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PATATO Documentation - Home

User Guide

  • Installation
  • Quick Start
  • Image Processing Parameters
  • Example data
  • Running Tests
  • Troubleshooting

Examples

  • 1. Reconstructing photoacoustic data
  • 2. Comparing image reconstruction methods
  • 3: Command Line Usage
  • 4: Time-Series MSOT Data Analysis
  • 5: Writing your own reconstruction algorithm
  • 6: Writing your own scan reader

Developers

  • File Format Specification
  • Contributing to PATATO

API Reference

  • Analysis Code
    • patato
      • read_reconstruction_preset
      • read_unmixing_preset
      • PreProcessor
      • ReferenceBackprojection
      • OpenCLBackprojection
      • ModelBasedReconstruction
      • SpectralUnmixer
      • SO2Calculator
      • THbCalculator
      • GasChallengeAnalyser
      • DCEAnalyser
      • PAData
      • SimpaImporter
      • iTheraMSOT
      • Reconstruction
      • UnmixedData
      • ImageSequence
      • ROI
      • PATimeSeries
      • core
        • image_structures
      • io
        • attribute_tags
        • hdf
        • hdf5_converter
        • ipasc
        • ithera
        • json
        • msot_data
        • simpa
      • recon
        • get_default_recon_preset
        • backprojection_implementation
        • backprojection_opencl
        • backprojection_reference
        • fourier_transform_rec
        • jax_model_based
        • model_based
        • numpy_backprojection
        • reconstruction_algorithm
      • unmixing
        • get_default_unmixing_preset
        • spectra
        • unmixer
      • processing
        • gpu_preprocessing_algorithm
        • jax_preprocessing_algorithm
        • preprocessing_algorithm
        • preprocessing_types
        • processing_algorithm
      • utils
        • sort_key
        • mask_operations
        • pipeline
        • plotting
        • process_study
        • roi_operations
        • rois
        • tests
        • time_series_analysis
      • data
        • get_msot_time_series_example
        • get_ithera_msot_time_series_example
        • get_msot_phantom_example
        • get_basic_p0
        • generate_basic_simulation
  • Convenience Scripts
    • convenience_scripts
      • convert_binary_to_hdf5
        • main
        • strtobool
      • convert_simpa
        • main
        • strtobool
      • copy_rois
        • init_argparse
        • main
      • data_analysis
        • analyse_dce
        • analyse_gas_challenge
      • generate_core
        • init_argparse
        • main
      • import_clinical_data
        • init_argparse
        • main
      • import_ithera_recons
        • init_argparse
        • main
      • print_speeds
        • init_argparse
        • main
      • process_msot
        • main
      • rename_scan
        • init_argparse
        • main
      • scan_status
        • init_argparse
        • main
      • split_rois
        • init_argparse
        • main
      • unmix
        • init_argparse
        • main
      • view
        • init_argparse
        • main
  • Useful Utilities
    • useful_utilities
      • add_axis_label
      • add_subfigure_label
      • extract_data_tables
      • invert_dictionary_tolist
      • linear_regression
      • process_scan_name
      • set_matplotlib_defaults
  • .rst

processing

Contents

  • Time-series data processing module

processing#

Time-series data processing module#

This module provides functions for commonly-used pre-processing procedures used in photoacoustic imaging. This includes, for example, band-pass filtering, Hilbert transforms and interpolation.

Modules

gpu_preprocessing_algorithm

jax_preprocessing_algorithm

preprocessing_algorithm

preprocessing_types

processing_algorithm

previous

find_dce_boundaries

next

gpu_preprocessing_algorithm

Contents
  • Time-series data processing module

By Thomas Else

© Copyright 2023, Thomas Else.