Merge branch 'master' into docs/seg_explanation

.codespellrc

@@ -0,0 +1,4 @@
+[codespell]
+skip = .git,*.pdf,*.svg,*.ipynb
+# te,fo - either abbreviations of variables
+ignore-words-list = te,fo

.github/workflows/codespell.yml

@@ -0,0 +1,22 @@
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

setup.py

@@ -51,7 +51,7 @@ def get_version():
     package_dir={'': 'src'},
     python_requires='>=3.6',
     install_requires=[
-        'pydicom>=2.3.0',
+        'pydicom>=2.3.0,!=2.4.0',
         'numpy>=1.19',
         'pillow>=8.3',
         'pillow-jpls>=1.0',

src/highdicom/ann/enum.py

@@ -57,7 +57,7 @@ class GraphicTypeValues(Enum):
     """
 
     POINT = 'POINT'
-    """An individual piont defined by a single coordinate."""
+    """An individual point defined by a single coordinate."""
 
     POLYLINE = 'POLYLINE'
     """Connected line segments defined by two or more ordered coordinates.

src/highdicom/frame.py

@@ -63,7 +63,7 @@ def encode_frame(
     -------
     bytes
         Encoded pixel data (potentially compressed in case of encapsulated
-        format encoding, depending on the transfer snytax)
+        format encoding, depending on the transfer syntax)
 
     Raises
     ------

src/highdicom/ko/sop.py

@@ -68,7 +68,7 @@ def __init__(
             Name of the department of the person or device that creates the
             document instance
         requested_procedures: Union[Sequence[pydicom.dataset.Dataset], None], optional
-            Requested procedures that are being fullfilled by creation of the
+            Requested procedures that are being fulfilled by creation of the
             document
         transfer_syntax_uid: str, optional
             UID of transfer syntax that should be used for encoding of

src/highdicom/legacy/sop.py

@@ -328,7 +328,7 @@ def _convert_legacy_to_enhanced(
     # All remaining unassigned attributes will be collected in either the
     # UnassignedSharedConvertedAttributesSequence or the
     # UnassignedPerFrameConvertedAttributesSequence, depending on whether
-    # values vary accross frames (original single-frame image instances).
+    # values vary across frames (original single-frame image instances).
     unassigned_shared_ca_item = Dataset()
     unassigned_perframe_ca_items = [
         Dataset()

src/highdicom/pm/sop.py

@@ -222,7 +222,7 @@ def __init__(
             Identifying information for the person who created the content of
             this parametric map.
         palette_color_lut_transformation: Union[highdicom.PaletteColorLUTTransformation, None], optional
-            Description of the Palette Color LUT Transformation for tranforming
+            Description of the Palette Color LUT Transformation for transforming
             grayscale into RGB color pixel values
         **kwargs: Any, optional
             Additional keyword arguments that will be passed to the constructor
@@ -737,9 +737,11 @@ def __init__(
                 # Frame Content
                 frame_content_item = Dataset()
                 frame_content_item.DimensionIndexValues = [
-                    np.where(
-                        (dimension_position_values[idx] == pos)
-                    )[0][0] + 1
+                    int(
+                        np.where(
+                            (dimension_position_values[idx] == pos)
+                        )[0][0] + 1
+                    )
                     for idx, pos in enumerate(plane_position_values[i])
                 ]
 

src/highdicom/pr/content.py

@@ -136,7 +136,7 @@ def __init__(
         label: str
             Name used to identify the Graphic Group (maximum 64 characters).
         description: Union[str, None], optional
-            Description of the group (maxiumum 10240 characters).
+            Description of the group (maximum 10240 characters).
 
         """
         super().__init__()
@@ -431,7 +431,7 @@ def __init__(
                 raise ValueError(
                     'All coordinates in the bounding box must be non-negative.'
                 )
-            self.AnchorPoint = anchor_point
+            self.AnchorPoint = list(anchor_point)
             self.AnchorPointAnnotationUnits = units.value
             self.AnchorPointVisibility = 'Y' if anchor_point_visible else 'N'
             if units == AnnotationUnitsValues.DISPLAY:

src/highdicom/pr/sop.py

@@ -389,7 +389,7 @@ def __init__(
         device_serial_number: Union[str, None]
             Manufacturer's serial number of the device
         palette_color_lut_transformation: highdicom.PaletteColorLUTTransformation
-            Description of the Palette Color LUT Transformation for tranforming
+            Description of the Palette Color LUT Transformation for transforming
             grayscale into RGB color pixel values
         content_label: str
             A label used to describe the content of this presentation state.
@@ -419,10 +419,10 @@ def __init__(
             Identifying information for the person who created the content of
             this presentation state.
         modality_lut_transformation: Union[highdicom.ModalityLUTTransformation, None], optional
-            Description of the Modality LUT Transformation for tranforming modality
+            Description of the Modality LUT Transformation for transforming modality
             dependent into modality independent pixel values
         voi_lut_transformations: Union[Sequence[highdicom.pr.SoftcopyVOILUTTransformation], None], optional
-            Description of the VOI LUT Transformation for tranforming
+            Description of the VOI LUT Transformation for transforming
             modality pixel values into pixel values that are of interest to a
             user or an application
         icc_profile: Union[bytes, None], optional

src/highdicom/seg/sop.py

@@ -589,7 +589,7 @@ def iterate_indices_by_source_instance(
         relabel: bool, optional
             If True and ``combine_segments`` is ``True``, the output segment
             numbers are relabelled into the range ``0`` to
-            ``len(segment_numbers)`` (inclusive) accoring to the position of
+            ``len(segment_numbers)`` (inclusive) according to the position of
             the original segment numbers in ``segment_numbers`` parameter.  If
             ``combine_segments`` is ``False``, this has no effect.
 
@@ -690,7 +690,7 @@ def iterate_indices_by_source_frame(
         relabel: bool, optional
             If True and ``combine_segments`` is ``True``, the output segment
             numbers are relabelled into the range ``0`` to
-            ``len(segment_numbers)`` (inclusive) accoring to the position of
+            ``len(segment_numbers)`` (inclusive) according to the position of
             the original segment numbers in ``segment_numbers`` parameter.  If
             ``combine_segments`` is ``False``, this has no effect.
 
@@ -793,7 +793,7 @@ def iterate_indices_by_dimension_index_values(
         relabel: bool, optional
             If True and ``combine_segments`` is ``True``, the output segment
             numbers are relabelled into the range ``0`` to
-            ``len(segment_numbers)`` (inclusive) accoring to the position of
+            ``len(segment_numbers)`` (inclusive) according to the position of
             the original segment numbers in ``segment_numbers`` parameter.  If
             ``combine_segments`` is ``False``, this has no effect.
 
@@ -1613,9 +1613,11 @@ def __init__(
                             CoordinateSystemNames.SLIDE
                         ):
                             index_values = [
-                                np.where(
-                                    (dimension_position_values[idx] == pos)
-                                )[0][0] + 1
+                                int(
+                                    np.where(
+                                        (dimension_position_values[idx] == pos)
+                                    )[0][0] + 1
+                                )
                                 for idx, pos in enumerate(
                                     plane_position_values[j]
                                 )
@@ -1626,11 +1628,12 @@ def __init__(
                             # Sequence points to (Image Position Patient) has a
                             # value multiplicity greater than one.
                             index_values = [
-                                np.where(
-                                    (dimension_position_values[idx] == pos).all(
-                                        axis=1
-                                    )
-                                )[0][0] + 1
+                                int(
+                                    np.where(
+                                        (dimension_position_values[idx] == pos)
+                                        .all(axis=1)
+                                    )[0][0] + 1
+                                )
                                 for idx, pos in enumerate(
                                     plane_position_values[j]
                                 )
@@ -1642,7 +1645,7 @@ def __init__(
                             'dimension index values: {}'.format(j, error)
                         )
                 frame_content_item.DimensionIndexValues = (
-                    [segment_number] + index_values
+                    [int(segment_number)] + index_values
                 )
                 pffp_item.FrameContentSequence = [frame_content_item]
                 if has_ref_frame_uid:
@@ -1697,7 +1700,7 @@ def __init__(
                     logger.warning('spatial locations not preserved')
 
                 identification = Dataset()
-                identification.ReferencedSegmentNumber = segment_number
+                identification.ReferencedSegmentNumber = int(segment_number)
                 pffp_item.SegmentIdentificationSequence = [
                     identification,
                 ]
@@ -2638,7 +2641,7 @@ def _get_pixels_by_seg_frame(
         relabel: bool
             If True and ``combine_segments`` is ``True``, the pixel values in
             the output array are relabelled into the range ``0`` to
-            ``len(segment_numbers)`` (inclusive) accoring to the position of
+            ``len(segment_numbers)`` (inclusive) according to the position of
             the original segment numbers in ``segment_numbers`` parameter.  If
             ``combine_segments`` is ``False``, this has no effect.
         rescale_fractional: bool
@@ -3010,7 +3013,7 @@ def get_pixels_by_source_instance(
         relabel: bool, optional
             If True and ``combine_segments`` is ``True``, the pixel values in
             the output array are relabelled into the range ``0`` to
-            ``len(segment_numbers)`` (inclusive) accoring to the position of
+            ``len(segment_numbers)`` (inclusive) according to the position of
             the original segment numbers in ``segment_numbers`` parameter.  If
             ``combine_segments`` is ``False``, this has no effect.
         ignore_spatial_locations: bool, optional
@@ -3229,7 +3232,7 @@ def get_pixels_by_source_frame(
         relabel: bool, optional
             If True and ``combine_segments`` is ``True``, the pixel values in
             the output array are relabelled into the range ``0`` to
-            ``len(segment_numbers)`` (inclusive) accoring to the position of
+            ``len(segment_numbers)`` (inclusive) according to the position of
             the original segment numbers in ``segment_numbers`` parameter.  If
             ``combine_segments`` is ``False``, this has no effect.
         ignore_spatial_locations: bool, optional
@@ -3494,7 +3497,7 @@ def get_pixels_by_dimension_index_values(
         relabel: bool, optional
             If True and ``combine_segments`` is ``True``, the pixel values in
             the output array are relabelled into the range ``0`` to
-            ``len(segment_numbers)`` (inclusive) accoring to the position of
+            ``len(segment_numbers)`` (inclusive) according to the position of
             the original segment numbers in ``segment_numbers`` parameter.  If
             ``combine_segments`` is ``False``, this has no effect.
         assert_missing_frames_are_empty: bool, optional

src/highdicom/sr/__init__.py

@@ -1,4 +1,4 @@
-"""Package for creationg of Structured Report (SR) instances."""
+"""Package for creation of Structured Report (SR) instances."""
 from highdicom.sr.coding import CodedConcept
 from highdicom.sr.content import (
     FindingSite,

src/highdicom/sr/sop.py

@@ -127,7 +127,7 @@ def __init__(
         performed_procedure_codes: Union[List[highdicom.sr.CodedConcept], None], optional
             Codes of the performed procedures that resulted in the SR document
         requested_procedures: Union[List[pydicom.dataset.Dataset], None], optional
-            Requested procedures that are being fullfilled by creation of the
+            Requested procedures that are being fulfilled by creation of the
             SR document
         previous_versions: Union[List[pydicom.dataset.Dataset], None], optional
             Instances representing previous versions of the SR document
@@ -432,7 +432,7 @@ def __init__(
         performed_procedure_codes: Union[List[highdicom.sr.CodedConcept], None], optional
             Codes of the performed procedures that resulted in the SR document
         requested_procedures: Union[List[pydicom.dataset.Dataset], None], optional
-            Requested procedures that are being fullfilled by creation of the
+            Requested procedures that are being fulfilled by creation of the
             SR document
         previous_versions: Union[List[pydicom.dataset.Dataset], None], optional
             Instances representing previous versions of the SR document
@@ -563,7 +563,7 @@ def __init__(
         performed_procedure_codes: Union[List[highdicom.sr.CodedConcept], None], optional
             Codes of the performed procedures that resulted in the SR document
         requested_procedures: Union[List[pydicom.dataset.Dataset], None], optional
-            Requested procedures that are being fullfilled by creation of the
+            Requested procedures that are being fulfilled by creation of the
             SR document
         previous_versions: Union[List[pydicom.dataset.Dataset], None], optional
             Instances representing previous versions of the SR document
@@ -725,7 +725,7 @@ def __init__(
         performed_procedure_codes: Union[List[highdicom.sr.CodedConcept], None], optional
             Codes of the performed procedures that resulted in the SR document
         requested_procedures: Union[List[pydicom.dataset.Dataset], None], optional
-            Requested procedures that are being fullfilled by creation of the
+            Requested procedures that are being fulfilled by creation of the
             SR document
         previous_versions: Union[List[pydicom.dataset.Dataset], None], optional
             Instances representing previous versions of the SR document

src/highdicom/sr/templates.py

@@ -2350,7 +2350,7 @@ def __init__(
             "General Region of Interest Measurement Modifiers"
             for options)
         finding_sites: Union[Sequence[highdicom.sr.FindingSite], None], optional
-            Coded description of one or more anatomic locations corresonding
+            Coded description of one or more anatomic locations corresponding
             to the image region from which measurement was taken
         method: Union[highdicom.sr.CodedConcept, pydicom.sr.coding.Code, None], optional
             Measurement method (see
@@ -3274,7 +3274,7 @@ def __init__(
         algorithm_id: Union[highdicom.sr.AlgorithmIdentification, None], optional
             Identification of algorithm used for making measurements
         finding_sites: Union[Sequence[highdicom.sr.FindingSite], None], optional
-            Coded description of one or more anatomic locations corresonding
+            Coded description of one or more anatomic locations corresponding
             to the image region from which measurement was taken
         session: Union[str, None], optional
             Description of the session

src/highdicom/sr/value_types.py

@@ -1458,7 +1458,7 @@ def __init__(
             Number of frame(s) to which the reference applies in case of a
             multi-frame image
         referenced_segment_numbers: Union[int, Sequence[int], None], optional
-            Number of segment(s) to which the refernce applies in case of a
+            Number of segment(s) to which the reference applies in case of a
             segmentation image
         relationship_type: Union[highdicom.sr.RelationshipTypeValues, str, None], optional
             Type of relationship with parent content item
@@ -1702,7 +1702,7 @@ class Scoord3DContentItem(ContentItem):
     Note
     ----
     Spatial coordinates are defined in the patient or specimen-based coordinate
-    system and have milimeter unit.
+    system and have millimeter unit.
 
     """
 
@@ -1955,7 +1955,7 @@ def __init__(
         referenced_waveform_channels: Union[Sequence[Tuple[int, int]], None], optional
             Pairs of waveform number (number of item in the Waveform Sequence)
             and channel definition number (number of item in the Channel
-            Defition Sequence) to which the reference applies in case of a
+            Definition Sequence) to which the reference applies in case of a
             multi-channel waveform
         relationship_type: Union[highdicom.sr.RelationshipTypeValues, str, None], optional
             Type of relationship with parent content item

src/highdicom/utils.py

@@ -106,7 +106,7 @@ def compute_plane_position_tiled_full(
     Returns
     -------
     highdicom.PlanePositionSequence
-        Positon of the plane in the slide coordinate system
+        Position, of the plane in the slide coordinate system
 
     Raises
     ------
@@ -262,7 +262,7 @@ def _compute_plane_position_tiled_full_efficiently(
         Returns
         -------
         highdicom.PlanePositionSequence
-            Positon of the plane in the slide coordinate system
+            Position, of the plane in the slide coordinate system
 
         """
         row_offset_frame = ((row_index - 1) * rows)

tests/test_ko.py

@@ -89,8 +89,8 @@ def test_construction(self):
         container = content[0]
         assert isinstance(container, ContainerContentItem)
         assert container.ContentTemplateSequence[0].TemplateIdentifier == '2010'
-        # Oberver Context (Person): 2
-        # Oberver Context (Device): 3
+        # Observer Context (Person): 2
+        # Observer Context (Device): 3
         # Description: 1
         # Referenced Objects: 4
         assert len(container.ContentSequence) == 10