def __init__(self):
self.bridge = MagellanBridge()
self.core = self.bridge.get_core()
print('MicroManager Socket:')
print(self.core.socket)
self.magellan = self.bridge.get_magellan()
print('MicroMagellan Socket:')
print(self.magellan.socket)
self.channelGroup = self.core.getChannelGroup()
from pygellan.acquire import MagellanBridge #establish communication with Magellan bridge = MagellanBridge() #get object representing micro-magellan API magellan = bridge.get_magellan() #get this list of acquisitions in the magellan GUI acquistions = magellan.get_acquisitions() #grab the first acquisition in the list acq = acquistions[0] acq.start() # block until the acquisition is complete acq.wait_for_completion()
"""
This example shows how to use pygellan to interact with the micro-manager core. Aside from
the setup section, each following section can be run independently
"""
from pygellan.acquire import MagellanBridge
import numpy as np
import matplotlib.pyplot as plt
#### Setup ####
#establish communication with Magellan
bridge = MagellanBridge()
#get object representing micro-manager core
core = bridge.get_core()
#### Calling core functions ###
exposure = core.getExposure()
#### Setting and getting properties ####
#Here we set a property of the core itself, but same code works for device properties
auto_shutter = core.getProperty('Core', 'AutoShutter')
core.setProperty('Core', 'AutoShutter', 0)
#### Acquiring images ####
#The micro-manager core exposes several mechanisms foor acquiring images. In order to not interfere
#with other pygellan functionality, this is the one that should be used
core.snapImage()
tagged_image = core.getTaggedImage()
#If using micro-manager multi-camera adapter, use core.getTaggedImage(i), where i is the camera index
#tagged_image is a tuple containing the raw pixel data (as a numpy array) and the image metadata (as a python dictionary)
pixels_flat = tagged_image[0]