Version = 1.0
Pip = 1
[Field = InputFile]
short = in
type = FN
usage = Input model filename
tooltip =
manpage = Name of input model file. If it is not entered with this option it
must be entered with the first non-option argument.
[Field = OutputFile]
type = FN
usage = Output model filename
tooltip =
manpage = Name of output model file. If it is not entered with this option it
must be entered with the second non-option argument.
[Field = WindowLength]
short = wl
type = F
usage = Window length over which to fit circle
tooltip =
manpage = Length in pixels over which to fit a circle to the contour data
around a point. The default is the sum of the lower and upper radius
criteria (i.e., the mean diameter). The radius will not be determined in
contours less than this length for closed contour objects, or less than half
this length for open contour objects. In the latter case, the window will be
reduced for fitting to points near the ends of the contour.
[Field = ZRangeToFit]
short = zr
type = F
usage = Range of contours in Z to include for fitting to a sphere
tooltip =
manpage = Range of contours in Z to include for fitting to a sphere. The
value should specify the actual distance in Z after Z-scaling, if any.
The default is 0 to fit just one contour at a time to a circle.
[Field = CylinderSearchAngle]
short = cy
type = F
usage = Angular increment for searching for best-fitting cylinder
tooltip =
manpage = If this option is entered, points will be fit to a cylinder instead
of a sphere by doing an exhaustive search of all possible orientations. The
value entered is the angular increment for this search. Increments of 5 to 10
degrees are useful. Computation time will increase inversely with the square
of this increment. A value of 10 is recommended for initial testing, and a
value of 5 for final computations.
[Field = RadiusCriterion]
short = rc
type = FP
usage = Lower and upper criteria for radius of curvature
tooltip =
manpage = Lower and upper criteria for radius of curvature. When the radius
at a point is within this range, it will be encoded into the model.
[Field = FitCriterion]
short = fc
type = F
usage = Criterion for RMS error of circle fit (default 0)
tooltip =
manpage = Criterion for root mean squared error of the local fit to a circle.
If a non-zero value is entered, then the RMS error must be less than the given
value for a radius of curvature to be encoded at that point. With the default
value of 0, the curvature will be encoded regardless of the error of the fit.
[Field = ObjectsToDo]
short = ob
type = LI
usage = List of objects to encode
tooltip =
manpage =
[Field = RotateToXYPlane]
short = ro
type = B
usage = Rotate out-of-plane contours into X/Y plane
tooltip =
manpage = Rotate contours that are not all in one X/Y plane into the
best-fitting X/Y plane. Circles will be fit to the rotated contour. This
option cannot be used with the -zr option for spherical fitting.
[Field = StoreValues]
short = st
type = B
usage = Store radius of curvature values in the model
tooltip =
manpage = Store the radius of curvature values directly in the model. They
can then be visualized as intensity variations or in false color by activating
the option to "Show stored values" in the Values panel of the model view
Object Edit window of 3dmod. This option allows dynamic adjustment of the
displayed colors. These radius values will be scaled by the pixel size
defined in the model, unlike all other radius values, which are in pixels.
[Field = KappaValues]
short = kappa
type = B
usage = Store curvature values (1/radius) in the model
tooltip =
manpage = Store curvature values, which are the inverse of the radius of
curvature, in the model. This curvature is commonly referred to as kappa.
To keep values from becoming too small, they will be multiplied by 1000 if
the pixel size is greater than 0.05. Thus, for typical pixel sizes in
nanometers, the curvatures will be in reciprocal microns.
This measure could be advantageous if you are interested in seeing the
values for regions with little or no curvature while still seeing distinctions
among regions with moderate curvature. The curvature value
goes to zero, while radius of curvature becomes very large and compresses the
dynamic range.
[Field = PointSize]
short = ps
type = B
usage = Use spherical point size to encode radius of curvature
tooltip =
manpage = Use spherical point size to encode radius of curvature. Each point
that meets
the criterion will be given a point size equal to the radius of curvature;
other points will have individual point sizes set to 0.
[Field = SymbolZoom]
short = sy
type = F
usage = Use circular symbols to encode radius with given zoom factor
tooltip =
manpage = Use circular symbols to encode radius of curvature, where the
circles will have the right size when the image is displayed with the given
zoom factor.
[Field = Color]
short = co
type = ITM
usage = Color to set for points meeting criteria (r,g,b between 0 and 255)
tooltip =
manpage = Use this entry to specify one or more colors to change points to
when their radius of curvature meets the criteria. Enter r,g,b values
between 0 and 255. When multiple colors are entered, the behavior is
controlled by the -di option.
[Field = DivideRange]
short = di
type = B
usage = Subdivide radius range to use all colors entered
tooltip =
manpage = When multiple colors are entered, by default they will be
applied to successive objects being analyzed. If this option is
entered, then the range of radii between the low and high criterion will be
subdivided by the number of colors, and points within each subrange will be
assigned to a different color.
[Field = UsePalette]
short = pa
type = FN
usage = Use false color palette (follow with s, i, or filename)
tooltip =
manpage = Use a 256-color false color palette for the colors. Enter a filename
to read a color table from a file, or "s", "standard", or any abbreviation
thereof for the standard palette from 3dmod, or "i", "inverted", or any
abbreviation thereof for an inverted palette from 3dmod.
This option will automatically subdivide the radius range into 256 levels.
A color table file can have one of two forms. One form starts with a line
with 256, then has 256 lines with red, green, and blue values from 0-255.
The other form starts with the number of lines to follow; then each following
line has a red, green, and blue value (0-255) plus an arbitrary integer
indicating the relative location of that value along the 256-color range.
These location values must be in order. If the colors being specified are to
be equally spaced, the location values can simply be sequential values.
[Field = SampleSpacing]
short = sa
type = F
usage = Spacing of sample points along contour for fitting (default 2)
tooltip =
manpage =
[Field = MeanStored]
short = me
type = I
usage = 1 or 2 for mean of values stored for each object or contour
tooltip =
manpage = Use this option to get an output of the mean value stored in the
model for each object (1) or for each contour (2).
[Field = Verbose]
short = ve
type = B
usage = Verbose output for testing or seeing mean errors
tooltip =
manpage = The verbose output will show the number of points being fit, the
center and radius, and the root mean squared error for each point being fit.
It could be useful for getting a sense of the RMS errors.
[Field = TestCircleFits]
short = tc
type = B
usage = Test circle fitting
tooltip =
manpage = Test circle fitting by fitting a circle to each contour in object 1
and putting a point with the given location and radius in a new object.
[Field = TestSphereFits]
short = ts
type = IP
usage = Test sphere fits at given contour and point #
tooltip =
manpage = Test sphere fitting by making a new object with the points being
fit to and the fitted sphere for the given contour and point number. If
cylinder fitting is being done instead, 3 spheres will be shown along the axis
of the fitted cyclinder, and the results for each search angle will be
printed. If the -ve option is given, the program will also output the
projection points at each search angle.
[Field = SignedValues]
short = si
type = CH
usage = Store radii / curvatures as signed values
tooltip =
manpage = If "+", radii and curvatures will be stored as positive values
when the contour follows a locally clockwise path as viewed from the
+z axis, and negative for counterclockwise. If "-", these signs will be
reversed. SignedValues are not allowed in combination with ZRangeToFit (-zr)
or CylinderSearchAngles (-cy) .
[Field = usage]
short = help
type = B
usage = Print help output
tooltip =
manpage =