mycelyso.tunables¶

Module contents¶

This file contains all the tunables available in mycelyso.

You can set them via -t Name=value on the command line.

class mycelyso.tunables.BorderArtifactRemovalBorderSize[source]¶

Bases: tunable.tunable.Tunable

Remove structures, whose centroid lies within that distance [µm] of a border

default = 10.0¶

value = 10.0¶

class mycelyso.tunables.BoxDetection[source]¶

Bases: tunable.tunable.Tunable

Whether to run the rectangular microfluidic growth structure detection as ROI detection

default = False¶

value = False¶

class mycelyso.tunables.CleanUpGaussianSigma[source]¶

Bases: tunable.tunable.Tunable

Clean up step: Sigma [µm] used for Gaussian filter

default = 0.075¶

value = 0.075¶

class mycelyso.tunables.CleanUpGaussianThreshold[source]¶

Bases: tunable.tunable.Tunable

Clean up step: Threshold used after Gaussian filter (values range from 0 to 1)

default = 0.5¶

value = 0.5¶

class mycelyso.tunables.CleanUpHoleFillSize[source]¶

Bases: tunable.tunable.Tunable

Clean up step: Maximum size of holes [µm²] which will be filled

default = 1.0¶

value = 1.0¶

class mycelyso.tunables.CropHeight[source]¶

Bases: tunable.tunable.Tunable

Crop value (vertical) of the image [pixels]

default = 0¶

value = 0¶

class mycelyso.tunables.CropWidth[source]¶

Bases: tunable.tunable.Tunable

Crop value (horizontal) of the image [pixels]

default = 0¶

value = 0¶

class mycelyso.tunables.NodeEndpointMergeRadius[source]¶

Bases: tunable.tunable.Tunable

Radius in which endpoints are going to be merged [µm]

default = 0.5¶

value = 0.5¶

class mycelyso.tunables.NodeJunctionMergeRadius[source]¶

Bases: tunable.tunable.Tunable

Radius in which junctions are going to be merged [µm]

default = 0.5¶

value = 0.5¶

class mycelyso.tunables.NodeLookupCutoffRadius[source]¶

Bases: tunable.tunable.Tunable

Radius at which nodes will be ignored if they are further away [µm]

default = 2.5¶

value = 2.5¶

class mycelyso.tunables.NodeLookupRadius[source]¶

Bases: tunable.tunable.Tunable

Radius in which nodes will be searched for found pixel structures [µm]

default = 0.5¶

value = 0.5¶

class mycelyso.tunables.NodeTrackingEndpointShiftRadius[source]¶

Bases: tunable.tunable.Tunable

Maximum search radius for endpoints [µm·h⁻¹]

default = 100.0¶

value = 100.0¶

class mycelyso.tunables.NodeTrackingJunctionShiftRadius[source]¶

Bases: tunable.tunable.Tunable

Maximum search radius for junctions [µm·h⁻¹]

default = 5.0¶

value = 5.0¶

class mycelyso.tunables.RemoveSmallStructuresSize[source]¶

Bases: tunable.tunable.Tunable

Remove structures up to this size [µm²]

default = 10.0¶

value = 10.0¶

class mycelyso.tunables.SkipBinarization[source]¶

Bases: tunable.tunable.Tunable

Whether to directly use the input image as binary mask. Use in case external binarization is desired.

default = False¶

value = False¶

class mycelyso.tunables.StoreImage[source]¶

Bases: tunable.tunable.Tunable

Whether to store images in the resulting HDF5. This leads to a potentially much larger output file.

default = False¶

value = False¶

class mycelyso.tunables.ThresholdingParameters[source]¶

Bases: tunable.tunable.Tunable

Parameters for the used binarization method, passed as key1:value1,key2:value2,… string

default = ''¶

value = ''¶

class mycelyso.tunables.ThresholdingTechnique[source]¶

Bases: tunable.tunable.Tunable

Binarization method to use, for available methods see documentation (mycelyso.processing.binarization)

default = 'experimental_thresholding'¶

classmethod test(value)[source]¶

value = 'experimental_thresholding'¶

class mycelyso.tunables.TrackingMaximumCoverage[source]¶

Bases: tunable.tunable.Tunable

Tracking, maximum covered area ratio at which tracking is still performed

default = 0.2¶

value = 0.2¶

class mycelyso.tunables.TrackingMaximumRelativeShrinkage[source]¶

Bases: tunable.tunable.Tunable

Tracking, maximal relative shrinkage

default = 0.2¶

value = 0.2¶

class mycelyso.tunables.TrackingMaximumTipElongationRate[source]¶

Bases: tunable.tunable.Tunable

Tracking, maximum tip elongation rate [µm·h⁻¹]

default = 100.0¶

value = 100.0¶

class mycelyso.tunables.TrackingMinimalGrownLength[source]¶

Bases: tunable.tunable.Tunable

Tracking, minimal hyphae gained length in track filter [µm]

default = 5.0¶

value = 5.0¶

class mycelyso.tunables.TrackingMinimalMaximumLength[source]¶

Bases: tunable.tunable.Tunable

Tracking, minimal hyphae end length in track filter [µm]

default = 10.0¶

value = 10.0¶

class mycelyso.tunables.TrackingMinimumTipElongationRate[source]¶

Bases: tunable.tunable.Tunable

Tracking, minimum tip elongation rate [µm·h⁻¹]

default = -0.0¶

value = -0.0¶

class mycelyso.tunables.TrackingMinimumTrackedPointCount[source]¶

Bases: tunable.tunable.Tunable

Tracking, minimal time steps in track filter [#]

default = 5¶

value = 5¶