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@scaramallion
scaramallion committed Apr 1, 2024
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154 changes: 77 additions & 77 deletions doc/release_notes/v3.0.0.rst
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Expand Up @@ -3,67 +3,67 @@ Version 3.0.0

Changes
-------
* Removed support for Python <= 3.9
* All tag formats changed to upper case, no space e.g. "(7FE0,0010)" rather than "(7fe0, 0010)"
* Removed support for Python <= 3.9.
* All tag formats changed to upper case, no space e.g. "(7FE0,0010)" rather than "(7fe0, 0010)".
* Values with VR **AE** with an incorrect value length are now handled
gracefully (extra bytes are ignored with a warning)
gracefully (extra bytes are ignored with a warning).
* A value of 0 for *Number of Frames* is now handled as 1 frame, with a user warning issued
on reading the pixel data (:issue:`1844`)
on reading the pixel data (:issue:`1844`).
* The value for :attr:`~pydicom.uid.JPEGLossless` has changed from
1.2.840.10008.1.2.4.70 to 1.2.840.10008.1.2.4.57 to match its UID keyword. Use
:attr:`~pydicom.uid.JPEGLosslessSV1` instead for 1.2.840.10008.1.2.4.70
:attr:`~pydicom.uid.JPEGLosslessSV1` instead for 1.2.840.10008.1.2.4.70.
* The theoretical maximum number of instances supported by
:class:`~pydicom.fileset.FileSet` has been reduced to 1838265625 to ensure support
for 32-bit systems (:issue:`1743`)
for 32-bit systems (:issue:`1743`).
* The characters used by :func:`~pydicom.fileset.generate_filename` when
`alphanumeric` is ``True`` has been reduced to [0-9][A-I,K-Z]
`alphanumeric` is ``True`` has been reduced to [0-9][A-I,K-Z].
* :func:`~pydicom.data.get_testdata_file` and
:func:`~pydicom.data.get_testdata_files`
now raise ``ValueError`` if called with an absolute path or pattern
now raise ``ValueError`` if called with an absolute path or pattern.
* :func:`~pydicom.uid.generate_uid` has been changed to use a random suffix
generated using :func:`~secrets.randbelow` when `entropy_srcs` isn't used, and
the maximum allowed length of the `prefix` has been changed to 54 characters
(:issue:`1773`)
(:issue:`1773`).
* :attr:`DataElement.VM<pydicom.dataelem.DataElement.VM>` always returns ``1``
for **SQ** elements (:issue:`1481`)
* DICOM dictionary updated to 2023d
for **SQ** elements (:issue:`1481`).
* DICOM dictionary updated to 2023d.
* :func:`~pydicom.dataset.validate_file_meta` now checks to ensure required
Type 1 elements aren't empty
Type 1 elements aren't empty.
* `implicit_vr` and `little_endian` optional arguments added to
:meth:`Dataset.save_as()<pydicom.dataset.Dataset.save_as>`. In addition, this
method will now raise an exception if the user tries to convert between little
and big endian datasets. If this is something you need, use
:func:`~pydicom.filewriter.dcmwrite` instead.
* `implicit_vr`, `little_endian` and `force_encoding` optional arguments
added to :func:`~pydicom.filewriter.dcmwrite`
added to :func:`~pydicom.filewriter.dcmwrite`.
* The priority used to decide which encoding to use with
:meth:`Dataset.save_as()<pydicom.dataset.Dataset.save_as>` and
:func:`~pydicom.filewriter.dcmwrite` has been changed to:

1. The set *Transfer Syntax UID*
2. The `implicit_vr` and `little_endian` arguments
1. The set *Transfer Syntax UID*,
2. The `implicit_vr` and `little_endian` arguments,
3. :attr:`Dataset.is_implicit_VR<pydicom.dataset.Dataset.is_implicit_VR>` and
:attr:`Dataset.is_little_endian<pydicom.dataset.Dataset.is_little_endian>`
4. :attr:`Dataset.original_encoding<pydicom.dataset.Dataset.original_encoding>`
:attr:`Dataset.is_little_endian<pydicom.dataset.Dataset.is_little_endian>`,
4. :attr:`Dataset.original_encoding<pydicom.dataset.Dataset.original_encoding>`.
* Datasets containing *Command Set* (0000,eeee) elements can no longer be written using
:meth:`Dataset.save_as()<pydicom.dataset.Dataset.save_as>` or
:func:`~pydicom.filewriter.dcmwrite`, use :func:`~pydicom.filewriter.write_dataset`
instead.
* A dataset's :attr:`~pydicom.dataset.FileDataset.file_meta` elements are no longer
modified when writing
modified when writing.
* :class:`~pydicom.filebase.DicomIO` now requires a readable or writeable buffer
during initialisation and :class:`~pydicom.filebase.DicomBytesIO` directly
inherits from it.
* The ``pydicom.encoders`` module has been moved to :mod:`pydicom.pixels.encoders
<pydicom.pixels.encoders>`, the original import path will be removed in v4.0
<pydicom.pixels.encoders>`, the original import path will be removed in v4.0.
* Using GDCM v3.0.23 or lower to decode JPEG-LS datasets with a *Bits Stored* of
6 or 7 produces incorrect results, so attempting to do so now raises an exception.
``pyjpegls`` or ``pylibjpeg`` with ``pylibjpeg-libjpeg`` can be used instead (:issue:`2008`)
``pyjpegls`` or ``pylibjpeg`` with ``pylibjpeg-libjpeg`` can be used instead (:issue:`2008`).


Removals
~~~~~~~~
* The ``compat`` module has been removed
* The ``compat`` module has been removed.
* The ``dicomdir`` module and ``DicomDir`` class have been removed and reading a
DICOMDIR dataset now returns a normal :class:`~pydicom.dataset.FileDataset` instance.
For handling DICOM File-sets and DICOMDIR datasets use the
Expand Down Expand Up @@ -93,30 +93,30 @@ Removals
:attr:`~pydicom.uid.UncompressedTransferSyntaxes`
* ``PILSupportedCompressedPixelTransferSyntaxes``
* The ``PersonNameUnicode`` class has been removed, use
:class:`~pydicom.valuerep.PersonName` instead
:class:`~pydicom.valuerep.PersonName` instead.
* The ``DataElement.description`` attribute has been removed, use
:attr:`DataElement.name<pydicom.dataelem.DataElement.name>` instead
:attr:`DataElement.name<pydicom.dataelem.DataElement.name>` instead.
* The ``pixel_data_handlers.rle_handler.rle_encode_frame`` function has been
removed, use :meth:`Dataset.compress()<pydicom.dataset.Dataset.compress>` or
:attr:`~pydicom.pixels.encoders.base.RLELosslessEncoder` instead.
* The ``_storage_sopclass_uids`` module has been removed, import UIDs from the
:mod:`~pydicom.uid` module instead
:mod:`~pydicom.uid` module instead.
* The following properties have been removed:

* ``Dataset.parent`` and ``Dataset.parent_seq``
* ``Sequence.parent`` and ``Sequence.parent_dataset``
* ``DataElement.parent``
* The ``overlay_data_handlers`` module has been removed, use the :mod:`~pydicom.overlays`
module instead
* ``config.overlay_data_handlers`` has been removed
module instead.
* ``config.overlay_data_handlers`` has been removed.
* ``Dataset.fix_meta_info()`` has been removed as encoding state now follows the
transfer syntax instead of the other way around
transfer syntax instead of the other way around.


Enhancements
------------
* Added details of missing required tag information when adding a dataset to a
File-set (:issue:`1752`)
File-set (:issue:`1752`).
* The following UID constants have been added:

* :attr:`~pydicom.uid.MPEG2MPMLF`
Expand All @@ -134,27 +134,27 @@ Enhancements
* :attr:`~pydicom.uid.SMPTEST211020UncompressedProgressiveActiveVideo`
* :attr:`~pydicom.uid.SMPTEST211020UncompressedInterlacedActiveVideo`
* :attr:`~pydicom.uid.SMPTEST211030PCMDigitalAudio`
* Added convenience method :meth:`~pydicom.dataset.Dataset.add_new_private` to add a private tag
* Added convenience method :meth:`~pydicom.dataset.Dataset.add_new_private` to add a private tag.
* Added the :ref:`examples<api_examples>` module to make it easier and less
confusing for users to work with the example datasets used by the documentation
confusing for users to work with the example datasets used by the documentation.
* Added the ability to set the corresponding dataset encoding for private transfer
syntaxes to :class:`~pydicom.uid.UID` via the :meth:`~pydicom.uid.UID.set_private_encoding`
method
method.
* Added the ability to register private transfer syntaxes with
:func:`~pydicom.uid.register_transfer_syntax` so they can be used when reading
datasets with :func:`~pydicom.filereader.dcmread`
* Warning messages are also sent to the pydicom logger (:issue:`1529`)
datasets with :func:`~pydicom.filereader.dcmread`.
* Warning messages are also sent to the pydicom logger (:issue:`1529`).
* Added the following to the :mod:`~pydicom.encaps` module:

* :func:`~pydicom.encaps.parse_basic_offsets` for parsing the Basic Offset Table
* :func:`~pydicom.encaps.parse_basic_offsets` for parsing the Basic Offset Table.
* :func:`~pydicom.encaps.parse_fragments` for determining the number of encapsulated
fragments and their byte offsets
* :func:`~pydicom.encaps.generate_fragments` for yielding encapsulated fragments
fragments and their byte offsets.
* :func:`~pydicom.encaps.generate_fragments` for yielding encapsulated fragments.
* :func:`~pydicom.encaps.generate_fragmented_frames` for yielding encapsulated frame
fragments
* :func:`~pydicom.encaps.generate_frames` for yielding whole encapsulated frames
fragments.
* :func:`~pydicom.encaps.generate_frames` for yielding whole encapsulated frames.
* :func:`~pydicom.encaps.get_frame` for returning the specific encapsulated frame at `index`
without necessarily having to read the preceding frames into memory
without necessarily having to read the preceding frames into memory.

These new functions support reading encapsulated data from both :class:`bytes`
or any Python object with ``read()``, ``seek()`` and ``tell()`` methods such
Expand All @@ -163,22 +163,22 @@ Enhancements
<part03/sect_C.7.6.3.html#sect_C.7.6.3.1.8>` for determining frame boundaries.
* Added the `keep_deferred` keyword argument to :meth:`Dataset.get_item()
<pydicom.dataset.Dataset.get_item>` to allow accessing the file offset and
element length without having to read the element value. (:issue:`1873`)
element length without having to read the element value. (:issue:`1873`).
* Added the :mod:`~pydicom.pixels` module and a new more flexible backend for
decoding pixel data via :class:`~pydicom.pixels.decoders.base.Decoder` factory class
instances. The new decoding backend adds support for the following:

* Returning a view over the original pixel data buffer (:issue:`746`)
* Retrieving specific frames (:issue:`1263`, :issue:`1243`)
* Returning a view over the original pixel data buffer (:issue:`746`).
* Retrieving specific frames (:issue:`1263`, :issue:`1243`).
* Returning RGB pixel data by default for JPEG (:issue:`1781`, :issue:`1133`
and many others)
and many others).
* Returning excess frames for JPEG when there is no Basic or Extended Offset
Table and the *Number of Frames* is incorrect (:issue:`1666`)
Table and the *Number of Frames* is incorrect (:issue:`1666`).
* Returning the decoded pixel data as either a NumPy :class:`~numpy.ndarray` or
`buffer-like object <https://docs.python.org/3/c-api/buffer.html#bufferobjects>`_
* Iterating through either all or specific frames
`buffer-like object <https://docs.python.org/3/c-api/buffer.html#bufferobjects>`_.
* Iterating through either all or specific frames.

* Added support for decoding HTJ2K transfer syntaxes (:issue:`1848`)
* Added support for decoding HTJ2K transfer syntaxes (:issue:`1848`).
* Added two functions for returning pixel data as a NumPy :class:`~numpy.ndarray`
from a path to a dataset while minimizing memory-usage: :func:`~pydicom.pixels.pixel_array`
and :func:`~pydicom.pixels.iter_pixels`.
Expand All @@ -198,64 +198,64 @@ Fixes
-----
* Fixed the GDCM and pylibjpeg handlers changing the *Pixel Representation* value to 0
when the J2K stream disagrees with the dataset and
:attr:`~pydicom.config.APPLY_J2K_CORRECTIONS` is ``True`` (:issue:`1689`)
* Fixed pydicom codify error when relative path did not exist
* Fixed the VR enum sometimes returning invalid values for Python 3.11+ (:issue:`1874`)
* Fixed pixel data handler for Pillow 10.1 raising an AttributeError (:issue:`1907`)
:attr:`~pydicom.config.APPLY_J2K_CORRECTIONS` is ``True`` (:issue:`1689`).
* Fixed pydicom codify error when relative path did not exist.
* Fixed the VR enum sometimes returning invalid values for Python 3.11+ (:issue:`1874`).
* Fixed pixel data handler for Pillow 10.1 raising an AttributeError (:issue:`1907`).
* Fixed a possible security issue with :class:`~pydicom.fileset.FileInstance` instances
being able to escape the temporary directory when being added to a
:class:`~pydicom.fileset.FileSet` (:issue:`1922`)
:class:`~pydicom.fileset.FileSet` (:issue:`1922`).
* Fixed an ``AttributeError`` when running :py:func:`~copy.deepcopy` after
:meth:`Dataset.update<pydicom.dataset.Dataset.update>` (:issue:`1816`)
:meth:`Dataset.update<pydicom.dataset.Dataset.update>` (:issue:`1816`).
* Fixed :func:`~pydicom.encaps.encapsulate_extended` not returning the correct
values for odd-length frames (:issue:`1968`)
values for odd-length frames (:issue:`1968`).
* Fixed using the incorrect encoding when writing datasets converted between
explicit and implicit VR when only the *Transfer Syntax UID* was changed (:issue:`1943`)
explicit and implicit VR when only the *Transfer Syntax UID* was changed (:issue:`1943`).
* Fixed the ``jpeg_ls``, ``pillow`` and ``rle`` pixel data handlers not working
correctly when a frame is spread across multiple fragments (:issue:`1774`)
correctly when a frame is spread across multiple fragments (:issue:`1774`).
* Added mitigation for a rare case where clearing the pixel data value prior
to updating it may sometimes result in :attr:`~pydicom.dataset.Dataset.pixel_array`
returning the previous array instead of creating a new one (:issue:`1983`)
returning the previous array instead of creating a new one (:issue:`1983`).
* Fixed a ``KeyError`` when comparing codes with one of the codes having
``scheme_designator`` set to ``SRT`` but not being included in the ``SRT``
to ``SCT`` code mapping (:issue:`1994`)
to ``SCT`` code mapping (:issue:`1994`).
* Fixed JPEG-LS datasets with a *Pixel Representation* of 1 returning incorrect
image data when *Bits Stored* is less than *Bits Allocated* (:issue:`2009`)
image data when *Bits Stored* is less than *Bits Allocated* (:issue:`2009`).
* Fixed decoding failures for JPEG-LS datasets with *Bits Allocated* of 16 and
*Bits Stored* <= 8 (:issue:`2010`)
*Bits Stored* <= 8 (:issue:`2010`).
* Fixed the *Pixel Data* VR not being set correctly with :func:`Dataset.compress()
<pydicom.dataset.Dataset.compress>` (:issue:`2013`)
<pydicom.dataset.Dataset.compress>` (:issue:`2013`).


Deprecations
------------
* :attr:`Dataset.is_little_endian <pydicom.dataset.Dataset.is_little_endian>` and
:attr:`Dataset.is_implicit_VR<pydicom.dataset.Dataset.is_implicit_VR>` will be removed in v4.0
:attr:`Dataset.is_implicit_VR<pydicom.dataset.Dataset.is_implicit_VR>` will be removed in v4.0.
* :attr:`Dataset.read_little_endian<pydicom.dataset.Dataset.read_little_endian>` and
:attr:`Dataset.read_implicit_vr<pydicom.dataset.Dataset.read_implicit_vr>` will be removed in v4.0,
use :attr:`Dataset.original_encoding<pydicom.dataset.Dataset.original_encoding>` instead
use :attr:`Dataset.original_encoding<pydicom.dataset.Dataset.original_encoding>` instead.
* :attr:`Dataset.read_encoding<pydicom.dataset.Dataset.read_encoding>` will be removed in v4.0,
use :attr:`Dataset.original_character_set<pydicom.dataset.Dataset.original_character_set>` instead
use :attr:`Dataset.original_character_set<pydicom.dataset.Dataset.original_character_set>` instead.
* The `write_like_original` optional argument to
:meth:`Dataset.save_as<pydicom.dataset.Dataset.save_as>` and
:func:`~pydicom.filewriter.dcmwrite` will be removed in v4.0, use
`enforce_file_format` instead
`enforce_file_format` instead.
* The following :mod:`~pydicom.encaps` module functions will be removed in v4.0:

* :func:`~pydicom.encaps.get_frame_offsets`, use :func:`~pydicom.encaps.parse_basic_offsets`
instead
instead.
* :func:`~pydicom.encaps.generate_pixel_data_fragment`, use :func:`~pydicom.encaps.generate_fragments`
instead
instead.
* :func:`~pydicom.encaps.generate_pixel_data_frame`, use :func:`~pydicom.encaps.generate_fragmented_frames`
instead
instead.
* :func:`~pydicom.encaps.generate_pixel_data`, use :func:`~pydicom.encaps.generate_frames`
instead
instead.
* :func:`~pydicom.encaps.decode_data_sequence`, use :func:`~pydicom.encaps.generate_fragments`
instead
instead.
* :func:`~pydicom.encaps.defragment_data`, use :func:`~pydicom.encaps.generate_frames`
instead
instead.
* :func:`~pydicom.encaps.read_item`, use :func:`~pydicom.encaps.generate_fragments`
instead
instead.

* The :mod:`pydicom.pixel_data_handlers` module will be removed in v4.0. All pixel
data processing will use the :mod:`pydicom.pixels` module instead starting
Expand Down Expand Up @@ -286,12 +286,12 @@ Deprecations
* :func:`~pydicom.pixels.utils.unpack_bits`

* :func:`~pydicom.pixel_data_handlers.util.dtype_corrected_for_endianness` will be
removed in v4.0
removed in v4.0.


Pydicom Internals
-----------------
* Repository folder structure refactored
* Renamed top level ``source`` folder to ``util``
* New CI tools - `dependabot`, and `pre-commit` using black and ruff
* Added a script to hotfix the documentation search function (:issue:`1965`)
* Repository folder structure refactored.
* Renamed top level ``source`` folder to ``util``.
* New CI tools - `dependabot`, and `pre-commit` using black and ruff.
* Added a script to hotfix the documentation search function (:issue:`1965`).

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