Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | Z A abspath() (in module deepali.core.pathlib) abspath_template() (in module deepali.core.pathlib) abspow() (in module deepali.core.math) Activation (class in deepali.networks.layers.acti) activation() (in module deepali.networks.layers.acti) add_summary_image() (in module deepali.utils.tensorboard) add_summary_images() (in module deepali.utils.tensorboard) affine() (Cube method) (Grid method) affine_first() (in module deepali.spatial.generic) affine_flow() (in module deepali.core.flow) affine_model (TransformConfig attribute) AFFINE_NAMES (in module deepali.spatial.generic) affine_rotation_matrix() (in module deepali.core.affine) AFFINE_TRANSFORMS (in module deepali.spatial.generic) AffineTransform (class in deepali.spatial.linear) align_centers() (ImageTransformer method) (SampleImage method) ALIGN_CORNERS (in module deepali.core.grid) align_corners() (Grid method) (Image method) (ImageBatch method) (SampleImage method) (SpatialTransform method) align_corners_() (Grid method) AlignImage (class in deepali.modules.sample) all() (FlowDerivativeKeys class method) (SpatialDerivativeKeys static method) all_central_image_slices() (in module deepali.utils.tensorboard) angle_axis_to_quaternion() (in module deepali.core._kornia) angle_axis_to_rotation_matrix() (in module deepali.core._kornia) angles() (EulerRotation method) (Shearing method) angles_() (EulerRotation method) (Shearing method) AnisotropicScaling (class in deepali.spatial.linear) append() (ImageBatch method) apply_transform() (Cube method) (Grid method) (in module deepali.core.affine) apply_warp_field_to_points() (in module deepali.utils.vtk.simpleitk) apply_warp_field_to_pointset() (in module deepali.utils.vtk.simpleitk) ArgumentParser (class in deepali.core.argparse) array_from_image() (in module deepali.utils.simpleitk.numpy) as_float_tensor() (in module deepali.core.tensor) as_homogeneous_matrix() (in module deepali.core.linalg) as_homogeneous_tensor() (in module deepali.core.linalg) as_immutable_container() (in module deepali.core.nnutils) as_module_dict() (RegistrationLoss static method) as_one_hot_tensor() (in module deepali.core.tensor) as_tensor() (in module deepali.core.tensor) asdict() (DataclassConfig method) atanh() (in module deepali.core.math) atleast_1d() (in module deepali.core.tensor) avg_pool() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) AvgPoolImage (class in deepali.data.transforms.image) Axes (class in deepali.core.grid) axes() (FlowField method) (FlowFields method) (Grid method) (SampleImage method) (SpatialTransform method) axis_coords() (GridAttrs method) axis_indices() (GridAttrs method) B balanced_binary_cross_entropy_with_logits() (in module deepali.losses.functional) batch() (FlowField method) (Image method) batched_index_select() (in module deepali.core.tensor) Bending (class in deepali.losses.flow) bending_loss() (in module deepali.losses.functional) binary_image_stencil_mask() (in module deepali.utils.vtk.image) BlurImage (class in deepali.modules.image) bool() (CompositeTransform method) bool_from_arg() (in module deepali.core.argparse) bounding_box() (in module deepali.core.pointset) bspline1d() (in module deepali.core.kernels) bspline_bending_loss() (in module deepali.losses.functional) bspline_interpolation_weights() (in module deepali.core.bspline) BSplineBending (class in deepali.losses.bspline) BSplineLoss (class in deepali.losses.base) BSplineTransform (class in deepali.spatial.bspline) bucket (S3Object property) C CastImage (class in deepali.data.transforms.image) cat_scalars() (in module deepali.core.tensor) center (GridAttrs property) center() (Cube method) (Grid method) (Image method) (ImageBatch method) center_() (Cube method) (Grid method) center_crop() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) center_pad() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) CenterCropImage (class in deepali.data.transforms.image) CenterPadImage (class in deepali.data.transforms.image) check() (SpatialDerivativeKeys static method) check_cuda_visible_devices() (in module deepali.core.environ) check_sample_grid() (in module deepali.core.image) circle_image() (in module deepali.core.image) ClampImage (class in deepali.data.transforms.image) clear_buffers() (CompositeTransform method) (NonRigidTransform method) (SpatialTransform method) clone() (Cube method) (Grid method) close() (S3Client method) closest_point_distances() (in module deepali.core.pointset) closest_point_indices() (in module deepali.core.pointset) ClosestPointDistance (class in deepali.losses.pointset) collate_samples() (in module deepali.data.collate) compose_flows() (in module deepali.core.flow) compose_svfs() (in module deepali.core.flow) CompositeTransform (class in deepali.spatial.composite) condition() (CompositeTransform method) (SpatialTransform method) (SpatialTransformer method) condition_() (CompositeTransform method) (SpatialTransform method) (SpatialTransformer method) config (S3Client property) config_has_read_image_transform() (in module deepali.data.transforms.image) configure_logging() (in module deepali.core.logging) connect() (S3Client method) control_point_spacing (TransformConfig attribute) conv() (Image method) (ImageBatch method) (in module deepali.core.image) Conv1d (class in deepali.networks.layers.conv) conv1d() (in module deepali.core.image) Conv2d (class in deepali.networks.layers.conv) Conv3d (class in deepali.networks.layers.conv) conv_mode() (PaddingMode method) conv_module() (in module deepali.networks.layers.conv) conv_output_size() (in module deepali.core.nnutils) conv_transposed_output_size() (in module deepali.core.nnutils) ConvLayer (class in deepali.networks.layers.conv) convolution() (in module deepali.networks.layers.conv) ConvTranspose1d (class in deepali.networks.layers.conv) ConvTranspose2d (class in deepali.networks.layers.conv) ConvTranspose3d (class in deepali.networks.layers.conv) coords (GridAttrs property) coords() (Grid method) copy_file() (in module deepali.core.storage) corners (GridAttrs property) cpu_count() (in module deepali.core.psutil) crop() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) cshape_image() (in module deepali.core.image) CUBE (Axes attribute) Cube (class in deepali.core.cube) cube() (Grid method) (Image method) (ImageBatch method) CUBE_CORNERS (Axes attribute) cube_extent() (Grid method) cube_points_transform() (in module deepali.core.cube) cube_to_index() (Grid method) cube_to_world() (Cube method) (Grid method) cube_vectors_transform() (in module deepali.core.cube) cubes() (ImageBatch method) cubic_bspline() (in module deepali.core.kernels) cubic_bspline1d() (in module deepali.core.kernels) cubic_bspline2d() (in module deepali.core.kernels) cubic_bspline3d() (in module deepali.core.kernels) cubic_bspline_control_point_grid() (in module deepali.core.bspline) cubic_bspline_control_point_grid_size() (in module deepali.core.bspline) cubic_bspline_interpolation_weights() (in module deepali.core.bspline) cubic_bspline_value() (in module deepali.core.kernels) cuda_visible_devices() (in module deepali.core.environ) Curl (class in deepali.modules.flow) curl() (FlowField method) (in module deepali.core.flow) Curvature (class in deepali.losses.flow) curvature_loss() (in module deepali.losses.functional) D data() (ParametricTransform method) data_() (ParametricTransform method) data_shape (AnisotropicScaling property) (BSplineTransform property) (DenseVectorFieldTransform property) (EulerRotation property) (HomogeneousTransform property) (IsotropicScaling property) (ParametricTransform property) (QuaternionRotation property) (Shearing property) (Translation property) Dataclass (class in deepali.core.typing) DataclassConfig (class in deepali.core.config) Dataset (class in deepali.data.dataset) dataset_split_lengths() (in module deepali.data.partition) DataTensor (class in deepali.data.tensor) dcm (GridAttrs property) deepali.core module deepali.core._kornia module deepali.core.affine module deepali.core.argparse module deepali.core.bspline module deepali.core.collections module deepali.core.config module deepali.core.cube module deepali.core.enum module deepali.core.environ module deepali.core.flow module deepali.core.functional module deepali.core.grid module deepali.core.image module deepali.core.itertools module deepali.core.kernels module deepali.core.linalg module deepali.core.logging module deepali.core.math module deepali.core.nnutils module deepali.core.pathlib module deepali.core.pointset module deepali.core.psutil module deepali.core.random module deepali.core.storage module deepali.core.tempfile module deepali.core.tensor module deepali.core.typing module deepali.data module deepali.data.collate module deepali.data.dataset module deepali.data.flow module deepali.data.image module deepali.data.partition module deepali.data.prepare module deepali.data.sample module deepali.data.sampler module deepali.data.tensor module deepali.data.transforms module deepali.data.transforms.image module deepali.data.transforms.item module deepali.losses module deepali.losses.base module deepali.losses.bspline module deepali.losses.flow module deepali.losses.functional module deepali.losses.image module deepali.losses.params module deepali.losses.pointset module deepali.modules module deepali.modules.basic module deepali.modules.flow module deepali.modules.image module deepali.modules.lambd module deepali.modules.mixins module deepali.modules.output module deepali.modules.sample module deepali.modules.utilities module deepali.networks module deepali.networks.blocks module deepali.networks.blocks.residual module deepali.networks.blocks.skip module deepali.networks.layers module deepali.networks.layers.acti module deepali.networks.layers.conv module deepali.networks.layers.join module deepali.networks.layers.lambd module deepali.networks.layers.linear module deepali.networks.layers.norm module deepali.networks.layers.pool module deepali.networks.layers.upsample module deepali.networks.resnet module deepali.networks.unet module deepali.networks.utils module deepali.spatial module deepali.spatial.base module deepali.spatial.bspline module deepali.spatial.composite module deepali.spatial.generic module deepali.spatial.image module deepali.spatial.linear module deepali.spatial.nonrigid module deepali.spatial.parametric module deepali.spatial.transformer module deepali.utils module deepali.utils.aws module deepali.utils.aws.s3 module deepali.utils.aws.s3.client module deepali.utils.aws.s3.config module deepali.utils.aws.s3.object module deepali.utils.imageio module deepali.utils.imageio.meta module deepali.utils.imageio.nifti module deepali.utils.imageio.sitk module deepali.utils.ipython module deepali.utils.simpleitk module deepali.utils.simpleitk.grid module deepali.utils.simpleitk.imageio module deepali.utils.simpleitk.numpy module deepali.utils.simpleitk.sample module deepali.utils.simpleitk.torch module deepali.utils.tensorboard module deepali.utils.vtk module deepali.utils.vtk.idlist module deepali.utils.vtk.image module deepali.utils.vtk.numpy module deepali.utils.vtk.polydataio module deepali.utils.vtk.simpleitk module default() (S3Client class method) default_path() (S3Object static method) delete() (in module deepali.core.pathlib) (StorageObject method) delete_file() (S3Client method) delete_files() (S3Client method) denormalize_flow() (in module deepali.core.flow) denormalize_grid() (in module deepali.core.pointset) DenseBlock (class in deepali.networks.blocks.skip) DenseVectorFieldTransform (class in deepali.spatial.nonrigid) deregister_kernels() (BSplineTransform method) device (Cube property) (DeviceProperty property) (Grid property) DeviceProperty (class in deepali.modules.mixins) Dice (class in deepali.losses.image) dice_loss() (in module deepali.losses.functional) dice_score() (in module deepali.losses.functional) Diffusion (class in deepali.losses.flow) diffusion_loss() (in module deepali.losses.functional) dim() (Cube method) (Grid method) (SpatialTransform method) direction() (Cube method) (Grid method) (Image method) (ImageBatch method) direction_() (Cube method) (Grid method) disp() (CompositeTransform method) (SpatialTransform method) DisplacementFieldTransform (class in deepali.spatial.nonrigid) DisplacementLoss (class in deepali.losses.base) distance_matrix() (in module deepali.core.pointset) DistributedWeightedRandomSampler (class in deepali.data.sampler) Divergence (class in deepali.losses.flow) divergence() (in module deepali.core.flow) divergence_free_flow() (in module deepali.core.flow) divergence_loss() (in module deepali.losses.functional) domain() (Grid method) (Image method) (ImageBatch method) domains() (ImageBatch method) dot_batch() (in module deepali.core.image) dot_channels() (in module deepali.core.image) down() (GridAttrs method) download_file() (S3Client method) download_files() (S3Client method) downsample() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) dtype (Cube property) (Grid property) E Elasticity (class in deepali.losses.flow) elasticity_loss() (in module deepali.losses.functional) empty_image() (in module deepali.core.image) entry_point() (in module deepali.core.argparse) escape_channel_index_format_string() (in module deepali.utils.tensorboard) euler_rotation_angles() (in module deepali.core.affine) euler_rotation_matrix() (in module deepali.core.affine) euler_rotation_order() (in module deepali.core.affine) EulerRotation (class in deepali.spatial.linear) eval() (RegistrationLoss method) evaluate() (DenseVectorFieldTransform method) evaluate_cubic_bspline() (in module deepali.core.bspline) evaluate_spline() (BSplineTransform method) exceptions (S3Client property) exists() (S3Client method) (S3Object method) (StorageObject method) exp() (FlowField method) (FlowFields method) ExpFlow (class in deepali.modules.flow) expv() (in module deepali.core.flow) extent() (Cube method) (Grid method) extent_() (Cube method) extra_repr() (AnisotropicScaling method) (BlurImage method) (BSplineLoss method) (ClosestPointDistance method) (Curl method) (Dice method) (Elasticity method) (EulerRotation method) (ExpFlow method) (FilterImage method) (GetItem method) (GradLoss method) (HomogeneousTransform method) (InvertibleParametricTransform method) (IsotropicScaling method) (JoinLayer method) (LandmarkPointDistance method) (LCC method) (MI method) (Narrow method) (NCC method) (NMI method) (NormalizedPairwiseImageLoss method) (Pad method) (QuaternionRotation method) (Reshape method) (SampleImage method) (Shearing method) (SpatialTransform method) (ToImmutableOutput method) (Translation method) (View method) (WLCC method) F fill_border() (in module deepali.core.image) FilterImage (class in deepali.modules.image) finite_differences() (in module deepali.core.image) first_central_image_slice() (in module deepali.utils.tensorboard) fit() (DisplacementFieldTransform method) (SpatialTransform method) flatten_channels() (in module deepali.core.image) flip_grid_coords (TransformConfig attribute) flow() (SpatialTransform method) flow_derivatives() (in module deepali.core.flow) FlowChannelIndex (class in deepali.core.enum) FlowDerivativeKeys (class in deepali.core.enum) FlowField (class in deepali.data.flow) FlowFields (class in deepali.data.flow) focal_loss_with_logits() (in module deepali.losses.functional) forward() (AlignImage method) (Bending method) (BSplineBending method) (BSplineLoss method) (ClosestPointDistance method) (Curvature method) (Dice method) (Diffusion method) (DisplacementLoss method) (Divergence method) (Elasticity method) (ExpFlow method) (FilterImage method) (GaussianConv method) (GradLoss method) (HuberImageLoss method) (ImageTransformer method) (ItemTransform method) (L1ImageLoss method) (L1Norm method) (L2ImageLoss method) (L2Norm method) (LandmarkPointDistance method) (LCC method) (MI method) (MultiLevelTransform method) (NCC method) (PairwiseImageLoss method) (ParamsLoss method) (PatchwiseImageLoss method) (PointSetDistance method) (PointSetTransformer method) (RegistrationLoss method) (SampleImage method) (SequentialTransform method) (SmoothL1ImageLoss method) (Sparsity method) (SpatialTransform method) (SSD method) (SubpixelUpsample method) (TotalVariation method) (TransformImage method) (WLCC method) FreeFormDeformation (class in deepali.spatial.bspline) from_align_corners() (Axes class method) from_arg() (Axes class method) (FlowChannelIndex class method) (FlowDerivativeKeys class method) (PaddingMode class method) (Partition class method) (S3Client class method) (Sampling class method) (SpatialDim class method) from_batch() (Grid class method) from_depth() (ResNetConfig class method) from_dict() (DataclassConfig class method) from_encoder() (UNetDecoder class method) (UNetDecoderConfig class method) from_file() (Grid class method) from_grid() (Axes class method) (Cube class method) from_image() (FlowField class method) from_images() (ImageBatch class method) from_numpy() (Cube class method) (Grid class method) from_path() (DataclassConfig class method) (S3Object static method) (StorageObject static method) from_reader() (Grid class method) from_seq() (Cube class method) (Grid class method) from_sitk() (FlowField class method) (Grid class method) (Image class method) from_uri() (Image class method) (S3Object class method) (StorageObject static method) FullAffineTransform (class in deepali.spatial.linear) G gaussian() (in module deepali.core.kernels) gaussian1d() (in module deepali.core.kernels) gaussian1d_I() (in module deepali.core.kernels) gaussian2d() (in module deepali.core.kernels) gaussian3d() (in module deepali.core.kernels) gaussian_kernel_radius() (in module deepali.core.kernels) gaussian_pyramid() (in module deepali.core.image) GaussianConv (class in deepali.modules.image) GenericSpatialTransform (class in deepali.spatial.generic) get() (CompositeTransform method) get_tensor() (in module deepali.core.collections) GetItem (class in deepali.modules.basic) grad_loss() (in module deepali.losses.functional) GradLoss (class in deepali.losses.flow) GRID (Axes attribute) Grid (class in deepali.core.grid) grid() (Cube method) (Image method) (ImageBatch method) (SpatialTransform method) grid_() (BSplineTransform method) (DenseVectorFieldTransform method) (Image method) (ImageBatch method) (SpatialTransform method) (StationaryVelocityFieldTransform method) grid_image() (in module deepali.core.image) grid_points_transform() (in module deepali.core.grid) grid_resample() (in module deepali.core.image) grid_reshape() (in module deepali.core.image) grid_resize() (in module deepali.core.image) grid_sample() (in module deepali.core.image) grid_sample_mask() (in module deepali.core.image) grid_sample_mode() (PaddingMode method) (Sampling method) grid_transform_points() (in module deepali.core.grid) grid_transform_vectors() (in module deepali.core.grid) grid_vectors_transform() (in module deepali.core.grid) GridAttrs (class in deepali.utils.simpleitk.grid) grids() (ImageBatch method) GroupDataset (class in deepali.data.dataset) H has_affine_component() (in module deepali.spatial.generic) has_children() (in module deepali.modules.utilities) has_meta_image_suffix() (in module deepali.utils.imageio.meta) has_nifti_image_suffix() (in module deepali.utils.imageio.nifti) has_nonrigid_component() (in module deepali.spatial.generic) has_norm_after_conv() (ConvLayer method) has_parameters() (ParametricTransform method) HelpFormatter (class in deepali.core.argparse) hmm() (in module deepali.core.linalg) homogeneous_coords() (in module deepali.utils.simpleitk.grid) homogeneous_matmul() (in module deepali.core.linalg) homogeneous_matrix() (in module deepali.core.linalg) (in module deepali.utils.simpleitk.grid) homogeneous_transform() (in module deepali.core.linalg) HomogeneousTransform (class in deepali.spatial.linear) HuberImageLoss (class in deepali.losses.image) I identity_transform() (in module deepali.core.affine) Image (class in deepali.data.image) image_data_grid() (in module deepali.utils.vtk.simpleitk) image_dtype() (in module deepali.utils.simpleitk.numpy) image_from_array() (in module deepali.utils.simpleitk.numpy) image_from_tensor() (in module deepali.utils.simpleitk.torch) image_grid_attributes() (in module deepali.utils.simpleitk.grid) image_slice() (in module deepali.core.image) image_transform() (in module deepali.data.transforms.image) image_transforms() (in module deepali.data.transforms.image) ImageBatch (class in deepali.data.image) ImageDataset (class in deepali.data.dataset) ImageDatasetConfig (class in deepali.data.dataset) ImageToTensor (class in deepali.data.transforms.image) ImageTransform (class in deepali.spatial.image) ImageTransformer (class in deepali.spatial.transformer) index() (FlowChannelIndex method) index_to_cube() (Grid method) index_to_physical_space() (GridAttrs method) index_to_world() (Grid method) indices (GridAttrs property) init_conv_modules() (ResNet method) init_default() (S3Client class method) init_norm_layers() (ResNet method) init_num_threads() (in module deepali.core.environ) init_omp_num_threads() (in module deepali.core.environ) interpolate_griddata() (in module deepali.utils.simpleitk.sample) interpolate_mode() (Sampling method) interpolate_ndimage() (in module deepali.utils.simpleitk.sample) interpolate_regular_grid() (in module deepali.utils.simpleitk.sample) inv (ExpFlow property) (SpatialTransform property) inverse() (ExpFlow method) (GenericSpatialTransform method) (InvertibleParametricTransform method) (SequentialTransform method) (SpatialTransform method) (StationaryVelocityFieldTransform method) (StationaryVelocityFreeFormDeformation method) inverse_affine() (Cube method) (Grid method) inverse_consistency_loss() (in module deepali.losses.functional) inverse_transform (GridAttrs property) inverse_transform() (Cube method) (Grid method) InvertibleParametricTransform (class in deepali.spatial.parametric) is_absolute() (in module deepali.core.pathlib) is_activation() (in module deepali.networks.layers.acti) is_batch_norm() (in module deepali.networks.layers.norm) is_bool_dtype() (in module deepali.core.typing) is_bottleneck() (ResidualUnit method) is_closed() (S3Client method) is_conv_module() (in module deepali.networks.layers.conv) is_convolution() (in module deepali.networks.layers.conv) is_dir() (S3Object method) (StorageObject method) is_displacement_loss() (in module deepali.losses) is_even_permutation() (in module deepali.core.itertools) is_file() (S3Object method) (StorageObject method) is_float_dtype() (in module deepali.core.typing) is_group_norm() (in module deepali.networks.layers.norm) is_instance_norm() (in module deepali.networks.layers.norm) is_int_dtype() (in module deepali.core.typing) is_jupyter_notebook() (in module deepali.utils.ipython) is_linear_transform() (in module deepali.spatial) is_mixed() (FlowDerivativeKeys class method) (SpatialDerivativeKeys static method) is_namedtuple() (in module deepali.core.typing) is_nonrigid_transform() (in module deepali.spatial) is_norm_layer() (in module deepali.networks.layers.norm) is_open() (S3Client method) is_optional_field() (in module deepali.core.typing) is_optional_type_hint() (in module deepali.core.typing) is_pairwise_image_loss() (in module deepali.losses) is_path_str() (in module deepali.core.typing) is_path_str_field() (in module deepali.core.typing) is_path_str_type_hint() (in module deepali.core.typing) is_pointset_distance() (in module deepali.losses) is_spatial_transform() (in module deepali.spatial) is_transposed_convolution() (in module deepali.networks.layers.conv) is_uint_dtype() (in module deepali.core.typing) is_uri() (in module deepali.core.pathlib) is_valid() (SpatialDerivativeKeys class method) IsotropicScaling (class in deepali.spatial.linear) item() (ItemwiseTransform class method) ItemTransform (class in deepali.data.transforms.item) ItemwiseTransform (class in deepali.data.transforms.item) iter_cell_point_ids() (in module deepali.utils.vtk.idlist) iter_id_list() (in module deepali.utils.vtk.idlist) iter_point_cell_ids() (in module deepali.utils.vtk.idlist) iterdir() (S3Client method) (S3Object method) (StorageObject method) J jacobian_det() (in module deepali.core.flow) jacobian_dict() (in module deepali.core.flow) jacobian_matrix() (in module deepali.core.flow) join() (SpatialDerivativeKeys static method) join_func() (in module deepali.networks.layers.join) join_kwargs_in_sequence() (in module deepali.core.config) JoinDataset (class in deepali.data.dataset) JoinLayer (class in deepali.networks.layers.join) K kernel() (BSplineTransform method) kernel_name() (BSplineTransform static method) key (S3Object property) keys() (S3Client method) kld_loss() (in module deepali.losses.functional) L L1ImageLoss (class in deepali.losses.image) L1Norm (class in deepali.losses.params) L2ImageLoss (class in deepali.losses.image) L2Norm (class in deepali.losses.params) label_smoothing() (in module deepali.losses.functional) LambdaLayer (class in deepali.modules.lambd) LandmarkPointDistance (class in deepali.losses.pointset) last_conv_layer (ResidualUnit property) LCC (class in deepali.losses.image) lcc_loss() (in module deepali.losses.functional) lie_bracket() (in module deepali.core.flow) Linear (class in deepali.networks.layers.linear) linear (CompositeTransform property) (SpatialTransform property) LinearTransform (class in deepali.spatial.base) link() (ParametricTransform method) link_() (ParametricTransform method) listdir() (S3Client method) LocalObject (class in deepali.core.storage) log_grad_hook() (in module deepali.core.tensor) LogLevel (class in deepali.core.logging) logv() (in module deepali.core.flow) M mae_loss() (in module deepali.losses.functional) main_func() (in module deepali.core.argparse) MainCallable (class in deepali.core.argparse) make_parent_dir() (in module deepali.core.pathlib) make_temp_file() (in module deepali.core.tempfile) manual_seed() (in module deepali.core.random) masked_loss() (in module deepali.losses.functional) match_all() (in module deepali.utils.aws.s3.client) matrix() (LinearTransform method) matrix_() (EulerRotation method) (HomogeneousTransform method) (QuaternionRotation method) max_difference() (in module deepali.core.math) max_pool() (in module deepali.core.image) memory_from_arg() (in module deepali.core.argparse) memory_limit() (in module deepali.core.psutil) meta_image_bytes() (in module deepali.utils.imageio.meta) MetaDataset (class in deepali.data.dataset) MI (class in deepali.losses.image) mi_loss() (in module deepali.losses.functional) min_pool() (in module deepali.core.image) module deepali.core deepali.core._kornia deepali.core.affine deepali.core.argparse deepali.core.bspline deepali.core.collections deepali.core.config deepali.core.cube deepali.core.enum deepali.core.environ deepali.core.flow deepali.core.functional deepali.core.grid deepali.core.image deepali.core.itertools deepali.core.kernels deepali.core.linalg deepali.core.logging deepali.core.math deepali.core.nnutils deepali.core.pathlib deepali.core.pointset deepali.core.psutil deepali.core.random deepali.core.storage deepali.core.tempfile deepali.core.tensor deepali.core.typing deepali.data deepali.data.collate deepali.data.dataset deepali.data.flow deepali.data.image deepali.data.partition deepali.data.prepare deepali.data.sample deepali.data.sampler deepali.data.tensor deepali.data.transforms deepali.data.transforms.image deepali.data.transforms.item deepali.losses deepali.losses.base deepali.losses.bspline deepali.losses.flow deepali.losses.functional deepali.losses.image deepali.losses.params deepali.losses.pointset deepali.modules deepali.modules.basic deepali.modules.flow deepali.modules.image deepali.modules.lambd deepali.modules.mixins deepali.modules.output deepali.modules.sample deepali.modules.utilities deepali.networks deepali.networks.blocks deepali.networks.blocks.residual deepali.networks.blocks.skip deepali.networks.layers deepali.networks.layers.acti deepali.networks.layers.conv deepali.networks.layers.join deepali.networks.layers.lambd deepali.networks.layers.linear deepali.networks.layers.norm deepali.networks.layers.pool deepali.networks.layers.upsample deepali.networks.resnet deepali.networks.unet deepali.networks.utils deepali.spatial deepali.spatial.base deepali.spatial.bspline deepali.spatial.composite deepali.spatial.generic deepali.spatial.image deepali.spatial.linear deepali.spatial.nonrigid deepali.spatial.parametric deepali.spatial.transformer deepali.utils deepali.utils.aws deepali.utils.aws.s3 deepali.utils.aws.s3.client deepali.utils.aws.s3.config deepali.utils.aws.s3.object deepali.utils.imageio deepali.utils.imageio.meta deepali.utils.imageio.nifti deepali.utils.imageio.sitk deepali.utils.ipython deepali.utils.simpleitk deepali.utils.simpleitk.grid deepali.utils.simpleitk.imageio deepali.utils.simpleitk.numpy deepali.utils.simpleitk.sample deepali.utils.simpleitk.torch deepali.utils.tensorboard deepali.utils.vtk deepali.utils.vtk.idlist deepali.utils.vtk.image deepali.utils.vtk.numpy deepali.utils.vtk.polydataio deepali.utils.vtk.simpleitk module_counts_by_class_name() (in module deepali.modules.utilities) module_ids_by_class_name() (in module deepali.modules.utilities) module_output_size() (in module deepali.networks.utils) move_dim() (in module deepali.core.tensor) mse_loss() (in module deepali.losses.functional) MultiLevelTransform (class in deepali.spatial.composite) multinomial() (in module deepali.core.random) N name (S3Object property) (StorageObject property) named_transforms() (CompositeTransform method) nangles (EulerRotation property) (Shearing property) Narrow (class in deepali.modules.basic) narrow() (Grid method) (Image method) (ImageBatch method) NarrowImage (class in deepali.data.transforms.image) NCC (class in deepali.losses.image) ncc_loss() (in module deepali.losses.functional) nchannels (Image property) (ImageBatch property) ndim (Cube property) (Grid property) (GridAttrs property) (SpatialTransform property) new_loss() (in module deepali.losses) new_spatial_transform() (in module deepali.spatial) NMI (class in deepali.losses.image) nonrigid (SpatialTransform property) nonrigid_components() (in module deepali.spatial.generic) NONRIGID_TRANSFORMS (in module deepali.spatial.generic) NonRigidTransform (class in deepali.spatial.base) norm_layer() (in module deepali.networks.layers.norm) norm_uri() (in module deepali.core.pathlib) normalization() (in module deepali.networks.layers.norm) normalize() (Image method) (ImageBatch method) normalize_() (Image method) (ImageBatch method) normalize_flow() (in module deepali.core.flow) normalize_grid() (in module deepali.core.pointset) normalize_image() (in module deepali.core.image) normalize_quaternion() (in module deepali.core._kornia) normalize_summary_image() (in module deepali.utils.tensorboard) NormalizedPairwiseImageLoss (class in deepali.losses.base) NormalizeImage (class in deepali.data.transforms.image) normkey() (S3Object static method) NormLayer (class in deepali.networks.layers.norm) npoints (GridAttrs property) num_levels (UNetDecoderConfig property) (UNetEncoderConfig property) numel() (Grid method) numpy() (Cube method) (Grid method) numpy_to_vtk_array() (in module deepali.utils.vtk.numpy) numpy_to_vtk_cell_array() (in module deepali.utils.vtk.numpy) numpy_to_vtk_matrix4x4() (in module deepali.utils.vtk.numpy) numpy_to_vtk_points() (in module deepali.utils.vtk.numpy) O offset() (Translation method) offset_() (Translation method) ones_image() (in module deepali.core.image) ops (S3Client property) order() (FlowDerivativeKeys class method) (SpatialDerivativeKeys static method) origin() (Cube method) (Grid method) (Image method) (ImageBatch method) origin_() (Cube method) (Grid method) output_is_dict() (UNet method) output_is_tensor() (UNet method) output_is_tuple() (UNet method) output_size() (SequentialUNet method) (UNetDecoder method) (UNetEncoder method) output_sizes() (UNetDecoder method) (UNetEncoder method) P Pad (class in deepali.modules.basic) pad() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) pad_mode() (PaddingMode method) pad_output_size() (in module deepali.core.nnutils) padding() (SampleImage method) padding_mode() (SampleImage method) padding_value() (SampleImage method) PaddingMode (class in deepali.core.enum) PairwiseImageLoss (class in deepali.losses.base) ParametricTransform (class in deepali.spatial.parametric) ParamsLoss (class in deepali.losses.base) ParserCallable (class in deepali.core.argparse) Partition (class in deepali.data.partition) PatchwiseImageLoss (class in deepali.losses.image) path (StorageObject property) path_suffix() (in module deepali.core.pathlib) path_uri() (in module deepali.core.pathlib) physical_space_to_continuous_index() (GridAttrs method) physical_space_to_index() (GridAttrs method) points (GridAttrs property) points() (Grid method) (SpatialTransform method) PointSetDistance (class in deepali.losses.base) PointSetTransformer (class in deepali.spatial.transformer) polyline_directions() (in module deepali.core.pointset) polyline_tangents() (in module deepali.core.pointset) pool() (Grid method) pool_output_size() (in module deepali.core.nnutils) pooling() (in module deepali.networks.layers.pool) PoolLayer (class in deepali.networks.layers.pool) prepare_batch() (in module deepali.data.prepare) prepend_read_image_transform() (in module deepali.data.transforms.image) pull() (S3Object method) (StorageObject method) push() (S3Object method) (StorageObject method) pyramid() (Grid method) (Image method) (ImageBatch method) Q quaternion() (QuaternionRotation method) quaternion_() (QuaternionRotation method) quaternion_exp_to_log() (in module deepali.core._kornia) quaternion_log_to_exp() (in module deepali.core._kornia) quaternion_to_angle_axis() (in module deepali.core._kornia) quaternion_to_rotation_matrix() (in module deepali.core._kornia) QuaternionRotation (class in deepali.spatial.linear) R rand_sample() (in module deepali.core.image) random_split_indices() (in module deepali.data.partition) read() (DataclassConfig class method) (FlowField class method) (Image class method) read_bytes() (S3Client method) (S3Object method) (StorageObject method) read_config_dict() (in module deepali.core.config) read_image() (in module deepali.utils.imageio) (in module deepali.utils.simpleitk.imageio) read_meta_image() (in module deepali.utils.imageio.meta) read_nifti_image() (in module deepali.utils.imageio.nifti) read_off() (in module deepali.utils.vtk.polydataio) read_polydata() (in module deepali.utils.vtk.polydataio) read_polydata_off() (in module deepali.utils.vtk.polydataio) read_sitk_image() (in module deepali.utils.imageio.sitk) read_table() (in module deepali.data.dataset) read_text() (S3Client method) (S3Object method) (StorageObject method) ReadImage (class in deepali.data.transforms.image) ReadOnlyParameters reduce_loss() (in module deepali.losses.functional) region_of_interest() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) register_backward_hook() (in module deepali.core.tensor) register_kernels() (BSplineTransform method) register_update_hook() (SpatialTransform method) RegistrationLoss (class in deepali.losses.base) release() (LocalObject method) (StorageObject method) remove_layers_in_state_dict() (in module deepali.modules.utilities) remove_update_hook() (SpatialTransform method) rename_layers_in_state_dict() (in module deepali.modules.utilities) repeat_last() (in module deepali.core.itertools) replace_all_sample_field_values() (in module deepali.data.sample) ReprWithCrossReferences (class in deepali.modules.mixins) resample() (Grid method) (Image method) (ImageBatch method) resample_image() (in module deepali.utils.simpleitk.sample) ResampleImage (class in deepali.data.transforms.image) rescale() (Image method) (ImageBatch method) (in module deepali.core.image) RescaleImage (class in deepali.data.transforms.image) reset_parameters() (AnisotropicScaling method) (IsotropicScaling method) (ParametricTransform method) (QuaternionRotation method) reset_path() (S3Object method) Reshape (class in deepali.modules.basic) reshape() (Grid method) ResidualUnit (class in deepali.networks.blocks.residual) resize() (Grid method) (Image method) (ImageBatch method) ResizeImage (class in deepali.data.transforms.image) ResNet (class in deepali.networks.resnet) ResNetConfig (class in deepali.networks.resnet) RigidQuaternionTransform (class in deepali.spatial.linear) RigidTransform (class in deepali.spatial.linear) rmdir() (S3Object method) (StorageObject method) rotation_matrix() (in module deepali.core.affine) rotation_matrix_to_angle_axis() (in module deepali.core._kornia) rotation_matrix_to_quaternion() (in module deepali.core._kornia) rotation_model (TransformConfig attribute) round_decimals() (in module deepali.core.math) row() (MetaDataset method) S s3 (S3Object property) S3Client (class in deepali.utils.aws.s3.client) S3Client.Operation (class in deepali.utils.aws.s3.client) S3Config (class in deepali.utils.aws.s3.config) S3Object (class in deepali.utils.aws.s3.object) same_domain_as() (Grid method) (Image method) same_domains_as() (ImageBatch method) same_padding() (in module deepali.core.nnutils) sample (ImageTransformer property) sample() (Dataset method) (FlowFields method) (Image method) (ImageBatch method) (JoinDataset method) (MetaDataset method) sample_field_names() (in module deepali.data.sample) sample_field_value() (in module deepali.data.sample) sample_flow() (in module deepali.core.flow) sample_image() (in module deepali.core.image) SampleImage (class in deepali.modules.sample) samples() (Dataset method) (MetaDataset method) Sampling (class in deepali.core.enum) sampling() (SampleImage method) scales() (AnisotropicScaling method) (IsotropicScaling method) scales_() (AnisotropicScaling method) (IsotropicScaling method) scaling_and_squaring_steps (TransformConfig attribute) scaling_transform() (in module deepali.core.affine) sdim (Image property) (ImageBatch property) section() (DataclassConfig static method) SequentialTransform (class in deepali.spatial.composite) SequentialUNet (class in deepali.networks.unet) set_epoch() (DistributedWeightedRandomSampler method) shape (Grid property) (GridAttrs property) shear_matrix() (in module deepali.core.affine) Shearing (class in deepali.spatial.linear) SimilarityTransform (class in deepali.spatial.linear) sitk() (FlowField method) (Image method) sitk_image_from_vtk_image() (in module deepali.utils.vtk.simpleitk) size (GridAttrs property) size() (Grid method) size_tensor() (Grid method) SkipConnection (class in deepali.networks.blocks.skip) SmoothL1ImageLoss (class in deepali.losses.image) sorted() (FlowDerivativeKeys class method) (SpatialDerivativeKeys class method) source_axes() (PointSetTransformer method) source_grid() (ImageTransformer method) (PointSetTransformer method) (SampleImage method) spacing() (Cube method) (Grid method) (Image method) (ImageBatch method) spacing_() (Grid method) Sparsity (class in deepali.losses.params) spatial_derivatives() (in module deepali.core.image) SpatialDerivativeKeys (class in deepali.core.enum) SpatialDim (class in deepali.core.enum) SpatialTransform (class in deepali.spatial.base) SpatialTransformer (class in deepali.spatial.transformer) split() (FlowDerivativeKeys static method) (SpatialDerivativeKeys static method) SSD (class in deepali.losses.image) ssd_loss() (in module deepali.losses.functional) StationaryVelocityFieldTransform (class in deepali.spatial.nonrigid) StationaryVelocityFreeFormDeformation (class in deepali.spatial.bspline) StorageObject (class in deepali.core.storage) str_to_seed() (in module deepali.core.random) subdivide_cubic_bspline() (in module deepali.core.bspline) SubpixelUpsample (class in deepali.networks.layers.upsample) surface_image_stencil() (in module deepali.utils.vtk.image) surface_mesh_grid() (in module deepali.utils.vtk.image) symbol() (FlowChannelIndex method) (SpatialDim method) T target_axes() (PointSetTransformer method) target_grid() (ImageTransformer method) (PointSetTransformer method) (SampleImage method) temp_dir() (in module deepali.core.tempfile) temp_file() (in module deepali.core.tempfile) tensor() (AnisotropicScaling method) (DataTensor method) (EulerRotation method) (HomogeneousTransform method) (IsotropicScaling method) (MultiLevelTransform method) (NonRigidTransform method) (QuaternionRotation method) (SequentialTransform method) (Shearing method) (SpatialTransform method) (Translation method) tensor_collection_entry() (in module deepali.core.collections) tensor_dim() (SpatialDim method) tensor_from_image() (in module deepali.utils.simpleitk.torch) tensordot() (in module deepali.core.linalg) threshold() (in module deepali.core.math) to_uri() (Image method) (in module deepali.core.pathlib) ToImmutableOutput (class in deepali.modules.output) total_variation_loss() (in module deepali.losses.functional) TotalVariation (class in deepali.losses.flow) transform (GridAttrs property) (SpatialTransformer property) (TransformConfig attribute) transform() (Cube method) (Dataset method) (Grid method) transform_() (Dataset method) transform_components() (in module deepali.spatial.generic) transform_grid() (in module deepali.core.pointset) transform_point() (in module deepali.utils.simpleitk.grid) transform_points() (Cube method) (Grid method) (in module deepali.core.affine) (in module deepali.core.pointset) transform_vector() (in module deepali.utils.simpleitk.grid) transform_vectors() (Cube method) (Grid method) (in module deepali.core.affine) TransformConfig (class in deepali.spatial.generic) TransformImage (class in deepali.modules.sample) transforms() (CompositeTransform method) (Dataset method) transforms_() (Dataset method) Translation (class in deepali.spatial.linear) translation() (in module deepali.core.affine) translation_matrix() (in module deepali.utils.simpleitk.grid) tversky_index() (in module deepali.losses.functional) tversky_index_with_logits() (in module deepali.losses.functional) tversky_loss() (in module deepali.losses.functional) tversky_loss_with_logits() (in module deepali.losses.functional) U UNet (class in deepali.networks.unet) unet_conv_block() (in module deepali.networks.unet) UNetConfig (class in deepali.networks.unet) UNetDecoder (class in deepali.networks.unet) UNetDecoderConfig (class in deepali.networks.unet) UNetDownsampleConfig (class in deepali.networks.unet) UNetEncoder (class in deepali.networks.unet) UNetEncoderConfig (class in deepali.networks.unet) UNetLayerConfig (class in deepali.networks.unet) UNetOutputConfig (class in deepali.networks.unet) UNetUpsampleConfig (class in deepali.networks.unet) unique() (FlowDerivativeKeys class method) (SpatialDerivativeKeys class method) unlink() (ParametricTransform method) (S3Object method) (StorageObject method) unlink_() (ParametricTransform method) unlink_or_mkdir() (in module deepali.core.pathlib) unmixed() (FlowDerivativeKeys class method) (SpatialDerivativeKeys static method) unpool_output_size() (in module deepali.core.nnutils) unravel_coords() (in module deepali.core.tensor) unravel_index() (in module deepali.core.tensor) up() (GridAttrs method) update() (CompositeTransform method) (DisplacementFieldTransform method) (FreeFormDeformation method) (GenericSpatialTransform method) (NonRigidTransform method) (ParametricTransform method) (SpatialTransform method) (SpatialTransformer method) (StationaryVelocityFieldTransform method) (StationaryVelocityFreeFormDeformation method) upload_file() (S3Client method) upload_files() (S3Client method) Upsample (class in deepali.networks.layers.upsample) upsample() (Grid method) (Image method) (ImageBatch method) (in module deepali.core.image) upsample_output_padding() (in module deepali.core.nnutils) upsample_output_size() (in module deepali.core.nnutils) upsample_padding() (in module deepali.core.nnutils) UpsampleMode (class in deepali.networks.layers.upsample) uri (S3Object property) (StorageObject property) V VALID_COMPONENTS (in module deepali.spatial.generic) valid_transform_model() (in module deepali.spatial.generic) vector_rotation() (in module deepali.core.linalg) vectordot() (in module deepali.core.linalg) View (class in deepali.modules.basic) vtk_image_from_sitk_image() (in module deepali.utils.vtk.simpleitk) vtk_to_numpy_array() (in module deepali.utils.vtk.numpy) vtk_to_numpy_points() (in module deepali.utils.vtk.numpy) W warp_grid() (in module deepali.core.flow) warp_image() (FlowField method) (FlowFields method) (in module deepali.core.flow) (in module deepali.utils.simpleitk.sample) warp_points() (in module deepali.core.flow) with_bucket() (S3Object method) with_key() (S3Object method) with_margin() (GridAttrs method) with_path() (StorageObject method) with_properties() (StorageObject method) with_spacing() (GridAttrs method) WLCC (class in deepali.losses.image) wlcc_loss() (in module deepali.losses.functional) WORLD (Axes attribute) world_to_cube() (Cube method) (Grid method) world_to_index() (Grid method) write() (DataclassConfig method) (FlowField method) (Image method) write_bytes() (S3Client method) (S3Object method) (StorageObject method) write_config_dict() (in module deepali.core.config) write_image() (in module deepali.utils.imageio) (in module deepali.utils.simpleitk.imageio) write_meta_image() (in module deepali.utils.imageio.meta) write_nifti_image() (in module deepali.utils.imageio.nifti) write_polydata() (in module deepali.utils.vtk.polydataio) write_polydata_off() (in module deepali.utils.vtk.polydataio) write_sitk_image() (in module deepali.utils.imageio.sitk) write_text() (S3Client method) (S3Object method) (StorageObject method) Z zero_init_residual() (ResidualUnit method) zero_init_residuals() (ResNet method) zeros_flow() (in module deepali.core.flow) zeros_image() (in module deepali.core.image)
