scikitimage_sart.rst

{% extends "plugin_template.rst" %}

{% block title %}Scikitimage Sart{% endblock %}

{% block description %} A Plugin to reconstruct an image by filter back projection using the inverse radon transform from scikit-image. {% endblock %}

{% block parameter_yaml %}

in_datasets:

visibility: datasets dtype: "[list[],list[str]]" description: summary: A list of the dataset(s) to process. verbose: A list of strings, where each string gives the name of a dataset that was either specified by a loader plugin or created as output to a previous plugin. The length of the list is the number of input datasets requested by the plugin. If there is only one dataset and the list is left empty it will default to that dataset. default: "[]"

out_datasets:

visibility: datasets dtype: "[list[],list[str]]" description: summary: A list of the dataset(s) to create. verbose: A list of strings, where each string is a name to be assigned to a dataset output by the plugin. If there is only one input dataset and one output dataset and the list is left empty, the output will take the name of the input dataset. The length of the list is the number of output datasets created by the plugin. default: "[]"

centre_of_rotation:

visibility: basic dtype: "[float, str, dict{int:float}]" description: Centre of rotation to use for the reconstruction. default: "0.0" example: It could be a fixed value, a dictionary of (sinogram number, value) pairs for a polynomial fit of degree 1, or a dataset name.

init_vol:

visibility: intermediate dtype: "[None, str]" description: Dataset to use as volume initialiser (does not currently work with preview) default: None example: "Type the name of the initialised dataset e.g. ['tomo']"

log:

visibility: intermediate dtype: bool description: summary: Option to take the log of the data before reconstruction. verbose: Should be set to false if you use PaganinFilter default: "True" example: Set to True to take the log of the data before reconstruction.

preview:

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

force_zero:

visibility: intermediate dtype: "[list[float,float],list[None,None]]" description: Set any values in the reconstructed image outside of this range to zero. default: "['None', 'None']" example: "[0, 1]"

ratio:

visibility: intermediate dtype: "[float, list[float, float]]" description: Ratio of the masks diameter in pixels to the smallest edge size along given axis. If a list of two floats is given, the second value is used to fill up the area outside the mask. default: "0.95"

log_func:

visibility: advanced dtype: str description: Override the default log function with a numpy statement default: np.nan_to_num(-np.log(sino))

vol_shape:

visibility: hidden dtype: "[str, int]" description: summary: Override the size of the reconstruction volume with an integer value. verbose: When fixed, you get the dimension of the horizontal detector or you can specify any reconstruction size you like with an integer. default: fixed

iterations:

visibility: basic dtype: int description: Number of iterations in the reconstruction. default: "1"

output_size:

visibility: intermediate dtype: "[None, int, list[int,int], str]" description: Number of rows and columns in the reconstruction. default: auto

filter:

visibility: intermediate dtype: str description: Filter used in frequency domain filtering. Ramp filter used by default. Assign None to use no filter. options: "['ramp', 'shepp-logan', 'cosine', 'hamming', 'hann', 'None']" default: ramp

interpolation:

visibility: intermediate dtype: int description: Interpolation method used in reconstruction. Methods available: linear, nearest, and cubic (cubic is slow). options: "['linear', 'nearest', 'cubic']" default: linear

circle:

visibility: intermediate dtype: bool description: Assume the reconstructed image is zero outside the inscribed circle. Also changes the default output_size to match the behaviour of radon called with circle=True. default: "False"

image:

visibility: intermediate dtype: "[None,list]" description: "2D array, dtype=float, optional. Image containing an initial reconstruction estimate. Shape of this array should be (radon_image.shape[0], radon_image.shape[0]). The default is a filter backprojection using scikit.image.iradon as 'result'." default: None

clip:

visibility: intermediate dtype: "[list,None]" description: "length-2 sequence of floats. Force all values in the reconstructed tomogram to lie in the range [clip[0], clip[1]]." default: None

relaxation:

visibility: advanced dtype: float description: Float. Relaxation parameter for the update step. A higher value can improve the convergence rate, but one runs the risk of instabilities. Values close to or higher than 1 are not recommended. default: "0.15"

{% endblock %}

{% block plugin_citations %}

Principles of computerized tomographic imaging by Kak, Avinash C et al.

Bibtex

@article{kak2002principles,
title={Principles of computerized tomographic imaging},
author={Kak, Avinash C and Slaney, Malcolm and Wang, Ge},
journal={Medical Physics},
volume={29},
number={1},
pages={107--107},
year={2002},
publisher={Wiley Online Library}
}

Endnote

%0 Journal Article
%T Principles of computerized tomographic imaging
%A Kak, Avinash C
%A Slaney, Malcolm
%A Wang, Ge
%J Medical Physics
%V 29
%N 1
%P 107-107
%@ 0094-2405
%D 2002
%I Wiley Online Library

{% endblock %}

{% block plugin_file %}../../../plugin_api/plugins.reconstructions.scikitimage_sart.rst{% endblock %}