Fix pydicom support by replacing dicomio with dcmread for reading DICOM files

Author: PierreRaybaut

CHANGELOG.md

@@ -17,6 +17,10 @@ Supported versions of Python have been updated (drop support for Python 3.8, add
   * The `info_callback` is a function that takes the annotation object and returns a string with the information to display
   * Default `info_callback` is redirected to the `get_infos` method of the annotation object (this makes the feature backward compatible)
 
+🛠️ Bug fixes:
+
+* Fixed `pydicom` support: use `dcmread` instead of `read_file` to read DICOM files
+
 ## Version 2.6.3 ##
 
 🧯 In this release, test coverage is 79%.

plotpy/builder/image.py

@@ -226,9 +226,9 @@ def image(
         if isinstance(filename, str) and filename.lower().endswith(".dcm"):
             # pylint: disable=import-outside-toplevel
             # pylint: disable=import-error
-            from pydicom import dicomio  # type:ignore
+            from pydicom import dcmread  # type:ignore
 
-            template = dicomio.read_file(filename, stop_before_pixels=True, force=True)
+            template = dcmread(filename, stop_before_pixels=True, force=True)
             ipp = getattr(template, "ImagePositionPatient", ["0", "0", "0"])
             pxs = getattr(template, "PixelSpacing", ["1", "1"])
             ipx, ipy = float(ipp[0]), float(ipp[1])

plotpy/io.py

@@ -374,7 +374,7 @@ def _import_dcm():
     # is to check if pydicom is installed:
     # pylint: disable=import-outside-toplevel
     # pylint: disable=import-error
-    from pydicom import dicomio  # type:ignore # noqa: F401
+    from pydicom import dcmread  # type:ignore # noqa: F401
 
     logger.setLevel(logging.WARNING)
 
@@ -383,9 +383,9 @@ def _imread_dcm(filename, **kwargs):
     """Open DICOM image with pydicom and return a NumPy array"""
     # pylint: disable=import-outside-toplevel
     # pylint: disable=import-error
-    from pydicom import dicomio  # type:ignore
+    from pydicom import dcmread  # type:ignore
 
-    dcm = dicomio.read_file(filename, force=True)
+    dcm = dcmread(filename, force=True)
     # **********************************************************************
     # The following is necessary until pydicom numpy support is improved:
     # (after that, a simple: 'arr = dcm.PixelArray' will work the same)

plotpy/tools/misc.py

@@ -176,11 +176,11 @@ class SnapshotParam(DataSet):
         # the extension .dcm is not registered in the io module, so we will not
         # get here.
         try:
-            from pydicom import dicomio  # pylint: disable=import-outside-toplevel
+            from pydicom import dcmread  # pylint: disable=import-outside-toplevel
         except ImportError:
             raise ImportError("This should not happen (pydicom is not installed)")
 
-        model_dcm = dicomio.read_file(model_fname)
+        model_dcm = dcmread(model_fname)
         try:
             ps_attr = "ImagerPixelSpacing"
             ps_x, ps_y = getattr(model_dcm, ps_attr)