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mednet 1.3.1
mednet 1.3.1
  • Installation
  • Usage
    • Running complete experiments
    • Training and Analysis
    • Prediction and Evaluation
    • Saliency Generation and Analysis (classification)
    • Annotation visualisation and analysis (segmentation)
  • Baselines and Pre-trained Models
  • Data model
  • Databases
    • Classification
      • HIV-TB
      • Indian (Dataset A/Dataset B)
      • Montgomery County
      • NIH-CXR14
      • PAD-Chest
      • Shenzhen Hospital
      • TB-POC
      • TBX11k
      • Visceral
      • Aggregated databases (Montgomery County and Shenzhen)
      • Aggregated databases (Montgomery County, Shenzhen and Indian)
      • Aggregated databases (Montgomery County, Shenzhen, Indian and TBX11k)
    • Semantic Segmentation
      • AV-Drive
      • CHASE-DB1
      • CXR-8
      • Dr. Hagis
      • DRIONS-DB
      • DRISHTI-GS1
      • DRIVE
      • HRF
      • IOSTAR
      • JSRT
      • Montgomery County
      • REFUGE
      • RIM One (r3)
      • Shenzhen Hospital
      • STARE
    • Object Detection
      • CXR-8
      • JSRT
      • Montgomery County
      • Shenzhen Hospital
  • Model Architectures
  • Command-line Interface
  • Python API
    • mednet
      • mednet.data
        • mednet.data.augmentations
        • mednet.data.classify
          • mednet.data.classify.hivtb
          • mednet.data.classify.indian
          • mednet.data.classify.montgomery
          • mednet.data.classify.montgomery_shenzhen
          • mednet.data.classify.montgomery_shenzhen_indian
          • mednet.data.classify.montgomery_shenzhen_indian_tbx11k
          • mednet.data.classify.nih_cxr14
          • mednet.data.classify.padchest
          • mednet.data.classify.shenzhen
          • mednet.data.classify.tbpoc
          • mednet.data.classify.tbx11k
          • mednet.data.classify.visceral
        • mednet.data.datamodule
        • mednet.data.detect
          • mednet.data.detect.cxr8
          • mednet.data.detect.jsrt
          • mednet.data.detect.montgomery
          • mednet.data.detect.shenzhen
        • mednet.data.image_utils
        • mednet.data.segment
          • mednet.data.segment.avdrive
          • mednet.data.segment.chasedb1
          • mednet.data.segment.cxr8
          • mednet.data.segment.drhagis
          • mednet.data.segment.drionsdb
          • mednet.data.segment.drishtigs1
          • mednet.data.segment.drive
          • mednet.data.segment.hrf
          • mednet.data.segment.iostar
          • mednet.data.segment.jsrt
          • mednet.data.segment.montgomery
          • mednet.data.segment.refuge
          • mednet.data.segment.rimoner3
          • mednet.data.segment.shenzhen
          • mednet.data.segment.stare
        • mednet.data.split
        • mednet.data.typing
      • mednet.engine
        • mednet.engine.callbacks
        • mednet.engine.classify
          • mednet.engine.classify.evaluator
          • mednet.engine.classify.predictor
          • mednet.engine.classify.saliency
            • mednet.engine.classify.saliency.completeness
            • mednet.engine.classify.saliency.generator
            • mednet.engine.classify.saliency.interpretability
            • mednet.engine.classify.saliency.utils
            • mednet.engine.classify.saliency.viewer
        • mednet.engine.detect
          • mednet.engine.detect.evaluator
          • mednet.engine.detect.predictor
        • mednet.engine.device
        • mednet.engine.loggers
        • mednet.engine.segment
          • mednet.engine.segment.dumper
          • mednet.engine.segment.evaluator
          • mednet.engine.segment.predictor
          • mednet.engine.segment.viewer
        • mednet.engine.trainer
        • mednet.engine.uploader
      • mednet.models
        • mednet.models.classify
          • mednet.models.classify.alexnet
          • mednet.models.classify.cnn3d
          • mednet.models.classify.densenet
          • mednet.models.classify.logistic_regression
          • mednet.models.classify.mlp
          • mednet.models.classify.model
          • mednet.models.classify.pasa
          • mednet.models.classify.typing
        • mednet.models.detect
          • mednet.models.detect.faster_rcnn
          • mednet.models.detect.model
          • mednet.models.detect.typing
        • mednet.models.losses
        • mednet.models.model
        • mednet.models.normalizer
        • mednet.models.segment
          • mednet.models.segment.backbones
            • mednet.models.segment.backbones.mobilenetv2
            • mednet.models.segment.backbones.vgg
          • mednet.models.segment.driu
          • mednet.models.segment.driu_bn
          • mednet.models.segment.driu_od
          • mednet.models.segment.driu_pix
          • mednet.models.segment.hed
          • mednet.models.segment.lwnet
          • mednet.models.segment.m2unet
          • mednet.models.segment.make_layers
          • mednet.models.segment.model
          • mednet.models.segment.unet
        • mednet.models.transforms
        • mednet.models.typing
      • mednet.scripts
        • mednet.scripts.classify
          • mednet.scripts.classify.cli
          • mednet.scripts.classify.evaluate
          • mednet.scripts.classify.saliency
            • mednet.scripts.classify.saliency.completeness
            • mednet.scripts.classify.saliency.generate
            • mednet.scripts.classify.saliency.interpretability
            • mednet.scripts.classify.saliency.view
        • mednet.scripts.cli
        • mednet.scripts.click
        • mednet.scripts.config
        • mednet.scripts.database
        • mednet.scripts.detect
          • mednet.scripts.detect.cli
          • mednet.scripts.detect.evaluate
        • mednet.scripts.experiment
        • mednet.scripts.info
        • mednet.scripts.logging
        • mednet.scripts.predict
        • mednet.scripts.preprocess
        • mednet.scripts.segment
          • mednet.scripts.segment.cli
          • mednet.scripts.segment.dump_annotations
          • mednet.scripts.segment.evaluate
          • mednet.scripts.segment.view
        • mednet.scripts.train
        • mednet.scripts.train_analysis
        • mednet.scripts.upload
        • mednet.scripts.utils
      • mednet.utils
        • mednet.utils.checkpointer
        • mednet.utils.rc
        • mednet.utils.resources
        • mednet.utils.string
        • mednet.utils.summary
        • mednet.utils.tensorboard
  • Config Modules
    • mednet.config
      • mednet.config.augmentations
        • mednet.config.augmentations.affine
        • mednet.config.augmentations.elastic
        • mednet.config.augmentations.hflip
        • mednet.config.augmentations.hflip_affine
        • mednet.config.augmentations.hflip_jitter_affine
        • mednet.config.augmentations.jitter
      • mednet.config.classify
        • mednet.config.classify.data
          • mednet.config.classify.data.hivtb
            • mednet.config.classify.data.hivtb.fold_0
            • mednet.config.classify.data.hivtb.fold_1
            • mednet.config.classify.data.hivtb.fold_2
            • mednet.config.classify.data.hivtb.fold_3
            • mednet.config.classify.data.hivtb.fold_4
            • mednet.config.classify.data.hivtb.fold_5
            • mednet.config.classify.data.hivtb.fold_6
            • mednet.config.classify.data.hivtb.fold_7
            • mednet.config.classify.data.hivtb.fold_8
            • mednet.config.classify.data.hivtb.fold_9
          • mednet.config.classify.data.indian
            • mednet.config.classify.data.indian.default
            • mednet.config.classify.data.indian.fold_0
            • mednet.config.classify.data.indian.fold_1
            • mednet.config.classify.data.indian.fold_2
            • mednet.config.classify.data.indian.fold_3
            • mednet.config.classify.data.indian.fold_4
            • mednet.config.classify.data.indian.fold_5
            • mednet.config.classify.data.indian.fold_6
            • mednet.config.classify.data.indian.fold_7
            • mednet.config.classify.data.indian.fold_8
            • mednet.config.classify.data.indian.fold_9
          • mednet.config.classify.data.montgomery
            • mednet.config.classify.data.montgomery.default
            • mednet.config.classify.data.montgomery.fold_0
            • mednet.config.classify.data.montgomery.fold_1
            • mednet.config.classify.data.montgomery.fold_2
            • mednet.config.classify.data.montgomery.fold_3
            • mednet.config.classify.data.montgomery.fold_4
            • mednet.config.classify.data.montgomery.fold_5
            • mednet.config.classify.data.montgomery.fold_6
            • mednet.config.classify.data.montgomery.fold_7
            • mednet.config.classify.data.montgomery.fold_8
            • mednet.config.classify.data.montgomery.fold_9
            • mednet.config.classify.data.montgomery.multiclass
          • mednet.config.classify.data.montgomery_shenzhen
            • mednet.config.classify.data.montgomery_shenzhen.default
            • mednet.config.classify.data.montgomery_shenzhen.fold_0
            • mednet.config.classify.data.montgomery_shenzhen.fold_1
            • mednet.config.classify.data.montgomery_shenzhen.fold_2
            • mednet.config.classify.data.montgomery_shenzhen.fold_3
            • mednet.config.classify.data.montgomery_shenzhen.fold_4
            • mednet.config.classify.data.montgomery_shenzhen.fold_5
            • mednet.config.classify.data.montgomery_shenzhen.fold_6
            • mednet.config.classify.data.montgomery_shenzhen.fold_7
            • mednet.config.classify.data.montgomery_shenzhen.fold_8
            • mednet.config.classify.data.montgomery_shenzhen.fold_9
          • mednet.config.classify.data.montgomery_shenzhen_indian
            • mednet.config.classify.data.montgomery_shenzhen_indian.default
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_0
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_1
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_2
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_3
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_4
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_5
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_6
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_7
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_8
            • mednet.config.classify.data.montgomery_shenzhen_indian.fold_9
          • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_0
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_1
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_2
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_3
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_4
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_5
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_6
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_7
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_8
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_fold_9
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v1_healthy_vs_atb
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_0
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_1
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_2
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_3
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_4
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_5
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_6
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_7
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_8
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_fold_9
            • mednet.config.classify.data.montgomery_shenzhen_indian_tbx11k.v2_others_vs_atb
          • mednet.config.classify.data.nih_cxr14
            • mednet.config.classify.data.nih_cxr14.default
            • mednet.config.classify.data.nih_cxr14.first_100
          • mednet.config.classify.data.padchest
            • mednet.config.classify.data.padchest.cardiomegaly_idiap
            • mednet.config.classify.data.padchest.idiap
            • mednet.config.classify.data.padchest.no_tb_idiap
            • mednet.config.classify.data.padchest.tb_idiap
          • mednet.config.classify.data.shenzhen
            • mednet.config.classify.data.shenzhen.alltest
            • mednet.config.classify.data.shenzhen.default
            • mednet.config.classify.data.shenzhen.fold_0
            • mednet.config.classify.data.shenzhen.fold_1
            • mednet.config.classify.data.shenzhen.fold_2
            • mednet.config.classify.data.shenzhen.fold_3
            • mednet.config.classify.data.shenzhen.fold_4
            • mednet.config.classify.data.shenzhen.fold_5
            • mednet.config.classify.data.shenzhen.fold_6
            • mednet.config.classify.data.shenzhen.fold_7
            • mednet.config.classify.data.shenzhen.fold_8
            • mednet.config.classify.data.shenzhen.fold_9
          • mednet.config.classify.data.tbpoc
            • mednet.config.classify.data.tbpoc.fold_0
            • mednet.config.classify.data.tbpoc.fold_1
            • mednet.config.classify.data.tbpoc.fold_2
            • mednet.config.classify.data.tbpoc.fold_3
            • mednet.config.classify.data.tbpoc.fold_4
            • mednet.config.classify.data.tbpoc.fold_5
            • mednet.config.classify.data.tbpoc.fold_6
            • mednet.config.classify.data.tbpoc.fold_7
            • mednet.config.classify.data.tbpoc.fold_8
            • mednet.config.classify.data.tbpoc.fold_9
          • mednet.config.classify.data.tbx11k
            • mednet.config.classify.data.tbx11k.v1_fold_0
            • mednet.config.classify.data.tbx11k.v1_fold_1
            • mednet.config.classify.data.tbx11k.v1_fold_2
            • mednet.config.classify.data.tbx11k.v1_fold_3
            • mednet.config.classify.data.tbx11k.v1_fold_4
            • mednet.config.classify.data.tbx11k.v1_fold_5
            • mednet.config.classify.data.tbx11k.v1_fold_6
            • mednet.config.classify.data.tbx11k.v1_fold_7
            • mednet.config.classify.data.tbx11k.v1_fold_8
            • mednet.config.classify.data.tbx11k.v1_fold_9
            • mednet.config.classify.data.tbx11k.v1_healthy_vs_atb
            • mednet.config.classify.data.tbx11k.v2_fold_0
            • mednet.config.classify.data.tbx11k.v2_fold_1
            • mednet.config.classify.data.tbx11k.v2_fold_2
            • mednet.config.classify.data.tbx11k.v2_fold_3
            • mednet.config.classify.data.tbx11k.v2_fold_4
            • mednet.config.classify.data.tbx11k.v2_fold_5
            • mednet.config.classify.data.tbx11k.v2_fold_6
            • mednet.config.classify.data.tbx11k.v2_fold_7
            • mednet.config.classify.data.tbx11k.v2_fold_8
            • mednet.config.classify.data.tbx11k.v2_fold_9
            • mednet.config.classify.data.tbx11k.v2_others_vs_atb
          • mednet.config.classify.data.visceral
            • mednet.config.classify.data.visceral.default
        • mednet.config.classify.models
          • mednet.config.classify.models.alexnet
          • mednet.config.classify.models.alexnet_pretrained
          • mednet.config.classify.models.cnn3d
          • mednet.config.classify.models.densenet
          • mednet.config.classify.models.densenet_pretrained
          • mednet.config.classify.models.logistic_regression
          • mednet.config.classify.models.mlp
          • mednet.config.classify.models.pasa
      • mednet.config.detect
        • mednet.config.detect.data
          • mednet.config.detect.data.cxr8
            • mednet.config.detect.data.cxr8.default
          • mednet.config.detect.data.jsrt
            • mednet.config.detect.data.jsrt.default
          • mednet.config.detect.data.montgomery
            • mednet.config.detect.data.montgomery.default
          • mednet.config.detect.data.shenzhen
            • mednet.config.detect.data.shenzhen.default
        • mednet.config.detect.models
          • mednet.config.detect.models.faster_rcnn
      • mednet.config.segment
        • mednet.config.segment.data
          • mednet.config.segment.data.avdrive
            • mednet.config.segment.data.avdrive.default
          • mednet.config.segment.data.chasedb1
            • mednet.config.segment.data.chasedb1.first_annotator
            • mednet.config.segment.data.chasedb1.second_annotator
          • mednet.config.segment.data.cxr8
            • mednet.config.segment.data.cxr8.default
          • mednet.config.segment.data.drhagis
            • mednet.config.segment.data.drhagis.default
          • mednet.config.segment.data.drionsdb
            • mednet.config.segment.data.drionsdb.expert1
            • mednet.config.segment.data.drionsdb.expert2
          • mednet.config.segment.data.drishtigs1
            • mednet.config.segment.data.drishtigs1.optic_cup_all
            • mednet.config.segment.data.drishtigs1.optic_cup_any
            • mednet.config.segment.data.drishtigs1.optic_disc_all
            • mednet.config.segment.data.drishtigs1.optic_disc_any
          • mednet.config.segment.data.drive
            • mednet.config.segment.data.drive.default
            • mednet.config.segment.data.drive.drive_2nd
          • mednet.config.segment.data.hrf
            • mednet.config.segment.data.hrf.default
          • mednet.config.segment.data.iostar
            • mednet.config.segment.data.iostar.optic_disc
            • mednet.config.segment.data.iostar.vessel
          • mednet.config.segment.data.jsrt
            • mednet.config.segment.data.jsrt.default
          • mednet.config.segment.data.montgomery
            • mednet.config.segment.data.montgomery.default
          • mednet.config.segment.data.refuge
            • mednet.config.segment.data.refuge.cup
            • mednet.config.segment.data.refuge.disc
          • mednet.config.segment.data.rimoner3
            • mednet.config.segment.data.rimoner3.cup_exp1
            • mednet.config.segment.data.rimoner3.cup_exp2
            • mednet.config.segment.data.rimoner3.disc_exp1
            • mednet.config.segment.data.rimoner3.disc_exp2
          • mednet.config.segment.data.shenzhen
            • mednet.config.segment.data.shenzhen.default
          • mednet.config.segment.data.stare
            • mednet.config.segment.data.stare.ah
            • mednet.config.segment.data.stare.vk
        • mednet.config.segment.models
          • mednet.config.segment.models.driu
          • mednet.config.segment.models.driu_bn
          • mednet.config.segment.models.driu_od
          • mednet.config.segment.models.driu_pix
          • mednet.config.segment.models.hed
          • mednet.config.segment.models.lwnet
          • mednet.config.segment.models.m2unet
          • mednet.config.segment.models.unet
  • Getting Involved and Contributing
  • Bibliography
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REFUGEΒΆ

  • DataModule and support code: data.segment.refuge

  • Splits:

    Config. key

    Module

    refuge-cup

    config.segment.data.refuge.cup

    refuge-disc

    config.segment.data.refuge.disc
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