A pre-trained model for the endoscopic inbody classification task and trained using the SEResNet50 structure, whose details can be found in [1]. All datasets are from private samples of Activ Surgical. Samples in training and validation dataset are from the same 4 videos, while test samples are from different two videos.
The PyTorch model and torchscript model are shared in google drive. Modify the bundle_root
parameter specified in configs/train.json
and configs/inference.json
to reflect where models are downloaded. Expected directory path to place downloaded models is models/
under bundle_root
.
The datasets used in this work were provided by Activ Surgical.
Since datasets are private, we provide a link of 20 samples (10 in-body and 10 out-body) to show what they look like.
After downloading this dataset, python script in scripts
folder named data_process
can be used to generate label json files by running the command below and modifying datapath
to path of unziped downloaded data. Generated label json files will be stored in label
folder under the bundle path.
python scripts/data_process.py --datapath /path/to/data/root
By default, label path parameter in train.json
and inference.json
of this bundle is point to the generated label
folder under bundle path. If you move these generated label files to another place, please modify the train_json
, val_json
and test_json
parameters specified in configs/train.json
and configs/inference.json
to where these label files are.
The input label json should be a list made up by dicts which includes image
and label
keys. An example format is shown below.
[
{
"image":"/path/to/image/image_name0.jpg",
"label": 0
},
{
"image":"/path/to/image/image_name1.jpg",
"label": 0
},
{
"image":"/path/to/image/image_name2.jpg",
"label": 1
},
....
{
"image":"/path/to/image/image_namek.jpg",
"label": 0
},
]
The training as performed with the following:
A three channel video frame
Two Channels
Accuracy was used for evaluating the performance of the model. This model achieves an accuracy score of 0.99
The endoscopic_inbody_classification
bundle supports acceleration with TensorRT through the ONNX-TensorRT method. The table below displays the speedup ratios observed on an A100 80G GPU.
method | torch_fp32(ms) | torch_amp(ms) | trt_fp32(ms) | trt_fp16(ms) | speedup amp | speedup fp32 | speedup fp16 | amp vs fp16 |
---|---|---|---|---|---|---|---|---|
model computation | 6.50 | 9.23 | 2.78 | 2.31 | 0.70 | 2.34 | 2.81 | 4.00 |
end2end | 23.54 | 23.78 | 7.37 | 7.14 | 0.99 | 3.19 | 3.30 | 3.33 |
Where:
model computation
means the speedup ratio of model's inference with a random input without preprocessing and postprocessingend2end
means run the bundle end-to-end with the TensorRT based model.torch_fp32
and torch_amp
are for the PyTorch models with or without amp
mode.trt_fp32
and trt_fp16
are for the TensorRT based models converted in corresponding precision.speedup amp
, speedup fp32
and speedup fp16
are the speedup ratios of corresponding models versus the PyTorch float32 modelamp vs fp16
is the speedup ratio between the PyTorch amp model and the TensorRT float16 based model.Currently, the only available method to accelerate this model is through ONNX-TensorRT. However, the Torch-TensorRT method is under development and will be available in the near future.
This result is benchmarked under:
In addition to the Pythonic APIs, a few command line interfaces (CLI) are provided to interact with the bundle. The CLI supports flexible use cases, such as overriding configs at runtime and predefining arguments in a file.
For more details usage instructions, visit the MONAI Bundle Configuration Page.
python -m monai.bundle run --config_file configs/train.json
Please note that if the default dataset path is not modified with the actual path in the bundle config files, you can also override it by using --dataset_dir
:
python -m monai.bundle run --config_file configs/train.json --dataset_dir <actual dataset path>
train
config to execute multi-GPU training:torchrun --standalone --nnodes=1 --nproc_per_node=2 -m monai.bundle run \
--config_file "['configs/train.json','configs/multi_gpu_train.json']"
Please note that the distributed training-related options depend on the actual running environment; thus, users may need to remove --standalone
, modify --nnodes
, or do some other necessary changes according to the machine used. For more details, please refer to pytorch's official tutorial.
In addition, if using the 20 samples example dataset, the preprocessing script will divide the samples to 16 training samples, 2 validation samples and 2 test samples. However, pytorch multi-gpu training requires number of samples in dataloader larger than gpu numbers. Therefore, please use no more than 2 gpus to run this bundle if using the 20 samples example dataset.
train
config to execute evaluation with the trained model:python -m monai.bundle run --config_file "['configs/train.json','configs/evaluate.json']"
python -m monai.bundle run --config_file configs/inference.json
The classification result of every images in test.json
will be printed to the screen.
python -m monai.bundle ckpt_export network_def --filepath models/model.ts --ckpt_file models/model.pt --meta_file configs/metadata.json --config_file configs/inference.json
python -m monai.bundle trt_export --net_id network_def \
--filepath models/model_trt.ts --ckpt_file models/model.pt \
--meta_file configs/metadata.json --config_file configs/inference.json \
--precision <fp32/fp16> --use_onnx "True" --use_trace "True"
python -m monai.bundle run --config_file "['configs/inference.json', 'configs/inference_trt.json']"
[1] J. Hu, L. Shen and G. Sun, Squeeze-and-Excitation Networks, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2018, pp. 7132-7141. https://arxiv.org/pdf/1709.01507.pdf
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