dicom_parser package¶
Subpackages¶
Submodules¶
dicom_parser.header module¶
Definition of the Header class, which extends the functionality of pydicom.
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class
dicom_parser.header.Header(raw, parser=<class 'dicom_parser.parser.Parser'>, sequence_detector=<class 'dicom_parser.utils.sequence_detector.sequence_detector.SequenceDetector'>)¶ Bases:
objectFacilitates access to DICOM header information from pydicom’s FileDataset.
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detect_sequence() → str¶ Returns the detected imaging sequence using the modality’s sequence identifying header information.
- Returns
Imaging sequence name
- Return type
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get(tag_or_keyword, default=None, parsed: bool = True, missing_ok: bool = True)¶ 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
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get_csa_element_by_keyword(keyword: str)¶ Returns the CSA header for Siemens scans.
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get_element(tag_or_keyword) → pydicom.dataelem.DataElement¶ Returns a pydicom DataElement 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.
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get_element_by_keyword(keyword: str) → pydicom.dataelem.DataElement¶ Returns a pydicom DataElement 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
DataElement
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get_element_by_tag(tag: tuple) → pydicom.dataelem.DataElement¶ Returns a pydicom DataElement 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
DataElement
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get_parsed_value(tag_or_keyword)¶ 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.
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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.
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sequence_identifiers= {'mr': ['ScanningSequence', 'SequenceVariant']}¶
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dicom_parser.parser module¶
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class
dicom_parser.parser.Parser¶ Bases:
object-
CODE_STRINGS_DICT= {'(0008, 0060)': <enum 'Modality'>, '(0010, 0040)': <enum 'Sex'>, '(0018, 0020)': <enum 'ScanningSequence'>, '(0018, 0021)': <enum 'SequenceVariant'>, '(0018, 5100)': <enum 'PatientPosition'>}¶
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N_IN_YEAR= {'D': 365.2422, 'M': 12, 'W': 52.1429, 'Y': 1}¶
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PARSING_METHOD= {<ValueRepresentation.AGE_STRING: 'AS'>: 'parse_age_string', <ValueRepresentation.DATE: 'DA'>: 'parse_date', <ValueRepresentation.TIME: 'TM'>: 'parse_time', <ValueRepresentation.DATE_TIME: 'DT'>: 'parse_datetime', <ValueRepresentation.INTEGER_STRING: 'IS'>: 'parse_integer_string', <ValueRepresentation.DECIMAL_STRING: 'DS'>: 'parse_decimal_string', <ValueRepresentation.UNKNOWN: 'UN'>: 'parse_unknown', <ValueRepresentation.CODE_STRING: 'CS'>: 'parse_code_string'}¶
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SINGLE_VALUE_CODE_STRINGS= ['(0010, 0040)', '(0018, 5100)', '(0008, 0060)']¶
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parse(element: pydicom.dataelem.DataElement)¶ Tries to parse a pydicom DICOM data element using its value-representation (VR) attribute. If no parser method is registered for the VR under the PARSING_METHOD dictionary, will simply return the raw value.
- Parameters
element (DataElement) – DICOM data element as represented by pydicom.
- Returns
Parsed DICOM data element value.
- Return type
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parse_age_string(element: pydicom.dataelem.DataElement) → float¶ Parses Age String (AS) data elements into a float representation of the age in years.
- Parameters
element (DataElement) – DICOM Age String (AS) data element.
- Returns
The age in years.
- Return type
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parse_code_string(element: pydicom.dataelem.DataElement)¶ Parses Code String (CS) data elements to a more readable string or list of strings. This method relies on an Enum representation of the data element’s possible values to be registered in the Parser’s CODE_STRINGS_DICT by tag. If no Enum is registered, will return None.
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parse_date(element: pydicom.dataelem.DataElement) → None.datetime.date¶ Parses Date (DA) data elements to date objects.
- Parameters
element (DataElement) – DICOM Date (DA) data element.
- Returns
Native python date object.
- Return type
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parse_datetime(element: pydicom.dataelem.DataElement) → datetime.datetime¶ Parses Date Time (DT) data elements to datetime objects.
- Parameters
element (DataElement) – DICOM Date Time (DT) data element.
- Returns
Native python datetime object.
- Return type
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parse_decimal_string(element: pydicom.dataelem.DataElement)¶ Parses Decimal String (DS) data elements to floats. In case the Value Multiplicity (VM) is greater than one, returns a list of floats.
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parse_integer_string(element: pydicom.dataelem.DataElement) → int¶ Parses DICOM Integer String (IS) data elements to integers.
- Parameters
element (DataElement) – DICOM Integer String (IS) data element.
- Returns
Data element value.
- Return type
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parse_siemens_gradient_direction(value: bytes) → list¶ Parses a SIEMENS MR image’s B-vector as represented in the private (0019, 100E) DiffusionGradientDirection DICOM tag.
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parse_siemens_slice_timing(value: bytes) → list¶ Parses a SIEMENS MR image’s slice timing as saved in the private (0019, 1029) MosaicRefAcqTimes tag to a list of floats representing slice times in milliseconds.
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parse_time(element: pydicom.dataelem.DataElement) → None.datetime.time¶ Parses Time (TM) data elements to time objects.
- Parameters
element (DataElement) – DICOM Time (TM) data element.
- Returns
Native python time object.
- Return type
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parse_unknown(element: pydicom.dataelem.DataElement)¶ Parses private tags and other Unknown (UN) data elememts.
- Parameters
element (DataElement) – DICOM Unknown (UN) data element.
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