import numpy as np

import data_transforms

import data_iterators

import pathfinder

import lasagne as nn

from collections import namedtuple

from functools import partial

import lasagne.layers.dnn as dnn

import theano.tensor as T

import utils

import nn_lung

restart_from_save = None

rng = np.random.RandomState(42)

# transformations

p_transform = {'patch_size': (64, 64, 64),

               'mm_patch_size': (64, 64, 64),

               'pixel_spacing': (1., 1., 1.)

               }

p_transform_augment = {

    'translation_range_z': [-27, 27],

    'translation_range_y': [-27, 27],

    'translation_range_x': [-27, 27],

    'rotation_range_z': [-180, 180],

    'rotation_range_y': [-180, 180],

    'rotation_range_x': [-180, 180]

}

# data preparation function

def data_prep_function(data, patch_center, luna_annotations, pixel_spacing, luna_origin, p_transform,

                       p_transform_augment, **kwargs):

    x, patch_annotation_tf, annotations_tf = data_transforms.transform_patch3d(data=data,

                                                                               luna_annotations=luna_annotations,

                                                                               patch_center=patch_center,

                                                                               p_transform=p_transform,

                                                                               p_transform_augment=p_transform_augment,

                                                                               pixel_spacing=pixel_spacing,

                                                                               luna_origin=luna_origin)

    x = data_transforms.hu2normHU(x)

    y = data_transforms.make_3d_mask_from_annotations(img_shape=x.shape, annotations=annotations_tf, shape='sphere')

    return x, y

data_prep_function_train = partial(data_prep_function, p_transform_augment=p_transform_augment, p_transform=p_transform)

data_prep_function_valid = partial(data_prep_function, p_transform_augment=None, p_transform=p_transform)

# data iterators

batch_size = 1

nbatches_chunk = 4

chunk_size = batch_size * nbatches_chunk

train_valid_ids = utils.load_pkl(pathfinder.LUNA_VALIDATION_SPLIT_PATH)

train_pids, valid_pids = train_valid_ids['train'], train_valid_ids['valid']

train_data_iterator = data_iterators.PatchPositiveLunaDataGenerator(data_path=pathfinder.LUNA_DATA_PATH,

                                                                    batch_size=chunk_size,

                                                                    transform_params=p_transform,

                                                                    data_prep_fun=data_prep_function_train,

                                                                    rng=rng,

                                                                    patient_ids=train_pids,

                                                                    full_batch=True, random=True, infinite=True)

valid_data_iterator = data_iterators.PatchPositiveLunaDataGenerator(data_path=pathfinder.LUNA_DATA_PATH,

                                                                    batch_size=1,

                                                                    transform_params=p_transform,

                                                                    data_prep_fun=data_prep_function_valid,

                                                                    rng=rng,

                                                                    patient_ids=valid_pids,

                                                                    full_batch=False, random=False, infinite=False)

nchunks_per_epoch = train_data_iterator.nsamples / chunk_size

max_nchunks = nchunks_per_epoch * 30

validate_every = int(1. * nchunks_per_epoch)

save_every = int(0.5 * nchunks_per_epoch)

learning_rate_schedule = {

    0: 1e-5,

    int(max_nchunks * 0.4): 5e-6,

    int(max_nchunks * 0.5): 3e-6,

    int(max_nchunks * 0.6): 2e-6,

    int(max_nchunks * 0.85): 1e-6,

    int(max_nchunks * 0.95): 5e-7

}

# model

conv3d = partial(dnn.Conv3DDNNLayer,

                 filter_size=3,

                 pad='same',

                 W=nn.init.Orthogonal(),

                 b=nn.init.Constant(0.01),

                 nonlinearity=nn.nonlinearities.linear)

max_pool3d = partial(dnn.MaxPool3DDNNLayer,

                     pool_size=2)

def build_model():

    l_in = nn.layers.InputLayer((None, 1,) + p_transform['patch_size'])

    l_target = nn.layers.InputLayer((None, 1,) + p_transform['patch_size'])

    net = {}

    base_n_filters = 64

    net['contr_1_1'] = conv3d(l_in, base_n_filters)

    net['contr_1_1'] = nn.layers.ParametricRectifierLayer(net['contr_1_1'])

    net['contr_1_2'] = conv3d(net['contr_1_1'], base_n_filters)

    net['contr_1_2'] = nn.layers.ParametricRectifierLayer(net['contr_1_2'])

    net['contr_1_3'] = conv3d(net['contr_1_2'], base_n_filters)

    net['contr_1_3'] = nn.layers.ParametricRectifierLayer(net['contr_1_3'])

    net['pool1'] = max_pool3d(net['contr_1_3'])

    net['encode_1'] = conv3d(net['pool1'], base_n_filters)

    net['encode_1'] = nn.layers.ParametricRectifierLayer(net['encode_1'])

    net['encode_2'] = conv3d(net['encode_1'], base_n_filters)

    net['encode_2'] = nn.layers.ParametricRectifierLayer(net['encode_2'])

    net['encode_3'] = conv3d(net['encode_2'], base_n_filters)

    net['encode_3'] = nn.layers.ParametricRectifierLayer(net['encode_3'])

    net['upscale1'] = nn_lung.Upscale3DLayer(net['encode_3'], 2)

    net['concat1'] = nn.layers.ConcatLayer([net['upscale1'], net['contr_1_3']],

                                           cropping=(None, None, "center", "center", "center"))

    net['expand_1_1'] = conv3d(net['concat1'], 2 * base_n_filters)

    net['expand_1_1'] = nn.layers.ParametricRectifierLayer(net['expand_1_1'])

    net['expand_1_2'] = conv3d(net['expand_1_1'], 2 * base_n_filters)

    net['expand_1_2'] = nn.layers.ParametricRectifierLayer(net['expand_1_2'])

    net['expand_1_3'] = conv3d(net['expand_1_2'], base_n_filters)

    net['expand_1_3'] = nn.layers.ParametricRectifierLayer(net['expand_1_3'])

    l_out = dnn.Conv3DDNNLayer(net['expand_1_3'], num_filters=1,

                               filter_size=1,

                               W=nn.init.Constant(0.),

                               nonlinearity=nn.nonlinearities.sigmoid)

    return namedtuple('Model', ['l_in', 'l_out', 'l_target'])(l_in, l_out, l_target)

def build_objective(model, deterministic=False, epsilon=1e-12):

    predictions = T.flatten(nn.layers.get_output(model.l_out))

    targets = T.flatten(nn.layers.get_output(model.l_target))

    dice = (2. * T.sum(targets * predictions) + epsilon) / (T.sum(predictions) + T.sum(targets) + epsilon)

    return -1. * dice

def build_updates(train_loss, model, learning_rate):

    updates = nn.updates.adam(train_loss, nn.layers.get_all_params(model.l_out), learning_rate)

    return updates