pyemma.coordinates.data.DataInMemory

class pyemma.coordinates.data.DataInMemory(*args, **kwargs)

multi-dimensional data fully stored in memory.

Used to pass arbitrary coordinates to pipeline. Data is being flattened to two dimensions to ensure it is compatible.

Parameters

data (ndarray (nframe, ndim) or list of ndarrays (nframe, ndim)) – Data has to be either one 2d array which stores amount of frames in first dimension and coordinates/features in second dimension or a list of this arrays.

__init__(data, chunksize=None, **kw)

Initialize self. See help(type(self)) for accurate signature.

Methods

_Loggable__create_logger()
_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__(data[, chunksize])	Initialize self.
__init_subclass__(*args, **kwargs)	This method is called when a class is subclassed.
__iter__()
__le__(value, /)	Return self<=value.
__lt__(value, /)	Return self<value.
__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 str(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().
_add_array_to_storage(array)	checks shapes, eg convert them (2d), raise if not possible after checks passed, add array to self._data
_chunk_finite(data)
_cleanup_logger(logger_id, logger_name)
_clear_in_memory()
_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.
_get_classes_to_inspect()	gets classes self derives from which 1.
_get_interpolation_map(cls)
_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.
_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.
_set_dimensions_and_lenghts()
_set_state_from_serializeable_fields_and_state(…)	set only fields from state, which are present in klass.__serialize_fields
_source_from_memory([data_producer])
describe()
dimension()
get_output([dimensions, stride, skip, chunk])	Maps all input data of this transformer and returns it as an array or list of arrays
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.
load_from_files(files)	construct this by loading all files into memory
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.
save(file_name[, model_name, overwrite, …])	saves the current state of this object to given file and name.
trajectory_length(itraj[, stride, skip])	Returns the length of trajectory of the requested index.
trajectory_lengths([stride, skip])	Returns the length of each trajectory.
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

IN_MEMORY_FILENAME
_DataInMemory__serialize_version
_DataSource__serialize_fields
_FALLBACK_CHUNKSIZE
_InMemoryMixin__serialize_fields
_InMemoryMixin__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
_loglevel_CRITICAL
_loglevel_DEBUG
_loglevel_ERROR
_loglevel_INFO
_loglevel_WARN
_save_data_producer
_serialize_version
chunksize
data	Property that returns the data that was hold in storage (data in memory mode).
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.
filenames	list of file names the data is originally being read from.
in_memory	are results stored in memory?
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
name	The name of this instance
ndim
ntraj
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.