patato

PATATO Reference

All the functions, classes and modules contained in the PATATO package are detailed here.

For examples of how to use PATATO, please see the examples page.

Functions

read_reconstruction_preset(json_path)	Load and parse the reconstruction preset from the specified JSON file or dictionary.
read_unmixing_preset(json_path, ...)	Load and parse the unmixing preset from the specified JSON file or dictionary.

Classes

PreProcessor([time_factor, detector_factor, ...])	Preprocesses MSOT time series data.
ReferenceBackprojection(n_pixels, ...)	Reference backprojection: Uses JAX in the background.
OpenCLBackprojection(n_pixels, ...)	An OpenCL implemntation of the photoacoustic backprojection.
ModelBasedReconstruction(n_pixels, field_of_view)	Model based reconstruction algorithm processor.
SpectralUnmixer(chromophores, wavelengths[, ...])	The spectral unmixer.
SO2Calculator([algorithm_id, nan_invalid])	The SO2 calculator.
THbCalculator([algorithm_id])	The Total Haemoglobin calculator.
GasChallengeAnalyser([...])	Analyser for oxygen-enhanced datasets.
DCEAnalyser([smoothing_window_size, ...])	Analyser for DCE datasets.
PAData(scan_reader[, scan_writer])	A class that contains the interface to access data from a single scan.
SimpaImporter(filename)	An importer for HDF5 files created by the SIMPA toolkit.
iTheraMSOT(folder[, scan_name])	An interface for iThera MSOT datasets.
Reconstruction(*args, **kwargs)	Data structure for reconstructed images.
UnmixedData(raw_data[, ax_1_labels, ...])	UnmixedData stores unmixed datasets.
ImageSequence(raw_data[, ax_1_labels, ...])
ROI(points, z_position, run, repetition, ...)	Class to store regions of interests.
PATimeSeries(data, dimensions[, ...])	PATimeSeries is the data structure for time-domain raw PA data.

Modules

patato.core	Core datastructures
patato.io	Input/output module
patato.recon	Reconstruction module
patato.unmixing	Unmixing module
patato.processing	Time-series data processing module
patato.utils	Utility module
patato.data	Data examples