cataract_classification: A Python repository from shenmishajing

Installation

install pytorch, torchvision etc. and mmcv-full from their official site.
install required packages with pip install -r requirements.txt
install this project with pip install -e .

For the versions of packages, you can check freeze.yml.

Usage

This project base on the CLI of pytorch-lightning, you can get more information on here.

Config and config files

Predefined config files

The predefined config files are located at configs/.

Every config file under configs/runs is a complete config file, so you can run an experiment with just a config file from configs/runs. But every other config file is just a part of complete config file, you should use them by combining them with each other or write a complete config file under configs/runs using __base__ to inherit from them.

Syntax

The syntax of config file is yaml and some additional keyword described as follow.

keyword	value	effect
`__base__`	`str` or `list[str]`,(each `str` should be a relative path from current cofig file)	Merge every config one by one, current last.
`__delete__`	`True` or `str,int` or `list[str,int]`,`True` for delete all keys from other config, `str,int` only delete the specific key (for dict) or index (for list)	Delete some part of config from other.
`__import__`	Any	Just delete this, for convenience of reference in yaml
`change_item`	`list[[index, item]]`,used only when merge list	Add ability of merg list, change the `list[index]` from other to `item`
`insert_item`	`list[[index, item, (extend)]]`,used only when merge list	Add ability of merg list, insert iterm to the `list` at `index`, extend=True if insert a list of items
`pre_item`	`Any`or `list[Any]`,used only when merge list	Add ability of merg list, add the value in the start of the list from other to item
`post_item`	`Any`or `list[Any]`,used only when merge list	Add ability of merg list, add the value in the end of the list from other to item

CLI

CLI script is located at tools/cli.py, so you can run it with python tools/cli.py.

For commands and options, you can get all available options and commands from python tools/cli.py --help.

Train

You can start a experiment with command as follow, in which, gpu_ids is comma-separated id list or just one int.

CUDA_VISIBLE_DEVICES=<gpu_ids> python tools/cli.py fit --config configs/runs/path/to/config

Validation test and predict etc.

CUDA_VISIBLE_DEVICES=<gpu_ids> python tools/cli.py {validation, test, predict, tune} --config configs/runs/path/to/config

Experiments

See configs/runs/image_classifier/. You can run them with python tools/cli.py fit --config configs/runs/image_classifier/path/to/config.

Run teacher model:

CUDA_VISIBLE_DEVICES=<gpu_ids> python tools/cli.py fit --config configs/runs/image_classifier/resnet50_transformer_with_label_cataract

Run student model:

First, modify the checkpoint in configs/runs/image_classifier/resnet50_transformer_distillation_label_cataract.yaml to the ckpt path of teacher model.

Then, run:

CUDA_VISIBLE_DEVICES=<gpu_ids> python tools/cli.py fit --config configs/runs/image_classifier/resnet50_transformer_distillation_label_cataract.yaml

shenmishajing/cataract_classification