pyemma.coordinates.clustering.KmeansClustering

class pyemma.coordinates.clustering.KmeansClustering(*args, **kwargs)

k-means clustering

__init__(n_clusters, max_iter=5, metric='euclidean', tolerance=1e-05, init_strategy='kmeans++', fixed_seed=False, oom_strategy='memmap', stride=1, n_jobs=None, skip=0, clustercenters=None, keep_data=False)

Kmeans clustering

Parameters

• n_clusters (int) – amount of cluster centers. When not specified (None), min(sqrt(N), 5000) is chosen as default value, where N denotes the number of data points

• max_iter (int) – maximum number of iterations before stopping.

• tolerance (float) –

  stop iteration when the relative change in the cost function

  \[C(S) = \sum_{i=1}^{k} \sum_{\mathbf x \in S_i} \left\| \mathbf x - \boldsymbol\mu_i \right\|^2\]

  is smaller than tolerance.

• metric (str) – metric to use during clustering (‘euclidean’, ‘minRMSD’)

• init_strategy (string) – can be either ‘kmeans++’ or ‘uniform’, determining how the initial cluster centers are being chosen

• fixed_seed (bool or int) – if True, the seed gets set to 42. Use time based seeding otherwise. if an integer is given, use this to initialize the random generator.

• oom_strategy (string, default='memmap') –

  how to deal with out of memory situation during accumulation of all data.

  • ’memmap’: if no memory is available to store all data, a memory

    mapped file is created and written to

  • ’raise’: raise OutOfMemory exception.

• stride (int) – stridden data

• n_jobs (int or None, default None) – Number of threads to use during assignment of the data. If None, all available CPUs will be used.

• clustercenters (None or array(k, dim)) – This is used to resume the kmeans iteration. Note, that if this is set, the init_strategy is ignored and the centers are directly passed to the kmeans iteration algorithm.

• keep_data (boolean, default False) – If you intend to resume the kmeans iteration later on, in case it did not converge, this parameter controls whether the input data is kept in memory or not.

Methods

_Loggable__create_logger()
_ProgressReporterMixin__check_stage_registered(stage)
_SerializableMixIn__interpolate(state, klass)
__delattr__(name, /)	Implement delattr(self, name).
__dir__()	Default dir() implementation.
__eq__(value, /)	Return self==value.
__format__(format_spec, /)	Default object formatter.
__ge__(value, /)	Return self>=value.
__getattribute__(name, /)	Return getattr(self, name).
__getstate__()
__gt__(value, /)	Return self>value.
__hash__()	Return hash(self).
__init__(n_clusters[, max_iter, metric, …])	Kmeans clustering
__init_subclass__(*args, **kwargs)	This method is called when a class is subclassed.
__iter__()
__le__(value, /)	Return self<=value.
__lt__(value, /)	Return self<value.
__my_getstate__()
__my_setstate__(state)
__ne__(value, /)	Return self!=value.
__new__(cls, *args, **kwargs)	Create and return a new object.
__reduce__()	Helper for pickle.
__reduce_ex__(protocol, /)	Helper for pickle.
__repr__()	Return repr(self).
__setattr__(name, value, /)	Implement setattr(self, name, value).
__setstate__(state)
__sizeof__()	Size of object in memory, in bytes.
__str__()	Return str(self).
__subclasshook__	Abstract classes can override this to customize issubclass().
_check_estimated()
_check_resume_iteration()
_chunk_finite(data)
_cleanup_logger(logger_id, logger_name)
_clear_in_memory()
_collect_data(X, first_chunk, last_chunk)
_compute_default_cs(dim, itemsize[, logger])
_create_iterator([skip, chunk, stride, …])	Should be implemented by non-abstract subclasses.
_data_flow_chain()	Get a list of all elements in the data flow graph.
_estimate(iterable, **kw)
_finish_estimate()
_get_classes_to_inspect()	gets classes self derives from which 1.
_get_interpolation_map(cls)
_get_model_param_names()	Get parameter names for the model
_get_param_names()	Get parameter names for the estimator
_get_private_field(cls, name[, default])
_get_serialize_fields(cls)
_get_state_of_serializeable_fields(klass, state)	:return a dictionary {k:v} for k in self.serialize_fields and v=getattr(self, k)
_get_traj_info(filename)
_get_version(cls[, require])
_get_version_for_class_from_state(state, klass)	retrieves the version of the current klass from the state mapping from old locations to new ones.
_init_estimate()
_init_in_memory_chunks(size)
_initialize_centers(X, itraj, t, last_chunk)
_logger_is_active(level)	@param level: int log level (debug=10, info=20, warn=30, error=40, critical=50)
_map_to_memory([stride])	Maps results to memory.
_progress_context([stage])	param stage
_progress_force_finish([stage, description])	forcefully finish the progress for given stage
_progress_register(amount_of_work[, …])	Registers a progress which can be reported/displayed via a progress bar.
_progress_set_description(stage, description)	set description of an already existing progress
_progress_update(numerator_increment[, …])	Updates the progress.
_set_random_access_strategies()
_set_state_from_serializeable_fields_and_state(…)	set only fields from state, which are present in klass.__serialize_fields
_source_from_memory([data_producer])
_transform_array(X)	get closest index of point in clustercenters to x.
assign([X, stride])	Assigns the given trajectory or list of trajectories to cluster centers by using the discretization defined by this clustering method (usually a Voronoi tesselation).
describe()	Get a descriptive string representation of this class.
dimension()	output dimension of clustering algorithm (always 1).
estimate(X, **kwargs)	Estimates the model given the data X
fit(X[, y])	Estimates parameters - for compatibility with sklearn.
fit_predict(X[, y])	Performs clustering on X and returns cluster labels.
fit_transform(X[, y])	Fit to data, then transform it.
get_model_params([deep])	Get parameters for this model.
get_output([dimensions, stride, skip, chunk])	Maps all input data of this transformer and returns it as an array or list of arrays
get_params([deep])	Get parameters for this estimator.
iterator([stride, lag, chunk, …])	creates an iterator to stream over the (transformed) data.
load(file_name[, model_name])	Loads a previously saved PyEMMA object from disk.
n_chunks(chunksize[, stride, skip])	how many chunks an iterator of this sourcde will output, starting (eg.
n_frames_total([stride, skip])	Returns total number of frames.
number_of_trajectories([stride])	Returns the number of trajectories.
output_type()	By default transformers return single precision floats.
sample_indexes_by_cluster(clusters, nsample)	Samples trajectory/time indexes according to the given sequence of states.
save(file_name[, model_name, overwrite, …])	saves the current state of this object to given file and name.
save_dtrajs([trajfiles, prefix, output_dir, …])	saves calculated discrete trajectories.
set_model_params(clustercenters)
set_params(**params)	Set the parameters of this estimator.
trajectory_length(itraj[, stride, skip])	Returns the length of trajectory of the requested index.
trajectory_lengths([stride, skip])	Returns the length of each trajectory.
transform(X)	Maps the input data through the transformer to correspondingly shaped output data array/list.
update_model_params(**params)	Update given model parameter if they are set to specific values
write_to_csv([filename, extension, …])	write all data to csv with numpy.savetxt
write_to_hdf5(filename[, group, …])	writes all data of this Iterable to a given HDF5 file.

Attributes

_AbstractClustering__serialize_fields
_AbstractClustering__serialize_version
_DataSource__serialize_fields
_Estimator__serialize_fields
_FALLBACK_CHUNKSIZE
_InMemoryMixin__serialize_fields
_InMemoryMixin__serialize_version
_KmeansClustering__serialize_fields
_KmeansClustering__serialize_version
_Loggable__ids
_Loggable__refs
_SerializableMixIn__serialize_fields
_SerializableMixIn__serialize_modifications_map
_SerializableMixIn__serialize_version
__abstractmethods__
__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_abc_impl
_estimated
_estimator_type
_loglevel_CRITICAL
_loglevel_DEBUG
_loglevel_ERROR
_loglevel_INFO
_loglevel_WARN
_pg_threshold
_prog_rep_callbacks
_prog_rep_descriptions
_prog_rep_progressbars
_progress_num_registered
_progress_registered_stages
_save_data_producer
_serialize_version
chunksize	chunksize defines how much data is being processed at once.
cluster_centers_	Array containing the coordinates of the calculated cluster centers.
clustercenters	Array containing the coordinates of the calculated cluster centers.
converged
data_producer	The data producer for this data source object (can be another data source object).
default_chunksize	How much data will be processed at once, in case no chunksize has been provided.
dtrajs	Discrete trajectories (assigned data to cluster centers).
filenames	list of file names the data is originally being read from.
fixed_seed	seed for random choice of initial cluster centers.
in_memory	are results stored in memory?
index_clusters	Returns trajectory/time indexes for all the clusters
init_strategy	Strategy to get an initial guess for the centers.
is_random_accessible	Check if self._is_random_accessible is set to true and if all the random access strategies are implemented.
is_reader	Property telling if this data source is a reader or not.
logger	The logger for this class instance
model	The model estimated by this Estimator
n_jobs	Returns number of jobs/threads to use during assignment of data.
name	The name of this instance
ndim
ntraj
overwrite_dtrajs	Should existing dtraj files be overwritten.
ra_itraj_cuboid	Implementation of random access with slicing that can be up to 3-dimensional, where the first dimension corresponds to the trajectory index, the second dimension corresponds to the frames and the third dimension corresponds to the dimensions of the frames.
ra_itraj_jagged	Behaves like ra_itraj_cuboid just that the trajectories are not truncated and returned as a list.
ra_itraj_linear	Implementation of random access that takes arguments as the default random access (i.e., up to three dimensions with trajs, frames and dims, respectively), but which considers the frame indexing to be contiguous.
ra_linear	Implementation of random access that takes a (maximal) two-dimensional slice where the first component corresponds to the frames and the second component corresponds to the dimensions.
show_progress	whether to show the progress of heavy calculations on this object.