"""
atomic reference. Used for predicting extensive properties.
"""

import logging
from typing import List, Optional

import numpy as np
import tensorflow as tf
from ase import Atoms
from pymatgen.core import Element, Molecule, Structure

from m3gnet.config import DataType
from m3gnet.graph import Index
from m3gnet.utils import get_segment_indices_from_n, register

logger = logging.getLogger(__name__)


@register
class BaseAtomRef(tf.keras.layers.Layer):
    """
    Base AtomRef that predicts 0 correction
    """

    def call(self, graph: List, **kwargs):
        """

        Args:
            graph (list): list repr of a graph
            **kwargs:

        Returns: 0
        """
        return 0.0


@register
class AtomRef(BaseAtomRef):
    """
    Atom reference values. For example, if the average H energy is -20.0, and
    the average O energy is -10.0, the AtomRef predicts -20 * 2 + (-10.) =
    -50.0 for the atom reference energy for H2O
    """

    def __init__(
        self,
        property_per_element: Optional[np.ndarray] = None,
        max_z: int = 94,
        **kwargs,
    ):
        """
        Args:
            property_per_element (np.ndarray): element reference value
            max_z (int): maximum atomic number
            **kwargs:
        """
        super().__init__(**kwargs)
        if property_per_element is None:
            self.property_per_element = np.zeros(shape=(max_z + 1,))
        else:
            self.property_per_element = np.array(property_per_element).ravel()
        self.max_z = max_z

    def _get_feature_matrix(self, structs_or_graphs):
        n = len(structs_or_graphs)
        features = np.zeros(shape=(n, self.max_z + 1))
        for i, s in enumerate(structs_or_graphs):
            if isinstance(s, (Structure, Molecule)):
                atomic_numbers = [i.specie.Z for i in s.sites]
            elif isinstance(s, (list, np.ndarray)):
                atomic_numbers = s
            elif isinstance(s, Atoms):
                atomic_numbers = s.get_atomic_numbers()
            else:
                atomic_numbers = s.atoms[:, 0]
            features[i] = np.bincount(atomic_numbers, minlength=self.max_z + 1)
        return features

    def fit(self, structs_or_graphs, properties):
        """
        Fit the elemental reference values for the properties
        Args:
            structs_or_graphs (list): list of graphs or structures
            properties (np.ndarray): array of extensive properties
        Returns:
        """
        features = self._get_feature_matrix(structs_or_graphs)
        self.property_per_element = np.linalg.pinv(features.T.dot(features)).dot(features.T.dot(properties))
        string_prop = ""
        for i, j in enumerate(self.property_per_element):
            if abs(j) > 1e-5:
                string_prop += f"{str(Element.from_Z(i))}: {j:.5f}"
        logger.info("Property offset values: " + string_prop)
        return True

    def transform(self, structs_or_graphs, properties):
        """
        Correct the extensive properties by subtracting the atom reference
        values
        Args:
            structs_or_graphs (list): list of graphs or structures
            properties (np.ndarray): array of extensive properties
        Returns: corrected property values

        """
        properties = np.array(properties)
        atom_properties = self.predict_properties(structs_or_graphs)
        return properties - np.reshape(atom_properties, properties.shape)

    def inverse_transform(self, structs_or_graphs, properties):
        """
        Take the transformed values and get the original values
        Args:
            structs_or_graphs (list): list of graphs or structures
            properties (np.ndarray): array of extensive properties
        Returns: corrected property values

        """
        properties = np.array(properties)
        property_atoms = self.predict_properties(structs_or_graphs)
        final_properties = properties + np.reshape(property_atoms, properties.shape)
        return final_properties

    def predict_properties(self, structs_or_graphs):
        """
        Args:
            structs_or_graphs (list): calculate the atom summed property
                values
        Returns:

        """
        if not isinstance(structs_or_graphs, list):
            structs_or_graphs = [structs_or_graphs]
        features = self._get_feature_matrix(structs_or_graphs)
        return features.dot(self.property_per_element)

    def call(self, graph: List, **kwargs):
        """
        Args:
            graph (list): a list repr of a graph
            **kwargs:
        Returns:
        """
        atomic_numbers = graph[Index.ATOMS][:, 0]
        atom_energies = tf.gather(tf.cast(self.property_per_element, DataType.tf_float), atomic_numbers)
        res = tf.math.segment_sum(atom_energies, get_segment_indices_from_n(graph[Index.N_ATOMS]))
        return tf.reshape(res, (-1, 1))

    def set_property_per_element(self, property_per_element):
        """
        Set the property per atom value
        Args:
            property_per_element (np.ndarray): array of elemental properties,
                the i-th row is the elemental value for atomic number i.
        Returns:
        """
        self.property_per_element = property_per_element

    def get_config(self):
        """
        Get dict config for serialization
        Returns (dict):
        """
        config = super().get_config()
        config.update(**{"property_per_element": self.property_per_element, "max_z": self.max_z})
        return config

"""
atomic reference. Used for predicting extensive properties.
"""

import logging
from typing import List, Optional

import numpy as np
import tensorflow as tf
from ase import Atoms
from pymatgen.core import Element, Molecule, Structure

from m3gnet.config import DataType
from m3gnet.graph import Index
from m3gnet.utils import get_segment_indices_from_n, register

logger = logging.getLogger(__name__)


@register
class BaseAtomRef(tf.keras.layers.Layer):
    """
    Base AtomRef that predicts 0 correction
    """

    def call(self, graph: List, **kwargs):
        """

        Args:
            graph (list): list repr of a graph
            **kwargs:

        Returns: 0
        """
        return 0.0


@register
class AtomRef(BaseAtomRef):
    """
    Atom reference values. For example, if the average H energy is -20.0, and
    the average O energy is -10.0, the AtomRef predicts -20 * 2 + (-10.) =
    -50.0 for the atom reference energy for H2O
    """

    def __init__(
        self,
        property_per_element: Optional[np.ndarray] = None,
        max_z: int = 94,
        **kwargs,
    ):
        """
        Args:
            property_per_element (np.ndarray): element reference value
            max_z (int): maximum atomic number
            **kwargs:
        """
        super().__init__(**kwargs)
        if property_per_element is None:
            self.property_per_element = np.zeros(shape=(max_z + 1,))
        else:
            self.property_per_element = np.array(property_per_element).ravel()
        self.max_z = max_z

    def _get_feature_matrix(self, structs_or_graphs):
        n = len(structs_or_graphs)
        features = np.zeros(shape=(n, self.max_z + 1))
        for i, s in enumerate(structs_or_graphs):
            if isinstance(s, (Structure, Molecule)):
                atomic_numbers = [i.specie.Z for i in s.sites]
            elif isinstance(s, (list, np.ndarray)):
                atomic_numbers = s
            elif isinstance(s, Atoms):
                atomic_numbers = s.get_atomic_numbers()
            else:
                atomic_numbers = s.atoms[:, 0]
            features[i] = np.bincount(atomic_numbers, minlength=self.max_z + 1)
        return features

    def fit(self, structs_or_graphs, properties):
        """
        Fit the elemental reference values for the properties
        Args:
            structs_or_graphs (list): list of graphs or structures
            properties (np.ndarray): array of extensive properties
        Returns:
        """
        features = self._get_feature_matrix(structs_or_graphs)
        self.property_per_element = np.linalg.pinv(features.T.dot(features)).dot(features.T.dot(properties))
        string_prop = ""
        for i, j in enumerate(self.property_per_element):
            if abs(j) > 1e-5:
                string_prop += f"{str(Element.from_Z(i))}: {j:.5f}"
        logger.info("Property offset values: " + string_prop)
        return True

    def transform(self, structs_or_graphs, properties):
        """
        Correct the extensive properties by subtracting the atom reference
        values
        Args:
            structs_or_graphs (list): list of graphs or structures
            properties (np.ndarray): array of extensive properties
        Returns: corrected property values

        """
        properties = np.array(properties)
        atom_properties = self.predict_properties(structs_or_graphs)
        return properties - np.reshape(atom_properties, properties.shape)

    def inverse_transform(self, structs_or_graphs, properties):
        """
        Take the transformed values and get the original values
        Args:
            structs_or_graphs (list): list of graphs or structures
            properties (np.ndarray): array of extensive properties
        Returns: corrected property values

        """
        properties = np.array(properties)
        property_atoms = self.predict_properties(structs_or_graphs)
        final_properties = properties + np.reshape(property_atoms, properties.shape)
        return final_properties

    def predict_properties(self, structs_or_graphs):
        """
        Args:
            structs_or_graphs (list): calculate the atom summed property
                values
        Returns:

        """
        if not isinstance(structs_or_graphs, list):
            structs_or_graphs = [structs_or_graphs]
        features = self._get_feature_matrix(structs_or_graphs)
        return features.dot(self.property_per_element)

    def call(self, graph: List, **kwargs):
        """
        Args:
            graph (list): a list repr of a graph
            **kwargs:
        Returns:
        """
        atomic_numbers = graph[Index.ATOMS][:, 0]
        atom_energies = tf.gather(tf.cast(self.property_per_element, DataType.tf_float), atomic_numbers)
        res = tf.math.segment_sum(atom_energies, get_segment_indices_from_n(graph[Index.N_ATOMS]))
        return tf.reshape(res, (-1, 1))

    def set_property_per_element(self, property_per_element):
        """
        Set the property per atom value
        Args:
            property_per_element (np.ndarray): array of elemental properties,
                the i-th row is the elemental value for atomic number i.
        Returns:
        """
        self.property_per_element = property_per_element

    def get_config(self):
        """
        Get dict config for serialization
        Returns (dict):
        """
        config = super().get_config()
        config.update(**{"property_per_element": self.property_per_element, "max_z": self.max_z})
        return config

atomic reference. Used for predicting extensive properties. Base AtomRef that predicts 0 correction Args:             graph (list): list repr of a graph             **kwargs:          Returns: 0 Atom reference values. For example, if the average H energy is -20.0, and     the average O energy is -10.0, the AtomRef predicts -20 * 2 + (-10.) =     -50.0 for the atom reference energy for H2O Args:             property_per_element (np.ndarray): element reference value             max_z (int): maximum atomic number             **kwargs: Fit the elemental reference values for the properties         Args:             structs_or_graphs (list): list of graphs or structures             properties (np.ndarray): array of extensive properties         Returns: Correct the extensive properties by subtracting the atom reference         values         Args:             structs_or_graphs (list): list of graphs or structures             properties (np.ndarray): array of extensive properties         Returns: corrected property values Take the transformed values and get the original values         Args:             structs_or_graphs (list): list of graphs or structures             properties (np.ndarray): array of extensive properties         Returns: corrected property values Args:             structs_or_graphs (list): calculate the atom summed property                 values         Returns: Args:             graph (list): a list repr of a graph             **kwargs:         Returns: Set the property per atom value         Args:             property_per_element (np.ndarray): array of elemental properties,                 the i-th row is the elemental value for atomic number i.         Returns: Get dict config for serialization         Returns (dict):