Fix import PR docstrings (#72)

* Fix all sphinx warnings * Removed all unnecessary modules from doc content tree, fixed all docstrings to match * Fix unused import
ImagingDataCommons · May 19, 2021 · 448351f · 448351f
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diff --git a/docs/package.rst b/docs/package.rst
@@ -23,15 +23,6 @@ highdicom.color module
    :undoc-members:
    :show-inheritance:
 
-highdicom.content module
-++++++++++++++++++++++++
-
-.. automodule:: highdicom.content
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
 highdicom.enum module
 +++++++++++++++++++++
 
@@ -68,15 +59,6 @@ highdicom.spatial module
    :undoc-members:
    :show-inheritance:
 
-highdicom.uid module
-++++++++++++++++++++++
-
-.. automodule:: highdicom.uid
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
 highdicom.utils module
 ++++++++++++++++++++++
 
@@ -99,16 +81,6 @@ highdicom.legacy package
    :show-inheritance:
 
 
-highdicom.legacy.sop module
-+++++++++++++++++++++++++++
-
-.. automodule:: highdicom.legacy.sop
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-
 .. _highdicom-seg-subpackage:
 
 highdicom.seg package
@@ -120,33 +92,6 @@ highdicom.seg package
    :undoc-members:
    :show-inheritance:
 
-highdicom.seg.content module
-++++++++++++++++++++++++++++
-
-.. automodule:: highdicom.seg.content
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-highdicom.seg.enum module
-+++++++++++++++++++++++++
-
-.. automodule:: highdicom.seg.enum
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-highdicom.seg.sop module
-++++++++++++++++++++++++
-
-.. automodule:: highdicom.seg.sop
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
 highdicom.seg.utils module
 ++++++++++++++++++++++++++
 
@@ -167,42 +112,6 @@ highdicom.sr package
    :undoc-members:
    :show-inheritance:
 
-highdicom.sr.coding module
-++++++++++++++++++++++++++
-
-.. automodule:: highdicom.sr.coding
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-highdicom.sr.content module
-+++++++++++++++++++++++++++
-
-.. automodule:: highdicom.sr.content
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-highdicom.sr.enum module
-++++++++++++++++++++++++
-
-.. automodule:: highdicom.sr.enum
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-highdicom.sr.sop module
-+++++++++++++++++++++++
-
-.. automodule:: highdicom.sr.sop
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
 highdicom.sr.utils module
 +++++++++++++++++++++++++
 
@@ -212,25 +121,6 @@ highdicom.sr.utils module
    :undoc-members:
    :show-inheritance:
 
-highdicom.sr.templates module
-+++++++++++++++++++++++++++++
-
-.. automodule:: highdicom.sr.templates
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-highdicom.sr.value\_types module
-++++++++++++++++++++++++++++++++
-
-.. automodule:: highdicom.sr.value_types
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-
 .. _highdicom-sc-subpackage:
 
 highdicom.sc package
@@ -241,21 +131,3 @@ highdicom.sc package
    :special-members: __call__
    :undoc-members:
    :show-inheritance:
-
-highdicom.sc.enum module
-+++++++++++++++++++++++++
-
-.. automodule:: highdicom.sc.enum
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
-
-highdicom.sc.sop module
-++++++++++++++++++++++++
-
-.. automodule:: highdicom.sc.sop
-   :members:
-   :special-members: __call__
-   :undoc-members:
-   :show-inheritance:
diff --git a/src/highdicom/base.py b/src/highdicom/base.py
@@ -93,7 +93,7 @@ def __init__(
             Name of the referring physician
         content_qualification: Union[str, highdicom.enum.ContentQualificationValues], optional
             Indicator of content qualification
-        coding_schemes: Sequence[highdicom.sr.coding.CodingSchemeIdentificationItem], optional
+        coding_schemes: Sequence[highdicom.sr.CodingSchemeIdentificationItem], optional
             private or public coding schemes that are not part of the
             DICOM standard
         series_description: str, optional

diff --git a/src/highdicom/content.py b/src/highdicom/content.py
@@ -41,7 +41,7 @@ def __init__(
         ----------
         name: str
             Name of the algorithm
-        family: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
+        family: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Kind of algorithm family
         version: str
             Version of the algorithm
@@ -175,7 +175,7 @@ def __eq__(self, other: Any) -> bool:
 
         Parameters
         ----------
-        other: highdicom.content.PlanePositionSequence
+        other: highdicom.PlanePositionSequence
             Plane position of other image that should be compared
 
         Returns
@@ -255,7 +255,7 @@ def __eq__(self, other: Any) -> bool:
 
         Parameters
         ----------
-        other: highdicom.content.PlaneOrientationSequence
+        other: highdicom.PlaneOrientationSequence
             Plane position of other image that should be compared
 
         Returns
@@ -338,7 +338,7 @@ def __init__(
         """
         Parameters
         ----------
-        procedure: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
+        procedure: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Procedure used to collect the examined specimen
 
         """  # noqa
@@ -368,13 +368,13 @@ def __init__(
         """
         Parameters
         ----------
-        method: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
+        method: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Method used to sample the examined specimen from a parent specimen
         parent_specimen_id: str
             Identifier of the parent specimen
-        parent_specimen_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
+        parent_specimen_type: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Type of the parent specimen
-        issuer_of_parent_specimen_id: highdicom.content.IssuerOfIdentifier, optional
+        issuer_of_parent_specimen_id: highdicom.IssuerOfIdentifier, optional
             Issuer who created the parent specimen
 
         """  # noqa
@@ -423,7 +423,7 @@ def __init__(
         """
         Parameters
         ----------
-        substances: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]]
+        substances: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]]
             Substances used to stain examined specimen(s)
 
         """  # noqa
@@ -467,18 +467,18 @@ def __init__(
         ----------
         specimen_id: str
             Identifier of the processed specimen
-        processing_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
+        processing_type: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Type of processing
-        processing_procedure: Union[highdicom.content.SpecimenCollection, highdicom.content.SpecimenSampling, highdicom.content.SpecimenStaining]
+        processing_procedure: Union[highdicom.SpecimenCollection, highdicom.SpecimenSampling, highdicom.SpecimenStaining]
             Procedure used during processing
         processing_datetime: datetime.datetime, optional
             Datetime of processing
-        processing_description: Union[str, pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional
+        processing_description: Union[str, pydicom.sr.coding.Code, highdicom.sr.CodedConcept], optional
             Description of processing
-        issuer_of_specimen_id: highdicom.content.IssuerOfIdentifier, optional
-        fixative: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional
+        issuer_of_specimen_id: highdicom.IssuerOfIdentifier, optional
+        fixative: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept], optional
             Fixative used during processing
-        embedding_medium: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept], optional
+        embedding_medium: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept], optional
             Embedding medium used during processing
 
         """  # noqa
@@ -566,10 +566,10 @@ def __init__(
             provided either in form of text or in form of spatial x, y, z
             coordinates specifying the position (offset) relative to the
             three-dimensional slide coordinate system
-        specimen_preparation_steps: Sequence[highdicom.content.SpecimenPreparationStep], optional
+        specimen_preparation_steps: Sequence[highdicom.SpecimenPreparationStep], optional
             Steps that were applied during the preparation of the examined
             specimen in the laboratory prior to image acquisition
-        issuer_of_specimen_id: highdicom.content.IssuerOfIdentifier, optional
+        issuer_of_specimen_id: highdicom.IssuerOfIdentifier, optional
             Description of the issuer of the specimen identifier
 
         """  # noqa

diff --git a/src/highdicom/sc/sop.py b/src/highdicom/sc/sop.py
@@ -158,9 +158,9 @@ def __init__(
         container_identifier: str, optional
             Identifier of the container holding the specimen (required if
             `coordinate_system` is ``"SLIDE"``)
-        issuer_of_container_identifier: highdicom.content.IssuerOfIdentifier, optional
+        issuer_of_container_identifier: highdicom.IssuerOfIdentifier, optional
             Issuer of `container_identifier`
-        specimen_descriptions: Sequence[highdicom.content.SpecimenDescriptions], optional
+        specimen_descriptions: Sequence[highdicom.SpecimenDescriptions], optional
             Description of each examined specimen (required if
             `coordinate_system` is ``"SLIDE"``)
         transfer_syntax_uid: str, optional

diff --git a/src/highdicom/seg/__init__.py b/src/highdicom/seg/__init__.py
@@ -7,6 +7,10 @@
     SpatialLocationsPreservedValues,
     SegmentsOverlapValues,
 )
+from highdicom.seg.content import (
+    SegmentDescription,
+    DimensionIndexSequence,
+)
 from highdicom.seg import utils
 
 SOP_CLASS_UIDS = {

diff --git a/src/highdicom/seg/content.py b/src/highdicom/seg/content.py
@@ -47,32 +47,32 @@ def __init__(
             Number of the segment.
         segment_label: str
             Label of the segment
-        segmented_property_category: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
+        segmented_property_category: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Category of the property the segment represents,
             e.g. ``Code("49755003", "SCT", "Morphologically Abnormal Structure")``
             (see `CID 7150 <http://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_CID_7150.html>`_
             "Segmentation Property Categories")
-        segmented_property_type: Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]
+        segmented_property_type: Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]
             Property the segment represents,
             e.g. ``Code("108369006", "SCT", "Neoplasm")``
             (see `CID 7151 <http://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_CID_7151.html>`_
             "Segmentation Property Types")
-        algorithm_type: Union[str, highdicom.seg.enum.SegmentAlgorithmTypeValues]
+        algorithm_type: Union[str, highdicom.seg.SegmentAlgorithmTypeValues]
             Type of algorithm
-        algorithm_identification: highdicom.content.AlgorithmIdentificationSequence, optional
+        algorithm_identification: highdicom.AlgorithmIdentificationSequence, optional
             Information useful for identification of the algorithm, such
             as its name or version. Required unless the algorithm type is `MANUAL`
         tracking_uid: str, optional
             Unique tracking identifier (universally unique)
         tracking_id: str, optional
             Tracking identifier (unique only with the domain of use)
-        anatomic_regions: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]], optional
+        anatomic_regions: Sequence[Union[pydicom.sr.coding.Code, highdicom.sr.CodedConcept]], optional
             Anatomic region(s) into which segment falls,
             e.g. ``Code("41216001", "SCT", "Prostate")``
             (see `CID 4 <http://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_CID_4.html>`_
             "Anatomic Region", `CID 4031 <http://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_CID_4031.html>`_ "Common Anatomic Regions", as
             as well as other CIDs for domain-specific anatomic regions)
-        primary_anatomic_structures: Sequence[Union[highdicom.sr.coding.Code, highdicom.sr.coding.CodedConcept]], optional
+        primary_anatomic_structures: Sequence[Union[highdicom.sr.Code, highdicom.sr.CodedConcept]], optional
             Anatomic structure(s) the segment represents
             (see CIDs for domain-specific primary anatomic structures)
 
@@ -307,7 +307,7 @@ def get_plane_positions_of_image(
 
         Returns
         -------
-        List[PlanePositionSequence]
+        List[highdicom.PlanePositionSequence]
             Plane position of each frame in the image
 
         """
@@ -348,7 +348,7 @@ def get_plane_positions_of_series(
 
         Returns
         -------
-        List[PlanePositionSequence]
+        List[highdicom.PlanePositionSequence]
             Plane position of each frame in the image
 
         """
@@ -376,7 +376,7 @@ def get_index_values(
 
         Parameters
         ----------
-        plane_positions: Sequence[PlanePositionSequence]
+        plane_positions: Sequence[highdicom.PlanePositionSequence]
             Plane position of frames in a multi-frame image or in a series of
             single-frame images