Version = 1.0
Pip = 1
[Field = InputFile]
short = input
type = FN
usage = Input model file with scattered points for 3D gold bead positions
tooltip =
manpage = Input model file with scattered points for 3D gold bead positions.
If this option is not entered, the first non-option argument will be used
for this file.
[Field = OutputFile]
short = output
type = FN
usage = Output file for processed model or surface information
tooltip =
manpage = Output file for processed model or surface information
If this option is not entered, the second non-option argument will be used
for this file.
[Field = TextFileWithSurfaces]
short = text
type = FN
usage = Name of text file to output with top/bottom assignments
tooltip =
manpage = Output a text file with the original contour
number and the top/bottom assignments (values 1 and 2) for each point. This
is meant to be used by Pickbestseed(1), so input data should have only one object
and only one point per contour.
[Field = FlipYandZ]
short = flipyz
type = I
usage = 1 to flip Y and Z coordinates, 0 not to, or -1 to flip if nz > ny
tooltip =
manpage = This option allows control over whether the Y and Z coordinates of
the model are flipped. By default, flipping will be done if the Z dimension
(nz) of the modeled volume is greater than the Y dimension (ny). Enter 1
to force flipping even if this is not the case, or 0 to prevent it if this is
the case.
[Field = SubareaSize]
short = subarea
type = I
usage = Size of subareas over which to analyze for two surfaces
tooltip =
manpage = Size of subareas over which to analyze for two surfaces. This
option is needed only if the area coated with beads is large enough and warped
enough that the analysis fails to separate the two surfaces. The area
occupied by beads will
be divided into non-overlapping subregions of approximately the given size in
each dimension. Each will be analyzed separately to sort all of the beads
between the two surfaces. Make this value as large as possible, since the
analysis can easily fail if there are only ~10 beads in any of the subareas.
[Field = PickAreasMinNumAndSize]
short = pick
type = IP
usage = Minimum bead number and area size for having program pick subarea size
tooltip =
manpage = The program can divide the analysis in to subareas automatically if
this option is used to enter the minimum number of beads required in each area
and the minimum subarea size allowed. The program will pick the smallest
possible subarea size that fits these constraints.
[Field = MajorityObjectOnly]
short = majority
type = B
usage = Retain only the points on the surface with more beads
tooltip =
manpage = Output a model with only one object containing
the points on the surface that has the most beads. Use this option if
there are too few fiducials on one surface to fit a smooth surface to in
Flattenwarp(1).
[Field = XAxisTilt]
short = xaxis
type = F
usage = X axis tilt used to generate the tomogram (for Tiltalign output only)
tooltip =
manpage = The value of X axis tilt used when the tomogram was generated. This
value is needed for a 3D fiducial model output by Tiltalign(1) (and only for
such a model).
[Field = InvertZAxis]
short = invert
type = B
usage = Invert the Z coordinates of points to match a flipped reconstruction
tooltip =
manpage = Invert the Z coordinates of the points so that they will match a
reconstruction that was Y-Z flipped rather than rotated around the X axis.
This option is needed only for a 3D fiducial model output by Tiltalign(1).
[Field = AlreadySorted]
short = already
type = B
usage = Points are already sorted into two surfaces
tooltip =
manpage = Use this option to skip the analysis that sorts beads between two
surfaces, and combine multiple objects by color if there are any. You would
use this for a 3D fiducial model from Tiltalign(1) if the beads are already
correctly sorted into two surfaces, or if they are on only one surface and in
only one object.
[Field = OneSurface]
short = one
type = B
usage = Points are all on one surface
tooltip =
manpage = Use this option to skip the analysis that sorts beads between two
surfaces, and to combine all points into one object. You would use this for a
3D fiducial model from Tiltalign(1) if the beads are all on one surface but in
different objects.
[Field = AlignedSizeXandY]
short = aligned
type = IP
usage = Unbinned X and Y size of aligned stack used to make reconstruction
tooltip =
manpage = Unbinned X and Y size of the aligned stack used to make the
reconstruction.
Use this option if the reconstruction is based on a final aligned
stack whose unbinned size is smaller or larger than that of the raw stack, and
if you are processing a 3D fiducial model from Tiltalign(1). If the
prealigned stack was binned, you must also enter the -prebin option.
[Field = XTrimStartAndEnd]
short = xtrim
type = IP
usage = Starting and ending X coordinates of aligned stack in final volume
tooltip =
manpage = Starting and ending X coordinates of the aligned stack that appear
in the final trimmed reconstruction, numbered from 1. See next option.
[Field = YTrimStartAndEnd]
short = ytrim
type = IP
usage = Starting and ending Y coordinates of aligned stack in final volume
tooltip =
manpage = Starting and ending Y coordinates of the aligned stack that appear
in the final trimmed reconstruction, numbered from 1. These two options are
needed only for a 3D fiducial model from Tiltalign(1). If you built the full
reconstruction (no SLICE or WIDTH and OFFSET entries to Tilt(1)), then the
coordinates for these two options are just the ones used to trim the volume
with Trimvol(1). If you built a subset of the reconstruction, the WIDTH and
OFFSET entries can be used to derive the X coordinates, and the SLICE entries
provide the Y coordinates. If you then trimmed the volume, you need to
combine the trimming coordinates with the one used to build the
reconstruction. If you enter these coordinates, you must enter the
prealigned and the aligned stack binning if either is different from one.
[Field = PrealignedBinning]
short = prebin
type = I
usage = Binning of prealigned stack used to build 3D fiducial model
tooltip =
manpage = Binning of prealigned stack used to build a 3D fiducial model. This
option is needed for a binning other than 1 if you enter the aligned stack
size or trimming coordinates, or if you want to rescale to the coordinates of
the reconstruction.
[Field = ReconstructionBinning]
short = recbin
type = I
usage = Binning of aligned stack used to build reconstruction
tooltip =
manpage = Binning of aligned stack used to build the reconstruction. This
option is needed for a 3D fiducial model if you are entering trimming
coordinates or if you want to rescale coordinates to match the reconstruction.
[Field = RescaleByBinnings]
short = rescale
type = B
usage = Rescale the model coordinates to account for binning
tooltip =
manpage = Rescale the model coordinates to account for binning of the
prealigned or final aligned stack. By default output coordinates will still
have the scaling of the prealigned stack; use this option to rescale them so
that they match the scaling of the reconstruction.
[Field = CheckExistingGroups]
short = check
type = B
usage = Check that the sorting is the same as in the input model
tooltip =
manpage = Check that the sorting is the same as in the input model, which must
already have points divided into two groups. All other output is suppressed,
and if the sorting matches the program just exits with 0 status; if there is
a mismatch it prints the number of incorrect points and exits with an error
status.
[Field = ValuesToRestrainSorting]
short = values
type = I
usage = Use general values of points to exclude some points from initial pairings
tooltip =
manpage = Use the general values of the points or contours in the model to
identify a fraction of points as outliers that should be excluded from the
initial pairing of points at steep angles to each other. Enter 1 to exclude
points with particularly high values (e.g., for mean residual values from
Beadtrack(1)), or -1 to exclude points with low values (e.g., for peak values
from imodFindBeads(1)).
[Field = OutlierCriterionDeviation]
short = outlier
type = F
usage = Criterion value for MAD-Median outlier identification from values
tooltip =
manpage = When the -values option is entered, the values of points are
analyzed to determine the normalized median absolute deviation (MADN) from the
median value. Points with an absolute deviation from the median bigger than
a criterion times the MADN are identified as outliers and excluded from
initial pairing. Use this option to change the criterion, whose default is
2.24.
[Field = SetSurfaceSortParam]
short = set
type = FPM
usage = Set given parameter (0-13) to given value in surfaceSort routine
tooltip =
manpage = Set one parameter specified by the first number to the value
specified by the second number in the surfaceSort routine. See the library
documentation of surfaceSort (in libcfshr - "Other utilty functions") for an
explanation and a list of the parameters.
To set the verbose level, use "-set 13,1" or "-set 13,2".
[Field = usage]
short = help
long = usage
type = B
usage = Print help output
tooltip =
manpage = Print help output.