Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W _ __call__() (clinicadl.data.dataloader.collate.CollateFn method) (clinicadl.data.dataloader.collate.MergeBatchesCollate method) (clinicadl.data.dataloader.collate.ToBatchCollate method) (clinicadl.data.dataloader.collate.ToBatchesCollate method) (clinicadl.infer.Inferer method) (clinicadl.infer.PatchesToImageInferer method) (clinicadl.infer.SimpleInferer method) (clinicadl.infer.SlicesToImageInferer method) (clinicadl.metrics.Metric method) (clinicadl.metrics.MetricsHandler method) (clinicadl.transforms.extraction.Image method) (clinicadl.transforms.extraction.Patch method) (clinicadl.transforms.extraction.Slice method) (clinicadl.transforms.Format method) (clinicadl.transforms.MergeFields method) __getitem__() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.Dataset method) (clinicadl.data.datasets.PairedDataset method) (clinicadl.data.datasets.TensorDataset method) (clinicadl.data.datasets.UnpairedDataset method) __len__() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.Dataset method) (clinicadl.data.datasets.PairedDataset method) (clinicadl.data.datasets.TensorDataset method) (clinicadl.data.datasets.UnpairedDataset method) _accumulate() (clinicadl.metrics.Metric method) _aggregate() (clinicadl.metrics.Metric method) A act (clinicadl.networks.config.AttentionUNetConfig attribute) (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.networks.config.DenseNetConfig attribute) (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.MLPOptions attribute) (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) (clinicadl.networks.config.UNetConfig attribute) add_callbacks() (clinicadl.callbacks.CallbacksHandler method) (clinicadl.train.Trainer method) add_field() (clinicadl.data.dataloader.Batch method) add_image() (clinicadl.data.structures.DataPoint method) (clinicadl.data.structures.Sample2D method) add_images() (clinicadl.data.dataloader.Batch method) add_mask() (clinicadl.data.structures.DataPoint method) (clinicadl.data.structures.Sample2D method) add_masks() (clinicadl.data.dataloader.Batch method) add_metrics() (clinicadl.metrics.MetricsHandler method) (clinicadl.train.Trainer method) adn_ordering (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.MLPOptions attribute) affine (clinicadl.data.structures.DataPoint property) aggregate() (clinicadl.metrics.Metric method) (clinicadl.metrics.MetricsHandler method) all_callbacks (clinicadl.callbacks.CallbacksHandler property) alpha (clinicadl.optim.optimizers.config.RMSpropConfig attribute) AMP amsgrad (clinicadl.optim.optimizers.config.AdamConfig attribute) anneal_strategy (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) applied_labels (clinicadl.transforms.config.FillHolesConfig attribute) (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) (clinicadl.transforms.config.LabelFilterConfig attribute) apply_augmentations() (clinicadl.transforms.TransformsHandler method) apply_image_transforms() (clinicadl.transforms.TransformsHandler method) apply_sample_transforms() (clinicadl.transforms.TransformsHandler method) argmax (clinicadl.transforms.config.AsDiscreteConfig attribute) AttentionUNet (class in clinicadl.networks.nn) AutoEncoder (class in clinicadl.networks.nn) average (clinicadl.metrics.config.AveragePrecisionMetricConfig attribute) (clinicadl.metrics.config.ROCAUCMetricConfig attribute) axes (clinicadl.transforms.config.RandomAnisotropyConfig attribute) (clinicadl.transforms.config.RandomFlipConfig attribute) (clinicadl.transforms.config.RandomGhostingConfig attribute) B backward_step() (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) base_momentum (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) Batch (class in clinicadl.data.dataloader) beta (clinicadl.losses.config.SmoothL1LossConfig attribute) betas (clinicadl.optim.optimizers.config.AdamConfig attribute) bias (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.MLPOptions attribute) BIDS Bids (class in clinicadl.io.bids) BIDS derivative BidsDataset (class in clinicadl.data.datasets) BidsFileType (class in clinicadl.io.bids) block_type (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) bottleneck_factor (clinicadl.networks.config.DenseNetConfig attribute) bottleneck_reduction (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) build_optimizers() (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) build_path() (clinicadl.io.bids.Bids method) build_train_loader() (clinicadl.split.Split method) build_val_loader() (clinicadl.split.Split method) by_measure (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) C call_event() (clinicadl.callbacks.CallbacksHandler method) Callback (class in clinicadl.callbacks) callbacks (clinicadl.callbacks.CallbacksHandler property) (clinicadl.train.Trainer property) CallbacksHandler (class in clinicadl.callbacks) CAPS capturable (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) center (clinicadl.transforms.config.RandomAffineConfig attribute) centered (clinicadl.optim.optimizers.config.RMSpropConfig attribute) channels (clinicadl.networks.config.AttentionUNetConfig attribute) (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.networks.config.UNetConfig attribute) channels_last (clinicadl.data.dataloader.Batch property) check_metric_name() (clinicadl.metrics.MetricsHandler method) check_shape (clinicadl.transforms.config.RandomAffineConfig attribute) class_thresholds (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) clinicadl.callbacks module clinicadl.data module clinicadl.data.dataloader module clinicadl.data.dataloader.collate module clinicadl.data.datasets module clinicadl.data.structures module clinicadl.data.structures.examples module clinicadl.data.utils module clinicadl.infer module clinicadl.io module clinicadl.io.bids module clinicadl.io.maps module clinicadl.losses module clinicadl.losses.config module clinicadl.metrics module clinicadl.metrics.config module clinicadl.models module clinicadl.networks module clinicadl.networks.config module clinicadl.networks.nn module clinicadl.optim module clinicadl.optim.lr_schedulers.config module clinicadl.optim.optimizers.config module clinicadl.split module clinicadl.train module clinicadl.transforms module clinicadl.transforms.config module clinicadl.transforms.extraction module clinicadl.utils module CNN (class in clinicadl.networks.nn) coefficients (clinicadl.transforms.config.RandomBiasFieldConfig attribute) Colin27DataPoint (class in clinicadl.data.structures.examples) Colin27Sample (class in clinicadl.data.structures.examples) Colin27Sample2D (class in clinicadl.data.structures.examples) CollateFn (class in clinicadl.data.dataloader.collate) ComputationalConfig (class in clinicadl.train) compute_sample (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) ConcatDataset (class in clinicadl.data.datasets) connectivity (clinicadl.transforms.config.FillHolesConfig attribute) (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) conv_args (clinicadl.networks.config.AutoEncoderConfig attribute) (clinicadl.networks.config.CNNConfig attribute) (clinicadl.networks.config.GeneratorConfig attribute) (clinicadl.networks.config.VAEConfig attribute) ConvDecoder (class in clinicadl.networks.nn) ConvEncoder (class in clinicadl.networks.nn) cooldown (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) copy_ (clinicadl.transforms.config.ActivationsConfig attribute) (clinicadl.transforms.config.AsDiscreteConfig attribute) (clinicadl.transforms.config.ClampConfig attribute) (clinicadl.transforms.config.CropConfig attribute) (clinicadl.transforms.config.CropOrPadConfig attribute) (clinicadl.transforms.config.DistanceTransformEDTConfig attribute) (clinicadl.transforms.config.EnsureShapeMultipleConfig attribute) (clinicadl.transforms.config.FillHolesConfig attribute) (clinicadl.transforms.config.FormatConfig attribute) (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) (clinicadl.transforms.config.LabelFilterConfig attribute) (clinicadl.transforms.config.MaskConfig attribute) (clinicadl.transforms.config.MergeFieldsConfig attribute) (clinicadl.transforms.config.OneHotConfig attribute) (clinicadl.transforms.config.OneOfConfig attribute) (clinicadl.transforms.config.PadConfig attribute) (clinicadl.transforms.config.RandomAffineConfig attribute) (clinicadl.transforms.config.RandomAnisotropyConfig attribute) (clinicadl.transforms.config.RandomBiasFieldConfig attribute) (clinicadl.transforms.config.RandomBlurConfig attribute) (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) (clinicadl.transforms.config.RandomFlipConfig attribute) (clinicadl.transforms.config.RandomGammaConfig attribute) (clinicadl.transforms.config.RandomGhostingConfig attribute) (clinicadl.transforms.config.RandomMotionConfig attribute) (clinicadl.transforms.config.RandomNoiseConfig attribute) (clinicadl.transforms.config.RandomSpikeConfig attribute) (clinicadl.transforms.config.RandomSwapConfig attribute) (clinicadl.transforms.config.RemapLabelsConfig attribute) (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) (clinicadl.transforms.config.ResampleConfig attribute) (clinicadl.transforms.config.RescaleIntensityConfig attribute) (clinicadl.transforms.config.ResizeConfig attribute) (clinicadl.transforms.config.SobelGradientsConfig attribute) (clinicadl.transforms.config.ToCanonicalConfig attribute) (clinicadl.transforms.config.ZNormalizationConfig attribute) create() (clinicadl.io.maps.Maps method) cropping (clinicadl.transforms.config.CropConfig attribute) cycle_momentum (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) D dampening (clinicadl.optim.optimizers.config.SGDConfig attribute) data leakage data_range (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) DataLoader (class in clinicadl.data.dataloader) DataPoint (class in clinicadl.data.structures) Dataset (class in clinicadl.data.datasets) default_pad_value (clinicadl.transforms.config.RandomAffineConfig attribute) degrees (clinicadl.transforms.config.RandomAffineConfig attribute) (clinicadl.transforms.config.RandomMotionConfig attribute) delete_split() (clinicadl.io.maps.Maps method) delta (clinicadl.losses.config.HuberLossConfig attribute) DenseNet (class in clinicadl.networks.nn) DenseNet121 (class in clinicadl.networks.nn) DenseNet161 (class in clinicadl.networks.nn) DenseNet169 (class in clinicadl.networks.nn) DenseNet201 (class in clinicadl.networks.nn) describe() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.TensorDataset method) detailed_df (clinicadl.metrics.MetricsHandler property) device (clinicadl.data.dataloader.Batch property) df (clinicadl.data.datasets.BidsDataset property) (clinicadl.data.datasets.ConcatDataset property) (clinicadl.data.datasets.Dataset property) (clinicadl.data.datasets.PairedDataset property) (clinicadl.data.datasets.TensorDataset property) (clinicadl.data.datasets.UnpairedDataset property) (clinicadl.metrics.MetricsHandler property) differentiable (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) dilation (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) dim (clinicadl.transforms.config.ActivationsConfig attribute) (clinicadl.transforms.config.AsDiscreteConfig attribute) directed (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) distance_metric (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) div_factor (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) downsampling (clinicadl.transforms.config.RandomAnisotropyConfig attribute) dropout (clinicadl.networks.config.AttentionUNetConfig attribute) (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.networks.config.DenseNetConfig attribute) (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.MLPOptions attribute) (clinicadl.networks.config.UNetConfig attribute) (clinicadl.networks.config.ViTConfig attribute) dtype (clinicadl.transforms.config.AsDiscreteConfig attribute) (clinicadl.transforms.config.FormatConfig attribute) (clinicadl.transforms.config.SobelGradientsConfig attribute) DwiDti (class in clinicadl.io.bids) E EarlyStoppingCallback (class in clinicadl.callbacks) embedding_dim (clinicadl.networks.config.ViTConfig attribute) end_factor (clinicadl.optim.lr_schedulers.config.LinearLRConfig attribute) epochs (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) eps (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) eval() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.Dataset method) (clinicadl.data.datasets.PairedDataset method) (clinicadl.data.datasets.TensorDataset method) (clinicadl.data.datasets.UnpairedDataset method) evaluation_step() (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) exclude (clinicadl.transforms.config.ActivationsConfig attribute) (clinicadl.transforms.config.AsDiscreteConfig attribute) (clinicadl.transforms.config.ClampConfig attribute) (clinicadl.transforms.config.CropConfig attribute) (clinicadl.transforms.config.CropOrPadConfig attribute) (clinicadl.transforms.config.DistanceTransformEDTConfig attribute) (clinicadl.transforms.config.EnsureShapeMultipleConfig attribute) (clinicadl.transforms.config.FillHolesConfig attribute) (clinicadl.transforms.config.FormatConfig attribute) (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) (clinicadl.transforms.config.LabelFilterConfig attribute) (clinicadl.transforms.config.MaskConfig attribute) (clinicadl.transforms.config.MergeFieldsConfig attribute) (clinicadl.transforms.config.OneHotConfig attribute) (clinicadl.transforms.config.OneOfConfig attribute) (clinicadl.transforms.config.PadConfig attribute) (clinicadl.transforms.config.RandomAffineConfig attribute) (clinicadl.transforms.config.RandomAnisotropyConfig attribute) (clinicadl.transforms.config.RandomBiasFieldConfig attribute) (clinicadl.transforms.config.RandomBlurConfig attribute) (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) (clinicadl.transforms.config.RandomFlipConfig attribute) (clinicadl.transforms.config.RandomGammaConfig attribute) (clinicadl.transforms.config.RandomGhostingConfig attribute) (clinicadl.transforms.config.RandomMotionConfig attribute) (clinicadl.transforms.config.RandomNoiseConfig attribute) (clinicadl.transforms.config.RandomSpikeConfig attribute) (clinicadl.transforms.config.RandomSwapConfig attribute) (clinicadl.transforms.config.RemapLabelsConfig attribute) (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) (clinicadl.transforms.config.ResampleConfig attribute) (clinicadl.transforms.config.RescaleIntensityConfig attribute) (clinicadl.transforms.config.ResizeConfig attribute) (clinicadl.transforms.config.SobelGradientsConfig attribute) (clinicadl.transforms.config.ToCanonicalConfig attribute) (clinicadl.transforms.config.ZNormalizationConfig attribute) extract_sample() (clinicadl.transforms.TransformsHandler method) F factor (clinicadl.optim.lr_schedulers.config.ConstantLRConfig attribute) (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) final_div_factor (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) FlairLinear (class in clinicadl.io.bids) flip_probability (clinicadl.transforms.config.RandomFlipConfig attribute) foreach (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) Format (class in clinicadl.transforms) forward() (clinicadl.networks.nn.UNet method) (clinicadl.networks.nn.VAE method) (clinicadl.networks.nn.ViT method) forward_step() (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) freeze (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) from_maps() (clinicadl.train.Trainer class method) fused (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) G gamma (clinicadl.optim.lr_schedulers.config.ExponentialLRConfig attribute) (clinicadl.optim.lr_schedulers.config.MultiStepLRConfig attribute) (clinicadl.optim.lr_schedulers.config.StepLRConfig attribute) Generator (class in clinicadl.networks.nn) get_all_participants_sessions() (clinicadl.io.bids.Bids method) get_detailed_metric_values() (clinicadl.metrics.MetricsHandler method) get_field() (clinicadl.data.dataloader.Batch method) get_image_tensor() (clinicadl.data.structures.DataPoint method) (clinicadl.data.structures.Sample2D method) get_images_dict() (clinicadl.data.structures.DataPoint method) get_keys() (clinicadl.data.structures.DataPoint method) get_loss_functions() (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) get_masks_dict() (clinicadl.data.structures.DataPoint method) get_metric_value() (clinicadl.metrics.MetricsHandler method) get_metric_values() (clinicadl.metrics.MetricsHandler method) get_non_images_dict() (clinicadl.data.structures.DataPoint method) get_not_nans (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) (clinicadl.metrics.config.MAEMetricConfig attribute) (clinicadl.metrics.config.MeanIoUConfig attribute) (clinicadl.metrics.config.MSEMetricConfig attribute) (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.PSNRMetricConfig attribute) (clinicadl.metrics.config.RMSEMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) get_participant_session_couples() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.Dataset method) (clinicadl.data.datasets.PairedDataset method) (clinicadl.data.datasets.TensorDataset method) (clinicadl.data.datasets.UnpairedDataset method) get_participants_sessions_with() (clinicadl.io.bids.Bids method) get_path() (clinicadl.io.bids.Bids method) get_sample_info() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.Dataset method) (clinicadl.data.datasets.PairedDataset method) (clinicadl.data.datasets.TensorDataset method) (clinicadl.data.datasets.UnpairedDataset method) get_split() (clinicadl.split.SingleSplit method) get_splits() (clinicadl.split.KFold method) get_summary() (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) growth_rate (clinicadl.networks.config.DenseNetConfig attribute) H has_file_type() (clinicadl.io.bids.Bids method) hidden_dims (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.MLPOptions attribute) I ignore_empty (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.metrics.config.MeanIoUConfig attribute) ignore_index (clinicadl.losses.config.CrossEntropyLossConfig attribute) (clinicadl.losses.config.NLLLossConfig attribute) Image (class in clinicadl.transforms.extraction) image_interpolation (clinicadl.transforms.config.RandomAffineConfig attribute) (clinicadl.transforms.config.RandomAnisotropyConfig attribute) (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) (clinicadl.transforms.config.RandomMotionConfig attribute) (clinicadl.transforms.config.ResampleConfig attribute) (clinicadl.transforms.config.ResizeConfig attribute) in_channels (clinicadl.networks.config.AttentionUNetConfig attribute) (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.DenseNetConfig attribute) (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) (clinicadl.networks.config.UNetConfig attribute) in_min_max (clinicadl.transforms.config.RescaleIntensityConfig attribute) in_shape (clinicadl.networks.config.AutoEncoderConfig attribute) (clinicadl.networks.config.CNNConfig attribute) (clinicadl.networks.config.VAEConfig attribute) (clinicadl.networks.config.ViTConfig attribute) include (clinicadl.transforms.config.ActivationsConfig attribute) (clinicadl.transforms.config.AsDiscreteConfig attribute) (clinicadl.transforms.config.ClampConfig attribute) (clinicadl.transforms.config.CropConfig attribute) (clinicadl.transforms.config.CropOrPadConfig attribute) (clinicadl.transforms.config.DistanceTransformEDTConfig attribute) (clinicadl.transforms.config.EnsureShapeMultipleConfig attribute) (clinicadl.transforms.config.FillHolesConfig attribute) (clinicadl.transforms.config.FormatConfig attribute) (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) (clinicadl.transforms.config.LabelFilterConfig attribute) (clinicadl.transforms.config.MaskConfig attribute) (clinicadl.transforms.config.MergeFieldsConfig attribute) (clinicadl.transforms.config.OneHotConfig attribute) (clinicadl.transforms.config.OneOfConfig attribute) (clinicadl.transforms.config.PadConfig attribute) (clinicadl.transforms.config.RandomAffineConfig attribute) (clinicadl.transforms.config.RandomAnisotropyConfig attribute) (clinicadl.transforms.config.RandomBiasFieldConfig attribute) (clinicadl.transforms.config.RandomBlurConfig attribute) (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) (clinicadl.transforms.config.RandomFlipConfig attribute) (clinicadl.transforms.config.RandomGammaConfig attribute) (clinicadl.transforms.config.RandomGhostingConfig attribute) (clinicadl.transforms.config.RandomMotionConfig attribute) (clinicadl.transforms.config.RandomNoiseConfig attribute) (clinicadl.transforms.config.RandomSpikeConfig attribute) (clinicadl.transforms.config.RandomSwapConfig attribute) (clinicadl.transforms.config.RemapLabelsConfig attribute) (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) (clinicadl.transforms.config.ResampleConfig attribute) (clinicadl.transforms.config.RescaleIntensityConfig attribute) (clinicadl.transforms.config.ResizeConfig attribute) (clinicadl.transforms.config.SobelGradientsConfig attribute) (clinicadl.transforms.config.ToCanonicalConfig attribute) (clinicadl.transforms.config.ZNormalizationConfig attribute) include_background (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.metrics.config.GeneralizedDiceScoreConfig attribute) (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) (clinicadl.metrics.config.MeanIoUConfig attribute) (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) independent (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) independent_channels (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) index (clinicadl.split.Split property) Inferer (class in clinicadl.infer) init_conv_size (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) init_conv_stride (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) init_features (clinicadl.networks.config.DenseNetConfig attribute) init_metrics() (clinicadl.metrics.MetricsHandler method) initial_accumulator_value (clinicadl.optim.optimizers.config.AdagradConfig attribute) intensity (clinicadl.transforms.config.RandomGhostingConfig attribute) (clinicadl.transforms.config.RandomSpikeConfig attribute) is_onehot (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) isotropic (clinicadl.transforms.config.RandomAffineConfig attribute) K k1 (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) k2 (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) kernel_sigma (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) kernel_size (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.transforms.config.SobelGradientsConfig attribute) kernel_type (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) keys (clinicadl.transforms.config.MergeFieldsConfig attribute) KFold (class in clinicadl.split) L label_interpolation (clinicadl.transforms.config.RandomAffineConfig attribute) (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) (clinicadl.transforms.config.ResampleConfig attribute) (clinicadl.transforms.config.ResizeConfig attribute) label_key (clinicadl.metrics.config.AveragePrecisionMetricConfig attribute) (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.metrics.config.GeneralizedDiceScoreConfig attribute) (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) (clinicadl.metrics.config.LossMetricConfig attribute) (clinicadl.metrics.config.MAEMetricConfig attribute) (clinicadl.metrics.config.MeanIoUConfig attribute) (clinicadl.metrics.config.MSEMetricConfig attribute) (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.PSNRMetricConfig attribute) (clinicadl.metrics.config.RMSEMetricConfig attribute) (clinicadl.metrics.config.ROCAUCMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) label_smoothing (clinicadl.losses.config.CrossEntropyLossConfig attribute) labels (clinicadl.transforms.config.CropOrPadConfig attribute) (clinicadl.transforms.config.MaskConfig attribute) last_epoch (clinicadl.optim.lr_schedulers.config.ConstantLRConfig attribute) (clinicadl.optim.lr_schedulers.config.ExponentialLRConfig attribute) (clinicadl.optim.lr_schedulers.config.LinearLRConfig attribute) (clinicadl.optim.lr_schedulers.config.MultiStepLRConfig attribute) (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) (clinicadl.optim.lr_schedulers.config.PolynomialLRConfig attribute) (clinicadl.optim.lr_schedulers.config.StepLRConfig attribute) latent_size (clinicadl.networks.config.AutoEncoderConfig attribute) (clinicadl.networks.config.GeneratorConfig attribute) (clinicadl.networks.config.VAEConfig attribute) load() (clinicadl.metrics.MetricsHandler method) load_state_dict() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.EarlyStoppingCallback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.ModelCheckpointCallback method) (clinicadl.callbacks.MonitorCallback method) locked_borders (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) log_gamma (clinicadl.transforms.config.RandomGammaConfig attribute) log_target (clinicadl.losses.config.KLDivLossConfig attribute) LoggerCallback (class in clinicadl.callbacks) loss_name (clinicadl.metrics.config.LossMetricConfig attribute) lr (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) lr_decay (clinicadl.optim.optimizers.config.AdagradConfig attribute) LRSchedulerCallback (class in clinicadl.callbacks) M make_kfold() (in module clinicadl.split) make_split() (in module clinicadl.split) mapping (clinicadl.data.datasets.UnpairedDataset property) MAPS Maps (class in clinicadl.io.maps) maps (clinicadl.train.Trainer property) margin (clinicadl.losses.config.MultiMarginLossConfig attribute) mask_name (clinicadl.transforms.config.CropOrPadConfig attribute) masking_method (clinicadl.transforms.config.MaskConfig attribute) (clinicadl.transforms.config.RemapLabelsConfig attribute) (clinicadl.transforms.config.RescaleIntensityConfig attribute) (clinicadl.transforms.config.ZNormalizationConfig attribute) max_displacement (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) max_lr (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) max_momentum (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) max_val (clinicadl.metrics.config.PSNRMetricConfig attribute) maximize (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) mean (clinicadl.transforms.config.RandomNoiseConfig attribute) merge() (clinicadl.metrics.MetricsHandler method) MergeBatchesCollate (class in clinicadl.data.dataloader.collate) MergeFields (class in clinicadl.transforms) method (clinicadl.transforms.config.EnsureShapeMultipleConfig attribute) Metric (class in clinicadl.metrics) metric_name (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) metrics (clinicadl.metrics.MetricsHandler property) (clinicadl.train.Trainer property) MetricsHandler (class in clinicadl.metrics) milestones (clinicadl.optim.lr_schedulers.config.MultiStepLRConfig attribute) min_lr (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) min_size (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) MLP (class in clinicadl.networks.nn) mlp_args (clinicadl.networks.config.AutoEncoderConfig attribute) (clinicadl.networks.config.CNNConfig attribute) (clinicadl.networks.config.GeneratorConfig attribute) (clinicadl.networks.config.VAEConfig attribute) mlp_dim (clinicadl.networks.config.ViTConfig attribute) mode (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) Model (class in clinicadl.models) model (clinicadl.train.Trainer property) ModelCheckpointCallback (class in clinicadl.callbacks) module clinicadl.callbacks clinicadl.data clinicadl.data.dataloader clinicadl.data.dataloader.collate clinicadl.data.datasets clinicadl.data.structures clinicadl.data.structures.examples clinicadl.data.utils clinicadl.infer clinicadl.io clinicadl.io.bids clinicadl.io.maps clinicadl.losses clinicadl.losses.config clinicadl.metrics clinicadl.metrics.config clinicadl.models clinicadl.networks clinicadl.networks.config clinicadl.networks.nn clinicadl.optim clinicadl.optim.lr_schedulers.config clinicadl.optim.optimizers.config clinicadl.split clinicadl.train clinicadl.transforms clinicadl.transforms.config clinicadl.transforms.extraction clinicadl.utils momentum (clinicadl.optim.optimizers.config.RMSpropConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) MonitorCallback (class in clinicadl.callbacks) N n_dense_layers (clinicadl.networks.config.DenseNetConfig attribute) n_features (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) n_iterations (clinicadl.callbacks.MonitorCallback property) n_res_blocks (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) nesterov (clinicadl.optim.optimizers.config.SGDConfig attribute) NIfTI norm (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.MLPOptions attribute) normalize_gradients (clinicadl.transforms.config.SobelGradientsConfig attribute) normalize_kernels (clinicadl.transforms.config.SobelGradientsConfig attribute) num_classes (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.transforms.config.OneHotConfig attribute) num_components (clinicadl.transforms.config.KeepLargestConnectedComponentConfig attribute) num_control_points (clinicadl.transforms.config.RandomElasticDeformationConfig attribute) num_ghosts (clinicadl.transforms.config.RandomGhostingConfig attribute) num_heads (clinicadl.networks.config.ViTConfig attribute) num_inputs (clinicadl.networks.config.MLPConfig attribute) num_iterations (clinicadl.transforms.config.RandomSwapConfig attribute) num_layers (clinicadl.networks.config.ViTConfig attribute) num_outputs (clinicadl.networks.config.CNNConfig attribute) (clinicadl.networks.config.DenseNet121Config attribute) (clinicadl.networks.config.DenseNet161Config attribute) (clinicadl.networks.config.DenseNet169Config attribute) (clinicadl.networks.config.DenseNet201Config attribute) (clinicadl.networks.config.DenseNetConfig attribute) (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.ResNet101Config attribute) (clinicadl.networks.config.ResNet152Config attribute) (clinicadl.networks.config.ResNet18Config attribute) (clinicadl.networks.config.ResNet34Config attribute) (clinicadl.networks.config.ResNet50Config attribute) (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNet101Config attribute) (clinicadl.networks.config.SEResNet152Config attribute) (clinicadl.networks.config.SEResNet50Config attribute) (clinicadl.networks.config.SEResNetConfig attribute) (clinicadl.networks.config.ViTB16Config attribute) (clinicadl.networks.config.ViTB32Config attribute) (clinicadl.networks.config.ViTConfig attribute) (clinicadl.networks.config.ViTL16Config attribute) (clinicadl.networks.config.ViTL32Config attribute) num_samples_per_image() (clinicadl.transforms.extraction.Image method) (clinicadl.transforms.extraction.Patch method) (clinicadl.transforms.extraction.Slice method) num_spikes (clinicadl.transforms.config.RandomSpikeConfig attribute) num_transforms (clinicadl.transforms.config.RandomMotionConfig attribute) O on_backward_step_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.MonitorCallback method) on_backward_step_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.MonitorCallback method) on_batch_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.MonitorCallback method) on_batch_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) on_epoch_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.ModelCheckpointCallback method) (clinicadl.callbacks.MonitorCallback method) (clinicadl.callbacks.TrainingCheckpointCallback method) on_epoch_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.MonitorCallback method) on_evaluation_step_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.MonitorCallback method) on_exception() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.MonitorCallback method) (clinicadl.callbacks.TrainingCheckpointCallback method) on_forward_step_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.MonitorCallback method) on_metrics_computation_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.MonitorCallback method) on_metrics_computation_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.MonitorCallback method) on_optimization_step_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.MonitorCallback method) on_optimization_step_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.MonitorCallback method) on_resume() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.EarlyStoppingCallback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.ModelCheckpointCallback method) (clinicadl.callbacks.MonitorCallback method) (clinicadl.callbacks.TrainingCheckpointCallback method) on_test_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) on_test_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) on_train_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.ModelCheckpointCallback method) (clinicadl.callbacks.MonitorCallback method) (clinicadl.callbacks.TrainingCheckpointCallback method) on_train_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.EarlyStoppingCallback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.ModelCheckpointCallback method) (clinicadl.callbacks.MonitorCallback method) (clinicadl.callbacks.TrainingCheckpointCallback method) on_trainer_init() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) on_validate_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) on_validate_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) on_validation_end() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.EarlyStoppingCallback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.ModelCheckpointCallback method) (clinicadl.callbacks.MonitorCallback method) on_validation_start() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.LoggerCallback method) (clinicadl.callbacks.MonitorCallback method) open_file() (clinicadl.io.maps.Maps static method) optimization (clinicadl.train.Trainer property) optimization_step() (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) OptimizationConfig (class in clinicadl.optim) optimum (clinicadl.metrics.Metric property) order (clinicadl.transforms.config.RandomBiasFieldConfig attribute) other (clinicadl.transforms.config.ActivationsConfig attribute) out_channels (clinicadl.networks.config.AttentionUNetConfig attribute) (clinicadl.networks.config.AutoEncoderConfig attribute) (clinicadl.networks.config.UNetConfig attribute) (clinicadl.networks.config.VAEConfig attribute) out_max (clinicadl.transforms.config.ClampConfig attribute) out_min (clinicadl.transforms.config.ClampConfig attribute) out_min_max (clinicadl.transforms.config.RescaleIntensityConfig attribute) output_act (clinicadl.networks.config.AttentionUNetConfig attribute) (clinicadl.networks.config.AutoEncoderConfig attribute) (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.networks.config.DenseNet121Config attribute) (clinicadl.networks.config.DenseNet161Config attribute) (clinicadl.networks.config.DenseNet169Config attribute) (clinicadl.networks.config.DenseNet201Config attribute) (clinicadl.networks.config.DenseNetConfig attribute) (clinicadl.networks.config.MLPConfig attribute) (clinicadl.networks.config.MLPOptions attribute) (clinicadl.networks.config.ResNet101Config attribute) (clinicadl.networks.config.ResNet152Config attribute) (clinicadl.networks.config.ResNet18Config attribute) (clinicadl.networks.config.ResNet34Config attribute) (clinicadl.networks.config.ResNet50Config attribute) (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNet101Config attribute) (clinicadl.networks.config.SEResNet152Config attribute) (clinicadl.networks.config.SEResNet50Config attribute) (clinicadl.networks.config.SEResNetConfig attribute) (clinicadl.networks.config.UNetConfig attribute) (clinicadl.networks.config.VAEConfig attribute) (clinicadl.networks.config.ViTB16Config attribute) (clinicadl.networks.config.ViTB32Config attribute) (clinicadl.networks.config.ViTConfig attribute) (clinicadl.networks.config.ViTL16Config attribute) (clinicadl.networks.config.ViTL32Config attribute) output_key (clinicadl.transforms.config.MergeFieldsConfig attribute) output_padding (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) outside_value (clinicadl.transforms.config.MaskConfig attribute) P p (clinicadl.losses.config.MultiMarginLossConfig attribute) padding (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) (clinicadl.transforms.config.PadConfig attribute) padding_mode (clinicadl.transforms.config.CropOrPadConfig attribute) (clinicadl.transforms.config.PadConfig attribute) (clinicadl.transforms.config.SobelGradientsConfig attribute) PairedDataset (class in clinicadl.data.datasets) participants_dir (clinicadl.io.bids.Bids property) Patch (class in clinicadl.transforms.extraction) patch_size (clinicadl.networks.config.ViTConfig attribute) (clinicadl.transforms.config.RandomSwapConfig attribute) PatchesToImageInferer (class in clinicadl.infer) patience (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) pct_start (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) percentile (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) percentiles (clinicadl.transforms.config.RescaleIntensityConfig attribute) PetLinear (class in clinicadl.io.bids) pixdim (clinicadl.transforms.config.RemoveSmallObjectsConfig attribute) plot() (clinicadl.data.structures.DataPoint method) pooling (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) pooling_indices (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) pos_embed_type (clinicadl.networks.config.ViTConfig attribute) pos_weight (clinicadl.losses.config.BCEWithLogitsLossConfig attribute) postprocessing (clinicadl.metrics.config.AveragePrecisionMetricConfig attribute) (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.metrics.config.GeneralizedDiceScoreConfig attribute) (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) (clinicadl.metrics.config.LossMetricConfig attribute) (clinicadl.metrics.config.MAEMetricConfig attribute) (clinicadl.metrics.config.MeanIoUConfig attribute) (clinicadl.metrics.config.MSEMetricConfig attribute) (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.PSNRMetricConfig attribute) (clinicadl.metrics.config.RMSEMetricConfig attribute) (clinicadl.metrics.config.ROCAUCMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) power (clinicadl.optim.lr_schedulers.config.PolynomialLRConfig attribute) pre_affine_name (clinicadl.transforms.config.ResampleConfig attribute) pred_key (clinicadl.metrics.config.AveragePrecisionMetricConfig attribute) (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.metrics.config.GeneralizedDiceScoreConfig attribute) (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) (clinicadl.metrics.config.LossMetricConfig attribute) (clinicadl.metrics.config.MAEMetricConfig attribute) (clinicadl.metrics.config.MeanIoUConfig attribute) (clinicadl.metrics.config.MSEMetricConfig attribute) (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.PSNRMetricConfig attribute) (clinicadl.metrics.config.RMSEMetricConfig attribute) (clinicadl.metrics.config.ROCAUCMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) pretrained (clinicadl.networks.config.DenseNet121Config attribute) (clinicadl.networks.config.DenseNet161Config attribute) (clinicadl.networks.config.DenseNet169Config attribute) (clinicadl.networks.config.DenseNet201Config attribute) (clinicadl.networks.config.ResNet101Config attribute) (clinicadl.networks.config.ResNet152Config attribute) (clinicadl.networks.config.ResNet18Config attribute) (clinicadl.networks.config.ResNet34Config attribute) (clinicadl.networks.config.ResNet50Config attribute) (clinicadl.networks.config.ViTB16Config attribute) (clinicadl.networks.config.ViTB32Config attribute) (clinicadl.networks.config.ViTL16Config attribute) (clinicadl.networks.config.ViTL32Config attribute) probabilities (clinicadl.transforms.config.OneOfConfig attribute) R RAS+ read() (clinicadl.io.maps.Maps method) ReconstructionModel (class in clinicadl.models) reduction (clinicadl.losses.config.BCELossConfig attribute) (clinicadl.losses.config.BCEWithLogitsLossConfig attribute) (clinicadl.losses.config.CrossEntropyLossConfig attribute) (clinicadl.losses.config.HuberLossConfig attribute) (clinicadl.losses.config.KLDivLossConfig attribute) (clinicadl.losses.config.L1LossConfig attribute) (clinicadl.losses.config.MSELossConfig attribute) (clinicadl.losses.config.MultiMarginLossConfig attribute) (clinicadl.losses.config.NLLLossConfig attribute) (clinicadl.losses.config.SmoothL1LossConfig attribute) (clinicadl.metrics.config.ConfusionMatrixMetricConfig attribute) (clinicadl.metrics.config.DiceMetricConfig attribute) (clinicadl.metrics.config.GeneralizedDiceScoreConfig attribute) (clinicadl.metrics.config.HausdorffDistanceMetricConfig attribute) (clinicadl.metrics.config.MAEMetricConfig attribute) (clinicadl.metrics.config.MeanIoUConfig attribute) (clinicadl.metrics.config.MSEMetricConfig attribute) (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.PSNRMetricConfig attribute) (clinicadl.metrics.config.RMSEMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) remapping (clinicadl.transforms.config.RemapLabelsConfig attribute) remove() (clinicadl.io.maps.Maps method) remove_image() (clinicadl.data.structures.DataPoint method) remove_metrics() (clinicadl.metrics.MetricsHandler method) remove_tensors() (in module clinicadl.data.utils) reparameterize() (clinicadl.networks.nn.VAE method) reset() (clinicadl.metrics.MetricsHandler method) (clinicadl.models.Model method) (clinicadl.models.ReconstructionModel method) (clinicadl.models.SupervisedModel method) ResNet (class in clinicadl.networks.nn) ResNet101 (class in clinicadl.networks.nn) ResNet152 (class in clinicadl.networks.nn) ResNet18 (class in clinicadl.networks.nn) ResNet34 (class in clinicadl.networks.nn) ResNet50 (class in clinicadl.networks.nn) restore (clinicadl.transforms.config.RandomGhostingConfig attribute) resume() (clinicadl.train.Trainer method) return_with_label (clinicadl.metrics.config.DiceMetricConfig attribute) rho (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) rounding (clinicadl.transforms.config.AsDiscreteConfig attribute) S Sample (class in clinicadl.data.structures) Sample2D (class in clinicadl.data.structures) sample_type (clinicadl.transforms.extraction.Image property) (clinicadl.transforms.extraction.Patch property) (clinicadl.transforms.extraction.Slice property) sampling (clinicadl.transforms.config.DistanceTransformEDTConfig attribute) sanity_check() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.TensorDataset method) save() (clinicadl.metrics.MetricsHandler method) save_file() (clinicadl.io.maps.Maps static method) scalars_only (clinicadl.transforms.config.ResampleConfig attribute) scales (clinicadl.transforms.config.RandomAffineConfig attribute) se_reduction (clinicadl.networks.config.SEResNetConfig attribute) seed_everything() (in module clinicadl.utils.seed) seed_everything_context() (in module clinicadl.utils.seed) SEResNet (class in clinicadl.networks.nn) SEResNet101 (class in clinicadl.networks.nn) SEResNet152 (class in clinicadl.networks.nn) SEResNet50 (class in clinicadl.networks.nn) set_epoch() (clinicadl.data.dataloader.DataLoader method) (clinicadl.data.datasets.UnpairedDataset method) shape (clinicadl.data.structures.DataPoint property) sigmoid (clinicadl.transforms.config.ActivationsConfig attribute) SimpleInferer (class in clinicadl.infer) SingleSplit (class in clinicadl.split) Slice (class in clinicadl.transforms.extraction) SlicesToImageInferer (class in clinicadl.infer) softmax (clinicadl.transforms.config.ActivationsConfig attribute) sort() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.TensorDataset method) spacing (clinicadl.data.structures.DataPoint property) spatial_axes (clinicadl.transforms.config.SobelGradientsConfig attribute) spatial_dims (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) (clinicadl.metrics.config.SSIMMetricConfig attribute) (clinicadl.networks.config.AttentionUNetConfig attribute) (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.DenseNetConfig attribute) (clinicadl.networks.config.ResNetConfig attribute) (clinicadl.networks.config.SEResNetConfig attribute) (clinicadl.networks.config.UNetConfig attribute) spatial_shape (clinicadl.data.structures.DataPoint property) Split (class in clinicadl.split) split_dir (clinicadl.split.Split property) squeeze (clinicadl.transforms.config.FormatConfig attribute) start_factor (clinicadl.optim.lr_schedulers.config.LinearLRConfig attribute) start_shape (clinicadl.networks.config.GeneratorConfig attribute) state (clinicadl.train.Trainer property) state_dict() (clinicadl.callbacks.Callback method) (clinicadl.callbacks.EarlyStoppingCallback method) (clinicadl.callbacks.LRSchedulerCallback method) (clinicadl.callbacks.ModelCheckpointCallback method) (clinicadl.callbacks.MonitorCallback method) std (clinicadl.transforms.config.RandomBlurConfig attribute) (clinicadl.transforms.config.RandomNoiseConfig attribute) step_size (clinicadl.optim.lr_schedulers.config.StepLRConfig attribute) steps_per_epoch (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) stride (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) (clinicadl.networks.config.ConvEncoderConfig attribute) (clinicadl.networks.config.ConvEncoderOptions attribute) subset() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.Dataset method) (clinicadl.data.datasets.PairedDataset method) (clinicadl.data.datasets.TensorDataset method) (clinicadl.data.datasets.UnpairedDataset method) (clinicadl.metrics.MetricsHandler method) SupervisedModel (class in clinicadl.models) symmetric (clinicadl.metrics.config.SurfaceDistanceMetricConfig attribute) T T1Linear (class in clinicadl.io.bids) target (clinicadl.transforms.config.ResampleConfig attribute) target_multiple (clinicadl.transforms.config.EnsureShapeMultipleConfig attribute) target_shape (clinicadl.transforms.config.CropOrPadConfig attribute) (clinicadl.transforms.config.ResizeConfig attribute) TensorDataset (class in clinicadl.data.datasets) tensors_dir (clinicadl.io.bids.Bids property) test() (clinicadl.train.Trainer method) three_phase (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) threshold (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) (clinicadl.transforms.config.AsDiscreteConfig attribute) threshold_mode (clinicadl.optim.lr_schedulers.config.ReduceLROnPlateauConfig attribute) to() (clinicadl.data.dataloader.Batch method) to_onehot (clinicadl.transforms.config.AsDiscreteConfig attribute) to_tensors() (clinicadl.data.datasets.BidsDataset method) ToBatchCollate (class in clinicadl.data.dataloader.collate) ToBatchesCollate (class in clinicadl.data.dataloader.collate) total_iters (clinicadl.optim.lr_schedulers.config.ConstantLRConfig attribute) (clinicadl.optim.lr_schedulers.config.LinearLRConfig attribute) (clinicadl.optim.lr_schedulers.config.PolynomialLRConfig attribute) total_steps (clinicadl.optim.lr_schedulers.config.OneCycleLRConfig attribute) train() (clinicadl.data.datasets.BidsDataset method) (clinicadl.data.datasets.ConcatDataset method) (clinicadl.data.datasets.Dataset method) (clinicadl.data.datasets.PairedDataset method) (clinicadl.data.datasets.TensorDataset method) (clinicadl.data.datasets.UnpairedDataset method) (clinicadl.train.Trainer method) train_dataset (clinicadl.split.Split property) train_loader (clinicadl.split.Split property) Trainer (class in clinicadl.train) TrainerState (class in clinicadl.train) TrainingCheckpointCallback (class in clinicadl.callbacks) transforms (clinicadl.transforms.config.OneOfConfig attribute) TransformsHandler (class in clinicadl.transforms) translation (clinicadl.transforms.config.RandomAffineConfig attribute) (clinicadl.transforms.config.RandomMotionConfig attribute) U UNet (class in clinicadl.networks.nn) UnpairedDataset (class in clinicadl.data.datasets) unpooling (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) unpooling_indices (clinicadl.networks.config.ConvDecoderConfig attribute) (clinicadl.networks.config.ConvDecoderOptions attribute) unpooling_mode (clinicadl.networks.config.AutoEncoderConfig attribute) (clinicadl.networks.config.VAEConfig attribute) unsqueeze (clinicadl.transforms.config.FormatConfig attribute) use_subvoxels (clinicadl.metrics.config.SurfaceDiceMetricConfig attribute) V VAE (class in clinicadl.networks.nn) val_dataset (clinicadl.split.Split property) val_loader (clinicadl.split.Split property) validate() (clinicadl.train.Trainer method) ViT (class in clinicadl.networks.nn) ViTB16 (class in clinicadl.networks.nn) ViTB32 (class in clinicadl.networks.nn) ViTL16 (class in clinicadl.networks.nn) ViTL32 (class in clinicadl.networks.nn) W weight (clinicadl.losses.config.BCELossConfig attribute) (clinicadl.losses.config.BCEWithLogitsLossConfig attribute) (clinicadl.losses.config.CrossEntropyLossConfig attribute) (clinicadl.losses.config.MultiMarginLossConfig attribute) (clinicadl.losses.config.NLLLossConfig attribute) weight_decay (clinicadl.optim.optimizers.config.AdadeltaConfig attribute) (clinicadl.optim.optimizers.config.AdagradConfig attribute) (clinicadl.optim.optimizers.config.AdamConfig attribute) (clinicadl.optim.optimizers.config.RMSpropConfig attribute) (clinicadl.optim.optimizers.config.SGDConfig attribute) weight_type (clinicadl.metrics.config.GeneralizedDiceScoreConfig attribute) weights (clinicadl.metrics.config.MultiScaleSSIMMetricConfig attribute) win_size (clinicadl.metrics.config.SSIMMetricConfig attribute)