Models¶

Module contents¶

Definition of the app’s models.

Subpackages¶

Submodules¶

django_mri.models.common_sequences module¶

A list of common MRI sequences and their respective DICOM header attributes.

django_mri.models.fields module¶

Definition of a custom ArrayField subclass.

Copied from https://blogs.gnome.org/danni/2016/03/08/multiple-choice-using-djangos-postgres-arrayfield/.

class django_mri.models.fields.ChoiceArrayField(base_field, size=None, **kwargs)¶

Bases: django.contrib.postgres.fields.array.ArrayField

A field that allows us to store an array of choices.

Uses Django’s PostgreSQL ArrayField and a MultipleChoiceField for its formfield.

formfield(**kwargs)¶: Return a django.forms.Field instance for this field.

django_mri.models.help_text module¶

A module storing strings used to populate the fields’ help_text attributes.

django_mri.models.messages module¶

A module storing strings used to display messages.

django_mri.models.nifti module¶

Definition of the NIfTI model.

class django_mri.models.nifti.NIfTI(*args, **kwargs)¶

Bases: django_extensions.db.models.TimeStampedModel

A model representing a NIfTI file in the database.

b_value¶

Returns the B-value of DWI scans as calculated by dcm2niix.

See also

get_b_value()

Returns:	B-value
Return type:	List[int]

b_vector¶

Returns the B-vector of DWI scans as calculated by dcm2niix.

See also

get_b_vector()

Returns:	B-vector
Return type:	List[List[float]]

compress(keep_source: bool = False) → pathlib.Path¶

Compress the associated .nii using gzip, if it isn’t already compressed.

Parameters:	keep_source (bool, optional) – Whether to keep a copy of the uncompressed file, by default False
Returns:	Path of the compressed (.nii.gz) file
Return type:	Path

compressed¶

Compresses the associated .nii file using gzip if it isn’t and returns its path.

Returns:	Compressed .nii.gz file associated with this instance
Return type:	Path

get_b_value() → List[int]¶

Returns the degree of diffusion weighting applied (b-value) for each diffusion direction. This method relies on dcm2niix’s default configuration in which when diffusion-weighted images (DWI) are converted, another file with the same name and a “bval” extension is created alongside.

Hint

For more information, see dcm2niix’s Diffusion Tensor Imaging section of the user guide.

See also

b_value

Returns:	b-value for each diffusion direction.
Return type:	List[int]

get_b_vector() → List[List[float]]¶

Returns the b-vectors representing the diffusion weighting gradient scheme. This method relies on dcm2niix’s default configuration in which when diffusion-weighted images (DWI) are converted, another file with the same name and a “bvec” extension is created alongside.

Hint

For more information, see dcm2niix’s Diffusion Tensor Imaging section of the user guide.

See also

b_vector

Returns:	b-value for each diffusion direction
Return type:	List[List[float]]

get_data() → numpy.ndarray¶

Uses NiBabel to return the underlying pixel data as a NumPy array.

Returns:	Pixel data.
Return type:	np.ndarray

get_effective_spacing() → float¶

Reads the effective echo spacing value extracted by dcm2niix upon conversion.

Returns:	Effective echo spacing
Return type:	float

get_phase_encoding_direction() → float¶

Reads the phase encoding direction value extracted by dcm2niix upon conversion.

Returns:	Phase encoding direction
Return type:	float

get_total_readout_time() → float¶

Reads the total readout time extracted by dcm2niix upon conversion.

Hint

Total readout time is defined as the time from the center of the first echo to the center of the last (in seconds).

Returns:	Total readout time
Return type:	float

is_compressed¶

Whether the associated .nii file is compressed with gzip or not.

Returns:	Associated .nii file gzip compression state
Return type:	bool

is_raw¶: Whether the created instance is the product of a direct conversion from some raw format to NIfTI or of a manipulation of the data.

json_data¶

Reads BIDS sidecar information and caches within a local variable to prevent multiple reads.

See also

read_json()

Returns:	“BIDS sidecar” JSON data
Return type:	dict

objects = <django.db.models.manager.Manager object>¶

path¶: Path of the .nii file within the application’s media directory.

read_json() → dict¶

Returns the JSON data generated alognside .nii files generated using dcm2niix’s “BIDS sidecar” option.

Notes

For more information about dcm2niix and the BIDS sidecar, see dcm2niix’s general usage manual.
For more information about the extracted properties and their usage see Acquiring and Using Field-maps

Returns:	BIDS sidecar information stored in a JSON file, or {} if the file doesn’t exist
Return type:	dict

run_input_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

run_output_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

scan¶

Accessor to the related object on the reverse side of a one-to-one relation.

In the example:

class Restaurant(Model):
    place = OneToOneField(Place, related_name='restaurant')

Place.restaurant is a ReverseOneToOneDescriptor instance.

uncompress(keep_source: bool = False) → pathlib.Path¶

Uncompress the associated .nii using gzip, if it isn’t already uncompressed.

Parameters:	keep_source (bool, optional) – Whether to keep a copy of the compressed file, by default False
Returns:	Path of the uncompressed (.nii) file
Return type:	Path

uncompressed¶

Uncompresses the associated .nii file using gzip if it isn’t and returns its path.

Returns:	Uncompressed .nii file associated with this instance
Return type:	Path

django_mri.models.scan module¶

Definition of the Scan model.

class django_mri.models.scan.Scan(*args, **kwargs)¶

Bases: django_extensions.db.models.TimeStampedModel

A model used to represent an MRI scan independently from the file-format in which it is saved. This model handles any conversions between formats in case they are required, and allows for easy querying of MRI scans based on universal attributes.

added_by¶: Keeps a record of the user that added this scan.

comments¶: Any other comments about this scan.

compile_to_bids(bids_path: pathlib.Path)¶

convert_to_mif() → pathlib.Path¶

Creates a .mif version of this scan using mrconvert.

Returns:	Created file path
Return type:	Path

description¶: Short description of the scan’s acquisition parameters.

dicom¶: If this instance’s origin is a DICOM file, or it was saved as one, this field stores the association with the appropriate :class`django_dicom.models.series.Series` instance.

dicom_to_nifti(destination: pathlib.Path = None, compressed: bool = True, generate_json: bool = True) → django_mri.models.nifti.NIfTI¶

Convert this scan from DICOM to NIfTI using _dcm2niix.

Parameters:	destination (Path, optional) – The desired path for conversion output (the default is None, which will create the file in some default location)
Raises:	`AttributeError` – If no DICOM series is related to this scan
Returns:	A `django_mri.NIfTI` instance referencing the conversion output
Return type:	NIfTI

echo_time¶: The time between the application of the radio-frequency excitation pulse and the peak of the signal induced in the coil (in milliseconds).

get_bids_destination() → pathlib.Path¶

Returns the BIDS-compatible destination of this scan’s associated NIfTI file.

Returns:	BIDS-compatible NIfTI file destination
Return type:	pathlib.Path

get_default_mif_path() → pathlib.Path¶

Returns the default .mif path for this scan.

Returns:	Default .mif path
Return type:	Path

get_default_nifti_destination() → pathlib.Path¶

Returns the default path for a NIfTI version of this scan.

Returns:	Default path for NIfTI file
Return type:	str

get_default_nifti_dir() → pathlib.Path¶

Returns the default location for the creation of a NIfTI version of the scan. Currently only conversion from DICOM is supported.

Returns:	Default location for conversion output
Return type:	str

get_default_nifti_name() → str¶

Returns the default file name for a NIfTI version of this scan.

Returns:	Default file name
Return type:	str

infer_sequence_type() → django_mri.models.sequence_type.SequenceType¶

Tries to infer the sequence type using associated data.

Returns:	The inferred sequence type
Return type:	SequenceType

infer_sequence_type_from_dicom() → django_mri.models.sequence_type.SequenceType¶

Returns the appropriate django_mri.SequenceType instance according to the scan’s “ScanningSequence” and “SequenceVariant” header values.

Returns:	The inferred sequence type
Return type:	SequenceType

institution_name¶: The institution in which this scan was acquired.

inversion_time¶: The time between the 180-degree inversion pulse and the following spin-echo (SE) sequence (in milliseconds).

is_updated_from_dicom¶: Keeps track of whether we’ve updated the instance’s fields from DICOM header data or not.

mif¶

Returns the .mif version of this scan, creating it if it doesn’t exist.

Returns:	.mif file path
Return type:	Path

See also

convert_to_mif()

nifti¶

Returns the associated NIfTI instance if one exists, or tries to create one if it doesn’t.

Returns:	Associated NIfTI instance
Return type:	NIfTI

number¶: The relative number of this scan in the session in which it was acquired.

objects = <django_mri.models.managers.scan.ScanManager object>¶

repetition_time¶: The time between two successive RF pulses (in milliseconds).

run_input_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

save(*args, **kwargs) → None¶: Overrides the model’s save() method to provide custom validation.

Hint

For more information, see Django’s documentation on overriding model methods.

sequence_type¶

Returns the sequence type instance fitting this scan if one exists.

See also

infer_sequence_type()
django_mri.models.sequence_type.SequenceType

Returns:	Inferred sequence type
Return type:	SequenceType

spatial_resolution¶: The spatial resolution of the image in millimeters.

study_groups¶: Individual scans may be associated with multiple Group instances. This is meant to provide flexibility in managing access to data between researchers working on different studies. The Group model is expected to be specified as STUDY_GROUP_MODEL in the project’s settings.

subject¶: Associates this scan with some subject. Subjects are expected to be represented by a model specified as SUBJECT_MODEL in the project’s settings.

suggest_subject(subject) → None¶

time¶: Acquisition datetime.

update_fields_from_dicom() → None¶

Sets instance fields from related DICOM series.

Raises:	`AttributeError` – If not DICOM series is related to this scan

warn_subject_mismatch(subject)¶

Warns the user regarding a mismatch in subject identity.

Parameters:	subject (django.db.models.Model) – Suggested subject identity

django_mri.models.sequence_type module¶

class django_mri.models.sequence_type.SequenceType(*args, **kwargs)¶

Bases: django_extensions.db.models.TitleDescriptionModel, django_extensions.db.models.TimeStampedModel

The purpose of this model is to provide a title and description for: commonly used sequences, as well as to facilitate queries.

Each particular sequence is defined as a unique combination of DICOM’s “ScanningSequence” and “SequenceVariant” attributes. This model is a wrapper for the known combinations.

objects = <django_mri.models.managers.sequence_type.SequenceTypeManager object>¶

sequence_definition_set¶

Accessor to the related objects manager on the reverse side of a many-to-one relation.

In the example:

class Child(Model):
    parent = ForeignKey(Parent, related_name='children')

Parent.children is a ReverseManyToOneDescriptor instance.

Most of the implementation is delegated to a dynamically defined manager class built by create_forward_many_to_many_manager() defined below.

sequence_definitions¶