PYME.Acquire.acquisition_base module

Base class for acquisition modules

This exists to document the interface which acquisition types should implement in order to be able to be used with spooling etc …

class PYME.Acquire.acquisition_base.AcquisitionBase(*args, **kwargs)

Bases: ABC

Create an Acquisition object

abort()

Abort the acquisition

This should stop the acquisition as quickly as practical. In many cases this can just be a call to stop(), but there is no expectation that buffers will be flushed, remaining protocol steps executed or hardware returned to a starting state. Especially for cases which involve moving translation stages or other hardware it is desirable that the abort method not result in further movement of hardware unless to a known safe state (e.g. lasers off).

Abort should, however, finalise the backend and emit the on_stop signal. TODO - should abort set spool_complete?

abstract classmethod from_spool_settings(scope, settings, backend, backend_kwargs={}, series_name=None, spool_controller=None)

Create an Acquisition object from settings and a backend.

Parameters

scopemicroscope.Microscope

The microscope object to use for acquisition. Supplied in order to allow hardware control and access to the frameWrangler.

settingsdict

A dictionary of settings for the acquisition

backedclass

The class of the backend to use for the acquisition. Generally one of PYME.IO.acquisition_backends

backend_kwargsdict

A dictionary of keyword arguments to pass to the backend constructor

series_namestr

The name of the series to create. series_name should be defined unless the MemoryBackend is used, in which case it is ignored.

spool_controllerobject

The spool controller object to use for the acquisition. Generally scope.spoolController. Currently used by ProtocolAcquisition to access default protocol settings held by the spoolController, but a bit of a legacy hack. May be removed in the future.

getURL()

classmethod get_frozen_settings(scope, spool_controller=None)

Return a dictionary of settings for the acquisition

Used to “freeze” the state of the spool_controller and/or other settings objects when queueing acquisitions for subsequent execution via the ActionManager

abstract md()

Return acqusition metadata (a PYME.IO.MetaDataHandler object)

generally just a short wrapper around the backend metadata

#TODO - rename this to .mdh, or remove entirely and standardise backend access?

abstract on_frame(sender, frameData, **kwargs)

Frame source handler

This method should be connected to the frame source signal (i.e. scope.frameWrangler.onFrame) and be responsible for handling incoming frames, passing them off to storage and performing anything that needs to be done (e.g. hardware movements or protocol task handling) before the next frame. NOTE - this method is called when the frame is retrieved by the frame wrangler - if the camera is running in continuous mode, this may be several frames after the camera has actually acquired the frame.

abstract start()

Start the acquisition

This will usually record any metadata, connect self.on_frame to a frame source (i.e. scope.frameWrangler.onFrame), and initialise the backend. It should not block, with the bulk of the acquisition logic taking place in frame source handler.

abstract stop()

Stop the acquisition

This should disconnect from the frame souce, flush any remaining buffers, return hardware to starting state (if modified), do any cleanup, and finalise the backend.

It is desirable to send a final on_progress signal so that the GUI reflects the actual number of frames spooled etc… .

Once everything is complete, the on_stop signal should be emitted and the spool_complete flag set.

property storage

Return the storage object for the acquisition