dials.search_beam_position¶
Introduction¶
A function to find beam center from diffraction images
The default method (based on the work of Sauter et al., J. Appl. Cryst. 37, 399-409 (2004)) is using the results from spot finding.
- Example:
dials.search_beam_position imported.expt strong.refl
Other methods are based on horizontal and vertical projection, and only require an imported experiment.
- Example:
dials.search_beam_position method=midpoint imported.exp
More information about the projection methods can be found at https://autoed.readthedocs.io/en/latest/pages/beam_position_methods.html
Basic parameters¶
method = default midpoint maximum inversion
default {
nproc = Auto
plot_search_scope = False
max_cell = None
image_range = None
max_reflections = 10000
mm_search_scope = 4.0
wide_search_binning = 2
n_macro_cycles = 1
d_min = None
seed = 42
}
projection {
method_x = midpoint maximum inversion
method_y = midpoint maximum inversion
image_ranges = "::"
imageset_ranges = "::"
plot = True
verbose = True
exclude_pixel_range_x = None
exclude_pixel_range_y = None
per_image = False
save_average_image = False
load_average_image = False
color_cutoff = None
midpoint {
exclude_intensity_percent = 0.01
intersection_range = (0.3, 0.9, 0.01)
convolution_width = 80
dead_pixel_range_x = None
dead_pixel_range_y = None
intersection_min_width = 10
}
maximum {
bad_pixel_threshold = None
n_convolutions = 1
convolution_width = 1
bin_width = 20
bin_step = 10
}
inversion {
bad_pixel_threshold = None
guess_position = None
inversion_window_width = 400
background_cutoff = None
convolution_width = 1
}
}
output {
experiments = optimised.expt
log = "dials.search_beam_position.log"
json = "beam_positions.json"
}
Full parameter definitions¶
method = default midpoint maximum inversion
default {
nproc = Auto
.type = int(value_min=1, allow_none=True)
plot_search_scope = False
.type = bool
max_cell = None
.help = "Known max cell (otherwise will compute from spot positions)"
.type = float(allow_none=True)
image_range = None
.help = "The range of images to use in indexing. Number of arguments must"
"be a factor of two. Specifying 0 0\" will use all images\" by"
"default. The given range follows C conventions (e.g. j0 <= j <"
"j1)."
.type = ints(size=2)
.multiple = True
max_reflections = 10000
.help = "Maximum number of reflections to use in the search for better"
"experimental model. If the number of input reflections is "
"greater then a random subset of reflections will be used."
.type = int(value_min=1, allow_none=True)
mm_search_scope = 4.0
.help = "Global radius of origin offset search."
.type = float(value_min=0, allow_none=True)
wide_search_binning = 2
.help = "Modify the coarseness of the wide grid search for the beam"
"centre."
.type = float(value_min=0, allow_none=True)
n_macro_cycles = 1
.help = "Number of macro cycles for an iterative beam centre search."
.type = int(allow_none=True)
d_min = None
.type = float(value_min=0, allow_none=True)
seed = 42
.type = int(value_min=0, allow_none=True)
}
projection {
method_x = midpoint maximum inversion
.help = "The projection method along the x-axis."
.type = str
method_y = midpoint maximum inversion
.help = "The projection method along the y-axis."
.type = str
image_ranges = "::"
.help = "A list of comma-separated numpy slices used to select specific "
"images in the dataset (e.g. 0:5:2,1,7:15)."
.type = str
imageset_ranges = "::"
.help = "A list of comma-separated numpy slices used to select specific "
"imagesets (see image_ranges)."
.type = str
plot = True
.help = "Plot the diffraction image with the computed beam center."
.type = bool
verbose = True
.help = "Print the beam position to the output."
.type = bool
exclude_pixel_range_x = None
.help = "List of comma-separated pairs of numbers specifying pixel ranges "
"in the x direction to exclude from projection to the y-axis "
"(e.g., exclude_pixel_range_x=20,350,700,800 would exclude ranges "
"20-350 and 700-800). Indexing assumes Python (or C) conventions."
"The first pixel has an index 0, the last pixel has an index N-1"
"(here N is the number of pixels along the x-axis). The last"
"pixel in the range is not included, e.g., '0,N' would exclude"
"the entire range, while '0,3' would exclude pixels 0, 1, and 2."
.type = ints
.multiple = True
exclude_pixel_range_y = None
.help = "List of pixel ranges to exclude from projection to the y-axis. "
"See `exclude_pixel_range_x` for more details."
.type = ints
.multiple = True
per_image = False
.help = "Compute the beam position for each image. Otherwise, compute the "
"beam position for a single (average) image."
.type = bool
save_average_image = False
.help = "Saves the average diffraction image to an npz file (i.e.,"
"average_image.npz). Works only when per_image=False. Use this to"
"save the average image for later use (see the load_average_image"
"option)."
.type = bool
load_average_image = False
.help = "Loads the average diffraction image from an npz file. Works only"
"when `per_image=False`. If an average image was saved before,"
"DIALS will use that image instead of computing it again."
.type = bool
color_cutoff = None
.help = "The maximum of the colorbar range in the plotted beam position "
"figure. Use this option to adjust the visibility of the plotted "
"diffraction image."
.type = float(allow_none=True)
midpoint {
exclude_intensity_percent = 0.01
.help = "Order all pixels by intensity and discard this percentage from"
"the top (by setting them to zero)."
.type = float(allow_none=True)
intersection_range = (0.3, 0.9, 0.01)
.help = "Compute midpoints in this range (start, end, step)."
.type = floats
convolution_width = 80
.help = "Convolution kernel width used for smoothing (in pixels)."
.type = int(allow_none=True)
dead_pixel_range_x = None
.help = "List of comma-separated pairs of numbers specifying pixel "
"ranges in the x direction to exclude from midpoint "
"calculation. Indexing assumes the same rules as with the"
"exclude_pixel_range_x."
.type = ints
.multiple = True
dead_pixel_range_y = None
.help = "List of comma-separated pairs of numbers specifying pixel "
"ranges in the y direction to exclude from midpoint "
"calculation. Indexing assumes the same rules as with "
"exclude_pixel_range_y."
.type = ints
.multiple = True
intersection_min_width = 10
.help = "Do not consider midpoint intersections below this width."
.type = int(allow_none=True)
}
maximum {
bad_pixel_threshold = None
.help = "Set all pixels above this value to zero."
.type = int(allow_none=True)
n_convolutions = 1
.help = "The number of smoothing convolutions."
.type = int(allow_none=True)
convolution_width = 1
.help = "Convolution kernel width used for smoothing (in pixels)."
.type = int(allow_none=True)
bin_width = 20
.help = "The width of the averaging bin used to find the region of max"
"intensity (pixels)."
.type = int(allow_none=True)
bin_step = 10
.help = "Distance in pixels between neighboring bins used to find the "
"region of maximal intensity."
.type = int(allow_none=True)
}
inversion {
bad_pixel_threshold = None
.help = "Set all pixels above this value to zero."
.type = int(allow_none=True)
guess_position = None
.help = "Initial guess for the beam position (x, y) in pixels. If not"
"supplied, it will be set to the center of the image."
.type = ints(size=2)
inversion_window_width = 400
.help = "Do profile inversion within this window (in pixels)."
.type = int(allow_none=True)
background_cutoff = None
.help = "Set all the pixels with intensity above this value to zero."
.type = int(allow_none=True)
convolution_width = 1
.help = "Convolution kernel width used for smoothing (in pixels)."
.type = int(allow_none=True)
}
}
output {
experiments = optimised.expt
.type = path
log = "dials.search_beam_position.log"
.type = str
json = "beam_positions.json"
.type = str
}
