PYME.IO.acquisition_backends module

class PYME.IO.acquisition_backends.Backend(dim_order='XYCZT', shape=[-1, -1, -1, 1, 1], spoof_timestamps=False, cycle_time=None, dtype=dtype('uint16'), **kwargs)

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 …

finished()

classmethod gen_sequence_id()

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

getURL()

Get URL for the series to pass to other processes so they can open it

Implement in derived classes if appropriate.

get_n_frames()

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 md

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

supported_dtypes = [dtype('uint16')]

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='runnervm0kj6c', dtype='uint16', **kwargs)

Bases: Backend

default_compression_settings = {'compression': 1, 'quantization': 0, 'quantizationOffset': -1000000.0, 'quantizationScale': 1.0}

finalise()

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

getURL()

Get URL for the series to pass to other processes so they can open it

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

supported_dtypes = [dtype('uint8'), dtype('uint16'), dtype('float32')]

class PYME.IO.acquisition_backends.HDFBackend(series_name, dim_order='XYCZT', shape=[-1, -1, -1, 1, 1], complevel=6, complib='zlib', evt_time_fcn=<built-in function time>, dtype='uint16', **kwargs)

Bases: Backend

Parameters

dtypestr, optional

dtype of image data, in PyTables type str format. Default is ‘uint16’.

finalise(events=None)

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

getURL()

Get URL for the series to pass to other processes so they can open it

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

supported_dtypes = [dtype('uint8'), dtype('uint16'), dtype('float32'), dtype('float64')]

class PYME.IO.acquisition_backends.MemoryBackend(size_x, size_y, n_frames, dtype='uint16', series_name=None, dim_order='XYCZT', shape=[-1, -1, 1, 1, 1], **kwargs)

Bases: Backend

finalise()

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.TiffFolderBackend(series_name, dim_order='XYCZT', shape=[-1, -1, -1, 1, 1], dtype='uint16', **kwargs)

Bases: Backend

finalise()

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

getURL()

Get URL for the series to pass to other processes so they can open it

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

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

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