PYME.IO.acquisition_backends module

class PYME.IO.acquisition_backends.Backend(dim_order='XYCZT', shape=[-1, -1, -1, 1, 1])

Bases: ABC

Base class for acquisition backends.

finalise(events=None)

Called after acquisition is complete, may be overridden to e.g. flush buffers, close files, , write events etc …

classmethod gen_sequence_id()

Generate a unique sequence ID which belongs to this acquisition and can be used as, e.g. a database key

initialise()

Called before acquisition starts, may be overridden to e.g. save metadata. NOTE: We typically save metadata in advance of the data so that analysis can start while acquisition is underway.

property sequence_id

This sequences unique ID

abstract store_frame(n, frame_data)

Store frame data (over-ride in derived classes)

Parameters
nint

frame index / position in sequence

frame_datanp.ndarray

data for the frame as a numpy array

class PYME.IO.acquisition_backends.ClusterBackend(series_name, dim_order='XYCZT', shape=[-1, -1, -1, 1, 1], distribution_fcn=None, compression_settings={}, cluster_h5=False, serverfilter='fv-az569-89')

Bases: Backend

default_compression_settings = {'compression': 1, 'quantization': 0, 'quantizationOffset': -1000000.0, 'quantizationScale': 1.0}
finalise(events='[]')

Called after acquisition is complete, may be overridden to e.g. flush buffers, close files, , write events etc …

initialise()

Called before acquisition starts, may be overridden to e.g. save metadata. NOTE: We typically save metadata in advance of the data so that analysis can start while acquisition is underway.

store_frame(n, frame_data)

Store frame data (over-ride in derived classes)

Parameters
nint

frame index / position in sequence

frame_datanp.ndarray

data for the frame as a numpy array

class PYME.IO.acquisition_backends.HDFBackend(series_name, dim_order='XYCZT', shape=[-1, -1, -1, 1, 1], complevel=6, complib='zlib')

Bases: Backend

finalise(events=None)

Called after acquisition is complete, may be overridden to e.g. flush buffers, close files, , write events etc …

store_frame(n, frame_data)

Store frame data (over-ride in derived classes)

Parameters
nint

frame index / position in sequence

frame_datanp.ndarray

data for the frame as a numpy array

class PYME.IO.acquisition_backends.MemoryBackend(size_x, size_y, n_frames, dtype='uint16', dim_order='XYCZT', shape=[-1, -1, 1, 1, 1])

Bases: Backend

store_frame(n, frame_data)

Store frame data (over-ride in derived classes)

Parameters
nint

frame index / position in sequence

frame_datanp.ndarray

data for the frame as a numpy array

PYME.IO.acquisition_backends.distfcn_oidic(n_servers, i=None)