xmipp3.protocols.protocol_cl2d_clustering module

class xmipp3.protocols.protocol_cl2d_clustering.XmippProtCL2DClustering(**args)

Bases: ProtAnalysis2D, XmippProtocol

Groups similar 2D class averages using clustering. This process helps identify homogeneous subsets within the dataset, improving classification and downstream analysis.

AVERAGES = 1

BOTH = 2

CLASSES = 0

clusterClasses()

xmipp_cl2d_clustering -i path/to/inputAverages.mrcs -o path/to/outputDir -m 10 -M 20 -j 8

convertStep()

createOutputSetOfAverages(inputSet2D, result_dict, output_dict)

createOutputSetOfClasses(inputSet2D, result_dict, output_dict)

createOutputStep()

getClusterImagesPlot()

getClusterPlot()

read_clusters_from_txt(file_path)

Reads a cluster dictionary from a .txt file formatted as: Cluster 0:

6

Cluster 1:

36 34 44

…

Args:

file_path (str): The path to the .txt file.

Returns:

dict: A dictionary where the key is the cluster number and the value is a list of associated numbers.