Index

_

__call__() (minerva.transforms._Transform method) (minerva.transforms.Flip method) (minerva.transforms.PerlinMasker method) (minerva.transforms.transform._Transform method) (minerva.transforms.transform.CastTo method) (minerva.transforms.transform.Flip method) (minerva.transforms.transform.Padding method) (minerva.transforms.transform.PerlinMasker method) (minerva.transforms.transform.Squeeze method) (minerva.transforms.transform.TransformPipeline method) (minerva.transforms.transform.Unsqueeze method) (minerva.transforms.TransformPipeline method) __getitem__() (minerva.data.datasets.base.SimpleDataset method) (minerva.data.datasets.SimpleDataset method) (minerva.data.datasets.supervised_dataset.SupervisedReconstructionDataset method) (minerva.data.datasets.SupervisedReconstructionDataset method) (minerva.data.readers._Reader method) (minerva.data.readers.patched_array_reader.PatchedArrayReader method) (minerva.data.readers.PatchedArrayReader method) (minerva.data.readers.png_reader.PNGReader method) (minerva.data.readers.PNGReader method) (minerva.data.readers.reader._Reader method) (minerva.data.readers.tabular_reader.TabularReader method) (minerva.data.readers.tiff_reader.TiffReader method) (minerva.data.readers.TiffReader method) (minerva.utils.data.SimpleDataset method) __len__() (minerva.data.datasets.base.SimpleDataset method) (minerva.data.datasets.SimpleDataset method) (minerva.data.readers._Reader method) (minerva.data.readers.patched_array_reader.PatchedArrayReader method) (minerva.data.readers.PatchedArrayReader method) (minerva.data.readers.png_reader.PNGReader method) (minerva.data.readers.PNGReader method) (minerva.data.readers.reader._Reader method) (minerva.data.readers.tabular_reader.TabularReader method) (minerva.data.readers.tiff_reader.TiffReader method) (minerva.data.readers.TiffReader method) (minerva.utils.data.SimpleDataset method) __repr__() (minerva.models.nets.cnn_ha_etal.ZeroPadder2D method) (minerva.models.nets.cnn_pf.ZeroPadder2D method) __str__() (minerva.models.nets.cnn_ha_etal.ZeroPadder2D method) (minerva.models.nets.cnn_pf.ZeroPadder2D method) _calculate_fc_input_features() (minerva.models.nets.cnn_ha_etal.CNN_HaEtAl_1D method) (minerva.models.nets.cnn_ha_etal.CNN_HaEtAl_2D method) (minerva.models.nets.cnn_pf.CNN_PF_2D method) (minerva.models.nets.imu_transformer.IMUCNN method) (minerva.models.nets.inception_time.InceptionTime method) (minerva.models.nets.resnet_1d.ResNet1DBase method) _calculate_metrics() (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline method) _compute_metrics() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.SimpleSupervisedModel method) _create_backbone() (minerva.models.nets.cnn_ha_etal.CNN_HaEtAl_1D method) (minerva.models.nets.cnn_ha_etal.CNN_HaEtAl_2D method) (minerva.models.nets.imu_transformer.IMUCNN method) (minerva.models.nets.imu_transformer.IMUTransformerEncoder method)

_create_fc() (minerva.models.nets.cnn_ha_etal.CNN_HaEtAl_1D method) (minerva.models.nets.cnn_ha_etal.CNN_HaEtAl_2D method) (minerva.models.nets.cnn_pf.CNN_PF_2D method) (minerva.models.nets.imu_transformer.IMUCNN method) (minerva.models.nets.imu_transformer.IMUTransformerEncoder method) (minerva.models.nets.inception_time.InceptionTime method) _DoubleConv (class in minerva.models.nets.unet) _Down (class in minerva.models.nets.unet) _Encoder (class in minerva.models.nets.vit) _evaluate() (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline method) _fit() (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline method) _generate_data() (minerva.utils.data.RandomDataModule method) _get_patches() (minerva.data.readers.patched_array_reader.PatchedArrayReader method) (minerva.data.readers.PatchedArrayReader method) _IMUTransformerEncoder (class in minerva.models.nets.imu_transformer) _InceptionTime (class in minerva.models.nets.inception_time) _init_weights() (minerva.models.nets.sfm.MaskedAutoencoderViT method) _initialize_vars() (minerva.pipelines.base.Pipeline method) (minerva.pipelines.Pipeline method) _loss_func() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.DeepLabV3 method) (minerva.models.nets.deeplabv3.DeepLabV3 method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.SimpleSupervisedModel method) _OutConv (class in minerva.models.nets.unet) _pad_data() (minerva.data.readers.patched_array_reader.PatchedArrayReader method) (minerva.data.readers.PatchedArrayReader method) _predict() (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline method) _process_input() (minerva.models.nets.vit._VisionTransformerBackbone method) _Reader (class in minerva.data.readers) (class in minerva.data.readers.reader) _ResNet1D (class in minerva.models.nets.resnet_1d) _run() (minerva.pipelines.base.Pipeline method) (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline method) (minerva.pipelines.Pipeline method) _save_pipeline_info() (minerva.pipelines.base.Pipeline method) (minerva.pipelines.Pipeline method) _SetR_PUP (class in minerva.models.nets.setr) _SETRMLAHead (class in minerva.models.nets.setr) _SETRUPHead (class in minerva.models.nets.setr) _single_step() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.SimpleSupervisedModel method) (minerva.models.nets.WiseNet method) (minerva.models.nets.wisenet.WiseNet method) _test() (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline method) _Transform (class in minerva.transforms) (class in minerva.transforms.transform) _UNet (class in minerva.models.nets.unet) _Up (class in minerva.models.nets.unet) _VisionTransformerBackbone (class in minerva.models.nets.vit) _WiseNet (class in minerva.models.nets.wisenet)

A

aggregate_loss() (minerva.losses.dice.DiceLoss method)

B

BINARY_MODE (in module minerva.losses.dice)

build_model() (minerva.models.nets.inception_time._InceptionTime method) (minerva.models.nets.inception_time.InceptionModule method)

C

CastTo (class in minerva.transforms.transform) clone() (minerva.pipelines.base.Pipeline static method) (minerva.pipelines.Pipeline static method) CNN_HaEtAl_1D (class in minerva.models.nets.cnn_ha_etal) CNN_HaEtAl_2D (class in minerva.models.nets.cnn_ha_etal) CNN_PF_2D (class in minerva.models.nets.cnn_pf) CNN_PF_Backbone (class in minerva.models.nets.cnn_pf) CNN_PFF_2D (class in minerva.models.nets.cnn_pf) compute() (minerva.analysis.metrics.pixel_accuracy.PixelAccuracy method) (minerva.analysis.metrics.PixelAccuracy method) compute_score() (minerva.losses.dice.DiceLoss method)

config (minerva.pipelines.base.Pipeline property) (minerva.pipelines.Pipeline property) configure_optimizers() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.DeepLabV3 method) (minerva.models.nets.deeplabv3.DeepLabV3 method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.sfm.MaskedAutoencoderViT method) (minerva.models.nets.SimpleSupervisedModel method) ConvolutionalBlock (class in minerva.models.nets.resnet_1d) CSVReader (class in minerva.data.readers.csv_reader)

D

data (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline property) DeepLabV3 (class in minerva.models.nets) (class in minerva.models.nets.deeplabv3)

DeepLabV3Backbone (class in minerva.models.nets.deeplabv3) DeepLabV3PredictionHead (class in minerva.models.nets.deeplabv3) dice_score() (in module minerva.losses._functional) DiceLoss (class in minerva.losses.dice)

F

Flip (class in minerva.transforms) (class in minerva.transforms.transform) forward() (minerva.losses.dice.DiceLoss method) (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.cnn_ha_etal.ZeroPadder2D method) (minerva.models.nets.cnn_pf.CNN_PF_Backbone method) (minerva.models.nets.cnn_pf.ZeroPadder2D method) (minerva.models.nets.DeepLabV3 method) (minerva.models.nets.deeplabv3.DeepLabV3 method) (minerva.models.nets.deeplabv3.DeepLabV3Backbone method) (minerva.models.nets.imu_transformer._IMUTransformerEncoder method) (minerva.models.nets.inception_time._InceptionTime method) (minerva.models.nets.inception_time.InceptionModule method) (minerva.models.nets.inception_time.ShortcutLayer method) (minerva.models.nets.resnet_1d._ResNet1D method) (minerva.models.nets.resnet_1d.ConvolutionalBlock method) (minerva.models.nets.resnet_1d.ResNetBlock method) (minerva.models.nets.resnet_1d.SqueezeAndExcitation1D method) (minerva.models.nets.setr._SetR_PUP method) (minerva.models.nets.setr._SETRMLAHead method) (minerva.models.nets.setr._SETRUPHead method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.sfm.MaskedAutoencoderViT method) (minerva.models.nets.SimpleSupervisedModel method) (minerva.models.nets.unet._DoubleConv method) (minerva.models.nets.unet._Down method) (minerva.models.nets.unet._OutConv method) (minerva.models.nets.unet._UNet method) (minerva.models.nets.unet._Up method) (minerva.models.nets.vit._Encoder method) (minerva.models.nets.vit._VisionTransformerBackbone method) (minerva.models.nets.wisenet._WiseNet method) (minerva.utils.upsample.Upsample method)

forward_decoder() (minerva.models.nets.sfm.MaskedAutoencoderViT method) forward_encoder() (minerva.models.nets.sfm.MaskedAutoencoderViT method) forward_loss() (minerva.models.nets.sfm.MaskedAutoencoderViT method) freeze_weights() (minerva.models.nets.deeplabv3.DeepLabV3Backbone method) full_dataset_from_dataloader() (in module minerva.utils.data) full_info (minerva.pipelines.base.Pipeline property) (minerva.pipelines.Pipeline property)

G

get_1d_sincos_pos_embed_from_grid() (in module minerva.utils.position_embedding) get_2d_sincos_pos_embed() (in module minerva.utils.position_embedding)

get_2d_sincos_pos_embed_from_grid() (in module minerva.utils.position_embedding) get_full_data_split() (in module minerva.utils.data) get_split_dataloader() (in module minerva.utils.data)

I

IMUCNN (class in minerva.models.nets.imu_transformer) IMUTransformerEncoder (class in minerva.models.nets.imu_transformer) InceptionModule (class in minerva.models.nets.inception_time)

InceptionTime (class in minerva.models.nets.inception_time) initialize_weights() (minerva.models.nets.sfm.MaskedAutoencoderViT method) interpolate_pos_embed() (in module minerva.utils.position_embedding)

L

log_dir (minerva.pipelines.base.Pipeline property) (minerva.pipelines.Pipeline property)

M

mae_vit_base_patch16 (in module minerva.models.nets.sfm) mae_vit_base_patch16D4d256 (in module minerva.models.nets.sfm) mae_vit_huge_patch14 (in module minerva.models.nets.sfm) mae_vit_large_patch16 (in module minerva.models.nets.sfm) mae_vit_large_patch16D4d256 (in module minerva.models.nets.sfm) mae_vit_small_patch16 (in module minerva.models.nets.sfm) main() (in module minerva.pipelines.lightning_pipeline) MaskedAutoencoderViT (class in minerva.models.nets.sfm) minerva module minerva.analysis module minerva.analysis.metrics module minerva.analysis.metrics.pixel_accuracy module minerva.data module minerva.data.datasets module minerva.data.datasets.base module minerva.data.datasets.supervised_dataset module minerva.data.readers module minerva.data.readers.csv_reader module minerva.data.readers.patched_array_reader module minerva.data.readers.png_reader module minerva.data.readers.reader module minerva.data.readers.tabular_reader module minerva.data.readers.tiff_reader module minerva.data.readers.zarr_reader module minerva.losses module minerva.losses._functional module minerva.losses.dice module minerva.models module minerva.models.nets module minerva.models.nets.base module minerva.models.nets.cnn_ha_etal module minerva.models.nets.cnn_pf module minerva.models.nets.deeplabv3 module minerva.models.nets.imu_transformer module minerva.models.nets.inception_time module minerva.models.nets.resnet_1d module minerva.models.nets.setr module minerva.models.nets.sfm module minerva.models.nets.unet module minerva.models.nets.vit module

minerva.models.nets.wisenet module minerva.pipelines module minerva.pipelines.base module minerva.pipelines.lightning_pipeline module minerva.transforms module minerva.transforms.transform module minerva.utils module minerva.utils.data module minerva.utils.position_embedding module minerva.utils.tensor module minerva.utils.typing module minerva.utils.upsample module model (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline property) module minerva minerva.analysis minerva.analysis.metrics minerva.analysis.metrics.pixel_accuracy minerva.data minerva.data.datasets minerva.data.datasets.base minerva.data.datasets.supervised_dataset minerva.data.readers minerva.data.readers.csv_reader minerva.data.readers.patched_array_reader minerva.data.readers.png_reader minerva.data.readers.reader minerva.data.readers.tabular_reader minerva.data.readers.tiff_reader minerva.data.readers.zarr_reader minerva.losses minerva.losses._functional minerva.losses.dice minerva.models minerva.models.nets minerva.models.nets.base minerva.models.nets.cnn_ha_etal minerva.models.nets.cnn_pf minerva.models.nets.deeplabv3 minerva.models.nets.imu_transformer minerva.models.nets.inception_time minerva.models.nets.resnet_1d minerva.models.nets.setr minerva.models.nets.sfm minerva.models.nets.unet minerva.models.nets.vit minerva.models.nets.wisenet minerva.pipelines minerva.pipelines.base minerva.pipelines.lightning_pipeline minerva.transforms minerva.transforms.transform minerva.utils minerva.utils.data minerva.utils.position_embedding minerva.utils.tensor minerva.utils.typing minerva.utils.upsample MULTICLASS_MODE (in module minerva.losses.dice) MULTILABEL_MODE (in module minerva.losses.dice)

P

Padding (class in minerva.transforms.transform) PatchedArrayReader (class in minerva.data.readers) (class in minerva.data.readers.patched_array_reader) PatchedZarrReader (class in minerva.data.readers) (class in minerva.data.readers.zarr_reader) patchify() (minerva.models.nets.sfm.MaskedAutoencoderViT method) PathLike (in module minerva.utils.typing) PerlinMasker (class in minerva.transforms) (class in minerva.transforms.transform) Pipeline (class in minerva.pipelines) (class in minerva.pipelines.base) pipeline_id (minerva.pipelines.base.Pipeline property) (minerva.pipelines.Pipeline property)

pipeline_info (minerva.pipelines.base.Pipeline property) (minerva.pipelines.Pipeline property) PixelAccuracy (class in minerva.analysis.metrics) (class in minerva.analysis.metrics.pixel_accuracy) PNGReader (class in minerva.data.readers) (class in minerva.data.readers.png_reader) predict_dataloader() (minerva.utils.data.RandomDataModule method) predict_step() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.SimpleSupervisedModel method) (minerva.models.nets.WiseNet method) (minerva.models.nets.wisenet.WiseNet method)

R

random_masking() (minerva.models.nets.sfm.MaskedAutoencoderViT method) RandomDataModule (class in minerva.utils.data) resize() (in module minerva.utils.upsample) ResNet1D_8 (class in minerva.models.nets.resnet_1d) ResNet1DBase (class in minerva.models.nets.resnet_1d) ResNetBlock (class in minerva.models.nets.resnet_1d) ResNetSE1D_5 (class in minerva.models.nets.resnet_1d)

ResNetSE1D_8 (class in minerva.models.nets.resnet_1d) ResNetSEBlock (class in minerva.models.nets.resnet_1d) result (minerva.pipelines.base.Pipeline property) (minerva.pipelines.Pipeline property) run() (minerva.pipelines.base.Pipeline method) (minerva.pipelines.Pipeline method) run_status (minerva.pipelines.base.Pipeline property) (minerva.pipelines.Pipeline property)

S

SETR_PUP (class in minerva.models.nets) (class in minerva.models.nets.setr) setup() (minerva.utils.data.RandomDataModule method) ShortcutLayer (class in minerva.models.nets.inception_time) SimpleDataset (class in minerva.data.datasets) (class in minerva.data.datasets.base) (class in minerva.utils.data) SimpleLightningPipeline (class in minerva.pipelines.lightning_pipeline)

SimpleSupervisedModel (class in minerva.models.nets) (class in minerva.models.nets.base) Squeeze (class in minerva.transforms.transform) SqueezeAndExcitation1D (class in minerva.models.nets.resnet_1d) SupervisedReconstructionDataset (class in minerva.data.datasets) (class in minerva.data.datasets.supervised_dataset) system_info() (minerva.pipelines.base.Pipeline method) (minerva.pipelines.Pipeline method)

T

TabularReader (class in minerva.data.readers.tabular_reader) test_dataloader() (minerva.utils.data.RandomDataModule method) test_step() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.SimpleSupervisedModel method) TiffReader (class in minerva.data.readers) (class in minerva.data.readers.tiff_reader) to_tensor() (in module minerva.utils.tensor)

train_dataloader() (minerva.utils.data.RandomDataModule method) trainer (minerva.pipelines.lightning_pipeline.SimpleLightningPipeline property) training_step() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.sfm.MaskedAutoencoderViT method) (minerva.models.nets.SimpleSupervisedModel method) TransformPipeline (class in minerva.transforms) (class in minerva.transforms.transform)

U

UNet (class in minerva.models.nets) (class in minerva.models.nets.unet) unfreeze_weights() (minerva.models.nets.deeplabv3.DeepLabV3Backbone method) unpatchify() (minerva.models.nets.sfm.MaskedAutoencoderViT method)

Unsqueeze (class in minerva.transforms.transform) update() (minerva.analysis.metrics.pixel_accuracy.PixelAccuracy method) (minerva.analysis.metrics.PixelAccuracy method) Upsample (class in minerva.utils.upsample)

V

val_dataloader() (minerva.utils.data.RandomDataModule method) validation_step() (minerva.models.nets.base.SimpleSupervisedModel method) (minerva.models.nets.setr.SETR_PUP method) (minerva.models.nets.SETR_PUP method) (minerva.models.nets.sfm.MaskedAutoencoderViT method) (minerva.models.nets.SimpleSupervisedModel method)

W

WiseNet (class in minerva.models.nets) (class in minerva.models.nets.wisenet)

Z

ZeroPadder2D (class in minerva.models.nets.cnn_ha_etal) (class in minerva.models.nets.cnn_pf)