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readme.md

Constrained-CNN losses for weakly supervised segmentation

Code of our submission at MIDL 2018 and its Medical Image Analysis journal extension. Video of the MIDL talk is available: https://www.youtube.com/watch?v=2-0Ey5-If7o

Requirements

Non-exhaustive list:

  • python3.6+
  • Pytorch 1.0
  • nibabel
  • Scipy
  • NumPy
  • Matplotlib
  • Scikit-image
  • zsh

Usage

Instruction to download the data are contained in the lineage files acdc.lineage, zenodo_spine and prostate.lineage. They are just text files containing the md5sum (or sha256sum) of the original zip.

Once the zip is in place, everything should be automatic:

make -f acdc.make
make -f prostate.make
make -f zenodo_spine.make

Usually takes a little bit more than a day per makefile.

This perform in the following order:

  • Unpacking of the data
  • Remove unwanted big files
  • Normalization and slicing of the data
  • Training with the different methods
  • Plotting of the metrics curves
  • Display of a report
  • Archiving of the results in an .tar.gz stored in the archives folder

The main advantage of the makefile is that it will handle by itself the dependencies between the different parts. For instance, once the data has been pre-processed, it won't do it another time, even if you delete the training results. It is also a good way to avoid overwriting existing results by relaunching the exp by accident.

Of course, parts can be launched separately :

make -f acdc.make data/acdc # Unpack only
make -f acdc.make data/MIDL # unpack if needed, then slice the data
make -f acdc.make results/acdc/fs # train only with full supervision. Create the data if needed
make -f acdc.make results/acdc/val_dice.png # Create only this plot. Do the trainings if needed

The number of option for the main script is fairly dense, but the recipes in the different makefiles should give you a good idea on how to modify the training parameters and create new targets. In case of questions, feel free to contact me.

Data scheme

datasets

For instance

MIDL/
    train/
        img/
            case_10_0_0.png
            ...
        gt/
            case_10_0_0.png
            ...
        random/
            ...
        ...
    val/
        img/
            case_10_0_0.png
            ...
        gt/
            case_10_0_0.png
            ...
        random/
            ...
        ...

The network takes png files as an input. The gt folder contains gray-scale images of the ground-truth, where the gray-scale level are the number of the class (namely, 0 and 1). This is because I often use my segmentation viewer to visualize the results, so that does not really matter. If you want to see it directly in an image viewer, you can either use the remap script, or use imagemagick:

mogrify -normalize data/ISLES/val/gt/*.png

results

results/
    acdc/
        fs/
            best_epoch/
                val/
                    case_10_0_0.png
                    ...
            iter000/
                val/
            ...
        size_595/
            ...
        best.pkl # best model saved
        metrics.csv # metrics over time, csv
        best_epoch.txt # number of the best epoch
        val_dice.npy # log of all the metric over time for each image and class
        val_dice.png # Plot over time
        ...
    prostate/
        ...
archives/
    $(REPO)-$(DATE)-$(HASH)-$(HOSTNAME)-acdc.tar.gz
    $(REPO)-$(DATE)-$(HASH)-$(HOSTNAME)-prostate.tar.gz

Interesting bits

The losses are defined in the losses.py file. Explaining the remaining of the code is left as an exercise for the reader.

Cool tricks

Remove all assertions from the code. Usually done after making sure it does not crash for one complete epoch:

make -f acdc.make <anything really> CFLAGS=-O

Use a specific python executable:

make -f acdc.make <super target> CC=/path/to/the/executable

Train for only 5 epochs, with a dummy network, and only 10 images per data loader. Useful for debugging:

make -f acdc.make <really> NET=Dimwit EPC=5 DEBUG=--debug

Rebuild everything even if already exist:

make -f acdc.make <a> -B

Only print the commands that will be run (useful to check recipes are properly defined):

make -f acdc.make <a> -n

Create a gif for the predictions over time of a specific patient:

cd results/acdc/fs
convert iter*/val/case_14_0_0.png case_14_0_0.gif
mogrify -normalize case_14_0_0.gif

About

Code of our MIDL 2018 paper and MedIA extension: https://arxiv.org/abs/1805.04628

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