PYME.Acquire.microscope module

class PYME.Acquire.microscope.Microscope

Bases: object

Attributes

frameWranglerPYME.Acquire.frameWrangler.FrameWrangler

Initialized in between hardware initializations and gui initializations.

AddVoxelSizeSetting(name, x, y)

Adds a new voxel size setting.

The reason for multiple settings is to easily support switching between different cameras and/or optical configurations such as tube lenses, splitters, etc …

Parameters

namestring

The name to use for the new setting

xfloat

the pixelsize along the x axis in um

yfloat

the pixelsize along the y axis in um

EnableJoystick(enable=True)

GenStartMetadata(mdh)

Collects the metadata we want to record at the start of a sequence

Parameters

mdhobject derived from PYME.IO.MetaDataHandler.MDHandlerBase

The metadata handler to which we should write our metadata

GetActiveCameraName()

Get the name / key of the currently active camera

GetPixelSize(cam=None)

Get the (sample space) pixel size for the current camera

Returns

pixelsizetuple

the pixel size in the x and y axes, in um

GetPos()

GetPosRange()

PanCamera(dx, dy)

Moves / pans the stage my a given offset, in pixels relative to the camera, correcting for any differences in rotation and mirroring between camera and stage axes.

TODO: fix to use state based position setting

SetPos(**kwargs)

SetVoxelSize(voxelsizename, camName=None)

Set the camera voxel size, from a pre-existing voxel size seting.

Parameters

voxelsizenamestring

The name of the voxelsize setting to use. This should have been created using the AddVoxelSize function.

camNamestring

The name of the camera to ascociate the setting with. If None, then the currently selected camera is used.

centre_roi_on(x, y)

Convenience function to center the ROI on a given location

genStatus()

Generate a status message. TODO - move this to the GUI?

get_roi_centre()

Convenience function to get the centre of the ROI

exists to allow both automatically and manually specified actions to use the same code

get_roi_offset()

Stage (positioning) coordinates are referenced to the (0,0) pixel of the primary camera. Return the offset to the centre of the current ROI. Used when, e.g. moving the stage to centre the current view on a given set of coordinates.

Returns

roi_offset_x, roi_offset_yfloat

offsets in um

initialize(init_script_name, locals={})

property initialized

Checks if the initialisation thread has run (replaces check of initDone flag which needed to be manually set in initialisation script). Semantics are slightly different in that this returns true even if there is an error whist the old way of checking would get forever stuck at the splash screen.

Returns

True if the initialisation script has run, False otherwise

property pa

property to catch access of what was previously called the scope.frameWrangler (the PreviewAcquisator)

register_camera(cam, name, port='', rotate=False, flipx=False, flipy=False)

Register a camera with the microscope

Parameters

camThe camera object

nameA human-readable name

portWhich sideport the camera is attached to (used to automatically select the right camera when changing

sideports & vice versa, but currently only works on the Nikon Ti stand)

rotateIs this camera rotated with respect to the cardinal camera (used for multi-camera support)

flipxIs this camera flipped in x w.r.t. the cardinal camera (used for multi-camera support)

flipyIs this camera flipped in y w.r.t. the cardinal camera (used for multi-camera support)

Notes

The optional port, rotate, flipx, and flipy parameters all relate to multiple camera support and should be defined with respect to the principle camera (not stages etc which should be in the frame of the principle camera). The support for these parameters is currently pretty limited - they work when panning the sample using the mouse, but are generally ignored in other parts of the code.

register_piezo(piezo, axis_name, multiplier=1, needCamRestart=False, channel=0)

Register a piezo with the microscope object

Parameters

piezoPYME.Acquire.Hardware.Piezos.base_piezo.PiezoBase instance

the piezo to register

axis_namestring

the axis name, e.g. ‘x’, ‘y’, ‘z’

multiplierfloat, typically either 1 or -1

what to multiply the positions by to match the directionality in the displayed image and make panning etc work.

needCamRestartbool

whether to restart the camera after changing the position (mostly for simulation and fake piezos)

Notes

The ‘x’ and ‘y’ axes should be defined in terms of the axes of the principle camera (i.e. if a stage moves the image on the camera left and right it is the ‘x’ stage, regardless of the physical motion of the sample). Likewise, the multipliers should be set so that a positive movement of the x stage moves the image right, and a positive movement of the y stage moves the image down.

satCheck(source, **kwargs)

Check to see if the current frame is saturated and stop the camera/ close the shutter if necessary

TODO: could use a rewrite / new inspection.

property settingsDB

startFrameWrangler(event_loop=None)

Start the frame wrangler. Gets called during post-init phase of aquiremainframe.

turnAllLasersOff()

Turn all attached lasers off.

TODO - does this fit with the new state based paradigm?

wait_for_init()

class PYME.Acquire.microscope.StateHandler(key, getFcn=None, setFcn=None, needCamRestart=False)

Bases: object

Define a state-change handler for a give state key, based on supplied get and set functions which interact with the underlying hardware.

This wrapper class serves two functions - a) allowing the get and set methods to be stored under a single dictionary key in the StateManager, and b) making sure a signal is fired when the state changes.

Parameters

keystring

The hardware key - e.g. “Positioning.x”, or “Lasers.405.Power”. This will also be how the hardware state is recorder in the metadata.

getFcnfunction

The function to call to get the value of the parameter. Should take one parameter which is the value to get

setFcnfunction

The function to call to set the value of the parameter. Should take one parameter which is the value to set. Not providing a setFcn results in a read-only property.

needCamRestartbool

Does this absolutely need a camera restart (e.g. we are changing which camera we are using). Will override other preferences.

setValue(value, force=False)

Set the state of the controlled hardware to the given value and fire a signal. The underlying function will not be called if old and new values are the same unless force=True.

class PYME.Acquire.microscope.StateManager(scope, handlers={})

Bases: object

Manages object (microscope) state by calling an appropriate state-handler for a given key.

Looks and behaves like a dictionary to the user, with individual pieces of hardware registering themselves to handle individual keys.

get(key, default=None)

keys()

registerChangeListener(key, callback)

Registers a function to be called when the state of a particular key changes.

The key and value are provided as keyword arguments to the callback the callback should accept have the signature callback(**kwargs), or callback(key, value, **kwargs). Other keyword arguments might also be given.

registerHandler(key, getFcn=None, setFcn=None, needCamRestart=False)

Register a harware key and the ascociated handlers

Parameters

keystring

The hardware key - e.g. “Positioning.x”, or “Lasers.405.Power”. This will also be how the hardware state is recorded in the metadata.

getFcnfunction

The function to call to get the value of the parameter. Should take one parameter which is the value to get

setFcnfunction

The function to call to set the value of the parameter. Should take one parameter which is the value to set. Not providing a setFcn results in a read-only property.

needCamRestartbool

Does this absolutely need a camera restart (e.g. we are changing which camera we are using). Will override other preferences.

Notes

There are a few conventions and special key names which should be observed as this is how the camera will find hardware.

• Keys should be hierachial, separated by dots

• Piezos and stages should start with “Positioning.”, followed by an axis name, and use um as a unit.

• Lasers should start with “Laser.” and define both “<lasername>.Power” and “<lasername>.On” (this is to allow lasers with external switches/shutters as well as )

setItem(key, value, stopCamera=False, force=False)

Set the value of one of our hardware components

Parameters

keystring

The parameter identifier - e.g. “Positioning.x”

valueobject

The value to set. This can be anything the registered handler understands but designing the handlers to accept something which is easily converted to text for the Metadata (see PYME.IO.MetaDataHandler) is advised.

stopCamerabool

Should we stop the camera before setting the value and restart afterwards. Useful for things like integration time which might not be able to be changed on the fly, but also potentially as a way of achieving hardware synchronization.

forcebool

Whether we should call the set method even if the current state is already the desired state.

setItems(stateDict, stopCamera=False, force=False, ignoreMissing=False)

Set multiple items at once - see setItem for details.

Parameters

stateDictdictionary (or dictionary like object)

a dictionary of key : value pairs for each piece of hardware which wants to be updated.

stopCamerabool

Should we stop the camera before setting the values and restart afterwards? Useful for things like integration time which might not be able to be changed on the fly, but also potentially as a way of achieving hardware synchronization.

forcebool

Whether we should call the set method even if the current state is already the desired state.

ignoreMissingbool

Should we silently ignore keys that we don’t have handlers for. Used when setting state from e.g. sequence metadata which might have other irrelevent info.

update(state)

Update state from a dictionary

Parameters

statedict

A dictionary containing the new state