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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Loop
Step1:  SETUP
Step2:  Autosipper
Step3:  Manifold
Step4:  Micromanager
Step5:  Preset
Step6:  MM Get info
Step7:  Video
Step8:  EXIT
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Python Code:
# WELL
# all valves closed
st = 'A01'
x1,y1,z1 = locs[st]
Z.move(42)
XY.move_xy(x1,y1)
Z.move(z1)
log.append([time.ctime(time.time()), 'AT '+st])
# ACQUIRE 120 frames 11000 ms
# OPEN Hep_1 + W_1 (tree in + out)
log.append([time.ctime(time.time()), 'OPEN tree in + out'])
# flow 20 min (fill tube + tree)
# ACQUIRE 120 frames  5000 ms
# CLOSE W_1 (tree out); OPEN in_1 + out_1 (chip in + out)
log.append([time.ctime(time.time()), 'CLOSE tree out; OPEN chip in + out'])
# flow 10 min (fill chip)
# CLOSE out_1 + in_1 (chip out + in); CLOSE Hep_1 (tree in)
log.append([time.ctime(time.time()), 'CLOSE chip out + in; CLOSE tree in'])
# incubate... WASH in meantime
# WASH
Z.move(42)
XY.move_xy(-8.9473,1.0592)
Z.move(62)
log.append([time.ctime(time.time()), 'AT wash'])
Explanation: Loop
End of explanation
import time
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
Explanation: SETUP
End of explanation
# config director must have "__init__.py" file
# from the 'config' directory, import the following classes:
from config import Motor, ASI_Controller, Autosipper
from config import utils as ut
autosipper = Autosipper(Motor('config/motor.yaml'), ASI_Controller('config/asi_controller.yaml'))
autosipper.coord_frames
# add/determine deck info
autosipper.coord_frames.deck.position_table = ut.read_delim_pd('config/position_tables/deck')
# check deck alignment
# CLEAR DECK OF OBSTRUCTIONS!!
autosipper.go_to('deck', ['name'],'align')
# add plate
Explanation: Autosipper
End of explanation
from config import Manifold
manifold = Manifold('192.168.1.3', 'config/valvemaps/valvemap.csv', 512)
manifold.valvemap[manifold.valvemap.name>0]
Explanation: Manifold
End of explanation
# !!!! Also must have MM folder on system PATH
# mm_version = 'C:\Micro-Manager-1.4'
# cfg = 'C:\Micro-Manager-1.4\SetupNumber2_05102016.cfg'
mm_version = 'C:\Program Files\Micro-Manager-2.0beta'
cfg = 'C:\Program Files\Micro-Manager-2.0beta\Setup2_20170413.cfg'
import sys
sys.path.insert(0, mm_version) # make it so python can find MMCorePy
import MMCorePy
from PIL import Image
core = MMCorePy.CMMCore()
core.loadSystemConfiguration(cfg)
core.setProperty("Spectra", "White_Enable", "1")
core.waitForDevice("Spectra")
core.setProperty("Cam Andor_Zyla4.2", "Sensitivity/DynamicRange", "16-bit (low noise & high well capacity)") # NEED TO SET CAMERA TO 16 BIT (ceiling 12 BIT = 4096)
# core.initializeCircularBuffer()
# core.setCircularBufferMemoryFootprint(4096) # MiB 
Explanation: Micromanager
End of explanation
core.setConfig('Channel','1_PBP')
core.setProperty(core.getCameraDevice(), "Exposure", 300)
core.snapImage()
img = core.getImage()
plt.imshow(img,cmap='gray')
image = Image.fromarray(img)
image.save('TESTIMAGE.tif')
for i in range(5):
    x = core.getXPosition()
    y = core.getYPosition()
    core.setXYPosition(x-1500,y)
    core.waitForDevice(core.getXYStageDevice())
    
    core.snapImage()
    img = core.getImage()
    image = Image.fromarray(img)
    image.save('images/images_{}.tif'.format(i))
Explanation: Preset: 1_PBP 
ConfigGroup,Channel,1_PBP,TIFilterBlock1,Label,1-PBP
Preset: 2_BF  
ConfigGroup,Channel,2_BF,TIFilterBlock1,Label,2-BF
Preset: 3_DAPI 
ConfigGroup,Channel,3_DAPI,TIFilterBlock1,Label,3-DAPI
Preset: 4_eGFP 
ConfigGroup,Channel,4_eGFP,TIFilterBlock1,Label,4-GFP
Preset: 5_Cy5 
ConfigGroup,Channel,5_Cy5,TIFilterBlock1,Label,5-Cy5
Preset: 6_AttoPhos 
ConfigGroup,Channel,6_AttoPhos,TIFilterBlock1,Label,6-AttoPhos
EXPERIMENT
End of explanation
core.getFocusDevice()
core.getCameraDevice()
core.XYStageDevice()
core.getDevicePropertyNames(core.getCameraDevice())
Explanation: MM Get info
End of explanation
# cv2.startWindowThread()
cv2.namedWindow('Video')
cv2.imshow('Video',img)
cv2.waitKey(0)
cv2.destroyAllWindows()
core.stopSequenceAcquisition()
import cv2
cv2.namedWindow('Video')
core.startContinuousSequenceAcquisition(1)
while True:
    img = core.getLastImage()
    if core.getRemainingImageCount() > 0:
#         img = core.popNextImage()
        img = core.getLastImage()
        cv2.imshow('Video', img)
        cv2.waitkey(0)
    else:
        print('No frame')
    if cv2.waitKey(20) >= 0:
        break
cv2.destroyAllWindows()
core.stopSequenceAcquisition()
# core.reset()
Explanation: Video
End of explanation
autosipper.exit()
manifold.exit()
core.unloadAllDevices()
core.reset()
print 'closed'
Explanation: EXIT
End of explanation
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