411 Adding depth map estimation bundle

models/bronchoscopic_depthmap_estimation/LICENSE

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+This work is licensed under a Creative Commons Attribution 4.0 International License: https://creativecommons.org/licenses/by/4.0/

models/bronchoscopic_depthmap_estimation/configs/inference.json

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+{
+    "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": [
+        "[email protected]()"
+    ]
+}

models/bronchoscopic_depthmap_estimation/configs/metadata.json

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+{
+    "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"
+                }
+            }
+        }
+    }
+}

models/bronchoscopic_depthmap_estimation/docs/README.md

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+# 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}
+}

models/bronchoscopic_depthmap_estimation/docs/license.txt

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+This work is licensed under a Creative Commons Attribution 4.0 International License: https://creativecommons.org/licenses/by/4.0/

models/bronchoscopic_depthmap_estimation/large_files.yml

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+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"