DPC protocol in ImSwitch

[AaronRiSa]

Hi, @beniroquai !

I am trying to solve the DPC problem in ImSwitch script, here's the code :)

import tifffile
import time 
import matplotlib.pyplot as plt
import numpy as np

mainWindow.setCurrentModule('imcontrol')
def fft2c(x):

    axes = (-2, -1)
    return np.fft.fftshift(
        np.fft.fft2(np.fft.ifftshift(x, axes=axes), norm="ortho"), axes=axes
        )

def ifft2c(X):
    
    axes = (-2, -1)
    return np.fft.fftshift(
        np.fft.ifft2(np.fft.ifftshift(X, axes=axes), norm="ortho"), axes=axes
        )

tWait = 2
Path = r'C:\Users\T490\Documents\GitHub\ImSwitch\imswitch\ImSwitch\recordings\DPC'


#Top pattern
api.imcontrol.setAllLEDOff()
time.sleep(.2)

topPattern = [{"id":8, "r":0, "g":1, "b":0}, 
{"id":9, "r":0, "g":1, "b":0}, 
{"id":10, "r":0, "g":1, "b":0}, 
{"id":11, "r":0, "g":1, "b":0}, 
{"id":12, "r":0, "g":0, "b":0}, 
{"id":13, "r":0, "g":1, "b":0}, 
{"id":14, "r":0, "g":1, "b":0}, 
{"id":15, "r":0, "g":0, "b":0}
]

api.imcontrol.setSpecial(topPattern, 255, True)
time.sleep(tWait)
mImage = api.imcontrol.snapImage(True, False)
tifffile.imsave(Path+r'\toppattern.tif', mImage)
	

#Bottom pattern
api.imcontrol.setAllLEDOff()
time.sleep(0.2)

bottomPattern= [{"id":0, "r":0, "g":0, "b":0}, 
{"id":1, "r":0, "g":1, "b":0}, 
{"id":2, "r":0, "g":1, "b":0}, 
{"id":3, "r":0, "g":0, "b":0}, 
{"id":4, "r":0, "g":1, "b":0}, 
{"id":5, "r":0, "g":1, "b":0}, 
{"id":6, "r":0, "g":1, "b":0}, 
{"id":7, "r":0, "g":1, "b":0}
]

api.imcontrol.setSpecial(bottomPattern, 255, True)
time.sleep(tWait)

mImage = api.imcontrol.snapImage(True, False)
tifffile.imsave(Path + r'\bottompattern.tif', mImage)
	



#right pattern
api.imcontrol.setAllLEDOff()
time.sleep(.1)

rightPattern = [{"id":2, "r":0, "g":1, "b":0}, 
{"id":3, "r":0, "g":0, "b":0}, 
{"id":4, "r":0, "g":1, "b":0}, 
{"id":5, "r":0, "g":1, "b":0}, 
{"id":11, "r":0, "g":1, "b":0}, 
{"id":10, "r":0, "g":1, "b":0}, 
{"id":12, "r":0, "g":0, "b":0}, 
{"id":13, "r":0, "g":1, "b":0}
]

api.imcontrol.setSpecial(rightPattern, 255, True)
time.sleep(tWait)
mImage = api.imcontrol.snapImage(True, False)
tifffile.imsave(Path+r'\rightpattern.tif', mImage)
	


#left pattern
api.imcontrol.setAllLEDOff()
time.sleep(.1)


leftPattern = [{"id":0, "r":0, "g":0, "b":0}, 
{"id":1, "r":0, "g":1, "b":0}, 
{"id":6, "r":0, "g":1, "b":0}, 
{"id":7, "r":0, "g":1, "b":0}, 
{"id":8, "r":0, "g":1, "b":0}, 
{"id":9, "r":0, "g":1, "b":0}, 
{"id":14, "r":0, "g":1, "b":0}, 
{"id":15, "r":0, "g":0, "b":0}
]

api.imcontrol.setSpecial(leftPattern, 255, True)
time.sleep(tWait)
mImage = api.imcontrol.snapImage(True, False)
tifffile.imsave(Path+r'\leftpattern.tif', mImage)


#Brightfield pattern
api.imcontrol.setAllLEDOff()
time.sleep(.1)

rightPattern = [{"id":2, "r":0, "g":1, "b":0}, 
{"id":3, "r":0, "g":0, "b":0}, 
{"id":4, "r":0, "g":1, "b":0}, 
{"id":5, "r":0, "g":1, "b":0}, 
{"id":11, "r":0, "g":1, "b":0}, 
{"id":10, "r":0, "g":1, "b":0}, 
{"id":12, "r":0, "g":0, "b":0}, 
{"id":13, "r":0, "g":1, "b":0}
]

api.imcontrol.setSpecial(rightPattern, 255, True)

leftPattern = [{"id":0, "r":0, "g":0, "b":0}, 
{"id":1, "r":0, "g":1, "b":0}, 
{"id":6, "r":0, "g":1, "b":0}, 
{"id":7, "r":0, "g":1, "b":0}, 
{"id":8, "r":0, "g":1, "b":0}, 
{"id":9, "r":0, "g":1, "b":0}, 
{"id":14, "r":0, "g":1, "b":0}, 
{"id":15, "r":0, "g":0, "b":0}
]

api.imcontrol.setSpecial(leftPattern, 255, True)

time.sleep(tWait)

#Read Intensity images for the four patterns

#I_Bf = tiff.imread(str(path_name + '/Wide_field.tiff'))
I_bottom = tifffile.imread(str(Path + '/bottompattern.tif'))
I_top = tifffile.imread(str(Path + '/toppattern.tif'))
I_left = tifffile.imread(str(Path + '/leftpattern.tif'))
I_right = tifffile.imread(str(Path + '/rightpattern.tif'))

m = I_bottom.shape[0]
n = I_bottom.shape[1]
scaling_x =  n/2
scaling_y =  m/2
x = np.linspace(-n/2,n/2-1,n).reshape(1,n)/scaling_x
y = np.linspace(-m/2,m/2-1,m).reshape(m,1)/scaling_y


#Definition of gradients (Differences)
I_DPC_y = -(np.float32(I_right) - np.float32(I_left)) #/ (I_right + I_left)
I_DPC_x = (np.float32(I_bottom) - np.float32(I_top)) #/ (I_bottom + I_top)

#Definition of transfer functions 
H_x = np.tanh(x)
H_y = np.tanh(y)

I_x_ft = fft2c(I_DPC_x)
I_y_ft = fft2c(I_DPC_y)

numerator = I_x_ft * H_x + I_y_ft * H_y
alpha = 1e-3
denominator = H_x**2 + H_y**2 + alpha
phase_ft = numerator / denominator
phase = np.imag(ifft2c(phase_ft))

api.imcontrol.displayImageNapari(phase, "DPC Phase")
tifffile.imsave(Path+r'\Phase.tiff', phase)
api.imcontrol.displayImageNapari(I_DPC_y, "DPCy")
api.imcontrol.displayImageNapari(I_DPC_x, "DPCx")
api.imcontrol.displayImageNapari(np.float32(I_right)+np.float32(I_left), "DPCxy")
snap = np.float32(api.imcontrol.snapImage(True, False))
bfPseudo = np.float32(I_right)+np.float32(I_left)
api.imcontrol.displayImageNapari(bfPseudo/np.max(bfPseudo)-snap/np.max(snap), "DPCxyCheck")

Let me know if you find the issue.

HG

Aaron

[beniroquai]

On it...