ColabSegData#

class ColabSegData#

Docstring for ColabSegData data structure framework.

Methods

`ColabSegData.analyze_protein_membrane_min_distance`([...])	analyze distance between particle positions and a membrane segmentation
`ColabSegData.backup_step_to_previous`()	takes the current value and overwrites the previous step
`ColabSegData.calculate_normals`([...])	Calculate the normals of each voxel based on nearest neighbors uses a plane fit (very basic method)
`ColabSegData.compile_xyz_string`(point_cloud)	Compiles an xyz file string for viz in py3DMol
`ColabSegData.convert_tomo`([step_size])	optimized version of conversion code
`ColabSegData.crop_fit_around_membrane`([...])	use kdtree for distance calculation
`ColabSegData.dbscan_clustering`([...])	DBSCAN subclustering of the individual clusters after processing If the clusters are all numbered the same
`ColabSegData.delete_cluster`(cluster_index)	delete a single cluster from data
`ColabSegData.delete_fit`(fit_index)	delete a fit from data
`ColabSegData.delete_multiple_clusters`(...)	delete Multiple clusters
`ColabSegData.delete_multiple_fits`(fit_index)	delete a fit from data
`ColabSegData.delete_normals`()
`ColabSegData.delete_protein_position`()	delete the positions from the gui
`ColabSegData.eigenvalue_outlier_removal`(...)	Uses the covaiance based edge detection to remove points from the point cloud.
`ColabSegData.extract_slice`(filename[, slice])	Extract a slice from the original tomogram and visualize
`ColabSegData.flip_normals`()
`ColabSegData.get_lamina_rotation_matrix`([...])
`ColabSegData.get_selected_sphere_radii`([...])	return a list of sphere radii based on a selection
`ColabSegData.interpolate_membrane_closed_surface`(...)	Least square fit for a perfect sphere and adding of points.
`ColabSegData.interpolate_membrane_rbf`([...])	Interpolate extended membrane using scipy RBF fit.
`ColabSegData.load_hdf`(filename)	read all class variables from hdf5 file format and populate instance
`ColabSegData.load_pickle`(filename)
`ColabSegData.load_point_cloud`(filename)	Load a plain point cloud from a txt file.
`ColabSegData.load_protein_position`(filename)	Load a protein position list (XYZ file)
`ColabSegData.load_stl_file`(filename)	Load an stl file.
`ColabSegData.load_tomogram`(filename)	load_tomogram with pyto library
`ColabSegData.merge_clusters`([cluster_indices])	Merge two or more clusters by vstacking them
`ColabSegData.plain_fit_and_rotate_lamina`([...])	Fits plane through extracted point cloud and rotates the positions
`ColabSegData.read_mrc`(filename)
`ColabSegData.reload_original_values`()	Reload the origial values
`ColabSegData.reload_previous_step`()
`ColabSegData.save_hdf`(filename)	write all class variables into hdf5 file format
`ColabSegData.save_pickle`(filename)
`ColabSegData.save_values_txt`(value_array, ...)
`ColabSegData.split_clusters`([cluster_indices])	Split one cluster by kmeans
`ColabSegData.statistical_outlier_removal`([...])	Remove the statistical outliers of the membrane
`ColabSegData.trim_cluster_egdes_cluster`(...)	Trim lamina at top and bottom
`ColabSegData.trim_cluster_egdes_fit`(fit_indices)	Trim lamina at top and bottom
`ColabSegData.write_output_mrc`(positions, ...)	writes a merged mrc file from the fit
`ColabSegData.write_txt`(point_cloud, ...)	Write a simple txt file to disc
`ColabSegData.write_xyz`(point_cloud, ...)	Write an XYZ file for viewing in VMD