pyalfe.data_structure

pyalfe.data_structure#

class pyalfe.data_structure.Modality(value)[source]#

Bases: StrEnum

An enumeration.

T1 = 'T1'#
T1Post = 'T1Post'#
T2 = 'T2'#
FLAIR = 'FLAIR'#
SWI = 'SWI'#
DWI = 'DWI'#
SingleDWI = 'SingleDWI'#
ADC = 'ADC'#
EADC = 'EADC'#
CBF = 'CBF'#
ASL = 'ASL'#
PERFUSION = 'PERFUSION'#
class pyalfe.data_structure.Orientation(value)[source]#

Bases: StrEnum

An enumeration.

AXIAL = 'AXIAL'#
SAGITTAL = 'SAGITTAL'#
CORONAL = 'CORONAL'#
class pyalfe.data_structure.Tissue(value)[source]#

Bases: IntEnum

An enumeration.

BACKGROUND = 0#
CSF = 1#
CORTICAL_GRAY_MATTER = 2#
WHITE_MATTER = 3#
DEEP_GRAY_MATTER = 4#
BRAIN_STEM = 5#
CEREBELLUM = 6#
class pyalfe.data_structure.Series(series_path, instances)#

Bases: tuple

instances#

Alias for field number 1

series_path#

Alias for field number 0

class pyalfe.data_structure.PipelineDataDir[source]#

Bases: ABC

Abstract PipelineDataDir

get_output_image(accession, modality, image_type=None, resampling_target=None, resampling_origin=None, sub_dir_name=None, extension='.nii.gz')[source]#
Generates the path for an output image. All the implementations

should make the parent directories if they do not exist.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • image_type (str, default=None) – Image type. For example: skullstripped.

  • resampling_target (Modality or str, default=None) – The target space that the image has been resampled to. For example, for a T2 image that is resampled to FLAIR, resampling target is FLAIR.

  • resampling_origin (Modality, str, default=None) – The origin of image before resampling. For example, if a template image is resampled to T1, the resampling origin is template.

  • sub_dir_name (str, default=None) – The name of the sub directory inside the modality directory in which the image is stored. If None the image is stored directory inside the modality directory.

  • extension (str, default='.nii.gz') – The extension of the image.

Returns:

The path to output image.

Return type:

str

get_input_image(accession, modality, extension='.nii.gz')[source]#

Generates the path for an input image.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • extension (str, default='.nii.gz') – The extension of the image.

Returns:

The path to input image.

Return type:

str

get_quantification_file(accession, modality, quantification_file_type, extension='.csv')[source]#

Generates the path for an output quantification file. All the implementations should make the parent directories if they do not exist.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • quantification_file_type (str, default=None) – Image type. For example: SummaryLesionMeasures.

  • extension (str, default='.csv') – The extension of the quantification.

Returns:

The path to quantification file.

Return type:

str

class pyalfe.data_structure.DefaultALFEDataDir(output_dir, input_dir)[source]#

Bases: PipelineDataDir

Default implementation of PipelineDataDir

create_dir(dir_type, accession, *sub_dir_names, exists=True)[source]#
get_output_image(accession, modality, image_type=None, resampling_target=None, resampling_origin=None, sub_dir_name=None, extension='.nii.gz')[source]#

Generate the path for an output image in ALFE default dir structure format.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • image_type (str, default=None) – Image type. For example: skullstripped.

  • resampling_target (Modality or str, default=None) – The target space that the image has been resampled to. For example, for a T2 image that is resampled to FLAIR, resampling target is FLAIR.

  • resampling_origin (Modality, str, default=None) – The origin of image before resampling. For example, if a template image is resampled to T1, the resampling origin is template.

  • sub_dir_name (str, default=None) – The name of the sub directory inside the modality directory in which the image is stored. If None the image is stored directory inside the modality directory.

  • extension (str, default='.nii.gz') – The extension of the image.

Returns:

The path to output image.

Return type:

str

Examples

>>> from pyalfe.data_structure import DefaultALFEDataDir
>>> data_dir = DefaultALFEDataDir(
output_dir='/mri-data/processed', input_dir='/mri-data/input')
>>> data_dir.get_output_image('34521', 'T1')
'/mri-data/processed/34521/T1/34521_T1.nii.gz'

>>> data_dir.get_output_image(
'34521', 'T2', image_type='skullstrippied')
'/mri-data/processed/34521/T2/34521_T2_skullstrippied.nii.gz'

>>> data_dir.get_output_image(
'34521', 'T1Post', resampling_target='T1Post', resampling_origin='template')
'/mri-data/processed/34521/T1Post/34521_template_to_T1Post.nii.gz'

>>> data_dir.get_output_image(
'34521', 'T2', image_type='abnormal_seg', sub_dir_name='abnormalmap')
'/mri-data/processed/34521/T2/abnormalmap/34521_T2_abnormal_seg.nii.gz'
get_input_image(accession, modality, extension='.nii.gz')[source]#

Generate the path for an input image in ALFE default dir structure format.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • extension (str, default='.nii.gz') – The extension of the image.

Returns:

The path to input image.

Return type:

str

Examples

>>> from pyalfe.data_structure import DefaultALFEDataDir
>>> data_dir = DefaultALFEDataDir(
output_dir='/mri-data/processed', input_dir='/mri-data/input')
>>> data_dir.get_input_image('34521', 'T1')
'/mri-data/input/34521/T1/T1.nii.gz'
get_quantification_file(accession, modality, quantification_file_type, extension='.csv')[source]#

Generate the path for a quantification file in ALFE default dir structure format.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • quantification_file_type (str, default=None) – Image type. For example: SummaryLesionMeasures.

  • extension (str, default='.csv') – The extension of the quantification.

Returns:

The path to quantification file.

Return type:

str

Examples

>>> from pyalfe.data_structure import DefaultALFEDataDir
>>> data_dir = DefaultALFEDataDir(
output_dir='/mri-data/processed', input_dir='/mri-data/input')
>>> data_dir.get_quantification_file(
'34521', 'T1Post', quantification_file_type='IndividualLesionMeasures')
'/mri-data/processed/34521/T1Post/quantification/34521_IndividualLesionMeasures.csv'
class pyalfe.data_structure.BIDSDataDir(output_dir, input_dir)[source]#

Bases: PipelineDataDir

BIDS almost-compliant implementation of PipelineDataDir

logger = <Logger BIDSDataDir (DEBUG)>#
modality_dict = {Modality.ADC: {'datatype': 'dwi', 'suffix': 'md'}, Modality.ASL: {'datatype': 'perf', 'suffix': 'asl'}, Modality.CBF: {'datatype': 'perf', 'suffix': 'cbf'}, Modality.FLAIR: {'datatype': 'anat', 'suffix': 'FLAIR'}, Modality.SWI: {'datatype': 'swi', 'suffix': 'swi'}, Modality.T1: {'datatype': 'anat', 'suffix': 'T1w'}, Modality.T1Post: {'ceagent': 'gadolinium', 'datatype': 'anat', 'suffix': 'T1w'}, Modality.T2: {'datatype': 'anat', 'suffix': 'T2w'}}#
get_input_image(accession, modality, extension='.nii.gz')[source]#

Generates the path for an input image in BIDS dir structure format.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • extension (str, default='.nii.gz') – The extension of the image.

Returns:

The path to input image.

Return type:

str

Examples

>>> from pyalfe.data_structure import BIDSDataDir
>>> data_dir = BIDSDataDir(
output_dir='/mri-data/processed', input_dir='/mri-data/input')
>>> data_dir.get_input_image('34521', 'T1')
'/mri-data/input/sub-34521/anat/sub-34521_T1w.nii.gz'

>>> data_dir.get_input_image('34521', 'ADC')
'/mri-data/input/sub-34521/derivative/dwi/sub-34521_md.nii.gz'

>>> data_dir.get_input_image('34521', 'CBF')
'/mri-data/input/sub-34521/derivative/perf/sub-34521_cbf.nii.gz'

>>> data_dir.get_input_image('34521', 'SWI')
'/mri-data/input/sub-34521/derivative/swi/sub-34521_swi.nii.gz'

>>> data_dir.get_input_image('34521', 'T1Post')
'/mri-data/input/sub-34521/anat/sub-34521_ce-gadolinium_T1w.nii.gz'
get_output_image(accession, modality, image_type=None, resampling_target=None, resampling_origin=None, sub_dir_name=None, extension='.nii.gz')[source]#

Generates the path for an output image in BIDS dir structure format.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • image_type (str, default=None) – Image type. For example: skullstripped.

  • resampling_target (Modality or str, default=None) – The target space that the image has been resampled to. For example, for a T2 image that is resampled to FLAIR, resampling target is FLAIR.

  • resampling_origin (Modality, str, default=None) – The origin of image before resampling. For example, if a template image is resampled to T1, the resampling origin is template.

  • sub_dir_name (str, default=None) – The name of the sub directory inside the modality directory in which the image is stored. If None the image is stored directory inside the modality directory.

  • extension (str, default='.nii.gz') – The extension of the image.

Returns:

The path to output image.

Return type:

str

Examples

>>> from pyalfe.data_structure import BIDSDataDir
>>> data_dir = BIDSDataDir(
output_dir='/mri-data/processed', input_dir='/mri-data/input')
>>> data_dir.get_output_image('34521', 'T1')
'/mri-data/processed/sub-34521/anat/sub-34521_T1w.nii.gz'

>>> data_dir.get_output_image('34521', 'T2', image_type='skullstrippied')
'/mri-data/processed/sub-34521/anat/sub-34521_desc-skullstrippied_T2w.nii.gz'

>>> data_dir.get_output_image(
'34521', 'T1Post', resampling_target='T1Post', resampling_origin='template')
'/mri-data/processed/sub-34521/anat/sub-34521_ce-gadolinium_space-orig_desc-template_T1w.nii.gz'

>>> data_dir.get_output_image(
'34521', 'T2', image_type='abnormal_seg', sub_dir_name='abnormalmap')
'/mri-data/processed/sub-34521/anat/sub-34521_desc-abnormalseg_dseg.nii.gz'
get_quantification_file(accession, modality, quantification_file_type, extension='.csv')[source]#

Generate the path for a quantification file in BIDS dir structure format.

Parameters:

  • accession (str) – The accession or study number.

  • modality (Modality or str) – Image modality.

  • quantification_file_type (str, default=None) – Image type. For example: SummaryLesionMeasures.

  • extension (str, default='.csv') – The extension of the quantification.

Returns:

The path to quantification file.

Return type:

str

Examples

>>> from pyalfe.data_structure import BIDSDataDir
>>> data_dir = BIDSDataDir(
output_dir='/mri-data/processed', input_dir='/mri-data/input')
>>> data_dir.get_quantification_file(
'34521', 'T1Post', quantification_file_type='IndividualLesionMeasures')
'/mri-data/processed/sub-34521/anat/quantification/sub-34521_ce-gadolinium_desc-T1Post_IndividualLesionMeasures.csv'
class pyalfe.data_structure.PatientDicomDataDir(dicom_dir)[source]#

Bases: object

This class is designed to work with directories containing raw dicom files for a patient that are organized as: dicom_dir

└─ accession (study)
└─ series

├─ instance_0.dcm └─ instance_1.dcm

is_dicom_file(file)[source]#

Function to check if file is a dicom file. The first 128 bytes are preamble the next 4 bytes should contain DICM otherwise it is not a dicom file. Adapted from icometrix/dicom2nifti

Parameters:

file (str) – file to check for the DICM header block

Returns:

True if it is a dicom file otherwise False.

Return type:

bool

get_all_dicom_series_instances(accession)[source]#

This method returns a list of Series each containing a series path and all of the instances in the series.

Parameters:

accession (str) – The accession or study number.

Returns:

A list of Series (series_path, instances)

Return type:

list[Series]

get_series(accession, series_uid)[source]#

This method returns the path to a series.

Parameters:

  • patient_id (str) – The patient_id.

  • accession (str) – The accession or study number.

  • series_uid (str) – The series ID.

Returns:

  • str

  • The path to the series directory