Tomo Phantom Loader

Description

A hdf5 dataset of a specified size is created at runtime using Tomophantom to generate synthetic data , saved with relevant meta_data to a NeXus file, and used as input. It recreates the behaviour of the nxtomo loader but with synthetic data. The input file path passed to Savu will be ignored (use a dummy).

Parameters

preview:
    visibility: basic
    dtype: preview
    description: A slice list of required frames.
    default: "[]"

proj_data_dims:
    visibility: basic
    dtype: "[list[float], list[]]"
    description: "A list specifiying the sizes of dimensions of the generated 3D               projection data in the following format [Angles, DetectorsY, DetectorsX]."
    default: "[180, 128, 160]"

axis_labels:
    visibility: basic
    dtype: "list[str]"
    description: A list of axis labels.
    default: "['rotation_angle.degrees', 'detector_y.pixels', 'detector_x.pixels']"

tomo_model:
    visibility: basic
    dtype: int
    description: Select a model number from the library (see TomoPhantom dat files).
    default: "13"

patterns:
    visibility: hidden
    dtype: "list[str]"
    description: projection data object patterns.
    default: "['SINOGRAM.0c.1s.2c', 'PROJECTION.0s.1c.2c']"

axis_labels_phantom:
    visibility: hidden
    dtype: "list[str]"
    description: A list of axis labels.
    default: "['detector_z.pixels', 'detector_y.pixels', 'detector_x.pixels']"

patterns_tomo2:
    visibility: hidden
    dtype: "list[str]"
    description: Phantom data object patterns.
    default: "['VOLUME_XZ.0c.1s.2c', 'VOLUME_XY.0s.1c.2c']"

out_datasets:
    visibility: datasets
    dtype: "list[str]"
    description: The names assigned to the datasets.
    default: "['synth_proj_data', 'phantom']"

Key

visibility: The visibility level of the parameter
dtype: The type of data
description: A short explanation of the parameter
default: The default value
options: A list of permitted values
dependency: The name of the parameter and value which this parameter depends upon
range: A guide for the range of the parameter

Citations

TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks by Kazantsev, Daniil et al.

Bibtex

@article{kazantsev2018tomophantom,
  title={TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks},
  author={Kazantsev, Daniil and Pickalov, Valery and Nagella, Srikanth and Pasca, Edoardo and Withers, Philip J},
  journal={SoftwareX},
  volume={7},
  pages={150--155},
  year={2018},
  publisher={Elsevier}
}

Endnote

%0 Journal Article
%T TomoPhantom, a software package to generate 2D-4D analytical phantoms for CT image reconstruction algorithm benchmarks
%A Kazantsev, Daniil
%A Pickalov, Valery
%A Nagella, Srikanth
%A Pasca, Edoardo
%A Withers, Philip J
%J SoftwareX
%V 7
%P 150-155
%@ 2352-7110
%D 2018
%I Elsevier

API

class TomoPhantomLoader(name='TomoPhantomLoader')

setup()

This method is first to be called after the plugin has been created. It determines input/output datasets and plugin specific dataset information such as the pattern (e.g. sinogram/projection).