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Fixing some minor Python problems #68

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109 changes: 58 additions & 51 deletions cipher_parse/cipher_input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@
from pathlib import Path
from dataclasses import dataclass
from textwrap import indent
from typing import Optional, List, Union, Tuple, Dict

import numpy as np
from numpy.typing import NDArray
import h5py
from parse import parse
from ruamel.yaml import YAML
Expand All @@ -14,12 +14,13 @@
from cipher_parse.geometry import CIPHERGeometry
from cipher_parse.interface import InterfaceDefinition
from cipher_parse.material import MaterialDefinition
from cipher_parse.utilities import set_by_path, read_shockley, grain_boundary_mobility
from cipher_parse.utilities import (
set_by_path, read_shockley, grain_boundary_mobility)


def compress_1D_array(arr):
vals = []
nums = []
def compress_1D_array(arr: NDArray) -> tuple[list[int], list[int]]:
vals: list[int] = []
nums: list[int] = []
for idx, i in enumerate(arr):
if idx == 0:
vals.append(i)
Expand All @@ -37,16 +38,16 @@ def compress_1D_array(arr):
return nums, vals


def compress_1D_array_string(arr, item_delim="\n"):
def compress_1D_array_string(arr: NDArray, item_delim="\n"):
out = []
for n, v in zip(*compress_1D_array(arr)):
out.append(f"{n} of {v}" if n > 1 else f"{v}")

return item_delim.join(out)


def decompress_1D_array_string(arr_str, item_delim="\n"):
out = []
def decompress_1D_array_string(arr_str: str, item_delim="\n") -> NDArray:
out: list[int] = []
for i in arr_str.split(item_delim):
if not i:
continue
Expand All @@ -62,10 +63,10 @@ def decompress_1D_array_string(arr_str, item_delim="\n"):
@dataclass
class CIPHERInput:
geometry: CIPHERGeometry
components: List
outputs: List
solution_parameters: Dict
quiet: Optional[bool] = False
components: list
outputs: list
solution_parameters: dict
quiet: bool | None = False

def __post_init__(self):
self._validate()
Expand All @@ -89,11 +90,13 @@ def _validate(self):
)
if not np.all(check_grid_size == np.array(self.geometry.grid_size)):
raise ValueError(
f"`grid_size` (specifed: {self.geometry.grid_size}) must be equal to: "
f"`initblocksize` (specified: {self.solution_parameters['initblocksize']}) "
f"multiplied by 2 raised to the power of `initrefine` (specified: "
f"{self.solution_parameters['initrefine']}), calculated to be: "
f"{check_grid_size}."
f"`grid_size` "
f"(specifed: {self.geometry.grid_size}) "
f"must be equal to: `initblocksize` "
f"(specified: {self.solution_parameters['initblocksize']}) "
f"multiplied by 2 raised to the power of `initrefine` "
f"(specified: {self.solution_parameters['initrefine']}), "
f"calculated to be: {check_grid_size}."
)

def to_JSON_file(self, path):
Expand Down Expand Up @@ -175,7 +178,7 @@ def get_input_maps_from_files(
return (voxel_phase, phase_material, interface_map)

@classmethod
def from_input_YAML_file(cls, path):
def from_input_YAML_file(cls, path: Path):
"""Generate a CIPHERInput object from a CIPHER input YAML file."""

with Path(path).open("rt") as fp:
Expand All @@ -198,14 +201,14 @@ def from_input_YAML_file(cls, path):
)

@classmethod
def read_input_YAML_file(cls, path):
def read_input_YAML_file(cls, path: str | Path):
with Path(path).open("rt") as fp:
file_str = "".join(fp.readlines())

return cls.read_input_YAML_string(file_str=file_str)

@staticmethod
def read_input_YAML_string(file_str, parse_interface_map=True):
def read_input_YAML_string(file_str: str, parse_interface_map=True):
yaml = YAML(typ="safe")
data = yaml.load(file_str)

Expand Down Expand Up @@ -256,7 +259,7 @@ def read_input_YAML_string(file_str, parse_interface_map=True):
@classmethod
def from_input_YAML_str(
cls,
file_str,
file_str: str,
input_map_voxel_phase=None,
input_map_phase_material=None,
input_map_interface=None,
Expand All @@ -283,7 +286,7 @@ def from_input_YAML_str(
)
for idx, (name, props) in enumerate(yaml_dat["material"].items())
]
interfaces = []
interfaces: list[InterfaceDefinition] = []
for idx, (int_name, props) in enumerate(yaml_dat["interface"].items()):
phase_pairs = np.vstack(np.where(yaml_dat["interface_map"] == idx)).T
if phase_pairs.size:
Expand Down Expand Up @@ -325,14 +328,14 @@ def from_voronoi(
grid_size,
size,
materials,
interfaces,
interfaces: list[InterfaceDefinition],
components,
outputs,
solution_parameters,
seeds=None,
num_phases=None,
random_seed=None,
is_periodic=False,
is_periodic: bool = False,
combine_phases=None,
):
geometry = CIPHERGeometry.from_voronoi(
Expand Down Expand Up @@ -362,7 +365,7 @@ def from_seed_voronoi(
grid_size,
size,
materials,
interfaces,
interfaces: list[InterfaceDefinition],
components,
outputs,
solution_parameters,
Expand Down Expand Up @@ -391,7 +394,7 @@ def from_random_voronoi(
grid_size,
size,
materials,
interfaces,
interfaces: list[InterfaceDefinition],
components,
outputs,
solution_parameters,
Expand Down Expand Up @@ -419,7 +422,7 @@ def from_voxel_phase_map(
voxel_phase,
size,
materials,
interfaces,
interfaces: list[InterfaceDefinition],
components,
outputs,
solution_parameters,
Expand Down Expand Up @@ -447,7 +450,7 @@ def from_dream3D(
cls,
path,
materials,
interfaces,
interfaces: list[InterfaceDefinition],
components,
outputs,
solution_parameters,
Expand Down Expand Up @@ -576,15 +579,15 @@ def materials(self):
return self.geometry.materials

@property
def material_properties(self):
def material_properties(self) -> dict:
return self.geometry.material_properties

@property
def interfaces(self):
def interfaces(self) -> list[InterfaceDefinition]:
return self.geometry.interfaces

@property
def interface_names(self):
def interface_names(self) -> list[str]:
return self.geometry.interface_names

def get_header(self):
Expand All @@ -599,10 +602,10 @@ def get_header(self):
}
return out

def get_interfaces(self):
def get_interfaces(self) -> dict[str, dict]:
return {i.name: i.properties for i in self.geometry.interfaces}

def write_yaml(self, path, separate_mappings=False):
def write_yaml(self, path: str, separate_mappings: bool = False) -> Path:
"""Write the CIPHER input YAML file.

Parameters
Expand Down Expand Up @@ -659,22 +662,22 @@ def write_yaml(self, path, separate_mappings=False):
}

yaml = YAML()
path = Path(path)
with path.open("wt", newline="\n") as fp:
path_ = Path(path)
with path_.open("wt", newline="\n") as fp:
yaml.dump(cipher_input_data, fp)

return path
return path_

def bin_interfaces_by_misorientation_angle(
self,
base_interface_name,
base_interface_name: str,
theta_max,
energy_range=None,
mobility_range=None,
n=4,
B=5,
bin_width=5,
degrees=True,
n: int = 4,
B: int = 5,
bin_width: int = 5,
degrees: bool = True,
**kwargs,
):
if energy_range is None and mobility_range is None:
Expand Down Expand Up @@ -795,8 +798,8 @@ def bin_interfaces_by_misorientation_angle(

def apply_interface_property(
self,
base_interface_name,
property_name,
base_interface_name: str,
property_name: str | list[str] | tuple[str, ...],
property_values,
additional_metadata=None,
bin_edges=None,
Expand All @@ -818,8 +821,10 @@ def apply_interface_property(

"""

if not isinstance(property_name, list):
property_name = [property_name]
if isinstance(property_name, list):
property_name = tuple(property_name)
elif isinstance(property_name, str):
property_name = (property_name, )

if not isinstance(property_values, list):
property_values = [property_values]
Expand All @@ -843,8 +848,9 @@ def apply_interface_property(
else:
value = bin_i
print(
f"Adding {pp_idx_i.size!r} phase pair(s) to {property_name!r} bin "
f"{idx + 1} with edge value: {bin_i!r} and centre: {value!r}."
f"Adding {pp_idx_i.size!r} phase pair(s) to "
f"{property_name!r} bin {idx + 1} with edge "
f"value: {bin_i!r} and centre: {value!r}."
)
new_interfaces_data.append(
{
Expand Down Expand Up @@ -879,9 +885,10 @@ def apply_interface_property(
)
)
raise RuntimeError(
f"Not all phase pairs have been added to a property value bin. The "
f"following {len(missing_dat)}/{phase_pairs.shape[1]} phase pairs (and "
f"property values) are missing: {missing_dat}."
f"Not all phase pairs have been added to a property "
f"value bin. The following "
f"{len(missing_dat)}/{phase_pairs.shape[1]} "
f"phase pairs (and property values) are missing: {missing_dat}."
)
else:
print(
Expand All @@ -900,7 +907,7 @@ def apply_interface_property(
for idx, i in enumerate(new_interfaces_data):
props = copy.deepcopy(base_defn.properties)
for name, val in zip(property_name, i["values"]):
new_value = val.item() # convert from numpy to native
new_value = val.item() # convert from numpy to native
set_by_path(root=props, path=name, value=new_value)

new_type_lab = str(idx)
Expand Down
11 changes: 3 additions & 8 deletions cipher_parse/cipher_output.py
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Original file line number Diff line number Diff line change
@@ -1,19 +1,14 @@
import copy
import json
import shutil
from subprocess import run, PIPE
from pathlib import Path
import re
import os
from textwrap import dedent

import numpy as np
import pyvista as pv
import pandas as pd
import plotly.express as px
import zarr

from cipher_parse.cipher_input import CIPHERInput, decompress_1D_array_string
from cipher_parse.cipher_input import CIPHERInput
from cipher_parse.geometry import CIPHERGeometry
from cipher_parse.utilities import (
get_subset_indices,
Expand Down Expand Up @@ -753,7 +748,7 @@ def _prepare_phase_size_dist_evolution_dataframe(
max_phase_size = df.phase_size.max()

if num_bins is not None and bin_size is not None:
raise TypeError(f"Specify exactly one of `num_bins` and `bin_size`.")
raise TypeError("Specify exactly one of `num_bins` and `bin_size`.")
elif num_bins is None and bin_size is None:
num_bins = 50

Expand Down Expand Up @@ -933,7 +928,7 @@ def show_misorientation_dist_evolution(
max_misori = max_misori_i

if num_bins is not None and bin_size is not None:
raise TypeError(f"Specify exactly one of `num_bins` and `bin_size`.")
raise TypeError("Specify exactly one of `num_bins` and `bin_size`.")
elif num_bins is None and bin_size is None:
num_bins = 50

Expand Down
5 changes: 3 additions & 2 deletions cipher_parse/discrete_voronoi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,8 +39,8 @@ def __init__(
Parameters
----------
region_seeds : list or ndarray of shape (N, 2) or (N, 3)
Row vectors of seed positions in 2D or 3D. Must be coordinates within real-space
`size`.
Row vectors of seed positions in 2D or 3D.
Must be coordinates within real-space `size`.
grid_size : list or ndarray of length 2 or 3
size : list or ndarray of length 2 or 3, optional
If not specified, a unit square/box is used.
Expand Down Expand Up @@ -133,6 +133,7 @@ def get_unique_random_seeds(cls, num_regions, size, grid_size, random_seed=None)
"""Get random seeds that occupy unique elements on the voxel grid."""
max_search_iter = 10_000
idx = 0
counts = np.array([0])
while idx == 0 or np.any(counts > 1):
random_seed = random_seed + idx if random_seed else None
seeds = cls.get_random_seeds(num_regions, size, random_seed)
Expand Down
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