == i] = root_ID

reassignment_inv[root_ID] = shared_IDs

pt_i.phases = kept_IDs # modify phase type phases

# reindex phases across all materials to maintain consecutive phase IDs:
voxel_phase_new_flat = voxel_phase_new.reshape(-1)
uniq, inv = np.unique(voxel_phase_new_flat, return_inverse=True)
reindex = dict(zip(uniq, range(len(uniq))))
voxel_phase_new = inv.reshape(voxel_phase_new.shape)
for mat_j in materials:
for pt_j in mat_j.phase_types:
pt_j.phases = np.array([reindex[i] for i in pt_j.phases])

return voxel_phase_new

def __eq__(self, other):
# Note we don't check seeds (not stored in YAML file)
if not isinstance(other, self.__class__):
Expand Down Expand Up @@ -456,7 +562,7 @@ def _get_phase_material(self):
"Not all phases are accounted for in the phase type definitions."
) # TODO: test raise

# check all phase indices form a consequtive range:
# check all phase indices form a consecutive range:
num_phases_range = set(np.arange(self.num_phases))
known_phases = set(np.hstack(all_phase_idx))
miss_phase_idx = num_phases_range - known_phases
Expand Down Expand Up @@ -740,6 +846,7 @@ def from_voronoi(
num_phases=None,
random_seed=None,
is_periodic=False,
combine_phases=None,
):
if sum(i is not None for i in (seeds, num_phases)) != 1:
raise ValueError(f"Specify exactly one of `seeds` and `num_phases`")
Expand Down Expand Up @@ -769,6 +876,7 @@ def from_voronoi(
size=size,
seeds=seeds,
random_seed=random_seed,
combine_phases=combine_phases,
)

@classmethod
Expand Down
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