dicom_parser package

Module contents

Subpackages

Submodules

dicom_parser.header module

Definition of the Header class, which extends the functionality of pydicom.

class dicom_parser.header.Header(raw: Union[pydicom.dataset.FileDataset, str, pathlib.Path], sequence_detector=<class 'dicom_parser.utils.sequence_detector.sequence_detector.SequenceDetector'>)

Bases: object

Facilitates access to DICOM header information from pydicom’s FileDataset.

DATAFRAME_COLUMNS = ('Tag', 'Keyword', 'VR', 'VM', 'Value')
DATAFRAME_INDEX = 'Tag'
property as_dict
property data_elements
detect_sequence()str

Returns the detected imaging sequence using the modality’s sequence identifying header information.

Returns

Imaging sequence name

Return type

str

get(tag_or_keyword, default=None, parsed: bool = True, missing_ok: bool = True, as_json: bool = False) → Any

Returns the value of a pydicom data element, selected by tag (tuple) or keyword (str). Input may also be a list of such identifiers, in which case a dictionary will be returned with the identifiers as keys and header information as values.

Parameters
  • tag_or_keyword (tuple or str, or list) – Tag or keyword representing the requested data element, or a list of such

  • parsed (bool, optional) – Whether to return a parsed or raw value (the default is True, which will return the parsed value)

Returns

The requested data element value (or a dict for multiple values)

Return type

Any

get_data_element(tag_or_keyword) → dicom_parser.data_element.DataElement
get_data_elements(value_representation=None, exclude=None, private: bool = None)list
get_parsed_value(tag_or_keyword) → Any

Returns the parsed value of pydicom data element using the this class’s parser attribute. The data element may be represented by tag or by its pydicom keyword. If none is found will return None.

Parameters

tag_or_keyword (tuple or str) – Tag or keyword representing the requested data element

Returns

Parsed data element value

Return type

Any

get_private_tag(keyword: str)tuple

Returns a vendor-specific private tag corresponding to the provided keyword, if the tag is registered (see the private_tags module). This is required because pydicom does not offer keyword access to private tags.

Parameters

keyword (str) – Private data element keyword

Returns

Private data element tag

Return type

tuple

get_raw_element(tag_or_keyword)pydicom.dataelem.DataElement

Returns a pydicom PydicomDataElement from the associated FileDataset either by tag (passed as a tuple) or a keyword (passed as a string). If none found or the tag or keyword are invalid, returns None.

Parameters

tag_or_keyword (tuple or str) – Tag or keyword representing the requested data element

Returns

The requested data element

Return type

PydicomDataElement

get_raw_element_by_keyword(keyword: str)pydicom.dataelem.DataElement

Returns a pydicom PydicomDataElement from the header (FileDataset isntance) by keyword.

Parameters

keyword (str) – The keyword representing the DICOM data element in pydicom

Returns

The requested data element

Return type

PydicomDataElement

get_raw_element_by_tag(tag: tuple)pydicom.dataelem.DataElement

Returns a pydicom PydicomDataElement from the header (FileDataset isntance) by tag.

Parameters

tag (tuple) – The DICOM tag of the desired data element

Returns

The requested data element

Return type

PydicomDataElement

get_raw_value(tag_or_keyword)

Returns the raw value for the requested data element, as returned by pydicom. If none is found will return None.

Parameters

tag_or_keyword (tuple or str) – Tag or keyword representing the requested data element.

Returns

The raw value of the data element

Return type

type

property keys
sequence_identifiers = {'Magnetic Resonance': ['ScanningSequence', 'SequenceVariant']}
to_dataframe(data_elements: list = None, value_representation=None, exclude=None, private: bool = None) → pandas.core.frame.DataFrame
to_dict(parsed: bool = True)dict

dicom_parser.image module

Definition of the Image class, representing a single pair of Header and data (3D NumPy array).

class dicom_parser.image.Image(raw: Union[pydicom.dataset.FileDataset, str, pathlib.Path])

Bases: object

This class represents a single DICOM image (i.e. .dcm file) and provides unified access to it’s header information and data.

property data

Returns the pixel data array after having applied any required transformations.

Returns

Pixel data array

Return type

np.ndarray

property default_relative_path
fix_data() → numpy.ndarray

Applies any required transformation to the data.

Returns

Pixel array data

Return type

np.ndarray

get_default_relative_path()pathlib.Path
property is_fmri

Returns True for fMRI images according to their header information.

Returns

Whether this image represents fMRI data

Return type

bool

property is_mosaic

Checks whether a 3D volume is encoded as a 2D Mosaic. For more information, see the Mosaic class.

Returns

Whether the image is a mosaic encoded volume

Return type

bool

read_raw_data() → numpy.ndarray

Reads the pixel array data as returned by pydicom.

Returns

Pixel array data

Return type

np.ndarray

dicom_parser.series module

Definition of the Series class.

class dicom_parser.series.Series(path: pathlib.Path)

Bases: object

This class represents a complete collection of Image instances originating from a single directory and ordered by InstanceNumber.

check_path(path)pathlib.Path

Converts to a Path instance if required and checks that it represents an existing directory.

Parameters

path (str or Path) – The provided path.

Returns

A pathlib.Path instance representing an existing directory

Return type

Path

Raises

ValueError – If the provided path is not an existing directory

property data

Caches the stacked 3D array containing the entire series’ data.

Returns

Series 3D data

Return type

np.ndarray

get(tag_or_keyword, default=None, parsed: bool = True, missing_ok: bool = True) → Any

Returns header information from the Image that compose this series. If one distinct value is returned from all the images’ headers, returns that value. Otherwise, returns a list of the values (ordered the same as the images attribute, by instance number).

Parameters

tag_or_keyword (tuple or str, or list) – Tag or keyword representing the requested data element, or a list of such

Returns

The requested data element value for the entire series

Return type

Any

get_dcm_paths() → generator

Returns a generator of .dcm files within the provided directory path.

Returns

DICOM images (.dcm files) generator

Return type

GeneratorType

Raises

FileNotFoundError – No DICOM images found under provided directory

get_images()tuple

Returns a tuple of Image instances ordered by instance number.

Returns

Image instance by instance number

Return type

tuple

get_spatial_resolution()tuple
property spatial_resolution

Returns the spatial resolution of the series.

Returns

Spatial resolution

Return type

tuple