pyfibre.pyfibre_runner module

class pyfibre.pyfibre_runner.PyFibreRunner[source]

Bases: traits.has_traits.HasStrictTraits

Set parameters for ImageAnalyser routines

alpha = None

Metric for hysterisis segmentation

ow_metric = None

Toggles force overwrite of existing metric analysis

ow_network = None

Toggles force overwrite of existing fibre network

ow_segment = None

Toggles force overwrite of existing segmentation

p_denoise = None

Parameters for non-linear means algorithm (used to remove noise)

run(file_sets, analyser, reader)[source]

Generator that returns databases of metrics from each image in dictionary. Analyses input image by calculating metrics and segmenting via FIRE algorithm

Parameters

  • file_sets (list of IFileSet) – Contains file sets corresponding to each BaseMultiImage to be analysed

  • analyser (BaseAnalyser) – Contains reference to MultiImage and analysis script to be performed

  • reader (BaseMultiImageReader) – Contains loading routines for a BaseMultiImage class

Yields

databases (list of pd.DataFrame) – Calculated metrics for further analysis

save_figures = None

Toggles creation of figures

scale = None

Unit of scale to resize image

sigma = None

Standard deviation of Gaussian smoothing