Tomopy Recon¶

Description¶

A wrapper to the tomopy reconstruction library.

Parameters

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: hidden
    dtype: "[None,int]"
    description: Not an option.
    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: intermediate
    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

algorithm:
    visibility: basic
    dtype: str
    description: The reconstruction algorithm
    default: gridrec
    options: "['art', 'bart', 'fbp', 'gridrec', 'mlem', 'osem', 'ospml_hybrid', 'ospml_quat', 'pml_hybrid', 'pml_quad', 'sirt']"

filter_name:
    visibility: intermediate
    dtype: "[None, str]"
    description: Name of the filter for analytic reconstruction
    default: ramlak
    options: "['None', 'shepp', 'cosine', 'hann', 'hamming', 'ramlak', 'parzen', 'butterworth']"
    dependency:
        algorithm:
            fbp
            gridrec

reg_par:
    visibility: intermediate
    dtype: float
    description: Regularization parameter for smoothing
    default: "0.0"
    dependency:
        algorithm:
            ospml_hybrid
            ospml_quad
            pml_hybrid
            pml_quad

n_iterations:
    visibility: basic
    dtype: int
    description: Number of iterations.
    default: "1"
    dependency:
        algorithm:
            art
            bart
            mlem
            osem
            ospml_hybrid
            ospml_quad
            pml_hybrid
            pml_quad
            sirt

outer_pad:
    visibility: intermediate
    dtype: "[bool, float]"
    description: Pad the sinogram width to fill the reconstructed volume for asthetic purposes. Choose from True (defaults to sqrt(2)), False or float <= 2.1.
    warning: This will increase the size of the data and the time to compute the reconstruction. Only available for selected algorithms and will be ignored otherwise.
    default: "False"
    dependency:
        algorithm:
            fbp
            gridrec

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