Data

Tools

Indexes

Applications

Experiments

Open Source Science

ftu_seg

https://github.com/zezeze97/ftu_seg

Science Score: 44.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.1%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: zezeze97
  • License: apache-2.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 18.1 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Created over 3 years ago · Last pushed over 3 years ago
Metadata Files
Readme Contributing License Code of conduct Citation

README.md

Kaggle 比赛

该仓库用于HuBMAP + HPA - Hacking the Human Body比赛

数据集探索

环境安装

```sh

conda create -n mmseg-kaggle python=3.10 -y

conda activate mmseg-kaggle

conda install pytorch=1.11.0 torchvision cudatoolkit=11.3 -c pytorch

pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu113

pip install mmcv-full -f https://download.openmmlab.com/mmcv/dist/cu113/torch1.11.0/index.html pip install segmentationmodelspytorch git clone https://github.com/zezeze97/FTU_seg.git

cd {path of project}

pip install -e .

```

数据集下载，预处理

从官网下载好数据集后，放在该项目的data目录下，运行kagglesegmentation/edamask.ipynb

训练，测试

```sh

训练

bash run.sh train $GPU

测试

bash run.sh test$GPU

```

可视化预测

kagglesegmentation/inferencedemo.ipynb

Note

  • 虽然有多个类别，但是比赛只要求区分FTU，我先处理成2分类问题
  • 使用multilabel segmentor, 最后的激活用sigmoid而不是softmax
  • 图片分辨率很大3000x3000, 使用slide模式进行inference，而不是whole!
  • baseline使用的convnext-base

TODO

  • 实验结果整理
  • Multi Class Dateset

Owner

  • Login: zezeze97
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
  - name: "MMSegmentation Contributors"
title: "OpenMMLab Semantic Segmentation Toolbox and Benchmark"
date-released: 2020-07-10
url: "https://github.com/open-mmlab/mmsegmentation"
license: Apache-2.0

GitHub Events

Total
Last Year

Dependencies

requirements/docs.txt pypi
  • docutils ==0.16.0
  • myst-parser *
  • sphinx ==4.0.2
  • sphinx_copybutton *
  • sphinx_markdown_tables *
requirements/mminstall.txt pypi
  • mmcls >=0.20.1
  • mmcv-full >=1.4.4,<1.7.0
requirements/optional.txt pypi
  • cityscapesscripts *
requirements/readthedocs.txt pypi
  • mmcv *
  • prettytable *
  • torch *
  • torchvision *
requirements/runtime.txt pypi
  • matplotlib *
  • mmcls >=0.20.1
  • numpy *
  • packaging *
  • prettytable *
requirements/tests.txt pypi
  • codecov * test
  • flake8 * test
  • interrogate * test
  • pytest * test
  • xdoctest >=0.10.0 test
  • yapf * test
.github/workflows/build.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • codecov/codecov-action v1.0.10 composite
  • codecov/codecov-action v2 composite
.github/workflows/deploy.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/lint.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
.github/workflows/test_mim.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
docker/Dockerfile docker
  • pytorch/pytorch ${PYTORCH}-cuda${CUDA}-cudnn${CUDNN}-devel build
docker/serve/Dockerfile docker
  • pytorch/pytorch ${PYTORCH}-cuda${CUDA}-cudnn${CUDNN}-devel build