# Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import math
from typing import Optional, Callable, List, Tuple, Sequence
import numpy as np

import torch
import torch.nn as nn
from scipy.stats import truncnorm

from openfold.utils.tensor_utils import (
    permute_final_dims,
    flatten_final_dims,
    _chunk_slice,
)


def _prod(nums):
    out = 1
    for n in nums:
        out = out * n
    return out


def _calculate_fan(linear_weight_shape, fan="fan_in"):
    fan_out, fan_in = linear_weight_shape

    if fan == "fan_in":
        f = fan_in
    elif fan == "fan_out":
        f = fan_out
    elif fan == "fan_avg":
        f = (fan_in + fan_out) / 2
    else:
        raise ValueError("Invalid fan option")

    return f


def trunc_normal_init_(weights, scale=1.0, fan="fan_in"):
    shape = weights.shape
    f = _calculate_fan(shape, fan)
    scale = scale / max(1, f)
    a = -2
    b = 2
    std = math.sqrt(scale) / truncnorm.std(a=a, b=b, loc=0, scale=1)
    size = _prod(shape)
    samples = truncnorm.rvs(a=a, b=b, loc=0, scale=std, size=size)
    samples = np.reshape(samples, shape)
    with torch.no_grad():
        weights.copy_(torch.tensor(samples, device=weights.device))


def lecun_normal_init_(weights):
    trunc_normal_init_(weights, scale=1.0)


def he_normal_init_(weights):
    trunc_normal_init_(weights, scale=2.0)


def glorot_uniform_init_(weights):
    nn.init.xavier_uniform_(weights, gain=1)


def final_init_(weights):
    with torch.no_grad():
        weights.fill_(0.0)


def gating_init_(weights):
    with torch.no_grad():
        weights.fill_(0.0)


def normal_init_(weights):
    torch.nn.init.kaiming_normal_(weights, nonlinearity="linear")


def ipa_point_weights_init_(weights):
    with torch.no_grad():
        softplus_inverse_1 = 0.541324854612918
        weights.fill_(softplus_inverse_1)


class Linear(nn.Linear):
    """
    A Linear layer with built-in nonstandard initializations. Called just
    like torch.nn.Linear.

    Implements the initializers in 1.11.4, plus some additional ones found
    in the code.
    """

    def __init__(
        self,
        in_dim: int,
        out_dim: int,
        bias: bool = True,
        init: str = "default",
        init_fn: Optional[Callable[[torch.Tensor, torch.Tensor], None]] = None,
    ):
        """
        Args:
            in_dim:
                The final dimension of inputs to the layer
            out_dim:
                The final dimension of layer outputs
            bias:
                Whether to learn an additive bias. True by default
            init:
                The initializer to use. Choose from:

                "default": LeCun fan-in truncated normal initialization
                "relu": He initialization w/ truncated normal distribution
                "glorot": Fan-average Glorot uniform initialization
                "gating": Weights=0, Bias=1
                "normal": Normal initialization with std=1/sqrt(fan_in)
                "final": Weights=0, Bias=0

                Overridden by init_fn if the latter is not None.
            init_fn:
                A custom initializer taking weight and bias as inputs.
                Overrides init if not None.
        """
        super(Linear, self).__init__(in_dim, out_dim, bias=bias)

        if bias:
            with torch.no_grad():
                self.bias.fill_(0)

        if init_fn is not None:
            init_fn(self.weight, self.bias)
        else:
            if init == "default":
                lecun_normal_init_(self.weight)
            elif init == "relu":
                he_normal_init_(self.weight)
            elif init == "glorot":
                glorot_uniform_init_(self.weight)
            elif init == "gating":
                gating_init_(self.weight)
                if bias:
                    with torch.no_grad():
                        self.bias.fill_(1.0)
            elif init == "normal":
                normal_init_(self.weight)
            elif init == "final":
                final_init_(self.weight)
            else:
                raise ValueError("Invalid init string.")


class Attention(nn.Module):
    """
    Standard multi-head attention using AlphaFold's default layer
    initialization. Allows multiple bias vectors.
    """
    def __init__(
        self,
        c_q: int,
        c_k: int,
        c_v: int,
        c_hidden: int,
        no_heads: int,
        gating: bool = True,
    ):
        """
        Args:
            c_q:
                Input dimension of query data
            c_k:
                Input dimension of key data
            c_v:
                Input dimension of value data
            c_hidden:
                Per-head hidden dimension
            no_heads:
                Number of attention heads
            gating:
                Whether the output should be gated using query data
        """
        super(Attention, self).__init__()

        self.c_q = c_q
        self.c_k = c_k
        self.c_v = c_v
        self.c_hidden = c_hidden
        self.no_heads = no_heads
        self.gating = gating

        # DISCREPANCY: c_hidden is not the per-head channel dimension, as
        # stated in the supplement, but the overall channel dimension.

        self.linear_q = Linear(
            self.c_q, self.c_hidden * self.no_heads, bias=False, init="glorot"
        )
        self.linear_k = Linear(
            self.c_k, self.c_hidden * self.no_heads, bias=False, init="glorot"
        )
        self.linear_v = Linear(
            self.c_v, self.c_hidden * self.no_heads, bias=False, init="glorot"
        )
        self.linear_o = Linear(
            self.c_hidden * self.no_heads, self.c_q, init="final"
        )

        self.linear_g = None
        if self.gating:
            self.linear_g = Linear(
                self.c_q, self.c_hidden * self.no_heads, init="gating"
            )

        self.sigmoid = nn.Sigmoid()
        self.softmax = nn.Softmax(dim=-1)

    def forward(
        self,
        q_x: torch.Tensor,
        k_x: torch.Tensor,
        v_x: torch.Tensor,
        biases: Optional[List[torch.Tensor]] = None,
    ) -> torch.Tensor:
        """
        Args:
            q_x:
                [*, Q, C_q] query data
            k_x:
                [*, K, C_k] key data
            v_x:
                [*, V, C_v] value data
        Returns
            [*, Q, C_q] attention update
        """
        # [*, Q/K/V, H * C_hidden]
        q = self.linear_q(q_x)
        k = self.linear_k(k_x)
        v = self.linear_v(v_x)

        # [*, Q/K, H, C_hidden]
        q = q.view(q.shape[:-1] + (self.no_heads, -1))
        k = k.view(k.shape[:-1] + (self.no_heads, -1))
        v = v.view(v.shape[:-1] + (self.no_heads, -1))

        # [*, H, Q, C_hidden]
        q = permute_final_dims(q, (1, 0, 2))

        # [*, H, C_hidden, K]
        k = permute_final_dims(k, (1, 2, 0))

        # [*, H, Q, K]
        a = torch.matmul(q, k)

        del q, k

        norm = 1 / math.sqrt(self.c_hidden)  # [1]
        a *= norm

        if biases is not None:
            for b in biases:
                a += b

        a = self.softmax(a)

        # [*, H, V, C_hidden]
        v = permute_final_dims(v, (1, 0, 2))

        # [*, H, Q, C_hidden]
        o = torch.matmul(a, v)

        # [*, Q, H, C_hidden]
        o = o.transpose(-2, -3)
        if(self.linear_g is not None):
            g = self.sigmoid(self.linear_g(q_x))
            # [*, Q, H, C_hidden]
            g = g.view(g.shape[:-1] + (self.no_heads, -1))
            o = o * g

        # [*, Q, H * C_hidden]
        o = flatten_final_dims(o, 2)

        # [*, Q, C_q]
        o = self.linear_o(o)

        return o


class GlobalAttention(nn.Module):
    def __init__(self, c_in, c_hidden, no_heads, inf, eps):
        super(GlobalAttention, self).__init__()

        self.c_in = c_in
        self.c_hidden = c_hidden
        self.no_heads = no_heads
        self.inf = inf
        self.eps = eps

        self.linear_q = Linear(
            c_in, c_hidden * no_heads, bias=False, init="glorot"
        )

        self.linear_k = Linear(
            c_in, c_hidden, bias=False, init="glorot",
        )
        self.linear_v = Linear(
            c_in, c_hidden, bias=False, init="glorot",
        )
        self.linear_g = Linear(c_in, c_hidden * no_heads, init="gating")
        self.linear_o = Linear(c_hidden * no_heads, c_in, init="final")

        self.sigmoid = nn.Sigmoid()
        self.softmax = nn.Softmax(dim=-1)

    def forward(self, m: torch.Tensor, mask: torch.Tensor) -> torch.Tensor:
        # [*, N_res, C_in]
        q = torch.sum(m * mask.unsqueeze(-1), dim=-2) / (
            torch.sum(mask, dim=-1)[..., None] + self.eps
        )

        # [*, N_res, H * C_hidden]
        q = self.linear_q(q)
        q = q * (self.c_hidden ** (-0.5))

        # [*, N_res, H, C_hidden]
        q = q.view(q.shape[:-1] + (self.no_heads, -1))

        # [*, N_res, N_seq, C_hidden]
        k = self.linear_k(m)
        v = self.linear_v(m)

        # [*, N_res, H, N_seq]
        a = torch.matmul(
            q,
            k.transpose(-1, -2),  # [*, N_res, C_hidden, N_seq]
        )
        bias = (self.inf * (mask - 1))[..., :, None, :]
        a = a + bias
        a = self.softmax(a)

        # [*, N_res, H, C_hidden]
        o = torch.matmul(
            a,
            v,
        )

        # [*, N_res, N_seq, C_hidden]
        g = self.sigmoid(self.linear_g(m))

        # [*, N_res, N_seq, H, C_hidden]
        g = g.view(g.shape[:-1] + (self.no_heads, -1))

        # [*, N_res, N_seq, H, C_hidden]
        o = o.unsqueeze(-3) * g

        # [*, N_res, N_seq, H * C_hidden]
        o = o.reshape(o.shape[:-2] + (-1,))

        # [*, N_res, N_seq, C_in]
        m = self.linear_o(o)

        return m


@torch.jit.script
def _lma(
    q: torch.Tensor, 
    k: torch.Tensor, 
    v: torch.Tensor, 
    biases: List[torch.Tensor], 
    q_chunk_size: int, 
    kv_chunk_size: int
):
    no_q, no_kv = q.shape[-3], k.shape[-3]

    # [*, Q, H, C_hidden]
    o = q.new_zeros(q.shape)
    for q_s in range(0, no_q, q_chunk_size):
        q_chunk = q[..., q_s: q_s + q_chunk_size, :, :]
        big_bias_chunks = [
            b[..., q_s: q_s + q_chunk_size, :] for b in biases
        ] 
        
        maxes = []
        weights = []
        values = []
        for kv_s in range(0, no_kv, kv_chunk_size):
            k_chunk = k[..., kv_s: kv_s + kv_chunk_size, :, :]
            v_chunk = v[..., kv_s: kv_s + kv_chunk_size, :, :] 
            small_bias_chunks = [
                b[..., kv_s: kv_s + kv_chunk_size] for b in big_bias_chunks
            ]

            a = torch.einsum(
                "...qhd,...khd->...hqk", q_chunk, k_chunk
            )
        
            for b in small_bias_chunks:
                a += b
        
            a = a.transpose(-2, -3)
  
            max_a = torch.max(a, dim=-1, keepdim=True)[0].detach()
            exp_a = torch.exp(a - max_a)
            exp_v = torch.einsum("...vhf,...qhv->...qhf", v_chunk, exp_a)

            maxes.append(max_a.squeeze(-1))
            weights.append(torch.sum(exp_a, dim=-1))
            values.append(exp_v)

        chunk_max = torch.stack(maxes, dim=-3)
        chunk_weights = torch.stack(weights, dim=-3)
        chunk_values = torch.stack(values, dim=-4)

        global_max = torch.max(chunk_max, dim=-3, keepdim=True)[0]
        max_diffs = torch.exp(chunk_max - global_max)
        chunk_values *= max_diffs.unsqueeze(-1)
        chunk_weights *= max_diffs

        all_values = torch.sum(chunk_values, dim=-4)
        all_weights = torch.sum(chunk_weights.unsqueeze(-1), dim=-4)

        q_chunk_out = all_values / all_weights

        o[..., q_s: q_s + q_chunk_size, :, :] = q_chunk_out

    return o


class LowMemoryAttention(nn.Module):
    """
    Standard multi-head attention using AlphaFold's default layer
    initialization. Allows multiple bias vectors. Implements Rabe and Staats'
    low-memory self-attention algorithm.
    """
    def __init__(
        self,
        c_q: int,
        c_k: int,
        c_v: int,
        c_hidden: int,
        no_heads: int,
        gating: bool = True,
    ):
        """
        Args:
            c_q:
                Input dimension of query data
            c_k:
                Input dimension of key data
            c_v:
                Input dimension of value data
            c_hidden:
                Per-head hidden dimension
            no_heads:
                Number of attention heads
            gating:
                Whether the output should be gated using query data
            chunk_size:
                Trades memory for better parallelization. A low value
                corresponds to lower memory usage.
        """
        super().__init__()

        self.c_q = c_q
        self.c_k = c_k
        self.c_v = c_v
        self.c_hidden = c_hidden
        self.no_heads = no_heads
        self.gating = gating

        self.linear_q = Linear(
            self.c_q, self.c_hidden * self.no_heads, bias=False, init="glorot"
        )
        self.linear_k = Linear(
            self.c_k, self.c_hidden * self.no_heads, bias=False, init="glorot"
        )
        self.linear_v = Linear(
            self.c_v, self.c_hidden * self.no_heads, bias=False, init="glorot"
        )
        self.linear_o = Linear(
            self.c_hidden * self.no_heads, self.c_q, init="final"
        )

        if self.gating:
            self.linear_g = Linear(
                self.c_q, self.c_hidden * self.no_heads, init="gating"
            )

        self.sigmoid = nn.Sigmoid()
        self.softmax = nn.Softmax(dim=-1)

    def forward(self, 
        q_x: torch.Tensor,
        k_x: torch.Tensor,
        v_x: torch.Tensor,
        q_chunk_size: int,
        kv_chunk_size: int,
        biases: Optional[List[torch.Tensor]] = None,
    ):
        if(biases is None):
            biases = []
        else:
            biases = [
                b.expand(b.shape[:-2] + (q_x.shape[-2],) + (k_x.shape[-2],)) 
                for b in biases
            ]

        # [*, Q/K/V, H * C_hidden]
        q = self.linear_q(q_x)
        k = self.linear_k(k_x)
        v = self.linear_v(v_x)

        # [*, Q/K, H, C_hidden]
        q = q.view(q.shape[:-1] + (self.no_heads, -1))
        k = k.view(k.shape[:-1] + (self.no_heads, -1))
        v = v.view(v.shape[:-1] + (self.no_heads, -1))

        q = q / math.sqrt(q.shape[-1])

        o = _lma(q, k, v, biases, q_chunk_size, kv_chunk_size)

        if self.gating:
            g = self.sigmoid(self.linear_g(q_x))
            # [*, Q, H, C_hidden]
            g = g.view(g.shape[:-1] + (self.no_heads, -1))
            o = o * g

        # [*, Q, H * C_hidden]
        o = flatten_final_dims(o, 2)

        # [*, Q, C_q]
        o = self.linear_o(o)

        return o
