Mask Initialiser

Description

A plugin to initialise a binary mask for level sets and distance transform segmentations. Seeds are generated by providing coordinates of three points in 3D space (start-middle-finish) and connecting them with a cylinder of a certain radius. Importantly the Z coordinate is given following VOLUME_XY vertical pattern

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: The default names
    default: "['INIT_MASK']"

mask1_coordinates:
    visibility: basic
    dtype: list
    description: X0,Y0,Z0 (start) X1,Y1,Z1 (middle) and X2,Y2,Z2 (finish) coordinates of three points.
    default: "[10, 10, 0, 15, 15, 15, 20, 20, 20]"

mask1_radius:
    visibility: basic
    dtype: int
    description: Mask1 will be initialised with an ellipse of radius.
    default: "5"

mask2_coordinates:
    visibility: basic
    dtype: "[None,list]"
    description: The second mask coordinates.
    default: None

mask2_radius:
    visibility: basic
    dtype: "[None,int]"
    description: Mask2 will be initialised with an ellipse of radius.
    default: None

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

No citations

API

class MaskInitialiser

A plugin to initialise a binary mask for level sets and distance transform segmentations. Seeds are generated by providing coordinates of three points in 3D space (start-middle-finish) and connecting them with a cylinder of a certain radius. Importantly the Z coordinate is given following VOLUME_XY vertical pattern

Parameters

• mask1_coordinates – X0,Y0,Z0 (start) X1,Y1,Z1 (middle) and X2,Y2,Z2 (finish) coordinates of three points. Default: [10, 10, 0, 15, 15, 15, 20, 20, 20].

• mask1_radius – Mask1 will be initialised with an ellipse of radius. Default: 5.

• mask2_coordinates – The second mask coordinates. Default: None.

• mask2_radius – Mask2 will be initialised with an ellipse of radius. Default: None.

• out_datasets – The default names . Default: [‘INIT_MASK’].

get_max_frames()

nInput_datasets()

The number of datasets required as input to the plugin

Returns

Number of input datasets

nOutput_datasets()

The number of datasets created by the plugin

Returns

Number of output datasets

pre_process()

This method is called immediately after base_pre_process().

process_frames(data)

This method is called after the plugin has been created by the pipeline framework and forms the main processing step

Parameters

data (list(np.array)) – A list of numpy arrays for each input dataset.

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).

mask_gen(mask, coordX, coordY, coordZ, mask_radius, dimX, dimY, index_current)