# Copyright 2008-2021 pydicom authors. See LICENSE file for details. """Define the Dataset and FileDataset classes. The Dataset class represents the DICOM Dataset while the FileDataset class adds extra functionality to Dataset when data is read from or written to file. Overview of DICOM object model ------------------------------ Dataset (dict subclass) Contains DataElement instances, each of which has a tag, VR, VM and value. The DataElement value can be: * A single value, such as a number, string, etc. (i.e. VM = 1) * A list of numbers, strings, etc. (i.e. VM > 1) * A Sequence (list subclass), where each item is a Dataset which contains its own DataElements, and so on in a recursive manner. """ import copy import io import json import os import os.path import re from bisect import bisect_left from collections.abc import ( ValuesView, Iterator, Callable, MutableSequence, MutableMapping, Set, ) from contextlib import nullcontext from importlib.util import find_spec as have_package from itertools import takewhile from types import TracebackType from typing import ( TypeAlias, Any, AnyStr, cast, BinaryIO, TypeVar, overload, ) try: import numpy except ImportError: pass import pydicom # for dcmwrite from pydicom import jsonrep, config from pydicom._version import __version_info__ from pydicom.charset import default_encoding, convert_encodings from pydicom.config import logger from pydicom.datadict import ( dictionary_description, dictionary_VR, tag_for_keyword, keyword_for_tag, repeater_has_keyword, get_private_entry, ) from pydicom.dataelem import DataElement, convert_raw_data_element, RawDataElement from pydicom.filebase import ReadableBuffer, WriteableBuffer from pydicom.fileutil import path_from_pathlike, PathType from pydicom.misc import warn_and_log from pydicom.pixels import compress, convert_color_space, decompress, pixel_array from pydicom.pixels.utils import ( reshape_pixel_array, get_image_pixel_ids, set_pixel_data, ) from pydicom.tag import Tag, BaseTag, tag_in_exception, TagType, TAG_PIXREP from pydicom.uid import PYDICOM_IMPLEMENTATION_UID, UID from pydicom.valuerep import VR as VR_, AMBIGUOUS_VR from pydicom.waveforms import numpy_handler as wave_handler # FloatPixelData, DoubleFloatPixelData, PixelData PIXEL_KEYWORDS = {0x7FE00008, 0x7FE00009, 0x7FE00010} class PrivateBlock: """Helper class for a private block in the :class:`Dataset`. See the DICOM Standard, Part 5, :dcm:`Section 7.8.1` - Private Data Element Tags Attributes ---------- group : int The private group where the private block is located as a 32-bit :class:`int`. private_creator : str The private creator string related to the block. dataset : Dataset The parent dataset. block_start : int The start element of the private block as a 32-bit :class:`int`. Note that the 2 low order hex digits of the element are always 0. """ def __init__( self, key: tuple[int, str], dataset: "Dataset", private_creator_element: int ) -> None: """Initializes an object corresponding to a private tag block. Parameters ---------- key : tuple The private (tag group, creator) as ``(int, str)``. The group must be an odd number. dataset : Dataset The parent :class:`Dataset`. private_creator_element : int The element of the private creator tag as a 32-bit :class:`int`. """ self.group = key[0] self.private_creator = key[1] self.dataset = dataset self.block_start = private_creator_element << 8 def get_tag(self, element_offset: int) -> BaseTag: """Return the private tag ID for the given `element_offset`. Parameters ---------- element_offset : int The lower 16 bits (e.g. 2 hex numbers) of the element tag. Returns ------- The tag ID defined by the private block location and the given element offset. Raises ------ ValueError If `element_offset` is too large. """ if element_offset > 0xFF: raise ValueError("Element offset must be less than 256") return Tag(self.group, self.block_start + element_offset) def __contains__(self, element_offset: int) -> bool: """Return ``True`` if the tag with given `element_offset` is in the parent :class:`Dataset`. """ return self.get_tag(element_offset) in self.dataset def __getitem__(self, element_offset: int) -> DataElement: """Return the data element in the parent dataset for the given element offset. Parameters ---------- element_offset : int The lower 16 bits (e.g. 2 hex numbers) of the element tag. Returns ------- The data element of the tag in the parent dataset defined by the private block location and the given element offset. Raises ------ ValueError If `element_offset` is too large. KeyError If no data element exists at that offset. """ return self.dataset.__getitem__(self.get_tag(element_offset)) def __delitem__(self, element_offset: int) -> None: """Delete the tag with the given `element_offset` from the dataset. Parameters ---------- element_offset : int The lower 16 bits (e.g. 2 hex numbers) of the element tag to be deleted. Raises ------ ValueError If `element_offset` is too large. KeyError If no data element exists at that offset. """ del self.dataset[self.get_tag(element_offset)] def add_new(self, element_offset: int, VR: str, value: object) -> None: """Add a private element to the parent :class:`Dataset`. Adds the private tag with the given `VR` and `value` to the parent :class:`Dataset` at the tag ID defined by the private block and the given `element_offset`. Parameters ---------- element_offset : int The lower 16 bits (e.g. 2 hex numbers) of the element tag to be added. VR : str The 2 character DICOM value representation. value The value of the data element. See :meth:`Dataset.add_new()` for a description. """ tag = self.get_tag(element_offset) self.dataset.add_new(tag, VR, value) self.dataset[tag].private_creator = self.private_creator def __deepcopy__(self, memo: Any) -> "PrivateBlock": copied = self.__class__( (self.group, self.private_creator), self.dataset, self.block_start >> 8, ) memo[id(self)] = copied return copied def _dict_equal(a: "Dataset", b: Any, exclude: list[str] | None = None) -> bool: """Common method for Dataset.__eq__ and FileDataset.__eq__ Uses .keys() as needed because Dataset iter return items not keys `exclude` is used in FileDataset__eq__ ds.__dict__ compare, which would also compare the wrapped _dict member (entire dataset) again. """ return ( len(a) == len(b) and all(key in b for key in a.keys()) and all( a[key] == b[key] for key in a.keys() if exclude is None or key not in exclude ) ) _DatasetValue = DataElement | RawDataElement _DatasetType: TypeAlias = "Dataset | MutableMapping[BaseTag, _DatasetValue]" class Dataset: """A DICOM dataset as a mutable mapping of DICOM Data Elements. Examples -------- Add an element to the :class:`Dataset` (for elements in the DICOM dictionary): >>> ds = Dataset() >>> ds.PatientName = "CITIZEN^Joan" >>> ds.add_new(0x00100020, 'LO', '12345') >>> ds[0x0010, 0x0030] = DataElement(0x00100030, 'DA', '20010101') Add a sequence element to the :class:`Dataset` >>> ds.BeamSequence = [Dataset(), Dataset(), Dataset()] >>> ds.BeamSequence[0].Manufacturer = "Linac, co." >>> ds.BeamSequence[1].Manufacturer = "Linac and Sons, co." >>> ds.BeamSequence[2].Manufacturer = "Linac and Daughters, co." Add private elements to the :class:`Dataset` >>> block = ds.private_block(0x0041, 'My Creator', create=True) >>> block.add_new(0x01, 'LO', '12345') Updating and retrieving element values: >>> ds.PatientName = "CITIZEN^Joan" >>> ds.PatientName 'CITIZEN^Joan' >>> ds.PatientName = "CITIZEN^John" >>> ds.PatientName 'CITIZEN^John' Retrieving an element's value from a Sequence: >>> ds.BeamSequence[0].Manufacturer 'Linac, co.' >>> ds.BeamSequence[1].Manufacturer 'Linac and Sons, co.' Accessing the :class:`~pydicom.dataelem.DataElement` items: >>> elem = ds['PatientName'] >>> elem (0010,0010) Patient's Name PN: 'CITIZEN^John' >>> elem = ds[0x00100010] >>> elem (0010,0010) Patient's Name PN: 'CITIZEN^John' >>> elem = ds.data_element('PatientName') >>> elem (0010,0010) Patient's Name PN: 'CITIZEN^John' Accessing a private :class:`~pydicom.dataelem.DataElement` item: >>> block = ds.private_block(0x0041, 'My Creator') >>> elem = block[0x01] >>> elem (0041,1001) Private tag data LO: '12345' >>> elem.value '12345' Alternatively: >>> ds.get_private_item(0x0041, 0x01, 'My Creator').value '12345' Deleting an element from the :class:`Dataset` >>> del ds.PatientID >>> del ds.BeamSequence[1].Manufacturer >>> del ds.BeamSequence[2] Deleting a private element from the :class:`Dataset` >>> block = ds.private_block(0x0041, 'My Creator') >>> if 0x01 in block: ... del block[0x01] Determining if an element is present in the :class:`Dataset` >>> 'PatientName' in ds True >>> 'PatientID' in ds False >>> (0x0010, 0x0030) in ds True >>> 'Manufacturer' in ds.BeamSequence[0] True Iterating through the top level of a :class:`Dataset` only (excluding Sequences): >>> for elem in ds: ... print(elem) (0010,0010) Patient's Name PN: 'CITIZEN^John' Iterating through the entire :class:`Dataset` (including Sequences): >>> for elem in ds.iterall(): ... print(elem) (0010,0010) Patient's Name PN: 'CITIZEN^John' Recursively iterate through a :class:`Dataset` (including Sequences): >>> def recurse(ds): ... for elem in ds: ... if elem.VR == 'SQ': ... [recurse(item) for item in elem.value] ... else: ... # Do something useful with each DataElement Converting the :class:`Dataset` to and from JSON: >>> ds = Dataset() >>> ds.PatientName = "Some^Name" >>> jsonmodel = ds.to_json() >>> ds2 = Dataset() >>> ds2.from_json(jsonmodel) (0010,0010) Patient's Name PN: 'Some^Name' Attributes ---------- default_element_format : str The default formatting for string display. default_sequence_element_format : str The default formatting for string display of sequences. indent_chars : str For string display, the characters used to indent nested Sequences. Default is ``" "``. """ indent_chars = " " def __init__(self, *args: _DatasetType, **kwargs: Any) -> None: """Create a new :class:`Dataset` instance.""" self._parent_encoding: str | list[str] = kwargs.get( "parent_encoding", default_encoding ) self._dict: MutableMapping[BaseTag, _DatasetValue] if not args: self._dict = {} elif isinstance(args[0], Dataset): self._dict = args[0]._dict else: self._dict = args[0] self.is_decompressed = False # the following read_XXX attributes are used internally to store # the properties of the dataset after read from a file # set depending on the endianness of the read dataset self._read_little: bool | None = None # set depending on the VR handling of the read dataset self._read_implicit: bool | None = None # The dataset's original character set encoding self._read_charset: str | MutableSequence[str] = "" # TODO: v4.0 # Remove is_little_endian and is_implicit_VR if not config._use_future: self._is_little_endian: bool | None = None self._is_implicit_VR: bool | None = None # True if the dataset is a sequence item with undefined length self.is_undefined_length_sequence_item = False # known private creator blocks self._private_blocks: dict[tuple[int, str], PrivateBlock] = {} self._pixel_array: numpy.ndarray | None = None self._pixel_array_opts: dict[str, Any] = {"use_pdh": False} self._pixel_id: dict[str, int] = {} self.file_meta: FileMetaDataset # Used after reading an implicit dataset to help determine the VR of # ambiguous US or SS elements that depend on the value of (0028,0103) # *Pixel Representation* # It gets set by __getitem__() and __setitem()__ and is used by the # ambiguous VR correction function self._pixel_rep: int def __enter__(self) -> "Dataset": """Method invoked on entry to a with statement.""" return self def __exit__( self, exc_type: type[BaseException] | None, exc_val: BaseException | None, exc_tb: TracebackType | None, ) -> bool | None: """Method invoked on exit from a with statement.""" # Returning anything other than True will re-raise any exceptions return None def add(self, data_element: DataElement) -> None: """Add an element to the :class:`Dataset`. Equivalent to ``ds[data_element.tag] = data_element`` Parameters ---------- data_element : dataelem.DataElement The :class:`~pydicom.dataelem.DataElement` to add. """ self[data_element.tag] = data_element def add_new(self, tag: TagType, VR: str, value: Any) -> None: """Create a new element and add it to the :class:`Dataset`. Parameters ---------- tag The DICOM (group, element) tag in any form accepted by :func:`~pydicom.tag.Tag` such as ``[0x0010, 0x0010]``, ``(0x10, 0x10)``, ``0x00100010``, etc. VR : str The 2 character DICOM value representation (see DICOM Standard, Part 5, :dcm:`Section 6.2`). value The value of the data element. One of the following: * a single string or number * a :class:`list` or :class:`tuple` with all strings or all numbers * a multi-value string with backslash separator * for a sequence element, an empty :class:`list` or ``list`` of :class:`Dataset` """ self.add(DataElement(tag, VR, value)) def add_new_private( self, private_creator: str, group: int, element_offset: int, value: Any, vr: str | None = None, ) -> None: """Create a new private element and add it to the :class:`Dataset`. Parameters ---------- private_creator : str The private creator string related to the new tag. group : int The group ID (0x0009 - 0xFFFF) for the private tag. Must be an odd number. element_offset : int The tag offset, e.g. the lower byte of the tag element of the private tag (0x00 - 0xFF). The higher byte is defined by the location of the private creator tag. value : Any The value of the data element. One of the following: * a single string or number * a :class:`list` or :class:`tuple` with all strings or all numbers * a multi-value string with backslash separator * for a sequence element, an empty :class:`list` or ``list`` of :class:`Dataset` vr : str | None The two-letter DICOM value representation, or ``None``. If set to ``None``, it is taken from the private tag dictionary. Raises ------ ValueError If `group` doesn't belong to a private tag or `private_creator` is empty. KeyError If `vr` is ``None`` and the tag is not found in the private tag dictionary. """ block = self.private_block(group, private_creator, create=True) if vr is None: vr = get_private_entry((group, element_offset), private_creator)[0] block.add_new(element_offset, vr, value) def __array__(self) -> "numpy.ndarray": """Support accessing the dataset from a numpy array.""" return numpy.asarray(self._dict) def data_element(self, name: str) -> DataElement | None: """Return the element corresponding to the element keyword `name`. Parameters ---------- name : str A DICOM element keyword. Returns ------- dataelem.DataElement or None For the given DICOM element `keyword`, return the corresponding :class:`~pydicom.dataelem.DataElement` if present, ``None`` otherwise. """ tag = tag_for_keyword(name) # Test against None as (0000,0000) is a possible tag if tag is not None: return self[tag] return None def __contains__(self, name: TagType) -> bool: """Simulate dict.__contains__() to handle DICOM keywords. Examples -------- >>> ds = Dataset() >>> ds.SliceLocation = '2' >>> 'SliceLocation' in ds True Parameters ---------- name : str or int or 2-tuple The element keyword or tag to search for. Returns ------- bool ``True`` if the corresponding element is in the :class:`Dataset`, ``False`` otherwise. """ try: return Tag(name) in self._dict except Exception as exc: msg = ( f"Invalid value '{name}' used with the 'in' operator: must be " "an element tag as a 2-tuple or int, or an element keyword" ) if isinstance(exc, OverflowError): msg = ( "Invalid element tag value used with the 'in' operator: " "tags have a maximum value of (0xFFFF, 0xFFFF)" ) if config.INVALID_KEY_BEHAVIOR == "WARN": warn_and_log(msg) elif config.INVALID_KEY_BEHAVIOR == "RAISE": raise ValueError(msg) from exc return False def decode(self) -> None: """Apply character set decoding to the elements in the :class:`Dataset`. See DICOM Standard, Part 5, :dcm:`Section 6.1.1`. """ # Find specific character set. 'ISO_IR 6' is default # May be multi-valued, but let pydicom.charset handle all logic on that dicom_character_set = self._character_set # Shortcut to the decode function in pydicom.charset decode_data_element = pydicom.charset.decode_element # Callback for walk(), to decode the chr strings if necessary # This simply calls the pydicom.charset.decode_element function def decode_callback(ds: "Dataset", data_element: DataElement) -> None: """Callback to decode `data_element`.""" if data_element.VR == VR_.SQ: for dset in data_element.value: dset._parent_encoding = dicom_character_set dset.decode() else: decode_data_element(data_element, dicom_character_set) self.walk(decode_callback, recursive=False) def copy(self) -> "Dataset": """Return a shallow copy of the dataset.""" return copy.copy(self) def __delattr__(self, name: str) -> None: """Intercept requests to delete an attribute by `name`. Examples -------- >>> ds = Dataset() >>> ds.PatientName = 'foo' >>> ds.some_attribute = True If `name` is a DICOM keyword - delete the corresponding :class:`~pydicom.dataelem.DataElement` >>> del ds.PatientName >>> 'PatientName' in ds False If `name` is another attribute - delete it >>> del ds.some_attribute >>> hasattr(ds, 'some_attribute') False Parameters ---------- name : str The keyword for the DICOM element or the class attribute to delete. """ # First check if a valid DICOM keyword and if we have that data element tag = cast(BaseTag, tag_for_keyword(name)) if tag is not None and tag in self._dict: del self._dict[tag] # Deleting pixel data resets the stored array if tag in PIXEL_KEYWORDS: self._pixel_array = None self._pixel_id = {} # If not a DICOM name in this dataset, check for regular instance name # can't do delete directly, that will call __delattr__ again elif name in self.__dict__: del self.__dict__[name] # Not found, raise an error in same style as python does else: raise AttributeError(name) def __delitem__(self, key: "slice | BaseTag | TagType") -> None: """Intercept requests to delete an attribute by key. Examples -------- Indexing using :class:`~pydicom.dataelem.DataElement` tag >>> ds = Dataset() >>> ds.CommandGroupLength = 100 >>> ds.PatientName = 'CITIZEN^Jan' >>> del ds[0x00000000] >>> ds (0010,0010) Patient's Name PN: 'CITIZEN^Jan' Slicing using :class:`~pydicom.dataelem.DataElement` tag >>> ds = Dataset() >>> ds.CommandGroupLength = 100 >>> ds.SOPInstanceUID = '1.2.3' >>> ds.PatientName = 'CITIZEN^Jan' >>> del ds[:0x00100000] >>> ds (0010,0010) Patient's Name PN: 'CITIZEN^Jan' Parameters ---------- key The key for the attribute to be deleted. If a ``slice`` is used then the tags matching the slice conditions will be deleted. """ # If passed a slice, delete the corresponding DataElements if isinstance(key, slice): for tag in self._slice_dataset(key.start, key.stop, key.step): del self._dict[tag] # invalidate private blocks in case a private creator is # deleted - will be re-created on next access if self._private_blocks and BaseTag(tag).is_private_creator: self._private_blocks = {} if tag in PIXEL_KEYWORDS: self._pixel_array = None self._pixel_id = {} elif isinstance(key, BaseTag): del self._dict[key] if self._private_blocks and key.is_private_creator: self._private_blocks = {} # Deleting pixel data resets the stored array if key in PIXEL_KEYWORDS: self._pixel_array = None self._pixel_id = {} else: # If not a standard tag, than convert to Tag and try again tag = Tag(key) del self._dict[tag] if self._private_blocks and tag.is_private_creator: self._private_blocks = {} # Deleting pixel data resets the stored array if tag in PIXEL_KEYWORDS: self._pixel_array = None self._pixel_id = {} def __dir__(self) -> list[str]: """Return a list of methods, properties, attributes and element keywords available in the :class:`Dataset`. List of attributes is used, for example, in auto-completion in editors or command-line environments. """ names = set(super().__dir__()) keywords = set(self.dir()) return sorted(names | keywords) def dir(self, *filters: str) -> list[str]: """Return an alphabetical list of element keywords in the :class:`Dataset`. Intended mainly for use in interactive Python sessions. Only lists the element keywords in the current level of the :class:`Dataset` (i.e. the contents of any sequence elements are ignored). Parameters ---------- filters : str Zero or more string arguments to the function. Used for case-insensitive match to any part of the DICOM keyword. Returns ------- list of str The matching element keywords in the dataset. If no filters are used then all element keywords are returned. """ allnames = [keyword_for_tag(tag) for tag in self._dict.keys()] # remove blanks - tags without valid names (e.g. private tags) allnames = [x for x in allnames if x] # Store found names in a dict, so duplicate names appear only once matches = {} for filter_ in filters: filter_ = filter_.lower() match = [x for x in allnames if x.lower().find(filter_) != -1] matches.update({x: 1 for x in match}) if filters: return sorted(matches.keys()) return sorted(allnames) def __eq__(self, other: Any) -> bool: """Compare `self` and `other` for equality. Returns ------- bool The result if `self` and `other` are the same class NotImplemented If `other` is not the same class as `self` then returning :class:`NotImplemented` delegates the result to ``superclass.__eq__(subclass)``. """ # When comparing against self this will be faster if other is self: return True if isinstance(other, self.__class__): return _dict_equal(self, other) return NotImplemented @overload def get(self, key: str, default: Any | None = None) -> Any: pass # pragma: no cover @overload def get( self, key: int | tuple[int, int] | BaseTag, default: Any | None = None ) -> DataElement: pass # pragma: no cover def get( self, key: str | int | tuple[int, int] | BaseTag, default: Any | None = None ) -> Any | DataElement: """Simulate ``dict.get()`` to handle element tags and keywords. Parameters ---------- key : str or int or Tuple[int, int] or BaseTag The element keyword or tag or the class attribute name to get. default : obj or None, optional If the element or class attribute is not present, return `default` (default ``None``). Returns ------- value If `key` is the keyword for an element in the :class:`Dataset` then return the element's value. dataelem.DataElement If `key` is a tag for a element in the :class:`Dataset` then return the :class:`~pydicom.dataelem.DataElement` instance. value If `key` is a class attribute then return its value. """ if isinstance(key, str): try: return getattr(self, key) except AttributeError: return default # is not a string, try to make it into a tag and then hand it # off to the underlying dict try: key = Tag(key) except Exception as exc: raise TypeError("Dataset.get key must be a string or tag") from exc try: return self.__getitem__(key) except KeyError: return default def items(self) -> Set[tuple[BaseTag, _DatasetValue]]: """Return the :class:`Dataset` items to simulate :meth:`dict.items`. Returns ------- dict_items The top-level (:class:`~pydicom.tag.BaseTag`, :class:`~pydicom.dataelem.DataElement`) items for the :class:`Dataset`. """ return self._dict.items() def keys(self) -> Set[BaseTag]: """Return the :class:`Dataset` keys to simulate :meth:`dict.keys`. Returns ------- dict_keys The :class:`~pydicom.tag.BaseTag` of all the elements in the :class:`Dataset`. """ return self._dict.keys() def values(self) -> ValuesView[_DatasetValue]: """Return the :class:`Dataset` values to simulate :meth:`dict.values`. Returns ------- dict_keys The :class:`DataElements` that make up the values of the :class:`Dataset`. """ return self._dict.values() def __getattr__(self, name: str) -> Any: """Intercept requests for :class:`Dataset` attribute names. If `name` matches a DICOM keyword, return the value for the element with the corresponding tag. Parameters ---------- name : str An element keyword or a class attribute name. Returns ------- value If `name` matches a DICOM keyword, returns the corresponding element's value. Otherwise returns the class attribute's value (if present). """ tag = tag_for_keyword(name) if tag is not None: # None means `name` isn't a DICOM element keyword tag = Tag(tag) if tag in self._dict: return self[tag].value # no tag or tag not contained in the dataset if name == "_dict": # special handling for contained dict, needed for pickle return {} # Try the base class attribute getter (fix for issue 332) return object.__getattribute__(self, name) @property def _character_set(self) -> str | list[str]: """The character set used to encode text values.""" char_set = self.get(BaseTag(0x00080005), None) if not char_set: return self._parent_encoding return convert_encodings(char_set.value) @property def original_character_set(self) -> str | MutableSequence[str]: """Return the original character set encoding for a dataset decoded from a file or buffer. Returns ------- str | MutableSequence[str] The original character set encoding of the dataset as given by the (0008,0005) *Specific Character Set*, or `iso8859 `_ if the dataset has been created from scratch. """ return self._read_charset @property def read_encoding(self) -> str | MutableSequence[str]: """Return the original character set encoding for a decoded dataset. .. deprecated:: 3.0 ``read_encoding`` will be removed in v4.0, use :attr:`~pydicom.dataset.Dataset.original_character_set` instead. """ name = type(self).__name__ if config._use_future: raise AttributeError(f"'{name}' object has no attribute 'read_encoding'") warn_and_log( ( f"'{name}.read_encoding' will be removed in v4.0, use " f"'{name}.original_character_set' instead" ), DeprecationWarning, ) return self.original_character_set @read_encoding.setter def read_encoding(self, value: str | MutableSequence[str]) -> None: name = type(self).__name__ if config._use_future: raise AttributeError(f"'{name}' object has no attribute 'read_encoding'") warn_and_log( ( f"'{name}.read_encoding' will be removed in v4.0, use " f"'{name}.original_character_set' instead" ), DeprecationWarning, ) self._read_charset = value @overload def __getitem__(self, key: slice) -> "Dataset": pass # pragma: no cover @overload def __getitem__(self, key: TagType) -> DataElement: pass # pragma: no cover def __getitem__(self, key: "slice | TagType") -> "Dataset | DataElement": """Operator for ``Dataset[key]`` request. Any deferred data elements will be read in and an attempt will be made to correct any elements with ambiguous VRs. Examples -------- Indexing using :class:`~pydicom.dataelem.DataElement` tag >>> ds = Dataset() >>> ds.SOPInstanceUID = '1.2.3' >>> ds.PatientName = 'CITIZEN^Jan' >>> ds.PatientID = '12345' >>> ds[0x00100010].value 'CITIZEN^Jan' Slicing using element tags; all group ``0x0010`` elements in the dataset >>> ds[0x00100000:0x00110000] (0010,0010) Patient's Name PN: 'CITIZEN^Jan' (0010,0020) Patient ID LO: '12345' All group ``0x0002`` elements in the dataset >>> ds[(0x0002, 0x0000):(0x0003, 0x0000)] Parameters ---------- key The DICOM (group, element) tag in any form accepted by :func:`~pydicom.tag.Tag` such as ``[0x0010, 0x0010]``, ``(0x10, 0x10)``, ``0x00100010``, etc. May also be a :class:`slice` made up of DICOM tags. Returns ------- dataelem.DataElement or Dataset If a single DICOM element tag is used then returns the corresponding :class:`~pydicom.dataelem.DataElement`. If a :class:`slice` is used then returns a :class:`Dataset` object containing the corresponding :class:`DataElements`. """ # If passed a slice, return a Dataset containing the corresponding # DataElements if isinstance(key, slice): return self._dataset_slice(key) if isinstance(key, BaseTag): tag = key else: try: tag = Tag(key) except Exception as exc: raise KeyError(f"'{key}'") from exc elem = self._dict[tag] if isinstance(elem, RawDataElement): # If a deferred read, then go get the value now if elem.value is None and elem.length != 0: from pydicom.filereader import read_deferred_data_element src = self.filename or self.buffer if ( self.filename and self.buffer and not getattr(self.buffer, "closed", False) ): src = self.buffer elem = read_deferred_data_element( self.fileobj_type, src, self.timestamp, elem ) if tag != BaseTag(0x00080005): character_set = self.original_character_set or self._character_set else: character_set = default_encoding # Not converted from raw form read from file yet; do so now self[tag] = convert_raw_data_element(elem, encoding=character_set, ds=self) # On initial read of the dataset, propagate the pixel representation # (if any) to child datasets in any sequences. # This is used as part of the ambiguous VR correction for US or SS if self[tag].VR == VR_.SQ: self._set_pixel_representation(self[tag]) # If the Element has an ambiguous VR, try to correct it if self[tag].VR in AMBIGUOUS_VR: from pydicom.filewriter import correct_ambiguous_vr_element self[tag] = correct_ambiguous_vr_element(self[tag], self, elem[6]) return cast(DataElement, self._dict.get(tag)) def private_block( self, group: int, private_creator: str, create: bool = False ) -> PrivateBlock: """Return the block for the given tag `group` and `private_creator`. If `create` is ``True`` and the `private_creator` does not exist, the private creator tag is added. Notes ----- We ignore the unrealistic case that no free block is available. Parameters ---------- group : int The group of the private tag to be found as a 32-bit :class:`int`. Must be an odd number (e.g. a private group). private_creator : str The private creator string associated with the tag. create : bool, optional If ``True`` and `private_creator` does not exist, a new private creator tag is added at the next free block. If ``False`` (the default) and `private_creator` does not exist, :class:`KeyError` is raised instead. Returns ------- PrivateBlock The existing or newly created private block. Raises ------ ValueError If `group` doesn't belong to a private tag or `private_creator` is empty. KeyError If the private creator tag is not found in the given group and the `create` parameter is ``False``. """ def new_block(element: int) -> PrivateBlock: block = PrivateBlock(key, self, element) self._private_blocks[key] = block return block key = (group, private_creator) if key in self._private_blocks: return self._private_blocks[key] if not private_creator: raise ValueError("Private creator must have a value") if group % 2 == 0: raise ValueError("Tag must be private if private creator is given") # find block with matching private creator block = self[(group, 0x10):(group, 0x100)] # type: ignore[misc] data_el = next((elem for elem in block if elem.value == private_creator), None) if data_el is not None: return new_block(data_el.tag.element) if not create: # not found and shall not be created - raise raise KeyError(f"Private creator '{private_creator}' not found") # private creator not existing - find first unused private block # and add the private creator first_free_el = next( el for el in range(0x10, 0x100) if Tag(group, el) not in self._dict ) self.add_new(Tag(group, first_free_el), "LO", private_creator) return new_block(first_free_el) def private_creators(self, group: int) -> list[str]: """Return a list of private creator names in the given group. Examples -------- This can be used to check if a given private creator exists in the group of the dataset: >>> ds = Dataset() >>> if 'My Creator' in ds.private_creators(0x0041): ... block = ds.private_block(0x0041, 'My Creator') Parameters ---------- group : int The private group as a 32-bit :class:`int`. Must be an odd number. Returns ------- list of str All private creator names for private blocks in the group. Raises ------ ValueError If `group` is not a private group. """ if group % 2 == 0: raise ValueError("Group must be an odd number") block = self[(group, 0x10):(group, 0x100)] # type: ignore[misc] return [x.value for x in block] def get_private_item( self, group: int, element_offset: int, private_creator: str ) -> DataElement: """Return the data element for the given private tag `group`. This is analogous to ``Dataset.__getitem__()``, but only for private tags. This allows to find the private tag for the correct private creator without the need to add the tag to the private dictionary first. Parameters ---------- group : int The private tag group where the item is located as a 32-bit int. element_offset : int The lower 16 bits (e.g. 2 hex numbers) of the element tag. private_creator : str The private creator for the tag. Must match the private creator for the tag to be returned. Returns ------- dataelem.DataElement The corresponding element. Raises ------ ValueError If `group` is not part of a private tag or `private_creator` is empty. KeyError If the private creator tag is not found in the given group. If the private tag is not found. """ block = self.private_block(group, private_creator) return self.__getitem__(block.get_tag(element_offset)) @overload def get_item(self, key: slice, *, keep_deferred: bool = ...) -> "Dataset": pass # pragma: no cover @overload def get_item(self, key: TagType, *, keep_deferred: bool = ...) -> DataElement: pass # pragma: no cover def get_item( self, key: "slice | TagType", *, keep_deferred: bool = False, ) -> "Dataset | DataElement | RawDataElement | None": """Return the raw data element if possible. It will be raw if the user has never accessed the value, or set their own value. Note if the data element is a deferred-read element, then it is read and converted before being returned. .. versionchanged: 3.0 Added the `keep_deferred` keyword argument. Parameters ---------- key The DICOM (group, element) tag in any form accepted by :func:`~pydicom.tag.Tag` such as ``[0x0010, 0x0010]``, ``(0x10, 0x10)``, ``0x00100010``, etc. May also be a :class:`slice` made up of DICOM tags. keep_deferred : bool, optional If ``True`` then when returning :class:`~pydicom.dataelem.RawDataElement` do not perform the deferred read of the element's value (accessing the value will return ``None`` instead). Default ``False``. Returns ------- dataelem.DataElement | dataelem.RawDataElement The corresponding element. """ if isinstance(key, slice): return self._dataset_slice(key) elem = self._dict.get(Tag(key)) # If a deferred read, return using __getitem__ to read and convert it if ( isinstance(elem, RawDataElement) and not keep_deferred and elem.value is None ): return self[key] return elem def _dataset_slice(self, slce: slice) -> "Dataset": """Return a slice that has the same properties as the original dataset. That includes properties related to endianness and VR handling, and the specific character set. No element conversion is done, e.g. elements of type ``RawDataElement`` are kept. """ tags = self._slice_dataset(slce.start, slce.stop, slce.step) ds = Dataset({tag: self.get_item(tag) for tag in tags}) is_implicit, is_little = self.original_encoding ds.set_original_encoding(is_implicit, is_little, self.original_character_set) if not config._use_future: ds._is_little_endian = self.is_little_endian ds._is_implicit_VR = self.is_implicit_VR return ds @property def is_implicit_VR(self) -> bool | None: """Get/set the VR method used when encoding the dataset. .. deprecated:: 3.0 ``is_implicit_VR`` will be removed in v4.0, set the *Transfer Syntax UID* or use the `implicit_vr` argument with :meth:`~pydicom.dataset.Dataset.save_as` or :func:`~pydicom.filewriter.dcmwrite` instead. Returns ------- bool | None If the dataset has been created from scratch then returns ``None``, otherwise returns the VR encoding method used by the decoded dataset. """ if config._use_future: raise AttributeError( f"'{type(self).__name__}' object has no attribute 'is_implicit_VR'" ) return self._is_implicit_VR @is_implicit_VR.setter def is_implicit_VR(self, value: bool | None) -> None: name = type(self).__name__ if config._use_future: raise AttributeError(f"'{name}' object has no attribute 'is_implicit_VR'") warn_and_log( ( f"'{name}.is_implicit_VR' will be removed in v4.0, set the " "Transfer Syntax UID or use the 'implicit_vr' argument with " f"{name}.save_as() or dcmwrite() instead" ), DeprecationWarning, ) self._is_implicit_VR = value @property def is_little_endian(self) -> bool | None: """Get/set the endianness used when encoding the dataset. .. deprecated:: 3.0 ``is_little_endian`` will be removed in v4.0, set the *Transfer Syntax UID* or use the `little_endian` argument with :meth:`~pydicom.dataset.Dataset.save_as` or :func:`~pydicom.filewriter.dcmwrite` instead. Returns ------- bool | None If the dataset has been created from scratch then returns ``None``, otherwise returns the endianness of the encoding used by the decoded dataset. """ if config._use_future: raise AttributeError( f"'{type(self).__name__}' object has no attribute 'is_little_endian'" ) return self._is_little_endian @is_little_endian.setter def is_little_endian(self, value: bool | None) -> None: name = type(self).__name__ if config._use_future: raise AttributeError(f"'{name}' object has no attribute 'is_little_endian'") warn_and_log( ( f"'{name}.is_little_endian' will be removed in v4.0, set the " "Transfer Syntax UID or use the 'little_endian' argument with " f"{name}.save_as() or dcmwrite() instead" ), DeprecationWarning, ) self._is_little_endian = value @property def is_original_encoding(self) -> bool: """Return ``True`` if the encoding to be used for writing is set and is the same as that used to originally encode the :class:`Dataset`. This includes properties related to endianness, VR handling and the (0008,0005) *Specific Character Set*. """ if config._use_future: return self.original_character_set == self._character_set current_encoding = (self.is_implicit_VR, self.is_little_endian) return ( None not in current_encoding and self.original_encoding == current_encoding and self.original_character_set == self._character_set ) @property def original_encoding(self) -> tuple[bool, bool] | tuple[None, None]: """Return the original encoding used for a dataset decoded from a file or buffer. Returns ------- tuple[bool, bool] | tuple[None, None] For a dataset decoded from a file or buffer this is whether the encoding used implicit/explicit VR and little/big endian as ``(encoded as implicit VR, encoded as little endian)``. Returns ``(None, None)`` for a dataset created from scratch. """ return cast( tuple[bool, bool] | tuple[None, None], (self._read_implicit, self._read_little), ) def set_original_encoding( self, is_implicit_vr: bool | None, is_little_endian: bool | None, character_encoding: str | MutableSequence[str] | None = None, ) -> None: """Set the values for the original dataset encoding. Can be used for a :class:`Dataset` with raw data elements to enable optimized writing (e.g. without decoding the data elements). .. versionchanged:: 3.0 `character_encoding` is now optional Parameters ---------- is_implicit_vr : bool | None The the original VR encoding of the dataset, ``True`` for implicit VR, ``False`` for explicit VR or ``None`` to reset. is_little_endian : bool | None Set the original endianness of the dataset, ``True`` for little endian, ``False`` for big or ``None`` to reset. character_encoding : str | MutableSequence[str], optional Set the original character set encoding of the dataset. If ``None`` then no changes will be made to the original character set encoding. """ self._read_implicit = is_implicit_vr self._read_little = is_little_endian if character_encoding is not None: self._read_charset = character_encoding def group_dataset(self, group: int) -> "Dataset": """Return a :class:`Dataset` containing only elements of a certain group. Parameters ---------- group : int The group part of a DICOM (group, element) tag. Returns ------- Dataset A :class:`Dataset` containing elements of the group specified. """ return self[(group, 0x0000) : (group + 1, 0x0000)] # type: ignore[misc] def __iter__(self) -> Iterator[DataElement]: """Iterate through the top-level of the Dataset, yielding DataElements. Examples -------- >>> ds = Dataset() >>> for elem in ds: ... print(elem) The :class:`DataElements` are returned in increasing tag value order. Sequence items are returned as a single :class:`~pydicom.dataelem.DataElement`, so it is up to the calling code to recurse into the Sequence items if desired. Yields ------ dataelem.DataElement The :class:`Dataset`'s :class:`DataElements`, sorted by increasing tag order. """ # Note this is different than the underlying dict class, # which returns the key of the key:value mapping. # Here the value is returned (but data_element.tag has the key) taglist = sorted(self._dict.keys()) for tag in taglist: yield self[tag] def elements(self) -> Iterator[DataElement | RawDataElement]: """Yield the top-level elements of the :class:`Dataset`. Examples -------- >>> ds = Dataset() >>> for elem in ds.elements(): ... print(elem) The elements are returned in the same way as in ``Dataset.__getitem__()``. Yields ------ dataelem.DataElement or dataelem.RawDataElement The unconverted elements sorted by increasing tag order. """ taglist = sorted(self._dict.keys()) for tag in taglist: yield self.get_item(tag) def __len__(self) -> int: """Return the number of elements in the top level of the dataset.""" return len(self._dict) def __ne__(self, other: Any) -> bool: """Compare `self` and `other` for inequality.""" return not self == other def clear(self) -> None: """Delete all the elements from the :class:`Dataset`.""" self._dict.clear() def pop(self, key: "BaseTag | TagType", *args: Any) -> _DatasetValue: """Emulate :meth:`dict.pop` with support for tags and keywords. Removes the element for `key` if it exists and returns it, otherwise returns a default value if given or raises :class:`KeyError`. Parameters ---------- key : int or str or 2-tuple * If :class:`tuple` - the group and element number of the DICOM tag * If :class:`int` - the combined group/element number * If :class:`str` - the DICOM keyword of the tag *args : zero or one argument Defines the behavior if no tag exists for `key`: if given, it defines the return value, if not given, :class:`KeyError` is raised Returns ------- RawDataElement or DataElement The element for `key` if it exists, or the default value if given. Raises ------ KeyError If the `key` is not a valid tag or keyword. If the tag does not exist and no default is given. """ try: key = Tag(key) except Exception: pass return self._dict.pop(cast(BaseTag, key), *args) def popitem(self) -> tuple[BaseTag, _DatasetValue]: """Emulate :meth:`dict.popitem`. Returns ------- tuple of (BaseTag, DataElement) """ return self._dict.popitem() def setdefault(self, key: TagType, default: Any | None = None) -> DataElement: """Emulate :meth:`dict.setdefault` with support for tags and keywords. Examples -------- >>> ds = Dataset() >>> elem = ds.setdefault((0x0010, 0x0010), "Test") >>> elem (0010,0010) Patient's Name PN: 'Test' >>> elem.value 'Test' >>> elem = ds.setdefault('PatientSex', ... DataElement(0x00100040, 'CS', 'F')) >>> elem.value 'F' Parameters ---------- key : int, str or 2-tuple of int * If :class:`tuple` - the group and element number of the DICOM tag * If :class:`int` - the combined group/element number * If :class:`str` - the DICOM keyword of the tag default : pydicom.dataelem.DataElement or object, optional The :class:`~pydicom.dataelem.DataElement` to use with `key`, or the value of the :class:`~pydicom.dataelem.DataElement` to use with `key` (default ``None``). Returns ------- pydicom.dataelem.DataElement or object The :class:`~pydicom.dataelem.DataElement` for `key`. Raises ------ ValueError If `key` is not convertible to a valid tag or a known element keyword. KeyError If :attr:`~pydicom.config.settings.reading_validation_mode` is ``RAISE`` and `key` is an unknown non-private tag. """ tag = Tag(key) if tag in self: return self[tag] vr: str | VR_ if not isinstance(default, DataElement): if tag.is_private: vr = VR_.UN else: try: vr = dictionary_VR(tag) except KeyError: if config.settings.writing_validation_mode == config.RAISE: raise KeyError(f"Unknown DICOM tag {tag}") vr = VR_.UN warn_and_log(f"Unknown DICOM tag {tag} - setting VR to 'UN'") default = DataElement(tag, vr, default) self[key] = default return default def convert_pixel_data(self, handler_name: str = "") -> None: """Convert pixel data to a :class:`numpy.ndarray` internally. .. deprecated:: 3.0 This method will be removed in v4.0, use :meth:`~pydicom.dataset.Dataset.pixel_array_options` instead. Parameters ---------- handler_name : str, optional The name of the pixel handler or decoding plugin to use to decode the dataset's pixel data. Support values are: * If using the :mod:`~pydicom.pixel_data_handlers` backend: ``'gdcm'``, ``'pillow'``, ``'jpeg_ls'``, ``'rle'``, ``'numpy'`` and ``'pylibjpeg'``. * If using the :mod:`~pydicom.pixels` backend see the :doc:`documentation for the decoder` corresponding to the dataset's *Transfer Syntax UID*. If not used (the default) then all available handlers or plugins will be tried and the data from first successful one will be used. Returns ------- None Converted pixel data is stored internally in the dataset, it can be accessed with the :attr:`~pydicom.dataset.Dataset.pixel_array` property. Raises ------ ValueError If `handler_name` is not a valid handler name. NotImplementedError If the given handler or any handler, if none given, is unable to decompress pixel data with the current transfer syntax RuntimeError If the given handler, or the handler that has been selected if none given, is not available. Notes ----- If the pixel data is in a compressed image format, the data is decompressed and any related data elements are changed accordingly. """ # TODO: Remove in v4.0 if config._use_future: raise AttributeError( f"'{type(self).__name__}' object has no attribute 'convert_pixel_data'" ) # Check if already have converted to a NumPy array # Also check if pixel data has changed. If so, get new NumPy array already_have = True if not hasattr(self, "_pixel_array"): already_have = False elif self._pixel_array is None: already_have = False # Checking `_pixel_id` may sometimes give a false result if the pixel # data memory has been freed (such as with ds.PixelData = None) # prior to setting a new value; Python may reuse that freed memory # for the new value and therefore give the same `id()` value if self._pixel_id != get_image_pixel_ids(self): already_have = False if already_have: return opts = self._pixel_array_opts.copy() name = handler_name.lower() if handler_name else opts.get("decoding_plugin", "") if not opts["use_pdh"]: # Use 'pydicom.pixels' backend opts["decoding_plugin"] = name self._pixel_array = pixel_array(self, **opts) self._pixel_id = get_image_pixel_ids(self) else: # Use 'pydicom.pixel_data_handlers' backend if name: self._convert_pixel_data_using_handler(name) else: self._convert_pixel_data_without_handler() def _convert_pixel_data_using_handler(self, name: str) -> None: """Convert the pixel data using handler with the given name. See :meth:`~Dataset.convert_pixel_data` for more information. """ # TODO: Remove in v4.0 # handle some variations in name handler_name = name.lower() if not handler_name.endswith("_handler"): handler_name += "_handler" if handler_name == "numpy_handler": handler_name = "np_handler" if handler_name == "jpeg_ls_handler": # the name in config differs from the actual handler name # we allow both handler_name = "jpegls_handler" if not hasattr(pydicom.config, handler_name): raise ValueError(f"'{name}' is not a known handler name") handler = getattr(pydicom.config, handler_name) tsyntax = self.file_meta.TransferSyntaxUID if not handler.supports_transfer_syntax(tsyntax): raise NotImplementedError( "Unable to decode pixel data with a transfer syntax UID" f" of '{tsyntax}' ({tsyntax.name}) using the pixel data " f"handler '{name}'. Please see the pydicom documentation for " "information on supported transfer syntaxes." ) if not handler.is_available(): raise RuntimeError( f"The pixel data handler '{name}' is not available on your " "system. Please refer to the pydicom documentation for " "information on installing needed packages." ) # if the conversion fails, the exception is propagated up self._do_pixel_data_conversion(handler) def _convert_pixel_data_without_handler(self) -> None: """Convert the pixel data using the first matching handler. See :meth:`~Dataset.convert_pixel_data` for more information. """ # TODO: Remove in v4.0 # Find all possible handlers that support the transfer syntax ts = self.file_meta.TransferSyntaxUID possible_handlers = [ hh for hh in pydicom.config.pixel_data_handlers if hh is not None and hh.supports_transfer_syntax(ts) ] # No handlers support the transfer syntax if not possible_handlers: raise NotImplementedError( "Unable to decode pixel data with a transfer syntax UID of " f"'{ts}' ({ts.name}) as there are no pixel data " "handlers available that support it. Please see the pydicom " "documentation for information on supported transfer syntaxes " ) # Handlers that both support the transfer syntax and have their # dependencies met available_handlers = [hh for hh in possible_handlers if hh.is_available()] # There are handlers that support the transfer syntax but none of them # can be used as missing dependencies if not available_handlers: # For each of the possible handlers we want to find which # dependencies are missing msg = ( "The following handlers are available to decode the pixel " "data however they are missing required dependencies: " ) pkg_msg = [] for hh in possible_handlers: hh_deps = hh.DEPENDENCIES # Missing packages missing = [dd for dd in hh_deps if have_package(dd) is None] # Package names names = [hh_deps[name][1] for name in missing] pkg_msg.append(f"{hh.HANDLER_NAME} (req. {', '.join(names)})") raise RuntimeError(msg + ", ".join(pkg_msg)) last_exception = None for handler in available_handlers: try: self._do_pixel_data_conversion(handler) return except Exception as exc: logger.debug("Exception raised by pixel data handler", exc_info=exc) last_exception = exc # The only way to get to this point is if we failed to get the pixel # array because all suitable handlers raised exceptions self._pixel_array = None self._pixel_id = {} logger.info( "Unable to decode the pixel data using the following handlers: {}." "Please see the list of supported Transfer Syntaxes in the " "pydicom documentation for alternative packages that might " "be able to decode the data".format( ", ".join([str(hh) for hh in available_handlers]) ) ) raise last_exception # type: ignore[misc] def _do_pixel_data_conversion(self, handler: Any) -> None: """Do the actual data conversion using the given handler.""" # TODO: Remove in v4.0 # Use the handler to get a 1D numpy array of the pixel data # Will raise an exception if no pixel data element arr = handler.get_pixeldata(self) self._pixel_array = reshape_pixel_array(self, arr) # Some handler/transfer syntax combinations may need to # convert the color space from YCbCr to RGB if handler.needs_to_convert_to_RGB(self): self._pixel_array = convert_color_space( self._pixel_array, "YBR_FULL", "RGB" ) self._pixel_id = get_image_pixel_ids(self) def compress( self, transfer_syntax_uid: str, arr: "numpy.ndarray | None" = None, encoding_plugin: str = "", encapsulate_ext: bool = False, *, generate_instance_uid: bool = True, jls_error: int | None = None, j2k_cr: list[float] | None = None, j2k_psnr: list[float] | None = None, **kwargs: Any, ) -> None: """Compress uncompressed pixel data and update `ds` in-place with the resulting :dcm:`encapsulated` codestream. .. versionadded:: 2.2 The dataset `ds` must already have the following :dcm:`Image Pixel` module elements present with correct values that correspond to the resulting compressed pixel data: * (0028,0002) *Samples per Pixel* * (0028,0004) *Photometric Interpretation* * (0028,0008) *Number of Frames* (if more than 1 frame will be present) * (0028,0010) *Rows* * (0028,0011) *Columns* * (0028,0100) *Bits Allocated* * (0028,0101) *Bits Stored* * (0028,0103) *Pixel Representation* If *Samples per Pixel* is greater than 1 then the following element is also required: * (0028,0006) *Planar Configuration* This method will add the file meta dataset if none is present and add or modify the following elements: * (0002,0010) *Transfer Syntax UID* * (7FE0,0010) *Pixel Data* If the compressed pixel data is too large for encapsulation using a basic offset table then an :dcm:`extended offset table ` will also be used, in which case the following elements will also be added: * (7FE0,0001) *Extended Offset Table* * (7FE0,0002) *Extended Offset Table Lengths* If `generate_instance_uid` is ``True`` (default) then a new (0008,0018) *SOP Instance UID* value will be generated. **Supported Transfer Syntax UIDs** +-----------------------------------------------+-----------+----------------------------------+ | UID | Plugins | Encoding Guide | +------------------------+----------------------+ | | | Name | Value | | | +========================+======================+===========+==================================+ |*JPEG-LS Lossless* |1.2.840.10008.1.2.4.80| pyjpegls | :doc:`JPEG-LS | +------------------------+----------------------+ | ` | | *JPEG-LS Near Lossless*|1.2.840.10008.1.2.4.81| | | +------------------------+----------------------+-----------+----------------------------------+ | *JPEG 2000 Lossless* |1.2.840.10008.1.2.4.90| pylibjpeg | :doc:`JPEG 2000 | +------------------------+----------------------+ | ` | | *JPEG 2000* |1.2.840.10008.1.2.4.91| | | +------------------------+----------------------+-----------+----------------------------------+ | *RLE Lossless* | 1.2.840.10008.1.2.5 | pydicom, | :doc:`RLE Lossless | | | | pylibjpeg,| ` | | | | gdcm | | +------------------------+----------------------+-----------+----------------------------------+ .. versionchanged:: 3.0 Added the `jls_error`, `j2k_cr`, `j2k_psnr` and `generate_instance_uid` keyword parameters. Examples -------- Compress the existing uncompressed *Pixel Data* in place: >>> from pydicom import examples >>> from pydicom.uid import RLELossless >>> ds = examples.ct >>> ds.compress(RLELossless) >>> ds.save_as("ct_rle_lossless.dcm") Parameters ---------- transfer_syntax_uid : pydicom.uid.UID The UID of the :dcm:`transfer syntax` to use when compressing the pixel data. arr : numpy.ndarray, optional Compress the uncompressed pixel data in `arr` and use it to set the *Pixel Data*. If `arr` is not used then the existing *Pixel Data* in the dataset will be compressed instead. The :attr:`~numpy.ndarray.shape`, :class:`~numpy.dtype` and contents of the array should match the dataset. encoding_plugin : str, optional Use the `encoding_plugin` to compress the pixel data. See the :doc:`user guide ` for a list of plugins available for each UID and their dependencies. If not specified then all available plugins will be tried (default). encapsulate_ext : bool, optional If ``True`` then force the addition of an extended offset table. If ``False`` (default) then an extended offset table will be added if needed for large amounts of compressed *Pixel Data*, otherwise just the basic offset table will be used. generate_instance_uid : bool, optional If ``True`` (default) then generate a new (0008,0018) *SOP Instance UID* value for the dataset using :func:`~pydicom.uid.generate_uid`, otherwise keep the original value. jls_error : int, optional **JPEG-LS Near Lossless only**. The allowed absolute compression error in the pixel values. j2k_cr : list[float], optional **JPEG 2000 only**. A list of the compression ratios to use for each quality layer. There must be at least one quality layer and the minimum allowable compression ratio is ``1``. When using multiple quality layers they should be ordered in decreasing value from left to right. For example, to use 2 quality layers with 20x and 5x compression ratios then `j2k_cr` should be ``[20, 5]``. Cannot be used with `j2k_psnr`. j2k_psnr : list[float], optional **JPEG 2000 only**. A list of the peak signal-to-noise ratios (in dB) to use for each quality layer. There must be at least one quality layer and when using multiple quality layers they should be ordered in increasing value from left to right. For example, to use 2 quality layers with PSNR of 80 and 300 then `j2k_psnr` should be ``[80, 300]``. Cannot be used with `j2k_cr`. **kwargs Optional keyword parameters for the encoding plugin may also be present. See the :doc:`encoding plugins options ` for more information. """ compress( self, transfer_syntax_uid, arr, encoding_plugin=encoding_plugin, encapsulate_ext=encapsulate_ext, generate_instance_uid=generate_instance_uid, jls_error=jls_error, j2k_cr=j2k_cr, j2k_psnr=j2k_psnr, **kwargs, ) def decompress( self, handler_name: str = "", *, as_rgb: bool = True, generate_instance_uid: bool = True, decoding_plugin: str = "", **kwargs: Any, ) -> None: """Perform an in-place decompression of a dataset with a compressed *Transfer Syntax UID*. .. warning:: This function requires `NumPy `_ and may require the installation of additional packages to perform the actual pixel data decoding. See the :doc:`pixel data decompression documentation ` for more information. * The dataset's *Transfer Syntax UID* will be set to *Explicit VR Little Endian*. * The *Pixel Data* will be decompressed in its entirety and the *Pixel Data* element's value updated with the decompressed data, padded to an even length. * The *Pixel Data* element's VR will be set to **OB** if *Bits Allocated* <= 8, otherwise it will be set to **OW**. * The :attr:`DataElement.is_undefined_length ` attribute for the *Pixel Data* element will be set to ``False``. * Any :dcm:`image pixel` module elements may be modified as required to match the uncompressed *Pixel Data*. * If `generate_instance_uid` is ``True`` (default) then a new (0008,0018) *SOP Instance UID* value will be generated. .. versionchanged:: 3.0 Added the `as_rgb` and `generate_instance_uid` keyword parameters. .. deprecated:: 3.0 The `handler_name` parameter will be removed in v4.0, use `decoding_plugin` instead. Parameters ---------- handler_name : str, optional Deprecated and will be removed in v4.0, use `decoding_plugin` instead. as_rgb : bool, optional :mod:`~pydicom.pixels` **backend only.** If ``True`` (default) then convert pixel data with a YCbCr :ref:`photometric interpretation ` such as ``"YBR_FULL_422"`` to RGB. generate_instance_uid : bool, optional If ``True`` (default) then generate a new (0008,0018) *SOP Instance UID* value for the dataset using :func:`~pydicom.uid.generate_uid`, otherwise keep the original value. decoding_plugin : str, optional The name of the decoding plugin to use when decoding compressed pixel data. If no `decoding_plugin` is specified (default) then all available plugins will be tried and the result from the first successful one yielded. * If using the :mod:`~pydicom.pixels` backend (default) then see the :doc:`API documentation` for the available plugins for each *Transfer Syntax UID*. * If using the deprecated :mod:`~pydicom.pixel_data_handlers` backend supported plugins are: ``'gdcm'``, ``'pillow'``, ``'jpeg_ls'``, ``'rle'``, ``'numpy'`` and ``'pylibjpeg'``. kwargs : dict[str, Any], optional :mod:`~pydicom.pixels` **backend only.** Optional keyword parameters for the decoding plugin may also be present. See the :doc:`decoding plugins options` for more information. """ # TODO: remove support for pixel_data_handlers module in v4.0 if config._use_future and kwargs.get("handler_name", handler_name): raise TypeError( f"{type(self).__name__}.decompress() got an unexpected " "keyword argument 'handler_name'" ) opts = self._pixel_array_opts.copy() if handler_name: opts["decoding_plugin"] = handler_name if decoding_plugin: opts["decoding_plugin"] = decoding_plugin opts.update(**kwargs) decompress( self, as_rgb=as_rgb, generate_instance_uid=generate_instance_uid, **opts, ) def overlay_array(self, group: int) -> "numpy.ndarray": """Return the *Overlay Data* in `group` as a :class:`numpy.ndarray`. Parameters ---------- group : int The group number of the overlay data. Returns ------- numpy.ndarray The (`group`,3000) *Overlay Data* converted to a :class:`numpy.ndarray`. """ if group < 0x6000 or group > 0x60FF: raise ValueError( "The group part of the 'Overlay Data' element tag must be " "between 0x6000 and 0x60FF (inclusive)" ) if not config.have_numpy: raise ImportError( f"NumPy is required for {type(self).__name__}.overlay_array()" ) from pydicom.overlays import get_overlay_array return get_overlay_array(self, group) @property def pixel_array(self) -> "numpy.ndarray": """Return the pixel data as a :class:`numpy.ndarray`. .. warning:: This property requires `NumPy `_ and may require the installation of additional packages to perform the actual pixel data decoding. See the :doc:`pixel data decompression documentation ` for more information. .. versionchanged:: 3.0 The backend used for pixel data decoding has changed from the :mod:`~pydicom.pixel_data_handlers` module to the :mod:`~pydicom.pixels` module. The behavior of the new backend is not backwards compatible with the old one, in particular the default color space should now be RGB when previously YCbCr data was returned. To revert to the deprecated :mod:`~pydicom.pixel_data_handlers` backend pass ``use_v2_backend=True`` to the :meth:`~pydicom.dataset.Dataset.pixel_array_options` method:: >>> from pydicom import examples >>> ds = examples.ct >>> ds.pixel_array_options(use_v2_backend=True) >>> arr = ds.pixel_array The :mod:`~pydicom.pixel_data_handlers` module and the `use_v2_backend` keyword argument will be removed in v4.0. Returns ------- numpy.ndarray The contents of the (7FE0,0008) *Float Pixel Data*, (7FE0,0009) *Double Float Pixel Data* or (7FE0,0010) *Pixel Data* elements converted to a :class:`numpy.ndarray`. The array will be shaped as: * (rows, columns) for single frame, single sample data * (rows, columns, samples) for single frame, multi-sample data * (frames, rows, columns) for multi-frame, single sample data * (frames, rows, columns, samples) for multi-frame, multi-sample data When using the :mod:`pydicom.pixels` backend the decoding options used with the returned array can be customized via the :meth:`~pydicom.dataset.Dataset.pixel_array_options` method. See Also -------- pydicom.pixels.pixel_array A function for returning the pixel data from the path to a dataset, a readable file-like containing a dataset or a :class:`~pydicom.dataset.Dataset` instance. Can be used to minimize the memory required to return the pixel data when used with a path or file-like. pydicom.pixels.iter_pixels Similar to :func:`pydicom.pixels.pixel_array` but returns a generator that iterates through the image frames. """ self.convert_pixel_data() return cast("numpy.ndarray", self._pixel_array) def pixel_array_options( self, *, index: int | None = None, raw: bool = False, decoding_plugin: str = "", use_v2_backend: bool = False, **kwargs: Any, ) -> None: """Set the decoding and processing options used by the :attr:`~pydicom.dataset.Dataset.pixel_array` property. .. versionadded:: 3.0 .. deprecated:: 3.0 The `use_v2_backend` keyword parameter will be removed in v4.0. **Processing** The following processing operations on the raw pixel data will always be performed: * Natively encoded bit-packed pixel data for a :ref:`bits allocated ` of ``1`` will be unpacked. * Natively encoded pixel data with a :ref:`photometric interpretation ` of ``"YBR_FULL_422"`` will have it's sub-sampling removed. * The output array will be reshaped to the specified dimensions. * JPEG-LS or JPEG 2000 encoded data whose signedness doesn't match the expected :ref:`pixel representation` will be converted to match. With the :mod:`pydicom.pixels` backend, if ``raw = False`` (the default) then the following processing operation will also be performed: * Pixel data with a :ref:`photometric interpretation ` of ``"YBR_FULL"`` or ``"YBR_FULL_422"`` will be converted to RGB. Examples -------- Convert the *Pixel Data* to an array that's a view on the original buffer:: >>> from pydicom import examples >>> ds = examples.ct >>> ds.pixel_array_options(view_only=True) >>> arr = ds.pixel_array Use the deprecated :mod:`~pydicom.pixel_data_handlers` backend to convert the *Pixel Data* to an array:: >>> from pydicom import examples >>> ds = examples.ct >>> ds.pixel_array_options(use_v2_backend=True) >>> arr = ds.pixel_array Parameters ---------- index : int | None, optional If ``None`` (default) then return an array containing all the frames in the pixel data, otherwise return one containing only the frame from the specified `index`, which starts at 0 for the first frame. Only available with the :mod:`~pydicom.pixels` backend. raw : bool, optional If ``True`` then return the decoded pixel data after only minimal processing (see the processing section above). If ``False`` (default) then additional processing may be applied to convert the pixel data to it's most commonly used form (such as converting from YCbCr to RGB). Only available with the :mod:`~pydicom.pixels` backend. decoding_plugin : str, optional The name of the decoding plugin to use when decoding compressed pixel data. If no `decoding_plugin` is specified (default) then all available plugins will be tried and the result from the first successful one returned. For information on the available plugins for each *Transfer Syntax UID*: * If using the :mod:`~pydicom.pixels` backend see the :doc:`documentation for the decoder` corresponding to the dataset's *Transfer Syntax UID*. * If using the :mod:`~pydicom.pixel_data_handlers` backend supported values are ``'gdcm'``, ``'pillow'``, ``'jpeg_ls'``, ``'rle'``, ``'numpy'`` and ``'pylibjpeg'``. use_v2_backend : bool, optional If ``False`` (default) then use the :mod:`pydicom.pixels` backend to decode the pixel data, otherwise use the deprecated :mod:`pydicom.pixel_data_handlers` backend. **kwargs Optional keyword parameters for controlling decoding with the :mod:`~pydicom.pixels` backend, please see the :doc:`decoding options documentation` for more information. """ if config._use_future and kwargs.get("use_v2_backend", use_v2_backend): raise TypeError( f"{type(self).__name__}.pixel_array_options() got an unexpected " "keyword argument 'use_v2_backend'" ) kwargs["index"] = index kwargs["raw"] = raw if decoding_plugin: kwargs["decoding_plugin"] = decoding_plugin.lower() kwargs["use_pdh"] = False if config._use_future else use_v2_backend self._pixel_array_opts = kwargs self._pixel_array = None self._pixel_id = {} def waveform_array(self, index: int) -> "numpy.ndarray": """Return an :class:`~numpy.ndarray` for the multiplex group at `index` in the (5400,0100) *Waveform Sequence*. .. versionadded:: 2.1 Parameters ---------- index : int The index of the multiplex group to return the array for. Returns ------ numpy.ndarray The *Waveform Data* for the multiplex group as an :class:`~numpy.ndarray` with shape (samples, channels). If (003A,0210) *Channel Sensitivity* is present then the values will be in the units specified by the (003A,0211) *Channel Sensitivity Units Sequence*. See Also -------- :func:`~pydicom.waveforms.numpy_handler.generate_multiplex` :func:`~pydicom.waveforms.numpy_handler.multiplex_array` """ if not wave_handler.is_available(): raise RuntimeError("The waveform data handler requires numpy") return wave_handler.multiplex_array(self, index, as_raw=False) # Format strings spec'd according to python string formatting options # See https://docs.python.org/3/library/stdtypes.html#printf-style-string-formatting default_element_format = "%(tag)s %(name)-35.35s %(VR)s: %(repval)s" default_sequence_element_format = "%(tag)s %(name)-35.35s %(VR)s: %(repval)s" def formatted_lines( self, element_format: str = default_element_format, sequence_element_format: str = default_sequence_element_format, indent_format: str | None = None, ) -> Iterator[str]: """Iterate through the :class:`Dataset` yielding formatted :class:`str` for each element. Parameters ---------- element_format : str The string format to use for non-sequence elements. Formatting uses the attributes of :class:`~pydicom.dataelem.DataElement`. Default is ``"%(tag)s %(name)-35.35s %(VR)s: %(repval)s"``. sequence_element_format : str The string format to use for sequence elements. Formatting uses the attributes of :class:`~pydicom.dataelem.DataElement`. Default is ``"%(tag)s %(name)-35.35s %(VR)s: %(repval)s"`` indent_format : str or None Placeholder for future functionality. Yields ------ str A string representation of an element. """ exclusion = ( "from_json", "to_json", "to_json_dict", "clear", "description", "validate", ) for elem in self.iterall(): # Get all the attributes possible for this data element (e.g. # gets descriptive text name too) # This is the dictionary of names that can be used in the format # string elem_dict = { attr: ( getattr(elem, attr)() if callable(getattr(elem, attr)) else getattr(elem, attr) ) for attr in dir(elem) if not attr.startswith("_") and attr not in exclusion } if elem.VR == VR_.SQ: yield sequence_element_format % elem_dict else: yield element_format % elem_dict def _pretty_str(self, indent: int = 0, top_level_only: bool = False) -> str: """Return a string of the DataElements in the Dataset, with indented levels. This private method is called by the ``__str__()`` method for handling print statements or ``str(dataset)``, and the ``__repr__()`` method. It is also used by ``top()``, therefore the `top_level_only` flag. This function recurses, with increasing indentation levels. ..versionchanged:: 2.0 The file meta information is returned in its own section, if :data:`~pydicom.config.show_file_meta` is ``True`` (default) Parameters ---------- indent : int, optional The indent level offset (default ``0``). top_level_only : bool, optional When True, only create a string for the top level elements, i.e. exclude elements within any Sequences (default ``False``). Returns ------- str A string representation of the Dataset. """ strings = [] indent_str = self.indent_chars * indent nextindent_str = self.indent_chars * (indent + 1) # Display file meta, if configured to do so, and have a non-empty one if ( hasattr(self, "file_meta") and self.file_meta and pydicom.config.show_file_meta ): strings.append(f"{'Dataset.file_meta ':-<49}") for elem in self.file_meta: with tag_in_exception(elem.tag): strings.append(indent_str + repr(elem)) strings.append(f"{'':-<49}") for elem in self: with tag_in_exception(elem.tag): if elem.VR == VR_.SQ: # a sequence strings.append( f"{indent_str}{elem.tag} {elem.name} " f"{len(elem.value)} item(s) ---- " ) if not top_level_only: for dataset in elem.value: strings.append(dataset._pretty_str(indent + 1)) strings.append(nextindent_str + "---------") else: strings.append(indent_str + repr(elem)) return "\n".join(strings) @property def read_implicit_vr(self) -> bool | None: """Get the VR method used by the original encoding of the dataset. .. deprecated:: 3.0 ``read_implicit_vr`` will be removed in v4.0, , use :attr:`~pydicom.dataset.Dataset.original_encoding` instead. Returns ------- bool | None Returns ``None`` if the dataset has been created from scratch, otherwise returns ``True`` if the dataset was decoded from file or buffer and used implicit VR, ``False`` if it used explicit VR. """ name = type(self).__name__ if config._use_future: raise AttributeError(f"'{name}' object has no attribute 'read_implicit_vr'") warn_and_log( ( f"'{name}.read_implicit_vr' will be removed in v4.0, use " f"'{name}.original_encoding[0]' instead" ), DeprecationWarning, ) return self._read_implicit @property def read_little_endian(self) -> bool | None: """Get the endianness used by the original encoding of the dataset. .. deprecated:: 3.0 ``read_little_endian`` will be removed in v4.0, use :attr:`~pydicom.dataset.Dataset.original_encoding` instead. Returns ------- bool | None Returns ``None`` if the dataset has been created from scratch, otherwise returns ``True`` if the dataset was decoded from file or buffer and used little endian encoding, ``False`` for big endian. """ name = type(self).__name__ if config._use_future: raise AttributeError( f"'{name}' object has no attribute 'read_little_endian'" ) warn_and_log( ( f"'{name}.read_little_endian' will be removed in v4.0, use " f"'{name}.original_encoding[1]' instead" ), DeprecationWarning, ) return self._read_little def remove_private_tags(self) -> None: """Remove all private elements from the :class:`Dataset`.""" def remove_callback(dataset: "Dataset", elem: DataElement) -> None: """Internal method to use as callback to walk() method.""" if elem.tag.is_private: # can't del self[tag] - won't be right dataset on recursion del dataset[elem.tag] self.walk(remove_callback) def save_as( self, filename: str | os.PathLike[AnyStr] | BinaryIO | WriteableBuffer, /, __write_like_original: bool | None = None, *, implicit_vr: bool | None = None, little_endian: bool | None = None, enforce_file_format: bool = False, overwrite: bool = True, **kwargs: Any, ) -> None: """Encode the current :class:`Dataset` and write it to `filename`. See the documentation for :func:`~pydicom.filewriter.dcmwrite` for more detailed information. .. warning:: Encoding a dataset with ``little_endian=False`` (i.e. as big endian) is not recommended. Big endian encoding was retired from the DICOM Standard in 2006. .. warning:: This function cannot be used to convert a decoded dataset to an encoding that uses a different endianness, such as from big to little endian. :func:`~pydicom.filewriter.dcmwrite()` must be used instead, however the process is not automatic. See the documentation of :func:`~pydicom.filewriter.dcmwrite()` for details. .. versionchanged:: 3.0 Added `implicit_vr`, `little_endian`, `enforce_file_format` and `overwrite` keyword arguments .. deprecated:: 3.0 `write_like_original` will be removed in v4.0, please use `enforce_file_format` instead Parameters ---------- filename : str | PathLike | BinaryIO The path, file-like or writeable buffer to write the encoded dataset to. If using a buffer it must have ``write()``, ``seek()`` and ``tell()`` methods. write_like_original : bool, optional If ``True`` (default) then write the dataset as-is, otherwise ensure that the dataset is written in the DICOM File Format or raise an exception is that isn't possible. This parameter is deprecated, please use `enforce_file_format` instead. implicit_vr : bool, optional Required if the dataset has no valid public *Transfer Syntax UID* set in the file meta and :attr:`~pydicom.dataset.Dataset.is_implicit_VR` or :attr:`~pydicom.dataset.Dataset.original_encoding` are ``None``. If ``True`` then encode using implicit VR, otherwise use explicit VR. little_endian : bool, optional Required if the dataset has no valid public *Transfer Syntax UID* set in the file meta and :attr:`~pydicom.dataset.Dataset.is_little_endian` or :attr:`~pydicom.dataset.Dataset.original_encoding` are ``None``. If ``True`` (default) then use little endian byte order when encoding, otherwise use big endian (not recommended). enforce_file_format : bool, optional If ``True`` then ensure the dataset is written in the DICOM File Format or raise an exception if that isn't possible. If ``False`` (default) then write the dataset as-is, preserving the following - which may result in a non-conformant file: - ``Dataset.preamble``: if the dataset has no preamble then none will be written - ``Dataset.file_meta``: if the dataset is missing any required *File Meta Information Group* elements then they will not be added or written overwrite : bool, optional If ``False`` and `filename` is a :class:`str` or PathLike, then raise a :class:`FileExistsError` if a file already exists with the given filename (default ``True``). See Also -------- pydicom.filewriter.dcmwrite Encode a :class:`Dataset` and write it to a file or buffer. """ # The default for little_endian is `None` so we can detect conversion # between little and big endian, but we actually default it to `True` # when `implicit_vr` is used if implicit_vr is not None and little_endian is None: little_endian = True # Disallow conversion between little and big endian encoding if self.original_encoding[1] is not None: file_meta = getattr(self, "file_meta", {}) syntax = file_meta.get("TransferSyntaxUID", None) use_little: bool | None = None try: use_little = syntax.is_little_endian except (AttributeError, ValueError): if little_endian is not None: use_little = little_endian elif not config._use_future: use_little = self.is_little_endian if use_little is not None and self.original_encoding[1] != use_little: raise ValueError( f"'{type(self).__name__}.save_as()' cannot be used to " "convert between little and big endian encoding. Please " "read the documentation for filewriter.dcmwrite() if this " "is what you really want to do" ) pydicom.dcmwrite( filename, self, __write_like_original, implicit_vr=implicit_vr, little_endian=little_endian, enforce_file_format=enforce_file_format, overwrite=overwrite, **kwargs, ) def ensure_file_meta(self) -> None: """Create an empty ``Dataset.file_meta`` if none exists.""" # Changed in v2.0 so does not re-assign self.file_meta with getattr() if not hasattr(self, "file_meta"): self.file_meta = FileMetaDataset() def __setattr__(self, name: str, value: Any) -> None: """Intercept any attempts to set a value for an instance attribute. If name is a DICOM keyword, set the corresponding tag and DataElement. Else, set an instance (python) attribute as any other class would do. Parameters ---------- name : str The keyword for the element you wish to add/change. If `name` is not a DICOM element keyword then this will be the name of the attribute to be added/changed. value The value for the attribute to be added/changed. """ # Save time for common Dataset attributes that are not DICOM keywords # This check is fast if `name` is a DICOM keyword (first chr is upper) # The startswith is needed for `is_implicit_VR` if name.startswith("is_") or name.islower(): if name == "file_meta": self._set_file_meta(value) else: object.__setattr__(self, name, value) return tag = tag_for_keyword(name) if tag is not None: # successfully mapped name to a tag if tag not in self: # don't have this tag yet->create the data_element instance vr = dictionary_VR(tag) elem = DataElement(tag, vr, value) else: # already have this data_element, just changing its value elem = self[tag] elem.value = value # Now have data_element - store it in this dict self[tag] = elem elif repeater_has_keyword(name): # Check if `name` is repeaters element raise ValueError( f"'{name}' is a DICOM repeating group element and must be " "added using the add() or add_new() methods." ) else: # Warn if `name` is camel case but not a keyword if _RE_CAMEL_CASE.match(name): msg = ( f"Camel case attribute '{name}' used which is not in the " "element keyword data dictionary" ) if config.INVALID_KEYWORD_BEHAVIOR == "WARN": warn_and_log(msg) elif config.INVALID_KEYWORD_BEHAVIOR == "RAISE": raise ValueError(msg) # name not in dicom dictionary - setting a non-dicom instance # attribute # XXX note if user misspells a dicom data_element - no error!!! object.__setattr__(self, name, value) def _set_file_meta(self, value: "Dataset | None") -> None: """Set the Dataset's File Meta Information attribute.""" if value is None: self.__dict__["file_meta"] = value return if not isinstance(value, Dataset): cls_name = self.__class__.__name__ raise TypeError( f"'{cls_name}.file_meta' must be a 'FileMetaDataset' instance" ) if not isinstance(value, FileMetaDataset): # Also validates for only group 2 elements value = FileMetaDataset(value) self.__dict__["file_meta"] = value def __setitem__(self, key: "slice | TagType", elem: _DatasetValue) -> None: """Operator for ``Dataset[key] = elem``. Parameters ---------- key : int or Tuple[int, int] or str The tag for the element to be added to the :class:`Dataset`. elem : dataelem.DataElement or dataelem.RawDataElement The element to add to the :class:`Dataset`. Raises ------ NotImplementedError If `key` is a :class:`slice`. ValueError If the `key` value doesn't match the corresponding :attr:`DataElement.tag`. """ if isinstance(key, slice): raise NotImplementedError( "Slicing is not supported when setting Dataset items" ) try: key = Tag(key) except Exception as exc: raise ValueError( f"Unable to convert the key '{key}' to an element tag" ) from exc if not isinstance(elem, DataElement | RawDataElement): raise TypeError("Dataset items must be 'DataElement' instances") if isinstance(elem.tag, BaseTag): elem_tag = elem.tag else: elem_tag = Tag(elem.tag) if key != elem_tag: raise ValueError( f"The key '{key}' doesn't match the 'DataElement' tag '{elem_tag}'" ) if elem_tag.is_private: # See PS 3.5-2008 section 7.8.1 (p. 44) for how blocks are reserved logger.debug(f"Setting private tag {elem_tag}") private_block = elem_tag.element >> 8 private_creator_tag = Tag(elem_tag.group, private_block) if private_creator_tag in self and elem_tag != private_creator_tag: if isinstance(elem, RawDataElement): elem = convert_raw_data_element( elem, encoding=self._character_set, ds=self ) elem.private_creator = self[private_creator_tag].value # Changing pixel data resets the stored array if elem_tag in PIXEL_KEYWORDS: self._pixel_array = None self._pixel_id = {} self._dict[elem_tag] = elem if elem.VR == VR_.SQ and isinstance(elem, DataElement): if not isinstance(elem.value, pydicom.Sequence): elem.value = pydicom.Sequence(elem.value) # type: ignore # Update the `_pixel_rep` attribute when nested sequences # containing RawDataElements are being added to a different # dataset self._set_pixel_representation(cast(DataElement, elem)) def set_pixel_data( self, arr: "numpy.ndarray", photometric_interpretation: str, bits_stored: int, *, generate_instance_uid: bool = True, ) -> None: """Use an :class:`~numpy.ndarray` to set the *Pixel Data* and related Image Pixel module elements. .. versionadded:: 3.0 The following :dcm:`Image Pixel` module elements values will be added, updated or removed as necessary: * (0028,0002) *Samples per Pixel* using a value corresponding to `photometric_interpretation`. * (0028,0104) *Photometric Interpretation* from `photometric_interpretation`. * (0028,0006) *Planar Configuration* will be added and set to ``0`` if *Samples per Pixel* is > 1, otherwise it will be removed. * (0028,0008) *Number of Frames* from the array :attr:`~numpy.ndarray.shape`, however it will be removed if `arr` only contains a single frame. * (0028,0010) *Rows* and (0028,0011) *Columns* from the array :attr:`~numpy.ndarray.shape`. * (0028,0100) *Bits Allocated* from the array :class:`~numpy.dtype`. * (0028,0101) *Bits Stored* and (0028,0102) *High Bit* from `bits_stored`. * (0028,0103) *Pixel Representation* from the array :class:`~numpy.dtype`. In addition: * The *Transfer Syntax UID* will be set to *Explicit VR Little Endian* if it doesn't already exist or uses a compressed (encapsulated) transfer syntax. * If `generate_instance_uid` is ``True`` (default) then the *SOP Instance UID* will be added or updated. Parameters ---------- arr : numpy.ndarray An array with :class:`~numpy.dtype` uint8, uint16, int8 or int16. The array must be shaped as one of the following: * (rows, columns) for a single frame of grayscale data. * (frames, rows, columns) for multi-frame grayscale data. * (rows, columns, samples) for a single frame of multi-sample data such as RGB. * (frames, rows, columns, samples) for multi-frame, multi-sample data. photometric_interpretation : str The value to use for (0028,0004) *Photometric Interpretation*. Valid values are ``"MONOCHROME1"``, ``"MONOCHROME2"``, ``"PALETTE COLOR"``, ``"RGB"``, ``"YBR_FULL"``, ``"YBR_FULL_422"``. bits_stored : int The value to use for (0028,0101) *Bits Stored*. Must be no greater than the number of bits used by the :attr:`~numpy.dtype.itemsize` of `arr`. generate_instance_uid : bool, optional If ``True`` (default) then add or update the (0008,0018) *SOP Instance UID* element with a value generated using :func:`~pydicom.uid.generate_uid`. Raises ------ NotImplementedError If the dataset has a big-endian *Transfer Syntax UID*. """ set_pixel_data( self, arr, photometric_interpretation, bits_stored, generate_instance_uid=generate_instance_uid, ) def _set_pixel_representation(self, elem: DataElement) -> None: """Set the `_pixel_rep` attribute for the current dataset and child datasets of the sequence element `elem`.""" # `TAG_PIXREP` is (0028,0103) *Pixel Representation* # May be DataElement or RawDataElement, also value may be None pr: int | bytes | None = None if TAG_PIXREP in self._dict: pr = self[TAG_PIXREP].value elif hasattr(self, "_pixel_rep"): # Must be second conditional pr = self._pixel_rep if pr is not None: self._pixel_rep = int(b"\x01" in pr) if isinstance(pr, bytes) else pr if elem.VR != VR_.SQ: return # Note that the value of `_pixel_rep` gets updated as we move # down the tree - the value used to correct ambiguous # elements will be from the closest dataset to that element for item in elem.value: if TAG_PIXREP in item._dict: pr = item._dict[TAG_PIXREP].value if pr is not None: item._pixel_rep = ( int(b"\x01" in pr) if isinstance(pr, bytes) else pr ) elif hasattr(self, "_pixel_rep"): item._pixel_rep = self._pixel_rep elif hasattr(self, "_pixel_rep"): item._pixel_rep = self._pixel_rep def _slice_dataset( self, start: "TagType | None", stop: "TagType | None", step: int | None ) -> list[BaseTag]: """Return the element tags in the Dataset that match the slice. Parameters ---------- start : int or 2-tuple of int or None The slice's starting element tag value, in any format accepted by :func:`~pydicom.tag.Tag`. stop : int or 2-tuple of int or None The slice's stopping element tag value, in any format accepted by :func:`~pydicom.tag.Tag`. step : int or None The slice's step size. Returns ------ list of BaseTag The tags in the :class:`Dataset` that meet the conditions of the slice. """ # Check the starting/stopping Tags are valid when used if start is not None: start = Tag(start) if stop is not None: stop = Tag(stop) all_tags = sorted(self._dict.keys()) # If the Dataset is empty, return an empty list if not all_tags: return [] # Special case the common situations: # - start and/or stop are None # - step is 1 if start is None: if stop is None: # For step=1 avoid copying the list return all_tags if step == 1 else all_tags[::step] else: # Have a stop value, get values until that point step1_list = list(takewhile(lambda x: x < stop, all_tags)) return step1_list if step == 1 else step1_list[::step] # Have a non-None start value. Find its index i_start = bisect_left(all_tags, start) if stop is None: return all_tags[i_start::step] i_stop = bisect_left(all_tags, stop) return all_tags[i_start:i_stop:step] def __str__(self) -> str: """Handle str(dataset). ..versionchanged:: 2.0 The file meta information was added in its own section, if :data:`pydicom.config.show_file_meta` is ``True`` """ return self._pretty_str() def top(self) -> str: """Return a :class:`str` representation of the top level elements.""" return self._pretty_str(top_level_only=True) def trait_names(self) -> list[str]: """Return a :class:`list` of valid names for auto-completion code. Used in IPython, so that data element names can be found and offered for autocompletion on the IPython command line. """ return dir(self) def update(self, d: _DatasetType) -> None: """Extend :meth:`dict.update` to handle DICOM tags and keywords. Parameters ---------- d : dict or Dataset The :class:`dict` or :class:`Dataset` to use when updating the current object. """ for key, value in list(d.items()): if isinstance(key, str): setattr(self, key, value) else: self[Tag(cast(int, key))] = value def iterall(self) -> Iterator[DataElement]: """Iterate through the :class:`Dataset`, yielding all the elements. Unlike ``iter(Dataset)``, this *does* recurse into sequences, and so yields all elements as if dataset were "flattened". Yields ------ dataelem.DataElement """ for elem in self: yield elem if elem.VR == VR_.SQ: for ds in elem.value: yield from ds.iterall() def walk( self, callback: Callable[["Dataset", DataElement], None], recursive: bool = True ) -> None: """Iterate through the :class:`Dataset's` elements and run `callback` on each. Visit all elements in the :class:`Dataset`, possibly recursing into sequences and their items. The `callback` function is called for each :class:`~pydicom.dataelem.DataElement` (including elements with a VR of 'SQ'). Can be used to perform an operation on certain types of elements. For example, :meth:`~Dataset.remove_private_tags` finds all elements with private tags and deletes them. The elements will be returned in order of increasing tag number within their current :class:`Dataset`. Parameters ---------- callback A callable function that takes two arguments: * a :class:`Dataset` * a :class:`~pydicom.dataelem.DataElement` belonging to that :class:`Dataset` recursive : bool, optional Flag to indicate whether to recurse into sequences (default ``True``). """ taglist = sorted(self._dict.keys()) for tag in taglist: with tag_in_exception(tag): data_element = self[tag] callback(self, data_element) # self = this Dataset # 'tag in self' below needed in case callback deleted # data_element if recursive and tag in self and data_element.VR == VR_.SQ: sequence = data_element.value for dataset in sequence: dataset.walk(callback) @classmethod def from_json( cls: type["Dataset"], json_dataset: dict[str, Any] | str | bytes | bytearray, bulk_data_uri_handler: ( Callable[[str, str, str], None | str | int | float | bytes] | Callable[[str], None | str | int | float | bytes] | None ) = None, ) -> "Dataset": """Return a :class:`Dataset` from a DICOM JSON Model object. See the DICOM Standard, Part 18, :dcm:`Annex F`. Parameters ---------- json_dataset : dict, str, bytes or bytearray :class:`dict`, :class:`str`, :class:`bytes` or :class:`bytearray` representing a DICOM Data Set formatted based on the :dcm:`DICOM JSON Model`. bulk_data_uri_handler : callable, optional Callable function that accepts either the tag, vr and "BulkDataURI" value or just the "BulkDataURI" value of the JSON representation of a data element and returns the actual value of that data element (retrieved via DICOMweb WADO-RS). If no `bulk_data_uri_handler` is specified (default) then the corresponding element will have an "empty" value such as ``""``, ``b""`` or ``None`` depending on the `vr` (i.e. the Value Multiplicity will be 0). Returns ------- Dataset """ if isinstance(json_dataset, str | bytes | bytearray): json_dataset = cast(dict[str, Any], json.loads(json_dataset)) dataset = cls() for tag, mapping in json_dataset.items(): # `tag` is an element tag in uppercase hex format as a str # `mapping` is Dict[str, Any] and should have keys 'vr' and at most # one of ('Value', 'BulkDataURI', 'InlineBinary') but may have # none of those if the element's VM is 0 vr = mapping["vr"] unique_value_keys = tuple( set(mapping.keys()) & set(jsonrep.JSON_VALUE_KEYS) ) if len(unique_value_keys) == 0: value_key = None value = [""] else: value_key = unique_value_keys[0] value = mapping[value_key] data_element = DataElement.from_json( cls, tag, vr, value, value_key, bulk_data_uri_handler ) dataset.add(data_element) return dataset def to_json_dict( self, bulk_data_threshold: int = 1024, bulk_data_element_handler: Callable[[DataElement], str] | None = None, suppress_invalid_tags: bool = False, ) -> dict[str, Any]: """Return a dictionary representation of the :class:`Dataset` conforming to the DICOM JSON Model as described in the DICOM Standard, Part 18, :dcm:`Annex F`. Parameters ---------- bulk_data_threshold : int, optional Threshold for the length of a base64-encoded binary data element above which the element should be considered bulk data and the value provided as a URI rather than included inline (default: ``1024``). Ignored if no bulk data handler is given. bulk_data_element_handler : callable, optional Callable function that accepts a bulk data element and returns a JSON representation of the data element (dictionary including the "vr" key and either the "InlineBinary" or the "BulkDataURI" key). suppress_invalid_tags : bool, optional Flag to specify if errors while serializing tags should be logged and the tag dropped or if the error should be bubbled up. Returns ------- dict :class:`Dataset` representation based on the DICOM JSON Model. """ json_dataset = {} context = config.strict_reading() if suppress_invalid_tags else nullcontext() with context: for key in self.keys(): json_key = f"{key:08X}" try: data_element = self[key] json_dataset[json_key] = data_element.to_json_dict( bulk_data_element_handler=bulk_data_element_handler, bulk_data_threshold=bulk_data_threshold, ) except Exception as exc: if not suppress_invalid_tags: logger.error(f"Error while processing tag {json_key}") raise exc logger.warning(f"Error while processing tag {json_key}: {exc}") return json_dataset def to_json( self, bulk_data_threshold: int = 1024, bulk_data_element_handler: Callable[[DataElement], str] | None = None, dump_handler: Callable[[dict[str, Any]], str] | None = None, suppress_invalid_tags: bool = False, ) -> str: """Return a JSON representation of the :class:`Dataset`. See the DICOM Standard, Part 18, :dcm:`Annex F`. Parameters ---------- bulk_data_threshold : int, optional Threshold for the length of a base64-encoded binary data element above which the element should be considered bulk data and the value provided as a URI rather than included inline (default: ``1024``). Ignored if no bulk data handler is given. bulk_data_element_handler : callable, optional Callable function that accepts a bulk data element and returns a JSON representation of the data element (dictionary including the "vr" key and either the "InlineBinary" or the "BulkDataURI" key). dump_handler : callable, optional Callable function that accepts a :class:`dict` and returns the serialized (dumped) JSON string (by default uses :func:`json.dumps`). .. note: Make sure to use a dump handler that sorts the keys (see example below) to create DICOM-conformant JSON. suppress_invalid_tags : bool, optional Flag to specify if errors while serializing tags should be logged and the tag dropped or if the error should be bubbled up. Returns ------- str :class:`Dataset` serialized into a string based on the DICOM JSON Model. Examples -------- >>> def my_json_dumps(data): ... return json.dumps(data, indent=4, sort_keys=True) >>> ds.to_json(dump_handler=my_json_dumps) """ if dump_handler is None: def json_dump(d: Any) -> str: return json.dumps(d, sort_keys=True) dump_handler = json_dump return dump_handler( self.to_json_dict( bulk_data_threshold, bulk_data_element_handler, suppress_invalid_tags=suppress_invalid_tags, ) ) def update_raw_element( self, tag: TagType, *, vr: str | None = None, value: bytes | None = None ) -> None: """Modify the VR or value for the raw element with `tag`. When a :class:`Dataset` is created most of it's elements are in their :class:`~pydicom.dataelem.RawDataElement` form, and only upon trying to access the element is it converted to a :class:`~pydicom.dataelem.DataElement`. When this conversion fails due to non-conformance issues, this method can be used to modify the raw element data prior to conversion in order to fix any issues. Example ------- Change the VR for the element with tag (0029,1026) before conversion to :class:`~pydicom.dataelem.DataElement`. >>> from pydicom import examples >>> ds = examples.ct >>> ds.update_raw_element(0x00291026, vr="US") >>> elem = ds[0x00291026] # conversion to DataElement occurs here >>> type(elem) >>> elem.VR "US" Parameters ---------- tag : int | str | tuple[int, int] | BaseTag The tag for a :class:`~pydicom.dataelem.RawDataElement` in the dataset. vr : str, optional Required if `value` is not used, the value to use for the modified element's VR, if not used then the existing VR will be kept. value : bytes, optional Required if `vr` is not used, the value to use for the modified element's raw encoded value, if not used then the existing value will be kept. """ if vr is None and value is None: raise ValueError("Either or both of 'vr' and 'value' are required") if vr is not None: try: VR_[vr] except KeyError: raise ValueError(f"Invalid VR value '{vr}'") if value is not None and not isinstance(value, bytes): raise TypeError(f"'value' must be bytes, not '{type(value).__name__}'") tag = Tag(tag) raw = self.get_item(tag) if raw is None: raise KeyError(f"No element with tag {tag} was found") if not isinstance(raw, RawDataElement): raise TypeError( f"The element with tag {tag} has already been converted to a " "'DataElement' instance, this method must be called earlier" ) vr = vr if vr is not None else raw.VR value = value if value is not None else raw.value self._dict[tag] = raw._replace(VR=vr, value=value) __repr__ = __str__ _FileDataset = TypeVar("_FileDataset", bound="FileDataset") class FileDataset(Dataset): """An extension of :class:`Dataset` to make reading and writing to file-like easier. .. versionchanged:: 3.0 Added the `buffer` attribute and the `filename` attribute has been changed to only contain the filename the dataset was read from (if any). Attributes ---------- preamble : str | bytes | None The optional DICOM preamble prepended to the :class:`FileDataset`, if available. file_meta : FileMetaDataset | None The Dataset's file meta information as a :class:`FileMetaDataset`, if available (``None`` if not present). Consists of group ``0x0002`` elements. filename : str | None The filename associated with the :class:`FileDataset` if read from a file or file-like, or ``None`` if the dataset has been read from a buffer-like object. buffer : ReadableBuffer | None The buffer-like object the :class:`FileDataset` was read from, or ``None`` if the dataset has been read from a file or file-like. fileobj_type The type of object the :class:`FileDataset` was read from. timestamp : float | None The modification time of the file the :class:`FileDataset` was read from, ``None`` if the modification time is not available. """ def __init__( self, filename_or_obj: PathType | BinaryIO | ReadableBuffer, dataset: _DatasetType, preamble: bytes | None = None, file_meta: "FileMetaDataset | None" = None, is_implicit_VR: bool = True, is_little_endian: bool = True, ) -> None: """Initialize a :class:`FileDataset` read from a DICOM file. Parameters ---------- filename_or_obj : str, PathLike, file-like or readable buffer * :class:`str` or path: the full path to the dataset file * file-like: a file-like object in "rb" mode * readable buffer: an object with ``read()``, ``tell()`` and ``seek()`` methods such as :class:`io.BytesIO`. dataset : Dataset or dict Some form of dictionary, usually a :class:`Dataset` returned from :func:`~pydicom.filereader.dcmread`. preamble : bytes or str, optional The 128-byte DICOM preamble. file_meta : FileMetaDataset, optional The file meta :class:`FileMetaDataset`, such as the one returned by :func:`~pydicom.filereader.read_file_meta_info`, or an empty :class:`FileMetaDataset` if no file meta information is in the file. is_implicit_VR : bool, optional ``True`` (default) if implicit VR transfer syntax used; ``False`` if explicit VR. is_little_endian : bool ``True`` (default) if little-endian transfer syntax used; ``False`` if big-endian. """ Dataset.__init__(self, dataset) self.preamble = preamble self.file_meta: FileMetaDataset = ( file_meta if file_meta is not None else FileMetaDataset() ) # TODO: Remove in v4.0 if not config._use_future: self._is_implicit_VR: bool = is_implicit_VR self._is_little_endian: bool = is_little_endian self._read_implicit: bool = is_implicit_VR self._read_little: bool = is_little_endian self.fileobj_type: Any = None self.filename: PathType | None = None self.buffer: ReadableBuffer | None = None filename_or_obj = path_from_pathlike(filename_or_obj) if isinstance(filename_or_obj, str): # Path to the dataset file self.filename = filename_or_obj self.fileobj_type = open elif isinstance(filename_or_obj, io.BufferedReader): # File-like in "rb" mode such as open(..., "rb") self.filename = filename_or_obj.name # This is the appropriate constructor for io.BufferedReader self.fileobj_type = open else: # Readable buffer with read(), seek() and tell() methods self.buffer = filename_or_obj self.fileobj_type = type(filename_or_obj) if getattr(filename_or_obj, "name", None): self.filename = filename_or_obj.name elif getattr(filename_or_obj, "filename", None): self.filename = filename_or_obj.filename # type: ignore[attr-defined] self.timestamp = None if self.filename and os.path.exists(self.filename): self.timestamp = os.stat(self.filename).st_mtime def __deepcopy__(self, memo: dict[int, Any]) -> "FileDataset": """Return a deep copy of the file dataset. Sets the `buffer` to ``None`` if it's been closed or is otherwise not copyable. Returns ------- FileDataset A deep copy of the file dataset. """ cls = self.__class__ result = cls.__new__(cls) memo[id(self)] = result for k, v in self.__dict__.items(): if k == "buffer": try: setattr(result, k, copy.deepcopy(v, memo)) except Exception as exc: warn_and_log( f"The {type(exc).__name__} exception '{exc}' occurred " "trying to deepcopy the buffer-like the dataset was read " "from, the 'buffer' attribute will be set to 'None' in the " "copied object" ) setattr(result, k, copy.deepcopy(None, memo)) else: setattr(result, k, copy.deepcopy(v, memo)) return result def validate_file_meta( file_meta: "FileMetaDataset", enforce_standard: bool = True ) -> None: """Validate the *File Meta Information* elements in `file_meta`. Parameters ---------- file_meta : Dataset The *File Meta Information* data elements. enforce_standard : bool, optional If ``False``, then only a check for invalid elements is performed. If ``True`` (default), the following elements will be added if not already present and the Type 1 elements given a value if empty: * (0002,0001) *File Meta Information Version*, Type 1 * (0002,0012) *Implementation Class UID*, Type 1 * (0002,0013) *Implementation Version Name*, Type 3 and the following elements will be checked to ensure they're present and have a non-empty value: * (0002,0002) *Media Storage SOP Class UID*, Type 1 * (0002,0003) *Media Storage SOP Instance UID*, Type 1 * (0002,0010) *Transfer Syntax UID*, Type 1 Raises ------ ValueError If `enforce_standard` is ``True`` and any of the Type 1 *File Meta Information* elements are missing from `file_meta` or have no value. ValueError If any non-Group 2 Elements are present in `file_meta`. """ # Check that no non-Group 2 Elements are present for elem in file_meta.elements(): if elem.tag.group != 0x0002: raise ValueError( "Only File Meta Information group (0002,eeee) elements may be " "present in 'file_meta'." ) if enforce_standard: if ( "FileMetaInformationVersion" not in file_meta or file_meta["FileMetaInformationVersion"].is_empty ): file_meta.FileMetaInformationVersion = b"\x00\x01" if ( "ImplementationClassUID" not in file_meta or file_meta["ImplementationClassUID"].is_empty ): file_meta.ImplementationClassUID = UID(PYDICOM_IMPLEMENTATION_UID) if "ImplementationVersionName" not in file_meta: file_meta.ImplementationVersionName = ( f"PYDICOM {'.'.join(__version_info__)}" ) invalid = [ f"{Tag(tag)} {dictionary_description(tag)}" for tag in (0x00020002, 0x00020003, 0x00020010) if tag not in file_meta or file_meta[tag].is_empty ] if invalid: raise AttributeError( "Required File Meta Information elements are either missing " f"or have an empty value: {', '.join(invalid)}" ) class FileMetaDataset(Dataset): """Contains a collection (dictionary) of group 2 DICOM Data Elements. .. versionadded:: 2.0 Derived from :class:`~pydicom.dataset.Dataset`, but only allows Group 2 (File Meta Information) data elements """ def __init__(self, *args: _DatasetType, **kwargs: Any) -> None: """Initialize a FileMetaDataset Parameters are as per :class:`Dataset`; this overrides the super class only to check that all are group 2 data elements Raises ------ ValueError If any data elements are not group 2. TypeError If the passed argument is not a :class:`dict` or :class:`Dataset` """ super().__init__(*args, **kwargs) FileMetaDataset.validate(self._dict) # Set type hints for the possible contents - VR, Type (1|1C|3) self.FileMetaInformationGroupLength: int # UL, 1 self.FileMetaInformationVersion: bytes # OB, 1 self.MediaStorageSOPClassUID: UID # UI, 1 self.MediaStorageSOPInstanceUID: UID # UI, 1 self.TransferSyntaxUID: UID # UI, 1 self.ImplementationClassUID: UID # UI, 1 self.ImplementationVersionName: str | None # SH, 3 self.SourceApplicationEntityTitle: str | None # AE, 3 self.SendingApplicationEntityTitle: str | None # AE, 3 self.ReceivingApplicationEntityTitle: str | None # AE, 3 self.SourcePresentationAddress: str | None # UR, 3 self.ReceivingPresentationAddress: str | None # UR, 3 self.PrivateInformationCreatorUID: UID | None # UI, 3 self.PrivateInformation: bytes # OB, 1C @staticmethod def validate(init_value: _DatasetType) -> None: """Raise errors if initialization value is not acceptable for file_meta Parameters ---------- init_value: dict or Dataset The tag:data element pairs to initialize a file meta dataset Raises ------ TypeError If the passed argument is not a :class:`dict` or :class:`Dataset` ValueError If any data elements passed are not group 2. """ if init_value is None: return if not isinstance(init_value, Dataset | dict): raise TypeError( f"Argument must be a dict or Dataset, not {type(init_value)}" ) non_group2 = [str(Tag(tag)) for tag in init_value.keys() if Tag(tag).group != 2] if non_group2: raise ValueError( "File meta datasets may only contain group 2 elements but the " f"following elements are present: {', '.join(non_group2)}" ) def __setitem__(self, key: "slice | TagType", value: _DatasetValue) -> None: """Override parent class to only allow setting of group 2 elements. Parameters ---------- key : int or Tuple[int, int] or str The tag for the element to be added to the Dataset. value : dataelem.DataElement or dataelem.RawDataElement The element to add to the :class:`FileMetaDataset`. Raises ------ ValueError If `key` is not a DICOM Group 2 tag. """ if isinstance(value.tag, BaseTag): tag = value.tag else: tag = Tag(value.tag) if tag.group != 2: raise ValueError( "Only group 2 data elements are allowed in a FileMetaDataset" ) super().__setitem__(key, value) @property def _tsyntax_encoding(self) -> tuple[bool, bool] | tuple[None, None]: """Return the transfer syntax encoding method (if any) Returns ------- tuple[bool, bool] | tuple[None, None] If the file meta has a valid public Transfer Syntax UID then returns (is implicit, is little), otherwise returns (None, None). """ tsyntax = self.get("TransferSyntaxUID", None) if not tsyntax or tsyntax.is_private or not tsyntax.is_transfer_syntax: return (None, None) return (tsyntax.is_implicit_VR, tsyntax.is_little_endian) _RE_CAMEL_CASE = re.compile( # Ensure mix of upper and lowercase and digits, no underscores # If first character is lowercase ensure at least one uppercase char "(?P(^[A-Za-z])((?=.+?[A-Z])[A-Za-z0-9]+)|(^[A-Z])([A-Za-z0-9]+))" "(?P[A-Za-z0-9][^_]$)" # Last character is alphanumeric )