Merge pull request #17 from ZviBaratz/isort

isort integration

dicom_parser/data_element.py

@@ -2,13 +2,14 @@
 Definition of the :class:`DataElement` class.
 """
 
-import pandas as pd
 import re
+from typing import Any
+
+import pandas as pd
+from pydicom.dataelem import DataElement as PydicomDataElement
 
 from dicom_parser.utils.parse_tag import parse_tag
 from dicom_parser.utils.value_representation import ValueRepresentation
-from pydicom.dataelem import DataElement as PydicomDataElement
-from typing import Any
 
 
 class DataElement:

dicom_parser/data_elements/code_string.py

@@ -4,17 +4,13 @@
 """
 
 import warnings
+from enum import Enum
 
 from dicom_parser.data_element import DataElement
-from dicom_parser.utils.code_strings import (
-    Modality,
-    Sex,
-    PatientPosition,
-    ScanningSequence,
-    SequenceVariant,
-)
+from dicom_parser.utils.code_strings import (Modality, PatientPosition,
+                                             ScanningSequence, SequenceVariant,
+                                             Sex)
 from dicom_parser.utils.value_representation import ValueRepresentation
-from enum import Enum
 
 
 class CodeString(DataElement):

dicom_parser/data_elements/date.py

@@ -3,6 +3,7 @@
 """
 
 from datetime import datetime
+
 from dicom_parser.data_element import DataElement
 from dicom_parser.data_elements.messages import DATE_PARSING_FAILURE
 from dicom_parser.utils.value_representation import ValueRepresentation

dicom_parser/data_elements/person_name.py

@@ -3,9 +3,10 @@
 element.
 """
 
+from pydicom.valuerep import PersonName as PydicomPersonName
+
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
-from pydicom.valuerep import PersonName as PydicomPersonName
 
 
 class PersonName(DataElement):

dicom_parser/data_elements/private_data_element.py

@@ -3,19 +3,17 @@
 data element.
 """
 
+from types import FunctionType
+from typing import Any
+
+from pydicom.dataelem import DataElement as PydicomDataElement
+
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.siemens.private_tags import (
-    parse_siemens_b_matrix,
-    parse_siemens_bandwith_per_pixel_phase_encode,
-    parse_siemens_csa_header,
-    parse_siemens_gradient_direction,
-    parse_siemens_number_of_slices_in_mosaic,
-    parse_siemens_slice_timing,
-)
+    parse_siemens_b_matrix, parse_siemens_bandwith_per_pixel_phase_encode,
+    parse_siemens_csa_header, parse_siemens_gradient_direction,
+    parse_siemens_number_of_slices_in_mosaic, parse_siemens_slice_timing)
 from dicom_parser.utils.value_representation import ValueRepresentation
-from pydicom.dataelem import DataElement as PydicomDataElement
-from types import FunctionType
-from typing import Any
 
 #: A dictionary matching private data elements to their appropriate parsing
 #: method.

dicom_parser/data_elements/sequence_of_items.py

@@ -4,12 +4,12 @@
 """
 
 import pandas as pd
+from pydicom.dataset import Dataset as PydicomDataset
 
 from dicom_parser.data_element import DataElement
 from dicom_parser.data_elements.messages import INVALID_SEQUENCE_PARSING
 from dicom_parser.utils.format_header_df import format_header_df
 from dicom_parser.utils.value_representation import ValueRepresentation
-from pydicom.dataset import Dataset as PydicomDataset
 
 
 class SequenceOfItems(DataElement):

dicom_parser/data_elements/time.py

@@ -3,6 +3,7 @@
 """
 
 from datetime import datetime
+
 from dicom_parser.data_element import DataElement
 from dicom_parser.data_elements.messages import TIME_PARSING_FAILURE
 from dicom_parser.utils.value_representation import ValueRepresentation

dicom_parser/header.py

@@ -4,23 +4,23 @@
 
 """
 import json
+from collections.abc import KeysView
+from pathlib import Path
+from types import GeneratorType
+from typing import Any, Union
+
 import pandas as pd
+from pydicom.dataelem import DataElement as PydicomDataElement
+from pydicom.dataset import FileDataset
 
-from collections.abc import KeysView
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.format_header_df import format_header_df
 from dicom_parser.utils.private_tags import PRIVATE_TAGS
 from dicom_parser.utils.read_file import read_file
-from dicom_parser.utils.sequence_detector.sequence_detector import (
-    SequenceDetector,
-)
+from dicom_parser.utils.sequence_detector.sequence_detector import \
+    SequenceDetector
 from dicom_parser.utils.value_representation import ValueRepresentation
 from dicom_parser.utils.vr_to_data_element import get_data_element_class
-from pathlib import Path
-from pydicom.dataelem import DataElement as PydicomDataElement
-from pydicom.dataset import FileDataset
-from types import GeneratorType
-from typing import Any, Union
 
 
 class Header:

dicom_parser/image.py

@@ -5,16 +5,17 @@
 
 """
 
-import numpy as np
 import warnings
+from pathlib import Path
+from typing import Union
+
+import numpy as np
+from pydicom.dataset import FileDataset
 
 from dicom_parser import messages
 from dicom_parser.header import Header
 from dicom_parser.utils.read_file import read_file
 from dicom_parser.utils.siemens.mosaic import Mosaic
-from pathlib import Path
-from pydicom.dataset import FileDataset
-from typing import Union
 
 
 class Image:

dicom_parser/series.py

@@ -9,11 +9,9 @@
 import numpy as np
 
 from dicom_parser.image import Image
-from dicom_parser.messages import (
-    EMPTY_SERIES_DIRECTORY,
-    INVALID_INDEXING_OPERATOR,
-    INVALID_SERIES_DIRECTORY,
-)
+from dicom_parser.messages import (EMPTY_SERIES_DIRECTORY,
+                                   INVALID_INDEXING_OPERATOR,
+                                   INVALID_SERIES_DIRECTORY)
 from dicom_parser.utils.mime_generator import generate_by_mime
 from dicom_parser.utils.peek import peek
 

dicom_parser/utils/code_strings/__init__.py

@@ -6,5 +6,5 @@
 from dicom_parser.utils.code_strings.modality import Modality
 from dicom_parser.utils.code_strings.patient_position import PatientPosition
 from dicom_parser.utils.code_strings.scanning_sequence import ScanningSequence
-from dicom_parser.utils.code_strings.sex import Sex
 from dicom_parser.utils.code_strings.sequence_variant import SequenceVariant
+from dicom_parser.utils.code_strings.sex import Sex

dicom_parser/utils/format_header_df.py

@@ -4,6 +4,7 @@
 """
 
 import functools
+
 import pandas as pd
 
 

dicom_parser/utils/peek.py

@@ -5,7 +5,6 @@
 """
 
 import itertools
-
 from types import GeneratorType
 
 

dicom_parser/utils/read_file.py

@@ -2,12 +2,13 @@
 Definition of the :func:`read_file` function.
 """
 
+from pathlib import Path
+from typing import Union
+
 import pydicom
+from pydicom.dataset import FileDataset
 
 from dicom_parser.utils.messages import BAD_FILE_INPUT
-from pathlib import Path
-from pydicom.dataset import FileDataset
-from typing import Union
 
 
 def read_file(

dicom_parser/utils/sequence_detector/__init__.py

@@ -1,3 +1,2 @@
-from dicom_parser.utils.sequence_detector.sequence_detector import (
-    SequenceDetector,
-)
+from dicom_parser.utils.sequence_detector.sequence_detector import \
+    SequenceDetector

dicom_parser/utils/sequence_detector/sequence_detector.py

@@ -4,9 +4,7 @@
 """
 
 from dicom_parser.utils.sequence_detector.messages import (
-    INVALID_MODALITY,
-    WRONG_DEFINITION_TYPE,
-)
+    INVALID_MODALITY, WRONG_DEFINITION_TYPE)
 from dicom_parser.utils.sequence_detector.sequences import SEQUENCES
 
 

dicom_parser/utils/vr_to_data_element.py

@@ -3,23 +3,21 @@
 :class:`dicom_parser.data_element.DataElement` subclass.
 """
 
+from dicom_parser.data_element import DataElement
 from dicom_parser.data_elements.age_string import AgeString
 from dicom_parser.data_elements.application_entity import ApplicationEntity
 from dicom_parser.data_elements.attribute_tag import AttributeTag
 from dicom_parser.data_elements.code_string import CodeString
 from dicom_parser.data_elements.date import Date
 from dicom_parser.data_elements.date_time import DateTime
 from dicom_parser.data_elements.decimal_string import DecimalString
-from dicom_parser.data_elements.floating_point_double import (
-    FloatingPointDouble,
-)
-from dicom_parser.data_elements.floating_point_single import (
-    FloatingPointSingle,
-)
+from dicom_parser.data_elements.floating_point_double import \
+    FloatingPointDouble
+from dicom_parser.data_elements.floating_point_single import \
+    FloatingPointSingle
 from dicom_parser.data_elements.integer_string import IntegerString
 from dicom_parser.data_elements.long_string import LongString
 from dicom_parser.data_elements.long_text import LongText
-from dicom_parser.data_element import DataElement
 from dicom_parser.data_elements.other_64bit_very_long import Other64bitVeryLong
 from dicom_parser.data_elements.other_byte import OtherByte
 from dicom_parser.data_elements.other_double import OtherDouble
@@ -31,25 +29,21 @@
 from dicom_parser.data_elements.sequence_of_items import SequenceOfItems
 from dicom_parser.data_elements.short_string import ShortString
 from dicom_parser.data_elements.short_text import ShortText
-from dicom_parser.data_elements.signed_64bit_very_long import (
-    Signed64bitVeryLong,
-)
+from dicom_parser.data_elements.signed_64bit_very_long import \
+    Signed64bitVeryLong
 from dicom_parser.data_elements.signed_long import SignedLong
 from dicom_parser.data_elements.signed_short import SignedShort
 from dicom_parser.data_elements.time import Time
 from dicom_parser.data_elements.unique_identifier import UniqueIdentifer
 from dicom_parser.data_elements.unlimited_characters import UnlimitedCharacters
 from dicom_parser.data_elements.unlimited_text import UnlimitedText
-from dicom_parser.data_elements.unsigned_64bit_very_long import (
-    Unsigned64bitVeryLong,
-)
+from dicom_parser.data_elements.unsigned_64bit_very_long import \
+    Unsigned64bitVeryLong
 from dicom_parser.data_elements.unsigned_long import UnsignedLong
 from dicom_parser.data_elements.unsigned_short import UnsignedShort
 from dicom_parser.data_elements.url import Url
-from dicom_parser.utils.value_representation import (
-    ValueRepresentation,
-    get_value_representation,
-)
+from dicom_parser.utils.value_representation import (ValueRepresentation,
+                                                     get_value_representation)
 
 #: A dictionary associating the various value representations with their
 #: appropriate :class:`dicom_parser.data_element.DataElement` subclasses.

docs/release_notes.rst

@@ -5,8 +5,11 @@ Release Notes
 -----
 
   * Lots of documentation updates and linting fixes.
+  * Integrated `isort`_.
   * Changed invalid integer strings ("IS" data elements) to return *None* (see
     :class:`~dicom_parser.data_elements.integer_string.IntegerString`).
+  * Added `mime` option to :class:`~dicom_parser.series.Series`.
+  * Updated development status classifier to beta.
 
 0.1.5
 -----
@@ -99,6 +102,7 @@ First release!
 .. _CSA Headers: https://nipy.org/nibabel/dicom/siemens_csa.html
 .. _dcm2niix: https://github.com/rordenlab/dcm2niix
 .. _django_dicom: https://github.com/TheLabbingProject/django_dicom
+.. _isort: https://pycqa.github.io/isort/
 .. _NIfTI: https://nifti.nimh.nih.gov/
 .. _pydicom: https://github.com/pydicom/pydicom
 .. _Siemens mosaic: https://nipy.org/nibabel/dicom/dicom_mosaic.html

requirements-dev.txt

@@ -4,6 +4,7 @@ coverage-badge~=1.0
 doc8~=0.8
 flake8~=3.7
 ipython~=7.19
+isort~=5.7
 pytest~=5.3
 sphinx~=3.3
 sphinx-rtd-theme~=0.4

setup.py

@@ -1,4 +1,5 @@
 import os
+
 from setuptools import find_packages, setup
 
 with open("README.md", "r") as fh:
@@ -30,7 +31,7 @@
     install_requires=requirements,
     extras_require={"dev": dev_requirements},
     classifiers=[
-        "Development Status :: 3 - Alpha",
+        "Development Status :: 4 - Beta",
         "Intended Audience :: Science/Research",
         "License :: OSI Approved :: GNU Affero General Public License v3",
         "Operating System :: OS Independent",

tests/fixtures.py

@@ -1,6 +1,6 @@
 import os
-
 from datetime import datetime
+
 from dicom_parser.utils.choice_enum import ChoiceEnum
 
 TESTS_DIRECTORY = os.path.dirname(os.path.realpath(__file__))

tests/test_header.py

@@ -1,15 +1,13 @@
-import pydicom
 import warnings
+from pathlib import Path
+from unittest import TestCase
+
+import pydicom
 
 from dicom_parser.header import Header
 from dicom_parser.utils.sequence_detector import SequenceDetector
-from pathlib import Path
-from tests.fixtures import (
-    TEST_IMAGE_PATH,
-    TEST_STUDY_FIELDS,
-    TEST_GE_LOCALIZER_PATH,
-)
-from unittest import TestCase
+from tests.fixtures import (TEST_GE_LOCALIZER_PATH, TEST_IMAGE_PATH,
+                            TEST_STUDY_FIELDS)
 
 
 class HeaderTestCase(TestCase):

tests/test_image.py

@@ -1,11 +1,12 @@
+from pathlib import Path
+from unittest import TestCase
+
 import numpy as np
 import pydicom
 
 from dicom_parser.header import Header
 from dicom_parser.image import Image
-from pathlib import Path
 from tests.fixtures import TEST_IMAGE_PATH, TEST_RSFMRI_IMAGE_PATH
-from unittest import TestCase
 
 
 class ImageTestCase(TestCase):