Contour Segmentation for Spread Through Air Spaces in Lung Adenocarcinom

Description

This is a competition from AI CUP 2022. The goal of this competition is to segment spread through air spaces (STAS) from a lung adenocarcinoma H&E image. We are TEAM1137.

Requirements

This repository is implemented by MATLAB2021a and python3.8.0 with third party package that stored in requirements.txt.

Dataset and Folder structure

The dataset can be downloaded from here.

• For reproduce our submission result only, you may just download Private_Image.zip and Public_Image.zip.
• For training scheme, you may need to download SEG_Train_Dataset.zip also.

For our training weight files, you may download the weight files a folder called checkpoint from here.

For convinence, you can follow the folder structure as follows

.
├─Dataset
|   ├─Private_Image      # From Private_Image.zip
|   ├─Public_Image       # From Private_Image.zip
|   ├─Train_Annotations  # From SEG_Train_Dataset.zip
|   └─Train_Images       # From SEG_Train_Dataset.zip
├─Json_Dataset           # Some .json file for our data pipeline
|   ├─Fold{i}_train.json
|   ├─Fold{i}_valid.json
|   ├─Private.json
|   ├─Public.json
|   └─Test.json
├─checkpoint             # put training weights here
|   ├─0531_4fold
|   ├─0601_4fold
|   └─mix_1
├─configs                # The config files that we train the model
|   ├─Fold0.yaml
|   ├─Fold1.yaml
|   ├─Fold2.yaml
|   └─Fold3.yaml
├─src
|   ├─python             # functions and classes written by python
|   └─matlab             # functions and classes written by matlab
├─requirements.txt       # python third party requirements
├─README.md              # this file
└─codes.py/mat           # other main step code

How to reproduce our result?

To reproduce our result, make sure that you have downloaded the Public data, Private data and checkpoint (model weights), then place them into the correct location, as described above. Then, execute STEP7_Inference.py and STEP8_PostProcess.py, which we are going to explain below.

How to use this code?

There are total 9 steps in our procedure (4 preprocess scripts, 2 training scripts and 3 inference scripts).

Preprocessing

STEP0: Convert train_annotation.json to label.png

First, we convert the annotation file (polygon, from Train_Annotations) to label (png file) by using the following command.

matlab21b < STEP0_Anno2Mask.m

You may find the png folder in Dataset/Train_Labels.

STEP1: Some simple statistics (optional)

We may observe some simple statistics by running

matlab21b < STEP1_Statistics.m

STEP2: Split training dataset

We handle the data IO by .json files (handling by filename).
In this step, we split the training dataset into Train and Test set.

• Test: Testing set, keep fixed.
• Train: Training set, split it into train/validation by five fold manner. Run the following command:

matlab21b < STEP2_SplitFiveFold.m

You may see those .json file in JsonDataset.
Note: We have provided an example in JsonDataset, you may skip this step if you want.

STEP3: Make augmentation images

As we state in our report, we have applied H & E staining extract for the training dataset. Decomposed an image into three parts: norm, H and E. This can be done by running

matlab21b < STEP3_MakeAugment.m

You may find the resulting image folders in Dataset/Train_Eimg', Dataset/Train_HimgandDataset/Train_norm`.

Training

STEP4: Training

There are two ways to run training script.

• Modify Config.py and run python3 STEP4_Train.py
• Prepare a config yaml file (e.g, configs/Fold0.yaml which we have provide), and run python3 STEP4_Train.py --config Fold0.yaml

After that, a checkpoint folder named by current date time (e.g. 2022-06-13-10-27-04) will be generated in checkpoint/2022-06-13-10-27-04, the usage of this folder is to store trained model weights, which can be catched during testing and inference.

STEP5: Testing

Execute testing scheme by running the following command, note that you should provide a checkpoint_folder that we have mentioned in STEP4.

python3 STEP5_Test.py --checkpont {checkpoint_folder}

You could find the testing result inside the checkpoint_folder.

Inference

STEP6: Generate Public and Private json files.

As we mentioned in STEP2, we need to generate a .json file to control data IO. We deal with it by running

matlab21b < STEP6_GenerateSubmitJson.m

You can find the .json files in JsonDataset.
Notice: We have provied an example in JsonDataset, If there is no change for the Public/Private dataset, you can skip this step.

STEP7: Inference by model

In order to implement model ensemble in our task, we maintain a checkpoint file so that we don't need to input a bunch of checkpoint folders.
You may modify it in Checkpoint_setting.py. After that, we may run inference step by

python3 STEP7_Inference.py

You may find the inferece result in prediction/public and prediction/private.

STEP8: Post process

For post processing, ensure that you have done STEP7 and prediction/public, prediction/private are exists. Then, we may run the following command

matlab21b < STEP8_PostProcess.m

You may find the post process result in prediciton/public-post and prediction/private-post.

Result

Public Score	Public Rank	Private Score	Private Rank
0.920027	3	0.910871	16

Citation

@misc{
    title  = {spread_through_air_spaces_segmentation},
    author = {Kuok-Tong Ng, Jia-Wei Liao, Yi-Cheng Hung},
    url    = {https://github.com/K-T-Ng/STAS_Final},
    year   = {2022}
}