@mat3ra/made 2026.8.7-0 → 2026.8.18-0

package/src/py/mat3ra/made/tools/utils.py

@@ -1,182 +0,0 @@
-from functools import wraps
-from typing import Any, Callable, List, Optional, Union
-
-import numpy as np
-from mat3ra.esse.models.materials_category_components.entities.auxiliary.two_dimensional.supercell_matrix_2d import (
-    SupercellMatrix2DSchema,
-    SupercellMatrix2DSchemaItem,
-)
-from mat3ra.utils.matrix import convert_2x2_to_3x3
-
-DEFAULT_SCALING_FACTOR = np.array([3, 3, 3])
-DEFAULT_TRANSLATION_VECTOR = 1 / DEFAULT_SCALING_FACTOR
-
-
-def is_primitive_2x2_matrix(matrix: Any) -> bool:
-    return (
-        isinstance(matrix, list) and len(matrix) == 2 and all(isinstance(row, list) and len(row) == 2 for row in matrix)
-    )
-
-
-def supercell_matrix_2d_schema_to_list(matrix: SupercellMatrix2DSchema) -> List[List[int]]:
-    """
-    Convert a SupercellMatrix2DSchema to a list of lists of integers.
-    This function is specifically designed to handle the structure of SupercellMatrix2DSchema
-    as seen in the error message.
-    """
-    if matrix is None or matrix.root is None:
-        return [[1, 0], [0, 1]]  # Default identity matrix
-
-    if is_primitive_2x2_matrix(matrix.root):
-        return matrix.root
-
-    if (
-        isinstance(matrix.root, list)
-        and len(matrix.root) == 2
-        and all(isinstance(row, SupercellMatrix2DSchemaItem) for row in matrix.root)
-    ):
-        return [[int(val) for val in row.root] for row in matrix.root]
-
-    # If we can't handle the specific structure, return a default identity matrix
-    return [[1, 0], [0, 1]]
-
-
-# TODO: remove, when propert solution for handling RootModel is added
-def unwrap(value: Any) -> Any:
-    """Recursively unwraps objects with a .root attribute and lists."""
-    if hasattr(value, "root"):
-        return unwrap(value.root)
-    if isinstance(value, list):
-        return [unwrap(item) for item in value]
-    return value
-
-
-def normalize_2x2_matrix(
-    matrix: Union[
-        List[List[float]],
-        SupercellMatrix2DSchema,
-    ]
-) -> Optional[List[List[float]]]:
-    """
-    Normalize any matrix-like structure to a plain 2x2 list of floats.
-    Returns None if normalization is not possible.
-    """
-    if isinstance(matrix, SupercellMatrix2DSchema):
-        return supercell_matrix_2d_schema_to_list(matrix)  # type: ignore
-
-    unwrapped_matrix = unwrap(matrix)
-
-    if is_primitive_2x2_matrix(unwrapped_matrix):
-        return unwrapped_matrix
-
-    return None
-
-
-def decorator_convert_supercell_matrix_2x2_to_3x3(func: Callable) -> Callable:
-    """
-    Decorator that converts a 2x2 matrix input to a 3x3 matrix.
-    Supports schema-based formats and raw nested lists.
-    """
-
-    @wraps(func)
-    def wrapper(*args, **kwargs):
-        def convert_if_matrix(arg):
-            matrix = normalize_2x2_matrix(arg)
-            return convert_2x2_to_3x3(matrix) if matrix else arg
-
-        args = tuple(convert_if_matrix(arg) for arg in args)
-
-        if "supercell_matrix" in kwargs:
-            kwargs["supercell_matrix"] = convert_if_matrix(kwargs["supercell_matrix"])
-
-        return func(*args, **kwargs)
-
-    return wrapper
-
-
-def decorator_convert_position_to_coordinate(func: Callable) -> Callable:
-    """
-    A decorator that converts a 2D position [x, y] to a 3D coordinate [x, y, 0.0].
-    """
-
-    @wraps(func)
-    def wrapper(*args, **kwargs):
-        if "coordinate" in kwargs:
-            coordinate = kwargs["coordinate"]
-        else:
-            # Find the position of the 'coordinate' argument and get its value
-            coordinate_index = func.__code__.co_varnames.index("coordinate")
-            coordinate = args[coordinate_index]
-
-        if len(coordinate) == 2:
-            coordinate = [coordinate[0], coordinate[1], 0.0]
-
-        if "coordinate" in kwargs:
-            kwargs["coordinate"] = coordinate
-        else:
-            args = list(args)
-            args[coordinate_index] = coordinate
-            args = tuple(args)
-
-        return func(*args, **kwargs)
-
-    return wrapper
-
-
-def get_distance_between_coordinates(coordinate1: List[float], coordinate2: List[float]) -> float:
-    """
-    Get the distance between two coordinates.
-    Args:
-        coordinate1 (List[float]): The first coordinate.
-        coordinate2 (List[float]): The second coordinate.
-
-    Returns:
-        float: The distance between the two coordinates.
-    """
-    return float(np.linalg.norm(np.array(coordinate1) - np.array(coordinate2)))
-
-
-def get_norm(vector: List[float]) -> float:
-    """
-    Get the norm of a vector.
-    Args:
-        vector (List[float]): The vector.
-
-    Returns:
-        float: The norm of the vector.
-    """
-    return float(np.linalg.norm(vector))
-
-
-def transform_coordinate_to_supercell(
-    coordinate: List[float],
-    scaling_factor: Optional[List[int]] = None,
-    translation_vector: Optional[List[float]] = None,
-    reverse: bool = False,
-) -> List[float]:
-    """
-    Convert a crystal coordinate of unit cell to a coordinate in a supercell.
-    Args:
-        coordinate (List[float]): The coordinates to convert.
-        scaling_factor (List[int]): The scaling factor for the supercell.
-        translation_vector (List[float]): The translation vector for the supercell.
-        reverse (bool): Whether to convert in the reverse transformation.
-
-    Returns:
-        List[float]: The converted coordinates.
-    """
-    if scaling_factor is None:
-        np_scaling_factor = np.array([3, 3, 3])
-    else:
-        np_scaling_factor = np.array(scaling_factor)
-
-    if translation_vector is None:
-        np_translation_vector = np.array([0, 0, 0])
-    else:
-        np_translation_vector = np.array(translation_vector)
-
-    np_coordinate = np.array(coordinate)
-    converted_array = np_coordinate * (1 / np_scaling_factor) + np_translation_vector
-    if reverse:
-        converted_array = (np_coordinate - np_translation_vector) * np_scaling_factor
-    return converted_array.tolist()

package/src/py/mat3ra/made/utils.py

@@ -1,144 +0,0 @@
-from typing import Any, Dict, List, Literal, Union
-
-import numpy as np
-from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
-from mat3ra.made.material import Material
-
-# TODO: move to mat3ra-code
-AXIS_TO_INDEX_MAP = {"x": 0, "y": 1, "z": 2}
-
-
-# TODO: use mat3ra-code
-def map_array_to_array_with_id_value(array: List[Any], remove_none: bool = False) -> List[Any]:
-    full_array = [{"id": i, "value": item} for i, item in enumerate(array)]
-    if remove_none:
-        return list(filter(lambda x: x["value"] is not None, full_array))
-    return full_array
-
-
-# TODO: use mat3ra-code
-def map_array_with_id_value_to_array(array: List[Dict[str, Any]]) -> List[Any]:
-    return [item["value"] for item in array]
-
-
-def get_center_of_coordinates(coordinates: List[List[float]]) -> List[float]:
-    """
-    Calculate the center of the coordinates.
-
-    Args:
-        coordinates (List[List[float]]): The list of coordinates.
-
-    Returns:
-        List[float]: The center of the coordinates.
-    """
-    return np.mean(np.array(coordinates), axis=0).tolist()
-
-
-def create_2d_supercell_matrices(max_search: int) -> List[np.ndarray]:
-    """
-    Create a list of 2D supercell matrices within a maximum search range.
-
-    Filtering conditions:
-    - Non-zero area constraint
-    - Positive determinant (to exclude mirroring transformations)
-
-    Args:
-        max_search: The maximum search range.
-    Returns:
-        List[np.ndarray]: The list of supercell matrices.
-    """
-    matrices = []
-    for s11 in range(-max_search, max_search + 1):
-        for s12 in range(-max_search, max_search + 1):
-            for s21 in range(-max_search, max_search + 1):
-                for s22 in range(-max_search, max_search + 1):
-                    matrix = np.array([[s11, s12], [s21, s22]])
-                    determinant = np.linalg.det(matrix)
-                    if determinant == 0 or determinant < 0:
-                        continue
-                    matrices.append(matrix)
-    return matrices
-
-
-def get_angle_from_rotation_matrix_2d(
-    matrix: np.ndarray, zero_tolerance: float = 1e-6, round_digits: int = 3
-) -> Union[float, None]:
-    """
-    Get the angle from a 2x2 rotation matrix in degrees if it's a pure rotation matrix.
-    Args:
-        matrix: The 2x2 rotation matrix.
-        zero_tolerance: The zero tolerance for the determinant.
-        round_digits: The number of digits to round the angle.
-
-    Returns:
-        Union[float, None]: The angle in degrees if it's a pure rotation matrix, otherwise None.
-    """
-    if matrix.shape != (2, 2):
-        return None
-    if np.abs(np.linalg.det(matrix) - 1) > zero_tolerance:
-        return None
-    if not np.all(np.abs(matrix) <= 1):
-        return None
-    # Check if it's in form of rotation matrix [cos(theta), -sin(theta); sin(theta), cos(theta)]
-    if not np.allclose(matrix @ matrix.T, np.eye(2), atol=zero_tolerance):
-        return None
-    cos_theta = matrix[0, 0]
-    sin_theta = matrix[1, 0]
-    angle_rad = np.arctan2(sin_theta, cos_theta)
-    angle_deg = np.round(np.degrees(angle_rad), round_digits)
-    return angle_deg
-
-
-def adjust_material_cell_to_set_gap_along_direction(
-    material: Material, gap: float, direction: AxisEnum = AxisEnum.z
-) -> Material:
-    """
-    Adjust the cell along the stacking direction to make the distance from the cell end to its closest atom
-    to be equal to the gap, in Angstroms.
-    """
-    direction_str = direction.value
-    axis_index = AXIS_TO_INDEX_MAP[direction_str]
-
-    max_fractional = get_atomic_coordinates_extremum(material, "max", direction_str, False)
-    current_vectors = material.lattice.vector_arrays
-    current_vector = np.array(current_vectors[axis_index])
-    current_length = np.linalg.norm(current_vector)
-
-    # Add a small nudge when gap=0 to prevent atoms at fractional coordinate 1.0 from being wrapped
-    nudge = 0.0001 if gap == 0 else 0
-    new_length = (max_fractional * current_length) + gap + nudge
-
-    new_vector = current_vector * (new_length / current_length)
-
-    new_lattice_vectors = list(current_vectors)
-    new_lattice_vectors[axis_index] = new_vector.tolist()
-
-    new_material = material.clone()
-    new_material.set_lattice_vectors_from_array(new_lattice_vectors)
-
-    return new_material
-
-
-def get_atomic_coordinates_extremum(
-    material: Material,
-    extremum: Literal["max", "min"] = "max",
-    axis: Literal["x", "y", "z"] = "z",
-    use_cartesian_coordinates: bool = False,
-) -> float:
-    """
-    Return minimum or maximum of coordinates along the specified axis.
-
-    Args:
-        material (Material): Material object.
-        extremum (str): "min" or "max".
-        axis (str):  "x", "y", or "z".
-        use_cartesian_coordinates (bool): Whether to use Cartesian coordinates.
-    Returns:
-        float: Minimum or maximum of coordinates along the specified axis.
-    """
-    new_material = material.clone()
-    if use_cartesian_coordinates:
-        new_material.to_cartesian()
-    else:
-        new_material.to_crystal()
-    return new_material.basis.coordinates.get_extremum_value_along_axis(extremum, axis)

package/tests/.gitattributes

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