DICOM File Handling

class pumpia.file_handling.dicom_structures.Patient(patient_id: str, name: str)

Represents a patient from a DICOM file.

Parameters:

patient_id (str) – The ID of the patient.
name (str) – The name of the patient.

patient_id

Type:: str

name

Type:: str

studies

Type:: list[Study]

tag

Type:: str

id_string

Type:: str

menu_options

Type:: list[tuple[str, Callable[[], None]]]

add_study(study: Study): Adds a study to the patient.

class pumpia.file_handling.dicom_structures.Study(patient: Patient, study_id: str, study_date: date, study_desc: str)

Represents a DICOM study.

Parameters:

patient (Patient) – The patient associated with the study.
study_id (str) – The ID of the study.
study_date (datetime.date) – The date of the study.
study_desc (str) – The description of the study.

patient

The patient associated with the study.

Type:: Patient

study_id

The ID of the study.

Type:: str

study_date

The date of the study.

Type:: datetime.date

study_description

The description of the study.

Type:: str

series

Type:: list[Series]

tag

Type:: str

id_string

Type:: str

menu_options

Type:: list[tuple[str, Callable[[], None]]]

add_series(series: Series): Adds a series to the study.

class pumpia.file_handling.dicom_structures.Series(study: Study, series_id: str, series_description: str, series_number: int, acquisition_number: int, instance_number: int | None = None, is_stack: bool = False, open_dicom: Dataset | None = None, filepath: Path | None = None)

Represents a DICOM series. Has the same attributes and methods as ImageCollection unless stated below.

Parameters:

study (Study) – The study associated with the series.
series_id (str) – The ID of the series.
series_description (str) – The description of the series.
series_number (int) – The number of the series.
acquisition_number (int) – The acquisition number of the series.
instance_number (int) – The instance number of the series. Required if series is a stack, ignored otherwise.
is_stack (bool, optional) – Whether the series is a stack (default is False).
open_dicom (pydicom.Dataset, optional) – The open DICOM dataset (default is None).
filepath (Path, optional) – The file path of the series (default is None).

study

The study associated with the series.

Type:: Study

series_id

The ID of the series.

Type:: str

series_number

The number of the series.

Type:: int

acquisition_number

The acquisition number of the series.

Type:: int

instance_number

The instance number of the series. Int if series is a stack, None otherwise.

Type:: int

series_description

The description of the series.

Type:: str

is_stack

Whether the series is a stack.

Type:: bool

loaded

Whether the series is loaded.

Type:: bool

dicom_dataset

Type:: pydicom.Dataset | None

instances

Type:: list[Instance]

raw_array

Type:: np.ndarray

add_instance(instance: 'Instance'): Adds an instance to the series.

get_tags(tag: Tag) → list: Gets the values of a dicom tag for all instances in the series.

get_tag(tag: Tag, instance_number: int): Gets the value of a tag for a specific instance in the series.

class pumpia.file_handling.dicom_structures.Instance(series: Series, slice_number: int, filepath: Path | None = None, is_frame: bool = False, dimension_index_values: list | tuple | None = None, open_dicom: Dataset | None = None)

Represents a DICOM instance if file has 1 frame or a frame if file has multiple frames. Has the same attributes and methods as FileImageSet unless stated below.

Parameters:

series (Series) – The series associated with the instance.
slice_number (int) – The slice number of the instance. For a frame this will be the frame number, otherwise this will be the instance number.
filepath (Path, optional) – The file path of the instance (default is None).
is_frame (bool, optional) – Whether the instance is a frame (default is False).
dimension_index_values (list or tuple, optional) – The dimension index values of the instance (default is None).

series

The series associated with the instance.

Type:: Series

slice_number

The slice number of the instance.

Type:: int

is_frame

Whether the instance is a frame.

Type:: bool

dimension_index_values

The dimension index values of the instance.

Type:: tuple | None

loaded

Whether the instance is loaded.

Type:: bool

dicom_dataset

Type:: pydicom.Dataset | None

raw_array

Type:: np.ndarray

get_tag(tag: Tag): Gets the value of a tag for the instance.