Exclude CharPyLS for Python 3.11

- does not compile

.github/workflows/merge-pytest.yml

@@ -76,7 +76,7 @@ jobs:
         python -m pip uninstall -y pillow
 
     - name: Install and test jpeg_ls
-      if: ${{ matrix.python-version != '3.12-dev' }}
+      if: ${{ matrix.python-version != '3.11' && matrix.python-version != '3.12-dev'}}
       run: |
         python -m pip install --upgrade cython
         python -m pip install git+https://github.com/Who8MyLunch/CharPyLS
@@ -101,7 +101,7 @@ jobs:
         pytest ${{ matrix.pytest-args }} pydicom/tests/test_pylibjpeg.py
 
     - name: Test all pixel handling
-      if: ${{ matrix.python-version != '3.12-dev' }}
+      if: ${{ matrix.python-version != '3.11' && matrix.python-version != '3.12-dev'}}
       run: |
         python -m pip install pillow python-gdcm
         python -m pip install git+https://github.com/Who8MyLunch/CharPyLS

doc/old/image_data_handlers.rst

@@ -51,8 +51,8 @@ handled by the given packages:
 
 +-------------------------------------------------------------+-------+-------------+----------+-----------------+-----------------+
 | Transfer Syntax                                             | NumPy | | NumPy +   | | NumPy +| | NumPy +       | | NumPy +       |
-+------------------------------------+------------------------+       | | JPEG-LS   | | GDCM   | | Pillow        | | pylibjpeg     |
-| Name                               | UID                    |       |             |          |                 |                 |
++------------------------------------+------------------------+       | | JPEG-LS\  | | GDCM   | | Pillow        | | pylibjpeg     |
+| Name                               | UID                    |       |  :sup:`7`   |          |                 |                 |
 +====================================+========================+=======+=============+==========+=================+=================+
 | Explicit VR Little Endian          | 1.2.840.10008.1.2.1    | |chk| | |chk|       | |chk|    |     |chk|       | |chk|           |
 +------------------------------------+------------------------+-------+-------------+----------+-----------------+-----------------+
@@ -92,6 +92,7 @@ handled by the given packages:
 | :sup:`4` *with the pylibjpeg-rle plugin and using the* :meth:`~pydicom.dataset.Dataset.decompress` *method, 4-5x faster than default*
 | :sup:`5` *with the pylibjpeg-libjpeg plugin*
 | :sup:`6` *with the pylibjpeg-openjpeg plugin*
+| :sup:`7` *only up to Python 3.10*
 
 Usage
 .....

doc/release_notes/v2.4.0.rst

@@ -44,3 +44,4 @@ Pydicom Internals
 -----------------
 * In test suites, renamed 'setup' and 'teardown' methods, deprecated starting
   in pytest 7.2
+* Do not try to use `CharPyLS` with Python > 3.10 (:issue:`1788`)

pydicom/tests/test_dataelem.py

@@ -1149,3 +1149,44 @@ def test_elem_description_deprecated():
     )
     with pytest.warns(DeprecationWarning, match=msg):
         assert elem.description() == "Patient's Name"
+
+
+def test_seg():
+    import numpy as np
+    import pydicom
+
+    orig = pydicom.dcmread(r"c:\dev\DICOM Data\pydicom\986\T1.dcm")
+    over = pydicom.dcmread(r"c:\dev\DICOM Data\pydicom\986\seg.dcm")
+
+    # rows_orig = orig[0x00280010].value
+    # cols_orig = orig[0x00280011].value
+    rows_orig = over[0x00280010].value
+    cols_orig = over[0x00280011].value
+
+    # segmented
+    im_data_over = over.pixel_array - 4203
+    # binarize segmented
+    im_data_over = np.where(im_data_over > 0, 1, 0)
+    im_data_over = im_data_over.astype('uint16')
+    from pydicom.pixel_data_handlers import pack_bits
+    im_data_over_bytes = pack_bits(im_data_over)
+    descrip = 'segmentation'
+
+    # Overlay fields
+    # filling in only Type 1 (mandatory) fields
+    orig.add_new([0x6000, 0x0010], 'US', rows_orig)  # Overlay Rows
+    orig.add_new([0x6000, 0x0011], 'US', cols_orig)  # Overlay Columns
+    orig.add_new([0x6000, 0x0015], 'US', 1)  # Overlay number of frames
+    orig.add_new([0x6000, 0x0022], 'LO', descrip)  # Overlay description
+    orig.add_new([0x6000, 0x0040], 'CS',
+                 'G')  # Overlay Type ('R','G'), ROI or Graphics
+    orig.add_new([0x6000, 0x0050], 'SS', [1, 1])  # Overlay Origin
+    orig.add_new([0x6000, 0x0051], 'US', 1)  # Image Frame Origin
+    orig.add_new([0x6000, 0x0100], 'US',
+                 1)  # Overlay Bits Allocated, mandatory fixed value = 1!!
+    orig.add_new([0x6000, 0x0102], 'US',
+                 0)  # Overlay Bit Position, mandatory fixed value = 0!!
+    orig.add_new([0x6000, 0x1001], 'CS', 'MASK')  # Overlay Activation Layer
+    orig.add_new([0x6000, 0x3000], 'OW', im_data_over_bytes)  # PixelData
+
+    orig.save_as(r"c:\dev\DICOM Data\pydicom\986\orig_with_overlay.dcm")

pydicom/tests/test_dataset.py

@@ -2302,3 +2302,36 @@ def test_setattr_ignore(setattr_ignore):
         with assert_no_warning():
             getattr(ds, s, None)
             setattr(ds, s, None)
+
+from pydicom.dataelem import _private_vr_for_tag
+from pydicom.valuerep import VR
+
+def remove_invalid_ds(raw_elem, **kwargs):
+    if raw_elem.tag.is_private and raw_elem.value:
+        vr = _private_vr_for_tag(kwargs["ds"], raw_elem.tag)
+        if vr == VR.DS:
+            try:
+                raw_elem.value.decode("ascii")
+            except UnicodeDecodeError:
+                print(f"Removing invalid tag value for tag {raw_elem.tag}")
+                return RawDataElement(raw_elem.tag, "DS", 0, None, 0,
+                                      raw_elem.is_implicit_VR,
+                                      raw_elem.is_little_endian)
+    return raw_elem
+
+
+def test_change_encoding():
+    ds = dcmread(r"c:\dev\DICOM Data\pydicom\1739\filename.dcm")
+    config.data_element_callback = remove_invalid_ds
+    config.data_element_callback_kwargs = {"ds": ds}
+    ds.decode()
+    ds['SpecificCharacterSet'].value = 'ISO_IR 192'
+    ds.save_as(r"c:\dev\DICOM Data\pydicom\1739\filename_utf8.dcm")
+
+def test_enhanced_mr():
+    filename = r"c:\dev\DICOM Data\EnhancedMR\BRUKER_WG30_1_Mouse_cardio_Brain_Mouse__E17_P1\EnIm1.dcm"
+    ds = dcmread(filename)
+    positions = []
+    for item in ds.PerFrameFunctionalGroupSequence:
+        positions.append(item.PlanePositionSequence[0].ImagePositionPatient)
+    print(positions)