Reference¶
Module contents¶
dicom_parser facilitates access to DICOM header information using the subpackages and submodules documented below.
Subpackages¶
Submodules¶
dicom_parser.data_element module¶
Definition of the DataElement
class.
-
class
dicom_parser.data_element.
DataElement
(raw: pydicom.dataelem.DataElement)¶ Bases:
object
A wrapper around pydicom’s
DataElement
class. This is a parent class for the data elements defined indata_elements
.-
PRIVATE_ELEMENT_DESCRIPTION_PATTERN
= '\\[(.*)\\]|Private Creator'¶
-
VALUE_REPRESENTATION
: dicom_parser.utils.value_representation.ValueRepresentation = None¶
-
get_private_element_keyword
() → str¶ Returns the keyword of private data elements if it can be extracted.
- Returns
Private data element keyword
- Return type
-
property
is_private
¶ Checks whether this data element is private or not.
- Returns
Whether this data element is private or not
- Return type
-
property
is_public
¶ Checks whether this data element is public or not.
- Returns
Whether this data element is public or not
- Return type
-
parse_keyword
() → str¶ Returns the keyword for this instance.
- Returns
This instance’s keyword
- Return type
-
parse_value
(value: Any) → Any¶ Default
parse_value()
method that simply decodes the raw value if it’s in bytes. This method is meant to be overridden by subclasses.- Parameters
value (Any) – This instance’s raw value
- Returns
This instance’s parsed value
- Return type
Any
-
parse_values
() → Any¶ Return the parsed value or values of this instance.
- Returns
This instance’s parsed value or values
- Return type
Any
-
to_dict
() → dict¶ Create a dictionary representation of this instance.
- Returns
This instance as a dictionary
- Return type
-
to_series
() → pandas.core.series.Series¶ Create a
Series
representation of this instance.- Returns
This instance as a
Series
- Return type
pd.Series
-
property
value
¶ Caches the parsed value or values of this instance.
- Returns
This instance’s parsed value or values
- Return type
Any
-
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
-
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
- 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_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.
-
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.
-
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.
-
get_raw_element_by_keyword
(keyword: str) → pydicom.dataelem.DataElement¶ Returns a pydicom PydicomDataElement from the header (FileDataset instance) 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 instance) 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.
-
property
keys
¶
-
sequence_identifiers
= {'Magnetic Resonance': ['ScanningSequence', 'SequenceVariant']}¶
-
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
-
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
-
read_raw_data
() → numpy.ndarray¶ Reads the pixel array data as returned by pydicom.
- Returns
Pixel array data
- Return type
np.ndarray
-
property
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).
-
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
-