KalbeDigitalLab/PathologyNucleiClassification

1{2    "imports": [3        "$import glob",4        "$import json",5        "$import pathlib",6        "$import os"7    ],8    "bundle_root": "/workspace/data/pathology_nuclei_classification",9    "output_dir": "$@bundle_root + '/eval'",10    "dataset_dir": "/workspace/data/CoNSePNuclei",11    "images": "$list(sorted(glob.glob(@dataset_dir + '/Test/Images/*.png')))[:1]",12    "labels": "$list(sorted(glob.glob(@dataset_dir + '/Test/Labels/*.png')))[:1]",13    "input_data": "$[{'image': i, 'label': l} for i,l in zip(@images, @labels)]",14    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",15    "network_def": {16        "_target_": "DenseNet121",17        "spatial_dims": 2,18        "in_channels": 4,19        "out_channels": 420    },21    "network": "$@network_def.to(@device)",22    "preprocessing": {23        "_target_": "Compose",24        "transforms": [25            {26                "_target_": "LoadImaged",27                "keys": [28                    "image",29                    "label"30                ],31                "dtype": "uint8"32            },33            {34                "_target_": "EnsureChannelFirstd",35                "keys": [36                    "image",37                    "label"38                ]39            },40            {41                "_target_": "ScaleIntensityRanged",42                "keys": "image",43                "a_min": 0.0,44                "a_max": 255.0,45                "b_min": -1.0,46                "b_max": 1.047            },48            {49                "_target_": "AddLabelAsGuidanced",50                "keys": "image",51                "source": "label"52            }53        ]54    },55    "dataset": {56        "_target_": "Dataset",57        "data": "@input_data",58        "transform": "@preprocessing"59    },60    "dataloader": {61        "_target_": "DataLoader",62        "dataset": "@dataset",63        "batch_size": 1,64        "shuffle": false,65        "num_workers": 466    },67    "inferer": {68        "_target_": "SimpleInferer"69    },70    "postprocessing": {71        "_target_": "Compose",72        "transforms": [73            {74                "_target_": "Activationsd",75                "keys": "pred",76                "softmax": true77            },78            {79                "_target_": "SaveImaged",80                "keys": "pred",81                "meta_keys": "pred_meta_dict",82                "output_dir": "@output_dir",83                "output_ext": ".json"84            }85        ]86    },87    "handlers": [88        {89            "_target_": "CheckpointLoader",90            "load_path": "$@bundle_root + '/models/model.pt'",91            "load_dict": {92                "model": "@network"93            }94        },95        {96            "_target_": "StatsHandler",97            "iteration_log": false98        }99    ],100    "evaluator": {101        "_target_": "SupervisedEvaluator",102        "device": "@device",103        "val_data_loader": "@dataloader",104        "network": "@network",105        "inferer": "@inferer",106        "postprocessing": "@postprocessing",107        "val_handlers": "@handlers",108        "amp": true109    },110    "evaluating": [111        "$setattr(torch.backends.cudnn, 'benchmark', True)",112        "$import scripts",113        "$monai.data.register_writer('json', scripts.ClassificationWriter)",114        "$@evaluator.run()"115    ]116}117