Version = 1.0
Pip = 1
[Field = InputSeedModel]
short =
type = FN
usage = Name of model file with starting bead coordinates
tooltip = Input model file of starting points to track.
manpage =
[Field = OutputModel]
short =
type = FN
usage = Name of output model file
tooltip = Output file for tracked model.
manpage =
[Field = ImageFile]
short =
type = FN
usage = Image file name
tooltip = Input file with images to track.
manpage =
[Field = PieceListFile]
short =
type = FN
usage = Name of piece list file if image is montaged or out of sequence
tooltip =
manpage = Name of piece list file if image is montaged or out of sequence.
A montaged file should not be be used unless the overlaps between pieces
are nearly exact.
[Field = PrealignTransformFile]
short = prexf
type = FN
usage = File with transforms used to align images being tracked
tooltip =
manpage = File with transformations applied to align the images. The program
will assume that the transformations consist only of shifts and will use this
information to avoid searching for a bead on a filled area that has no image
data.
[Field = XYZOutputFile]
short =
type = FN
usage = File name for output of X/Y/Z coordinates and mean residuals
tooltip =
manpage = File name for output of information that can be used by
Sortbeadsurfs(1) to determine which of two surfaces each bead is on. This
file has an entry for each bead with 5 columns: contour number, solved X, Y, Z
coordinates, and the mean of the mean residuals from each local area. The
program uses the X/Y/Z coordinates from beads that overlap between between
local areas to resolve the sets of coordinates from multiple local areas into
a single consistent set.
[Field = ElongationOutputFile]
short =
type = FN
usage = File name for output of mean residuals and bead elongation data
tooltip =
manpage = File name for output of mean residuals and bead elongation data,
which can be used by Pickbestseed(1) when selecting optimal beads for a seed
model. The file has an entry for each bead with 10 columns: object and contour
number, and mean of the contour's mean residuals from each local area that the
bead occurs in, the mean, median, and standard deviation of one measure of
elongation (the standard deviation of pixels around the edge of the bead when
measuring the centroid), the mean, median, and standard deviation of the
elongation of pixels above a threshold, and the mean bead integral.
[Field = ImagesAreBinned]
short =
type = I
usage = The binning of the images relative to the original data (default 1)
tooltip =
manpage = The current binning of the images relative to the original data.
This factor is used to scale the bead diameter
from unbinned to binned coordinates. The default is 1.
[Field = PixelSize]
short = pixel
type = F
usage = Pixel size of unbinned images in nanometers
tooltip =
manpage = Pixel size of unbinned images in nanometers. This entry is required
to use overall low pass filtering.
[Field = SkipViews]
short =
type = LI
usage = List of views to skip over (numbered from 1)
tooltip = List of views to skip over (comma-separated ranges without spaces).
manpage = List of views to skip over. Model contours will pass through
these views; points will need to be added by hand afterwards.
Ranges may be entered, e.g. 1,4-6. Views are numbered from 1.
[Field = RotationAngle]
short =
type = F
usage = Angle of rotation of the tilt axis in the images
tooltip =
manpage = Angle of rotation of the tilt axis in the images; specifically, the
angle from the vertical to the tilt axis (counterclockwise positive).
[Field = SeparateGroup]
short =
type = LIM
usage = List of views that should be grouped separately in automapping
tooltip = Lists of views to group separately from other views. Multiple lists
can be entered; separate them by spaces.
manpage = List of views that should be grouped separately in automapping
the tilt, magnification, and rotation variables.
Multiple entries can be used to specify more than one set of separate views.
[Field = FirstTiltAngle]
short = first
type = F
usage = Tilt angle of first view in degrees
tooltip =
manpage = Tilt angle of first view, in degrees. Use this option together with
TiltIncrement.
[Field = TiltIncrement]
short = increment
type = F
usage = Increment between tilt angles
tooltip =
manpage = Increment between tilt angles, in degrees. Use this option together
with FirstTiltAngle.
[Field = TiltFile]
short = tiltfile
type = FN
usage = File with tilt angles
tooltip =
manpage = Use this option if tilt angles are in a file, one per line.
[Field = TiltAngles]
short = angles
type = FAM
usage = Individual tilt angles for each view
tooltip =
manpage = Use this option to enter the tilt angles for each view individually,
in degrees.
[Field = TiltDefaultGrouping]
short =
type = I
usage = Average default group size when automapping tilt variables
tooltip = Basic grouping size for tilt angles (grouping will be less at high
tilt and more at low tilt).
manpage = Average default group size when automapping tilt variables
[Field = TiltNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
tilt variables.
tooltip = Sets of views with non-default grouping. For each set, enter
starting and ending view number and group size, separated by commas; separate
multiple sets with spaces.
manpage = Starting and ending view numbers and group size for a set of views
whose tilt variables should be grouped differently from the default.
[Field = MagDefaultGrouping]
short =
type = I
usage = Default group size when automapping magnification variables
tooltip = Grouping size for magnifications.
manpage = Default group size when automapping magnification variables
[Field = MagNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
magnification variables.
tooltip = Sets of views with non-default grouping. For each set, enter
starting and ending view number and group size, separated by commas; separate
multiple sets with spaces.
manpage = Starting and ending view numbers and group size for a set of views
whose magnification variables should be grouped differently from the default.
[Field = RotDefaultGrouping]
short =
type = I
usage = Default group size when automapping rotation variables
tooltip =
manpage =
[Field = RotNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
rotation variables.
tooltip =
manpage = Starting and ending view numbers and group size for a set of views
whose rotation variables should be grouped differently from the default.
Multiple entries can be used to specify more than one set of views with
nondefault grouping.
[Field = MinViewsForTiltalign]
short =
type = I
usage = Minimum number of views with data required to do a tilt alignment
tooltip = Minimum number of views with bead positions required to do a tilt
alignment.
manpage = Minimum number of views with bead positions available before trying
to do a tilt alignment. To skip the tilt alignment computations,
set this to a number higher than the number of views. (Default 4)
[Field = CentroidRadius]
short =
type = F
usage = Radius for centroid calculation
tooltip = Radius for calculation of centroid.
manpage = Radius for centroid calculation. The radius need not be a whole
number and should be somewhat larger than the bead radius. Either this option
or BeadDiameter must be entered, but not both. If this option is entered,
the diameter will be computed as 2 * radius - 3, then adjusted for binning,
and the radius will be taken as (adjusted diameter + 3) / 2.
[Field = BeadDiameter]
short =
type = F
usage = Actual diameter of beads in unbinned pixels
tooltip = Actual diameter of beads in unbinned pixels.
manpage = Actual diameter of beads in pixels in the original stack,
before any binning. If CentroidRadius is entered instead, the unbinned
diameter will be taken as 2 * radius - 3.
[Field = MedianForCentroid]
short =
type = B
usage = Use median instead of mean of surrounding pixels when computing centroid
tooltip =
manpage = Take the median instead of the mean of the pixels in the surrounding
annulus when computing the centroid.
[Field = LightBeads]
short =
type = B
usage = Beads are lighter than background rather than darker
tooltip = Not checked if beads are darker or checked if they are lighter than
background.
manpage =
[Field = FillGaps]
short =
type = B
usage = Fill in gaps in the seed model
tooltip = Fill in gaps in the seed model or leave them empty.
manpage =
[Field = MaxGapSize]
short =
type = I
usage = Maximum size of gap to create in the model (default 5)
tooltip = Maximum size of gap to create in the model before giving up on a
fiducial.
manpage = Maximum size of gap to create in the model. If a bead cannot be
tracked through some views, the tracking may be resumed as long as
the gap thus created is no larger than this amount. (Default 5)
[Field = ShiftsNearZeroTilt]
short =
type = FA
usage = Net shifts in bead positions between views near zero tilt
tooltip =
manpage = One or two entries for the net shift of bead positions when going
from a view near zero tilt to the next higher view. Each entry would be a
shift in X and Y in unbinned pixels. These shifts can help the tracking get
started properly when some of the beads are relatively far in Z from the plane of
material on which the coarse alignment is centered. They will be used when a
bead position is known on only one view near zero tilt. If only one shift is
provided, both the position of the bead on the adjacent view and this position
modified by the shift will be assessed in looking for the bead. If two shifts
are provided, they will be used to obtain both of the positions that are
assessed.
[Field = MinTiltRangeToFindAxis]
short =
type = F
usage = Minimum range of angles with data required for finding tilt axis
tooltip = Minimum range of tilt angles for which data must be available before
solving for tilt axis angle.
manpage = Minimum range of tilt angles for which data must be available before
trying to find the angle of the tilt axis (default 10).
[Field = MinTiltRangeToFindAngles]
short =
type = F
usage = Minimum range of angles with data required for finding tilt angles
tooltip = Minimum range of angles for which data must be available before
solving for tilt angles.
manpage = Minimum range of tilt angles for which data must be available before
trying to solve for tilt angles (default 20).
[Field = BoxSizeXandY]
short =
type = IP
usage = X and Y dimensions of the box used to search for a bead
tooltip = X and Y dimensions of the box used to search for a bead, in unbinned
pixels.
manpage = X and Y dimensions of the box used to search for a bead, in unbinned
pixels. Copytomocoms(1) sets this value initially from the unbinned bead
diameter to
^ max(32, 2 * diameter + 20, 3.3 * diameter + 2)
^If images are binned and the box size matches this value, then the same
formula with the binned diameter is used to adjust the box size. If the box size
has been changed from the initial value, then an unbinned effective diameter
is derived from the entered box size and a new box size is computed from the
formula with a binned effective diameter.
[Field = RoundsOfTracking]
short =
type = I
usage = Number of rounds of tracking through the views.
tooltip =
manpage = Number of rounds of tracking through the views.
Tracking proceeds from low to high tilt on odd rounds and from high to low
tilt on even rounds.
[Field = MaxViewsInAlign]
short =
type = I
usage = Maximum number of views to include in the tilt alignment
tooltip =
manpage = Maximum number of views to include in the tilt alignment. Use this
entry to do alignment only on a local subset of views at nearby tilt angles.
A value at least big enough to include half the views is recommended.
[Field = RestrictViewsOnRound]
short =
type = I
usage = Restrict the views in the tilt alignment on the given round of tracking
tooltip =
manpage = If MaxViewsInAlign is entered, this entry can be used to apply the
restriction on the number of the views in the tilt alignment on a particular
round of tracking.
[Field = UnsplitFirstRound]
short =
type = B
usage = In first round, track from seed view to first view then to last view (legacy)
tooltip =
manpage = On the first round, the program will track from the seed view
halfway down to the first view, then halfway up to the last view, then return
to the low views and finish with the high views. Use this option to return to
the old behavior (prior to IMOD 4.6.8) of tracking all the way to the first
view then tracking up to the last view.
[Field = InitialBidirectionalViews]
short =
type = I
usage = Number of views to track initially around bidirectional starting point
tooltip =
manpage = Number of views to track initially around bidirectional starting
point; default is 6. If tracking starts near the bidirectional starting
point, the program will track half of this number of views on each side of the
starting point before going on to more negative tilt angles. Set to 0 to
avoid this kind of tracking. The program assumes a tilt series is bidirection
if there is one separate view group defined at one end of the tilt series.
[Field = LocalAreaTracking]
short =
type = B
usage = Track subsets of beads in local areas
tooltip =
manpage = Track subsets of beads in local areas. The area containing beads
near zero tilt will be divided into subareas, and the subareas will be tracked
in order by increasing distance from the center of the image. Each subarea
will contain a minimum total number of beads (given by MinBeadsInArea), and
areas after the first will contain a minimum number that are shared with a
more central area (given by MinOverlapBeads)
[Field = LocalAreaTargetSize]
short =
type = I
usage = Target size for the local areas
tooltip =
manpage = Target size for the local areas. The program will try to make
typical areas have this size, but some will be bigger to contain enough beads.
[Field = MinBeadsInArea]
short =
type = I
usage = Minimum number of beads in a local area (default 8)
tooltip =
manpage = Minimum number of beads in a local area; areas will be expanded from
the target size to contain this minimum (default 8)
[Field = MaxBeadsInArea]
short =
type = I
usage = Maximum number of beads in a local area (default 500)
tooltip =
manpage = Maximum number of beads in a local area; the target size will be
shrunk if possible until no local areas exceed this limit (default 500)
[Field = MinOverlapBeads]
short =
type = I
usage = Minimum number of beads to overlap between areas (default 3)
tooltip =
manpage = Each area after the first one tracked will be required to have at
least this many beads shared with areas tracked earlier.
[Field = TrackObjectsTogether]
short =
type = B
usage = Track multiple objects together instead of separately
tooltip =
manpage = When there is more than one object in the seed model and local
area tracking is not specified, the objects will be tracked separately unless
this option is entered.
[Field = MaxBeadsToAverage]
short =
type = I
usage = Maximum number of views over which to average a bead (default 4)
tooltip = Maximum number of views over which to average a bead.
manpage = Maximum number of views over which to average a bead (default 4).
A running average is kept of the appearance of the bead over
the most recent views examined; this parameter specifies the
maximum number of views averaged.
[Field = LowPassCutoffInverseNm]
short =
type = F
usage = Cutoff for overall low-pass filter in reciprocal nanometers
tooltip = Cutoff for overall low-pass filter in reciprocal nanometers; values
around 0.3-0.4/nm are useful for cryo data sets in particular.
manpage = Cutoff radius for a low-pass filter that is
applied to all boxes when read in. The units are reciprocal nanometers; values
around 0.3-0.4/nm are useful for cryo data sets at a variety of unbinned pixel
sizes. The falloff (sigma) of the filter is set to 0.15 times the radius.
The \fB-PixelSize\fR option must be entered.
[Field = SobelFilterCentering]
short =
type = B
usage = Use edge-detecting Sobel filter to refine the bead positions
tooltip =
manpage = Use an edge-detecting Sobel filter to refine the centroid-based bead positions.
[Field = KernelSigmaForSobel]
short =
type = F
usage = Sigma for gaussian kernel filtering of single beads before Sobel filtering
tooltip = Sigma for gaussian kernel filtering of single beads before Sobel
filtering, in pixels. The default is 0.5 pixels; a value of around 1.5 is needed for
higher-noise (e.g., cryo) data with binned pixel sizes in the 0.6 - 1 nm range.
manpage = Sigma in pixels for gaussian kernel filtering of single bead before Sobel
filtering, which reduces the contribution of noise to the edge-filtered image. The
default is 0.5 pixels, which is optimal for relatively low-noise data. Higher-noise
data requires a higher sigma of around 1.5 when the binned pixel size is in
the 0.6 - 1 nm range, and correspondingly higher values for smaller pixel
sizes. This option cannot be entered with \fR-ScalableSigmaForSobel\fB.
[Field = ScalableSigmaForSobel]
short =
type = F
usage = Sigma for kernel filtering before Sobel filtering, as fraction of bead diameter.
tooltip = Sigma for gaussian kernel filtering of single beads before Sobel
filtering, as a fraction of bead diameter. The default sigma is 0.5 pixels
regardless of bead size.
A value of around 0.12 diameters is needed for higher-noise (e.g., cryo) data.
manpage = Sigma for gaussian kernel filtering of single beads before Sobel
filtering, as a fraction of the bead diameter. This filtering reduces the
contribution of noise to the edge-filtered image. If neither this option nor
\fB-KernelSigmaForSobel\fR is entered, the default sigma is 0.5 pixels,
which is optimal for relatively low-noise data. Higher-noise
data requires a value around 0.12 bead diameters, which can be used with
different binnings of data with a very small unbinned pixel size. This option cannot
be entered with \fR-KernelSigmaForSobel\fB.
[Field = AverageBeadsForSobel]
short =
type = I
usage = Number of beads to average for reference for Sobel filter correlation
tooltip =
manpage = Number of beads to average for the reference for Sobel filter
correlation. Images will be averaged from already-tracked nearby views
separately for each bead. If there are not enough already-tracked views,
averages will be combined from multiple beads to reach the desired number. If
the number of averaged beads is less than half of this value, a model bead is
used instead. The average or model is Sobel-filtered and correlated with the
Sobel-filtered image of the single bead. The default is 50.
[Field = InterpolationType]
short =
type = I
usage = 1 for linear or 0 for cubic interpolation or -1 for antialias
reduction in scaled Sobel filter
tooltip =
manpage = Type of interpolation to use in the scaled Sobel filter: 1 for
linear interpolation, 0 for cubic interpolation, and -1 for
image reduction with an antialias filter instead of with interpolation
combined with binning. The default is 0 if the sigma for kernel filtering is
less than 1.5, otherwise 1.
[Field = PositionTrialDiamFrac]
short =
type = F
usage = Threshold for trying both projection of 3D position and extrapolated position
tooltip =
manpage = When the projection of the 3D position from tilt alignment and the
extrapolated position from nearby views differ by more than this fraction
of the bead diameter, the program will try both positions. If a bead is found
from both starting positions, the two results will be evaluated by distance
from the expected position and integrated density. The default is 1.
[Field = MinDiamForParamScaling]
short =
type = F
usage = Minimum bead diameter for adjusting size-based parameters for binning
tooltip =
manpage = Minimum bead diameter, in binned pixels, for adjusting four
parameters that depend on bead size to account for binning: the distance
rescue criterion (DistanceRescueCriterion), the post-fitting rescue criterion
(PostFitRescueResidual), the maximum distance for rescues (MaxRescueDistance),
and the minimum residual criterion for deleting a point (first entry to
DeletionCriterionMinAndSD). This option should be entered only if these
parameters are already scaled up from their usual defaults to account for an
unbinned bead size larger than this minimum size. Copytomocoms does such
scaling when this option is present in the master track command file or added
or modified by a batch or template directive. Specifically, when the unbinned
bead diameter is greater than the minimum, the parameters in the master
command file are scaled up by the ratio of this diameter to the minimum. When
the ImageBinned entry is greater than 1, Beadtrack scales the parameters back
down by a ratio equal to the maximum of the minimum diameter (this option) and
the binned bead diameter, divided by the unbinned diameter. Regardless of
binning, if the binned bead size is bigger than this entry, an absolute
minimum residual value required for deleting points (not modifiable by option)
is scaled up by the ratio of the bead size to this entry.
[Field = PointsToFitMaxAndMin]
short =
type = IP
usage = Maximum and minimum number of positions to fit for extrapolation
tooltip = Number of positions to use for extrapolating a bead position to the
next view, and minimum required to use extrapolation rather than just the mean
of positions on the last few views.
manpage = Number of positions to use for extrapolating the bead position to
the next view when no tilt alignment is available, and minimum required to do
extrapolation rather than simply taking the mean of positions on the last few
views. (Defaults 7 and 3).
[Field = DensityRescueFractionAndSD]
short =
type = FP
usage = Criterion fraction of mean density and SDs below mean for rescue based
on density.
tooltip = Fraction of mean bead integral, and number of SDs below mean, to use
as the criterion for when to attempt a rescue based on bead density.
manpage = Fraction of mean bead integral, and number of standard deviations
below mean, to use as the criterion for when to attempt a rescue
based on bead density.
[Field = DistanceRescueCriterion]
short =
type = F
usage = Criterion distance for doing rescue based on excessive distance
tooltip = Distance away from expected position at which to attempt a rescue
based on excessive distance, in unbinned pixels for tilt series set up in IMOD 4.10.33+.
manpage = Criterion distance between found position and expected position for
attempting a rescue based on excessive distance. The distance should be in unbinned
pixels if \fB-MinDiamForParamScaling\fR is entered, namely if a tilt series
was set up in IMOD 4.10.33 or later, otherwise in binned pixels.
[Field = RescueRelaxationDensityAndDistance]
short =
type = FP
usage = Factors to relax density for rescues based on density and distance.
tooltip = Factors by which to relax the density criterion when trying to rescue
- a factor for density rescue and one for distance rescue.
manpage = Factors by which to adjust (relax) the density criterion when
trying to rescue. Enter one factor for density rescue and one for
distance rescue. A value of 1 does not relax the criterion.
[Field = PostFitRescueResidual]
short =
type = F
usage = Criterion distance for deletion of point after first-pass tilt
alignment.
tooltip = Criterion distance for deletion of a point on the first pass after
tilt alignment, in unbinned pixels for tilt series set up in IMOD 4.10.33+.
manpage = Criterion distance for deletion of a point after tilt alignment.
Points with residuals greater than this amount will be deleted on
the first pass, and a rescue search performed on the second pass. The
distance should be in unbinned pixels if \fB-MinDiamForParamScaling\fR is
entered, namely if a tilt series was set up in IMOD 4.10.33 or later,
otherwise in binned pixels.
[Field = DensityRelaxationPostFit]
short =
type = F
usage = Factor by which to relax the density criterion on the second pass.
tooltip = Factor by which to relax the density criterion on the second pass.
manpage =
[Field = MaxRescueDistance]
short =
type = F
usage = Max distance to search from expected position on second pass
tooltip = Maximum distance to search from the expected position, in unbinned
pixels for tilt series set up in IMOD 4.10.33+.
manpage = Maximum distance to search from the expected position on the second
pass. The distance should be in unbinned pixels if
\fB-MinDiamForParamScaling\fR is entered, namely if a tilt series was set up
in IMOD 4.10.33 or later, otherwise in binned pixels.
[Field = ResidualsToAnalyzeMaxAndMin]
short =
type = IP
usage = Max and min # of changes to use in analyzing changes in mean residual
tooltip = Maximum and minimum number of changes in mean residual to use in
finding the mean and SD of changes in the mean residual for a bead.
manpage = Maximum and minimum number of changes in mean residual to use in
finding the mean and SD of changes in the mean residual for a
bead as more points have been added. Default values 9 and 5.
[Field = DeletionCriterionMinAndSD]
short =
type = FP
usage = Min absolute and relative change in mean residual for deletion
tooltip = Minimum change in residual in unbinned pixels, and criterion number
of SDs from the mean residual change, to require for deletion of a point.
manpage = Minimum change in residual, and criterion number of SD's from the
mean residual change, to require for deletion of a point on pass 1 or 2. The
minimum change should be in unbinned pixels if
\fB-MinDiamForParamScaling\fR is entered, namely if a tilt series was set up
in IMOD 4.10.33 or later, otherwise in binned pixels.
[Field = SetIndexedParameter]
short =
type = FA
usage = One or more pairs consisting of a parameter number and a value to set
tooltip =
manpage = One or more pairs consisting of a parameter number and a value to
set. "bmr" refers to the analysis of background integrated densities and of
elongation when a point would be eliminated due to a big mean residual. "drb"
refers to analysis of background densities when evaluating a density rescue
result. Parameters are:
^ -1 maxBmrDeltaZ: Maximum delta Z from view for measuring elongations;
default 4.
^ -2 maxDrbDeltaZ: Maximum delta Z for analyzing background densities
^ -3 numBidirRelaxCrit: Number of views around bidirectional reversal over
which to relax the BMR criteria; default is 0.
^ -4 minzDelzNearZero: Maximum number of views away from the minimum-tilt
view at which to use the shifts near zero tilt; default is 2.
^ -5 maxDelzNearZero: Maximum number views from view with seed point at
which to use the shifts near zero tilt; default is 2.
^ 1 bmrLowerElongLim: Elongation below which the BMR criteria will be
raised without measuring on adjacent views; default 1.2.
^ 2 bmrUpperElongLim: Elongation below which the BMR criteria can be raised
after measuring on adjacent views; default 1.35
^ 3 bmrLowElongRaiseFac: Factor by which to raise BMR criteria when below the
lower limit; default 1.5
^ 4 bmrHighElongRaiseFac: Factor by which to raise BMR criteria when
between the two limits; default 1.3
^ 5 bmrMaxElongSD: Maximum allowed SD of elongation values over range of
views; default 0.2
^ 6 bmrMinWsumMADNratio: Minimum number of MADNS above the median
background density required to raise the BMR criteria; default 8.
^ 7 bmrMaxNumSDaboveMean: Maximum number of SDs above the mean elongation
allowed for raising the BMR criteria; default 1.
^ 8 drbJustAcceptCrit: After a successful density rescue, just accept when
density is above median background density by this number of MADNs. Set to 0
to accept all successful rescues; default 8.
^ 9 drbJustRejectCrit: After a failed density rescue, just drop the point
when density is below median background density by this number of MADNs. Set
to 0 to reject all failed rescues; default 3.
^ 10 drbAcceptMinMADNS: Minimum number of MADNs above median maximum
background density required to accept a bead despite a failed rescue; default 5.
^ 11 drbRejectMaxLowMADNS: Number of MADNs above median maximum
background density below which a successful rescue will be dropped for density
just below drbJustAcceptCrit; default 0.
^ 12 dbrAnyTypeMinMADNs: After any successful rescue, drop the point when
its density is below median background density by this number of MADNs;
default 1.5
^ 13 drbRejectMaxHighMADNS: Number of MADNs above median maximum
background density below which a successful rescue will be dropped for density
just above dbrAnyTypeMinMADNs; default 2.
^ 14 tiltIncMinForScaling - Winimum tilt increment for raising BMR
criteria by the ratio of tilt increment to this value; default 1.5.
Set to 0 to prevent raising the critera.
^ 15 cgEdgeDiamFrac - Width of annulus around bead in which background value
for centroid is measured; default 0.1
^ 16 cgGapDiamFrac - Width of annulus between pixels from which centroid and
background are measured; default 0.
^ 17 relaxBidirFac - Maximum amount by which to raise BMR criteria near a
bidirectional reversal.
[Field = ParameterFile]
short = param
type = PF
usage = Read parameter entries from file
tooltip =
manpage = Read parameter entries as keyword-value pairs from a parameter file.
[Field = usage]
short = help
type = B
usage = Print help output
tooltip =
manpage =
[SectionHeader = TestOptions]
usage = OPTIONS FOR TEST OUTPUT
manpage = OPTIONS FOR TEST OUTPUT
^ These options are used for program testing and development.
[Field = BoxOutputFile]
short =
long = BoxOutputFile
type = FN
usage = Root filename for diagnostic output of correlation boxes
tooltip =
manpage =
[Field = SnapshotViews]
short =
long = SnapshotViews
type = LI
usage = List of views at which to snapshot intermediate models
tooltip =
manpage = List of views at which to snapshot model before deletion on first and
second passes. The models will be named ...
[Field = SaveAllPointsAreaRound]
short =
long = SaveAllPointsAreaRound
type = IP
usage = Area/object and round at which to save all positions in new objects
tooltip =
manpage = Area or object and round at which to save all positions in new
objects. Enter negative of the area number to exit after finishing the area.
This option will also enable some debugging output for that area and round.