#!/usr/bin/env python

# Copyright 2018 Division of Medical Image Computing, German Cancer Research Center (DKFZ).

#

# 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.

# ==============================================================================

"""

Parts are based on https://github.com/multimodallearning/pytorch-mask-rcnn

published under MIT license.

"""

import sys

import numpy as np

import torch

import torch.nn as nn

import torch.nn.functional as F

import torch.utils

sys.path.append("..")

import utils.model_utils as mutils

import utils.exp_utils as utils

from custom_extensions.nms import nms

from custom_extensions.roi_align import roi_align

############################################################

# Networks on top of backbone

############################################################

class RPN(nn.Module):

    """

    Region Proposal Network.

    """

    def __init__(self, cf, conv):

        super(RPN, self).__init__()

        self.dim = conv.dim

        self.conv_shared = conv(cf.end_filts, cf.n_rpn_features, ks=3, stride=cf.rpn_anchor_stride, pad=1, relu=cf.relu)

        self.conv_class = conv(cf.n_rpn_features, 2 * len(cf.rpn_anchor_ratios), ks=1, stride=1, relu=None)

        self.conv_bbox = conv(cf.n_rpn_features, 2 * self.dim * len(cf.rpn_anchor_ratios), ks=1, stride=1, relu=None)

    def forward(self, x):

        """

        :param x: input feature maps (b, in_channels, y, x, (z))

        :return: rpn_class_logits (b, 2, n_anchors)

        :return: rpn_probs_logits (b, 2, n_anchors)

        :return: rpn_bbox (b, 2 * dim, n_anchors)

        """

        # Shared convolutional base of the RPN.

        x = self.conv_shared(x)

        # Anchor Score. (batch, anchors per location * 2, y, x, (z)).

        rpn_class_logits = self.conv_class(x)

        # Reshape to (batch, 2, anchors)

        axes = (0, 2, 3, 1) if self.dim == 2 else (0, 2, 3, 4, 1)

        rpn_class_logits = rpn_class_logits.permute(*axes)

        rpn_class_logits = rpn_class_logits.contiguous()

        rpn_class_logits = rpn_class_logits.view(x.size()[0], -1, 2)

        # Softmax on last dimension (fg vs. bg).

        rpn_probs = F.softmax(rpn_class_logits, dim=2)

        # Bounding box refinement. (batch, anchors_per_location * (y, x, (z), log(h), log(w), (log(d)), y, x, (z))

        rpn_bbox = self.conv_bbox(x)

        # Reshape to (batch, 2*dim, anchors)

        rpn_bbox = rpn_bbox.permute(*axes)

        rpn_bbox = rpn_bbox.contiguous()

        rpn_bbox = rpn_bbox.view(x.size()[0], -1, self.dim * 2)

        return [rpn_class_logits, rpn_probs, rpn_bbox]

class Classifier(nn.Module):

    """

    Head network for classification and bounding box refinement. Performs RoiAlign, processes resulting features through a

    shared convolutional base and finally branches off the classifier- and regression head.

    """

    def __init__(self, cf, conv):

        super(Classifier, self).__init__()

        self.dim = conv.dim

        self.in_channels = cf.end_filts

        self.pool_size = cf.pool_size

        self.pyramid_levels = cf.pyramid_levels

        # instance_norm does not work with spatial dims (1, 1, (1))

        norm = cf.norm if cf.norm != 'instance_norm' else None

        self.conv1 = conv(cf.end_filts, cf.end_filts * 4, ks=self.pool_size, stride=1, norm=norm, relu=cf.relu)

        self.conv2 = conv(cf.end_filts * 4, cf.end_filts * 4, ks=1, stride=1, norm=norm, relu=cf.relu)

        self.linear_class = nn.Linear(cf.end_filts * 4, cf.head_classes)

        self.linear_bbox = nn.Linear(cf.end_filts * 4, cf.head_classes * 2 * self.dim)

    def forward(self, x, rois):

        """

        :param x: input feature maps (b, in_channels, y, x, (z))

        :param rois: normalized box coordinates as proposed by the RPN to be forwarded through

        the second stage (n_proposals, (y1, x1, y2, x2, (z1), (z2), batch_ix). Proposals of all batch elements

        have been merged to one vector, while the origin info has been stored for re-allocation.

        :return: mrcnn_class_logits (n_proposals, n_head_classes)

        :return: mrcnn_bbox (n_proposals, n_head_classes, 2 * dim) predicted corrections to be applied to proposals for refinement.

        """

        x = pyramid_roi_align(x, rois, self.pool_size, self.pyramid_levels, self.dim)

        x = self.conv1(x)

        x = self.conv2(x)

        x = x.view(-1, self.in_channels * 4)

        mrcnn_class_logits = self.linear_class(x)

        mrcnn_bbox = self.linear_bbox(x)

        mrcnn_bbox = mrcnn_bbox.view(mrcnn_bbox.size()[0], -1, self.dim * 2)

        return [mrcnn_class_logits, mrcnn_bbox]

class Mask(nn.Module):

    """

    Head network for proposal-based mask segmentation. Performs RoiAlign, some convolutions and applies sigmoid on the

    output logits to allow for overlapping classes.

    """

    def __init__(self, cf, conv):

        super(Mask, self).__init__()

        self.pool_size = cf.mask_pool_size

        self.pyramid_levels = cf.pyramid_levels

        self.dim = conv.dim

        self.conv1 = conv(cf.end_filts, cf.end_filts, ks=3, stride=1, pad=1, norm=cf.norm, relu=cf.relu)

        self.conv2 = conv(cf.end_filts, cf.end_filts, ks=3, stride=1, pad=1, norm=cf.norm, relu=cf.relu)

        self.conv3 = conv(cf.end_filts, cf.end_filts, ks=3, stride=1, pad=1, norm=cf.norm, relu=cf.relu)

        self.conv4 = conv(cf.end_filts, cf.end_filts, ks=3, stride=1, pad=1, norm=cf.norm, relu=cf.relu)

        if conv.dim == 2:

            self.deconv = nn.ConvTranspose2d(cf.end_filts, cf.end_filts, kernel_size=2, stride=2)

        else:

            self.deconv = nn.ConvTranspose3d(cf.end_filts, cf.end_filts, kernel_size=2, stride=2)

        self.relu = nn.ReLU(inplace=True) if cf.relu == 'relu' else nn.LeakyReLU(inplace=True)

        self.conv5 = conv(cf.end_filts, cf.head_classes, ks=1, stride=1, relu=None)

        self.sigmoid = nn.Sigmoid()

    def forward(self, x, rois):

        """

        :param x: input feature maps (b, in_channels, y, x, (z))

        :param rois: normalized box coordinates as proposed by the RPN to be forwarded through

        the second stage (n_proposals, (y1, x1, y2, x2, (z1), (z2), batch_ix). Proposals of all batch elements

        have been merged to one vector, while the origin info has been stored for re-allocation.

        :return: x: masks (n_sampled_proposals (n_detections in inference), n_classes, y, x, (z))

        """

        x = pyramid_roi_align(x, rois, self.pool_size, self.pyramid_levels, self.dim)

        x = self.conv1(x)

        x = self.conv2(x)

        x = self.conv3(x)

        x = self.conv4(x)

        x = self.relu(self.deconv(x))

        x = self.conv5(x)

        x = self.sigmoid(x)

        return x

############################################################

#  Loss Functions

############################################################

def compute_rpn_class_loss(rpn_match, rpn_class_logits, shem_poolsize):

    """

    :param rpn_match: (n_anchors). [-1, 0, 1] for negative, neutral, and positive matched anchors.

    :param rpn_class_logits: (n_anchors, 2). logits from RPN classifier.

    :param shem_poolsize: int. factor of top-k candidates to draw from per negative sample

    (stochastic-hard-example-mining).

    :return: loss: torch tensor

    :return: np_neg_ix: 1D array containing indices of the neg_roi_logits, which have been sampled for training.

    """

    # filter out neutral anchors.

    pos_indices = torch.nonzero(rpn_match == 1)

    neg_indices = torch.nonzero(rpn_match == -1)

    # loss for positive samples

    if 0 not in pos_indices.size():

        pos_indices = pos_indices.squeeze(1)

        roi_logits_pos = rpn_class_logits[pos_indices]

        pos_loss = F.cross_entropy(roi_logits_pos, torch.LongTensor([1] * pos_indices.shape[0]).cuda())

    else:

        pos_loss = torch.FloatTensor([0]).cuda()

    # loss for negative samples: draw hard negative examples (SHEM)

    # that match the number of positive samples, but at least 1.

    if 0 not in neg_indices.size():

        neg_indices = neg_indices.squeeze(1)

        roi_logits_neg = rpn_class_logits[neg_indices]

        negative_count = np.max((1, pos_indices.cpu().data.numpy().size))

        roi_probs_neg = F.softmax(roi_logits_neg, dim=1)

        neg_ix = mutils.shem(roi_probs_neg, negative_count, shem_poolsize)

        neg_loss = F.cross_entropy(roi_logits_neg[neg_ix], torch.LongTensor([0] * neg_ix.shape[0]).cuda())

        np_neg_ix = neg_ix.cpu().data.numpy()

    else:

        neg_loss = torch.FloatTensor([0]).cuda()

        np_neg_ix = np.array([]).astype('int32')

    loss = (pos_loss + neg_loss) / 2

    return loss, np_neg_ix

def compute_rpn_bbox_loss(rpn_target_deltas, rpn_pred_deltas, rpn_match):

    """

    :param rpn_target_deltas:   (b, n_positive_anchors, (dy, dx, (dz), log(dh), log(dw), (log(dd)))).

    Uses 0 padding to fill in unsed bbox deltas.

    :param rpn_pred_deltas: predicted deltas from RPN. (b, n_anchors, (dy, dx, (dz), log(dh), log(dw), (log(dd))))

    :param rpn_match: (n_anchors). [-1, 0, 1] for negative, neutral, and positive matched anchors.

    :return: loss: torch 1D tensor.

    """

    if 0 not in torch.nonzero(rpn_match == 1).size():

        indices = torch.nonzero(rpn_match == 1).squeeze(1)

        # Pick bbox deltas that contribute to the loss

        rpn_pred_deltas = rpn_pred_deltas[indices]

        # Trim target bounding box deltas to the same length as rpn_bbox.

        target_deltas = rpn_target_deltas[:rpn_pred_deltas.size()[0], :]

        # Smooth L1 loss

        loss = F.smooth_l1_loss(rpn_pred_deltas, target_deltas)

    else:

        loss = torch.FloatTensor([0]).cuda()

    return loss

def compute_mrcnn_class_loss(target_class_ids, pred_class_logits):

    """

    :param target_class_ids: (n_sampled_rois) batch dimension was merged into roi dimension.

    :param pred_class_logits: (n_sampled_rois, n_classes)

    :return: loss: torch 1D tensor.

    """

    if 0 not in target_class_ids.size():

        loss = F.cross_entropy(pred_class_logits, target_class_ids.long())

    else:

        loss = torch.FloatTensor([0.]).cuda()

    return loss

def compute_mrcnn_bbox_loss(mrcnn_target_deltas, mrcnn_pred_deltas, target_class_ids):

    """

    :param mrcnn_target_deltas: (n_sampled_rois, (dy, dx, (dz), log(dh), log(dw), (log(dh)))

    :param mrcnn_pred_deltas: (n_sampled_rois, n_classes, (dy, dx, (dz), log(dh), log(dw), (log(dh)))

    :param target_class_ids: (n_sampled_rois)

    :return: loss: torch 1D tensor.

    """

    if 0 not in torch.nonzero(target_class_ids > 0).size():

        positive_roi_ix = torch.nonzero(target_class_ids > 0)[:, 0]

        positive_roi_class_ids = target_class_ids[positive_roi_ix].long()

        target_bbox = mrcnn_target_deltas[positive_roi_ix, :].detach()

        pred_bbox = mrcnn_pred_deltas[positive_roi_ix, positive_roi_class_ids, :]

        loss = F.smooth_l1_loss(pred_bbox, target_bbox)

    else:

        loss = torch.FloatTensor([0]).cuda()

    return loss

def compute_mrcnn_mask_loss(target_masks, pred_masks, target_class_ids):

    """

    :param target_masks: (n_sampled_rois, y, x, (z)) A float32 tensor of values 0 or 1. Uses zero padding to fill array.

    :param pred_masks: (n_sampled_rois, n_classes, y, x, (z)) float32 tensor with values between [0, 1].

    :param target_class_ids: (n_sampled_rois)

    :return: loss: torch 1D tensor.

    """

    if 0 not in torch.nonzero(target_class_ids > 0).size():

        # Only positive ROIs contribute to the loss. And only

        # the class specific mask of each ROI.

        positive_ix = torch.nonzero(target_class_ids > 0)[:, 0]

        positive_class_ids = target_class_ids[positive_ix].long()

        y_true = target_masks[positive_ix, :, :].detach()

        y_pred = pred_masks[positive_ix, positive_class_ids, :, :]

        loss = F.binary_cross_entropy(y_pred, y_true)

    else:

        loss = torch.FloatTensor([0]).cuda()

    return loss

############################################################

#  Helper Layers

############################################################

def refine_proposals(rpn_pred_probs, rpn_pred_deltas, proposal_count, batch_anchors, cf):

    """

    Receives anchor scores and selects a subset to pass as proposals

    to the second stage. Filtering is done based on anchor scores and

    non-max suppression to remove overlaps. It also applies bounding

    box refinment details to anchors.

    :param rpn_pred_probs: (b, n_anchors, 2)

    :param rpn_pred_deltas: (b, n_anchors, (y, x, (z), log(h), log(w), (log(d))))

    :return: batch_normalized_props: Proposals in normalized coordinates (b, proposal_count, (y1, x1, y2, x2, (z1), (z2), score))

    :return: batch_out_proposals: Box coords + RPN foreground scores

    for monitoring/plotting (b, proposal_count, (y1, x1, y2, x2, (z1), (z2), score))

    """

    std_dev = torch.from_numpy(cf.rpn_bbox_std_dev[None]).float().cuda()

    norm = torch.from_numpy(cf.scale).float().cuda()

    anchors = batch_anchors.clone()

    batch_scores = rpn_pred_probs[:, :, 1]

    # norm deltas

    batch_deltas = rpn_pred_deltas * std_dev

    batch_normalized_props = []

    batch_out_proposals = []

    # loop over batch dimension.

    for ix in range(batch_scores.shape[0]):

        scores = batch_scores[ix]

        deltas = batch_deltas[ix]

        # improve performance by trimming to top anchors by score

        # and doing the rest on the smaller subset.

        pre_nms_limit = min(cf.pre_nms_limit, anchors.size()[0])

        scores, order = scores.sort(descending=True)

        order = order[:pre_nms_limit]

        scores = scores[:pre_nms_limit]

        deltas = deltas[order, :]

        # apply deltas to anchors to get refined anchors and filter with non-maximum suppression.

        if batch_deltas.shape[-1] == 4:

            boxes = mutils.apply_box_deltas_2D(anchors[order, :], deltas)

            boxes = mutils.clip_boxes_2D(boxes, cf.window)

        else:

            boxes = mutils.apply_box_deltas_3D(anchors[order, :], deltas)

            boxes = mutils.clip_boxes_3D(boxes, cf.window)

        # boxes are y1,x1,y2,x2, torchvision-nms requires x1,y1,x2,y2, but consistent swap x<->y is irrelevant.

        keep = nms.nms(boxes, scores, cf.rpn_nms_threshold)

        keep = keep[:proposal_count]

        boxes = boxes[keep, :]

        rpn_scores = scores[keep][:, None]

        # pad missing boxes with 0.

        if boxes.shape[0] < proposal_count:

            n_pad_boxes = proposal_count - boxes.shape[0]

            zeros = torch.zeros([n_pad_boxes, boxes.shape[1]]).cuda()

            boxes = torch.cat([boxes, zeros], dim=0)

            zeros = torch.zeros([n_pad_boxes, rpn_scores.shape[1]]).cuda()

            rpn_scores = torch.cat([rpn_scores, zeros], dim=0)

        # concat box and score info for monitoring/plotting.

        batch_out_proposals.append(torch.cat((boxes, rpn_scores), 1).cpu().data.numpy())

        # normalize dimensions to range of 0 to 1.

        normalized_boxes = boxes / norm

        assert torch.all(normalized_boxes <= 1), "normalized box coords >1 found"

        # add again batch dimension

        batch_normalized_props.append(normalized_boxes.unsqueeze(0))

    batch_normalized_props = torch.cat(batch_normalized_props)

    batch_out_proposals = np.array(batch_out_proposals)

    return batch_normalized_props, batch_out_proposals

def pyramid_roi_align(feature_maps, rois, pool_size, pyramid_levels, dim):

    """

    Implements ROI Pooling on multiple levels of the feature pyramid.

    :param feature_maps: list of feature maps, each of shape (b, c, y, x , (z))

    :param rois: proposals (normalized coords.) as returned by RPN. contain info about original batch element allocation.

    (n_proposals, (y1, x1, y2, x2, (z1), (z2), batch_ixs)

    :param pool_size: list of poolsizes in dims: [x, y, (z)]

    :param pyramid_levels: list. [0, 1, 2, ...]

    :return: pooled: pooled feature map rois (n_proposals, c, poolsize_y, poolsize_x, (poolsize_z))

    Output:

    Pooled regions in the shape: [num_boxes, height, width, channels].

    The width and height are those specific in the pool_shape in the layer

    constructor.

    """

    boxes = rois[:, :dim*2]

    batch_ixs = rois[:, dim*2]

    # Assign each ROI to a level in the pyramid based on the ROI area.

    if dim == 2:

        y1, x1, y2, x2 = boxes.chunk(4, dim=1)

    else:

        y1, x1, y2, x2, z1, z2 = boxes.chunk(6, dim=1)

    h = y2 - y1

    w = x2 - x1

    # Equation 1 in https://arxiv.org/abs/1612.03144. Account for

    # the fact that our coordinates are normalized here.

    # divide sqrt(h*w) by 1 instead image_area.

    roi_level = (4 + torch.log2(torch.sqrt(h*w))).round().int().clamp(pyramid_levels[0], pyramid_levels[-1])

    # if Pyramid contains additional level P6, adapt the roi_level assignment accordingly.

    if len(pyramid_levels) == 5:

        roi_level[h*w > 0.65] = 5

    # Loop through levels and apply ROI pooling to each.

    pooled = []

    box_to_level = []

    fmap_shapes = [f.shape for f in feature_maps]

    for level_ix, level in enumerate(pyramid_levels):

        ix = roi_level == level

        if not ix.any():

            continue

        ix = torch.nonzero(ix)[:, 0]

        level_boxes = boxes[ix, :]

        # re-assign rois to feature map of original batch element.

        ind = batch_ixs[ix].int()

        # Keep track of which box is mapped to which level

        box_to_level.append(ix)

        # Stop gradient propogation to ROI proposals

        level_boxes = level_boxes.detach()

        if len(pool_size) == 2:

            # remap to feature map coordinate system

            y_exp, x_exp = fmap_shapes[level_ix][2:]  # exp = expansion

            level_boxes.mul_(torch.tensor([y_exp, x_exp, y_exp, x_exp], dtype=torch.float32).cuda())

            pooled_features = roi_align.roi_align_2d(feature_maps[level_ix],

                                                     torch.cat((ind.unsqueeze(1).float(), level_boxes), dim=1),

                                                     pool_size)

        else:

            y_exp, x_exp, z_exp = fmap_shapes[level_ix][2:]

            level_boxes.mul_(torch.tensor([y_exp, x_exp, y_exp, x_exp, z_exp, z_exp], dtype=torch.float32).cuda())

            pooled_features = roi_align.roi_align_3d(feature_maps[level_ix],

                                                     torch.cat((ind.unsqueeze(1).float(), level_boxes), dim=1),

                                                     pool_size)

        pooled.append(pooled_features)

    # Pack pooled features into one tensor

    pooled = torch.cat(pooled, dim=0)

    # Pack box_to_level mapping into one array and add another

    # column representing the order of pooled boxes

    box_to_level = torch.cat(box_to_level, dim=0)

    # Rearrange pooled features to match the order of the original boxes

    _, box_to_level = torch.sort(box_to_level)

    pooled = pooled[box_to_level, :, :]

    return pooled

def detection_target_layer(batch_proposals, batch_mrcnn_class_scores, batch_gt_class_ids, batch_gt_boxes, batch_gt_masks, cf):

    """

    Subsamples proposals for mrcnn losses and generates targets. Sampling is done per batch element, seems to have positive

    effects on training, as opposed to sampling over entire batch. Negatives are sampled via stochastic-hard-example-mining

    (SHEM), where a number of negative proposals are drawn from larger pool of highest scoring proposals for stochasticity.

    Scoring is obtained here as the max over all foreground probabilities as returned by mrcnn_classifier (worked better than

    loss-based class balancing methods like "online-hard-example-mining" or "focal loss".)

    :param batch_proposals: (n_proposals, (y1, x1, y2, x2, (z1), (z2), batch_ixs).

    boxes as proposed by RPN. n_proposals here is determined by batch_size * POST_NMS_ROIS.

    :param batch_mrcnn_class_scores: (n_proposals, n_classes)

    :param batch_gt_class_ids: list over batch elements. Each element is a list over the corresponding roi target labels.

    :param batch_gt_boxes: list over batch elements. Each element is a list over the corresponding roi target coordinates.

    :param batch_gt_masks: list over batch elements. Each element is binary mask of shape (n_gt_rois, y, x, (z), c)

    :return: sample_indices: (n_sampled_rois) indices of sampled proposals to be used for loss functions.

    :return: target_class_ids: (n_sampled_rois)containing target class labels of sampled proposals.

    :return: target_deltas: (n_sampled_rois, 2 * dim) containing target deltas of sampled proposals for box refinement.

    :return: target_masks: (n_sampled_rois, y, x, (z)) containing target masks of sampled proposals.

    """

    # normalization of target coordinates

    if cf.dim == 2:

        h, w = cf.patch_size

        scale = torch.from_numpy(np.array([h, w, h, w])).float().cuda()

    else:

        h, w, z = cf.patch_size

        scale = torch.from_numpy(np.array([h, w, h, w, z, z])).float().cuda()

    positive_count = 0

    negative_count = 0

    sample_positive_indices = []

    sample_negative_indices = []

    sample_deltas = []

    sample_masks = []

    sample_class_ids = []

    std_dev = torch.from_numpy(cf.bbox_std_dev).float().cuda()

    # loop over batch and get positive and negative sample rois.

    for b in range(len(batch_gt_class_ids)):

        gt_class_ids = torch.from_numpy(batch_gt_class_ids[b]).int().cuda()

        gt_masks = torch.from_numpy(batch_gt_masks[b]).float().cuda()

        if np.any(batch_gt_class_ids[b] > 0):  # skip roi selection for no gt images.

            gt_boxes = torch.from_numpy(batch_gt_boxes[b]).float().cuda() / scale

        else:

            gt_boxes = torch.FloatTensor().cuda()

        # get proposals and indices of current batch element.

        proposals = batch_proposals[batch_proposals[:, -1] == b][:, :-1]

        batch_element_indices = torch.nonzero(batch_proposals[:, -1] == b).squeeze(1)

        # Compute overlaps matrix [proposals, gt_boxes]

        if 0 not in gt_boxes.size():

            if gt_boxes.shape[1] == 4:

                assert cf.dim == 2, "gt_boxes shape {} doesnt match cf.dim{}".format(gt_boxes.shape, cf.dim)

                overlaps = mutils.bbox_overlaps_2D(proposals, gt_boxes)

            else:

                assert cf.dim == 3, "gt_boxes shape {} doesnt match cf.dim{}".format(gt_boxes.shape, cf.dim)

                overlaps = mutils.bbox_overlaps_3D(proposals, gt_boxes)

            # Determine postive and negative ROIs

            roi_iou_max = torch.max(overlaps, dim=1)[0]

            # 1. Positive ROIs are those with >= 0.5 IoU with a GT box

            positive_roi_bool = roi_iou_max >= (0.5 if cf.dim == 2 else 0.3)

            # 2. Negative ROIs are those with < 0.1 with every GT box.

            negative_roi_bool = roi_iou_max < (0.1 if cf.dim == 2 else 0.01)

        else:

            positive_roi_bool = torch.FloatTensor().cuda()

            negative_roi_bool = torch.from_numpy(np.array([1]*proposals.shape[0])).cuda()

        # Sample Positive ROIs

        if 0 not in torch.nonzero(positive_roi_bool).size():

            positive_indices = torch.nonzero(positive_roi_bool).squeeze(1)

            positive_samples = int(cf.train_rois_per_image * cf.roi_positive_ratio)

            rand_idx = torch.randperm(positive_indices.size()[0])

            rand_idx = rand_idx[:positive_samples].cuda()

            positive_indices = positive_indices[rand_idx]

            positive_samples = positive_indices.size()[0]

            positive_rois = proposals[positive_indices, :]

            # Assign positive ROIs to GT boxes.

            positive_overlaps = overlaps[positive_indices, :]

            roi_gt_box_assignment = torch.max(positive_overlaps, dim=1)[1]

            roi_gt_boxes = gt_boxes[roi_gt_box_assignment, :]

            roi_gt_class_ids = gt_class_ids[roi_gt_box_assignment]

            # Compute bbox refinement targets for positive ROIs

            deltas = mutils.box_refinement(positive_rois, roi_gt_boxes)

            deltas /= std_dev

            # Assign positive ROIs to GT masks

            roi_masks = gt_masks[roi_gt_box_assignment]

            assert roi_masks.shape[1] == 1, "desired to have more than one channel in gt masks?"

            # Compute mask targets

            boxes = positive_rois

            box_ids = torch.arange(roi_masks.shape[0]).cuda().unsqueeze(1).float()

            if len(cf.mask_shape) == 2:

                # need to remap normalized box coordinates to unnormalized mask coordinates.

                y_exp, x_exp = roi_masks.shape[2:]  # exp = expansion

                boxes.mul_(torch.tensor([y_exp, x_exp, y_exp, x_exp], dtype=torch.float32).cuda())

                masks = roi_align.roi_align_2d(roi_masks, torch.cat((box_ids, boxes), dim=1), cf.mask_shape)

            else:

                y_exp, x_exp, z_exp = roi_masks.shape[2:]  # exp = expansion

                boxes.mul_(torch.tensor([y_exp, x_exp, y_exp, x_exp, z_exp, z_exp], dtype=torch.float32).cuda())

                masks = roi_align.roi_align_3d(roi_masks, torch.cat((box_ids, boxes), dim=1), cf.mask_shape)

            masks = masks.squeeze(1)

            # Threshold mask pixels at 0.5 to have GT masks be 0 or 1 to use with

            # binary cross entropy loss.

            masks = torch.round(masks)

            sample_positive_indices.append(batch_element_indices[positive_indices])

            sample_deltas.append(deltas)

            sample_masks.append(masks)

            sample_class_ids.append(roi_gt_class_ids)

            positive_count += positive_samples

        else:

            positive_samples = 0

        # Negative ROIs. Add enough to maintain positive:negative ratio, but at least 1. Sample via SHEM.

        if 0 not in torch.nonzero(negative_roi_bool).size():

            negative_indices = torch.nonzero(negative_roi_bool).squeeze(1)

            r = 1.0 / cf.roi_positive_ratio

            b_neg_count = np.max((int(r * positive_samples - positive_samples), 1))

            roi_probs_neg = batch_mrcnn_class_scores[batch_element_indices[negative_indices]]

            raw_sampled_indices = mutils.shem(roi_probs_neg, b_neg_count, cf.shem_poolsize)

            sample_negative_indices.append(batch_element_indices[negative_indices[raw_sampled_indices]])

            negative_count += raw_sampled_indices.size()[0]

    if len(sample_positive_indices) > 0:

        target_deltas = torch.cat(sample_deltas)

        target_masks = torch.cat(sample_masks)

        target_class_ids = torch.cat(sample_class_ids)

    # Pad target information with zeros for negative ROIs.

    if positive_count > 0 and negative_count > 0:

        sample_indices = torch.cat((torch.cat(sample_positive_indices), torch.cat(sample_negative_indices)), dim=0)

        zeros = torch.zeros(negative_count).int().cuda()

        target_class_ids = torch.cat([target_class_ids, zeros], dim=0)

        zeros = torch.zeros(negative_count, cf.dim * 2).cuda()

        target_deltas = torch.cat([target_deltas, zeros], dim=0)

        zeros = torch.zeros(negative_count, *cf.mask_shape).cuda()

        target_masks = torch.cat([target_masks, zeros], dim=0)

    elif positive_count > 0:

        sample_indices = torch.cat(sample_positive_indices)

    elif negative_count > 0:

        sample_indices = torch.cat(sample_negative_indices)

        zeros = torch.zeros(negative_count).int().cuda()

        target_class_ids = zeros

        zeros = torch.zeros(negative_count, cf.dim * 2).cuda()

        target_deltas = zeros

        zeros = torch.zeros(negative_count, *cf.mask_shape).cuda()

        target_masks = zeros

    else:

        sample_indices = torch.LongTensor().cuda()

        target_class_ids = torch.IntTensor().cuda()

        target_deltas = torch.FloatTensor().cuda()

        target_masks = torch.FloatTensor().cuda()

    return sample_indices, target_class_ids, target_deltas, target_masks

############################################################

#  Output Handler

############################################################

# def refine_detections(rois, probs, deltas, batch_ixs, cf):

#     """

#     Refine classified proposals, filter overlaps and return final detections.

#

#     :param rois: (n_proposals, 2 * dim) normalized boxes as proposed by RPN. n_proposals = batch_size * POST_NMS_ROIS

#     :param probs: (n_proposals, n_classes) softmax probabilities for all rois as predicted by mrcnn classifier.

#     :param deltas: (n_proposals, n_classes, 2 * dim) box refinement deltas as predicted by mrcnn bbox regressor.

#     :param batch_ixs: (n_proposals) batch element assignemnt info for re-allocation.

#     :return: result: (n_final_detections, (y1, x1, y2, x2, (z1), (z2), batch_ix, pred_class_id, pred_score))

#     """

#     # class IDs per ROI. Since scores of all classes are of interest (not just max class), all are kept at this point.

#     class_ids = []

#     fg_classes = cf.head_classes - 1

#     # repeat vectors to fill in predictions for all foreground classes.

#     for ii in range(1, fg_classes + 1):

#         class_ids += [ii] * rois.shape[0]

#     class_ids = torch.from_numpy(np.array(class_ids)).cuda()

#

#     rois = rois.repeat(fg_classes, 1)

#     probs = probs.repeat(fg_classes, 1)

#     deltas = deltas.repeat(fg_classes, 1, 1)

#     batch_ixs = batch_ixs.repeat(fg_classes)

#

#     # get class-specific scores and  bounding box deltas

#     idx = torch.arange(class_ids.size()[0]).long().cuda()

#     class_scores = probs[idx, class_ids]

#     deltas_specific = deltas[idx, class_ids]

#     batch_ixs = batch_ixs[idx]

#

#     # apply bounding box deltas. re-scale to image coordinates.

#     std_dev = torch.from_numpy(np.reshape(cf.rpn_bbox_std_dev, [1, cf.dim * 2])).float().cuda()

#     scale = torch.from_numpy(cf.scale).float().cuda()

#     refined_rois = mutils.apply_box_deltas_2D(rois, deltas_specific * std_dev) * scale if cf.dim == 2 else \

#         mutils.apply_box_deltas_3D(rois, deltas_specific * std_dev) * scale

#

#     # round and cast to int since we're deadling with pixels now

#     refined_rois = mutils.clip_to_window(cf.window, refined_rois)

#     refined_rois = torch.round(refined_rois)

#

#     # filter out low confidence boxes

#     keep = idx

#     keep_bool = (class_scores >= cf.model_min_confidence)

#     if 0 not in torch.nonzero(keep_bool).size():

#

#         score_keep = torch.nonzero(keep_bool)[:, 0]

#         pre_nms_class_ids = class_ids[score_keep]

#         pre_nms_rois = refined_rois[score_keep]

#         pre_nms_scores = class_scores[score_keep]

#         pre_nms_batch_ixs = batch_ixs[score_keep]

#

#         for j, b in enumerate(mutils.unique1d(pre_nms_batch_ixs)):

#

#             bixs = torch.nonzero(pre_nms_batch_ixs == b)[:, 0]

#             bix_class_ids = pre_nms_class_ids[bixs]

#             bix_rois = pre_nms_rois[bixs]

#             bix_scores = pre_nms_scores[bixs]

#

#             for i, class_id in enumerate(mutils.unique1d(bix_class_ids)):

#

#                 ixs = torch.nonzero(bix_class_ids == class_id)[:, 0]

#                 # nms expects boxes sorted by score.

#                 ix_rois = bix_rois[ixs]

#                 ix_scores = bix_scores[ixs]

#                 ix_scores, order = ix_scores.sort(descending=True)

#                 ix_rois = ix_rois[order, :]

#

#                 if cf.dim == 2:

#                     class_keep = nms_2D(torch.cat((ix_rois, ix_scores.unsqueeze(1)), dim=1), cf.detection_nms_threshold)

#                 else:

#                     class_keep = nms_3D(torch.cat((ix_rois, ix_scores.unsqueeze(1)), dim=1), cf.detection_nms_threshold)

#

#                 # map indices back.

#                 class_keep = keep[score_keep[bixs[ixs[order[class_keep]]]]]

#                 # merge indices over classes for current batch element

#                 b_keep = class_keep if i == 0 else mutils.unique1d(torch.cat((b_keep, class_keep)))

#

#             # only keep top-k boxes of current batch-element

#             top_ids = class_scores[b_keep].sort(descending=True)[1][:cf.model_max_instances_per_batch_element]

#             b_keep = b_keep[top_ids]

#

#             # merge indices over batch elements.

#             batch_keep = b_keep if j == 0 else mutils.unique1d(torch.cat((batch_keep, b_keep)))

#

#         keep = batch_keep

#

#     else:

#         keep = torch.tensor([0]).long().cuda()

#

#     # arrange output

#     result = torch.cat((refined_rois[keep],

#                         batch_ixs[keep].unsqueeze(1),

#                         class_ids[keep].unsqueeze(1).float(),

#                         class_scores[keep].unsqueeze(1)), dim=1)

#

#     return result

def refine_detections(cf, batch_ixs, rois, deltas, scores):

    """

    Refine classified proposals (apply deltas to rpn rois), filter overlaps (nms) and return final detections.

    :param rois: (n_proposals, 2 * dim) normalized boxes as proposed by RPN. n_proposals = batch_size * POST_NMS_ROIS

    :param deltas: (n_proposals, n_classes, 2 * dim) box refinement deltas as predicted by mrcnn bbox regressor.

    :param batch_ixs: (n_proposals) batch element assignment info for re-allocation.

    :param scores: (n_proposals, n_classes) probabilities for all classes per roi as predicted by mrcnn classifier.

    :return: result: (n_final_detections, (y1, x1, y2, x2, (z1), (z2), batch_ix, pred_class_id, pred_score, *regression vector features))

    """

    # class IDs per ROI. Since scores of all classes are of interest (not just max class), all are kept at this point.

    class_ids = []

    fg_classes = cf.head_classes - 1

    # repeat vectors to fill in predictions for all foreground classes.

    for ii in range(1, fg_classes + 1):

        class_ids += [ii] * rois.shape[0]

    class_ids = torch.from_numpy(np.array(class_ids)).cuda()

    batch_ixs = batch_ixs.repeat(fg_classes)

    rois = rois.repeat(fg_classes, 1)

    deltas = deltas.repeat(fg_classes, 1, 1)

    scores = scores.repeat(fg_classes, 1)

    # get class-specific scores and  bounding box deltas

    idx = torch.arange(class_ids.size()[0]).long().cuda()

    # using idx instead of slice [:,] squashes first dimension.

    #len(class_ids)>scores.shape[1] --> probs is broadcasted by expansion from fg_classes-->len(class_ids)

    batch_ixs = batch_ixs[idx]

    deltas_specific = deltas[idx, class_ids]

    class_scores = scores[idx, class_ids]

    # apply bounding box deltas. re-scale to image coordinates.

    std_dev = torch.from_numpy(np.reshape(cf.rpn_bbox_std_dev, [1, cf.dim * 2])).float().cuda()

    scale = torch.from_numpy(cf.scale).float().cuda()

    refined_rois = mutils.apply_box_deltas_2D(rois, deltas_specific * std_dev) * scale if cf.dim == 2 else \

        mutils.apply_box_deltas_3D(rois, deltas_specific * std_dev) * scale

    # round and cast to int since we're dealing with pixels now

    refined_rois = mutils.clip_to_window(cf.window, refined_rois)

    refined_rois = torch.round(refined_rois)

    # filter out low confidence boxes

    keep = idx

    keep_bool = (class_scores >= cf.model_min_confidence)

    if not 0 in torch.nonzero(keep_bool).size():

        score_keep = torch.nonzero(keep_bool)[:, 0]

        pre_nms_class_ids = class_ids[score_keep]

        pre_nms_rois = refined_rois[score_keep]

        pre_nms_scores = class_scores[score_keep]

        pre_nms_batch_ixs = batch_ixs[score_keep]

        for j, b in enumerate(mutils.unique1d(pre_nms_batch_ixs)):

            bixs = torch.nonzero(pre_nms_batch_ixs == b)[:, 0]

            bix_class_ids = pre_nms_class_ids[bixs]

            bix_rois = pre_nms_rois[bixs]

            bix_scores = pre_nms_scores[bixs]

            for i, class_id in enumerate(mutils.unique1d(bix_class_ids)):

                ixs = torch.nonzero(bix_class_ids == class_id)[:, 0]

                # nms expects boxes sorted by score.

                ix_rois = bix_rois[ixs]

                ix_scores = bix_scores[ixs]

                ix_scores, order = ix_scores.sort(descending=True)

                ix_rois = ix_rois[order, :]

                class_keep = nms.nms(ix_rois, ix_scores, cf.detection_nms_threshold)

                # map indices back.

                class_keep = keep[score_keep[bixs[ixs[order[class_keep]]]]]

                # merge indices over classes for current batch element

                b_keep = class_keep if i == 0 else mutils.unique1d(torch.cat((b_keep, class_keep)))

            # only keep top-k boxes of current batch-element

            top_ids = class_scores[b_keep].sort(descending=True)[1][:cf.model_max_instances_per_batch_element]

            b_keep = b_keep[top_ids]

            # merge indices over batch elements.

            batch_keep = b_keep  if j == 0 else mutils.unique1d(torch.cat((batch_keep, b_keep)))

        keep = batch_keep

    else:

        keep = torch.tensor([0]).long().cuda()

    # arrange output

    output = [refined_rois[keep], batch_ixs[keep].unsqueeze(1)]

    output += [class_ids[keep].unsqueeze(1).float(), class_scores[keep].unsqueeze(1)]

    result = torch.cat(output, dim=1)

    # shape: (n_keeps, catted feats), catted feats: [0:dim*2] are box_coords, [dim*2] are batch_ics,

    # [dim*2+1] are class_ids, [dim*2+2] are scores, [dim*2+3:] are regression vector features (incl uncertainty)

    return result

def get_results(cf, img_shape, detections, detection_masks, box_results_list=None, return_masks=True):

    """

    Restores batch dimension of merged detections, unmolds detections, creates and fills results dict.

    :param img_shape:

    :param detections: (n_final_detections, (y1, x1, y2, x2, (z1), (z2), batch_ix, pred_class_id, pred_score)

    :param detection_masks: (n_final_detections, n_classes, y, x, (z)) raw molded masks as returned by mask-head.

    :param box_results_list: None or list of output boxes for monitoring/plotting.

    each element is a list of boxes per batch element.

    :param return_masks: boolean. If True, full resolution masks are returned for all proposals (speed trade-off).

    :return: results_dict: dictionary with keys:

             'boxes': list over batch elements. each batch element is a list of boxes. each box is a dictionary:

                      [[{box_0}, ... {box_n}], [{box_0}, ... {box_n}], ...]

             'seg_preds': pixel-wise class predictions (b, 1, y, x, (z)) with values [0, 1] only fg. vs. bg for now.

             class-specific return of masks will come with implementation of instance segmentation evaluation.

    """

    detections = detections.cpu().data.numpy()

    if cf.dim == 2:

        detection_masks = detection_masks.permute(0, 2, 3, 1).cpu().data.numpy()

    else:

        detection_masks = detection_masks.permute(0, 2, 3, 4, 1).cpu().data.numpy()

    # restore batch dimension of merged detections using the batch_ix info.

    batch_ixs = detections[:, cf.dim*2]

    detections = [detections[batch_ixs == ix] for ix in range(img_shape[0])]

    mrcnn_mask = [detection_masks[batch_ixs == ix] for ix in range(img_shape[0])]

    # for test_forward, where no previous list exists.

    if box_results_list is None:

        box_results_list = [[] for _ in range(img_shape[0])]

    seg_preds = []

    # loop over batch and unmold detections.

    for ix in range(img_shape[0]):

        if 0 not in detections[ix].shape:

            boxes = detections[ix][:, :2 * cf.dim].astype(np.int32)

            class_ids = detections[ix][:, 2 * cf.dim + 1].astype(np.int32)

            scores = detections[ix][:, 2 * cf.dim + 2]

            masks = mrcnn_mask[ix][np.arange(boxes.shape[0]), ..., class_ids]

            # Filter out detections with zero area. Often only happens in early

            # stages of training when the network weights are still a bit random.

            if cf.dim == 2:

                exclude_ix = np.where((boxes[:, 2] - boxes[:, 0]) * (boxes[:, 3] - boxes[:, 1]) <= 0)[0]

            else:

                exclude_ix = np.where(

                    (boxes[:, 2] - boxes[:, 0]) * (boxes[:, 3] - boxes[:, 1]) * (boxes[:, 5] - boxes[:, 4]) <= 0)[0]

            if exclude_ix.shape[0] > 0:

                boxes = np.delete(boxes, exclude_ix, axis=0)

                class_ids = np.delete(class_ids, exclude_ix, axis=0)

                scores = np.delete(scores, exclude_ix, axis=0)

                masks = np.delete(masks, exclude_ix, axis=0)

            # Resize masks to original image size and set boundary threshold.

            full_masks = []

            permuted_image_shape = list(img_shape[2:]) + [img_shape[1]]

            if return_masks:

                for i in range(masks.shape[0]):

                    # Convert neural network mask to full size mask.

                    full_masks.append(mutils.unmold_mask_2D(masks[i], boxes[i], permuted_image_shape)

                    if cf.dim == 2 else mutils.unmold_mask_3D(masks[i], boxes[i], permuted_image_shape))

            # if masks are returned, take max over binary full masks of all predictions in this image.

            # right now only binary masks for plotting/monitoring. for instance segmentation return all proposal masks.

            final_masks = np.max(np.array(full_masks), 0) if len(full_masks) > 0 else np.zeros(

                (*permuted_image_shape[:-1],))

            # add final predictions to results.

            if 0 not in boxes.shape:

                for ix2, score in enumerate(scores):

                    box_results_list[ix].append({'box_coords': boxes[ix2], 'box_score': score,

                                                 'box_type': 'det', 'box_pred_class_id': class_ids[ix2]})

        else:

            # pad with zero dummy masks.

            final_masks = np.zeros(img_shape[2:])

        seg_preds.append(final_masks)

    # create and fill results dictionary.

    results_dict = {'boxes': box_results_list,

                    'seg_preds': np.round(np.array(seg_preds))[:, np.newaxis].astype('uint8')}

    return results_dict

############################################################

#  Mask R-CNN Class

############################################################

class net(nn.Module):

    def __init__(self, cf, logger):

        super(net, self).__init__()

        self.cf = cf

        self.logger = logger

        self.build()

        if self.cf.weight_init is not None:

            logger.info("using pytorch weight init of type {}".format(self.cf.weight_init))

            mutils.initialize_weights(self)

        else:

            logger.info("using default pytorch weight init")

    def build(self):

        """Build Mask R-CNN architecture."""

        # Image size must be dividable by 2 multiple times.

        h, w = self.cf.patch_size[:2]

        if h / 2**5 != int(h / 2**5) or w / 2**5 != int(w / 2**5):

            raise Exception("Image size must be dividable by 2 at least 5 times "

                            "to avoid fractions when downscaling and upscaling."

                            "For example, use 256, 320, 384, 448, 512, ... etc. ")

        if len(self.cf.patch_size) == 3:

            d = self.cf.patch_size[2]

            if d / 2**3 != int(d / 2**3):

                raise Exception("Image z dimension must be dividable by 2 at least 3 times "

                                "to avoid fractions when downscaling and upscaling.")

        # instanciate abstract multi dimensional conv class and backbone class.

        conv = mutils.NDConvGenerator(self.cf.dim)

        backbone = utils.import_module('bbone', self.cf.backbone_path)

        # build Anchors, FPN, RPN, Classifier / Bbox-Regressor -head, Mask-head

        self.np_anchors = mutils.generate_pyramid_anchors(self.logger, self.cf)

        self.anchors = torch.from_numpy(self.np_anchors).float().cuda()

        self.fpn = backbone.FPN(self.cf, conv)

        self.rpn = RPN(self.cf, conv)

        self.classifier = Classifier(self.cf, conv)

        self.mask = Mask(self.cf, conv)

    def train_forward(self, batch, is_validation=False):

        """

        train method (also used for validation monitoring). wrapper around forward pass of network. prepares input data

        for processing, computes losses, and stores outputs in a dictionary.

        :param batch: dictionary containing 'data', 'seg', etc.

                    data_dict['roi_masks']: (b, n(b), 1, h(n), w(n) (z(n))) list like batch['class_target'] but with

                    arrays (masks) inplace of integers. n == number of rois per this batch element.

        :return: results_dict: dictionary with keys:

                'boxes': list over batch elements. each batch element is a list of boxes. each box is a dictionary:

                        [[{box_0}, ... {box_n}], [{box_0}, ... {box_n}], ...]

                'seg_preds': pixel-wise class predictions (b, 1, y, x, (z)) with values [0, n_classes].

                'monitor_values': dict of values to be monitored.

        """

        img = batch['data']

        if "roi_labels" in batch.keys():

            raise Exception("Key for roi-wise class targets changed in v0.1.0 from 'roi_labels' to 'class_target'.\n"

                            "If you use DKFZ's batchgenerators, please make sure you run version >= 0.20.1.")

        gt_class_ids = batch['class_target']

        gt_boxes = batch['bb_target']

        #axes = (0, 2, 3, 1) if self.cf.dim == 2 else (0, 2, 3, 4, 1)

        #gt_masks = [np.transpose(batch['roi_masks'][ii], axes=axes) for ii in range(len(batch['roi_masks']))]

        # --> now GT masks has c==channels in last dimension.

        gt_masks = batch['roi_masks']

        img = torch.from_numpy(img).float().cuda()

        batch_rpn_class_loss = torch.FloatTensor([0]).cuda()

        batch_rpn_bbox_loss = torch.FloatTensor([0]).cuda()

        # list of output boxes for monitoring/plotting. each element is a list of boxes per batch element.

        box_results_list = [[] for _ in range(img.shape[0])]

        #forward passes. 1. general forward pass, where no activations are saved in second stage (for performance

        # monitoring and loss sampling). 2. second stage forward pass of sampled rois with stored activations for backprop.

        rpn_class_logits, rpn_pred_deltas, proposal_boxes, detections, detection_masks = self.forward(img)

        mrcnn_class_logits, mrcnn_pred_deltas, mrcnn_pred_mask, target_class_ids, mrcnn_target_deltas, target_mask,  \

        sample_proposals = self.loss_samples_forward(gt_class_ids, gt_boxes, gt_masks)

        # loop over batch

        for b in range(img.shape[0]):

            if len(gt_boxes[b]) > 0:

                # add gt boxes to output list for monitoring.

                for ix in range(len(gt_boxes[b])):

                    box_results_list[b].append({'box_coords': batch['bb_target'][b][ix],

                                                'box_label': batch['class_target'][b][ix], 'box_type': 'gt'})

                # match gt boxes with anchors to generate targets for RPN losses.

                rpn_match, rpn_target_deltas = mutils.gt_anchor_matching(self.cf, self.np_anchors, gt_boxes[b])

                # add positive anchors used for loss to output list for monitoring.

                pos_anchors = mutils.clip_boxes_numpy(self.np_anchors[np.argwhere(rpn_match == 1)][:, 0], img.shape[2:])

                for p in pos_anchors:

                    box_results_list[b].append({'box_coords': p, 'box_type': 'pos_anchor'})

            else:

                rpn_match = np.array([-1]*self.np_anchors.shape[0])

                rpn_target_deltas = np.array([0])

            rpn_match_gpu = torch.from_numpy(rpn_match).cuda()

            rpn_target_deltas = torch.from_numpy(rpn_target_deltas).float().cuda()

            # compute RPN losses.

            rpn_class_loss, neg_anchor_ix = compute_rpn_class_loss(rpn_match_gpu, rpn_class_logits[b], self.cf.shem_poolsize)

            rpn_bbox_loss = compute_rpn_bbox_loss(rpn_target_deltas, rpn_pred_deltas[b], rpn_match_gpu)

            batch_rpn_class_loss += rpn_class_loss / img.shape[0]

            batch_rpn_bbox_loss += rpn_bbox_loss / img.shape[0]

            # add negative anchors used for loss to output list for monitoring.

            neg_anchors = mutils.clip_boxes_numpy(self.np_anchors[rpn_match == -1][neg_anchor_ix], img.shape[2:])

            for n in neg_anchors:

                box_results_list[b].append({'box_coords': n, 'box_type': 'neg_anchor'})

            # add highest scoring proposals to output list for monitoring.

            rpn_proposals = proposal_boxes[b][proposal_boxes[b, :, -1].argsort()][::-1]

            for r in rpn_proposals[:self.cf.n_plot_rpn_props, :-1]:

                box_results_list[b].append({'box_coords': r, 'box_type': 'prop'})

        # add positive and negative roi samples used for mrcnn losses to output list for monitoring.

        if 0 not in sample_proposals.shape:

            rois = mutils.clip_to_window(self.cf.window, sample_proposals).cpu().data.numpy()

            for ix, r in enumerate(rois):

                box_results_list[int(r[-1])].append({'box_coords': r[:-1] * self.cf.scale,

                                            'box_type': 'pos_class' if target_class_ids[ix] > 0 else 'neg_class'})

        batch_rpn_class_loss = batch_rpn_class_loss

        batch_rpn_bbox_loss = batch_rpn_bbox_loss

        # compute mrcnn losses.

        mrcnn_class_loss = compute_mrcnn_class_loss(target_class_ids, mrcnn_class_logits)

        mrcnn_bbox_loss = compute_mrcnn_bbox_loss(mrcnn_target_deltas, mrcnn_pred_deltas, target_class_ids)

        # mrcnn can be run without pixelwise annotations available (Faster R-CNN mode).

        # In this case, the mask_loss is taken out of training.

        if not self.cf.frcnn_mode:

            mrcnn_mask_loss = compute_mrcnn_mask_loss(target_mask, mrcnn_pred_mask, target_class_ids)

        else:

            mrcnn_mask_loss = torch.FloatTensor([0]).cuda()

        loss = batch_rpn_class_loss + batch_rpn_bbox_loss + mrcnn_class_loss + mrcnn_bbox_loss + mrcnn_mask_loss

        # monitor RPN performance: detection count = the number of correctly matched proposals per fg-class.

        dcount = [list(target_class_ids.cpu().data.numpy()).count(c) for c in np.arange(self.cf.head_classes)[1:]]

        # run unmolding of predictions for monitoring and merge all results to one dictionary.

        return_masks = True#self.cf.return_masks_in_val if is_validation else False

        results_dict = get_results(self.cf, img.shape, detections, detection_masks,

                                   box_results_list, return_masks=return_masks)

        results_dict['torch_loss'] = loss

        results_dict['monitor_values'] = {'loss': loss.item(), 'class_loss': mrcnn_class_loss.item()}

        results_dict['logger_string'] =  \

            "loss: {0:.2f}, rpn_class: {1:.2f}, rpn_bbox: {2:.2f}, mrcnn_class: {3:.2f}, mrcnn_bbox: {4:.2f}, " \

            "mrcnn_mask: {5:.2f}, dcount {6}".format(loss.item(), batch_rpn_class_loss.item(),

                                                     batch_rpn_bbox_loss.item(), mrcnn_class_loss.item(),

                                                     mrcnn_bbox_loss.item(), mrcnn_mask_loss.item(), dcount)

        return results_dict

    def test_forward(self, batch, return_masks=True):

        """

        test method. wrapper around forward pass of network without usage of any ground truth information.

        prepares input data for processing and stores outputs in a dictionary.

        :param batch: dictionary containing 'data'

        :param return_masks: boolean. If True, full resolution masks are returned for all proposals (speed trade-off).

        :return: results_dict: dictionary with keys:

               'boxes': list over batch elements. each batch element is a list of boxes. each box is a dictionary:

                       [[{box_0}, ... {box_n}], [{box_0}, ... {box_n}], ...]

               'seg_preds': pixel-wise class predictions (b, 1, y, x, (z)) with values [0, n_classes]

        """

        img = batch['data']

        img = torch.from_numpy(img).float().cuda()

        _, _, _, detections, detection_masks = self.forward(img)

        results_dict = get_results(self.cf, img.shape, detections, detection_masks, return_masks=return_masks)

        return results_dict

    def forward(self, img, is_training=True):

        """

        :param img: input images (b, c, y, x, (z)).

        :return: rpn_pred_logits: (b, n_anchors, 2)

        :return: rpn_pred_deltas: (b, n_anchors, (y, x, (z), log(h), log(w), (log(d))))

        :return: batch_proposal_boxes: (b, n_proposals, (y1, x1, y2, x2, (z1), (z2), batch_ix)) only for monitoring/plotting.

        :return: detections: (n_final_detections, (y1, x1, y2, x2, (z1), (z2), batch_ix, pred_class_id, pred_score)

        :return: detection_masks: (n_final_detections, n_classes, y, x, (z)) raw molded masks as returned by mask-head.

        """

        # extract features.

        fpn_outs = self.fpn(img)

        rpn_feature_maps = [fpn_outs[i] for i in self.cf.pyramid_levels]

        self.mrcnn_feature_maps = rpn_feature_maps

        # loop through pyramid layers and apply RPN.

        layer_outputs = []  # list of lists

        for p in rpn_feature_maps:

            layer_outputs.append(self.rpn(p))

        # concatenate layer outputs.

        # convert from list of lists of level outputs to list of lists of outputs across levels.

        # e.g. [[a1, b1, c1], [a2, b2, c2]] => [[a1, a2], [b1, b2], [c1, c2]]

        outputs = list(zip(*layer_outputs))

        outputs = [torch.cat(list(o), dim=1) for o in outputs]

        rpn_pred_logits, rpn_pred_probs, rpn_pred_deltas = outputs

        # generate proposals: apply predicted deltas to anchors and filter by foreground scores from RPN classifier.

        proposal_count = self.cf.post_nms_rois_training if is_training else self.cf.post_nms_rois_inference

        batch_rpn_rois, batch_proposal_boxes = refine_proposals(rpn_pred_probs, rpn_pred_deltas, proposal_count, self.anchors, self.cf)

        # merge batch dimension of proposals while storing allocation info in coordinate dimension.

        batch_ixs = torch.from_numpy(np.repeat(np.arange(batch_rpn_rois.shape[0]), batch_rpn_rois.shape[1])).float().cuda()

        rpn_rois = batch_rpn_rois.view(-1, batch_rpn_rois.shape[2])

        self.rpn_rois_batch_info = torch.cat((rpn_rois, batch_ixs.unsqueeze(1)), dim=1)

        # this is the first of two forward passes in the second stage, where no activations are stored for backprop.

        # here, all proposals are forwarded (with virtual_batch_size = batch_size * post_nms_rois.)

        # for inference/monitoring as well as sampling of rois for the loss functions.

        # processed in chunks of roi_chunk_size to re-adjust to gpu-memory.

        chunked_rpn_rois = self.rpn_rois_batch_info.split(self.cf.roi_chunk_size)