Version = 1.0
Pip = 1
[SectionHeader = IOOptions]
usage = INPUT AND OUTPUT FILE OPTIONS
manpage = INPUT AND OUTPUT FILE OPTIONS
^ These options give information about input and output files.
[Field = ModelFile]
short =
type = FN
usage = Input fiducial model file
tooltip =
manpage =
[Field = ImageFile]
short =
type = FN
usage = Image file that fiducial model was built on (optional)
tooltip =
manpage = Image file that fiducial model was built on, used to obtain
information for scaling the model. If this entry is
omitted, the program will use values entered with ImageSizeXandY,
ImageOriginXandY, and ImagePixelSizeXandY, or values from the model itself if
those options are omitted. In general, the information from the model header
should be sufficient and none of these entries should be needed.
[Field = ImageSizeXandY]
short =
type = IP
usage = Dimensions of image file (optional)
tooltip =
manpage =
[Field = ImageOriginXandY]
short =
type = FP
usage = X and Y origin values from image file header (optional)
tooltip =
manpage =
[Field = ImagePixelSizeXandY]
short =
type = FP
usage = X and Y Pixel spacing from image file header, in Angstroms (optional)
tooltip =
manpage =
[Field = UnbinnedPixelSize]
short =
type = F
usage = Pixel size of unbinned data in nanometers
tooltip =
manpage =
[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 values entered with AxisZShift and AxisXShift
from unbinned to binned coordinates. The default is 1.
[Field = OutputModelFile]
short =
type = FN
usage = Output file for 3-D model of solved fiducial positions
tooltip =
manpage = File in which to place 3-D model of the fiducials based on their
solved positions
[Field = OutputResidualFile]
short =
type = FN
usage = Output file for list of all residuals
tooltip =
manpage = Output file for a list of the residuals at all projection points,
which can be converted to a model with Patch2imod.
[Field = OutputModelAndResidual]
short =
type = FN
usage = Root name for output of both a 3-D model and residuals
tooltip =
manpage = Root name for output of both a 3-D model and residuals; the files
will have extensions .3dmod and .resid, respectively.
[Field = OutputFilledInModel]
short =
type = FN
usage = Output file for fiducial model with missing points filled in
tooltip =
manpage = Output file for fiducial model with missing points filled in on the
views included in the solution. This model can be used for erasing
fiducial markers. A missing point is first computed from the projection position of
the solved 3-D position of the fiducial. Then, a line is fit to the
residuals of points on the 6 nearest views and an estimated residual is
subtracted from the projection position, in order to incorporate a consistent
disparity between the fiducial positions and the solution. Projection
positions from a global solution are replaced by ones from local solutions, if
any, and ones from multiple local areas are averaged. This option is ignored
for a model from patch tracking.
[Field = OutputTopBotResiduals]
short =
type = FN
usage = Root name for separate output of residuals for top and bottom points
tooltip =
manpage = Root name for output of residuals for fiducials on the top and
bottom surfaces into separate files, with extensions .topres and .botres.
[Field = OutputFidXYZFile]
short =
type = FN
usage = File for text output of the solved X-Y-Z coordinates
tooltip =
manpage =
[Field = OutputTiltFile]
short =
type = FN
usage = Output file for the solved tilt angles after adjustment for beam tilt
tooltip =
manpage = Output file for the solved tilt angles after adjustment for beam
tilt, if any
[Field = OutputUnadjustedTiltFile]
short =
type = FN
usage = Output file for the solved tilt angles before adjustment for beam tilt
tooltip =
manpage = Output file for the solved tilt angles before adjustment for beam
tilt, if any
[Field = OutputXAxisTiltFile]
short =
type = FN
usage = Output file for tilts around the X axis.
tooltip =
manpage =
[Field = OutputTransformFile]
short =
type = FN
usage = Output file for 2-D transformations needed to align images
tooltip =
manpage =
[Field = OutputZFactorFile]
short =
type = FN
usage = Output file for factors to adjust X and Y as function of Z in
backprojection
tooltip =
manpage = Output file for factors to adjust X and Y as function of Z in
backprojection. When there is specimen stretch along an axis, a 2-D
transformation of the projections cannot fully correct for this effect, and
these factors are needed to adjust the backprojection position for different
Z heights in the reconstructed slice.
[SectionHeader = AngleViewOptions]
usage = ANGLE AND VIEW RELATED OPTIONS
manpage = ANGLE AND VIEW RELATED OPTIONS
^ These options provide information about tilt angles and the views to be
included in the analysis.
[Field = IncludeStartEndInc]
short =
type = IT
usage = Starting and ending view numbers, and increment between views, to
include in analysis
tooltip =
manpage = Starting and ending view numbers, and increment between views, to
include in analysis. This option, IncludeList, and ExcludeList are mutually
exclusive. The default is to include all views that have points in the model.
[Field = IncludeList]
short =
type = LI
usage = List of views to include in the analysis
tooltip =
manpage = List of views to include in the analysis (ranges allowed)
[Field = ExcludeList]
short =
type = LI
usage = List of views to exclude from the analysis
tooltip = List of views to exclude from alignment and reconstruction.
manpage = List of views to exclude from the analysis (ranges allowed)
[Field = RotationAngle]
short =
type = F
usage = Initial rotation angle from the Y axis to the tilt axis
tooltip =
manpage = Initial angle of rotation in the plane of projection. This is the
rotation (CCW positive) from the Y-axis (the tilt axis after the
views are aligned) to the suspected tilt axis in the unaligned views.
[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.
Multiple entries can be used to specify more than one set of separate views.
[Field = NoSeparateTiltGroups]
short =
type = I
usage = Group tilt angles across separate groups (1 for patch track, 2 for any)
tooltip =
manpage = Allow tilt angles to be grouped across separate view groups in order
to prevent large jumps in the solved tilt angles. Enter 1 to allow this grouping
with a patch tracking model, or 2 to allow it for any fiducial model.
[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 = AngleOffset]
short =
type = F
usage = Amount to add to all entered tilt angles
tooltip = Total amount to add to all tilt angles.
manpage = Amount to add to all entered tilt angles.
[SectionHeader = Options]
usage = VARIABLE SELECTION OPTIONS
manpage = VARIABLE SELECTION OPTIONS
^ These options specify the variables to be included in the analysis and
information about them, such as group sizes.
[Field = ProjectionStretch]
short =
type = B
usage = Solve for axis skew applying to projection of all images.
tooltip =
manpage = Solve for a parameter representing a skew between the microscope X
and Y axes that occurs during projection of all images. This is equivalent to
a stretch along a 45-degree line between the axes. A component of stretch
parallel to the axes cannot be distinguished from a stretch of the 3D fiducial
coordinates parallel to the axes, so as of IMOD 3.10.7 only this skew
component is solved for. The initial rotation angle of the tilt axis is used
to determine the approximate axis along which this stretch would occur after
the final image rotation.
[Field = BeamTiltOption]
short =
type = I
usage = Type of beam tilt solution: 0 for none, 1 to include in fit, 2 to
search
tooltip =
manpage = Type of solution for non-perpendicularity between tilt axis and beam
axis, referred to as beam tilt:
^ 0 for beam tilt fixed at the initial value,
^ 1 to include beam tilt as a variable in the minimization
^ procedure,
^ 2 to perform the minimization at a series of fixed beam tilt
^ values and search for the value that gives the smallest
^ error.
^Because some variables can covary with the beam tilt to give nearly equivalent
solutions, the second option for finding the beam tilt gives more reliable
results. Some combinations of variable simply cannot be solved for, in
particular the stretch variables and rotation together with beam tilt; either
omit the stretch variables or solve for a single rotation angle. Note that
only the component of the beam tilt around the X axis is solved for; the
component around the Y axis is indistinguishable from a change in tilt angle.
When the beam tilt is non-zero, either as a result of a search or because a
fixed value was entered, its effect is expressed as a varying tilt around the
X axis and a modification of the tilt angles and in-plane image rotations.
Thus, a file of X-tilt angles should be output when beam tilt is included in
the solution.
[Field = FixedOrInitialBeamTilt]
short =
type = F
usage = Initial value of beam tilt when solving for it, or fixed value when not
tooltip = Fixed value for beam tilt if it is not zero
manpage = The entry provides either an initial value for the beam tilt, when
it is being solved for, or a fixed value when it is not.
[Field = RotOption]
short =
type = I
usage = Type of rotation solution: 0 for none, 1 for independent, 2 for
mapped, 3 or 4 for automapped, -1 for single variable
tooltip =
manpage = Type of rotation solution:
^ 0 for all rotations fixed at the initial angle,
^ 1 for each view having an independent rotation,
^ 2 to enter general mapping of rotation variables,
^ 3 or 4 for automapping of rotation variables (3 for linearly
^ changing values or 4 for values all the same within a
^ group), or
^ -1 to solve for a single rotation variable.
enum.0.tooltip = Do not solve for rotations.
enum.1.tooltip = Solve for each rotation independently.
enum.3.tooltip = Group views to solve for fewer rotation variables.
enum.-1.tooltip = Solve for a single rotation variable.
[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 = RotationFixedView]
short =
type = I
usage = View to fix at the initial rotation angle
tooltip =
manpage = Number of view whose rotation should be fixed at the initial
rotation angle. This entry is relevant with any of the positive RotOption
entries.
[Field = LocalRotOption]
short =
type = I
usage = Type of local rotation solution: 0 for none, 1 for independent, 2 for
mapped, 3 or 4 for automapped, -1 for single variable
tooltip = Solve for local in-plane rotations.
manpage = Type of local rotation solution:
^ 0 for local rotations fixed,
^ 1 for each view having an independent rotation,
^ 2 to enter general mapping of variables,
^ 3 or 4 for automapping of rotation variables (3 for linearly
^ changing values or 4 for values all the same within a
^ group), or
^ -1 to solve for a single rotation variable.
[Field = LocalRotDefaultGrouping]
short =
type = I
usage = Default group size when automapping local rotation variables
tooltip = Grouping size for local rotations.
manpage = Default group size when automapping local rotation variables.
[Field = LocalRotNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
local rotation 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 local rotation variables should be grouped differently from the default.
[Field = TiltOption]
short =
type = I
usage = Type of tilt angle solution: 0 for all fixed, 2 for all independent, 5
for automapping
tooltip =
manpage = Type of tilt angle solution:
^ 0 to fix all tilt angles at their initial values,
^ 1 to solve for all tilt angles except for a specified view,
^ 2 to solve for all tilt angles except for the view at minimum
^ tilt,
^ 3 to solve for all tilt angles except for a specified view and
^ the view at minimum tilt,
^ 4 to specify a mapping of tilt angle variables,
^ 5 or 6 to automap groups of tilt angles (5 for linearly
^ changing values or 6 for values all the same within a
^ group), or
^ 7 or 8 to automap and fix two tilt angles (7 for linearly
^ changing values or 8 for values all the same within a group)
enum.0.tooltip = Do not solve for tilt angles.
enum.2.tooltip = Solve for each tilt angle independently.
enum.5.tooltip = Group views to solve for fewer tilt angle variables.
[Field = TiltFixedView]
short =
type = I
usage = View at which to fix the tilt angle (TiltOption 1, 3, 7, or 8)
tooltip =
manpage = Number of view at which to fix the tilt angle (required with
TiltOption 1, 3, 7, or 8)
[Field = TiltSecondFixedView]
short =
type = I
usage = Second view at which to fix the tilt angle (TiltOption 7 or 8)
tooltip =
manpage = Number of second view at which to fix the tilt angle (required with
TiltOption 7 or 8)
[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 = LocalTiltOption]
short =
type = I
usage = Type of local tilt angle solution; same values as for global
tooltip = Solve for local changes in tilt angle.
manpage = Type of local tilt angle solution; values 0-8 have same meaning as
for global solution.
[Field = LocalTiltFixedView]
short =
type = I
usage = View at which to fix the tilt angle (LocalTiltOption 1, 3, 7, or 8)
tooltip =
manpage = Number of view at which to fix the tilt angle in the local solution
(required with LocalTiltOption 1, 3, 7, or 8)
[Field = LocalTiltSecondFixedView]
short =
type = I
usage = Second view at which to fix the tilt angle (LocalTiltOption 7 or 8)
tooltip =
manpage = Number of second view at which to fix the tilt angle in the local
solution (required with LocalTiltOption 7 or 8)
[Field = LocalTiltDefaultGrouping]
short =
type = I
usage = Average default group size when automapping local tilt variables
tooltip = Grouping size for local tilt angle changes.
manpage = Average default group size when automapping local tilt variables
[Field = LocalTiltNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
local 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 local tilt variables should be grouped differently from the default.
[Field = MagReferenceView]
short =
type = I
usage = Reference view whose magnification will be fixed at 1.0
tooltip = View at which magnification will be fixed at 1.0.
manpage = Number of reference view whose magnification will be fixed at 1.0.
The default is the view at minimum tilt.
[Field = MagOption]
short =
type = I
usage = Type of magnification solution: 0 fixed, 1 independent, 2 mapped, 3 or
4 automapped.
tooltip =
manpage = Type of magnification solution:
^ 0 to fix all magnifications at 1.0,
^ 1 to vary all magnifications independently,
^ 2 to specify a mapping of magnification variables, or
^ 3 or 4 for automapping of variables (3 for linearly changing
^ values or 4 for values all the same within a group).
enum.0.tooltip = Do not solve for magnifications.
enum.1.tooltip = Solve for magnification at each view independently.
enum.3.tooltip = Group views to solve for fewer magnification variables.
[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 = LocalMagReferenceView]
short =
type = I
usage = Reference view whose local magnification will be fixed at 1.0
tooltip =
manpage = Number of reference view whose local magnification will be fixed at
1.0. The default is the view at minimum tilt.
[Field = LocalMagOption]
short =
type = I
usage = Type of local magnification solution; same values as for global
tooltip = Solve for local changes in magnification.
manpage = Type of local magnification solution; values 0-3 have same meaning as
for global solution.
[Field = LocalMagDefaultGrouping]
short =
type = I
usage = Default group size when automapping local magnification variables
tooltip = Grouping size for local magnification changes.
manpage = Default group size when automapping local magnification variables
[Field = LocalMagNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
local 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 local magnification variables should be grouped differently from the
default.
[Field = CompReferenceView]
short =
type = I
usage = View to fix at compression 1.0
tooltip =
manpage = Number of the view to fix at compression 1.0 (something
other than a view whose tilt angle is fixed at zero.) Required if CompOption
not 0.
[Field = CompOption]
short =
type = I
usage = Type of compression solution: 0 fixed, 1 independent, 2 mapped, 3 or
4 automapped
tooltip =
manpage = Type of compression solution:
^ 0 to fix all compressions at 1.0,
^ 1 to vary all compressions independently,
^ 2 to specify a mapping of compression variables, or
^ 3 or 4 for automapping of variables (3 for linearly changing
^ values or 4 for values all the same within a group).
[Field = CompDefaultGrouping]
short =
type = I
usage = Default group size when automapping compression variables
tooltip =
manpage =
[Field = CompNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
compression variables.
tooltip =
manpage = Starting and ending view numbers and group size for a set of views
whose compression variables should be grouped differently from the default.
[Field = XStretchOption]
short =
type = I
usage = Type of X-stretch solution: 0 fixed, 1 independent, 2 mapped, 3 or
4 automapped
tooltip =
manpage = Type of X-stretch solution:
^ 0 to fix all X stretches at 0,
^ 1 to vary all X stretches independently,
^ 2 to specify a mapping of X-stretch variables, or
^ 3 or 4 for automapping of variables (3 for values all the
^ same within a group or 4 for linearly changing values).
[Field = XStretchDefaultGrouping]
short =
type = I
usage = Default average group size when automapping X stretch variables
tooltip = Basic grouping size for X stretch (grouping will be less at high tilt
and more at low tilt).
manpage = Default average group size when automapping X stretch variables.
[Field = XStretchNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
X stretch variables.
tooltip = Sets of views with non-default grouping for X stretch. 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 X stretch variables should be grouped differently from the default.
[Field = LocalXStretchOption]
short =
type = I
usage = Type of local X-stretch solution; same values as for global
tooltip =
manpage = Type of local X-stretch solution; values 0-3 have same meaning as
for global solution.
[Field = LocalXStretchDefaultGrouping]
short =
type = I
usage = Default average group size when automapping local X stretch variables
tooltip = Grouping size for local X stretch variables.
manpage = Default average group size when automapping local X stretch variables
[Field = LocalXStretchNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
local X stretch variables.
tooltip = Sets of views with non-default grouping for X stretch. 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 local X stretch variables should be grouped differently from the
default.
[Field = SkewOption]
short =
type = I
usage = Type of skew solution: 0 fixed, 1 independent, 2 mapped, 3 or
4 automapped
tooltip = Solve for skew in the plane of section.
manpage = Type of skew solution:
^ 0 to fix all skew angles at 0.0,
^ 1 to vary all skew angles independently,
^ 2 to specify a mapping of skew variables, or
^ 3 or 4 for automapping of variables (3 for linearly changing
^ values or 4 for values all the same within a group).
[Field = SkewDefaultGrouping]
short =
type = I
usage = Default group size when automapping skew variables
tooltip = Grouping size for skew angles.
manpage = Default group size when automapping skew variables
[Field = SkewNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
skew variables.
tooltip = Sets of views with non-default grouping for skew angles. 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 skew variables should be grouped differently from the default.
[Field = LocalSkewOption]
short =
type = I
usage = Type of local skew solution; same values as for global
tooltip = Solve for local skew in the plane of section.
manpage = Type of local skew solution; values 0-3 have same meaning as
for global solution.
[Field = LocalSkewDefaultGrouping]
short =
type = I
usage = Default group size when automapping local skew variables
tooltip = Grouping size for local skew angle variables.
manpage = Default group size when automapping local skew variables
[Field = LocalSkewNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
local skew variables.
tooltip = Sets of views with non-default grouping for skew angles. 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 local skew variables should be grouped differently from the default.
[Field = XTiltOption]
short =
type = I
usage = Type of X-axis tilt solution: 0 fixed, 1 independent, 2 mapped, 3 or
4 automapped
tooltip =
manpage = Type of X-axis tilt solution:
^ 0 to fix all X tilts at 0.,
^ 1 to vary all X-tilts independently,
^ 2 to specify a mapping of X-tilt variables, or
^ 3 or 4 for automapping of variables (3 for linearly changing
^ values or 4 for values all the same within a group).
[Field = XTiltDefaultGrouping]
short =
type = I
usage = Default group size when automapping X-axis tilt variables
tooltip =
manpage =
[Field = XTiltNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
X-axis tilt variables.
tooltip =
manpage = Starting and ending view numbers and group size for a set of views
whose X-axis tilt variables should be grouped differently from the default.
[Field = LocalXTiltOption]
short =
type = I
usage = Type of local X-axis tilt solution; same values as for global
tooltip =
manpage = Type of local X-axis tilt solution; values 0-3 have same meaning as
for global solution.
[Field = LocalXTiltDefaultGrouping]
short =
type = I
usage = Default group size when automapping local X-axis tilt variables
tooltip =
manpage =
[Field = LocalXTiltNondefaultGroup]
short =
type = ITM
usage = Starting and ending views and group size for nondefault grouping of
local X-axis tilt variables.
tooltip =
manpage = Starting and ending view numbers and group size for a set of views
whose local X-axis tilt variables should be grouped differently from the
default.
[SectionHeader = Options]
usage = MINIMIZATION AND OUTPUT OPTIONS
manpage = MINIMIZATION AND OUTPUT OPTIONS
^ These options control the minimization procedure and the outputs of the
program.
[Field = ResidualReportCriterion]
short =
type = F
usage = Criterion number of SDs above mean residual error
to report (negative for SDs relative to neighbors)
tooltip = Threshold number of SDs above mean for reporting large residuals.
manpage = Criterion number of standard deviations above mean residual error
that should be reported. This can be based on either the overall
mean and S.d. of the residual errors, or on a mean and S.d.
computed from points in nearby views. Enter a positive value
for a report based on overall mean, or a negative value for a
report based on the mean residual in the same and nearby views.
enum.all.tooltip = Apply criterion relative to mean/SD of residuals on all
views.
enum.neighboring.tooltip = Apply criterion relative to mean/SD of residuals on
neighboring views.
[Field = SurfacesToAnalyze]
short =
type = I
usage = 1 or 2 to determine surface angles by fitting points to 1 or 2
surfaces, or 0 for no fit
tooltip =
manpage = 0 to omit surface analysis, or 1 or 2 to fit points to one or two
surfaces and derive a surface angles and recommended tilt angle offset. This
entry has no effect on the global alignment solution.
enum.1.tooltip = Fit one plane to all points to find angles of section.
enum.2.tooltip = Divide points into two groups and fit two planes to find
angles of section.
[Field = MetroFactor]
short =
type = F
usage = Step size for minimization procedure
tooltip = A step size factor; try changing by +/-10% if solutions fail.
manpage = This entry determines how large a step the variable metric
minimization procedure (METRO) tries to take. The default is 0.25,
which typically works even for large data sets.
When METRO fails for various reasons, the program will retry with several
other nearby values of the factor.
[Field = MaximumCycles]
short =
type = I
usage = Limit on number of cycles for minimization procedure (default 1000)
tooltip = Limit on number of iterations to find a solution.
manpage = Limit on number of cycles for minimization procedure (default 1000).
[Field = RobustFitting]
type = B
usage = Do robust fitting by giving less or no weight to outliers
tooltip =
manpage = Use a robust fitting method that gives less weight to points with
residuals higher than the median residual, and no weight to the most extreme
points.
[Field = WeightWholeTracks]
type = B
usage = Do robust fitting by weighting entire contours in patch track models
tooltip = Do robust fitting by finding weights for entire contours, giving the
same weight to all points in a contour (for patch tracking models only).
manpage = When doing robust fitting with a model from patch tracking,
assign the same weight to all the points in each contour. Contours with
mean residuals higher than the median will thus be given less weight, and ones
with the most extreme residuals will be given weights of 0.02.
[Field = KFactorScaling]
type = F
usage = Amount to scale the K factor that controls how many points are down-weighted
tooltip = Amount to scale the K factor that controls how many points are
down-weighted; the default is 1 and smaller values down-weight more points.
manpage = Amount to scale the K factor that controls how many points are
down-weighted in the robust fitting. The default scaling of 1 gives a K
factor of 4.685, the factor commonly used for the Tukey bisquare weighting. A
smaller factor will down-weight and eliminate more points.
[Field = WarnOnRobustFailure]
type = B
usage = Do not give error if robust fitting fails and alignment is just global
tooltip =
manpage = Give just a warning instead of exiting with an error if the robust
fitting fails and only a global alignment is being done. If local alignments
are being done, a failure in either the global alignment or a local area will
always result in just a warning. In all cases, the non-robust alignment is
restored after a failure.
[Field = MinWeightGroupSizes]
type = IP
usage = Minimum sizes of groups of points for computing weights, global and local
tooltip =
manpage = Minimum sizes of the groups of points used for computing weights,
in global and local alignment runs. In order to apply the robust method to
points that are relatively similar to each other, deviations from a median
residual are computed within subsets of points that are located on adjacent
views; and if there are enough points, the points in a global alignment run
are also sorted into rings based on distance from the center. These entries
set the minimum sizes of these groups. If the total number of points
available for fitting falls below the minimum, the robust fitting is not
done and a warning or error is issued. The defaults are 100 and 65 when
adjusting weights for individual points. When assigning weights to whole
contours with data from patch tracking, a similar approach is used to divide
the contours into groups that are analyzed together. Here, the defaults are
30 and 20.
[Field = AxisZShift]
short =
type = F
usage = Amount to shift tilt axis in Z, or 1000 to put at midpoint of range
tooltip = Distance to shift tilt axis in Z for reconstruction.
manpage = Amount to shift the tilt axis in Z, relative to the centroid in
Z of the fiducial points or relative to the original Z axis location if
ShiftZFromOriginal is entered. It is also possible to enter 1000 to shift the
tilt axis to the midpoint of the range of Z values. Enter this value in
unbinned pixels.
[Field = ShiftZFromOriginal]
short =
type = B
usage = Apply Z shift relative to original tilt axis location
tooltip =
manpage = Apply Z shift relative to original tilt axis location. If images
were initially aligned by cross-correlation, this option will keep specimen
material near the center of the reconstruction even if fiducials are on one
surface.
[Field = AxisXShift]
short =
type = F
usage = Amount to shift the tilt axis in X
tooltip =
manpage = Amount to shift the tilt axis in X away from the center of the
image. Enter this value in unbinned pixels.
[SectionHeader = LocalOptions]
usage = LOCAL ALIGNMENT OPTIONS
manpage = LOCAL ALIGNMENT OPTIONS
^ These options control local alignments.
[Field = LocalAlignments]
short =
type = B
usage = Do alignments with subsets of points in local areas
tooltip = Compute alignments in local areas after finding global solution.
manpage = Do alignments with subsets of points in local areas. When this
option is selected, the appropriate Local...Option values must be entered to
control what variables are solved for;
the default is 0 for all of the local option values.
[Field = OutputLocalFile]
short =
type = FN
usage = Output file for transformations for local alignments
tooltip =
manpage =
[Field = NumberOfLocalPatchesXandY]
short =
type = IP
usage = Number of local patches in X and Y for local solutions
tooltip = Number of overlapping local areas to use in the X and Y directions.
manpage = Number of local patches in X and in Y in which to obtain a solution
from the fiducials located in that patch. If this option is entered,
overlapping patches will be set up that fill the image area.
[Field = TargetPatchSizeXandY]
short =
type = IP
usage = Target minimum size for local patches in X and Y
tooltip = Target for the minimum size of local areas in the X and Y directions.
manpage = Target for the size of local patches in X and Y in which to obtain a
solution from the fiducials located in that patch. The number of patches will
be set so that patches smaller or up to 5% larger than this size and
overlapping by a fixed amount will fill the range occupied by fiducials (not
the image area). The patches on the edges should not have to expand as much
as when the patch centers are set up to fill the image area. If this option
is entered, NumberOfLocalPatchesXandY must not be entered, and
MinSizeOrOverlapXandY must specify an overlap instead of a size.
[Field = MinSizeOrOverlapXandY]
short =
type = FP
usage = Minimum size of patches in X and Y (if > 1) or minimum fractional
overlap (if < 1)
tooltip = Minimum size of patches in pixels, or minimum fractional overlap
between patches, in the X and Y directions.
manpage = Either the minimum size of each patch in X and Y (enter values > 1)
or the minimum fractional overlap between patches (values < 1). The default
is an overlap of 0.5.
[Field = MinFidsTotalAndEachSurface]
short =
type = IP
usage = Minimum total number of fiducials, and minimum number present on each
surface if two surfaces exist
tooltip = Minimum total number of fiducials required in each local area, and
minimum on each surface if two surfaces were analyzed for.
manpage = Minimum total number of fiducials, and minimum number present on each
surface if two surfaces were assumed in the analysis of
surfaces. A patch will be expanded about its center until it
contains enough points to meet both of these criteria.
[Field = FixXYZCoordinates]
short =
type = B
usage = Fix the X-Y-Z coordinates of the fiducials at their global values
tooltip =
manpage = Fix the X-Y-Z coordinates of the fiducials at their values from the
global solution; the default is to solve for them independently
in each local area. For more on the implications of this option, see the note
above in the section on local alignments.
[Field = LocalOutputOptions]
short =
type = IT
usage = 1 for parameter output, 1 for X-Y-Z coordinate output, and 1 for
high residual output
tooltip =
manpage = These three entries control the output of results for each local
alignment:
^ 1 to output the values of the parameters for each view or 0
^ not to;
^ 1 to output the X-Y-Z coordinates of fiducials or 0 not to;
^ and
^ 1 to output points with high residuals, or 0 not to
[SectionHeader = mappingOptions]
usage = MAPPING OPTIONS
manpage = MAPPING OPTIONS
^ These are obsolete options are for ultimate control of variable mapping.
[Field = RotMapping]
short =
type = IAM
usage = Rotation variable number for each view (if RotOption 2)
tooltip =
manpage = If RotOption is 2, this option must be used to enter a rotation
variable number for each view. These variable numbers can be completely
arbitrary, e.g. 1,1,1,3,3,3,5,5,5. The numbers are used to define block
grouping.
[Field = LocalRotMapping]
short =
type = IAM
usage = Local rotation variable number for each view (if LocalRotOption 2)
tooltip =
manpage = If LocalRotOption is 2, this option must be used to enter a local
rotation variable number for each view.
[Field = TiltMapping]
short =
type = IAM
usage = Tilt variable number for each view (if TiltOption 4)
tooltip =
manpage = If TiltOption is 2, this option must be used to enter a
tilt variable number for each view.
[Field = LocalTiltMapping]
short =
type = IAM
usage = Local tilt variable number for each view (if LocalTiltOption 4)
tooltip =
manpage = If LocalTiltOption is 4, this option must be used to enter a
local tilt variable number for each view.
[Field = MagMapping]
short =
type = IAM
usage = Magnification variable number for each view (if MagOption 2)
tooltip =
manpage = If MagOption is 2, this option must be used to enter a
magnification variable number for each view.
[Field = LocalMagMapping]
short =
type = IAM
usage = Local magnification variable number for each view (if LocalMagOption 2)
tooltip =
manpage = If LocalMagOption is 2, this option must be used to enter a
local magnification variable number for each view.
[Field = CompMapping]
short =
type = IAM
usage = Compression variable number for each view (if CompOption 2)
tooltip =
manpage = If CompOption is 2, this option must be used to enter a compression
variable number for each view.
[Field = XStretchMapping]
short =
type = IAM
usage = X stretch variable number for each view (if XStretchOption 2)
tooltip =
manpage = If XStretchOption is 2, this option must be used to enter an X
stretch variable number for each view.
[Field = LocalXStretchMapping]
short =
type = IAM
usage = Local X stretch variable number for each view (if
LocalXStretchOption 2)
tooltip =
manpage = If LocalXStretchOption is 2, this option must be used to enter a
local X stretch variable number for each view.
[Field = SkewMapping]
short =
type = IAM
usage = Skew variable number for each view (if SkewOption 2)
tooltip =
manpage = If SkewOption is 2, this option must be used to enter a skew
variable number for each view.
[Field = LocalSkewMapping]
short =
type = IAM
usage = Local skew variable number for each view (if LocalSkewOption 2)
tooltip =
manpage = If LocalSkewOption is 2, this option must be used to enter a local
skew variable number for each view.
[Field = XTiltMapping]
short =
type = IAM
usage = X-axis tilt variable number for each view (if XTiltOption 2)
tooltip =
manpage = If XTiltOption is 2, this option must be used to enter an X-axis
tilt variable number for each view.
[Field = LocalXTiltMapping]
short =
type = IAM
usage = Local X-axis tilt variable number for each view (if LocalXTiltOption 2)
tooltip =
manpage = If LocalXTiltOption is 2, this option must be used to enter a local
X-axis tilt variable number for each view.
[SectionHeader = UniversalOptions]
usage = UNIVERSAL OPTIONS
[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 =