Add inference example for bundle (#604)

* [DLMED] add inference example Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update based on latest design Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update config content Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update to latest design Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update according to comments Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] enhance the expression Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add more transforms Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] adjust config Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add checkpoint logic Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add checkpoint test Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update imports Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] update for _requires_ Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] add logging Signed-off-by: Nic Ma <nma@nvidia.com> * [DLMED] fix typo Signed-off-by: Nic Ma <nma@nvidia.com> * Update README.md * Update metadata.json * [DLMED] add hugging face download Signed-off-by: Nic Ma <nma@nvidia.com> Co-authored-by: Wenqi Li <831580+wyli@users.noreply.github.com>
Project-MONAI · Mar 25, 2022 · ac88fee · ac88fee
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diff --git a/modules/bundles/spleen_segmentation/configs/inference.json b/modules/bundles/spleen_segmentation/configs/inference.json
@@ -0,0 +1,147 @@
+{
+    "imports": [
+        "$import glob",
+        "$import os"
+    ],
+    "cudnn_opt": "$setattr(torch.backends.cudnn, 'benchmark', True)",
+    "dataset_dir": "/workspace/data/Task09_Spleen",
+    "ckpt_path": "/workspace/data/tutorials/modules/bundles/spleen_segmentation/models/model.pt",
+    "download_ckpt": "$monai.apps.utils.download_url('https://huggingface.co/MONAI/example_spleen_segmentation/resolve/main/model.pt', @ckpt_path)",
+    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
+    "datalist": "$list(sorted(glob.glob(@dataset_dir + '/imagesTs/*.nii.gz')))",
+    "network_def": {
+        "_target_": "UNet",
+        "spatial_dims": 3,
+        "in_channels": 1,
+        "out_channels": 2,
+        "channels": [
+            16,
+            32,
+            64,
+            128,
+            256
+        ],
+        "strides": [
+            2,
+            2,
+            2,
+            2
+        ],
+        "num_res_units": 2,
+        "norm": "batch"
+    },
+    "network": "$@network_def.to(@device)",
+    "preprocessing": {
+        "_target_": "Compose",
+        "transforms": [
+            {
+                "_target_": "LoadImaged",
+                "keys": "image"
+            },
+            {
+                "_target_": "EnsureChannelFirstd",
+                "keys": "image"
+            },
+            {
+                "_target_": "Orientationd",
+                "keys": "image",
+                "axcodes": "RAS"
+            },
+            {
+                "_target_": "Spacingd",
+                "keys": "image",
+                "pixdim": [1.5, 1.5, 2.0],
+                "mode": "bilinear"
+            },
+            {
+                "_target_": "ScaleIntensityRanged",
+                "keys": "image",
+                "a_min": -57,
+                "a_max": 164,
+                "b_min": 0,
+                "b_max": 1,
+                "clip": true
+            },
+            {
+                "_target_": "EnsureTyped",
+                "keys": "image"
+            }
+        ]
+    },
+    "dataset": {
+        "_target_": "Dataset",
+        "data": "$[{'image': i} for i in @datalist]",
+        "transform": "@preprocessing"
+    },
+    "dataloader": {
+        "_target_": "DataLoader",
+        "dataset": "@dataset",
+        "batch_size": 1,
+        "shuffle": false,
+        "num_workers": 4
+    },
+    "inferer": {
+        "_target_": "SlidingWindowInferer",
+        "roi_size": [
+            96,
+            96,
+            96
+        ],
+        "sw_batch_size": 4,
+        "overlap": 0.5
+    },
+    "postprocessing": {
+        "_target_": "Compose",
+        "transforms": [
+            {
+                "_target_": "Activationsd",
+                "keys": "pred",
+                "softmax": true
+            },
+            {
+                "_target_": "Invertd",
+                "keys": "pred",
+                "transform": "@preprocessing",
+                "orig_keys": "image",
+                "meta_key_postfix": "meta_dict",
+                "nearest_interp": false,
+                "to_tensor": true
+            },
+            {
+                "_target_": "AsDiscreted",
+                "keys": "pred",
+                "argmax": true
+            },
+            {
+                "_target_": "SaveImaged",
+                "keys": "pred",
+                "meta_keys": "pred_meta_dict",
+                "output_dir": "eval"
+            }
+        ]
+    },
+    "handlers": [
+        {
+            "_target_": "CheckpointLoader",
+            "_requires_": "@download_ckpt",
+            "_disabled_": "$not os.path.exists(@ckpt_path)",
+            "load_path": "@ckpt_path",
+            "load_dict": {"model": "@network"}
+        },
+        {
+            "_target_": "StatsHandler",
+            "iteration_log": false
+        }
+    ],
+    "evaluator": {
+        "_target_": "SupervisedEvaluator",
+        "_requires_": "@cudnn_opt",
+        "device": "@device",
+        "val_data_loader": "@dataloader",
+        "network": "@network",
+        "inferer": "@inferer",
+        "postprocessing": "@postprocessing",
+        "val_handlers": "@handlers",
+        "amp": false
+    }
+}
diff --git a/modules/bundles/spleen_segmentation/configs/logging.conf b/modules/bundles/spleen_segmentation/configs/logging.conf
@@ -0,0 +1,21 @@
+[loggers]
+keys=root
+
+[handlers]
+keys=consoleHandler
+
+[formatters]
+keys=fullFormatter
+
+[logger_root]
+level=INFO
+handlers=consoleHandler
+
+[handler_consoleHandler]
+class=StreamHandler
+level=INFO
+formatter=fullFormatter
+args=(sys.stdout,)
+
+[formatter_fullFormatter]
+format=%(asctime)s - %(name)s - %(levelname)s - %(message)s
diff --git a/modules/bundles/spleen_segmentation/configs/metadata.json b/modules/bundles/spleen_segmentation/configs/metadata.json
@@ -0,0 +1,76 @@
+{
+    "schema": "https://github.com/Project-MONAI/MONAI-extra-test-data/releases/download/0.8.1/meta_schema_202203171008.json",
+    "version": "0.1.0",
+    "changelog": {
+        "0.1.0": "complete the model package",
+        "0.0.1": "initialize the model package structure"
+    },
+    "monai_version": "0.8.0",
+    "pytorch_version": "1.10.0",
+    "numpy_version": "1.21.2",
+    "optional_packages_version": {
+        "nibabel": "3.2.1"
+    },
+    "task": "Decathlon spleen segmentation",
+    "description": "A pre-trained model for volumetric (3D) segmentation of the spleen from CT image",
+    "authors": "MONAI team",
+    "copyright": "Copyright (c) MONAI Consortium",
+    "data_source": "Task09_Spleen.tar from http://medicaldecathlon.com/",
+    "data_type": "dicom",
+    "image_classes": "single channel data, intensity scaled to [0, 1]",
+    "label_classes": "single channel data, 1 is spleen, 0 is everything else",
+    "pred_classes": "2 channels OneHot data, channel 1 is spleen, channel 0 is background",
+    "eval_metrics": {
+        "mean_dice": 0.96
+    },
+    "intended_use": "This is an example, not to be used for diagnostic purposes",
+    "references": [
+        "Xia, Yingda, et al. '3D Semi-Supervised Learning with Uncertainty-Aware Multi-View Co-Training. arXiv preprint arXiv:1811.12506 (2018). https://arxiv.org/abs/1811.12506.",
+        "Kerfoot E., Clough J., Oksuz I., Lee J., King A.P., Schnabel J.A. (2019) Left-Ventricle Quantification Using Residual U-Net. In: Pop M. et al. (eds) Statistical Atlases and Computational Models of the Heart. Atrial Segmentation and LV Quantification Challenges. STACOM 2018. Lecture Notes in Computer Science, vol 11395. Springer, Cham. https://doi.org/10.1007/978-3-030-12029-0_40"
+    ],
+    "network_data_format": {
+        "inputs": {
+            "image": {
+                "type": "image",
+                "format": "magnitude",
+                "num_channels": 1,
+                "spatial_shape": [
+                    160,
+                    160,
+                    160
+                ],
+                "dtype": "float32",
+                "value_range": [
+                    0,
+                    1
+                ],
+                "is_patch_data": false,
+                "channel_def": {
+                    "0": "image"
+                }
+            }
+        },
+        "outputs": {
+            "pred": {
+                "type": "image",
+                "format": "segmentation",
+                "num_channels": 2,
+                "spatial_shape": [
+                    160,
+                    160,
+                    160
+                ],
+                "dtype": "float32",
+                "value_range": [
+                    0,
+                    1
+                ],
+                "is_patch_data": false,
+                "channel_def": {
+                    "0": "background",
+                    "1": "spleen"
+                }
+            }
+        }
+    }
+}
diff --git a/modules/bundles/spleen_segmentation/docs/README.md b/modules/bundles/spleen_segmentation/docs/README.md
@@ -0,0 +1,49 @@
+# Description
+A pre-trained model for volumetric (3D) segmentation of the spleen from CT image.
+
+# Model Overview
+This model is trained using the runner-up [1] awarded pipeline of the "Medical Segmentation Decathlon Challenge 2018" using the UNet architecture [2] with 32 training images and 9 validation images.
+
+## Data
+The training dataset is Task09_Spleen.tar from http://medicaldecathlon.com/.
+
+## Training configuration
+The training was performed with at least 12GB-memory GPUs.
+
+Actual Model Input: 96 x 96 x 96
+
+## Input and output formats
+Input: 1 channel CT image
+
+Output: 2 channels: Label 1: spleen; Label 0: everything else
+
+## Scores
+This model achieves the following Dice score on the validation data (our own split from the training dataset):
+
+Mean Dice = 0.96
+
+## commands example
+Execute inference:
+```
+python -m monai.bundle run evaluator --meta_file configs/metadata.json --config_file configs/inference.json --logging_file configs/logging.conf
+```
+Verify the metadata format:
+```
+python -m monai.bundle verify_metadata --meta_file configs/metadata.json --filepath eval/schema.json
+```
+Verify the data shape of network:
+```
+python -m monai.bundle verify_net_in_out network_def --meta_file configs/metadata.json --config_file configs/inference.json
+```
+Export checkpoint to TorchScript file:
+```
+python -m monai.bundle export network_def --filepath models/model.ts --ckpt_file models/model.pt --meta_file configs/metadata.json --config_file configs/inference.json
+```
+
+# Disclaimer
+This is an example, not to be used for diagnostic purposes.
+
+# References
+[1] Xia, Yingda, et al. "3D Semi-Supervised Learning with Uncertainty-Aware Multi-View Co-Training." arXiv preprint arXiv:1811.12506 (2018). https://arxiv.org/abs/1811.12506.
+
+[2] Kerfoot E., Clough J., Oksuz I., Lee J., King A.P., Schnabel J.A. (2019) Left-Ventricle Quantification Using Residual U-Net. In: Pop M. et al. (eds) Statistical Atlases and Computational Models of the Heart. Atrial Segmentation and LV Quantification Challenges. STACOM 2018. Lecture Notes in Computer Science, vol 11395. Springer, Cham. https://doi.org/10.1007/978-3-030-12029-0_40
diff --git a/modules/bundles/spleen_segmentation/docs/license.txt b/modules/bundles/spleen_segmentation/docs/license.txt
@@ -0,0 +1,6 @@
+Third Party Licenses
+-----------------------------------------------------------------------
+
+/*********************************************************************/
+i. Medical Segmentation Decathlon
+   http://medicaldecathlon.com/