initial commit

2026-09-17 23:39:08 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
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+import numpy as np
+import scipy.io as sio #for read/write matlab file
+from scipy import ndimage
+
+class STEMprobe:
+      """Probe function for STEM"""
+      def __init__(self):
+          self.dx = 1.0
+          self.Nside = 256
+          self.px = 0
+          self.py = 0
+          self.voltage = 300 #keV
+          self.alpha_max = 30 #mrad
+          self.df = 0 #angstrom
+          self.cs = 0 #mm
+          self.f_a2 = 0 #angstrom
+          self.theta_a2 = 0
+          self.f_a3 = 0 #angstrom
+          self.theta_a3 = 0
+          self.f_c3 = 0 #angstrom
+          self.theta_c3 = 0
+          self.Fourier_mag = 1
+
+      def printParameters(self):
+          self.wavelength = 12.398/np.sqrt((2*511.0+self.voltage)*self.voltage)  #angstrom
+          #print out all the parameters in the dm reconstruction
+          print("probe size:",self.Nside,"x",self.Nside)
+          print("distance between adjacent pixels: dx =", self.dx)
+          print("distance between adjacent pixels in Fourier space: dk =", 1.0/(self.dx*self.Nside))
+
+          print("probe position: (px,py) =(",self.px,",",self.py,")")
+          print("beam voltage =", self.voltage, "keV")
+          print("beam wavelength =",self.wavelength, "angstrom")
+          print("semi-convergence angle =", self.alpha_max, "mrad")
+          print("defocus=", self.df, "angstrom")
+          print("spherical aberration =", self.cs, "angstrom")
+          print("two-fold astigmatism =", self.f_a2, "angstrom.", "azimuthal orientation=",self.theta_a2, "rad")
+          print("three-fold astigmatism =", self.f_a3, "angstrom.", "azimuthal orientation=",self.theta_a3, "rad")
+          print("coma =", self.f_c3, "angstrom.", "azimuthal orientation=",self.theta_c3, "rad")
+
+      def generateProbe(self):
+          print("generating probe function...")
+          self.wavelength = 12.398/np.sqrt((2*511.0+self.voltage)*self.voltage)  #angstrom
+          amax = self.alpha_max*1e-3 # in rad
+          amin = 0.0
+
+          k_max = amax/self.wavelength
+          k_min = amin/self.wavelength
+
+          dk= 1.0/(self.dx*self.Nside)
+          kx = np.linspace(-np.floor(self.Nside/2.0),np.ceil(self.Nside/2.0)-1,self.Nside)
+          [kY,kX] = np.meshgrid(kx,kx)
+          kX = kX*dk; kY = kY*dk;
+          kR = np.sqrt(kX**2+kY**2)
+          theta = np.arctan2(kY,kX)
+          
+          chi = -np.pi*self.wavelength*kR**2*self.df + np.pi/2*self.cs*1e7*self.wavelength**3*kR**4+np.pi*self.f_a2*self.wavelength*kR**2*np.sin(2*(theta-self.theta_a2))+2*np.pi/3*self.f_a3*self.wavelength**2*kR**3*np.sin(3*(theta-self.theta_a3))+2*np.pi/3*self.f_c3*self.wavelength**2*kR**3*np.sin(theta-self.theta_c3)
+
+          probe = np.exp(-1j*chi)*np.exp(-2*np.pi*1j*self.px*kX)*np.exp(-2*np.pi*1j*self.py*kY)
+          probe[kR>k_max] = 0
+          probe[kR<k_min] = 0
+          
+          if self.Fourier_mag != 1:
+              probe = probe/abs(probe) * self.Fourier_mag
+
+          #probe = probe/np.sum((np.abs(probe)**2)) #normalize probe
+          
+          probe = np.fft.fftshift(np.fft.ifft2(np.fft.ifftshift(probe)))
+          probe = probe/np.sqrt(np.sum((np.abs(probe)**2)*self.dx*self.dx)) #normalize probe
+          #probe = probe/np.sqrt(np.sum((np.abs(probe)**2))) #normalize probe
+          
+          mask = np.ones(kR.shape)
+          mask[kR>k_max] = 0
+          mask[kR<k_min] = 0
+
+          return probe