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Adding docstrings, cleaning up code
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@cophus
cophus committed Jun 27, 2024
1 parent 7f3eca7 commit b921a47
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Showing 2 changed files with 73 additions and 11 deletions.
12 changes: 7 additions & 5 deletions py4DSTEM/process/diffraction/crystal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -719,7 +719,11 @@ def generate_diffraction_pattern(
return_orientation_matrix=False,
):
"""
Generate a single diffraction pattern, return all peaks as a pointlist.
Generate a single diffraction pattern, return all peaks as a pointlist. This function performs a
kinematical calculation, with optional precession of the beam.
TODO - switch from numerical precession to analytic (requires geometry projection).
TODO - verify projection geometry for 2D material diffraction.
Parameters
----------
Expand All @@ -740,15 +744,13 @@ def generate_diffraction_pattern(
cartesian projection direction
proj_x_cartesian (3,) numpy.array
cartesian projection direction
foil_normal
3 element foil normal - set to None to use zone_axis
proj_x_axis (3,) numpy.array
3 element vector defining image x axis (vertical)
accel_voltage (float)
Accelerating voltage in Volts. If not specified,
we check to see if crystal already has voltage specified.
sigma_excitation_error (float)
sigma value for envelope applied to s_g (excitation errors) in units of inverse Angstroms
tol_excitation_error_mult (float)
Expand All @@ -768,8 +770,8 @@ def generate_diffraction_pattern(
----------
bragg_peaks (PointList)
list of all Bragg peaks with fields [qx, qy, intensity, h, k, l]
orientation_matrix (array)
3x3 orientation matrix (optional)
orientation_matrix (array, optional)
3x3 orientation matrix
"""

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72 changes: 66 additions & 6 deletions py4DSTEM/process/diffraction/crystal_phase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -106,29 +106,89 @@ def quantify_single_pattern(
"""
Quantify the phase for a single diffraction pattern.
TODO - determine the difference between false positive peaks and unmatched peaks (if any).
Parameters
----------
pointlistarray: (PointListArray)
Full array of all calibrated experimental bragg peaks, with shape = (num_x,num_y)
xy_position: (int,int)
The (x,y) or (row,column) position to be quantified.
corr_kernel_size: (float)
Correlation kernel size length. The size of the overlap kernel between the
measured Bragg peaks and diffraction library Bragg peaks. [1/Angstroms]
sigma_excitation_error: (float)
The out of plane excitation error tolerance. [1/Angstroms]
precession_angle_degrees: (float)
Tilt angle of illuminaiton cone in degrees for precession electron diffraction (PED).
power_radial: (float)
Power for scaling the correlation intensity as a function of the peak radius
power_intensity: (float)
Power for scaling the correlation intensity as a function of simulated peak intensity
Power for scaling the correlation intensity as a function of simulated peak intensity.
power_intensity_experiment: (float):
Power for scaling the correlation intensity as a function of experimental peak intensity
Power for scaling the correlation intensity as a function of experimental peak intensity.
k_max: (float)
Max k values included in fits, for both x and y directions.
max_number_patterns: int
Max number of orientations which can be included in a match.
single_phase: bool
Set to true to force result to output only the best-fit phase (minimum intensity residual).
allow_strain: bool,
Allow the simulated diffraction patterns to be distorted to improve the matches.
strain_iterations: int
Number of pattern position refinement iterations.
strain_max: float
Maximum strain fraction allowed - this value should be low, typically a few percent (~0.02).
include_false_positives: bool
Penalize patterns which generate false positive peaks.
weight_false_positives: float
Weight strength of false positive peaks.
weight_unmatched_peaks: float
Penalize unmatched peaks.
plot_result: bool
Plot the resulting fit.
plot_only_nonzero_phases: bool
Only plot phases with phase weights > 0.
plot_unmatched_peaks: bool
Plot the false postive peaks.
plot_correlation_radius: bool
In the visualization, draw the correlation radius.
scale_markers_experiment: float
Size of experimental diffraction peak markers.
scale_markers_calculated: float
Size of the calculate diffraction peak markers.
crystal_inds_plot: tuple of ints
Which crystal index / indices to plot.
phase_colors: np.array
Color of each phase, should have shape = (num_phases, 3)
figsize: (float,float)
Size of the output figure.
verbose: bool
Print the resulting fit weights to console.
returnfig: bool
Return the figure and axis handles for the plot.
Returns
-------
phase_weights: (np.array)
Estimated relative fraction of each phase for all probe positions.
shape = (num_x, num_y, num_orientations)
where num_orientations is the total number of all orientations for all phases.
phase_residual: (np.array)
Residual intensity not represented by the best fit phase weighting for all probe positions.
shape = (num_x, num_y)
phase_reliability: (np.array)
Estimated reliability of match(es) for all probe positions.
Typically calculated as the best fit score minus the second best fit.
shape = (num_x, num_y)
int_total: (np.array)
Sum of experimental peak intensities for all probe positions.
shape = (num_x, num_y)
fig,ax: (optional)
matplotlib figure and axis handles
"""


# tolerance
tol2 = 1e-6

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