-
Notifications
You must be signed in to change notification settings - Fork 0
Reference
Top-level package for radiome.
Strategy(self, forks=None, **kwargs)ResourceKey(
self,
key:
typing.Union[str, typing.Dict[str, str], ForwardRef('ResourceKey'), NoneType] = None,
tags: typing.Union[typing.Set[str], NoneType] = None,
**kwargs)Representation of a resource, matching BIDS specification.
Stores information contained in BIDS naming specs.
E.g. sub-001_ses-001_T1w.nii.gz
Entities are the key-value information encoded in the format
key-value in the file name.
The suffix is the last part of the name, after the last underscore.
Strategy is specific to radiome, and it is encoded in the desc entity,
in the format desc-strategy in which strategy is encoded as key-value
separated by +. E.g. desc-skullstripping-afni+registration-ants
In case there is an actual value for this entity, the strategy will
be encoded as key-value#strategy.
The resource key object can work as a filter, in case an entity of suffix is a quantifier: * and ^
Retrieve a copy of entities.
Retrieve the strategy. An empty strategy will be created if not set.
Retrieve the suffix.
Retrieve a copy of the tags.
ResourceKey.keys()Get a list of keys of defined entities and strategy.
ResourceKey.isfilter()Check if key is a filter.
It will be considered a filter if it contains a quantifier.
Returns: True, if an entity or suffix is a quantifier. False, otherwise.
ResourceKey.isbroad()Check if key is a broad key (*).
Returns: True, if there is no entity and suffix matches all. False, otherwise.
ResourceKey(
self,
key:
typing.Union[str, typing.Dict[str, str], ForwardRef('ResourceKey'), NoneType] = None,
tags: typing.Union[typing.Set[str], NoneType] = None,
**kwargs)Representation of a resource, matching BIDS specification.
Stores information contained in BIDS naming specs.
E.g. sub-001_ses-001_T1w.nii.gz
Entities are the key-value information encoded in the format
key-value in the file name.
The suffix is the last part of the name, after the last underscore.
Strategy is specific to radiome, and it is encoded in the desc entity,
in the format desc-strategy in which strategy is encoded as key-value
separated by +. E.g. desc-skullstripping-afni+registration-ants
In case there is an actual value for this entity, the strategy will
be encoded as key-value#strategy.
The resource key object can work as a filter, in case an entity of suffix is a quantifier: * and ^
Retrieve a copy of entities.
Retrieve the strategy. An empty strategy will be created if not set.
Retrieve the suffix.
Retrieve a copy of the tags.
ResourceKey.keys()Get a list of keys of defined entities and strategy.
ResourceKey.isfilter()Check if key is a filter.
It will be considered a filter if it contains a quantifier.
Returns: True, if an entity or suffix is a quantifier. False, otherwise.
ResourceKey.isbroad()Check if key is a broad key (*).
Returns: True, if there is no entity and suffix matches all. False, otherwise.
StrategyResourcePool(self, strategy: ResourceKey,
resource_pool: ResourcePool)A non-safe resource pool proxy for a specific strategy.
workflow(validate_inputs: bool = True, use_attr: bool = True)Decorator for a workflow. Control the behavior of create_workflow.
Args: validate_inputs: Validate inputs against the schema in spec.yml. use_attr: Use AttrDict instead of regular dicts. Retrieve values via attribute.
Returns: Should use as a decorator, return a decorated function.
Context(self, working_dir: typing.Union[str, os.PathLike], inputs_dir:
typing.Union[str, os.PathLike, radiome.core.utils.s3.S3Resource],
outputs_dir:
typing.Union[str, os.PathLike, radiome.core.utils.s3.S3Resource],
participant_label: typing.List, n_cpus: int, memory: int,
save_working_dir: bool, pipeline_config: typing.Dict,
diagnostics: bool)Context(working_dir: Union[str, os.PathLike], inputs_dir: Union[str, os.PathLike, radiome.core.utils.s3.S3Resource], outputs_dir: Union[str, os.PathLike, radiome.core.utils.s3.S3Resource], participant_label: List, n_cpus: int, memory: int, save_working_dir: bool, pipeline_config: Dict, diagnostics: bool)
PythonJob(self, function, reference=None)Radiome job for Python functions.
This job is to set up Python function in the steps of a workflow. Inputs of function should be set using attributes. Python functions must return a dict, which is mapping from names to values.
ComputedResource(self, job, field=None)Represents the future result from a job, but not the true result.
ComputedResource stores information that is needed to compute the result, but not the result itself. It can be used as inputs of other jobs and thus create a connection between jobs.
NipypeJob(self, interface: BaseInterface, reference=None)Radiome job for nipype interfaces,
NipypeJob is a uniform wrapper for all nipype interfaces such that nipype interfaces can receive results from or become inputs of other jobs.
NipypeJob(self, interface, reference=None)Nipype jobs mock for testing.
Mock that emulates the behavior and APIs of NipypeJob, but do not execute the commandline of nipype jobs. It will create fake outputs based on the outputs traits.
mock_nipype()Context manager which replaces Nipype jobs with mock at runtime.
Patch the nipype jobs with mocks at runtime, then recover it when exiting.
S3Resource(self,
content: str,
working_dir: str,
aws_cred_path: str = None,
aws_cred_profile: str = None)Amazon AWS S3 Resource.
An representation of S3 resource. It is bind to a specific s3 bucket url and credentials. Once the resource is initialized, files can be downloaded, cached and uoloaded to this bucket.
S3Resource.upload(path)Upload path to the S3 bucket.
Args: path: The source directory.
S3Resource.walk()Iterate the S3 bucket, the behavior is the same as os.walk.