dials.import¶
Introduction¶
This program is used to import image data files into a format that can be used within dials. The program looks at the metadata for each image along with the filenames to determine the relationship between sets of images. Once all the images have been analysed, a experiments object is written to file which specifies the relationship between files. For example if two sets of images which belong to two rotation scans have been given, two image sequences will be saved. Images to be processed are specified as command line arguments. Sometimes, there is a maximum number of arguments that can be given on the command line and the number of files may exceed this. In this case image filenames can be input on stdin as shown in the examples below. Alternatively a template can be specified using the template= parameter where the consecutive digits representing the image numbers in the filenames are replaced with ‘#’ characters.
The geometry can be set manually, either by using the reference_geometry= parameter to specify an experiment list .expt file containing the reference geometry, by using the mosflm_beam_centre= parameter to set the Mosflm beam centre, or by specifying each variable to be overridden using various geometry parameters.
Examples:
dials.import /data/directory-containing-images/
dials.import image_*.cbf
dials.import image_1_*.cbf image_2_*.cbf
dials.import directory/with/images
dials.import template=image_1_####.cbf
dials.import directory=directory/with/images
find . -name "image_*.cbf" | dials.import
dials.import << EOF
image_1.cbf
image_2.cbf
EOF
Basic parameters¶
output {
experiments = imported.expt
log = 'dials.import.log'
compact = False
}
identifier_type = *uuid timestamp None
input {
ignore_unhandled = True
template = None
directory = None
reference_geometry = None
allow_multiple_sequences = True
}
lookup {
mask = None
gain = None
pedestal = None
dx = None
dy = None
}
Full parameter definitions¶
output {
experiments = imported.expt
.help = "The output experiment file"
.type = str
log = 'dials.import.log'
.help = "The log filename"
.type = str
compact = False
.help = "For experiment output use compact JSON representation"
.type = bool
}
identifier_type = *uuid timestamp None
.help = "Type of unique identifier to generate."
.type = choice
input {
ignore_unhandled = True
.help = "Ignore unhandled input (e.g. log files)"
.type = bool
template = None
.help = "The image sequence template"
.type = str
.multiple = True
directory = None
.help = "A directory with images"
.type = str
.multiple = True
reference_geometry = None
.help = "Experimental geometry from this models.expt will override the"
"geometry from the image headers."
.type = path
check_reference_geometry = True
.help = "If True, assert the reference geometry is similar to the image"
"geometry"
.type = bool
.expert_level = 2
use_beam_reference = True
.help = "If True, the beam from reference_geometry will override the beam"
"from the image headers."
.type = bool
.expert_level = 2
use_gonio_reference = True
.help = "If True, the goniometer from reference_geometry will override "
"the goniometer from the image headers."
.type = bool
.expert_level = 2
use_detector_reference = True
.help = "If True, the detector from reference_geometry will override the"
"detector from the image headers."
.type = bool
.expert_level = 2
allow_multiple_sequences = True
.help = "If False, raise an error if multiple sequences are found"
.type = bool
}
format
.help = "Options to pass to the Format class"
.expert_level = 2
{
dynamic_shadowing = auto
.help = "Enable dynamic shadowing"
.type = bool
multi_panel = False
.help = "Enable a multi-panel detector model. (Not supported by all"
"detector formats)"
.type = bool
}
geometry
.help = "Allow overrides of experimental geometry"
.expert_level = 2
{
beam
.short_caption = "Beam overrides"
.expert_level = 1
{
type = *monochromatic polychromatic
.help = "Override the beam type"
.short_caption = beam_type
.type = choice
probe = *x-ray electron neutron
.help = "Override the beam probe"
.short_caption = beam_probe
.type = choice
wavelength = None
.help = "Override the beam wavelength"
.type = float(allow_none=True)
direction = None
.help = "Override the sample to source direction"
.short_caption = "Sample to source direction"
.type = floats(size=3)
divergence = None
.help = "Override the beam divergence"
.type = float(allow_none=True)
sigma_divergence = None
.help = "Override the beam sigma divergence"
.type = float(allow_none=True)
polarization_normal = None
.help = "Override the polarization normal"
.short_caption = "Polarization normal"
.type = floats(size=3)
polarization_fraction = None
.help = "Override the polarization fraction"
.short_caption = "Polarization fraction"
.type = float(value_min=0, value_max=1, allow_none=True)
transmission = None
.help = "Override the transmission"
.short_caption = transmission
.type = float(allow_none=True)
flux = None
.help = "Override the flux"
.short_caption = flux
.type = float(allow_none=True)
sample_to_source_distance = None
.help = "Override the distance between sample and source (mm)"
.type = float(allow_none=True)
wavelength_range = None
.help = "Override the wavelength range for polychromatic beams (A)"
.type = floats(size=2)
}
detector
.short_caption = "Detector overrides"
.expert_level = 1
{
panel
.multiple = True
{
id = 0
.help = "The panel number"
.short_caption = "Panel ID"
.type = int(allow_none=True)
name = None
.help = "Override the panel name"
.short_caption = "Panel name"
.type = str
type = None
.help = "Override the panel type"
.short_caption = "Panel type"
.type = str
gain = None
.help = "The gain of the detector panel"
.short_caption = "Gain value"
.type = float(value_min=0, allow_none=True)
pedestal = None
.help = "The pedestal of the detector panel"
.short_caption = "Pedestal value"
.type = float(allow_none=True)
pixel_size = None
.help = "Override the panel pixel size"
.short_caption = "Panel pixel size"
.type = floats(size=2)
image_size = None
.help = "Override the panel image size"
.short_caption = "Panel image size"
.type = ints(size=2)
trusted_range = None
.help = "Override the panel trusted range: [min-trusted-value,"
"max-trusted-value]"
.short_caption = "Panel trusted range"
.type = floats(size=2)
thickness = None
.help = "Override the panel thickness"
.short_caption = "Panel thickness"
.type = float(allow_none=True)
material = None
.help = "Override the panel material"
.short_caption = "Panel material"
.type = str
fast_axis = None
.help = "Override the panel fast axis. Requires slow_axis and origin."
.short_caption = "Panel fast axis direction"
.type = floats(size=3)
slow_axis = None
.help = "Override the panel slow axis. Requires fast_axis and origin."
.short_caption = "Panel slow axis direction"
.type = floats(size=3)
origin = None
.help = "Override the panel origin. Requires fast_axis and slow_axis."
.short_caption = "Panel origin vector"
.type = floats(size=3)
parallax_correction = None
.help = "Enable parallax correction. By default in overwrite mode, the"
"value of None does nothing."
.short_caption = "Enable parallax correction"
.type = bool
}
hierarchy
.expert_level = 2
{
name = None
.help = "Override the group name"
.short_caption = "group name"
.type = str
fast_axis = None
.help = "Override the panel fast axis. Requires slow_axis and origin."
.short_caption = "Panel fast axis direction"
.type = floats(size=3)
slow_axis = None
.help = "Override the panel slow axis. Requires fast_axis and origin."
.short_caption = "Panel slow axis direction"
.type = floats(size=3)
origin = None
.help = "Override the panel origin. Requires fast_axis and slow_axis."
.short_caption = "Panel origin vector"
.type = floats(size=3)
group
.multiple = True
{
id = None
.help = "The group identifier specifying the place in the hierarchy"
.short_caption = "Group ID"
.type = ints
name = None
.help = "Override the group name"
.short_caption = "Group name"
.type = str
fast_axis = None
.help = "Override the group fast axis. Requires slow_axis and"
"origin."
.short_caption = "Group fast axis direction"
.type = floats(size=3)
slow_axis = None
.help = "Override the group slow axis. Requires fast_axis and"
"origin."
.short_caption = "Group slow axis direction"
.type = floats(size=3)
origin = None
.help = "Override the group origin. Requires fast_axis and"
"slow_axis."
.short_caption = "Group origin vector"
.type = floats(size=3)
panel = None
.help = "The panel id"
.short_caption = "Panel ID"
.type = int(allow_none=True)
.multiple = True
}
}
mosflm_beam_centre = None
.help = "Override the beam centre from the image headers, following the"
"mosflm convention."
.short_caption = "Beam centre coordinates (mm, mm) using the Mosflm"
"convention"
.type = floats(size=2)
distance = None
.help = "The detector distance (used when mosflm_beam_centre is set)"
.short_caption = "Detector distance"
.type = float(allow_none=True)
fast_slow_beam_centre = None
.help = "Override the beam centre from the image headers. The first two"
"values are the fast and slow pixel coordinate. If the third is"
"supplied it specifies a panel number."
.short_caption = "Beam centre coordinates (px fast, px slow, [panel id])"
.type = floats(size_min=2, size_max=3)
slow_fast_beam_centre = None
.help = "Alternative to fast_slow_beam_centre in which the coordinates"
"are given in order (px slow, px fast, [panel id]). If"
"fast_slow_beam_centre is set it will take priority over any"
"values set here."
.short_caption = "Beam centre coordinates (px slow, px fast, [panel id])"
.type = ints(size_min=2, size_max=3)
}
goniometer
.short_caption = "Goniometer overrides"
.expert_level = 1
{
axis = None
.help = "Override the axis for a single axis goniometer. Equivalent to"
"providing a single 3D vector to 'axes'."
.short_caption = "Goniometer axis"
.type = floats(size=3)
axes = None
.help = "Override the goniometer axes. Axes must be provided in the"
"order crystal-to-goniometer, i.e. for a Kappa goniometer"
"phi,kappa,omega"
.short_caption = "Goniometer axes"
.type = floats
angles = None
.help = "Override the goniometer angles. Axes must be provided in the"
"order crystal-to-goniometer, i.e. for a Kappa goniometer"
"phi,kappa,omega"
.short_caption = "Goniometer angles"
.type = floats
names = None
.help = "The multi axis goniometer axis names"
.short_caption = "The axis names"
.type = str
scan_axis = None
.help = "The scan axis"
.short_caption = "The scan axis"
.type = int(allow_none=True)
fixed_rotation = None
.help = "Override the fixed rotation matrix"
.short_caption = "Fixed rotation matrix"
.type = floats(size=9)
setting_rotation = None
.help = "Override the setting rotation matrix"
.short_caption = "Setting rotation matrix"
.type = floats(size=9)
invert_rotation_axis = False
.help = "Invert the rotation axis"
.short_caption = "Invert rotation axis"
.type = bool
}
scan
.short_caption = "Scan overrides"
.expert_level = 1
{
image_range = None
.help = "Override the image range"
.short_caption = "Image range"
.type = ints(size=2)
extrapolate_scan = False
.help = "When overriding the image range, extrapolate exposure and epoch"
"information from existing images"
.short_caption = "Extrapolate scan"
.type = bool
oscillation = None
.help = "Override the image oscillation"
.short_caption = Oscillation
.type = floats(size=2)
batch_offset = None
.help = "Override the batch offset"
.short_caption = "Batch offset"
.type = int(value_min=0, allow_none=True)
}
convert_stills_to_sequences = False
.help = "When overriding the scan, convert stills into sequences"
.short_caption = "Convert stills into sequences"
.type = bool
convert_sequences_to_stills = False
.help = "When overriding the scan, convert sequences into stills"
.short_caption = "Convert sequences into stills"
.type = bool
}
lookup {
mask = None
.help = "Apply a mask to the imported data"
.type = str
gain = None
.help = "Apply a gain to the imported data"
.type = str
pedestal = None
.help = "Apply a pedestal to the imported data"
.type = str
dx = None
.help = "Apply an x geometry offset If both dx and dy are set then"
"OffsetParallaxCorrectedPxMmStrategy will be used"
.type = str
dy = None
.help = "Apply an y geometry offset If both dx and dy are set then"
"OffsetParallaxCorrectedPxMmStrategy will be used"
.type = str
}
