Upload UNetMSS3D

UNetConfigs.py

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+from transformers import PretrainedConfig
+from typing import List
+
+class UNet3DConfig(PretrainedConfig):
+    model_type = "UNet"
+    def __init__(
+            self,
+            in_ch=1, 
+            out_ch=1, 
+            init_features=64,
+            **kwargs):
+        self.in_ch = in_ch
+        self.out_ch = out_ch
+        self.init_features = init_features
+        super().__init__(**kwargs)
+
+class UNetMSS3DConfig(PretrainedConfig):
+    model_type = "UNetMSS"
+    def __init__(
+            self,
+            in_ch=1, 
+            out_ch=1, 
+            output_dir=None,
+            init_features=64,
+            **kwargs):
+        self.in_ch = in_ch
+        self.out_ch = out_ch
+        self.output_dir = output_dir
+        self.init_features = init_features
+        super().__init__(**kwargs)

UNets.py

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+from transformers import PreTrainedModel
+from .unet3d import U_Net, U_Net_DeepSup
+from .UNetConfigs import UNet3DConfig, UNetMSS3DConfig
+
+class UNet3D(PreTrainedModel):
+    config_class = UNet3DConfig
+    def __init__(self, config):
+        super().__init__(config)
+        self.model = U_Net(
+            in_ch=config.in_ch, 
+            out_ch=config.out_ch, 
+            init_features=config.init_features)
+    def forward(self, x):
+        return self.model(x)
+    
+class UNetMSS3D(PreTrainedModel):
+    config_class = UNetMSS3DConfig
+    def __init__(self, config):
+        super().__init__(config)
+        self.model = U_Net_DeepSup(
+            in_ch=config.in_ch, 
+            out_ch=config.out_ch, 
+            output_dir=config.output_dir,
+            init_features=config.init_features)
+    def forward(self, x):
+        return self.model(x)

config.json

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+{
+  "architectures": [
+    "UNetMSS3D"
+  ],
+  "auto_map": {
+    "AutoConfig": "UNetConfigs.UNetMSS3DConfig",
+    "AutoModel": "UNets.UNetMSS3D"
+  },
+  "in_ch": 1,
+  "init_features": 64,
+  "model_type": "UNetMSS",
+  "out_ch": 1,
+  "output_dir": null,
+  "torch_dtype": "float32",
+  "transformers_version": "4.44.2"
+}

model.safetensors

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+version https://git-lfs.github.com/spec/v1
+oid sha256:563f50ace879ccd7ac1846a2d6aa66cf9471a5243d5dbcdc8d0cb1196a465063
+size 414260220

unet3d.py

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+#!/usr/bin/env python
+ 
+# from __future__ import print_function, division
+'''
+
+This script is from the DS6 (https://github.com/soumickmj/DS6/blob/main/Models/unet3d.py), 
+and then the SPOCKMIP repository (https://github.com/soumickmj/SPOCKMIP/blob/master/Models/unet3d.py)
+
+Part of the DS6 paper: 
+"DS6, Deformation-Aware Semi-Supervised Learning: Application to Small Vessel Segmentation with Noisy Training Data" 
+(https://doi.org/10.3390/jimaging8100259)
+
+and the SPOCKMIP paper: 
+"SPOCKMIP: Segmentation of Vessels in MRAs with Enhanced Continuity using Maximum Intensity Projection as Loss" 
+(https://doi.org/10.48550/arXiv.2407.08655)
+
+'''
+
+
+import torch
+import torch.nn as nn
+import torch.utils.data
+import os
+
+__author__ = "Kartik Prabhu, Mahantesh Pattadkal, and Soumick Chatterjee"
+__copyright__ = "Copyright 2020, Faculty of Computer Science, Otto von Guericke University Magdeburg, Germany"
+__credits__ = ["Kartik Prabhu", "Mahantesh Pattadkal", "Soumick Chatterjee"]
+__license__ = "GPL"
+__version__ = "1.0.0"
+__maintainer__ = "Soumick Chatterjee"
+__email__ = "[email protected]"
+__status__ = "Production"
+
+class conv_block(nn.Module):
+    """
+    Convolution Block
+    """
+
+    def __init__(self, in_channels, out_channels, k_size=3, stride=1, padding=1, bias=True):
+        super(conv_block, self).__init__()
+        self.conv = nn.Sequential(
+            nn.Conv3d(in_channels=in_channels, out_channels=out_channels, kernel_size=k_size,
+                      stride=stride, padding=padding, bias=bias),
+            nn.BatchNorm3d(num_features=out_channels),
+            nn.LeakyReLU(inplace=True),
+            nn.Conv3d(in_channels=out_channels, out_channels=out_channels, kernel_size=k_size,
+                      stride=stride, padding=padding, bias=bias),
+            nn.BatchNorm3d(num_features=out_channels),
+            nn.LeakyReLU(inplace=True)
+        )
+
+    def forward(self, x):
+        x = self.conv(x)
+        return x
+
+
+class up_conv(nn.Module):
+    """
+    Up Convolution Block
+    """
+
+    # def __init__(self, in_ch, out_ch):
+    def __init__(self, in_channels, out_channels, k_size=3, stride=1, padding=1, bias=True):
+        super(up_conv, self).__init__()
+        self.up = nn.Sequential(
+            nn.Upsample(scale_factor=2),
+            nn.Conv3d(in_channels=in_channels, out_channels=out_channels, kernel_size=k_size,
+                      stride=stride, padding=padding, bias=bias),
+            nn.BatchNorm3d(num_features=out_channels),
+            nn.LeakyReLU(inplace=True))
+
+    def forward(self, x):
+        x = self.up(x)
+        return x
+
+
+class U_Net(nn.Module):
+    """
+    UNet - Basic Implementation
+    Input _ [batch * channel(# of channels of each image) * depth(# of frames) * height * width].
+    Paper : https://arxiv.org/abs/1505.04597
+    """
+
+    def __init__(self, in_ch=1, out_ch=1, init_features=64):
+        super(U_Net, self).__init__()
+
+        n1 = init_features 
+        filters = [n1, n1 * 2, n1 * 4, n1 * 8, n1 * 16]  # 64,128,256,512,1024
+
+        self.Maxpool1 = nn.MaxPool3d(kernel_size=2, stride=2)
+        self.Maxpool2 = nn.MaxPool3d(kernel_size=2, stride=2)
+        self.Maxpool3 = nn.MaxPool3d(kernel_size=2, stride=2)
+        self.Maxpool4 = nn.MaxPool3d(kernel_size=2, stride=2)
+
+        self.Conv1 = conv_block(in_ch, filters[0])
+        self.Conv2 = conv_block(filters[0], filters[1])
+        self.Conv3 = conv_block(filters[1], filters[2])
+        self.Conv4 = conv_block(filters[2], filters[3])
+        self.Conv5 = conv_block(filters[3], filters[4])
+
+        self.Up5 = up_conv(filters[4], filters[3])
+        self.Up_conv5 = conv_block(filters[4], filters[3])
+
+        self.Up4 = up_conv(filters[3], filters[2])
+        self.Up_conv4 = conv_block(filters[3], filters[2])
+
+        self.Up3 = up_conv(filters[2], filters[1])
+        self.Up_conv3 = conv_block(filters[2], filters[1])
+
+        self.Up2 = up_conv(filters[1], filters[0])
+        self.Up_conv2 = conv_block(filters[1], filters[0])
+
+        self.Conv = nn.Conv3d(filters[0], out_ch, kernel_size=1, stride=1, padding=0)
+
+    # self.active = torch.nn.Sigmoid()
+
+    def forward(self, x):
+        # print("unet")
+        # print(x.shape)
+        # print(padded.shape)
+
+        e1 = self.Conv1(x)
+        # print("conv1:")
+        # print(e1.shape)
+
+        e2 = self.Maxpool1(e1)
+        e2 = self.Conv2(e2)
+        # print("conv2:")
+        # print(e2.shape)
+
+        e3 = self.Maxpool2(e2)
+        e3 = self.Conv3(e3)
+        # print("conv3:")
+        # print(e3.shape)
+
+        e4 = self.Maxpool3(e3)
+        e4 = self.Conv4(e4)
+        # print("conv4:")
+        # print(e4.shape)
+
+        e5 = self.Maxpool4(e4)
+        e5 = self.Conv5(e5)
+        # print("conv5:")
+        # print(e5.shape)
+
+        d5 = self.Up5(e5)
+        # print("d5:")
+        # print(d5.shape)
+        # print("e4:")
+        # print(e4.shape)
+        d5 = torch.cat((e4, d5), dim=1)
+        d5 = self.Up_conv5(d5)
+        # print("upconv5:")
+        # print(d5.size)
+
+        d4 = self.Up4(d5)
+        # print("d4:")
+        # print(d4.shape)
+        d4 = torch.cat((e3, d4), dim=1)
+        d4 = self.Up_conv4(d4)
+        # print("upconv4:")
+        # print(d4.shape)
+        d3 = self.Up3(d4)
+        d3 = torch.cat((e2, d3), dim=1)
+        d3 = self.Up_conv3(d3)
+        # print("upconv3:")
+        # print(d3.shape)
+        d2 = self.Up2(d3)
+        d2 = torch.cat((e1, d2), dim=1)
+        d2 = self.Up_conv2(d2)
+        # print("upconv2:")
+        # print(d2.shape)
+        out = self.Conv(d2)
+        # print("out:")
+        # print(out.shape)
+        # d1 = self.active(out)
+
+        return [out]
+
+class U_Net_DeepSup(nn.Module):
+    """
+    UNet - Basic Implementation
+    Input _ [batch * channel(# of channels of each image) * depth(# of frames) * height * width].
+    Paper : https://arxiv.org/abs/1505.04597
+    """
+
+    def __init__(self, in_ch=1, out_ch=1, output_dir=None, init_features=64):
+        super(U_Net_DeepSup, self).__init__()
+
+        self.output_dir = output_dir
+        n1 = init_features
+        filters = [n1, n1 * 2, n1 * 4, n1 * 8, n1 * 16]  # 64,128,256,512,1024
+
+        self.Maxpool1 = nn.MaxPool3d(kernel_size=2, stride=2)
+        self.Maxpool2 = nn.MaxPool3d(kernel_size=2, stride=2)
+        self.Maxpool3 = nn.MaxPool3d(kernel_size=2, stride=2)
+        self.Maxpool4 = nn.MaxPool3d(kernel_size=2, stride=2)
+
+        self.Conv1 = conv_block(in_ch, filters[0])
+        self.Conv2 = conv_block(filters[0], filters[1])
+        self.Conv3 = conv_block(filters[1], filters[2])
+        self.Conv4 = conv_block(filters[2], filters[3])
+        self.Conv5 = conv_block(filters[3], filters[4])
+
+        #1x1x1 Convolution for Deep Supervision
+        self.Conv_d3 = conv_block(filters[1], 1)
+        self.Conv_d4 = conv_block(filters[2], 1)
+
+
+
+        self.Up5 = up_conv(filters[4], filters[3])
+        self.Up_conv5 = conv_block(filters[4], filters[3])
+
+        self.Up4 = up_conv(filters[3], filters[2])
+        self.Up_conv4 = conv_block(filters[3], filters[2])
+
+        self.Up3 = up_conv(filters[2], filters[1])
+        self.Up_conv3 = conv_block(filters[2], filters[1])
+
+        self.Up2 = up_conv(filters[1], filters[0])
+        self.Up_conv2 = conv_block(filters[1], filters[0])
+
+        self.Conv = nn.Conv3d(filters[0], out_ch, kernel_size=1, stride=1, padding=0)
+
+        for submodule in self.modules():
+            submodule.register_forward_hook(self.nan_hook)
+
+    # self.active = torch.nn.Sigmoid()
+
+    def nan_hook(self, module, inp, output):
+        for i, out in enumerate(output):
+            nan_mask = torch.isnan(out)
+            if nan_mask.any():
+                print("In", self.__class__.__name__)
+                torch.save(inp, os.path.join(self.output_dir, 'nan_values_ip.pt'))
+                module_params = module.named_parameters()
+                for name, param in module_params:
+                    torch.save(param, os.path.join(self.output_dir, 'nan_{}_param.pt'.format(name)))
+                torch.save(self.input_to_net, os.path.join(self.output_dir, 'nan_ip_batch.pt'))
+                raise RuntimeError(" classname "+self.__class__.__name__+"i "+str(i)+f" module: {module} classname {self.__class__.__name__} Found NAN in output {i} at indices: ", nan_mask.nonzero(), "where:", out[nan_mask.nonzero()[:, 0].unique(sorted=True)])
+
+    def forward(self, x):
+        # print("unet")
+        # print(x.shape)
+        # print(padded.shape)
+        self.input_to_net = x
+        e1 = self.Conv1(x)
+        # print("conv1:")
+        # print(e1.shape)
+
+        e2 = self.Maxpool1(e1)
+        e2 = self.Conv2(e2)
+        # print("conv2:")
+        # print(e2.shape)
+
+        e3 = self.Maxpool2(e2)
+        e3 = self.Conv3(e3)
+        # print("conv3:")
+        # print(e3.shape)
+
+        e4 = self.Maxpool3(e3)
+        e4 = self.Conv4(e4)
+        # print("conv4:")
+        # print(e4.shape)
+
+        e5 = self.Maxpool4(e4)
+        e5 = self.Conv5(e5)
+        # print("conv5:")
+        # print(e5.shape)
+
+        d5 = self.Up5(e5)
+        # print("d5:")
+        # print(d5.shape)
+        # print("e4:")
+        # print(e4.shape)
+        d5 = torch.cat((e4, d5), dim=1)
+        d5 = self.Up_conv5(d5)
+        # print("upconv5:")
+        # print(d5.size)
+
+        d4 = self.Up4(d5)
+        # print("d4:")
+        # print(d4.shape)
+        d4 = torch.cat((e3, d4), dim=1)
+        d4 = self.Up_conv4(d4)
+        d4_out  = self.Conv_d4(d4)
+        
+                
+        # print("upconv4:")
+        # print(d4.shape)
+        d3 = self.Up3(d4)
+        d3 = torch.cat((e2, d3), dim=1)
+        d3 = self.Up_conv3(d3)        
+        d3_out  = self.Conv_d3(d3)
+
+        # print("upconv3:")
+        # print(d3.shape)
+        d2 = self.Up2(d3)
+        d2 = torch.cat((e1, d2), dim=1)
+        d2 = self.Up_conv2(d2)
+        # print("upconv2:")
+        # print(d2.shape)
+        out = self.Conv(d2)
+        # print("out:")
+        # print(out.shape)
+        # d1 = self.active(out)
+
+        return [out, d3_out , d4_out]
+
+