Merge branch 'master' into check_unique_referenced_instances

.codespellrc

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

.github/workflows/codespell.yml

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+---
+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

docs/ann.rst

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+.. _ann:
+
+Microscopy Bulk Simple Annotation (ANN) Objects
+===============================================
+
+The Microscopy Bulk Simple Annotation IOD is an IOD designed specifically to
+store large numbers of similar annotations and measurements from microscopy
+images. Annotations of microscopy images typically refer to very large numbers
+of cells or cellular structures. Storing these in a Structured Report Document,
+with its highly nested structure, would be very inefficient in storage space
+and unnecessarily complex and slow to parse. Microscopy Bulk Simple Annotation
+objects ("bulk annotations") solve this problem by allowing you to store large
+number of similar annotations or measurements in efficient arrays without
+duplication of the descriptive metadata.
+
+Each bulk annotation object contains one or more Annotation Groups, each of
+which contains a set of graphical annotations, and optionally one or more
+numerical measurements relating to those graphical annotations.
+
+Constructing Annotation Groups
+------------------------------
+
+An Annotation Group is a set of multiple similar annotations from a microscopy
+image. For example, a single annotation group may contain all annotations of
+cell nuclei, lymphocytes, or regions of necrosis in the image. In *highdicom*,
+an annotation group is represented by a :class:`highdicom.ann.AnnotationGroup`.
+
+Each annotation group contains some required metadata that describes the
+contents of the group, as well as some further optional metadata that may
+contain further details about the group or the derivation of the annotations it
+contains. The required metadata elements include:
+
+* A ``number`` (``int``), an integer number for the group.
+* A ``label`` (``str``) giving a human-readable label for the group.
+* A ``uid`` (``str`` or :class:`highdicom.UID`) uniquely identifying the group.
+  Usually, you will want to generate UID for this.
+* An ``annotated_property_category`` and ``annotated_property_type``
+  (:class:`highdicom.sr.CodedConcept`) coded values (see :ref:`coding`)
+  describing the category and specific structure that has been annotated.
+* A ``graphic_type`` (:class:`highdicom.ann.GraphicTypeValues`) indicating the
+  "form" of the annotations. Permissible values are ``"ELLIPSE"``, ``"POINT"``,
+  ``"POLYGON"``, ``"RECTANGLE"``, and ``"POLYLINE"``.
+* The ``algorithm_type``
+  (:class:`highdicom.ann.AnnotationGroupGenerationTypeValues`), the type of the
+  algorithm used to generate the annotations (``"MANUAL"``,
+  ``"SEMIAUTOMATIC"``, or ``"AUTOMATIC"``).
+
+Further optional metadata may optionally be provided, see the API documentation
+for more information.
+
+The actual annotation data is passed to the group as a list of
+``numpy.ndarray`` objects, each of shape (*N* x *D*). *N* is the number of
+coordinates required for each individual annotation and is determined by the
+graphic type (see :class:`highdicom.ann.GraphicType`). *D* is either 2 -- meaning
+that the coordinates are expressed as a (Column,Row) pair in image coordinates
+-- or 3 -- meaning that the coordinates are expressed as a (X,Y,Z) triple in 3D
+frame of reference coordinates.
+
+When considering which type of coordinate to use, bear in mind that the 2D image
+coordinates refer only to one image in a image pyramid, whereas 3D frame of
+reference coordinates are more easily used with any image in the pyramid.
+Also note that although you can include multiple annotation groups in a single
+bulk annotation object, they must all use the same coordinate type.
+
+Here is a simple example of constructing an annotation group:
+
+.. code-block:: python
+
+    from pydicom.sr.codedict import codes
+    from pydicom.sr.coding import Code
+    import highdicom as hd
+    import numpy as np
+
+    # Graphic data containing two nuclei, each represented by a single point
+    # expressed in 2D image coordinates
+    graphic_data = [
+        np.array([[34.6, 18.4]]),
+        np.array([[28.7, 34.9]]),
+    ]
+
+    # Nuclei annotations produced by a manual algorithm
+    nuclei_group = hd.ann.AnnotationGroup(
+        number=1,
+        uid=hd.UID(),
+        label='nuclei',
+        annotated_property_category=codes.SCT.AnatomicalStructure,
+        annotated_property_type=Code('84640000', 'SCT', 'Nucleus'),
+        algorithm_type=hd.ann.AnnotationGroupGenerationTypeValues.MANUAL,
+        graphic_type=hd.ann.GraphicTypeValues.POINT,
+        graphic_data=graphic_data,
+    )
+
+Note that including two nuclei would be very unusual in practice: annotations
+often number in the thousands or even millions within a large whole slide image.
+
+Including Measurements
+----------------------
+
+In addition to the coordinates of the annotations themselves, it is also
+possible to attach one or more continuous-valued numeric *measurements*
+corresponding to those annotations. The measurements are passed as a
+:class:`highdicom.ann.Measurements` object, which contains the *name* of the
+measurement (as a coded value), the *unit* of the measurement (also as a coded
+value) and an array of the measurements themselves (as a ``numpy.ndarray``).
+
+The length of the measurement array for any measurements attached to an
+annotation group must match exactly the number of annotations in the group.
+Value *i* in the array therefore represents the measurement of annotation *i*.
+
+Here is the above example with an area measurement included:
+
+.. code-block:: python
+
+    from pydicom.sr.codedict import codes
+    from pydicom.sr.coding import Code
+    import highdicom as hd
+    import numpy as np
+
+    # Graphic data containing two nuclei, each represented by a single point
+    # expressed in 2D image coordinates
+    graphic_data = [
+        np.array([[34.6, 18.4]]),
+        np.array([[28.7, 34.9]]),
+    ]
+
+    # Measurement object representing the areas of each of the two nuclei
+    area_measurement = hd.ann.Measurements(
+        name=codes.SCT.Area,
+        unit=codes.UCUM.SquareMicrometer,
+        values=np.array([20.4, 43.8]),
+    )
+
+    # Nuclei annotations produced by a manual algorithm
+    nuclei_group = hd.ann.AnnotationGroup(
+        number=1,
+        uid=hd.UID(),
+        label='nuclei',
+        annotated_property_category=codes.SCT.AnatomicalStructure,
+        annotated_property_type=Code('84640000', 'SCT', 'Nucleus'),
+        algorithm_type=hd.ann.AnnotationGroupGenerationTypeValues.MANUAL,
+        graphic_type=hd.ann.GraphicTypeValues.POINT,
+        graphic_data=graphic_data,
+        measurements=[area_measurement],
+    )
+
+Constructing MicroscopyBulkSimpleAnnotation Objects
+---------------------------------------------------
+
+When you have constructed the annotation groups, you can include them into
+a bulk annotation object along with a bit more metadata using the
+:class:`highdicom.ann.MicroscopyBulkSimpleAnnotations` constructor. You also
+need to pass the image from which the annotations were derived so that
+`highdicom` can copy all the patient, study and slide-level metadata:
+
+.. code-block:: python
+
+    from pydicom import dcmread
+    import highdicom as hd
+
+    # Load a slide microscopy image from the highdicom test data (if you have
+    # cloned the highdicom git repo)
+    sm_image = dcmread('data/test_files/sm_image.dcm')
+
+    bulk_annotations = hd.ann.MicroscopyBulkSimpleAnnotations(
+        source_images=[sm_image],
+        annotation_coordinate_type=hd.ann.AnnotationCoordinateTypeValues.SCOORD,
+        annotation_groups=[nuclei_group],
+        series_instance_uid=hd.UID(),
+        series_number=10,
+        sop_instance_uid=hd.UID(),
+        instance_number=1,
+        manufacturer='MGH Pathology',
+        manufacturer_model_name='MGH Pathology Manual Annotations',
+        software_versions='0.0.1',
+        device_serial_number='1234',
+        content_description='Nuclei Annotations',
+    )
+
+    bulk_annotations.save_as('nuclei_annotations.dcm')
+
+The result is a complete DICOM object that can be written out as a DICOM file,
+transmitted over network, etc.
+
+Reading Existing Bulk Annotation Objects
+----------------------------------------
+
+You can read an existing bulk annotation object using `pydicom` and then convert
+to the `highdicom` object like this:
+
+.. code-block:: python
+
+    from pydicom import dcmread
+    import highdicom as hd
+
+    ann_dcm = dcmread('data/test_files/sm_annotations.dcm')
+
+    ann = hd.ann.MicroscopyBulkSimpleAnnotations.from_dataset(ann_dcm)
+
+    assert isinstance(ann, hd.ann.MicroscopyBulkSimpleAnnotations)
+
+Note that this example (and the following examples) uses an example file that
+you can access from the test data in the `highdicom` repository. It was created
+using exactly the code in the construction example above.
+
+Accessing Annotation Groups
+---------------------------
+
+Usually the next step when working with bulk annotation objects is to find the
+relevant annotation groups. You have two ways to do this.
+
+If you know either the number or the UID of the group, you can access the group
+directly (since either of these should uniquely identify a group). The
+:meth:`highdicom.ann.MicroscopyBulkSimpleAnnotations.get_annotation_group()`
+method is used for this purpose:
+
+.. code-block:: python
+
+    # Access a group by its number
+    group = ann.get_annotation_group(number=1)
+    assert isinstance(group, hd.ann.AnnotationGroup)
+
+    # Access a group by its UID
+    group = ann.get_annotation_group(
+        uid='1.2.826.0.1.3680043.10.511.3.40670836327971302375623613533993686'
+    )
+    assert isinstance(group, hd.ann.AnnotationGroup)
+
+Alternatively, you can search for groups that match certain filters such as
+the annotation property type or category, label, or graphic type. The
+:meth:`highdicom.ann.MicroscopyBulkSimpleAnnotations.get_annotation_groups()`
+method (note groups instead of group) is used for this. It returns a list
+of matching groups, since the filters may match multiple groups.
+
+.. code-block:: python
+
+    from pydicom.sr.coding import Code
+
+    # Search for groups by annotated property type
+    groups = ann.get_annotation_groups(
+        annotated_property_type=Code('84640000', 'SCT', 'Nucleus'),
+    )
+    assert len(groups) == 1 and isinstance(groups[0], hd.ann.AnnotationGroup)
+
+    # If there are no matches, an empty list is returned
+    groups = ann.get_annotation_groups(
+        annotated_property_type=Code('53982002', "SCT", "Cell membrane"),
+    )
+    assert len(groups) == 0
+
+    # Search for groups by label
+    groups = ann.get_annotation_groups(label='nuclei')
+    assert len(groups) == 1 and isinstance(groups[0], hd.ann.AnnotationGroup)
+
+    # Search for groups by label and graphic type together (results must match
+    # *all* provided filters)
+    groups = ann.get_annotation_groups(
+        label='nuclei',
+        graphic_type=hd.ann.GraphicTypeValues.POINT,
+    )
+    assert len(groups) == 1 and isinstance(groups[0], hd.ann.AnnotationGroup)
+
+
+Extracting Information From Annotation Groups
+---------------------------------------------
+
+When you have found a relevant group, you can use the Python properties on
+the object to conveniently access metadata and the graphic data of the
+annotations. For example (see :class:`highdicom.ann.AnnotationGroup` for a full
+list):
+
+.. code-block:: python
+
+    # Access the label
+    assert group.label == 'nuclei'
+
+    # Access the number
+    assert group.number == 1
+
+    # Access the UID
+    assert group.uid == '1.2.826.0.1.3680043.10.511.3.40670836327971302375623613533993686'
+
+    # Access the annotated property type (returns a CodedConcept)
+    assert group.annotated_property_type == Code('84640000', 'SCT', 'Nucleus')
+
+    # Access the graphic type, describing the "form" of each annotation
+    assert group.graphic_type == hd.ann.GraphicTypeValues.POINT
+
+
+You can access the entire array of annotations at once using
+:meth:`highdicom.ann.AnnotationGroup.get_graphic_data()`. You need to pass the
+annotation coordinate type from the parent bulk annotation object to the group
+so that it knows how to interpret the coordinate data. This method returns a
+list of 2D numpy arrays of shape (*N* x *D*), mirroring how you would have
+passed the data in to create the annotation with `highdicom`.
+
+.. code-block:: python
+
+    import numpy as np
+
+    graphic_data = group.get_graphic_data(
+        coordinate_type=ann.AnnotationCoordinateType,
+    )
+    assert len(graphic_data) == 2 and isinstance(graphic_data[0], np.ndarray)
+
+Alternatively, you can access the coordinate array for a specific annotation
+using its (one-based) index in the annotation list:
+
+.. code-block:: python
+
+    # Get the number of annotations
+    assert group.number_of_annotations == 2
+
+    # Access an annotation using 1-based index
+    first_annotation = group.get_coordinates(
+        annotation_number=1,
+        coordinate_type=ann.AnnotationCoordinateType,
+    )
+    assert np.array_equal(first_annotation, np.array([[34.6, 18.4]]))
+
+Extracting Measurements From Annotation Groups
+----------------------------------------------
+
+You can use the :meth:`highdicom.ann.AnnotationGroup.get_measurements()` method
+to access any measurements included in the group. By default, this will return
+all measurements in the group, but you can also filter for measurements matching
+a certain name.
+
+Measurements are returned as a tuple of ``(names, values, units)``, where
+``names`` is a list of nnames as :class:`highdicom.sr.CondedConcept` objects,
+``units`` is a list of units also as :class:`highdicom.sr.CondedConcept`
+objects, and the values is a ``numpy.ndarray`` of values of shape (*N* by *M*)
+where *N* is the number of annotations and *M* is the number of measurements.
+This return format is intended to facilitate the loading of measurements into
+tables or dataframes for further analysis.
+
+
+.. code-block:: python
+
+    from pydicom.sr.codedict import codes
+
+    names, values, units = group.get_measurements()
+    assert names[0] == codes.SCT.Area
+    assert units[0] == codes.UCUM.SquareMicrometer
+    assert values.shape == (2, 1)