Programming Reference

Here is the Programming Interface

• minerva
  • Subpackages
    • minerva.analysis
      • Subpackages
        • minerva.analysis.metrics
          • Submodules
            • minerva.analysis.metrics.pixel_accuracy
              • Classes
              • Module Contents
                • PixelAccuracy
                  • PixelAccuracy.compute()
                  • PixelAccuracy.update()
          • Classes
          • Package Contents
            • PixelAccuracy
              • PixelAccuracy.compute()
              • PixelAccuracy.update()
    • minerva.data
      • Subpackages
        • minerva.data.datasets
          • Submodules
            • minerva.data.datasets.base
              • Classes
              • Module Contents
                • SimpleDataset
                  • SimpleDataset.__getitem__()
                  • SimpleDataset.__len__()
            • minerva.data.datasets.supervised_dataset
              • Classes
              • Module Contents
                • SupervisedReconstructionDataset
                  • SupervisedReconstructionDataset.__getitem__()
          • Classes
          • Package Contents
            • SimpleDataset
              • SimpleDataset.__getitem__()
              • SimpleDataset.__len__()
            • SupervisedReconstructionDataset
              • SupervisedReconstructionDataset.__getitem__()
        • minerva.data.readers
          • Submodules
            • minerva.data.readers.csv_reader
              • Classes
              • Module Contents
                • CSVReader
            • minerva.data.readers.patched_array_reader
              • Classes
              • Module Contents
                • PatchedArrayReader
                  • PatchedArrayReader.__getitem__()
                  • PatchedArrayReader.__len__()
                  • PatchedArrayReader._get_patches()
                  • PatchedArrayReader._pad_data()
            • minerva.data.readers.png_reader
              • Classes
              • Module Contents
                • PNGReader
                  • PNGReader.__getitem__()
                  • PNGReader.__len__()
            • minerva.data.readers.reader
              • Classes
              • Module Contents
                • _Reader
                  • _Reader.__getitem__()
                  • _Reader.__len__()
            • minerva.data.readers.tabular_reader
              • Classes
              • Module Contents
                • TabularReader
                  • TabularReader.__getitem__()
                  • TabularReader.__len__()
            • minerva.data.readers.tiff_reader
              • Classes
              • Module Contents
                • TiffReader
                  • TiffReader.__getitem__()
                  • TiffReader.__len__()
            • minerva.data.readers.zarr_reader
              • Classes
              • Module Contents
                • PatchedZarrReader
          • Classes
          • Package Contents
            • PNGReader
              • PNGReader.__getitem__()
              • PNGReader.__len__()
            • PatchedArrayReader
              • PatchedArrayReader.__getitem__()
              • PatchedArrayReader.__len__()
              • PatchedArrayReader._get_patches()
              • PatchedArrayReader._pad_data()
            • PatchedZarrReader
            • TiffReader
              • TiffReader.__getitem__()
              • TiffReader.__len__()
            • _Reader
              • _Reader.__getitem__()
              • _Reader.__len__()
    • minerva.losses
      • Submodules
        • minerva.losses._functional
          • Functions
          • Module Contents
            • dice_score()
        • minerva.losses.dice
          • Attributes
          • Classes
          • Module Contents
            • BINARY_MODE
            • DiceLoss
              • DiceLoss.aggregate_loss()
              • DiceLoss.compute_score()
              • DiceLoss.forward()
            • MULTICLASS_MODE
            • MULTILABEL_MODE
    • minerva.models
      • Subpackages
        • minerva.models.nets
          • Submodules
            • minerva.models.nets.base
              • Classes
              • Module Contents
                • SimpleSupervisedModel
                  • SimpleSupervisedModel._compute_metrics()
                  • SimpleSupervisedModel._loss_func()
                  • SimpleSupervisedModel._single_step()
                  • SimpleSupervisedModel.configure_optimizers()
                  • SimpleSupervisedModel.forward()
                  • SimpleSupervisedModel.predict_step()
                  • SimpleSupervisedModel.test_step()
                  • SimpleSupervisedModel.training_step()
                  • SimpleSupervisedModel.validation_step()
            • minerva.models.nets.cnn_ha_etal
              • Classes
              • Module Contents
                • CNN_HaEtAl_1D
                  • CNN_HaEtAl_1D._calculate_fc_input_features()
                  • CNN_HaEtAl_1D._create_backbone()
                  • CNN_HaEtAl_1D._create_fc()
                • CNN_HaEtAl_2D
                  • CNN_HaEtAl_2D._calculate_fc_input_features()
                  • CNN_HaEtAl_2D._create_backbone()
                  • CNN_HaEtAl_2D._create_fc()
                • ZeroPadder2D
                  • ZeroPadder2D.__repr__()
                  • ZeroPadder2D.__str__()
                  • ZeroPadder2D.forward()
            • minerva.models.nets.cnn_pf
              • Classes
              • Module Contents
                • CNN_PFF_2D
                • CNN_PF_2D
                  • CNN_PF_2D._calculate_fc_input_features()
                  • CNN_PF_2D._create_fc()
                • CNN_PF_Backbone
                  • CNN_PF_Backbone.forward()
                • ZeroPadder2D
                  • ZeroPadder2D.__repr__()
                  • ZeroPadder2D.__str__()
                  • ZeroPadder2D.forward()
            • minerva.models.nets.deeplabv3
              • Classes
              • Module Contents
                • DeepLabV3
                  • DeepLabV3._loss_func()
                  • DeepLabV3.configure_optimizers()
                  • DeepLabV3.forward()
                • DeepLabV3Backbone
                  • DeepLabV3Backbone.forward()
                  • DeepLabV3Backbone.freeze_weights()
                  • DeepLabV3Backbone.unfreeze_weights()
                • DeepLabV3PredictionHead
            • minerva.models.nets.imu_transformer
              • Classes
              • Module Contents
                • IMUCNN
                  • IMUCNN._calculate_fc_input_features()
                  • IMUCNN._create_backbone()
                  • IMUCNN._create_fc()
                • IMUTransformerEncoder
                  • IMUTransformerEncoder._create_backbone()
                  • IMUTransformerEncoder._create_fc()
                • _IMUTransformerEncoder
                  • _IMUTransformerEncoder.forward()
            • minerva.models.nets.inception_time
              • Classes
              • Module Contents
                • InceptionModule
                  • InceptionModule.build_model()
                  • InceptionModule.forward()
                • InceptionTime
                  • InceptionTime._calculate_fc_input_features()
                  • InceptionTime._create_fc()
                • ShortcutLayer
                  • ShortcutLayer.forward()
                • _InceptionTime
                  • _InceptionTime.build_model()
                  • _InceptionTime.forward()
            • minerva.models.nets.resnet_1d
              • Classes
              • Module Contents
                • ConvolutionalBlock
                  • ConvolutionalBlock.forward()
                • ResNet1DBase
                  • ResNet1DBase._calculate_fc_input_features()
                • ResNet1D_8
                • ResNetBlock
                  • ResNetBlock.forward()
                • ResNetSE1D_5
                • ResNetSE1D_8
                • ResNetSEBlock
                • SqueezeAndExcitation1D
                  • SqueezeAndExcitation1D.forward()
                • _ResNet1D
                  • _ResNet1D.forward()
            • minerva.models.nets.setr
              • Classes
              • Module Contents
                • SETR_PUP
                  • SETR_PUP._compute_metrics()
                  • SETR_PUP._loss_func()
                  • SETR_PUP._single_step()
                  • SETR_PUP.configure_optimizers()
                  • SETR_PUP.forward()
                  • SETR_PUP.predict_step()
                  • SETR_PUP.test_step()
                  • SETR_PUP.training_step()
                  • SETR_PUP.validation_step()
                • _SETRMLAHead
                  • _SETRMLAHead.forward()
                • _SETRUPHead
                  • _SETRUPHead.forward()
                • _SetR_PUP
                  • _SetR_PUP.forward()
            • minerva.models.nets.sfm
              • Attributes
              • Classes
              • Module Contents
                • MaskedAutoencoderViT
                  • MaskedAutoencoderViT._init_weights()
                  • MaskedAutoencoderViT.configure_optimizers()
                  • MaskedAutoencoderViT.forward()
                  • MaskedAutoencoderViT.forward_decoder()
                  • MaskedAutoencoderViT.forward_encoder()
                  • MaskedAutoencoderViT.forward_loss()
                  • MaskedAutoencoderViT.initialize_weights()
                  • MaskedAutoencoderViT.patchify()
                  • MaskedAutoencoderViT.random_masking()
                  • MaskedAutoencoderViT.training_step()
                  • MaskedAutoencoderViT.unpatchify()
                  • MaskedAutoencoderViT.validation_step()
                • mae_vit_base_patch16
                • mae_vit_base_patch16D4d256
                • mae_vit_huge_patch14
                • mae_vit_large_patch16
                • mae_vit_large_patch16D4d256
                • mae_vit_small_patch16
            • minerva.models.nets.unet
              • Classes
              • Module Contents
                • UNet
                • _DoubleConv
                  • _DoubleConv.forward()
                • _Down
                  • _Down.forward()
                • _OutConv
                  • _OutConv.forward()
                • _UNet
                  • _UNet.forward()
                • _Up
                  • _Up.forward()
            • minerva.models.nets.vit
              • Classes
              • Module Contents
                • _Encoder
                  • _Encoder.forward()
                • _VisionTransformerBackbone
                  • _VisionTransformerBackbone._process_input()
                  • _VisionTransformerBackbone.forward()
            • minerva.models.nets.wisenet
              • Classes
              • Module Contents
                • WiseNet
                  • WiseNet._single_step()
                  • WiseNet.predict_step()
                • _WiseNet
                  • _WiseNet.forward()
          • Classes
          • Package Contents
            • DeepLabV3
              • DeepLabV3._loss_func()
              • DeepLabV3.configure_optimizers()
              • DeepLabV3.forward()
            • SETR_PUP
              • SETR_PUP._compute_metrics()
              • SETR_PUP._loss_func()
              • SETR_PUP._single_step()
              • SETR_PUP.configure_optimizers()
              • SETR_PUP.forward()
              • SETR_PUP.predict_step()
              • SETR_PUP.test_step()
              • SETR_PUP.training_step()
              • SETR_PUP.validation_step()
            • SimpleSupervisedModel
              • SimpleSupervisedModel._compute_metrics()
              • SimpleSupervisedModel._loss_func()
              • SimpleSupervisedModel._single_step()
              • SimpleSupervisedModel.configure_optimizers()
              • SimpleSupervisedModel.forward()
              • SimpleSupervisedModel.predict_step()
              • SimpleSupervisedModel.test_step()
              • SimpleSupervisedModel.training_step()
              • SimpleSupervisedModel.validation_step()
            • UNet
            • WiseNet
              • WiseNet._single_step()
              • WiseNet.predict_step()
    • minerva.pipelines
      • Submodules
        • minerva.pipelines.base
          • Classes
          • Module Contents
            • Pipeline
              • Pipeline._initialize_vars()
              • Pipeline._run()
              • Pipeline._save_pipeline_info()
              • Pipeline.clone()
              • Pipeline.config
              • Pipeline.full_info
              • Pipeline.log_dir
              • Pipeline.pipeline_id
              • Pipeline.pipeline_info
              • Pipeline.result
              • Pipeline.run()
              • Pipeline.run_status
              • Pipeline.system_info()
        • minerva.pipelines.lightning_pipeline
          • Classes
          • Functions
          • Module Contents
            • SimpleLightningPipeline
              • SimpleLightningPipeline._calculate_metrics()
              • SimpleLightningPipeline._evaluate()
              • SimpleLightningPipeline._fit()
              • SimpleLightningPipeline._predict()
              • SimpleLightningPipeline._run()
              • SimpleLightningPipeline._test()
              • SimpleLightningPipeline.data
              • SimpleLightningPipeline.model
              • SimpleLightningPipeline.trainer
            • main()
      • Classes
      • Package Contents
        • Pipeline
          • Pipeline._initialize_vars()
          • Pipeline._run()
          • Pipeline._save_pipeline_info()
          • Pipeline.clone()
          • Pipeline.config
          • Pipeline.full_info
          • Pipeline.log_dir
          • Pipeline.pipeline_id
          • Pipeline.pipeline_info
          • Pipeline.result
          • Pipeline.run()
          • Pipeline.run_status
          • Pipeline.system_info()
    • minerva.transforms
      • Submodules
        • minerva.transforms.transform
          • Classes
          • Module Contents
            • CastTo
              • CastTo.__call__()
            • Flip
              • Flip.__call__()
            • Padding
              • Padding.__call__()
            • PerlinMasker
              • PerlinMasker.__call__()
            • Squeeze
              • Squeeze.__call__()
            • TransformPipeline
              • TransformPipeline.__call__()
            • Unsqueeze
              • Unsqueeze.__call__()
            • _Transform
              • _Transform.__call__()
      • Classes
      • Package Contents
        • Flip
          • Flip.__call__()
        • PerlinMasker
          • PerlinMasker.__call__()
        • TransformPipeline
          • TransformPipeline.__call__()
        • _Transform
          • _Transform.__call__()
    • minerva.utils
      • Submodules
        • minerva.utils.data
          • Classes
          • Functions
          • Module Contents
            • RandomDataModule
              • RandomDataModule._generate_data()
              • RandomDataModule.predict_dataloader()
              • RandomDataModule.setup()
              • RandomDataModule.test_dataloader()
              • RandomDataModule.train_dataloader()
              • RandomDataModule.val_dataloader()
            • SimpleDataset
              • SimpleDataset.__getitem__()
              • SimpleDataset.__len__()
            • full_dataset_from_dataloader()
            • get_full_data_split()
            • get_split_dataloader()
        • minerva.utils.position_embedding
          • Functions
          • Module Contents
            • get_1d_sincos_pos_embed_from_grid()
            • get_2d_sincos_pos_embed()
            • get_2d_sincos_pos_embed_from_grid()
            • interpolate_pos_embed()
        • minerva.utils.tensor
          • Functions
          • Module Contents
            • to_tensor()
        • minerva.utils.typing
          • Attributes
          • Module Contents
            • PathLike
        • minerva.utils.upsample
          • Classes
          • Functions
          • Module Contents
            • Upsample
              • Upsample.forward()
            • resize()