API Reference

Annotation

Base

Credentials

Credentials([username, password, token, ...])

Construct an object that contains authentication information.

CVAT

CVAT Project

CVATProject([cas_connection, url, ...])	Defines a class to interact with a CVAT Project.
CVATProject.get_annotations(image_table, ...)	Fetch annotations from CVAT corresponding to the images in a CAS table.
CVATProject.post_images(image_table)	Create a CVAT task under the project and upload images from a CAS table to that task.
CVATProject.save([caslib, relative_path, ...])	Saves a CVATProject in the specified caslib and relative path.
CVATProject.resume(project_name, cas_connection)	Resumes a CVATProject by reading it from the specified caslib and relative path.

CVAT Authentication

CVATAuthenticator()	Defines a class with methods for CVAT authentication.
CVATAuthenticator.generate_cvat_token()	Authenticate a user against a CVAT server.

Tables

Biomedical Image Table

BiomedImageTable([table, image, dimension, ...])	Implement biomedical image processing functions.
BiomedImageTable.as_dict()	Create a dictionary representation of this object.
BiomedImageTable.fetch_image_array([n, qry, ...])	Fetch image array from this BiomedImageTable.
BiomedImageTable.fetch_geometry_info([n, ...])	Fetch geometry information from this BiomedImageTable.
BiomedImageTable.has_decoded_images()	Check if this table contains decoded images or encoded images.
BiomedImageTable.sphericity(use_spacing, ...)	Quantify the sphericity for the given component from this BiomedImageTable.
BiomedImageTable.morphological_gradient([...])	Compute the morphological gradient for each 3D grayscale image in this BiomedImageTable.

Image Table

ImageTable(table[, image, dimension, ...])	Base class for NaturalImageTable and BiomedImageTable classes.
ImageTable.as_dict()	Create a dictionary representation of this object.
ImageTable.has_decoded_images()	Check if this table contains decoded images or encoded images.
ImageTable.load(connection, path[, ...])	Loads images in an ImageTable.
ImageTable.from_table(cas_table[, ...])	Creates an ImageTable from a CASTable.

Natural Image Table

NaturalImageTable([table, image, dimension, ...])	Implement natural image processing functions.
NaturalImageTable.as_dict()	Create a dictionary representation of this object.
NaturalImageTable.has_decoded_images()	Check if this table contains decoded images or encoded images.
NaturalImageTable.mask_image(mask[, decode, ...])	Applies masking to an ImageTable.

Utilities

CAS Thread Tuner

CASThreadTuner()
CASThreadTuner.tune_thread_count(...[, ...])	Compute the optimal thread count for a given image action.

CAS Thread Tuner Results

CASThreadTunerResults([cas_server_mode, ...])	Store and present results for the CAS thread optimization tool.
CASThreadTunerResults.plot_exec_times([...])	Plot performance for given CAS thread tuner results.

Image Utilities

ImageUtils()
ImageUtils.convert_numpy_to_wide(numpy_array)	Convert a numpy image array to a wide image.
ImageUtils.convert_to_CAS_column(s)	Convert a string to CAS column name.
ImageUtils.convert_wide_to_numpy(wide_image)	Convert a wide image to a numpy image array.
ImageUtils.get_image_array(image_binaries, ...)	Get an image from a fetched array.
ImageUtils.get_image_array_const_ctype(...)	Get an image array with a constant channel type from a CAS table.
ImageUtils.get_image_array_from_row(...[, ...])	Get a 3D image from a row.

Visualization

display_image_slice(images, dims, ress, ...)	Display an image slice in 3D.
display_3D_image_slices_from_array(array[, ...])	Display 3D image slices in 3D.
display_3D_image_slices(self, image[, hold, ...])	Display 3D image slices in 3D.
display_3D_surface(surfaces, vdata, fdata[, ...])	Display the surfaces of an image.