Merge pull request #1489 from hackermd/patch-release-2.2.1

Patch release 2.2.1

.github/workflows/master-push.yml

@@ -127,7 +127,7 @@ jobs:
 
     - name: Install pymedphys
       if: ${{ matrix.pymedphys-dep == 'pymedphys' }}
-      run: python -m pip install pymedphys[user,tests]>=0.31.0
+      run: python -m pip install --pre pymedphys && python -m pip install pymedphys[user,tests]
     - name: Get PyMedPhys cache directory
       if: ${{ matrix.pymedphys-dep == 'pymedphys' }}
       id: pymedphys-cache-location

build_tools/circle/push_doc.sh

@@ -3,7 +3,7 @@
 # This script is meant to be called in the "deploy" step defined
 # in .circleci/config.yml. See https://circleci.com/docs/2.0 for more details.
 
-# We have three possibily workflows:
+# We have three possible workflows:
 #   If the git branch is 'master' then we want to commit and merge the dev/
 #       docs on gh-pages
 #   If the git branch is [0-9].[0.9].X (i.e. 0.9.X, 1.0.X, 1.2.X, 41.21.X) then

doc/old/ref_guide.rst

@@ -32,7 +32,7 @@ File Writing
 DICOM files can also be written using *pydicom*. There are two ways to do this.
 
 * The first is to use
-  :func:`~filewriter.dcmwrite` with a prexisting :class:`~dataset.FileDataset`
+  :func:`~filewriter.dcmwrite` with a preexisting :class:`~dataset.FileDataset`
   (derived from :class:`~dataset.Dataset`) instance.
 * The second is to use the :meth:`Dataset.save_as()<dataset.Dataset.save_as>`
   method on a ``FileDataset`` or ``Dataset`` instance.

doc/release_notes/v0.9.5.rst

@@ -38,6 +38,6 @@ Other
 .....
 
 * switch to Distribute for packaging
-* preliminary work on Python 3 compatiblity
+* preliminary work on Python 3 compatibility
 * preliminary work on using sphinx for documentation
 * preliminary work on better writing of files from scratch

doc/release_notes/v1.2.0.rst

@@ -63,7 +63,7 @@ Fixes
 * Fixed handling of private tags in repeater range (:issue:`689`)
 * Fixed Pillow pixel data handler for non-JPEG2k transfer syntax (:issue:`663`)
 * Fixed handling of elements with ambiguous VR (:pr:`700, 728`)
-* Adapted pixel handlers where endianess is explicitly adapted (:issue:`704`)
+* Adapted pixel handlers where endianness is explicitly adapted (:issue:`704`)
 * Improve performance of bit unpacking (:pr:`715`)
 * First character set no longer removed (:issue:`707`)
 * Fixed RLE decoded data having the wrong byte order (:pr:`729`)

doc/release_notes/v2.2.0.rst

@@ -116,3 +116,5 @@ Fixes
 * Fixed handling of code extensions with person name component delimiter
   (:pr:`1449`)
 * Fixed bug decoding RBG jpg with APP14 marker due to change in Pillow (:pr:`1444`)
+* Fixed decoding for `FloatPixelData` and `DoubleFloatPixelData` via
+  `pydicom.pixel_data_handlers.numpy_handler` (:issue:`1457`)

doc/tutorials/filesets.rst

@@ -332,7 +332,7 @@ use the :meth:`~pydicom.fileset.FileSet.add_custom` method.
 The :meth:`~pydicom.fileset.FileSet.add` method uses *pydicom's* default
 directory record creation functions to create the necessary records based on
 the SOP instance's attributes, such as *SOP Class UID* and *Modality*.
-Occassionally they may fail when an element required by these functions
+Occasionally they may fail when an element required by these functions
 is empty or missing:
 
 .. code-block:: python

doc/tutorials/installation.rst

@@ -156,7 +156,7 @@ RLE images provided a suitable plugin is installed.
 
 Using pip::
 
-  pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg pylibjpeg-rle
+  pip install -U "pylibjpeg>=1.2" pylibjpeg-libjpeg pylibjpeg-openjpeg pylibjpeg-rle
 
 
 .. _tut_install_dev:

examples/input_output/plot_read_fileset.py

@@ -7,7 +7,6 @@
 
 """
 
-import os
 from pathlib import Path
 from tempfile import TemporaryDirectory
 import warnings

examples/input_output/plot_write_dicom.py

@@ -17,7 +17,7 @@
 import datetime
 
 import pydicom
-from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
+from pydicom.dataset import FileDataset, FileMetaDataset
 
 # Create some temporary filenames
 suffix = '.dcm'

pydicom/_version.py

@@ -1,9 +1,9 @@
 """Pure python package for DICOM medical file reading and writing."""
 import re
-from typing import Tuple, cast, Match
+from typing import cast, Match
 
 
-__version__: str = '2.2.0'
+__version__: str = '2.2.1'
 
 result = cast(Match[str], re.match(r'(\d+\.\d+\.\d+).*', __version__))
 __version_info__ = tuple(result.group(1).split('.'))

pydicom/charset.py

@@ -519,24 +519,24 @@ def encode_string(value: str, encodings: Sequence[str]) -> bytes:
             return encoded
         except UnicodeError:
             continue
-    else:
-        # if we have more than one encoding, we retry encoding by splitting
-        # `value` into chunks that can be encoded with one of the encodings
-        if len(encodings) > 1:
-            try:
-                return _encode_string_parts(value, encodings)
-            except ValueError:
-                pass
-        # all attempts failed - raise or warn and encode with replacement
-        # characters
-        if config.enforce_valid_values:
-            # force raising a valid UnicodeEncodeError
-            value.encode(encodings[0])
 
-        warnings.warn("Failed to encode value with encodings: {} - using "
-                      "replacement characters in encoded string"
-                      .format(', '.join(encodings)))
-        return _encode_string_impl(value, encodings[0], errors='replace')
+    # if we have more than one encoding, we retry encoding by splitting
+    # `value` into chunks that can be encoded with one of the encodings
+    if len(encodings) > 1:
+        try:
+            return _encode_string_parts(value, encodings)
+        except ValueError:
+            pass
+    # all attempts failed - raise or warn and encode with replacement
+    # characters
+    if config.enforce_valid_values:
+        # force raising a valid UnicodeEncodeError
+        value.encode(encodings[0])
+
+    warnings.warn("Failed to encode value with encodings: {} - using "
+                  "replacement characters in encoded string"
+                  .format(', '.join(encodings)))
+    return _encode_string_impl(value, encodings[0], errors='replace')
 
 
 def _encode_string_parts(value: str, encodings: Sequence[str]) -> bytes:

pydicom/cli/main.py

@@ -8,15 +8,13 @@
 """
 
 import argparse
-import sys
 import pkg_resources
 import re
 from typing import Tuple, cast, List, Any, Dict, Optional, Callable
 
 from pydicom import dcmread
 from pydicom.data.data_manager import get_testdata_file
 from pydicom.dataset import Dataset
-from pydicom.dataelem import DataElement
 
 
 subparsers: Optional[argparse._SubParsersAction] = None

pydicom/cli/show.py

@@ -2,11 +2,8 @@
 """Pydicom command line interface program for `pydicom show`"""
 
 import argparse
-import sys
-from typing import Optional, List, Union, Callable, Any
+from typing import Optional, List, Union, Callable
 
-from pydicom import dcmread
-from pydicom.data.data_manager import get_testdata_file
 from pydicom.dataset import Dataset
 from pydicom.cli.main import filespec_help, filespec_parser
 

pydicom/config.py

@@ -5,10 +5,7 @@
 
 import logging
 import os
-from typing import (
-    Optional, Callable, Dict, Any, TYPE_CHECKING, List, Union, MutableSequence,
-    Union
-)
+from typing import Optional, Dict, Any, TYPE_CHECKING
 
 have_numpy = True
 try:

pydicom/data/__init__.py

@@ -9,7 +9,7 @@
 __all__ = [
     'fetch_data_files',
     'get_charset_files',
-    'get_palette_files'
+    'get_palette_files',
     'get_testdata_files',
     'get_testdata_file',
 ]

pydicom/data/download.py

@@ -185,7 +185,7 @@ def data_path_with_download(
     filename : str
         The filename of the file to return the path to.
     check_hash : bool, optional
-        ``True`` to perform a SHA256 checkum on the file, ``False`` otherwise.
+        ``True`` to perform a SHA256 checksum on the file, ``False`` otherwise.
     redownload_on_hash_mismatch : bool, optional
         ``True`` to redownload the file on checksum failure, ``False``
         otherwise.

pydicom/datadict.py

@@ -2,7 +2,7 @@
 # -*- coding: utf-8 -*-
 """Access dicom dictionary information"""
 
-from typing import Tuple, Optional, Dict, Union
+from typing import Tuple, Optional, Dict
 
 from pydicom.config import logger
 from pydicom.tag import Tag, BaseTag, TagType
@@ -602,7 +602,7 @@ def private_dictionary_VM(tag: TagType, private_creator: str) -> str:
         The tag for the element whose value multiplicity (VM) is being
         retrieved.
     private_creator : str
-        The name of the private creater.
+        The name of the private creator.
 
     Returns
     -------

pydicom/dataset.py

@@ -329,7 +329,7 @@ class Dataset:
     >>> def recurse(ds):
     ...     for elem in ds:
     ...         if elem.VR == 'SQ':
-    ...             [recurse(item) for item in elem]
+    ...             [recurse(item) for item in elem.value]
     ...         else:
     ...             # Do something useful with each DataElement
 
@@ -354,7 +354,7 @@ class Dataset:
     is_little_endian : bool
         Shall be set before writing with ``write_like_original=False``.
         The :class:`Dataset` (excluding the pixel data) will be written using
-        the given endianess.
+        the given endianness.
     is_implicit_VR : bool
         Shall be set before writing with ``write_like_original=False``.
         The :class:`Dataset` will be written using the transfer syntax with
@@ -382,7 +382,7 @@ def __init__(self, *args: _DatasetType, **kwargs: Any) -> None:
 
         # the following read_XXX attributes are used internally to store
         # the properties of the dataset after read from a file
-        # set depending on the endianess of the read dataset
+        # set depending on the endianness of the read dataset
         self.read_little_endian: Optional[bool] = None
         # set depending on the VR handling of the read dataset
         self.read_implicit_vr: Optional[bool] = None
@@ -1148,7 +1148,7 @@ def get_item(
     def _dataset_slice(self, slce: slice) -> "Dataset":
         """Return a slice that has the same properties as the original dataset.
 
-        That includes properties related to endianess and VR handling,
+        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.
         """
@@ -1168,7 +1168,7 @@ def is_original_encoding(self) -> bool:
 
         .. versionadded:: 1.1
 
-        This includes properties related to endianess, VR handling and the
+        This includes properties related to endianness, VR handling and the
         (0008,0005) *Specific Character Set*.
         """
         return (

pydicom/dicomdir.py

@@ -2,7 +2,7 @@
 """Module for DicomDir class."""
 
 import os
-from typing import Optional, List, Dict, Union, BinaryIO, AnyStr
+from typing import Optional, List, Dict, Union, BinaryIO
 import warnings
 
 from pydicom import config

pydicom/encoders/base.py

@@ -8,7 +8,6 @@
     TYPE_CHECKING, Any
 )
 
-from pydicom.encaps import encapsulate
 from pydicom.uid import (
     UID, JPEGBaseline8Bit, JPEGExtended12Bit, JPEGLosslessP14, JPEGLosslessSV1,
     JPEGLSLossless, JPEGLSNearLossless, JPEG2000Lossless, JPEG2000, RLELossless

pydicom/encoders/gdcm.py

@@ -2,7 +2,7 @@
 
 from typing import Any, cast
 
-from pydicom.uid import RLELossless, ImplicitVRLittleEndian
+from pydicom.uid import RLELossless
 
 try:
     import gdcm

pydicom/encoders/native.py

@@ -1,9 +1,8 @@
 # Copyright 2008-2021 pydicom authors. See LICENSE file for details.
 """Interface for *Pixel Data* encoding, not intended to be used directly."""
 
-from itertools import groupby, islice
+from itertools import groupby
 from struct import pack
-import sys
 from typing import List, Any
 
 from pydicom.uid import RLELossless
@@ -130,7 +129,7 @@ def _encode_row(src: bytes) -> bytes:
     Notes
     -----
     * 2-byte repeat runs are always encoded as Replicate Runs rather than
-      only when not preceeded by a Literal Run as suggested by the Standard.
+      only when not preceded by a Literal Run as suggested by the Standard.
     """
     out: List[int] = []
     out_append = out.append

pydicom/filereader.py

@@ -9,7 +9,7 @@
 import sys
 from typing import (
     BinaryIO, Union, Optional, List, Any, Callable, cast, MutableSequence,
-    Type, Iterator, Dict
+    Iterator, Dict
 )
 import warnings
 import zlib
@@ -24,6 +24,7 @@
 from pydicom.dataset import Dataset, FileDataset, FileMetaDataset
 from pydicom.dicomdir import DicomDir
 from pydicom.errors import InvalidDicomError
+from pydicom.filebase import DicomFileLike
 from pydicom.fileutil import (
     read_undefined_length_value, path_from_pathlike, PathType, _unpack_tag
 )
@@ -732,7 +733,8 @@ def read_preamble(fp: BinaryIO, force: bool) -> Optional[bytes]:
 
 
 def _at_pixel_data(tag: BaseTag, VR: Optional[str], length: int) -> bool:
-    return cast(bool, tag == 0x7fe00010)
+    pixel_data_tags = {0x7fe00010, 0x7fe00009, 0x7fe00008}
+    return tag in pixel_data_tags
 
 
 def read_partial(
@@ -901,7 +903,7 @@ def read_partial(
 
 
 def dcmread(
-    fp: Union[PathType, BinaryIO],
+    fp: Union[PathType, BinaryIO, DicomFileLike],
     defer_size: Optional[Union[str, int, float]] = None,
     stop_before_pixels: bool = False,
     force: bool = False,

pydicom/fileset.py

@@ -90,7 +90,7 @@ def generate_filename(
         The starting index to use for the suffixes, (default ``0``).
         i.e. if you want to start at ``'00010'`` then `start` should be ``10``.
     alphanumeric : bool, optional
-        If ``False`` (defalt) then only generate suffixes using the characters
+        If ``False`` (default) then only generate suffixes using the characters
         [0-9], otherwise use [0-9][A-Z].
 
     Yields

pydicom/fileutil.py

@@ -7,6 +7,7 @@
 from pydicom.misc import size_in_bytes
 from pydicom.tag import TupleTag, Tag, SequenceDelimiterTag, ItemTag, BaseTag
 from pydicom.datadict import dictionary_description
+from pydicom.filebase import DicomFileLike
 
 from pydicom.config import logger
 
@@ -411,7 +412,7 @@ def length_of_undefined_length(
 
 
 def path_from_pathlike(
-    file_object: Union[PathType, BinaryIO]
+    file_object: Union[PathType, BinaryIO, DicomFileLike]
 ) -> Union[str, BinaryIO]:
     """Returns the path if `file_object` is a path-like object, otherwise the
     original `file_object`.

pydicom/filewriter.py

@@ -830,7 +830,7 @@ def _write_dataset(
     if any, has been written.
     """
 
-    # if we want to write with the same endianess and VR handling as
+    # if we want to write with the same endianness and VR handling as
     # the read dataset we want to preserve raw data elements for
     # performance reasons (which is done by get_item);
     # otherwise we use the default converting item getter

pydicom/jsonrep.py

@@ -3,9 +3,8 @@
 
 import base64
 from inspect import signature
-import inspect
 from typing import (
-    Callable, Optional, Union, Any, cast, Type, TypeVar, Dict, TYPE_CHECKING,
+    Callable, Optional, Union, Any, cast, Type, Dict, TYPE_CHECKING,
     List
 )
 import warnings

pydicom/misc.py

@@ -3,7 +3,6 @@
 
 from itertools import groupby
 from pathlib import Path
-import re
 from typing import Optional, Union