microscopes module¶
A class for microscope objects.
Author: CD Phatak, ANL, 20.Feb.2015.
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class
microscopes.Microscope(E=200000.0, Cs=1000000.0, Cc=5000000.0, theta_c=0.0006, Ca=0.0, phi_a=0, def_spr=120.0, verbose=False)[source]¶ Bases:
objectClass for Microscope objects.
A class that describes a microscope for image simulation and reconstruction purposes. Along with accelerating voltage, aberrations, and other parameters, this also contains methods for propagating the electron wave and simulating images.
Notes:
- When initializing a Microscope you can set verbose=True to get a printout of the parameters.
- Unlike in TIE_reconstruct, here the qq frequency spectrum is expected to be shifted, i.e. rather than four dark corners it’s a dark circle.
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E¶ Accelerating voltage (V). Default 200kV.
Type: float
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Cs¶ Spherical aberration (nm). Default 1mm.
Type: float
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Cc¶ Chromatic aberration (nm). Default 5mm.
Type: float
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theta_c¶ Beam coherence (rad). Default 0.6mrad.
Type: float
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Ca¶ 2-fold astigmatism (nm). Default 0.
Type: float
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phi_a¶ 2-fold astigmatism angle (rad). Default 0.
Type: float
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def_spr¶ Defocus spread (nm). Default 120nm.
Type: float
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defocus¶ Defocus of the microscope (nm). Default 0nm.
Type: float
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lam¶ Electron wavelength (nm) calculated from E. Default 2.51pm.
Type: float
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gamma¶ Relativistic factor (unitless) from E. Default 1.39.
Type: float
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sigma¶ Interaction constant (1/(V*nm)) from E. Default 0.00729.
Type: float
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BackPropagateWave(ImgWave, qq, del_px)[source]¶ Back-propagate an image wave to get the object wave.
This function will back-propagate the image wave function to the object wave plane by convolving with exp(+i*Chiq). The damping envelope is not used for back propagation. Returns ObjWave in real space.
Parameters: - ObjWave (2D array) – Object wave function.
- qq (2D array) – Frequency array
- del_px (float) – Scale (nm/pixel)
Returns: Realspace object wave function. Complex 2D array same size as ObjWave.
Return type: ndarray
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PropagateWave(ObjWave, qq, del_px)[source]¶ Propagate object wave function to image plane.
This function will propagate the object wave function to the image plane by convolving with the transfer function of microscope, and returns the complex real-space ImgWave
Parameters: - ObjWave (2D array) – Object wave function.
- qq (2D array) – Frequency array
- del_px (float) – Scale (nm/pixel)
Returns: Realspace image wave function. Complex 2D array same size as ObjWave.
Return type: ndarray
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getBFPImage(ObjWave, qq, del_px)[source]¶ Produce the image in the backfocal plane (diffraction)
Parameters: - ObjWave (2D array) – Object wave function.
- qq (2D array) – Frequency array
- del_px (float) – Scale (nm/pixel)
Returns: Realspace image wave function. Real-valued 2D array same size as ObjWave.
Return type: ndarray
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getChiQ(qq, del_px)[source]¶ Calculate the phase transfer function.
Parameters: - qq (2D array) – Frequency array
- del_px (float) – Scale (nm/pixel)
Returns: 2D array same size as qq.
Return type: ndarray
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getDampEnv(qq, del_px)[source]¶ Calculate the complete damping envelope: spatial + temporal
Parameters: - qq (2D array) – Frequency array
- del_px (float) – Scale (nm/pixel)
Returns: Damping envelope. 2D array same size as qq.
Return type: ndarray
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getImage(ObjWave, qq, del_px)[source]¶ Produce the image at the set defocus using the methods in this class.
Parameters: - ObjWave (2D array) – Object wave function.
- qq (2D array) – Frequency array
- del_px (float) – Scale (nm/pixel)
Returns: Realspace image wave function. Real-valued 2D array same size as ObjWave.
Return type: ndarray
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getOptDef(qq, del_px)[source]¶ Calculate the Optimum or Lichte defocus (for holography).
Parameters: - qq (2D array) – Frequency array
- del_px (float) – Scale (nm/pixel)
Returns: Optimum defocus (nm)
Return type: float