model.py

import torch
from torch import nn
from torch.nn import functional as F
from torchvision import datasets
from torch.optim.lr_scheduler import StepLR
from torch.utils.tensorboard import SummaryWriter
from torchvision import datasets, transforms
import torch.utils.data as data_utils
from torch.autograd import Variable
import pickle
from sklearn.model_selection import train_test_split
import math
import os           
import re
import collections
from functools import partial
from torch.utils import model_zoo
from torch import optim

KERNEL_SIZE = 3


# Author: lukemelas (github username)
# Github repo: https://github.com/lukemelas/EfficientNet-PyTorch
# With adjustments and added comments by workingcoder (github username).


class MBConvBlock(nn.Module):
    """
    Mobile Inverted Residual Bottleneck Block
    Args:
        block_args (namedtuple): BlockArgs, see above
        global_params (namedtuple): GlobalParam, see above
    Attributes:
        has_se (bool): Whether the block contains a Squeeze and Excitation layer.
    """

    def __init__(self, block_args, global_params):
        super().__init__()
        self._block_args = block_args
        self._bn_mom = 1 - global_params.batch_norm_momentum
        self._bn_eps = global_params.batch_norm_epsilon
        self.has_se = (self._block_args.se_ratio is not None) and (0 < self._block_args.se_ratio <= 1)
        self.id_skip = block_args.id_skip  # skip connection and drop connect

        # Get static or dynamic convolution depending on image size
        Conv2d = get_same_padding_conv2d(image_size=global_params.image_size)

        # Expansion phase
        inp = self._block_args.input_filters  # number of input channels
        oup = self._block_args.input_filters * self._block_args.expand_ratio  # number of output channels
        if self._block_args.expand_ratio != 1:
            self._expand_conv = Conv2d(in_channels=inp, out_channels=oup, kernel_size=KERNEL_SIZE, bias=False)
            self._bn0 = nn.BatchNorm2d(num_features=oup, momentum=self._bn_mom, eps=self._bn_eps)

        # Depthwise convolution phase
        k = self._block_args.kernel_size
        s = self._block_args.stride
        self._depthwise_conv = Conv2d(
            in_channels=oup, out_channels=oup, groups=oup,  # groups makes it depthwise
            kernel_size=k, stride=s, bias=False)
        self._bn1 = nn.BatchNorm2d(num_features=oup, momentum=self._bn_mom, eps=self._bn_eps)

        # Squeeze and Excitation layer, if desired
        if self.has_se:
            num_squeezed_channels = max(1, int(self._block_args.input_filters * self._block_args.se_ratio))
            self._se_reduce = Conv2d(in_channels=oup, out_channels=num_squeezed_channels, kernel_size=KERNEL_SIZE)
            self._se_expand = Conv2d(in_channels=num_squeezed_channels, out_channels=oup, kernel_size=KERNEL_SIZE)

        # Output phase
        final_oup = self._block_args.output_filters
        self._project_conv = Conv2d(in_channels=oup, out_channels=final_oup, kernel_size=KERNEL_SIZE, bias=False)
        self._bn2 = nn.BatchNorm2d(num_features=final_oup, momentum=self._bn_mom, eps=self._bn_eps)
        self._mish = Mish()

    def forward(self, inputs, drop_connect_rate=None):
        """
        :param inputs: input tensor
        :param drop_connect_rate: drop connect rate (float, between 0 and 1)
        :return: output of block
        """

        # Expansion and Depthwise Convolution
        x = inputs
        if self._block_args.expand_ratio != 1:
            x = self._mish(self._bn0(self._expand_conv(inputs)))
        x = self._mish(self._bn1(self._depthwise_conv(x)))

        # Squeeze and Excitation
        if self.has_se:
            x_squeezed = F.adaptive_avg_pool2d(x, 1)
            x_squeezed = self._se_expand(self._mish(self._se_reduce(x_squeezed)))
            x = torch.sigmoid(x_squeezed) * x

        x = self._bn2(self._project_conv(x))

        # Skip connection and drop connect
        input_filters, output_filters = self._block_args.input_filters, self._block_args.output_filters
        if self.id_skip and self._block_args.stride == 1 and input_filters == output_filters:
            if drop_connect_rate:
                x = drop_connect(x, p=drop_connect_rate, training=self.training)
            x = x + inputs  # skip connection
        return x



global allele
allele = ''


class DeepNeo(nn.Module):
    """
    An DeepNeo model. Most easily loaded with the .from_name
    Args:
        blocks_args (list): A list of BlockArgs to construct blocks
        global_params (namedtuple): A set of GlobalParams shared between blocks
    Example:
        model = DeepNeo.from_pretrained('DeepNeo-b0')
    """


    def __init__(self, blocks_args=None, global_params=None):
        super().__init__()
        assert isinstance(blocks_args, list), 'blocks_args should be a list'
        assert len(blocks_args) > 0, 'block args must be greater than 0'
        self._global_params = global_params
        self._blocks_args = blocks_args

        # Get static or dynamic convolution depending on image size
        Conv2d = get_same_padding_conv2d(image_size=global_params.image_size)

        # Batch norm parameters
        bn_mom = 1 - self._global_params.batch_norm_momentum
        bn_eps = self._global_params.batch_norm_epsilon

        # Stem
        in_channels = 1  # 2D matrix has 1 channels
        out_channels = round_filters(3, self._global_params)  # number of output channels
        self._conv_stem = Conv2d(in_channels, out_channels, kernel_size=3, stride=2, bias=False)
        self._bn0 = nn.BatchNorm2d(num_features=out_channels, momentum=bn_mom, eps=bn_eps)

        # Build blocks
        self._blocks = nn.ModuleList([])
        for block_args in self._blocks_args:

            # Update block input and output filters based on depth multiplier.
            block_args = block_args._replace(
                input_filters=round_filters(block_args.input_filters, self._global_params),
                output_filters=round_filters(block_args.output_filters, self._global_params),
                num_repeat=round_repeats(block_args.num_repeat, self._global_params)
            )

            # The first block needs to take care of stride and filter size increase.
            self._blocks.append(MBConvBlock(block_args, self._global_params))
            if block_args.num_repeat > 1:
                block_args = block_args._replace(input_filters=block_args.output_filters, stride=1)
            for _ in range(block_args.num_repeat - 1):
                self._blocks.append(MBConvBlock(block_args, self._global_params))

        # Head
        in_channels = block_args.output_filters  # output of final block maybe 16?
        out_channels = round_filters(3, self._global_params)
        self._conv_head = Conv2d(in_channels, out_channels, kernel_size=KERNEL_SIZE, bias=False)
        self._bn1 = nn.BatchNorm2d(num_features=out_channels, momentum=bn_mom, eps=bn_eps)

        # Final linear layer
        self._avg_pooling = nn.AdaptiveAvgPool2d(1)
        self._dropout = nn.Dropout(self._global_params.dropout_rate)
        self._fc = nn.Linear(out_channels, self._global_params.num_classes)
        self._mish = Mish()

    def extract_features(self, inputs):
        """ Returns output of the final convolution layer """

        # Stem
        x = self._mish(self._bn0(self._conv_stem(inputs)))

        # Blocks
        for idx, block in enumerate(self._blocks):
            drop_connect_rate = self._global_params.drop_connect_rate
            if drop_connect_rate:
                drop_connect_rate *= float(idx) / len(self._blocks)
            x = block(x, drop_connect_rate=drop_connect_rate)

        # Head
        x = self._mish(self._bn1(self._conv_head(x)))

        return x

    def forward(self, inputs):
        """ Calls extract_features to extract features, applies final linear layer, and returns logits. """
        #bs = inputs.size(0)
        #print(bs)
        # Convolution layers
        x = self.extract_features(inputs)

        # Pooling and final linear layer
        x = self._avg_pooling(x)
        #x = x.view(bs, -1)
        #print(x.shape)
        
        x = x.flatten(start_dim=1)
        x = self._dropout(x)
        x = self._fc(x)

        return torch.sigmoid(x)

    @classmethod
    def from_name(cls, model_name, override_params=None):
        #cls._check_model_name_is_valid(model_name)
        global allele
        allele = model_name
        blocks_args, global_params = get_model_params(model_name, override_params)
        return cls(blocks_args, global_params)

    @classmethod
    def from_pretrained(cls, model_name, advprop=False, num_classes=1, in_channels=1):
        model = cls.from_name(model_name, override_params={'num_classes': num_classes})
        load_pretrained_weights(model, model_name, load_fc=(num_classes == 1000), advprop=advprop)
        if in_channels != 3:
            Conv2d = get_same_padding_conv2d(image_size=model._global_params.image_size)
            out_channels = round_filters(32, model._global_params)
            model._conv_stem = Conv2d(in_channels, out_channels, kernel_size=3, stride=2, bias=False)
        return model
    
    @classmethod
    def get_image_size(cls, model_name):
        cls._check_model_name_is_valid(model_name)
        _, _, res, _ = deepneo_params(model_name)
        return res

    @classmethod
    def _check_model_name_is_valid(cls, model_name):
        """ Validates model name. """ 
        valid_models = ['efficientnet-b'+str(i) for i in range(9)]
        if model_name not in valid_models:
            raise ValueError('model_name should be one of: ' + ', '.join(valid_models))
            
            


########################################################################
############### HELPERS FUNCTIONS FOR MODEL ARCHITECTURE ###############
########################################################################


# Parameters for the entire model (stem, all blocks, and head)
GlobalParams = collections.namedtuple('GlobalParams', [
    'batch_norm_momentum', 'batch_norm_epsilon', 'dropout_rate',
    'num_classes', 'width_coefficient', 'depth_coefficient',
    'depth_divisor', 'min_depth', 'drop_connect_rate', 'image_size'])

# Parameters for an individual model block
BlockArgs = collections.namedtuple('BlockArgs', [
    'kernel_size', 'num_repeat', 'input_filters', 'output_filters',
    'expand_ratio', 'id_skip', 'stride', 'se_ratio'])

# Change namedtuple defaults
GlobalParams.__new__.__defaults__ = (None,) * len(GlobalParams._fields)
BlockArgs.__new__.__defaults__ = (None,) * len(BlockArgs._fields)


class SwishImplementation(torch.autograd.Function):
    @staticmethod
    def forward(ctx, i):
        result = i * torch.sigmoid(i)
        ctx.save_for_backward(i)
        return result

    @staticmethod
    def backward(ctx, grad_output):
        i = ctx.saved_variables[0]
        sigmoid_i = torch.sigmoid(i)
        return grad_output * (sigmoid_i * (1 + i * (1 - sigmoid_i)))
    
    
class Mish(nn.Module):
    def __init__(self):
        super().__init__()

    def forward(self, x):
        return x * (torch.tanh(F.softplus(x)))


class MemoryEfficientSwish(nn.Module):
    def forward(self, x):
        return SwishImplementation.apply(x)


class Swish(nn.Module):
    def forward(self, x):
        return x * torch.sigmoid(x)


def round_filters(filters, global_params):
    """ Calculate and round number of filters based on depth multiplier. """
    multiplier = global_params.width_coefficient
    if not multiplier:
        return filters
    divisor = global_params.depth_divisor
    min_depth = global_params.min_depth
    filters *= multiplier
    min_depth = min_depth or divisor
    new_filters = max(min_depth, int(filters + divisor / 2) // divisor * divisor)
    if new_filters < 0.9 * filters:  # prevent rounding by more than 10%
        new_filters += divisor
    return int(new_filters)


def round_repeats(repeats, global_params):
    """ Round number of filters based on depth multiplier. """
    multiplier = global_params.depth_coefficient
    if not multiplier:
        return repeats
    return int(math.ceil(multiplier * repeats))


def drop_connect(inputs, p, training):
    """ Drop connect. """
    if not training: return inputs
    batch_size = inputs.shape[0]
    keep_prob = 1 - p
    random_tensor = keep_prob
    random_tensor += torch.rand([batch_size, 1, 1, 1], dtype=inputs.dtype, device=inputs.device)
    binary_tensor = torch.floor(random_tensor)
    output = inputs / keep_prob * binary_tensor
    return output


def get_same_padding_conv2d(image_size=None):
    """ Chooses static padding if you have specified an image size, and dynamic padding otherwise.
        Static padding is necessary for ONNX exporting of models. """
    if image_size is None:
        return Conv2dDynamicSamePadding
    else:
        return partial(Conv2dStaticSamePadding, image_size=image_size)


class Conv2dDynamicSamePadding(nn.Conv2d):
    """ 2D Convolutions like TensorFlow, for a dynamic image size """

    def __init__(self, in_channels, out_channels, kernel_size, stride=1, dilation=1, groups=1, bias=True):
        super().__init__(in_channels, out_channels, kernel_size, stride, 0, dilation, groups, bias)
        self.stride = self.stride if len(self.stride) == 2 else [self.stride[0]] * 2

    def forward(self, x):
        ih, iw = x.size()[-2:]
        kh, kw = self.weight.size()[-2:]
        sh, sw = self.stride
        oh, ow = math.ceil(ih / sh), math.ceil(iw / sw)
        pad_h = max((oh - 1) * self.stride[0] + (kh - 1) * self.dilation[0] + 1 - ih, 0)
        pad_w = max((ow - 1) * self.stride[1] + (kw - 1) * self.dilation[1] + 1 - iw, 0)
        if pad_h > 0 or pad_w > 0:
            x = F.pad(x, [pad_w // 2, pad_w - pad_w // 2, pad_h // 2, pad_h - pad_h // 2])
        return F.conv2d(x, self.weight, self.bias, self.stride, self.padding, self.dilation, self.groups)


class Conv2dStaticSamePadding(nn.Conv2d):
    """ 2D Convolutions like TensorFlow, for a fixed image size"""

    def __init__(self, in_channels, out_channels, kernel_size, image_size=None, **kwargs):
        super().__init__(in_channels, out_channels, kernel_size, **kwargs)
        self.stride = self.stride if len(self.stride) == 2 else [self.stride[0]] * 2

        # Calculate padding based on image size and save it
        assert image_size is not None
        ih, iw = image_size if type(image_size) == list else [image_size, image_size]
        kh, kw = self.weight.size()[-2:]
        sh, sw = self.stride
        oh, ow = math.ceil(ih / sh), math.ceil(iw / sw)
        pad_h = max((oh - 1) * self.stride[0] + (kh - 1) * self.dilation[0] + 1 - ih, 0)
        pad_w = max((ow - 1) * self.stride[1] + (kw - 1) * self.dilation[1] + 1 - iw, 0)
        if pad_h > 0 or pad_w > 0:
            self.static_padding = nn.ZeroPad2d((pad_w // 2, pad_w - pad_w // 2, pad_h // 2, pad_h - pad_h // 2))
        else:
            self.static_padding = Identity()

    def forward(self, x):
        x = self.static_padding(x)
        x = F.conv2d(x, self.weight, self.bias, self.stride, self.padding, self.dilation, self.groups)
        return x


class Identity(nn.Module):
    def __init__(self, ):
        super(Identity, self).__init__()

    def forward(self, input):
        return input


########################################################################
############## HELPERS FUNCTIONS FOR LOADING MODEL PARAMS ##############
########################################################################


def deepneo_params(model_name):
    """ Map DeepNeo model name to parameter coefficients. """
    params_dict = {
        # Coefficients:   width,depth,res,dropout
        'DeepNeo-HLA-A-9': (1.0, 1.0, [365,9], 0.2),
        'DeepNeo-HLA-B-9': (1.0, 1.0, [326,9], 0.2),
        'DeepNeo-HLA-C-9': (1.0, 1.0, [338,9], 0.2),
        'DeepNeo-HLA-A-10': (1.0, 1.0, [365,10], 0.2),
        'DeepNeo-HLA-B-10': (1.0, 1.0, [326,10], 0.2),
        'DeepNeo-HLA-C-10': (1.0, 1.0, [338,10], 0.2),
        'DeepNeo-HLA-A-9-short': (1.0, 1.0, [276,9], 0.2),
        'DeepNeo-HLA-B-9-short': (1.0, 1.0, [252,9], 0.2),
        'DeepNeo-HLA-C-9-short': (1.0, 1.0, [268,9], 0.2),
        'DeepNeo-HLA-A-10-short': (1.0, 1.0, [276,10], 0.2),
        'DeepNeo-HLA-B-10-short': (1.0, 1.0, [252,10], 0.2),
        'DeepNeo-HLA-C-10-short': (1.0, 1.0, [268,10], 0.2),
    }
    return params_dict[model_name]
        

class BlockDecoder(object):
    """ Block Decoder for readability, straight from the official TensorFlow repository """

    @staticmethod
    def _decode_block_string(block_string):
        """ Gets a block through a string notation of arguments. """
        assert isinstance(block_string, str)

        ops = block_string.split('_')
        options = {}
        for op in ops:
            splits = re.split(r'(\d.*)', op)
            if len(splits) >= 2:
                key, value = splits[:2]
                options[key] = value

        # Check stride
        assert (('s' in options and len(options['s']) == 1) or
                (len(options['s']) == 2 and options['s'][0] == options['s'][1]))

        return BlockArgs(
            kernel_size=int(options['k']),
            num_repeat=int(options['r']),
            input_filters=int(options['i']),
            output_filters=int(options['o']),
            expand_ratio=int(options['e']),
            id_skip=('noskip' not in block_string),
            se_ratio=float(options['se']) if 'se' in options else None,
            stride=[int(options['s'][0])])

    @staticmethod
    def _encode_block_string(block):
        """Encodes a block to a string."""
        args = [
            'r%d' % block.num_repeat,
            'k%d' % block.kernel_size,
            's%d%d' % (block.strides[0], block.strides[1]),
            'e%s' % block.expand_ratio,
            'i%d' % block.input_filters,
            'o%d' % block.output_filters
        ]
        if 0 < block.se_ratio <= 1:
            args.append('se%s' % block.se_ratio)
        if block.id_skip is False:
            args.append('noskip')
        return '_'.join(args)

    @staticmethod
    def decode(string_list):
        """
        Decodes a list of string notations to specify blocks inside the network.
        :param string_list: a list of strings, each string is a notation of block
        :return: a list of BlockArgs namedtuples of block args
        """
        assert isinstance(string_list, list)
        blocks_args = []
        for block_string in string_list:
            blocks_args.append(BlockDecoder._decode_block_string(block_string))
        return blocks_args

    @staticmethod
    def encode(blocks_args):
        """
        Encodes a list of BlockArgs to a list of strings.
        :param blocks_args: a list of BlockArgs namedtuples of block args
        :return: a list of strings, each string is a notation of block
        """
        block_strings = []
        for block in blocks_args:
            block_strings.append(BlockDecoder._encode_block_string(block))
        return block_strings


def efficientnet(width_coefficient=None, depth_coefficient=None, dropout_rate=0.2,
                 drop_connect_rate=0.2, image_size=None, num_classes=1):
    """ Creates a efficientnet model. """

    blocks_args = [
        'r1_k3_s11_e1_i1_o8_se0.25', 
        'r2_k3_s22_e6_i8_o16_se0.25',
        #'r2_k5_s22_e6_i24_o40_se0.25', 
        #'r3_k3_s22_e6_i40_o80_se0.25',
        #'r3_k5_s11_e6_i80_o112_se0.25', 
        #'r4_k5_s22_e6_i112_o192_se0.25',
        #'r1_k3_s11_e6_i192_o320_se0.25',
        #'r1_k3_s11_e6_i24_o48_se0.25',
    ]
    blocks_args = BlockDecoder.decode(blocks_args)

    global_params = GlobalParams(
        batch_norm_momentum=0.99,
        batch_norm_epsilon=1e-3,
        dropout_rate=dropout_rate,
        drop_connect_rate=drop_connect_rate,
        # data_format='channels_last',  # removed, this is always true in PyTorch
        num_classes=num_classes,
        width_coefficient=width_coefficient,
        depth_coefficient=depth_coefficient,
        depth_divisor=8,
        min_depth=None,
        image_size=image_size,
    )

    return blocks_args, global_params


def get_model_params(model_name, override_params):
    """ Get the block args and global params for a given model """
    if model_name.startswith('efficientnet'):
        w, d, s, p = deepneo_params(model_name)
        # note: all models have drop connect rate = 0.2
        blocks_args, global_params = efficientnet(
            width_coefficient=w, depth_coefficient=d, dropout_rate=p, image_size=s)
    else:
        raise NotImplementedError('model name is not pre-defined: %s' % model_name)
    if override_params:
        # ValueError will be raised here if override_params has fields not included in global_params.
        global_params = global_params._replace(**override_params)
    return blocks_args, global_params