PYME.IO.acquisition_backends module¶
- class PYME.IO.acquisition_backends.Backend(dim_order='XYCZT', shape=[-1, -1, -1, 1, 1])¶
Bases:
ABCBase 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)¶