PYME.LMVis.Extras.clusterAnalysis module

class PYME.LMVis.Extras.clusterAnalysis.ClusterAnalyser(visFr)

Methods

OnClumpDBSCAN([event]) Runs sklearn DBSCAN clustering algorithm on pipeline filtered results using the GUI defined in the DBSCAN recipe module.
OnClustersInTime([event])
OnFindMixedClusters([event]) FindMixedClusters first uses DBSCAN clustering on two color channels separately for denoising purposes, then after having removed noisy points, DBSCAN is run again on both channels combined, and the fraction of clumps containing both colors is determined.
OnMeasureClusters([event]) Calculates various measures for clusters using PYME.recipes.localisations.MeasureClusters
OnNearestNeighbor([event]) GUI front-end for the NearestNeighbourDistances recipe module.
OnPairwiseDistanceHistogram([event])
OnClumpDBSCAN(event=None)

Runs sklearn DBSCAN clustering algorithm on pipeline filtered results using the GUI defined in the DBSCAN recipe module.

Args are user defined through GUI
eps: search radius for clustering min_points: number of points within eps required for a given point to be considered a core point
OnClustersInTime(event=None)
OnFindMixedClusters(event=None)

FindMixedClusters first uses DBSCAN clustering on two color channels separately for denoising purposes, then after having removed noisy points, DBSCAN is run again on both channels combined, and the fraction of clumps containing both colors is determined.

OnMeasureClusters(event=None)

Calculates various measures for clusters using PYME.recipes.localisations.MeasureClusters

Parameters:labelsKey: pipeline key to access array of label assignments. Measurements will be calculated for each label.
OnNearestNeighbor(event=None)

GUI front-end for the NearestNeighbourDistances recipe module. Handling is in place for single species nearest neighbour calculations, as well as two species where the user is queried via the GUI as to which channels to use for building and querying the kdtree.

OnPairwiseDistanceHistogram(event=None)
PYME.LMVis.Extras.clusterAnalysis.Plug(visFr)

Plugs this module into the gui