pydicom.dataset.Dataset¶

class pydicom.dataset.Dataset(*args, **kwargs)¶

Contains a collection (dictionary) of DICOM Data Elements.

Behaves like a dict.

Note

Dataset is only derived from dict to make it work in a NumPy ndarray. The parent dict class is never called, as all dict methods are overridden.

Examples

Add an element to the 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 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 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 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 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 Dataset

>>> del ds.PatientID
>>> del ds.BeamSequence[1].Manufacturer
>>> del ds.BeamSequence[2]

Deleting a private element from the Dataset

>>> block = ds.private_block(0x0041, 'My Creator')
>>> if 0x01 in block:
...     del block[0x01]

Determining if an element is present in the 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 Dataset only (excluding Sequences):

>>> for elem in ds:
...    print(elem)
(0010, 0010) Patient's Name                      PN: 'CITIZEN^John'

Iterating through the entire Dataset (including Sequences):

>>> for elem in ds.iterall():
...     print(elem)
(0010, 0010) Patient's Name                      PN: 'CITIZEN^John'

Recursively iterate through a Dataset (including Sequences):

>>> def recurse(ds):
...     for elem in ds:
...         if elem.VR == 'SQ':
...             [recurse(item) for item in elem]
...         else:
...             # Do something useful with each DataElement

Converting the 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: u'Some^Name'

default_element_format¶

The default formatting for string display.

Type:	str

default_sequence_element_format¶

The default formatting for string display of sequences.

Type:	str

indent_chars¶

For string display, the characters used to indent nested Sequences. Default is " ".

Type:	str

is_little_endian¶

Shall be set before writing with write_like_original=False. The Dataset (excluding the pixel data) will be written using the given endianess.

Type:	bool

is_implicit_VR¶

Shall be set before writing with write_like_original=False. The Dataset will be written using the transfer syntax with the given VR handling, e.g Little Endian Implicit VR if True, and Little Endian Explicit VR or Big Endian Explicit VR (depending on Dataset.is_little_endian) if False.

Type:	bool

__init__(*args, **kwargs)¶: Create a new Dataset instance.

Methods

`__init__`(args, *kwargs)	Create a new `Dataset` instance.
`add`(data_element)	Add an element to the `Dataset`.
`add_new`(tag, VR, value)	Create a new element and add it to the `Dataset`.
`clear`()	Delete all the elements from the `Dataset`.
`convert_pixel_data`([handler_name])	Convert pixel data to a `numpy.ndarray` internally.
`copy`()
`data_element`(name)	Return the element corresponding to the element keyword name.
`decode`()	Apply character set decoding to the elements in the `Dataset`.
`decompress`([handler_name])	Decompresses Pixel Data and modifies the `Dataset` in-place.
`dir`(*filters)	Return an alphabetical list of element keywords in the `Dataset`.
`elements`()	Yield the top-level elements of the `Dataset`.
`ensure_file_meta`()	Create an empty `Dataset.file_meta` if none exists.
`fix_meta_info`([enforce_standard])	Ensure the file meta info exists and has the correct values for transfer syntax and media storage UIDs.
`formatted_lines`([element_format, …])	Iterate through the `Dataset` yielding formatted `str` for each element.
`from_json`(json_dataset[, bulk_data_uri_handler])	Add elements to the `Dataset` from DICOM JSON format.
`fromkeys`	Create a new dictionary with keys from iterable and values set to value.
`get`(key[, default])	Simulate `dict.get()` to handle element tags and keywords.
`get_item`(key)	Return the raw data element if possible.
`get_private_item`(group, element_offset, …)	Return the data element for the given private tag group.
`group_dataset`(group)	Return a `Dataset` containing only elements of a certain group.
`items`()	Return the `Dataset` items to simulate `dict.items()`.
`iterall`()	Iterate through the `Dataset`, yielding all the elements.
`keys`()	Return the `Dataset` keys to simulate `dict.keys()`.
`overlay_array`(group)	Return the Overlay Data in group as a `numpy.ndarray`.
`pop`(key, *args)	Emulate `dict.pop()` with support for tags and keywords.
`popitem`()	Remove and return a (key, value) pair as a 2-tuple.
`private_block`(group, private_creator[, create])	Return the block for the given tag group and private_creator.
`private_creators`(group)	Return a list of private creator names in the given group.
`remove_private_tags`()	Remove all private elements from the `Dataset`.
`save_as`(filename[, write_like_original])	Write the `Dataset` to filename.
`set_original_encoding`(is_implicit_vr, …)	Set the values for the original transfer syntax and encoding.
`setdefault`(key[, default])	Emulate `dict.setdefault()` with support for tags and keywords.
`to_json`([bulk_data_threshold, …])	Return a JSON representation of the `Dataset`.
`to_json_dict`([bulk_data_threshold, …])	Return a dictionary representation of the `Dataset` conforming to the DICOM JSON Model as described in the DICOM Standard, Part 18, Annex F.
`top`()	Return a `str` representation of the top level elements.
`trait_names`()	Return a `list` of valid names for auto-completion code.
`update`(dictionary)	Extend `dict.update()` to handle DICOM tags and keywords.
`values`()	Return the `Dataset` values to simulate `dict.values()`.
`walk`(callback[, recursive])	Iterate through the `Dataset's` elements and run callback on each.

Attributes

`default_element_format`
`default_sequence_element_format`
`indent_chars`
`is_original_encoding`	Return `True` if the encoding to be used for writing is set and is the same as that used to originally encode the `Dataset`.
`pixel_array`	Return the pixel data as a `numpy.ndarray`.

add(data_element)¶

Add an element to the Dataset.

Equivalent to ds[data_element.tag] = data_element

Parameters:	data_element (dataelem.DataElement) – The `DataElement` to add.

add_new(tag, VR, value)¶

Create a new element and add it to the Dataset.

Parameters:

tag – The DICOM (group, element) tag in any form accepted by Tag() such as [0x0010, 0x0010], (0x10, 0x10), 0x00100010, etc.
VR (str) – The 2 character DICOM value representation (see DICOM Standard, Part 5, Section 6.2).
value –
The value of the data element. One of the following:
- a single string or number
- a list or tuple with all strings or all numbers
- a multi-value string with backslash separator
- for a sequence element, an empty list or list of Dataset

clear()¶: Delete all the elements from the Dataset.

convert_pixel_data(handler_name='')¶

Convert pixel data to a numpy.ndarray internally.

Parameters:	handler_name (str, optional) – The name of the pixel handler that shall be used to decode the data. Supported names are: `'gdcm'`, `'pillow'`, `'jpeg_ls'`, `'rle'` and `'numpy'`. If not used (the default), a matching handler is used from the handlers configured in `pixel_data_handlers`.
Returns:	Converted pixel data is stored internally in the dataset.
Return type:	None
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.

data_element(name)¶

Return the element corresponding to the element keyword name.

Parameters:	name (str) – A DICOM element keyword.
Returns:	For the given DICOM element keyword, return the corresponding `DataElement` if present, `None` otherwise.
Return type:	dataelem.DataElement or None

decode()¶

Apply character set decoding to the elements in the Dataset.

See DICOM Standard, Part 5, Section 6.1.1.

decompress(handler_name='')¶

Decompresses Pixel Data and modifies the Dataset in-place.

New in version 1.4: The handler_name keyword argument was added

If not a compressed transfer syntax, then pixel data is converted to a numpy.ndarray internally, but not returned.

If compressed pixel data, then is decompressed using an image handler, and internal state is updated appropriately:

Dataset.file_meta.TransferSyntaxUID is updated to non-compressed form
is_undefined_length is False for the (7FE0,0010) Pixel Data element.

Changed in version 1.4: The handler_name keyword argument was added

Parameters:	handler_name (str, optional) – The name of the pixel handler that shall be used to decode the data. Supported names are: `'gdcm'`, `'pillow'`, `'jpeg_ls'`, `'rle'` and `'numpy'`. If not used (the default), a matching handler is used from the handlers configured in `pixel_data_handlers`.
Returns:
Return type:	None
Raises:	`NotImplementedError` – If the pixel data was originally compressed but file is not Explicit VR Little Endian as required by the DICOM Standard.

dir(*filters)¶

Return an alphabetical list of element keywords in the Dataset.

Intended mainly for use in interactive Python sessions. Only lists the element keywords in the current level of the 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:	The matching element keywords in the dataset. If no filters are used then all element keywords are returned.
Return type:	list of str

elements()¶

Yield the top-level elements of the Dataset.

New in version 1.1.

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.

ensure_file_meta()¶: Create an empty Dataset.file_meta if none exists.

New in version 1.2.

fix_meta_info(enforce_standard=True)¶

Ensure the file meta info exists and has the correct values for transfer syntax and media storage UIDs.

New in version 1.2.

Warning

The transfer syntax for is_implicit_VR = False and is_little_endian = True is ambiguous and will therefore not be set.

Parameters:	enforce_standard (bool, optional) – If `True`, a check for incorrect and missing elements is performed (see `validate_file_meta()`).

formatted_lines(element_format='%(tag)s %(name)-35.35s %(VR)s: %(repval)s', sequence_element_format='%(tag)s %(name)-35.35s %(VR)s: %(repval)s', indent_format=None)¶

Iterate through the Dataset yielding formatted str for each element.

Parameters:

element_format (str) – The string format to use for non-sequence elements. Formatting uses the attributes of 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 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.

classmethod from_json(json_dataset, bulk_data_uri_handler=None)¶

Add elements to the Dataset from DICOM JSON format.

New in version 1.3.

See the DICOM Standard, Part 18, Annex F.

Parameters:	json_dataset (dict or str) – `dict` or `str` representing a DICOM Data Set formatted based on the DICOM JSON Model. bulk_data_uri_handler (callable, optional) – Callable function that accepts the “BulkDataURI” of the JSON representation of a data element and returns the actual value of data element (retrieved via DICOMweb WADO-RS).
Returns:
Return type:	Dataset

get(key, default=None)¶

Simulate dict.get() to handle element tags and keywords.

Parameters:

key (str or 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 Dataset then return the element’s value.
dataelem.DataElement – If key is a tag for a element in the Dataset then return the DataElement instance.
value – If key is a class attribute then return its value.

get_item(key)¶

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.

Parameters:	key – The DICOM (group, element) tag in any form accepted by `Tag()` such as `[0x0010, 0x0010]`, `(0x10, 0x10)`, `0x00100010`, etc. May also be a `slice` made up of DICOM tags.
Returns:	The corresponding element.
Return type:	dataelem.DataElement

get_private_item(group, element_offset, private_creator)¶

Return the data element for the given private tag group.

New in version 1.3.

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:	The corresponding element.
Return type:	dataelem.DataElement
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.

group_dataset(group)¶

Return a Dataset containing only elements of a certain group.

Parameters:	group (int) – The group part of a DICOM (group, element) tag.
Returns:	A `Dataset` containing elements of the group specified.
Return type:	Dataset

is_original_encoding¶

Return True if the encoding to be used for writing is set and is the same as that used to originally encode the Dataset.

New in version 1.1.

This includes properties related to endianess, VR handling and the (0008,0005) Specific Character Set.

items()¶

Return the Dataset items to simulate dict.items().

Returns:	The top-level (`BaseTag`, `DataElement`) items for the `Dataset`.
Return type:	dict_items

iterall()¶

Iterate through the Dataset, yielding all the elements.

Unlike Dataset.__iter__(), this does recurse into sequences, and so yields all elements as if the file were “flattened”.

Yields:	dataelem.DataElement

keys()¶

Return the Dataset keys to simulate dict.keys().

Returns:	The `BaseTag` of all the elements in the `Dataset`.
Return type:	dict_keys

overlay_array(group)¶

Return the Overlay Data in group as a numpy.ndarray.

New in version 1.4.

Returns:	The (group,3000) Overlay Data converted to a `numpy.ndarray`.
Return type:	numpy.ndarray

pixel_array¶

Return the pixel data as a numpy.ndarray.

Changed in version 1.4: Added support for Float Pixel Data and Double Float Pixel Data

Returns:	The (7FE0,0008) Float Pixel Data, (7FE0,0009) Double Float Pixel Data or (7FE0,0010) Pixel Data converted to a `numpy.ndarray`.
Return type:	numpy.ndarray

pop(key, *args)¶

Emulate 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 KeyError.

Parameters:	key (int or str or 2-tuple) – If `tuple` - the group and element number of the DICOM tag If `int` - the combined group/element number If `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, `KeyError` is raised
Returns:
Return type:	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.

popitem()¶

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

private_block(group, private_creator, create=False)¶

Return the block for the given tag group and private_creator.

New in version 1.3.

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 `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, `KeyError` is raised instead.
Returns:	Element base for the given tag (the last 2 hex digits are always 0) as a 32-bit `int`.
Return type:	int
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`.

private_creators(group)¶

Return a list of private creator names in the given group.

New in version 1.3.

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 `int`. Must be an odd number.
Returns:	All private creator names for private blocks in the group.
Return type:	list of str
Raises:	`ValueError` – If group is not a private group.

remove_private_tags()¶: Remove all private elements from the Dataset.

save_as(filename, write_like_original=True)¶

Write the Dataset to filename.

Saving requires that the Dataset.is_implicit_VR and Dataset.is_little_endian attributes exist and are set appropriately. If Dataset.file_meta.TransferSyntaxUID is present then it should be set to a consistent value to ensure conformance.

Conformance with DICOM File Format

If write_like_original is False, the Dataset will be stored in the DICOM File Format. To do so requires that the Dataset.file_meta attribute exists and contains a Dataset with the required (Type 1) File Meta Information Group elements (see dcmwrite() and write_file_meta_info() for more information).

If write_like_original is True then the Dataset will be written as is (after minimal validation checking) and may or may not contain all or parts of the File Meta Information (and hence may or may not be conformant with the DICOM File Format).

Parameters:

filename (str or file-like) – Name of file or the file-like to write the new DICOM file to.
write_like_original (bool, optional) –
If True (default), preserves the following information from the Dataset (and may result in a non-conformant file):
- preamble – if the original file has no preamble then none will be written.
- file_meta – if the original file was missing any required File Meta Information Group elements then they will not be added or written. If (0002,0000) File Meta Information Group Length is present then it may have its value updated.
- seq.is_undefined_length – if original had delimiters, write them now too, instead of the more sensible length characters
- is_undefined_length_sequence_item – for datasets that belong to a sequence, write the undefined length delimiters if that is what the original had.
If False, produces a file conformant with the DICOM File Format, with explicit lengths for all elements.