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main.py

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+import gradio as gr
+
+def predict(img):
+    return "cat"
+
+
+demo = gr.Interface(
+    fn=predict,
+    inputs=gr.Image(type="pil"),
+    outputs=gr.Label(num_top_classes=3),
+)
+
+demo.launch(server_name="0.0.0.0", server_port=7860)

nnUNetTrainerV2_Loss_FL_and_CE.py

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+#    Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+#
+#    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.
+
+from torch import nn
+
+from nnunet.training.network_training.nnUNetTrainerV2 import nnUNetTrainerV2
+from nnunet.training.loss_functions.crossentropy import RobustCrossEntropyLoss
+from nnunet.training.network_training.nnUNet_variants.loss_function.nnUNetTrainerV2_focalLoss import FocalLoss
+# TODO: replace FocalLoss by fixed implemetation (and set smooth=0 in that one?)
+
+
+class FL_and_CE_loss(nn.Module):
+    def __init__(self, fl_kwargs=None, ce_kwargs=None, alpha=0.5, aggregate="sum"):
+        super(FL_and_CE_loss, self).__init__()
+        if fl_kwargs is None:
+            fl_kwargs = {}
+        if ce_kwargs is None:
+            ce_kwargs = {}
+
+        self.aggregate = aggregate
+        self.fl = FocalLoss(apply_nonlin=nn.Softmax(), **fl_kwargs)
+        self.ce = RobustCrossEntropyLoss(**ce_kwargs)
+        self.alpha = alpha
+
+    def forward(self, net_output, target):
+        fl_loss = self.fl(net_output, target)
+        ce_loss = self.ce(net_output, target)
+        if self.aggregate == "sum":
+            result = self.alpha*fl_loss + (1-self.alpha)*ce_loss
+        else:
+            raise NotImplementedError("nah son")
+        return result
+
+
+class nnUNetTrainerV2_Loss_FL_and_CE_checkpoints(nnUNetTrainerV2):
+    """
+    Set loss to FL + CE and set checkpoints
+    """
+    def __init__(self, plans_file, fold, output_folder=None, dataset_directory=None, batch_dice=True, stage=None,
+                 unpack_data=True, deterministic=True, fp16=False):
+        super().__init__(plans_file, fold, output_folder, dataset_directory, batch_dice, stage, unpack_data,
+                         deterministic, fp16)
+        self.loss = FL_and_CE_loss(alpha=0.5)
+        self.save_latest_only = False
+
+
+class nnUNetTrainerV2_Loss_FL_and_CE_checkpoints2(nnUNetTrainerV2_Loss_FL_and_CE_checkpoints):
+    """
+    Each run is stored in a folder with the training class name in it. This simply creates a new folder,
+    to allow investigating the variability between restarts.
+    """
+    def __init__(self, plans_file, fold, output_folder=None, dataset_directory=None, batch_dice=True, stage=None,
+                 unpack_data=True, deterministic=True, fp16=False):
+        super().__init__(plans_file, fold, output_folder, dataset_directory, batch_dice, stage, unpack_data,
+                         deterministic, fp16)
+
+
+class nnUNetTrainerV2_Loss_FL_and_CE_checkpoints3(nnUNetTrainerV2_Loss_FL_and_CE_checkpoints):
+    """
+    Each run is stored in a folder with the training class name in it. This simply creates a new folder,
+    to allow investigating the variability between restarts.
+    """
+    def __init__(self, plans_file, fold, output_folder=None, dataset_directory=None, batch_dice=True, stage=None,
+                 unpack_data=True, deterministic=True, fp16=False):
+        super().__init__(plans_file, fold, output_folder, dataset_directory, batch_dice, stage, unpack_data,
+                         deterministic, fp16)

nnUNetTrainerV2_focalLoss.py

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+#    Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+#
+#    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.
+
+
+import numpy as np
+import torch
+import torch.nn as nn
+from nnunet.training.network_training.nnUNetTrainerV2 import nnUNetTrainerV2
+
+
+class FocalLoss(nn.Module):
+    """
+    copy from: https://github.com/Hsuxu/Loss_ToolBox-PyTorch/blob/master/FocalLoss/FocalLoss.py
+    This is a implementation of Focal Loss with smooth label cross entropy supported which is proposed in
+    'Focal Loss for Dense Object Detection. (https://arxiv.org/abs/1708.02002)'
+        Focal_Loss= -1*alpha*(1-pt)*log(pt)
+    :param num_class:
+    :param alpha: (tensor) 3D or 4D the scalar factor for this criterion
+    :param gamma: (float,double) gamma > 0 reduces the relative loss for well-classified examples (p>0.5) putting more
+                    focus on hard misclassified example
+    :param smooth: (float,double) smooth value when cross entropy
+    :param balance_index: (int) balance class index, should be specific when alpha is float
+    :param size_average: (bool, optional) By default, the losses are averaged over each loss element in the batch.
+    """
+
+    def __init__(self, apply_nonlin=None, alpha=None, gamma=2, balance_index=0, smooth=1e-5, size_average=True):
+        super(FocalLoss, self).__init__()
+        self.apply_nonlin = apply_nonlin
+        self.alpha = alpha
+        self.gamma = gamma
+        self.balance_index = balance_index
+        self.smooth = smooth
+        self.size_average = size_average
+
+        if self.smooth is not None:
+            if self.smooth < 0 or self.smooth > 1.0:
+                raise ValueError('smooth value should be in [0,1]')
+
+    def forward(self, logit, target):
+        if self.apply_nonlin is not None:
+            logit = self.apply_nonlin(logit)
+        num_class = logit.shape[1]
+
+        if logit.dim() > 2:
+            # flatten spatial dimensions N,C,d1,d2 -> N,C,m (m=d1*d2*...)
+            logit = logit.view(logit.size(0), logit.size(1), -1)
+            logit = logit.permute(0, 2, 1).contiguous()
+            logit = logit.view(-1, logit.size(-1))
+        target = torch.squeeze(target, 1)
+        target = target.view(-1, 1)
+        # print(logit.shape, target.shape)
+
+        alpha = self.alpha
+
+        if alpha is None:
+            alpha = torch.ones(num_class, 1)
+        elif isinstance(alpha, (list, np.ndarray)):
+            assert len(alpha) == num_class
+            alpha = torch.FloatTensor(alpha).view(num_class, 1)
+            alpha = alpha / alpha.sum()
+        elif isinstance(alpha, float):
+            alpha = torch.ones(num_class, 1)
+            alpha = alpha * (1 - self.alpha)
+            alpha[self.balance_index] = self.alpha
+        else:
+            raise TypeError(f'Unsupported alpha type: {type(alpha)}')
+
+        if alpha.device != logit.device:
+            alpha = alpha.to(logit.device)
+
+        idx = target.cpu().long()
+
+        one_hot_key = torch.FloatTensor(target.size(0), num_class).zero_()
+        one_hot_key = one_hot_key.scatter_(1, idx, 1)
+        if one_hot_key.device != logit.device:
+            one_hot_key = one_hot_key.to(logit.device)
+
+        if self.smooth:
+            one_hot_key = torch.clamp(
+                one_hot_key, self.smooth/(num_class-1), 1.0 - self.smooth)
+        pt = (one_hot_key * logit).sum(1) + self.smooth
+        logpt = pt.log()
+
+        gamma = self.gamma
+
+        alpha = alpha[idx]
+        alpha = torch.squeeze(alpha)
+        loss = -1 * alpha * torch.pow((1 - pt), gamma) * logpt
+
+        if self.size_average:
+            loss = loss.mean()
+        else:
+            loss = loss.sum()
+
+        return loss
+
+
+class nnUNetTrainerV2_focalLossAlpha75(nnUNetTrainerV2):
+    def __init__(self, plans_file, fold, output_folder=None, dataset_directory=None, batch_dice=True, stage=None,
+                 unpack_data=True, deterministic=True, fp16=False):
+        super().__init__(plans_file, fold, output_folder, dataset_directory, batch_dice, stage, unpack_data,
+                         deterministic, fp16)
+        print("Setting up FocalLoss(alpha=[0.75, 0.25], apply_nonlin=nn.Softmax())")
+        self.loss = FocalLoss(alpha=[0.75, 0.25], apply_nonlin=nn.Softmax())
+
+
+class nnUNetTrainerV2_focalLossAlpha75_checkpoints(nnUNetTrainerV2_focalLossAlpha75):
+    def __init__(self, plans_file, fold, output_folder=None, dataset_directory=None, batch_dice=True, stage=None,
+                 unpack_data=True, deterministic=True, fp16=False):
+        super().__init__(plans_file, fold, output_folder, dataset_directory, batch_dice, stage, unpack_data,
+                         deterministic, fp16)
+        print("Saving checkpoint every 50th epoch")
+        self.save_latest_only = False
+
+
+class nnUNetTrainerV2_focalLossAlpha75_checkpoints2(nnUNetTrainerV2_focalLossAlpha75_checkpoints):
+    def __init__(self, plans_file, fold, output_folder=None, dataset_directory=None, batch_dice=True, stage=None,
+                 unpack_data=True, deterministic=True, fp16=False):
+        super().__init__(plans_file, fold, output_folder, dataset_directory, batch_dice, stage, unpack_data,
+                         deterministic, fp16)
+        pass  # this is just to get a new Trainer directory
+
+
+class nnUNetTrainerV2_focalLossAlpha75_checkpoints3(nnUNetTrainerV2_focalLossAlpha75_checkpoints):
+    def __init__(self, plans_file, fold, output_folder=None, dataset_directory=None, batch_dice=True, stage=None,
+                 unpack_data=True, deterministic=True, fp16=False):
+        super().__init__(plans_file, fold, output_folder, dataset_directory, batch_dice, stage, unpack_data,
+                         deterministic, fp16)
+        pass  # this is just to get a new Trainer directory