forked from mindspore-Ecosystem/mindspore
!14410 modify conv3d and conv3dtranspose for unet3d
From: @Somnus2020 Reviewed-by: @liangchenghui,@c_34 Signed-off-by: @liangchenghui
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@ -102,7 +102,6 @@ python eval.py --data_url=/path/to/data/ --seg_url=/path/to/segment/ --ckpt_path
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│ ├──transform.py // handle dataset
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│ ├──convert_nifti.py // convert dataset
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│ ├──loss.py // loss
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│ ├──conv.py // conv components
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│ ├──utils.py // General components (callback function)
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│ ├──unet3d_model.py // Unet3D model
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│ ├──unet3d_parts.py // Unet3D part
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@ -1,90 +0,0 @@
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# Copyright 2021 Huawei Technologies Co., Ltd
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# less required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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# ============================================================================
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import mindspore.nn as nn
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from mindspore import Parameter
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from mindspore import dtype as mstype
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from mindspore.ops import operations as P
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from mindspore.ops.operations import nn_ops as nps
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from mindspore.common.initializer import initializer
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def weight_variable(shape):
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init_value = initializer('Normal', shape, mstype.float32)
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return Parameter(init_value)
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class Conv3D(nn.Cell):
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def __init__(self,
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in_channel,
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out_channel,
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kernel_size,
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mode=1,
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pad_mode="valid",
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pad=0,
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stride=1,
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dilation=1,
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group=1,
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data_format="NCDHW",
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bias_init="zeros",
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has_bias=True):
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super().__init__()
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self.weight_shape = (out_channel, in_channel, kernel_size[0], kernel_size[1], kernel_size[2])
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self.weight = weight_variable(self.weight_shape)
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self.conv = nps.Conv3D(out_channel=out_channel, kernel_size=kernel_size, mode=mode, \
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pad_mode=pad_mode, pad=pad, stride=stride, dilation=dilation, \
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group=group, data_format=data_format)
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self.bias_init = bias_init
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self.has_bias = has_bias
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self.bias_add = P.BiasAdd(data_format=data_format)
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if self.has_bias:
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self.bias = Parameter(initializer(self.bias_init, [out_channel]), name='bias')
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def construct(self, x):
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output = self.conv(x, self.weight)
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if self.has_bias:
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output = self.bias_add(output, self.bias)
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return output
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class Conv3DTranspose(nn.Cell):
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def __init__(self,
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in_channel,
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out_channel,
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kernel_size,
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mode=1,
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pad=0,
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stride=1,
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dilation=1,
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group=1,
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output_padding=0,
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data_format="NCDHW",
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bias_init="zeros",
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has_bias=True):
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super().__init__()
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self.weight_shape = (in_channel, out_channel, kernel_size[0], kernel_size[1], kernel_size[2])
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self.weight = weight_variable(self.weight_shape)
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self.conv_transpose = nps.Conv3DTranspose(in_channel=in_channel, out_channel=out_channel,\
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kernel_size=kernel_size, mode=mode, pad=pad, stride=stride, \
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dilation=dilation, group=group, output_padding=output_padding, \
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data_format=data_format)
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self.bias_init = bias_init
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self.has_bias = has_bias
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self.bias_add = P.BiasAdd(data_format=data_format)
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if self.has_bias:
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self.bias = Parameter(initializer(self.bias_init, [out_channel]), name='bias')
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def construct(self, x):
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output = self.conv_transpose(x, self.weight)
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if self.has_bias:
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output = self.bias_add(output, self.bias)
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return output
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@ -16,7 +16,6 @@
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import mindspore.nn as nn
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from mindspore import dtype as mstype
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from mindspore.ops import operations as P
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from src.conv import Conv3D, Conv3DTranspose
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class BatchNorm3d(nn.Cell):
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def __init__(self, num_features):
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@ -39,22 +38,22 @@ class ResidualUnit(nn.Cell):
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self.down = down
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self.in_channel = in_channel
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self.out_channel = out_channel
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self.down_conv_1 = Conv3D(in_channel, out_channel, kernel_size=(3, 3, 3), \
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pad_mode="pad", stride=self.stride, pad=1)
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self.down_conv_1 = nn.Conv3d(in_channel, out_channel, kernel_size=(3, 3, 3), \
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pad_mode="pad", stride=self.stride, padding=1)
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self.is_output = is_output
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if not is_output:
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self.batchNormal1 = BatchNorm3d(num_features=self.out_channel)
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self.relu1 = nn.PReLU()
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if self.down:
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self.down_conv_2 = Conv3D(out_channel, out_channel, kernel_size=(3, 3, 3), \
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pad_mode="pad", stride=1, pad=1)
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self.down_conv_2 = nn.Conv3d(out_channel, out_channel, kernel_size=(3, 3, 3), \
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pad_mode="pad", stride=1, padding=1)
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self.relu2 = nn.PReLU()
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if kernel_size[0] == 1:
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self.residual = Conv3D(in_channel, out_channel, kernel_size=(1, 1, 1), \
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pad_mode="valid", stride=self.stride)
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self.residual = nn.Conv3d(in_channel, out_channel, kernel_size=(1, 1, 1), \
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pad_mode="valid", stride=self.stride)
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else:
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self.residual = Conv3D(in_channel, out_channel, kernel_size=(3, 3, 3), \
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pad_mode="pad", stride=self.stride, pad=1)
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self.residual = nn.Conv3d(in_channel, out_channel, kernel_size=(3, 3, 3), \
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pad_mode="pad", stride=self.stride, padding=1)
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self.batchNormal2 = BatchNorm3d(num_features=self.out_channel)
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@ -93,9 +92,10 @@ class Up(nn.Cell):
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self.down_in_channel = down_in_channel
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self.out_channel = out_channel
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self.stride = stride
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self.conv3d_transpose = Conv3DTranspose(in_channel=self.in_channel + self.down_in_channel, \
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pad=1, out_channel=self.out_channel, kernel_size=(3, 3, 3), \
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stride=self.stride, output_padding=(1, 1, 1))
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self.conv3d_transpose = nn.Conv3dTranspose(in_channels=self.in_channel + self.down_in_channel, \
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out_channels=self.out_channel, kernel_size=(3, 3, 3), \
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pad_mode="pad", stride=self.stride, \
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output_padding=(1, 1, 1), padding=1)
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self.concat = P.Concat(axis=1)
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self.conv = ResidualUnit(self.out_channel, self.out_channel, stride=1, down=False, \
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