Index

A

ACQ_CONTRAST_MAPPING (asldro.filters.bids_output_filter.BidsOutputFilter attribute) ACQ_DATE_TIME (asldro.filters.bids_output_filter.BidsOutputFilter attribute) AcquireMriImageFilter (class in asldro.filters.acquire_mri_image_filter) add_child_filter() (asldro.filters.basefilter.BaseFilter method) add_input() (asldro.filters.basefilter.BaseFilter method) add_inputs() (asldro.filters.basefilter.BaseFilter method) add_parent_filter() (asldro.filters.basefilter.BaseFilter method) AddComplexNoiseFilter (class in asldro.filters.add_complex_noise_filter) AddNoiseFilter (class in asldro.filters.add_noise_filter) affine() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property) AffineMatrixFilter (class in asldro.filters.affine_matrix_filter) AppendMetadataFilter (class in asldro.filters.append_metadata_filter) as_nifti() (asldro.containers.image.BaseImageContainer method) (asldro.containers.image.NiftiImageContainer method) (asldro.containers.image.NumpyImageContainer method) as_numpy() (asldro.containers.image.BaseImageContainer method) (asldro.containers.image.NiftiImageContainer method) (asldro.containers.image.NumpyImageContainer method) asl_context_length_validator_generator() (in module asldro.validators.user_parameter_input) asldro module asldro.cli module asldro.containers module asldro.containers.image module asldro.data module asldro.data.affine_test_data module asldro.data.filepaths module asldro.definitions module asldro.examples module asldro.filters module asldro.filters.acquire_mri_image_filter module asldro.filters.add_complex_noise_filter module asldro.filters.add_noise_filter module asldro.filters.affine_matrix_filter module

asldro.filters.append_metadata_filter module asldro.filters.basefilter module asldro.filters.bids_output_filter module asldro.filters.combine_time_series_filter module asldro.filters.filter_block module asldro.filters.fourier_filter module asldro.filters.gkm_filter module asldro.filters.ground_truth_loader module asldro.filters.invert_image_filter module asldro.filters.json_loader module asldro.filters.mri_signal_filter module asldro.filters.nifti_loader module asldro.filters.phase_magnitude_filter module asldro.filters.resample_filter module asldro.filters.scale_offset_filter module asldro.filters.transform_resample_image_filter module asldro.utils module asldro.utils.general module asldro.utils.resampling module asldro.validators module asldro.validators.ground_truth_json module asldro.validators.parameters module asldro.validators.schemas module asldro.validators.schemas.index module asldro.validators.user_parameter_input module

B

BaseFilter (class in asldro.filters.basefilter) BaseFilterException

BaseImageContainer (class in asldro.containers.image) BIDS_MAPPING (asldro.filters.bids_output_filter.BidsOutputFilter attribute) BidsOutputFilter (class in asldro.filters.bids_output_filter)

C

CASL (asldro.filters.gkm_filter.GkmFilter attribute) clone() (asldro.containers.image.BaseImageContainer method) CombineTimeSeriesFilter (class in asldro.filters.combine_time_series_filter)

COMPLEX_IMAGE_COMPONENT_MAPPING (asldro.filters.bids_output_filter.BidsOutputFilter attribute) CONTRAST_GE (asldro.filters.mri_signal_filter.MriSignalFilter attribute) CONTRAST_IR (asldro.filters.mri_signal_filter.MriSignalFilter attribute) CONTRAST_SE (asldro.filters.mri_signal_filter.MriSignalFilter attribute)

D

determine_asl_modality_label() (asldro.filters.bids_output_filter.BidsOutputFilter static method) DirType (class in asldro.cli)

DRO_SOFTWARE (asldro.filters.bids_output_filter.BidsOutputFilter attribute) DRO_SOFTWARE_URL (asldro.filters.bids_output_filter.BidsOutputFilter attribute) DRO_SOFTWARE_VERSION (asldro.filters.bids_output_filter.BidsOutputFilter attribute)

F

FftFilter (class in asldro.filters.fourier_filter) FileType (class in asldro.cli) FilterBlock (class in asldro.filters.filter_block) FilterInputKeyError

FilterInputValidationError FilterLoopError for_each_validator() (in module asldro.validators.parameters) from_list_validator() (in module asldro.validators.parameters)

G

generate() (in module asldro.cli) get_defaults() (asldro.validators.parameters.ParameterValidator method) get_example_input_params() (in module asldro.validators.user_parameter_input)

GkmFilter (class in asldro.filters.gkm_filter) greater_than_equal_to_validator() (in module asldro.validators.parameters) greater_than_validator() (in module asldro.validators.parameters) GroundTruthLoaderFilter (class in asldro.filters.ground_truth_loader)

H

has_attribute_value_validator() (in module asldro.validators.parameters) has_nifti() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property)

header() (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property) HrgtType (class in asldro.cli)

I

IfftFilter (class in asldro.filters.fourier_filter) image() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property)

IMAGE_TYPE (asldro.filters.bids_output_filter.BidsOutputFilter attribute) INPUT_IMAGE_REGEX_OBJ (asldro.filters.combine_time_series_filter.CombineTimeSeriesFilter attribute) InvertImageFilter (class in asldro.filters.invert_image_filter) isinstance_validator() (in module asldro.validators.parameters)

J

JsonLoaderFilter (class in asldro.filters.json_loader)

K

KEY_ACQ_CONTRAST (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_ACQ_TYPE (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_AFFINE (asldro.filters.affine_matrix_filter.AffineMatrixFilter attribute) (asldro.filters.resample_filter.ResampleFilter attribute) KEY_AFFINE_INVERSE (asldro.filters.affine_matrix_filter.AffineMatrixFilter attribute) KEY_AFFINE_LAST (asldro.filters.affine_matrix_filter.AffineMatrixFilter attribute) KEY_DELTA_M (asldro.filters.gkm_filter.GkmFilter attribute) KEY_ECHO_TIME (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_EXCITATION_FLIP_ANGLE (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_FILENAME (asldro.filters.bids_output_filter.BidsOutputFilter attribute) KEY_FILENAME_PREFIX (asldro.filters.bids_output_filter.BidsOutputFilter attribute) KEY_GROUND_TRUTH_MODULATE (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) KEY_IMAGE (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.add_complex_noise_filter.AddComplexNoiseFilter attribute) (asldro.filters.add_noise_filter.AddNoiseFilter attribute) (asldro.filters.append_metadata_filter.AppendMetadataFilter attribute) (asldro.filters.bids_output_filter.BidsOutputFilter attribute) (asldro.filters.combine_time_series_filter.CombineTimeSeriesFilter attribute) (asldro.filters.fourier_filter.FftFilter attribute) (asldro.filters.fourier_filter.IfftFilter attribute) (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) (asldro.filters.phase_magnitude_filter.PhaseMagnitudeFilter attribute) (asldro.filters.resample_filter.ResampleFilter attribute) (asldro.filters.scale_offset_filter.ScaleOffsetFilter attribute) (asldro.filters.transform_resample_image_filter.TransformResampleImageFilter attribute) KEY_IMAGE_FLAVOUR (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_IMAGE_OVERRIDE (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) KEY_INVERSION_FLIP_ANGLE (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_INVERSION_TIME (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_LABEL_DURATION (asldro.filters.gkm_filter.GkmFilter attribute) KEY_LABEL_EFFICIENCY (asldro.filters.gkm_filter.GkmFilter attribute) KEY_LABEL_TYPE (asldro.filters.gkm_filter.GkmFilter attribute) KEY_LAMBDA_BLOOD_BRAIN (asldro.filters.gkm_filter.GkmFilter attribute) KEY_M0 (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.gkm_filter.GkmFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_MAG_ENC (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_MAG_STRENGTH (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute)

KEY_MAGNITUDE (asldro.filters.phase_magnitude_filter.PhaseMagnitudeFilter attribute) KEY_METADATA (asldro.filters.append_metadata_filter.AppendMetadataFilter attribute) KEY_OFFSET (asldro.filters.scale_offset_filter.ScaleOffsetFilter attribute) KEY_OUTPUT_DIRECTORY (asldro.filters.bids_output_filter.BidsOutputFilter attribute) KEY_PARAMETER_OVERRIDE (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) KEY_PARAMETERS (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) KEY_PERFUSION_RATE (asldro.filters.gkm_filter.GkmFilter attribute) KEY_PHASE (asldro.filters.phase_magnitude_filter.PhaseMagnitudeFilter attribute) KEY_POST_LABEL_DELAY (asldro.filters.gkm_filter.GkmFilter attribute) KEY_QUANTITIES (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) KEY_QUANTITY (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) KEY_REF_IMAGE (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.add_complex_noise_filter.AddComplexNoiseFilter attribute) (asldro.filters.add_noise_filter.AddNoiseFilter attribute) KEY_REPETITION_TIME (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_ROTATION (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.affine_matrix_filter.AffineMatrixFilter attribute) (asldro.filters.transform_resample_image_filter.TransformResampleImageFilter attribute) KEY_ROTATION_ORIGIN (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.affine_matrix_filter.AffineMatrixFilter attribute) (asldro.filters.transform_resample_image_filter.TransformResampleImageFilter attribute) KEY_SCALE (asldro.filters.affine_matrix_filter.AffineMatrixFilter attribute) (asldro.filters.scale_offset_filter.ScaleOffsetFilter attribute) KEY_SEGMENTATION (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute) KEY_SHAPE (asldro.filters.resample_filter.ResampleFilter attribute) KEY_SIDECAR (asldro.filters.bids_output_filter.BidsOutputFilter attribute) KEY_SIGNAL_TIME (asldro.filters.gkm_filter.GkmFilter attribute) KEY_SNR (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.add_complex_noise_filter.AddComplexNoiseFilter attribute) (asldro.filters.add_noise_filter.AddNoiseFilter attribute) KEY_T1 (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_T1_ARTERIAL_BLOOD (asldro.filters.gkm_filter.GkmFilter attribute) KEY_T1_TISSUE (asldro.filters.gkm_filter.GkmFilter attribute) KEY_T2 (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_T2_STAR (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.mri_signal_filter.MriSignalFilter attribute) KEY_TARGET_SHAPE (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.transform_resample_image_filter.TransformResampleImageFilter attribute) KEY_TRANSIT_TIME (asldro.filters.gkm_filter.GkmFilter attribute) KEY_TRANSLATION (asldro.filters.acquire_mri_image_filter.AcquireMriImageFilter attribute) (asldro.filters.affine_matrix_filter.AffineMatrixFilter attribute) (asldro.filters.transform_resample_image_filter.TransformResampleImageFilter attribute) KEY_UNITS (asldro.filters.ground_truth_loader.GroundTruthLoaderFilter attribute)

L

LABEL_MAP_MAPPING (asldro.filters.bids_output_filter.BidsOutputFilter attribute)

list_of_type_validator() (in module asldro.validators.parameters) load_schemas() (in module asldro.validators.schemas.index)

M

main() (in module asldro.cli) map_dict() (in module asldro.utils.general) metadata() (asldro.containers.image.BaseImageContainer property) module asldro asldro.cli asldro.containers asldro.containers.image asldro.data asldro.data.affine_test_data asldro.data.filepaths asldro.definitions asldro.examples asldro.filters asldro.filters.acquire_mri_image_filter asldro.filters.add_complex_noise_filter asldro.filters.add_noise_filter asldro.filters.affine_matrix_filter asldro.filters.append_metadata_filter asldro.filters.basefilter asldro.filters.bids_output_filter asldro.filters.combine_time_series_filter asldro.filters.filter_block asldro.filters.fourier_filter asldro.filters.gkm_filter asldro.filters.ground_truth_loader asldro.filters.invert_image_filter asldro.filters.json_loader asldro.filters.mri_signal_filter asldro.filters.nifti_loader asldro.filters.phase_magnitude_filter asldro.filters.resample_filter asldro.filters.scale_offset_filter asldro.filters.transform_resample_image_filter asldro.utils asldro.utils.general asldro.utils.resampling asldro.validators asldro.validators.ground_truth_json asldro.validators.parameters asldro.validators.schemas asldro.validators.schemas.index asldro.validators.user_parameter_input

MriSignalFilter (class in asldro.filters.mri_signal_filter)

N

nifti_type() (asldro.containers.image.NiftiImageContainer property) NiftiImageContainer (class in asldro.containers.image)

NiftiLoaderFilter (class in asldro.filters.nifti_loader) non_empty_list_validator() (in module asldro.validators.parameters) NumpyImageContainer (class in asldro.containers.image)

O

of_length_validator() (in module asldro.validators.parameters)

output_hrgt() (in module asldro.cli) output_params() (in module asldro.cli)

P

Parameter (class in asldro.validators.parameters) ParameterValidator (class in asldro.validators.parameters)

PASL (asldro.filters.gkm_filter.GkmFilter attribute) PCASL (asldro.filters.gkm_filter.GkmFilter attribute) PhaseMagnitudeFilter (class in asldro.filters.phase_magnitude_filter)

R

range_exclusive_validator() (in module asldro.validators.parameters) range_inclusive_validator() (in module asldro.validators.parameters) regex_validator() (in module asldro.validators.parameters) ResampleFilter (class in asldro.filters.resample_filter) reserved_string_list_validator() (in module asldro.validators.parameters)

rot_x_mat() (in module asldro.utils.resampling) rot_y_mat() (in module asldro.utils.resampling) rot_z_mat() (in module asldro.utils.resampling) run() (asldro.filters.basefilter.BaseFilter method) (asldro.filters.filter_block.FilterBlock method) run_full_pipeline() (in module asldro.examples)

S

scale_mat() (in module asldro.utils.resampling) ScaleOffsetFilter (class in asldro.filters.scale_offset_filter) SERIES_DESCRIPTION (asldro.filters.bids_output_filter.BidsOutputFilter attribute) SERIES_NUMBER (asldro.filters.bids_output_filter.BidsOutputFilter attribute) SERIES_TYPE (asldro.filters.bids_output_filter.BidsOutputFilter attribute) shape() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property)

space_units() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property) splitext() (in module asldro.utils.general)

T

time_step_seconds() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property) time_units() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property)

transform_resample_affine() (in module asldro.utils.resampling) transform_resample_image() (in module asldro.utils.resampling) TransformResampleImageFilter (class in asldro.filters.transform_resample_image_filter) translate_mat() (in module asldro.utils.resampling)

V

validate() (asldro.validators.parameters.ParameterValidator method) validate_input() (in module asldro.validators.ground_truth_json) validate_input_params() (in module asldro.validators.user_parameter_input) ValidationError

Validator (class in asldro.validators.parameters) VOXEL_SIZE (asldro.filters.transform_resample_image_filter.TransformResampleImageFilter attribute) voxel_size_mm() (asldro.containers.image.BaseImageContainer property) (asldro.containers.image.NiftiImageContainer property) (asldro.containers.image.NumpyImageContainer property)