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Functions7,906 in github.com/Project-MONAI/MONAI

↓ 2 callersMethod_get_down_layer
In each down layer, the input is first downsampled using maxpooling, then passed through a convolution block, unless this is the top
monai/networks/nets/voxelmorph.py:220
↓ 2 callersMethod_get_down_layer
Returns the encoding (down) part of a layer of the network. This typically will downsample data at some point in its structure. Its o
monai/networks/nets/unet.py:198
↓ 2 callersFunction_get_fake_spatial_shape
Get spatial shape for fake data according to the specified shape pattern. It supports `int` number and `string` with formats like: "32", "32
monai/bundle/scripts.py:141
↓ 2 callersMethod_get_fft_amplitude
Calculate the amplitude of the fourier transformations representation of the images Args: images: Images that are to und
monai/losses/spectral_loss.py:74
↓ 2 callersMethod_get_filter_from_string
(self, filter: str, size: int, ndim: int)
monai/transforms/utility/array.py:1752
↓ 2 callersMethod_get_hidden_states
Extract hidden states from BertLayer output. Compatible with both older transformers (returns a tuple) and newer transformers >=5.0 (
monai/networks/nets/transchex.py:230
↓ 2 callersFunction_get_id_list
(gt: torch.Tensor)
monai/metrics/panoptic_quality.py:238
↓ 2 callersFunction_get_latest_bundle_version_ngc
(name: str, repo: str | None = None, headers: dict | None = None)
monai/bundle/scripts.py:376
↓ 2 callersMethod_get_layer
(self, in_channels: int, out_channels: int, bias: bool)
monai/networks/nets/fullyconnectednet.py:152
↓ 2 callersFunction_get_loss
(data: torch.Tensor | dict[str, torch.Tensor])
monai/utils/jupyter_utils.py:241
↓ 2 callersMethod_get_mean
Compute the mean of the posterior at timestep t. Args: timestep: current timestep. x0: the noise-free input.
monai/networks/schedulers/ddpm.py:128
↓ 2 callersFunction_get_named_tuple_like_type
(func)
monai/data/meta_tensor.py:35
↓ 2 callersFunction_get_net_io_info
Get the input and output information defined in the metadata. Args: parser: a ConfigParser of the given bundle. prefix: a pr
monai/bundle/scripts.py:1108
↓ 2 callersFunction_get_ngc_private_base_url
(repo: str)
monai/bundle/scripts.py:178
↓ 2 callersFunction_get_ngc_url
(model_name: str, version: str, model_prefix: str = "")
monai/apps/mmars/mmars.py:98
↓ 2 callersFunction_get_point
Select one of the indices within slice containing val. Args: val : value for comparison dim : dimension in w
monai/transforms/utils.py:1610
↓ 2 callersMethod_get_prev_sample
(self, sample: torch.Tensor, timestep: int, prev_timestep: int, model_output: torch.Tensor)
monai/networks/schedulers/pndm.py:279
↓ 2 callersMethod_get_prop_id
(self, name: str, property: dict)
monai/bundle/workflows.py:539
↓ 2 callersMethod_get_threshold
(self, image, mode)
monai/transforms/intensity/array.py:2741
↓ 2 callersMethod_get_unit_power
Calculate the power of the unit factor with respect to the base unit
monai/utils/misc.py:835
↓ 2 callersMethod_get_valid_unit_and_base
(self, unit)
monai/utils/misc.py:826
↓ 2 callersMethod_initialize_mergers
(self, inputs, outputs, patches, batch_size)
monai/inferers/inferer.py:252
↓ 2 callersMethod_iteration
Abstract callback function for the processing logic of 1 iteration in Ignite Engine. Need subclass to implement different logics, lik
monai/engines/workflow.py:284
↓ 2 callersFunction_join_path
(base_dir: PathLike, item: PathLike)
monai/data/decathlon_datalist.py:47
↓ 2 callersMethod_load_cache_item
Args: idx: the index of the input data sequence.
monai/data/dataset.py:917
↓ 2 callersMethod_load_engine
Loads TRT plan from disk and activates its execution context.
monai/networks/trt_compiler.py:409
↓ 2 callersFunction_load_legacy_pickle
Load an Algo object from a legacy pickle file. This is an internal function to support backward compatibility with pickle files. Gated b
monai/auto3dseg/utils.py:361
↓ 2 callersFunction_load_state_dict
(model: nn.Module, arch: str, progress: bool, adv_prop: bool)
monai/networks/nets/efficientnet.py:787
↓ 2 callersFunction_log_applied_info
(data: Any, key=None, logger_name: bool | str = False)
monai/transforms/lazy/functional.py:75
↓ 2 callersFunction_log_pending_info
( transform: Any, data: Any, activity: str, *, lazy: bool | None = None, key: str | No
monai/transforms/lazy/functional.py:40
↓ 2 callersFunction_log_stats
(data, prefix: str | None = "Data")
monai/transforms/transform.py:170
↓ 2 callersMethod_make_final_conv
(self, out_channels: int)
monai/networks/nets/segresnet.py:149
↓ 2 callersFunction_make_nconv
(spatial_dims: int, nchan: int, depth: int, act: tuple[str, dict] | str, bias: bool = False)
monai/networks/nets/vnet.py:54
↓ 2 callersFunction_modified_bessel_0
(x: torch.Tensor)
monai/networks/layers/convutils.py:156
↓ 2 callersMethod_normalize
(self, img: NdarrayOrTensor, sub=None, div=None)
monai/transforms/intensity/array.py:888
↓ 2 callersMethod_normalize
(self, img: NdarrayOrTensor)
monai/transforms/intensity/array.py:1412
↓ 2 callersFunction_pad_previous_mask
Helper function to pad inputs.
monai/apps/vista3d/inferer.py:170
↓ 2 callersMethod_pe_encoding
Positionally encode points that are normalized to [0,1].
monai/networks/nets/vista3d.py:878
↓ 2 callersMethod_pop_kwargs_to_get_image_save_transform
Pop the kwargs used to define ImageSave class for the ensemble output. Args: kwargs: image writing parameters for the en
monai/apps/auto3dseg/ensemble_builder.py:474
↓ 2 callersFunction_prepare_cmd_bcprun
Prepare the command for distributed job running using bcprun. Args: script: the script to run in the distributed job. cmd_pr
monai/auto3dseg/utils.py:606
↓ 2 callersFunction_prepare_cmd_default
Prepare the command for subprocess to run the script with the given arguments. Args: cmd: the command or script to run in the distri
monai/auto3dseg/utils.py:553
↓ 2 callersFunction_prepare_cmd_torchrun
Prepare the command for multi-gpu/multi-node job execution using torchrun. Args: cmd: the command or script to run in the distribute
monai/auto3dseg/utils.py:584
↓ 2 callersFunction_process_bundle_dir
(bundle_dir: PathLike | None = None)
monai/bundle/scripts.py:436
↓ 2 callersFunction_read_testing_data_answers
(fname: str | None = None, delimiter=",")
tests/testing_data/cpp_resample_answers.py:19
↓ 2 callersFunction_require_pickle_allowed
()
monai/auto3dseg/utils.py:60
↓ 2 callersFunction_resample_to_affine
linear resample
tests/integration/test_meta_affine.py:115
↓ 2 callersMethod_resolve_one_item
Resolve and return one ``ConfigItem`` of ``id``, cache the resolved result in ``resolved_content``. If it has unresolved references,
monai/bundle/reference_resolver.py:107
↓ 2 callersFunction_run_cmd_bcprun
Run the command with bcprun. Args: cmd: the command to run. Typically it is prepared by ``_prepare_cmd_bcprun``. kwargs: the
monai/auto3dseg/utils.py:655
↓ 2 callersFunction_run_cmd_torchrun
Run the command with torchrun. Args: cmd: the command to run. Typically it is prepared by ``_prepare_cmd_torchrun``. kwargs:
monai/auto3dseg/utils.py:629
↓ 2 callersMethod_run_inference
(self, network: Callable, patch: torch.Tensor, *args: Any, **kwargs: Any)
monai/inferers/inferer.py:240
↓ 2 callersMethod_set_spike
Helper function to introduce a given intensity at given location. Args: k: intensity array to alter. idx: in
monai/transforms/intensity/array.py:2175
↓ 2 callersFunction_sqrtm
Compute the square root of a matrix.
monai/metrics/fid.py:83
↓ 2 callersMethod_stdshift
(self, img: NdarrayOrTensor)
monai/transforms/intensity/array.py:355
↓ 2 callersFunction_strip_bias_field
Strip the optional PyTorch >= 2.13 ``, bias=True|False`` repr fragment. Args: text: Layer string representation to normalize. Return
tests/networks/layers/test_get_layers.py:22
↓ 2 callersMethod_sync
All gather the buffers across distributed ranks for aggregating. Each buffer will be concatenated as a PyTorch Tensor.
monai/metrics/metric.py:256
↓ 2 callersMethod_test_apply_metatensor_impl
(self, tensor, pending_transforms, expected_shape, pending_as_parameter)
tests/transforms/functional/test_apply.py:47
↓ 2 callersMethod_transform
Fetch single data item from `self.data`.
monai/data/dataset.py:90
↓ 2 callersMethod_transforms_match
Return whether a traced transform entry matches this transform. Matching succeeds when the traced ID matches this instance, when the ID
monai/transforms/inverse.py:324
↓ 2 callersMethod_upsample_and_post_process
(self, acti_map, x)
monai/visualize/class_activation_maps.py:208
↓ 2 callersFunction_wrap_parsed
Wrap a parsed dict/list in a :class:`_ConfigProxy` so nested access keeps chaining; pass scalars through. Args: parser: the owning :
monai/bundle/config_parser.py:44
↓ 2 callersMethod_write_to_file
(self, log_data)
monai/transforms/io/array.py:563
↓ 2 callersFunction_zdot
Complex dot product between tensors x1 and x2: sum(x1.*x2)
monai/networks/layers/conjugate_gradient.py:20
↓ 2 callersFunction_zdot_single
Complex dot product between tensor x and itself
monai/networks/layers/conjugate_gradient.py:31
↓ 2 callersMethodadd_factory_callable
Add the factory function to this object under the given name, with optional description.
monai/networks/layers/factories.py:90
↓ 2 callersMethodadd_property
Besides the default predefined properties, some 3rd party applications may need the bundle definition to provide additional propertie
monai/bundle/workflows.py:214
↓ 2 callersMethodadd_property
Besides the default predefined properties, some 3rd party applications may need the bundle definition to provide additional propertie
monai/bundle/workflows.py:579
↓ 2 callersFunctionaffine_from_pending
Extract the affine matrix from a pending transform item.
monai/transforms/lazy/utils.py:83
↓ 2 callersFunctionaffine_func
Functional implementation of affine. This function operates eagerly or lazily according to ``lazy`` (default ``False``). Args:
monai/transforms/spatial/functional.py:590
↓ 2 callersMethodaffine_transform
(self, theta: torch.Tensor)
monai/networks/nets/regunet.py:283
↓ 2 callersMethodaggregate
returns the total average value (averaged across processes) Args: to_numpy: whether to convert to numpy array. Defaults
monai/metrics/cumulative_average.py:81
↓ 2 callersMethodaggregate
Execute reduction logic for the output of `compute_average_surface_distance`. Args: reduction: define mode of reduction
monai/metrics/surface_distance.py:102
↓ 2 callersMethodaggregate
Execute reduction logic for the output of `compute_hausdorff_distance`. Args: reduction: define mode of reduction to the
monai/metrics/hausdorff_distance.py:111
↓ 2 callersMethodaggregate
Typically `y_pred` and `y` are stored in the cumulative buffers at each iteration, This function reads the buffers and computes the A
monai/metrics/average_precision.py:68
↓ 2 callersMethodaggregate
Returns the aggregated loss value across multiple iterations. Args: reduction: define mode of reduction to the metrics,
monai/metrics/loss_metric.py:80
↓ 2 callersMethodaggregate
Execute reduction logic for the output of `compute_iou`. Args: reduction: define mode of reduction to the metrics, will
monai/metrics/meaniou.py:84
↓ 2 callersMethodaggregate
Aggregate values for merging. Args: values: a tensor of shape BCHW[D], representing the values of inference output.
monai/inferers/merger.py:131
↓ 2 callersMethodaggregate
Aggregate values for merging. Args: values: a tensor of shape BCHW[D], representing the values of inference output.
monai/inferers/merger.py:430
↓ 2 callersMethodapply
(self, data: torch.Tensor)
monai/transforms/regularization/array.py:132
↓ 2 callersFunctionapply_affine_to_boxes
This function applies affine matrices to the boxes Args: boxes: bounding boxes, Nx4 or Nx6 torch tensor or ndarray. The box mode is
monai/apps/detection/transforms/box_ops.py:62
↓ 2 callersFunctionapply_pending_transforms
apply_pending_transforms is called with either a tensor or a dictionary, some entries of which contain tensors. When operating on a dict
monai/transforms/lazy/functional.py:85
↓ 2 callersFunctionargsort
`np.argsort` with equivalent implementation for torch. Args: a: the array/tensor to sort. axis: axis along which to sort. Re
monai/transforms/utils_pytorch_numpy_unification.py:174
↓ 2 callersMethodattach
Args: engine: Ignite Engine, it can be a trainer, validator or evaluator.
monai/handlers/metrics_saver.py:103
↓ 2 callersMethodattach
Args: engine: Ignite Engine, it can be a trainer, validator or evaluator.
monai/handlers/lr_schedule_handler.py:69
↓ 2 callersMethodattach
Args: engine: Ignite Engine, it can be a trainer, validator or evaluator.
monai/handlers/metric_logger.py:87
↓ 2 callersMethodattach
Args: engine: Ignite Engine, it can be a trainer, validator or evaluator.
monai/handlers/checkpoint_saver.py:233
↓ 2 callersMethodbbox
(self, patch_size, centroid, size)
monai/apps/nuclick/transforms.py:114
↓ 2 callersMethodboxes_to_corners
Convert the bounding boxes of the current mode to corners. Args: boxes: bounding boxes, Nx4 or Nx6 torch tensor
monai/data/box_utils.py:98
↓ 2 callersMethodbuild_conv_block
(self, in_channels, out_channels, kernel_size)
monai/networks/nets/regunet.py:134
↓ 2 callersFunctionbuild_sincos_position_embedding
Builds a sin-cos position embedding based on the given grid size, embed dimension, spatial dimensions, and temperature. Reference: https://gi
monai/networks/blocks/pos_embed_utils.py:87
↓ 2 callersFunctioncalculate_out_shape
Calculate the output tensor shape when applying a convolution to a tensor of shape `inShape` with kernel size `kernel_size`, stride value `st
monai/networks/layers/convutils.py:56
↓ 2 callersFunctioncast_all
Utility function to cast all tensors in a tuple from from_dtype to to_dtype
monai/networks/utils.py:1264
↓ 2 callersFunctioncenters_in_boxes
Checks which center points are within boxes Args: boxes: bounding boxes, Nx4 or Nx6 torch tensor or ndarray. The box mode is assumed
monai/data/box_utils.py:649
↓ 2 callersFunctioncheck_and_set_optional_args
convert `params` into '--key_1=value_1 --key_2=value_2 ...
monai/auto3dseg/utils.py:541
↓ 2 callersMethodcheck_ids
(self, a, b, should_match)
tests/data/meta_tensor/test_meta_tensor.py:65
↓ 2 callersMethodcheck_inverse
(self, name, keys, orig_d, fwd_bck_d, unmodified_d, acceptable_diff)
tests/transforms/inverse/test_inverse.py:400
↓ 2 callersFunctioncheck_kernels
(net, mode)
tests/networks/nets/test_hovernet.py:103
↓ 2 callersMethodcheck_properties
Check whether the required properties are existing in the bundle workflow. If no workflow type specified, return None, otherwise, ret
monai/bundle/workflows.py:232
↓ 2 callersMethodcheck_properties
Check whether the required properties are existing in the bundle workflow. If the optional properties have reference in the config, w
monai/bundle/workflows.py:497
↓ 2 callersMethodcheck_replaced_modules
(self, name, match_device)
tests/networks/utils/test_replace_module.py:47
↓ 2 callersFunctionclone
Clone data independent of type. Args: data (NdarrayTensor): This can be a Pytorch Tensor or numpy array. Returns: Any:
tests/test_utils.py:110
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