225 lines
7.4 KiB
Python
225 lines
7.4 KiB
Python
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import math
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import random
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from collections import namedtuple
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import torch
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from torch import nn as nn
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import torch.nn.functional as F
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from util.logconf import logging
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from util.unet import UNet
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log = logging.getLogger(__name__)
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# log.setLevel(logging.WARN)
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# log.setLevel(logging.INFO)
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log.setLevel(logging.DEBUG)
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class UNetWrapper(nn.Module):
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def __init__(self, **kwargs):
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super().__init__()
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self.input_batchnorm = nn.BatchNorm2d(kwargs['in_channels'])
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self.unet = UNet(**kwargs)
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self.final = nn.Sigmoid()
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self._init_weights()
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def _init_weights(self):
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init_set = {
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nn.Conv2d,
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nn.Conv3d,
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nn.ConvTranspose2d,
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nn.ConvTranspose3d,
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nn.Linear,
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}
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for m in self.modules():
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if type(m) in init_set:
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nn.init.kaiming_normal_(
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m.weight.data, mode='fan_out', nonlinearity='relu', a=0
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)
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if m.bias is not None:
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fan_in, fan_out = \
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nn.init._calculate_fan_in_and_fan_out(m.weight.data)
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bound = 1 / math.sqrt(fan_out)
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nn.init.normal_(m.bias, -bound, bound)
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# nn.init.constant_(self.unet.last.bias, -4)
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# nn.init.constant_(self.unet.last.bias, 4)
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def forward(self, input_batch):
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bn_output = self.input_batchnorm(input_batch)
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un_output = self.unet(bn_output)
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fn_output = self.final(un_output)
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return fn_output
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class SegmentationAugmentation(nn.Module):
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def __init__(
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self, flip=None, offset=None, scale=None, rotate=None, noise=None
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):
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super().__init__()
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self.flip = flip
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self.offset = offset
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self.scale = scale
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self.rotate = rotate
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self.noise = noise
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def forward(self, input_g, label_g):
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transform_t = self._build2dTransformMatrix()
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transform_t = transform_t.expand(input_g.shape[0], -1, -1)
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transform_t = transform_t.to(input_g.device, torch.float32)
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affine_t = F.affine_grid(transform_t[:,:2],
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input_g.size(), align_corners=False)
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augmented_input_g = F.grid_sample(input_g,
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affine_t, padding_mode='border',
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align_corners=False)
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augmented_label_g = F.grid_sample(label_g.to(torch.float32),
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affine_t, padding_mode='border',
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align_corners=False)
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if self.noise:
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noise_t = torch.randn_like(augmented_input_g)
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noise_t *= self.noise
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augmented_input_g += noise_t
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return augmented_input_g, augmented_label_g > 0.5
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def _build2dTransformMatrix(self):
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transform_t = torch.eye(3)
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for i in range(2):
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if self.flip:
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if random.random() > 0.5:
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transform_t[i,i] *= -1
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if self.offset:
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offset_float = self.offset
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random_float = (random.random() * 2 - 1)
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transform_t[2,i] = offset_float * random_float
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if self.scale:
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scale_float = self.scale
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random_float = (random.random() * 2 - 1)
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transform_t[i,i] *= 1.0 + scale_float * random_float
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if self.rotate:
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angle_rad = random.random() * math.pi * 2
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s = math.sin(angle_rad)
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c = math.cos(angle_rad)
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rotation_t = torch.tensor([
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[c, -s, 0],
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[s, c, 0],
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[0, 0, 1]])
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transform_t @= rotation_t
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return transform_t
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# MaskTuple = namedtuple('MaskTuple', 'raw_dense_mask, dense_mask, body_mask, air_mask, raw_candidate_mask, candidate_mask, lung_mask, neg_mask, pos_mask')
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#
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# class SegmentationMask(nn.Module):
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# def __init__(self):
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# super().__init__()
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#
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# self.conv_list = nn.ModuleList([
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# self._make_circle_conv(radius) for radius in range(1, 8)
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# ])
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#
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# def _make_circle_conv(self, radius):
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# diameter = 1 + radius * 2
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#
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# a = torch.linspace(-1, 1, steps=diameter)**2
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# b = (a[None] + a[:, None])**0.5
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#
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# circle_weights = (b <= 1.0).to(torch.float32)
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#
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# conv = nn.Conv2d(1, 1, kernel_size=diameter, padding=radius, bias=False)
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# conv.weight.data.fill_(1)
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# conv.weight.data *= circle_weights / circle_weights.sum()
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#
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# return conv
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#
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#
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# def erode(self, input_mask, radius, threshold=1):
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# conv = self.conv_list[radius - 1]
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# input_float = input_mask.to(torch.float32)
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# result = conv(input_float)
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#
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# # log.debug(['erode in ', radius, threshold, input_float.min().item(), input_float.mean().item(), input_float.max().item()])
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# # log.debug(['erode out', radius, threshold, result.min().item(), result.mean().item(), result.max().item()])
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#
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# return result >= threshold
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#
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# def deposit(self, input_mask, radius, threshold=0):
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# conv = self.conv_list[radius - 1]
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# input_float = input_mask.to(torch.float32)
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# result = conv(input_float)
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#
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# # log.debug(['deposit in ', radius, threshold, input_float.min().item(), input_float.mean().item(), input_float.max().item()])
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# # log.debug(['deposit out', radius, threshold, result.min().item(), result.mean().item(), result.max().item()])
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#
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# return result > threshold
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#
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# def fill_cavity(self, input_mask):
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# cumsum = input_mask.cumsum(-1)
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# filled_mask = (cumsum > 0)
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# filled_mask &= (cumsum < cumsum[..., -1:])
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# cumsum = input_mask.cumsum(-2)
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# filled_mask &= (cumsum > 0)
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# filled_mask &= (cumsum < cumsum[..., -1:, :])
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#
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# return filled_mask
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#
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#
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# def forward(self, input_g, raw_pos_g):
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# gcc_g = input_g + 1
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#
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# with torch.no_grad():
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# # log.info(['gcc_g', gcc_g.min(), gcc_g.mean(), gcc_g.max()])
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#
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# raw_dense_mask = gcc_g > 0.7
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# dense_mask = self.deposit(raw_dense_mask, 2)
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# dense_mask = self.erode(dense_mask, 6)
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# dense_mask = self.deposit(dense_mask, 4)
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#
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# body_mask = self.fill_cavity(dense_mask)
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# air_mask = self.deposit(body_mask & ~dense_mask, 5)
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# air_mask = self.erode(air_mask, 6)
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#
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# lung_mask = self.deposit(air_mask, 5)
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#
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# raw_candidate_mask = gcc_g > 0.4
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# raw_candidate_mask &= air_mask
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# candidate_mask = self.erode(raw_candidate_mask, 1)
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# candidate_mask = self.deposit(candidate_mask, 1)
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#
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# pos_mask = self.deposit((raw_pos_g > 0.5) & lung_mask, 2)
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#
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# neg_mask = self.deposit(candidate_mask, 1)
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# neg_mask &= ~pos_mask
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# neg_mask &= lung_mask
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#
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# # label_g = (neg_mask | pos_mask).to(torch.float32)
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# label_g = (pos_mask).to(torch.float32)
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# neg_g = neg_mask.to(torch.float32)
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# pos_g = pos_mask.to(torch.float32)
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#
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# mask_dict = {
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# 'raw_dense_mask': raw_dense_mask,
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# 'dense_mask': dense_mask,
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# 'body_mask': body_mask,
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# 'air_mask': air_mask,
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# 'raw_candidate_mask': raw_candidate_mask,
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# 'candidate_mask': candidate_mask,
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# 'lung_mask': lung_mask,
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# 'neg_mask': neg_mask,
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# 'pos_mask': pos_mask,
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# }
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#
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# return label_g, neg_g, pos_g, lung_mask, mask_dict
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