Merge branch 'update-requirements'

Author: hackermd

setup.py

@@ -53,7 +53,7 @@
         'gcp': [
             'google-auth>=1.6',
             'google-oauth>=1.0',
-        ]
+        ],
     },
     tests_require=[
         'mypy>=0.7',
@@ -62,10 +62,7 @@
         'pytest-flake8>=1.0',
     ],
     install_requires=[
-        'numpy>=1.13',
-        'pillow>=5.0',
         'pydicom>=1.0',
         'requests>=2.18',
-        'six>=1.11'
     ]
 )

src/dicomweb_client/api.py

@@ -4,7 +4,6 @@
 import sys
 import logging
 import email
-import six
 import xml.etree.ElementTree as ET
 from collections import OrderedDict
 from io import BytesIO
@@ -132,7 +131,7 @@ def _create_dataelement(
                 else:
                     elem_value = value
         else:
-            if len(value) == 1 and isinstance(value[0], six.string_types):
+            if len(value) == 1 and isinstance(value[0], str):
                 elem_value = value[0].split('\\')
             else:
                 elem_value = value
@@ -804,7 +803,7 @@ def _build_accept_header_field_value(
             )
         field_value_parts = []
         for media_type in media_types:
-            if not isinstance(media_type, six.string_types):
+            if not isinstance(media_type, str):
                 raise TypeError(
                     'Media type "{}" is not supported for '
                     'requested resource'.format(media_type)
@@ -1523,7 +1522,7 @@ def _get_common_media_type(
             raise ValueError('No acceptable media types provided.')
         common_media_types = []
         for item in media_types:
-            if isinstance(item, six.string_types):
+            if isinstance(item, str):
                 media_type = item
             else:
                 media_type = item[0]
@@ -1677,7 +1676,7 @@ def _assert_uid_format(self, uid: str) -> None:
             ``"^[.0-9]+$"``
 
         '''
-        if not isinstance(uid, six.string_types):
+        if not isinstance(uid, str):
             raise TypeError('DICOM UID must be a string.')
         pattern = re.compile('^[.0-9]+$')
         if not pattern.search(uid):

src/dicomweb_client/cli.py

@@ -9,9 +9,7 @@
 import getpass
 from io import BytesIO
 
-from PIL import Image
 import pydicom
-import numpy as np
 
 from dicomweb_client.api import DICOMwebClient, load_json_dataset
 from dicomweb_client.log import configure_logging
@@ -440,16 +438,6 @@ def _save_metadata(data, directory, sop_instance_uid, prettify=False,
                 json.dump(data, f, sort_keys=True)
 
 
-def _save_image(image, filename):
-    logger.info('save pixel data to file "{}"'.format(filename))
-    image.save(filename)
-
-
-def _show_image(image):
-    logger.info('show pixel data')
-    image.show()
-
-
 def _print_pixel_data(pixels):
     logger.info('print pixel data')
     print(pixels)
@@ -596,35 +584,34 @@ def _retrieve_instance_frames(client, args):
     image media types.
     '''
     pixel_data = client.retrieve_instance_frames(
-        args.study_instance_uid, args.series_instance_uid,
-        args.sop_instance_uid, args.frame_numbers,
+        args.study_instance_uid,
+        args.series_instance_uid,
+        args.sop_instance_uid,
+        args.frame_numbers,
         media_types=args.media_types,
     )
 
     for i, data in enumerate(pixel_data):
-        if args.save or args.show:
-            try:
-                image = Image.open(BytesIO(data))
-            except Exception:
-                try:
-                    import jpeg_ls
-                    image = jpeg_ls.decode(np.fromstring(data, dtype=np.uint8))
-                except Exception:
-                    raise IOError(
-                        'Cannot load retrieved frame as an image.'
-                    )
-            if args.save:
-                filename = (
-                    '{sop_instance_uid}_{frame_number}.{extension}'.format(
-                        sop_instance_uid=args.sop_instance_uid,
-                        frame_number=args.frame_numbers[i],
-                        extension=image.format.lower()
-                    )
+        if args.save:
+            if data[:2] == b'\xFF\xD8':       # SOI marker => JPEG
+                if data[2:4] == b'\xFF\xF7':  # SOF 55 marker => JPEG-LS
+                    extension = 'jls'
+                else:
+                    extension = 'jpg'
+            elif data[:2] == b'\xFF\x4F':     # SOC marker => JPEG 2000
+                extension = 'jp2'
+            else:
+                extension = 'dat'
+            filename = (
+                '{sop_instance_uid}_{frame_number}.{extension}'.format(
+                    sop_instance_uid=args.sop_instance_uid,
+                    frame_number=args.frame_numbers[i],
+                    extension=extension
                 )
-                filepath = os.path.join(args.output_dir, filename)
-                _save_image(image, filepath)
-            elif args.show:
-                _show_image(image)
+            )
+            filepath = os.path.join(args.output_dir, filename)
+            with open(filepath, 'bw') as fp:
+                fp.write(data)
         else:
             _print_pixel_data(data)