Utilities¶

Module contents¶

General app utilities.

Submodules¶

django_mri.utils.bids module¶

Definition of the Bids class.

class django_mri.utils.bids.Bids(scan)¶

Bases: object

A class to compose BIDS-appropriate paths for usage by dcm2niix In short, standard template for BIDS-appropriate path is: sub-<label>/<data_type>/sub-<label>_<modality_label>

References

The BIDS Specification.

DATASET_DESCRIPTION_FILE_NAME = 'dataset_description.json'¶

PARTICIPANTS_FILE_NAME = 'participants.tsv'¶

calculate_age(born: datetime.date) → float¶

Returns age by date of birth.

Parameters:	born (datetime.date) – Subject’s birth date
Returns:	Subject’s age
Return type:	float

clean_unwanted_files(bids_path: pathlib.Path)¶

Clean irrelevant .bvec and .bval files; Some versions of dcm2niix produce .bvec and .bval for fieldmap images as well as dwi images. Since BIDS specifications do now allow such files under “fmap” data-type, this method deletes them from the relevant directory.

Parameters:	bids_path (Path) – Path to the BIDS-compatible directory

compose_bids_path()¶

Uses parameters extracted by {self.get_data} to compose a BIDS- compatible file path

Returns:	Full path to a BIDS-compatible file, according to scan’s parameters.
Return type:	pathlib.Path

fix_functional_json(bids_path: pathlib.Path)¶

Add required “TaskName” field to functional scan, as stated in BIDS stucture.

Parameters:	bids_path (Path) – Path to the BIDS-compatible directory

References

BIDS MRI specification

generate_bidsignore(parent: pathlib.Path)¶

Some acquisitions do not conform to BIDS specification (mainly localizers), so we generate a .bidsignore file, pointing to them.

Parameters:	parent (Path) – BIDS-compatible directory, underwhich there are “sub-x” directories

References

BIDS validator specifications

generate_readme(parent: pathlib.Path)¶

It is recommended by BIDS specifications to have a README file at the base of our project, so we create a blank one for further usage.

Parameters:	parent (Path) – BIDS-compatible directory, underwhich there are “sub-x” directories

get_data()¶

Extracts relevant parameters for BIDS-compatible naming.

Returns:

parent (Path) – Parent BIDS directory, under which there will be “sub-x” directories
data_type (str) – sub-directory under “sub-x”. either “anat”,”func”,”fmap” or “dwi”
modality_label (str) – modality label as described in BIDS specifications. either “dwi”, “epi”,”T1w”,”FLAIR”,”bold” or “localizer”
task (Union[str, None]) – task name for functional scans. “rest” or None
pe_dir (Union[str, None]) – PhaseEncodingDirection for DWI-related images or fieldmap-related images. Either “AP”,”PA” or None

get_subject_data()¶

Extract relevant Scan-related subject’s parameters, as stated by BIDS structure.

Returns:	subject’s relevant parameters, sorted by “participant_id”, “handedness”,”age” and “sex” fields
Return type:	subject_dict[dict]

set_description_json(parent: pathlib.Path)¶

Generates required “dataset_description.json” file, as stated by BIDS structure.

Parameters:	parent (Path) – BIDS-compatible directory, underwhich there are “sub-x” directories

References

BIDS complementary files

set_participant_tsv_and_json(parent: pathlib.Path, subject_dict: dict)¶

Generates recommended “participants.tsv” by either copying the template from TEMPLATES_DiR or editing an existing one under {parent} directory.

Parameters:	parent (Path) – BIDS-compatible directory, underwhich there are “sub-x” directories subject_dict (dict) – Subject’s parameters dictionary, containing “participant_id”, “handedness”,”age”,”sex” fields

References

BIDS complementary files

class django_mri.utils.bids.DATA_TYPES¶

Bases: enum.Enum

An enumeration.

AP = 'dwi'¶

PA = 'fmap'¶

dwi = 'dwi'¶

flair = 'anat'¶

fmri = 'func'¶

ir_epi = 'anat'¶

ir_epi2 = 'anat'¶

localizer = 'anat'¶

mprage = 'anat'¶

class django_mri.utils.bids.MODALITY_LABELS¶

Bases: enum.Enum

An enumeration.

AP = 'dwi'¶

PA = 'epi'¶

dwi = 'dwi'¶

flair = 'FLAIR'¶

fmri = 'bold'¶

ir_epi = 'T1w'¶

ir_epi2 = 'T1w'¶

localizer = 'localizer'¶

mprage = 'T1w'¶

django_mri.utils.compression module¶

Definition of the compress() and uncompress() utility functions.

django_mri.utils.compression.compress(source: pathlib.Path, destination: pathlib.Path = None, keep_source: bool = True) → pathlib.Path¶

Compresses the provided source file.

Parameters:	source (Path) – File to compress destination (Path, optional) – Compressed output file path, by default None keep_source (bool, optional) – Whether to keep the source file or not, by default True
Returns:	Output file path
Return type:	Path

django_mri.utils.compression.uncompress(source: pathlib.Path, destination: pathlib.Path = None, keep_source: bool = True) → pathlib.Path¶

Uncompresses the provided (compressed) source file.

Parameters:	source (Path) – File to uncompress destination (Path, optional) – Uncompressed output file path, by default None keep_source (bool, optional) – Whether to keep the source file or not, by default True
Returns:	Output file path
Return type:	Path

django_mri.utils.messages module¶

A module storing strings used to display messages.

django_mri.utils.scan_type module¶

Definition of the django_mri.utils.scan_type.ScanType Enum.

class django_mri.utils.scan_type.ScanType¶

Bases: enum.Enum

Supported scan file formats.

DICOM = 'DICOM'¶

NIFTI = 'NIfTI'¶

django_mri.utils.utils module¶

General app utilites.

django_mri.utils.utils.DEFAULT_DICOM_DIR_NAME = 'DICOM'¶: The name of the subdirectory under the MRI data root in which DICOM files will be saved.

django_mri.utils.utils.DEFAULT_MRI_DIR_NAME = 'MRI'¶: The name of the subdirectory under MEDIA_ROOT in which MRI data will be saved.

django_mri.utils.utils.DEFAULT_STUDY_GROUP_MODEL = 'research.Group'¶: Default identifier for a study group model scans should be related to.

django_mri.utils.utils.DEFAULT_SUBJECT_MODEL = 'research.Subject'¶: Default identifier for a subject model scans should be related to.

django_mri.utils.utils.get_dicom_root() → pathlib.Path¶: Returns the path of the directory in which DICOM data should be saved.

django_mri.utils.utils.get_group_model()¶

Returns the study group model MRI scans should be related to.

Returns:	Study group model
Return type:	django.db.models.Model

django_mri.utils.utils.get_mri_root() → pathlib.Path¶: Returns the path of the directory in which MRI data should be saved.

django_mri.utils.utils.get_subject_model()¶

Returns the subject model MRI scans should be related to.

Returns:	Subject model
Return type:	django.db.models.Model