PCAGuidedTopVoxelsIDIFStep#

class petpal.pipelines.pca_guided_idif_steps.PCAGuidedTopVoxelsIDIFStep(input_image_path: str, mask_image_path: str, output_array_path: str, num_pca_components: int, verbose: bool, selected_component: int, num_of_voxels: int)#

Bases: petpal.pipelines.steps_base.ObjectBasedStep, PCAGuidedIDIFMixin

Pipeline step for PCA-guided IDIF calculation using top-ranked voxels.

This step extends the PCAGuidedIDIFMixin and provides functionality to select the top N voxels from a specified PCA component for IDIF generation. It uses the PCAGuidedTopVoxelsIDIF class for its calculations.

Inheritance:

Inherits from ObjectBasedStep and PCAGuidedIDIFMixin.

Variables:

  • selected_component (int) – PCA component selected for voxel ranking.

  • num_of_voxels (int) – Number of top-ranking voxels to select.

Example

from petpal.pipelines.pca_guided_idif_steps import PCAGuidedTopVoxelsIDIFStep

## Initializing the step
step = PCAGuidedTopVoxelsIDIFStep(input_image_path='/path/to/image.nii',
                                  mask_image_path='/path/to/mask.nii',
                                  output_array_path='/path/to/output.tsv',
                                  num_pca_components=3,
                                  verbose=False,
                                  selected_component=2,
                                  num_of_voxels=50)
## Running the step and saving the results
step()

Initializes the PCA-guided top voxels IDIF pipeline step.

Parameters:

  • input_image_path (str) – Path to the input 4D-PET image.

  • mask_image_path (str) – Path to the mask image in the same space as 4D-PET image.

  • output_array_path (str) – Path where the resulting TAC data will be saved.

  • num_pca_components (int) – Number of PCA components to consider.

  • verbose (bool) – If True, enables detailed diagnostic output.

  • selected_component (int) – PCA component to use for voxel ranking.

  • num_of_voxels (int) – Number of top voxels to select.

property selected_component#
property num_of_voxels#
classmethod default_pca_guided_idif_top_voxels(name: str = 'pca_guided_top_voxels_idif', verbose=False, **overrides)#

Creates a default instance for PCA-guided IDIF calculation based on selecting the top-ranked voxels from a single PCA component.

All paths are set to empty strings by default.

Parameters:

  • name (str) – Name of the step. Defaults to ‘pca_guided_top_voxels_idif’.

  • verbose (bool) – Whether to enable verbose mode (default: False).

  • **overrides – Parameter values to override the default settings.

Returns:

PCAGuidedTopVoxelsIDIFStep – A new instance of the PCA-guided top voxels IDIF step.

Default Parameters:

  • input_image_path: ‘’ (empty string)

  • mask_image_path: ‘’ (empty string)

  • output_array_path: ‘’ (empty string)

  • num_pca_components: 3

  • verbose: False

  • selected_component: 0

  • num_of_voxels: 50

Side Effects:

  • If an invalid override is provided, a warning is issued, and the default instance is returned instead.

validate_kwargs()#

Validates that all mandatory initialization and call arguments have been provided.

Raises:

RuntimeError – If any mandatory arguments are missing.

static get_args_not_set_in_kwargs(sig: inspect.Signature, kwargs: dict) → dict#

Retrieves arguments of the signature that are not set in the keyword arguments.

Parameters:

  • sig (inspect.Signature) – The signature of the function or method.

  • kwargs (dict) – The keyword arguments provided.

Returns:

dict – A dictionary of arguments that are not set in the keyword arguments.

get_empty_default_kwargs(sig: inspect.Signature, set_kwargs: dict) → list#

Identifies arguments that have not been provided and lack default values.

Parameters:

  • sig (inspect.Signature) – The signature of the function or method.

  • set_kwargs (dict) – The keyword arguments provided.

Returns:

list – A list of argument names that have no default values and are not provided.

execute() → None#

Instantiates the class and invokes it with the provided arguments.

Raises:

The function may raise any exceptions that its implementation can throw. –

__str__()#

Returns a detailed string representation of the ObjectBasedStep instance.

Returns:

str – A string describing the step, including its name, class, initialization, and call arguments.

__repr__()#

Returns an unambiguous string representation of the ObjectBasedStep instance.

Returns:

str – A string representation showing how the ObjectBasedStep can be recreated.

all_init_kwargs_non_empty_strings()#

Checks if all initialization keyword arguments are non-empty strings.

Returns:

bool – True if all initialization keyword arguments are non-empty strings, False otherwise.

all_call_kwargs_non_empty_strings()#

Checks if all call keyword arguments are non-empty strings.

Returns:

bool – True if all call keyword arguments are non-empty strings, False otherwise.

can_potentially_run()#

Determines if the step can potentially be executed based on argument validation. Very simply checks if all __init__ and __call__ keyword arguments for the object are non-empty strings.

Returns:

bool – True if the step can potentially run, False otherwise.

abstractmethod set_input_as_output_from(*sending_steps)#

Sets the input of the current step as the output from a list of steps.

Parameters:

*sending_steps – The previous steps from which the output will be used as input for the current step.

Raises:

NotImplementedError – This method should be implemented by subclasses.

Notes

For a concrete example, take a look at: TACsFromSegmentationStep

Important

If a step takes multiple input steps. the implementation will have a defined order for steps.

abstractmethod infer_outputs_from_inputs(out_dir: str, der_type: str, suffix: str = None, ext: str = None, **extra_desc)#

Infers output files from input data based on the specified output directory, derivative type, optional suffix and extension, plus any extra descriptions.

Parameters:

  • out_dir (str) – The directory where the output files will be saved.

  • der_type (str) – The type of derivative being produced.

  • suffix (str, optional) – An optional suffix for the output files.

  • ext (str, optional) – An optional extension for the output files.

  • **extra_desc – Additional keyword arguments for extra descriptions to be included.

Raises:

NotImplementedError – This method should be implemented by subclasses.

Notes

For a concrete example, take a look at: TACsFromSegmentationStep

__call__(*args, **kwargs)#
property input_image_path#
property mask_image_path#
property output_tac_path: str#
property num_pca_components#
property verbose#