def image_to_polar(
image,
delta_r=1.0,
delta_theta=1,
max_r=None,
find_direct_beam=False,
direct_beam_position=None,
):
"""Convert a single image to polar coordinates including the option to
find the direct beam and take this as the center.
Parameters
----------
image : 2D numpy.ndarray
Experimental image
delta_r : float, optional
The radial increment, determines how many columns will be in the polar
image.
delta_theta : float, optional
The angular increment, determines how many rows will be in the polar
image
max_r : float, optional
The maximum radial distance to include, in units of pixels. By default
this is the distance from the center of the image to a corner in pixel
units and rounded up to the nearest integer
find_direct_beam : bool
Whether to roughly find the direct beam using `find_beam_center_blur`
using a gaussian smoothing with sigma = 1. If False then the middle of
the image will be the center for the polar transform.
direct_beam_position : 2-tuple
(x, y) position of the central beam in pixel units. This overrides
the automatic find_maximum parameter if set to True.
Returns
-------
polar_image : 2D numpy.ndarray
Array representing the polar transform of the image with shape
(360/delta_theta, max_r/delta_r)
"""
half_x, half_y = image.shape[1] / 2, image.shape[0] / 2
if direct_beam_position is not None:
c_x, c_y = direct_beam_position
elif find_direct_beam:
c_y, c_x = find_beam_center_blur(image, 1)
else:
c_x, c_y = half_x, half_y
output_shape = get_polar_pattern_shape(image.shape,
delta_r,
delta_theta,
max_r=max_r)
return warp_polar(
image,
center=(c_y, c_x),
output_shape=output_shape,
radius=max_r,
preserve_range=True,
)
def test_find_beam_center_blur(center_expected, sigma):
z = np.zeros((50, 50))
z[28:31, 24:27] = 1
z = gaussian_filter(z, sigma=sigma)
shifts = find_beam_center_blur(z, 10)
assert np.allclose(shifts, center_expected, atol=0.2)
def plot_template_over_pattern(pattern,
simulation,
ax=None,
in_plane_angle=0.0,
max_r=None,
find_direct_beam=True,
direct_beam_position=None,
coordinate_system="cartesian",
marker_color="red",
marker_type="x",
size_factor=1.0,
**kwargs):
"""
A quick utility function to plot a simulated pattern over an experimental image
Parameters
----------
pattern : 2D np.ndarray
The diffraction pattern
simulation : diffsims.sims.diffraction_simulation.DiffractionSimulation
The simulated diffraction pattern. It must be calibrated.
axis : matplotlib.AxesSubplot, optional
An axis object on which to plot. If None is provided, one will be created.
in_plane_angle : float, optional
An in-plane rotation angle to apply to the template in degrees
max_r : float, optional
Maximum radius to consider in the polar transform in pixel coordinates.
Will only influence the result if `coordinate_system`="polar".
find_direct_beam: bool, optional
Roughly find the optimal direct beam position if it is not centered.
direct_beam_position: 2-tuple
The (x, y) position of the direct beam in pixel coordinates. Takes
precedence over `find_direct_beam`
coordinate_system : str, optional
Type of coordinate system to plot the image and template in. Either
`cartesian` or `polar`
marker_color : str, optional
Color of the spot markers
marker_type : str, optional
Type of marker used for the spots
size_factor : float, optional
Scaling factor for the spots. See notes on size.
**kwargs : See imshow
Returns
-------
ax : matplotlib.AxesSubplot
The axes object
im : matplotlib.image.AxesImage
The representation of the image on the axes
sp : matplotlib.collections.PathCollection
The scatter plot representing the diffraction pattern
Notes
-----
The spot marker sizes are scaled by the square root of their intensity
"""
if ax is None:
_, ax = plt.subplots()
if direct_beam_position is not None:
c_x, c_y = direct_beam_position
elif find_direct_beam:
c_y, c_x = find_beam_center_blur(pattern, 1)
else:
c_y, c_x = pattern.shape[0] // 2, pattern.shape[1] // 2
if coordinate_system == "polar":
pattern = image_to_polar(
pattern,
max_r=max_r,
find_direct_beam=find_direct_beam,
direct_beam_position=direct_beam_position,
)
x, y, intensities = get_template_polar_coordinates(
simulation, in_plane_angle=in_plane_angle, max_r=max_r)
elif coordinate_system == "cartesian":
x, y, intensities = get_template_cartesian_coordinates(
simulation,
center=(c_x, c_y),
in_plane_angle=in_plane_angle,
window_size=pattern.shape[::-1],
)
else:
raise NotImplementedError(
"Only polar and cartesian are accepted coordinate systems")
im = ax.imshow(pattern, **kwargs)
sp = ax.scatter(
x,
y,
s=size_factor * np.sqrt(intensities),
marker=marker_type,
color=marker_color,
)
return (ax, im, sp)