Basic U-Net example by MIC@DKFZ

This python code is an example project of how to use a U-Net [1] for segmentation on medical images using PyTorch (https://www.pytorch.org). It was developed at the Division of Medical Image Computing at the German Cancer Research Center (DKFZ). It is also an example of how to use our other python packages batchgenerators (https://github.com/MIC-DKFZ/batchgenerators) and Trixi (https://github.com/MIC-DKFZ/trixi) [2] to suit all our deep learning data augmentation needs.

If you have any questions or issues or you encounter a bug, feel free to contact us, open a GitHub issue or ask the community on Gitter:

WARNING: This repo was implemented and tested on Linux. We highly recommend using it within a Linux environment. If you use Windows you might experience some issues (see section "Errors and how to handle them")

How to set it up

The example is very easy to use. Just create a new virtual environment in python and install the requirements. This example requires python3. It was implemented with python 3.5.

WARNING: The newest supported version is python 3.7.9. For newer python versions there are some requirements that are not available in the needed version.

pip3 install -r requirements.txt

In this example code, we show how to use visdom for live visualization. See the Trixi documentation for more details or information about other tools like tensorboard. After setting up the virtual environment you have to start visdom once so it can download some needed files. You only have to do that once. You can stop the visdom server after a few seconds when it finished downloading the files.

python3 -m visdom.server

You can edit the paths for data storage and logging in the config file. By default, everything is stored in your working directory.

How to use it

To start the training simply run

python3 run_train_pipeline.py

This will download the Hippocampus dataset from the medical segmentation decathlon (http://medicaldecathlon.com), extract and preprocess it and then start the training. The preprocessing loads the images (imagesTr) and the corresponding labels (labelsTr), performs some normalization and padding operations and saves the data as NPY files. The available images are then split into train, validation and test sets. The splits are saved to a splits.pkl file. The images in imagesTs are not used in the example, because they are the test set for the medical segmentation decathlon and therefore no ground truth is provided.

If you run the pipeline again, the dataset will not be downloaded, extracted or preprocessed again. To enforce it, just delete the folder.

The training process will automatically be visualized using trixi/visdom. After starting the training you navigate in your browser to the port which is printed by the training script. Then you should see your loss curve and so on.

By default, a 2-dimensional U-Net is used. The example also comes with a 3-D version of the network (Özgün Cicek et al.). To use the 3-D version, simple use

python train3D.py

WARNING: The 3-D version is not yet tested thoroughly. Use it with caution!

How to use it for your own data

This description is work in progress. If you use this repo for your own data please share your experience, so we can update this part.

Config

The included Config_unet.py is an example config file. You have to adapt this to fit your local environment, e.g., if you run out of CUDA memory, try to reduce batch_size or patch_size. All the other parameters should be self-explanatory or described directly in the code comments.

Choose the #Train parameters to fit both, your data and your workstation. With fold you can choose which split from your splits.pkl you want to use for the training.

You may also need to adapt the paths (data_root_dir, data_dir, data_test_dir and split_dir).

You can change the Logging parameters if you want to. With append_rnd_string, you can give each experiment you start a unique name. If you want to start your visdom server manually, just set start_visdom=False. If you do not want to use visdom logging at all, just remove the visdom logger from your experiment, e.g. run_train_pipeline.py line 47:

loggers={
      "visdom": ("visdom", {"auto_start": c.start_visdom})
}

Datasets

If you want to use the provided DataLoader, you need to preprocess your data appropriately. An example can be found in the "example_dataset" folder. Make sure to load your images and your labels as numpy arrays. The required shape is (#slices, w,h). Then save both using:

result = np.stack((image, label))

np.save(output_filename, result)

The provided DataLoader requires a splits.pkl file, that contains a dictionary of all the files used for training, validation and testing. It looks like this:

[{'train': ['dataset_name_1',...], 'val': ['dataset_name_2', ...], 'test': ['dataset_name_3', ...]}]

We use the MIC/batchgenerators to perform data augmentation. The example uses cropping, mirroring and some elastic spatial transformation. You can change the data augmentation by editing the data_augmentation.py. Please see the MIC/batchgenerators documentation for more details.

To train your network, simply run

python train.py

You can either edit the config file or add command line parameters like this:

python train.py --n_epochs 100 [...]

Networks

This example contains a simple implementation of the U-Net [1], which can be found in networks>UNET.py. A little more generic version of the U-Net, as well as the 3D U-Net [3], can be found in networks>RecursiveUNet.py respectively networks>RecursiveUNet3D.py. This implementation is done recursively. It is therefore very easy to configure the number of downsamplings. Also, the type of normalization can be passed as a parameter (default is nn.InstanceNorm2d).

Errors and how to handle them

In this section, we want to collect common errors that may occur when using this repository. If you encounter something, feel free to let us know about it and we will include it here.

Windows related issues

If you want to use this repo on Windows, please note, that you have to adapt to some things. We recommend to install PyTorch via conda on Windows using: python -m conda install pytorch torchvision cpuonly -c pytorch You then have to remove torch from the requirements.txt.

If you run into issues like the following one:

AttributeError: Can't pickle local object 'MultiThreadedDataLoader.get_worker_init_fn.<locals>.init_fn'`

try to use SingleProcessDataLoader instead. This error is probably caused by how multithreading is handled in python on Windows. So fix this, add num_processes=0 to your dataloaders:

self.train_data_loader = NumpyDataSet(self.config.data_dir, target_size=self.config.patch_size, 
                                       batch_size=self.config.batch_size, keys=tr_keys, num_processes=0)
self.val_data_loader = NumpyDataSet(self.config.data_dir, target_size=self.config.patch_size, 
                                       batch_size=self.config.batch_size, keys=val_keys, mode="val", do_reshuffle=False, num_processes=0)
self.test_data_loader = NumpyDataSet(self.config.data_test_dir, target_size=self.config.patch_size, 
                                       batch_size=self.config.batch_size, keys=test_keys, mode="test", do_reshuffle=False, num_processes=0)

Multiple Labels

Depending on your dataset you might be dealing with multiple labels. For example the data from BRATS (https://www.med.upenn.edu/sbia/brats2017.html) has the following labels:

"labels": {
    "0": "background",
    "1": "edema",
    "2": "non-enhancing tumor",
    "3": "enhancing tumour"
},

If you run into an error like this:

Experiment exited. Checkpoints stored =)
INFO:default-z3HafHO4CS:Experiment exited. Checkpoints stored =)
Unhandled exception in thread started by <function PytorchExperimentLogger.save_checkpoint_static at 0x7fd07c3e8510>
Traceback (most recent call last):
  File "/python3.5/site-packages/trixi/logger/experiment/pytorchexperimentlogger.py", line 196, in save_checkpoint_static
   torch.save(to_cpu(kwargs), checkpoint_file)
  File "/python3.5/site-packages/trixi/logger/experiment/pytorchexperimentlogger.py", line 191, in to_cpu
    return {key: to_cpu(val) for key, val in obj.items()}
  File "//python3.5/site-packages/trixi/logger/experiment/pytorchexperimentlogger.py", line 191, in <dictcomp>
    return {key: to_cpu(val) for key, val in obj.items()}
  File "/python3.5/site-packages/trixi/logger/experiment/pytorchexperimentlogger.py", line 191, in to_cpu
    return {key: to_cpu(val) for key, val in obj.items()}
  File "/python3.5/site-packages/trixi/logger/experiment/pytorchexperimentlogger.py", line 191, in <dictcomp>
    return {key: to_cpu(val) for key, val in obj.items()}
  File "/python3.5/site-packages/trixi/logger/experiment/pytorchexperimentlogger.py", line 189, in to_cpu
    return obj.cpu()
RuntimeError: CUDA error: device-side assert triggered

make sure you updated num_classes in your config file. The value of num_classes should always equal the number of your labels including background.

If you run into an error like this:

File "/home/student/basic_unet/trixi/trixi/experiment/experiment.py", line 108, in run
  self.process_err(e)
File "/home/student/basic_unet/trixi/trixi/experiment/pytorchexperiment.py", line 391, in process_err
  raise e
File "/home/student/basic_unet/trixi/trixi/experiment/experiment.py", line 89, in run
  self.train(epoch=self._epoch_idx)
File "/home/student/PycharmProjects/new_unet/experiments/UNetExperiment.py", line 113, in train
  loss = self.dice_loss(pred_softmax, target.squeeze()) + self.ce_loss(pred, target.squeeze())
File "/opt/anaconda3/envs/a_new_test/lib/python3.6/site-packages/torch/nn/modules/module.py", line 493, in call
  result = self.forward(input, *kwargs)
File "/home/student/PycharmProjects/new_unet/loss_functions/dice_loss.py", line 125, in forward
  yonehot.scatter(1, y, 1)
RuntimeError: Invalid index in scatter at /pytorch/aten/src/TH/generic/THTensorEvenMoreMath.cpp:551

make sure to check your labels again. The error may be caused by the fact that the labels are not sequential. This causes scatter to crash. Consider changing the values of your labels.

References

[1] Ronneberger, Olaf, Philipp Fischer, and Thomas Brox. "U-net: Convolutional networks for biomedical image segmentation." International Conference on Medical image computing and computer-assisted intervention. Springer, Cham, 2015. [2] David Zimmerer, Jens Petersen, GregorKoehler, Jakob Wasserthal, dzimmm, Tim, … André Pequeño. (2018, November 23). MIC-DKFZ/trixi: Alpha (Version v0.1.1). Zenodo. http://doi.org/10.5281/zenodo.1495180 [3] Çiçek, Özgün, et al. "3D U-Net: learning dense volumetric segmentation from sparse annotation." International conference on medical image computing and computer-assisted intervention. Springer, Cham, 2016.

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