def __init__(self,
in_channels=3,
num_classes=2,
is_batchnorm=True,
is_deepsup=False,
is_CGM=False):
super(UNet3Plus, self).__init__()
# parameters
self.is_deepsup = True if is_CGM else is_deepsup
self.is_CGM = is_CGM
# internal definition
self.filters = [64, 128, 256, 512, 1024]
self.cat_channels = self.filters[0]
self.cat_blocks = 5
self.up_channels = self.cat_channels * self.cat_blocks
# layers
self.encoder = Encoder(in_channels, self.filters, is_batchnorm)
self.decoder = Decoder(self.filters, self.cat_channels,
self.up_channels)
if self.is_deepsup:
self.deepsup = DeepSup(self.up_channels, self.filters, num_classes)
if self.is_CGM:
self.cls = nn.Sequential(
nn.Dropout(p=0.5), nn.Conv2D(self.filters[4], 2, 1),
nn.AdaptiveMaxPool2D(1), nn.Sigmoid())
else:
self.outconv1 = nn.Conv2D(
self.up_channels, num_classes, 3, padding=1)
# initialise weights
for sublayer in self.sublayers():
if isinstance(sublayer, nn.Conv2D):
kaiming_normal_init(sublayer.weight)
elif isinstance(sublayer, (nn.BatchNorm, nn.SyncBatchNorm)):
kaiming_normal_init(sublayer.weight)
def __init__(self, block, depth):
super(ResNet, self).__init__()
layer_cfg = {
18: [2, 2, 2, 2],
34: [3, 4, 6, 3],
50: [3, 4, 6, 3],
101: [3, 4, 23, 3],
152: [3, 8, 36, 3]
}
layers = layer_cfg[depth]
self._norm_layer = nn.BatchNorm2D
self.inplanes = 64
self.dilation = 1
self.conv1 = nn.Conv2D(1,
self.inplanes,
kernel_size=7,
stride=2,
padding=3,
bias_attr=False)
self.bn1 = self._norm_layer(self.inplanes)
self.relu = nn.ReLU()
self.maxpool = nn.MaxPool2D(kernel_size=3, stride=2, padding=1)
self.layer1 = self._make_layer(block, 64, layers[0])
self.layer2 = self._make_layer(block, 128, layers[1], stride=2)
self.layer3 = self._make_layer(block, 256, layers[2], stride=2)
self.layer4 = self._make_layer(block, 512, layers[3], stride=2)
self.pool = nn.AdaptiveMaxPool2D((1, 1))
self.bn4 = nn.BatchNorm2D(512 * block.expansion)
self.dropout = nn.Dropout()
self.fc5 = nn.Linear(512 * block.expansion, 512)
self.bn5 = nn.BatchNorm1D(512)
def __init__(self, in_channels, ratio=8):
super(CAM, self).__init__()
self.avg_pool = nn.AdaptiveAvgPool2D(1)
self.max_pool = nn.AdaptiveMaxPool2D(1)
self.mlp = nn.Sequential(
nn.Conv2D(in_channels, in_channels//ratio, 1),
nn.ReLU(),
nn.Conv2D(in_channels//ratio, in_channels, 1)
)
def __init__(self, in_planes, ratio=16):
super(ChannelAttention, self).__init__()
self.avg_pool = nn.AdaptiveAvgPool2D(1)
self.max_pool = nn.AdaptiveMaxPool2D(1)
self.fc1 = nn.Conv2D(in_planes, in_planes // 16, 1)
self.relu1 = nn.ReLU()
self.fc2 = nn.Conv2D(in_planes // 16, in_planes, 1)
self.sigmoid = nn.Sigmoid()
def __init__(self, block, layers, use_se=True):
self.inplanes = 64
self.use_se = use_se
super(ResNet, self).__init__()
self.conv1 = nn.Conv2D(1, 64, kernel_size=3)
self.bn1 = nn.BatchNorm2D(64)
self.prelu = nn.PReLU()
self.maxpool = nn.MaxPool2D(kernel_size=3, stride=3)
self.layer1 = self._make_layer(block, 64, layers[0])
self.layer2 = self._make_layer(block, 128, layers[1], stride=2)
self.layer3 = self._make_layer(block, 256, layers[2], stride=2)
self.layer4 = self._make_layer(block, 512, layers[3], stride=2)
self.pool = nn.AdaptiveMaxPool2D((1, 1))
self.bn4 = nn.BatchNorm2D(512)
self.dropout = nn.Dropout()
self.flatten = nn.Flatten()
self.fc5 = nn.Linear(512, 512)
self.bn5 = nn.BatchNorm1D(512)
def func_test_layer_str(self):
module = nn.ELU(0.2)
self.assertEqual(str(module), 'ELU(alpha=0.2)')
module = nn.CELU(0.2)
self.assertEqual(str(module), 'CELU(alpha=0.2)')
module = nn.GELU(True)
self.assertEqual(str(module), 'GELU(approximate=True)')
module = nn.Hardshrink()
self.assertEqual(str(module), 'Hardshrink(threshold=0.5)')
module = nn.Hardswish(name="Hardswish")
self.assertEqual(str(module), 'Hardswish(name=Hardswish)')
module = nn.Tanh(name="Tanh")
self.assertEqual(str(module), 'Tanh(name=Tanh)')
module = nn.Hardtanh(name="Hardtanh")
self.assertEqual(str(module),
'Hardtanh(min=-1.0, max=1.0, name=Hardtanh)')
module = nn.PReLU(1, 0.25, name="PReLU", data_format="NCHW")
self.assertEqual(
str(module),
'PReLU(num_parameters=1, data_format=NCHW, init=0.25, dtype=float32, name=PReLU)'
)
module = nn.ReLU()
self.assertEqual(str(module), 'ReLU()')
module = nn.ReLU6()
self.assertEqual(str(module), 'ReLU6()')
module = nn.SELU()
self.assertEqual(
str(module),
'SELU(scale=1.0507009873554805, alpha=1.6732632423543772)')
module = nn.LeakyReLU()
self.assertEqual(str(module), 'LeakyReLU(negative_slope=0.01)')
module = nn.Sigmoid()
self.assertEqual(str(module), 'Sigmoid()')
module = nn.Hardsigmoid()
self.assertEqual(str(module), 'Hardsigmoid()')
module = nn.Softplus()
self.assertEqual(str(module), 'Softplus(beta=1, threshold=20)')
module = nn.Softshrink()
self.assertEqual(str(module), 'Softshrink(threshold=0.5)')
module = nn.Softsign()
self.assertEqual(str(module), 'Softsign()')
module = nn.Swish()
self.assertEqual(str(module), 'Swish()')
module = nn.Tanhshrink()
self.assertEqual(str(module), 'Tanhshrink()')
module = nn.ThresholdedReLU()
self.assertEqual(str(module), 'ThresholdedReLU(threshold=1.0)')
module = nn.LogSigmoid()
self.assertEqual(str(module), 'LogSigmoid()')
module = nn.Softmax()
self.assertEqual(str(module), 'Softmax(axis=-1)')
module = nn.LogSoftmax()
self.assertEqual(str(module), 'LogSoftmax(axis=-1)')
module = nn.Maxout(groups=2)
self.assertEqual(str(module), 'Maxout(groups=2, axis=1)')
module = nn.Linear(2, 4, name='linear')
self.assertEqual(
str(module),
'Linear(in_features=2, out_features=4, dtype=float32, name=linear)'
)
module = nn.Upsample(size=[12, 12])
self.assertEqual(
str(module),
'Upsample(size=[12, 12], mode=nearest, align_corners=False, align_mode=0, data_format=NCHW)'
)
module = nn.UpsamplingNearest2D(size=[12, 12])
self.assertEqual(
str(module),
'UpsamplingNearest2D(size=[12, 12], data_format=NCHW)')
module = nn.UpsamplingBilinear2D(size=[12, 12])
self.assertEqual(
str(module),
'UpsamplingBilinear2D(size=[12, 12], data_format=NCHW)')
module = nn.Bilinear(in1_features=5, in2_features=4, out_features=1000)
self.assertEqual(
str(module),
'Bilinear(in1_features=5, in2_features=4, out_features=1000, dtype=float32)'
)
module = nn.Dropout(p=0.5)
self.assertEqual(str(module),
'Dropout(p=0.5, axis=None, mode=upscale_in_train)')
module = nn.Dropout2D(p=0.5)
self.assertEqual(str(module), 'Dropout2D(p=0.5, data_format=NCHW)')
module = nn.Dropout3D(p=0.5)
self.assertEqual(str(module), 'Dropout3D(p=0.5, data_format=NCDHW)')
module = nn.AlphaDropout(p=0.5)
self.assertEqual(str(module), 'AlphaDropout(p=0.5)')
module = nn.Pad1D(padding=[1, 2], mode='constant')
self.assertEqual(
str(module),
'Pad1D(padding=[1, 2], mode=constant, value=0.0, data_format=NCL)')
module = nn.Pad2D(padding=[1, 0, 1, 2], mode='constant')
self.assertEqual(
str(module),
'Pad2D(padding=[1, 0, 1, 2], mode=constant, value=0.0, data_format=NCHW)'
)
module = nn.ZeroPad2D(padding=[1, 0, 1, 2])
self.assertEqual(str(module),
'ZeroPad2D(padding=[1, 0, 1, 2], data_format=NCHW)')
module = nn.Pad3D(padding=[1, 0, 1, 2, 0, 0], mode='constant')
self.assertEqual(
str(module),
'Pad3D(padding=[1, 0, 1, 2, 0, 0], mode=constant, value=0.0, data_format=NCDHW)'
)
module = nn.CosineSimilarity(axis=0)
self.assertEqual(str(module), 'CosineSimilarity(axis=0, eps=1e-08)')
module = nn.Embedding(10, 3, sparse=True)
self.assertEqual(str(module), 'Embedding(10, 3, sparse=True)')
module = nn.Conv1D(3, 2, 3)
self.assertEqual(str(module),
'Conv1D(3, 2, kernel_size=[3], data_format=NCL)')
module = nn.Conv1DTranspose(2, 1, 2)
self.assertEqual(
str(module),
'Conv1DTranspose(2, 1, kernel_size=[2], data_format=NCL)')
module = nn.Conv2D(4, 6, (3, 3))
self.assertEqual(str(module),
'Conv2D(4, 6, kernel_size=[3, 3], data_format=NCHW)')
module = nn.Conv2DTranspose(4, 6, (3, 3))
self.assertEqual(
str(module),
'Conv2DTranspose(4, 6, kernel_size=[3, 3], data_format=NCHW)')
module = nn.Conv3D(4, 6, (3, 3, 3))
self.assertEqual(
str(module),
'Conv3D(4, 6, kernel_size=[3, 3, 3], data_format=NCDHW)')
module = nn.Conv3DTranspose(4, 6, (3, 3, 3))
self.assertEqual(
str(module),
'Conv3DTranspose(4, 6, kernel_size=[3, 3, 3], data_format=NCDHW)')
module = nn.PairwiseDistance()
self.assertEqual(str(module), 'PairwiseDistance(p=2.0)')
module = nn.InstanceNorm1D(2)
self.assertEqual(str(module),
'InstanceNorm1D(num_features=2, epsilon=1e-05)')
module = nn.InstanceNorm2D(2)
self.assertEqual(str(module),
'InstanceNorm2D(num_features=2, epsilon=1e-05)')
module = nn.InstanceNorm3D(2)
self.assertEqual(str(module),
'InstanceNorm3D(num_features=2, epsilon=1e-05)')
module = nn.GroupNorm(num_channels=6, num_groups=6)
self.assertEqual(
str(module),
'GroupNorm(num_groups=6, num_channels=6, epsilon=1e-05)')
module = nn.LayerNorm([2, 2, 3])
self.assertEqual(
str(module),
'LayerNorm(normalized_shape=[2, 2, 3], epsilon=1e-05)')
module = nn.BatchNorm1D(1)
self.assertEqual(
str(module),
'BatchNorm1D(num_features=1, momentum=0.9, epsilon=1e-05, data_format=NCL)'
)
module = nn.BatchNorm2D(1)
self.assertEqual(
str(module),
'BatchNorm2D(num_features=1, momentum=0.9, epsilon=1e-05)')
module = nn.BatchNorm3D(1)
self.assertEqual(
str(module),
'BatchNorm3D(num_features=1, momentum=0.9, epsilon=1e-05, data_format=NCDHW)'
)
module = nn.SyncBatchNorm(2)
self.assertEqual(
str(module),
'SyncBatchNorm(num_features=2, momentum=0.9, epsilon=1e-05)')
module = nn.LocalResponseNorm(size=5)
self.assertEqual(
str(module),
'LocalResponseNorm(size=5, alpha=0.0001, beta=0.75, k=1.0)')
module = nn.AvgPool1D(kernel_size=2, stride=2, padding=0)
self.assertEqual(str(module),
'AvgPool1D(kernel_size=2, stride=2, padding=0)')
module = nn.AvgPool2D(kernel_size=2, stride=2, padding=0)
self.assertEqual(str(module),
'AvgPool2D(kernel_size=2, stride=2, padding=0)')
module = nn.AvgPool3D(kernel_size=2, stride=2, padding=0)
self.assertEqual(str(module),
'AvgPool3D(kernel_size=2, stride=2, padding=0)')
module = nn.MaxPool1D(kernel_size=2, stride=2, padding=0)
self.assertEqual(str(module),
'MaxPool1D(kernel_size=2, stride=2, padding=0)')
module = nn.MaxPool2D(kernel_size=2, stride=2, padding=0)
self.assertEqual(str(module),
'MaxPool2D(kernel_size=2, stride=2, padding=0)')
module = nn.MaxPool3D(kernel_size=2, stride=2, padding=0)
self.assertEqual(str(module),
'MaxPool3D(kernel_size=2, stride=2, padding=0)')
module = nn.AdaptiveAvgPool1D(output_size=16)
self.assertEqual(str(module), 'AdaptiveAvgPool1D(output_size=16)')
module = nn.AdaptiveAvgPool2D(output_size=3)
self.assertEqual(str(module), 'AdaptiveAvgPool2D(output_size=3)')
module = nn.AdaptiveAvgPool3D(output_size=3)
self.assertEqual(str(module), 'AdaptiveAvgPool3D(output_size=3)')
module = nn.AdaptiveMaxPool1D(output_size=16, return_mask=True)
self.assertEqual(
str(module), 'AdaptiveMaxPool1D(output_size=16, return_mask=True)')
module = nn.AdaptiveMaxPool2D(output_size=3, return_mask=True)
self.assertEqual(str(module),
'AdaptiveMaxPool2D(output_size=3, return_mask=True)')
module = nn.AdaptiveMaxPool3D(output_size=3, return_mask=True)
self.assertEqual(str(module),
'AdaptiveMaxPool3D(output_size=3, return_mask=True)')
module = nn.SimpleRNNCell(16, 32)
self.assertEqual(str(module), 'SimpleRNNCell(16, 32)')
module = nn.LSTMCell(16, 32)
self.assertEqual(str(module), 'LSTMCell(16, 32)')
module = nn.GRUCell(16, 32)
self.assertEqual(str(module), 'GRUCell(16, 32)')
module = nn.PixelShuffle(3)
self.assertEqual(str(module), 'PixelShuffle(upscale_factor=3)')
module = nn.SimpleRNN(16, 32, 2)
self.assertEqual(
str(module),
'SimpleRNN(16, 32, num_layers=2\n (0): RNN(\n (cell): SimpleRNNCell(16, 32)\n )\n (1): RNN(\n (cell): SimpleRNNCell(32, 32)\n )\n)'
)
module = nn.LSTM(16, 32, 2)
self.assertEqual(
str(module),
'LSTM(16, 32, num_layers=2\n (0): RNN(\n (cell): LSTMCell(16, 32)\n )\n (1): RNN(\n (cell): LSTMCell(32, 32)\n )\n)'
)
module = nn.GRU(16, 32, 2)
self.assertEqual(
str(module),
'GRU(16, 32, num_layers=2\n (0): RNN(\n (cell): GRUCell(16, 32)\n )\n (1): RNN(\n (cell): GRUCell(32, 32)\n )\n)'
)
module1 = nn.Sequential(
('conv1', nn.Conv2D(1, 20, 5)), ('relu1', nn.ReLU()),
('conv2', nn.Conv2D(20, 64, 5)), ('relu2', nn.ReLU()))
self.assertEqual(
str(module1),
'Sequential(\n '\
'(conv1): Conv2D(1, 20, kernel_size=[5, 5], data_format=NCHW)\n '\
'(relu1): ReLU()\n '\
'(conv2): Conv2D(20, 64, kernel_size=[5, 5], data_format=NCHW)\n '\
'(relu2): ReLU()\n)'
)
module2 = nn.Sequential(
nn.Conv3DTranspose(4, 6, (3, 3, 3)),
nn.AvgPool3D(kernel_size=2, stride=2, padding=0),
nn.Tanh(name="Tanh"), module1, nn.Conv3D(4, 6, (3, 3, 3)),
nn.MaxPool3D(kernel_size=2, stride=2, padding=0), nn.GELU(True))
self.assertEqual(
str(module2),
'Sequential(\n '\
'(0): Conv3DTranspose(4, 6, kernel_size=[3, 3, 3], data_format=NCDHW)\n '\
'(1): AvgPool3D(kernel_size=2, stride=2, padding=0)\n '\
'(2): Tanh(name=Tanh)\n '\
'(3): Sequential(\n (conv1): Conv2D(1, 20, kernel_size=[5, 5], data_format=NCHW)\n (relu1): ReLU()\n'\
' (conv2): Conv2D(20, 64, kernel_size=[5, 5], data_format=NCHW)\n (relu2): ReLU()\n )\n '\
'(4): Conv3D(4, 6, kernel_size=[3, 3, 3], data_format=NCDHW)\n '\
'(5): MaxPool3D(kernel_size=2, stride=2, padding=0)\n '\
'(6): GELU(approximate=True)\n)'
)
