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Tony Tung
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Fix docs build (#1696)
- Added top-level .rst files for a bunch of packages/modules that should be autodoc'ed. - Fixed places where things didn't generate correctly. - Added top-level constructs to starfish.morphology - Fixed inadvertent copy-pasta in `starfish/core/types/_constants.py` Test plan: make docs-html lint mypy
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‎docs/source/api/data_structures/binary_mask.rst

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.. _binary_mask:
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BinaryMaskCollection
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====================
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.. autoclass:: starfish.morphology.BinaryMaskCollection
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:members:

‎docs/source/api/data_structures/index.rst

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.. toctree::
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decoded_intensity_table.rst
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.. toctree::
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binary_mask.rst
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.. toctree::
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label_image.rst

‎docs/source/api/data_structures/label_image.rst

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.. _label_image:
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LabelImage
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==========
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.. autoclass:: starfish.morphology.LabelImage
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:members:

‎docs/source/api/index.rst

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.. toctree::
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spots/index.rst
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.. toctree::
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morphology/index.rst
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.. toctree::
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types/index.rst
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utils/index.rst
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.. toctree::
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datasets/index.rst
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datasets/index.rst

‎docs/source/api/morphology/index.rst

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.. _morphology:
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Morphology Transformations
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==========================
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starfish provides a variety of methods to perform transformations on morphological data. These include :py:class:`~starfish.morphology.Binarize`, which transform image data into morphological data and
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:py:class:`~starfish.morphology.Filter`, which performs filtering operations on morphological data.
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.. _binarize:
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Binarize
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--------
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Binarizing operations can be imported using ``starfish.morphology.Binarize``, which registers all classes that subclass :py:class:`~starfish.morphology.Binarize.BinarizeAlgorithm`:
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.. code-block:: python
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from starfish.morphology import Binarize
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.. automodule:: starfish.morphology.Binarize
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:members:
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.. _morphological_filter:
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Filter
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------
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Filtering operations can be imported using ``starfish.morphology.Filter``, which registers all classes that subclass :py:class:`~starfish.morphology.Filter.FilterAlgorithm`:
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.. code-block:: python
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from starfish.morphology import Filter
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.. automodule:: starfish.morphology.Filter
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:members:

‎docs/source/api/types/index.rst

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:members:
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Clip
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_____
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----
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Clip is deprecated in favor of :py:class:`~starfish.types.Levels`.
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.. autoclass:: starfish.core.types.Clip
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.. autoclass:: starfish.types.Clip
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:members:
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:undoc-members:
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Levels
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------
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.. autoclass:: starfish.types.Levels
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:members:
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:undoc-members:

‎starfish/core/morphology/binary_mask/binary_mask.py

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----------
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pixel_ticks : Union[Mapping[Axes, ArrayLike[int]], Mapping[str, ArrayLike[int]]]
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A map from the axis to the values for that axis.
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]],
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Mapping[str, ArrayLike[Number]]
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]], Mapping[str, ArrayLike[Number]]
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A map from the physical coordinate type to the values for axis. For 2D label images,
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X and Y physical coordinates must be provided. For 3D label images, Z physical
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coordinates must also be provided.
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the smallest size that contains the non-zero values, but pixel and physical coordinates
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ticks are retained. Masks extracted from BinaryMaskCollections will be cropped. To extract
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masks sized to the original label image, use
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:py:meth:`starfish.BinaryMaskCollection.uncropped_mask`.
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:py:meth:`starfish.morphology.BinaryMaskCollection.uncropped_mask`.
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Parameters
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----------
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arrays : Sequence[np.ndarray]
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A set of 2D or 3D binary arrays. The ordering of the axes must be Y, X for 2D images
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and ZPLANE, Y, X for 3D images. The arrays must have identical sizes and match the
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sizes of pixel_ticks and physical_ticks.
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pixel_ticks : Optional[Union[Mapping[Axes, ArrayLike[int]],
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Mapping[str, ArrayLike[int]]]]
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pixel_ticks : Optional[Union[Mapping[Axes, ArrayLike[int]], Mapping[str, ArrayLike[int]]]]
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A map from the axis to the values for that axis. For any axis that exist in the array
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but not in pixel_ticks, the pixel coordinates are assigned from 0..N-1, where N is
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the size along that axis.
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]],
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Mapping[str, ArrayLike[Number]]]
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]], Mapping[str,
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ArrayLike[Number]]]
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A map from the physical coordinate type to the values for axis. For 2D label images,
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X and Y physical coordinates must be provided. For 3D label images, Z physical
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coordinates must also be provided.
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the smallest size that contains the non-zero values, but pixel and physical coordinates
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ticks are retained. Masks extracted from BinaryMaskCollections will be cropped. To extract
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masks sized to the original label image, use
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:py:meth:`starfish.BinaryMaskCollection.uncropped_mask`.
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:py:meth:`starfish.morphology.BinaryMaskCollection.uncropped_mask`.
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Parameters
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----------
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array : np.ndarray
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A 2D or 3D array containing the labels. The ordering of the axes must be Y, X for 2D
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images and ZPLANE, Y, X for 3D images.
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pixel_ticks : Optional[Union[Mapping[Axes, ArrayLike[int]],
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Mapping[str, ArrayLike[int]]]]
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pixel_ticks : Optional[Union[Mapping[Axes, ArrayLike[int]], Mapping[str, ArrayLike[int]]]]
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A map from the axis to the values for that axis. For any axis that exist in the array
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but not in pixel_ticks, the pixel coordinates are assigned from 0..N-1, where N is
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the size along that axis.
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]],
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Mapping[str, ArrayLike[Number]]]
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]], Mapping[str,
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ArrayLike[Number]]]
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A map from the physical coordinate type to the values for axis. For 2D label images,
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X and Y physical coordinates must be provided. For 3D label images, Z physical
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coordinates must also be provided.

‎starfish/core/morphology/label_image/label_image.py

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array : np.ndarray
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A 2D or 3D array containing the labels. The ordering of the axes must be Y, X for 2D
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images and ZPLANE, Y, X for 3D images.
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pixel_ticks : Optional[Union[Mapping[Axes, ArrayLike[int]],
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Mapping[str, ArrayLike[int]]]]
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pixel_ticks : Optional[Union[Mapping[Axes, ArrayLike[int]], Mapping[str, ArrayLike[int]]]]
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A map from the axis to the values for that axis. For any axis that exist in the array
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but not in pixel_coordinates, the pixel coordinates are assigned from 0..N-1, where N is
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the size along that axis.
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]],
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Mapping[str, ArrayLike[Number]]]
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physical_ticks : Union[Mapping[Coordinates, ArrayLike[Number]], Mapping[str,
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ArrayLike[Number]]]
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A map from the physical coordinate type to the values for axis. For 2D label images,
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X and Y physical coordinates must be provided. For 3D label images, Z physical
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coordinates must also be provided.

‎starfish/core/types/_constants.py

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SCALE_BY_CHUNK = 'scale_by_chunk'
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"""Rescale the intensity of an image chunk by the peak intensity. Note that if the peak
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intensity of an image chunk is not saturated, this behaves differently than
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Clip.SCALE_BY_IMAGE."""
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Clip.SCALE_BY_CHUNK."""
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class TransformType(AugmentedEnum):

‎starfish/morphology.py

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from starfish.core.morphology import Filter # noqa: F401
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from starfish.core.morphology import ( # noqa: F401
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Binarize,
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Filter,
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)
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from starfish.core.morphology.binary_mask import BinaryMaskCollection # noqa: F401
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from starfish.core.morphology.label_image import LabelImage # noqa: F401

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