diff --git a/models/bronchoscopic_depthmap_estimation/LICENSE b/models/bronchoscopic_depthmap_estimation/LICENSE new file mode 100644 index 00000000..b085295c --- /dev/null +++ b/models/bronchoscopic_depthmap_estimation/LICENSE @@ -0,0 +1 @@ +This work is licensed under a Creative Commons Attribution 4.0 International License: https://creativecommons.org/licenses/by/4.0/ diff --git a/models/bronchoscopic_depthmap_estimation/configs/inference.json b/models/bronchoscopic_depthmap_estimation/configs/inference.json new file mode 100644 index 00000000..50317429 --- /dev/null +++ b/models/bronchoscopic_depthmap_estimation/configs/inference.json @@ -0,0 +1,85 @@ +{ + "imports": [ + "$import glob", + "$import os" + ], + "bundle_root": ".", + "ckpt_dir": "$@bundle_root + '/models'", + "output_dir": "$@bundle_root + '/eval'", + "data_list_file_path": "$@bundle_root + '/configs/datalist.json'", + "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')", + "amp": true, + "network_def": { + "_target_": "ResNet", + "init_filters": 16, + "in_channels": 1, + "out_channels": 1 + }, + "network": "$@network_def.to(@device)", + "preprocessing": { + "_target_": "Compose", + "transforms": [ + { + "_target_": "LoadImaged", + "keys": "image", + "image_only": false + }, + ] + }, + "dataset": { + "_target_": "Dataset", + "data": "@test_datalist", + "transform": "@preprocessing" + }, + "dataloader": { + "_target_": "DataLoader", + "dataset": "@dataset", + "batch_size": 1, + "shuffle": true, + "num_workers": 4 + }, + "postprocessing": { + "_target_": "Compose", + "transforms": [ + { + "_target_": "SaveImaged", + "keys": "depth", + "meta_keys": "pred_meta_dict", + "output_dir": "@output_dir", + "output_postfix": "depth", + "output_dtype": "float32", + "resample": false, + "squeeze_end_dims": true + } + ] + }, + "handlers": [ + { + "_target_": "CheckpointLoader", + "load_path": "$@bundle_root + '/models/model.pt'", + "load_dict": { + "model": "@network" + } + }, + { + "_target_": "StatsHandler", + "iteration_log": false + } + ], + "evaluator": { + "_target_": "SupervisedEvaluator", + "device": "@device", + "val_data_loader": "@dataloader", + "network": "@network", + "inferer": "@inferer", + "postprocessing": "@postprocessing", + "val_handlers": "@handlers", + "amp": true + }, + "initialize": [ + "$setattr(torch.backends.cudnn, 'benchmark', True)" + ], + "run": [ + "$@evaluator.run()" + ] +} diff --git a/models/bronchoscopic_depthmap_estimation/configs/metadata.json b/models/bronchoscopic_depthmap_estimation/configs/metadata.json new file mode 100644 index 00000000..bde2b71c --- /dev/null +++ b/models/bronchoscopic_depthmap_estimation/configs/metadata.json @@ -0,0 +1,62 @@ +{ + "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_20220324.json", + "version": "0.0.1", + "changelog": { + "0.0.1": "initializing the model package structure" + }, + "monai_version": "1.2.0rc5", + "pytorch_version": "1.13.1", + "numpy_version": "1.22.2", + "optional_packages_version": { + + }, + "name": "Bronchoscopy Depth Map Estimation", + "task": "Depth map generation from bronchoscopic images", + "copyright": "CC BY 4.0", + "description": "A model for generation of depth map images from bronchoscopic images", + "authors": "Surgical Navigation and Robotics Lab", + "image_classes": "single channel data, intensity scaled to [0, 255]", + "network_data_format": { + "inputs": { + "image": { + "type": "image", + "format": "magnitude", + "modality": "regular", + "num_channels": 1, + "spatial_shape": [ + 200, + 200 + ], + "dtype": "int", + "value_range": [ + 0, + 255 + ], + "is_patch_data": false, + "channel_def": { + "0": "image" + } + } + }, + "outputs": { + "pred": { + "type": "image", + "format": "magnitude", + "num_channels": 1, + "spatial_shape": [ + 200, + 200 + ], + "dtype": "float32", + "value_range": [ + 0, + 1 + ], + "is_patch_data": false, + "channel_def": { + "0": "depth" + } + } + } + } +} diff --git a/models/bronchoscopic_depthmap_estimation/docs/README.md b/models/bronchoscopic_depthmap_estimation/docs/README.md new file mode 100644 index 00000000..36151be7 --- /dev/null +++ b/models/bronchoscopic_depthmap_estimation/docs/README.md @@ -0,0 +1,28 @@ +# Model Title + +### **Authors** +Artur Banach, Franklin King, Fumitaro Masaki, Hisashi Tsukada, and Nobuhiko Hata +National Center for Image-guided Therapy, Brigham and Women’s Hospital and Harvard Medical School + +### **Tags** +Bronchoscopy, Grayscale, Lung, Depth map + +## **Model Description** +This model is in accordance with the following publication: Banach et al. "Visually Navigated Bronchoscopy using three cycle-Consistent generative adversarial network for depth estimation", Med. Image Anal. 73, 102164 (2021), https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8453111/ + +## **Data** +https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/8MNI49 + +#### **Preprocessing** +Model takes as input grayscale 200x200 images scaled from 0 to 255. + +## **Citation Info** +@article{banach2021visually, + title={Visually navigated bronchoscopy using three cycle-consistent generative adversarial network for depth estimation}, + author={Banach, Artur and King, Franklin and Masaki, Fumitaro and Tsukada, Hisashi and Hata, Nobuhiko}, + journal={Medical image analysis}, + volume={73}, + pages={102164}, + year={2021}, + publisher={Elsevier} +} diff --git a/models/bronchoscopic_depthmap_estimation/docs/license.txt b/models/bronchoscopic_depthmap_estimation/docs/license.txt new file mode 100644 index 00000000..b085295c --- /dev/null +++ b/models/bronchoscopic_depthmap_estimation/docs/license.txt @@ -0,0 +1 @@ +This work is licensed under a Creative Commons Attribution 4.0 International License: https://creativecommons.org/licenses/by/4.0/ diff --git a/models/bronchoscopic_depthmap_estimation/large_files.yml b/models/bronchoscopic_depthmap_estimation/large_files.yml new file mode 100644 index 00000000..d86eef7c --- /dev/null +++ b/models/bronchoscopic_depthmap_estimation/large_files.yml @@ -0,0 +1,9 @@ +large_files: + - path: "models/model.pt" + url: "https://drive.google.com/uc?export=download&id=1hBsBRrET40FbB9WJcNg5hIL67h2p2pRi" + hash_val: "5883296f3d06021b7068d024a00ac0c7" + hash_type: "md5" + - path: "models/model.onnx" + url: "https://drive.google.com/uc?export=download&id=184YGCmG7kHScBC8Cf5cxrt1qJCcfo9Zh" + hash_val: "636a469d5fbf72ab568dd232c8aa965c" + hash_type: "md5"