Paquo's most used class is the :class:`QuPathProject`. Through it you're accessing images, annotation, metadata and everything that QuPath has to offer (|:sweat_smile:| let us know if something's missing!)
.. autoclass:: paquo.projects.QuPathProject :members:
Classes are used to group your annotation into (you've guessed it) classes. :class:`QuPathPathClasses` can have names, a color and they can be children of other classes. If you want to create a new QuPathPathClass just instantiate it by providing a name and an optional color and optional parent class.
.. autoclass:: paquo.classes.QuPathPathClass :members:
Images in paquo cannot exist on their own and are always bound to a QuPathProject. You access them via :meth:`QuPathProject.images` or you make a new one from a file via :meth:`QuPathProject.add_image`. Images let you set a description, provide you with interfaces for metadata and properties and give you access to the various QuPath annotation and detections objects through the :class:`QuPathPathObjectHierarchy`.
.. autoclass:: paquo.images.QuPathProjectImageEntry :members:
.. autoclass:: paquo.images.QuPathImageType
.. autoattribute:: BRIGHTFIELD_H_DAB
.. autoattribute:: BRIGHTFIELD_H_E
.. autoattribute:: BRIGHTFIELD_OTHER
.. autoattribute:: FLUORESCENCE
.. autoattribute:: OTHER
.. autoattribute:: UNSET
Note
There's an additional :class:`paquo.images.ImageProvider` class which will be introduced when paquo settles on its implementation. See Paquo Issue #13.
The hierarchy is accessed via QuPathProjectImageEntry.hierarchy. It contains proxy objects that allow you to access annotations and detections, as well as importing and exporting them to geojson.
.. autoclass:: paquo.hierarchy.QuPathPathObjectHierarchy :members:
Annotations and detections are encapsulated via :class:`QuPathPathAnnotationObjects`.
.. autoclass:: paquo.pathobjects._PathROIObject
:members:
.. autoclass:: paquo.pathobjects.QuPathPathAnnotationObject
:show-inheritance:
.. autoattribute:: description
.. autoclass:: paquo.pathobjects.QuPathPathDetectionObject
:show-inheritance:
.. autoclass:: paquo.pathobjects.QuPathPathTileObject
:show-inheritance:
Colors in QuPath are represented as non-human-friendly integers. :class:`QuPathColor` provides a nicer interface to allow more intuitive color handling.
.. autoclass:: paquo.colors.QuPathColor :members:
If anything is not documented and you would love to know more about it, open an issue and let us know! We're happy to provide more documentation and clear things up! |:sparkling_heart:|