[Field = AImageFile]
short = aimage
type = FN
usage = Input image file with reference image to be aligned to
tooltip =
manpage = Input image file with reference image to be aligned to. If this
option is not entered, the first non-option argument will be used for this
input file.
[Field = BImageFile]
short = bimage
type = FN
usage = Name of image file with image to align to reference
tooltip =
manpage = Name of image file with image to align to reference. If this option
is not entered, the second non-option argument will be used for this input
file.
[Field = OutputFile]
short = output
type = FN
usage = Output file for transformation
tooltip =
manpage = Output file for transformation. If this
option is not entered, the third non-option argument will be used for this
output file.
[Field = InitialTransformFile]
short = initial
type = FN
usage = Input file with transformation to start search with
tooltip =
manpage = Input file with transformation to start search with. The final
reported transformation will include the initial one rather than being
incremental to it.
[Field = UseTransformLine]
short = useline
type = I
usage = Line number of initial transform in file, numbered from 0 (default 0)
tooltip =
manpage =
[Field = SectionsToUse]
short = sections
type = IP
usage = Sections to use from the first and second file (default 0,0)
tooltip =
manpage =
[Field = VariablesToSearch]
short = variables
type = I
usage = Number of variables to search, or 0 to search for formal parameters
tooltip =
manpage = Number of semi-natural variables to search, or 0 to search for formal
parameters. See above for the meaning and order of the variables
selected by this option.
[Field = LimitsOnSearch]
short = limits
type = FA
usage = Limits for each of the variables being searched
tooltip =
manpage = Limits for each of the variables being searched. Each number
entered specifies the maximum amount that the respective variable can change
from its initial value. Enter a 0 to avoid limiting a parameter. If the
search is being done on formal parameters, then only the first two (shift in X
and Y) can be limited, so only 1 or 2 values can be entered. If the search is
on semi-natural parameters, then you can enter more or fewer values than the
number of variables being searched. Extra values are ignored, missing values
are assumed to be zero.
[Field = EdgeToIgnore]
short = edge
type = F
usage = Fraction or number of pixels to ignore on edges of image
tooltip =
manpage = Fraction or number of pixels to ignore on edges of image. Enter a
value less than 0.5 for a fraction, or a value greater than 1 for a number of
pixels. The default is 0.05.
[Field = XMinAndMax]
short = xminmax
type = IP
usage = Starting and ending coordinates to analyze in X (overrides -edge)
tooltip =
manpage = Starting and ending coordinates to analyze in X (numbered from 1).
This entry overrides the X coordinates implied by the -edge entry or default.
[Field = YMinAndMax]
short = yminmax
type = IP
usage = Starting and ending coordinates to analyze in Y (overrides -edge)
tooltip =
manpage = Starting and ending coordinates to analyze in Y (numbered from 1).
This entry overrides the Y coordinates implied by the -edge entry or default.
[Field = BinningToApply]
short = binning
type = I
usage = Binning to apply to images (default 2)
tooltip =
manpage = Binning to apply to the images. The default is 2.
[Field = AntialiasFilter]
short = antialias
type = I
usage = Type of antialiasing filter to reduce images with instead of binning
tooltip =
manpage = Type of antialiasing filter to use for image reduction instead of
binning. Antialiasing becomes important when the images are highly reduced in size.
Ordinary binning reduces aliasing, but not as much as these filters
do. This option makes any filtering be applied after the image reduction
(thus it implies the -after option). As in Newstack(1), the available types
here are:
^ 2: Blackman - fast but not as good at antialiasing as slower
^ filters
^ 3: Triangle - fast but smooths more than Blackman
^ 4: Mitchell - good at antialiasing, smooths a bit
^ 5: Lanczos 2 lobes - good at antialiasing, less smoothing
^ than Mitchell
^ 6: Lanczos 3 lobes - slower, even less smoothing but more
^ risk of ringing
^ -1: Use the default filter, currently Lanczos 2
[Field = FilterSigma1]
short = sig1
type = F
usage = Sigma for low-frequency inverted Gaussian filter
tooltip =
manpage = Sigma value to filter low frequencies in both images with a
curve that is an inverted Gaussian. This filter is 0 at 0 frequency and decays
up to 1 with the given sigma value. However, if a negative value of radius1
is entered, this filter will be zero from 0 to |radius1| then decay up to 1.
[Field = FilterRadius1]
short = rad1
type = F
usage = Left cutoff radius for Gaussian filter
tooltip =
manpage = Low spatial frequencies in both images will be attenuated
by a Gaussian curve that is 1 at this cutoff radius and falls off below this
radius with a standard deviation specified by FilterSigma2. Spatial
frequency units range from 0 to 0.5. Use FilterSigma1 instead of this entry
for more predictable attenuation of low frequencies.
[Field = FilterRadius2]
short = rad2
type = F
usage = Right cutoff radius for Gaussian filter
tooltip = High frequency cutoff radius for Gaussian filter
manpage = High spatial frequencies in both images will be attenuated
by a Gaussian curve that is 1 at this cutoff radius and falls off above this
radius with a standard deviation specified by FilterSigma2.
[Field = FilterSigma2]
short = sig2
type = F
usage = Sigma for Gaussian rolloff below radius1 and above radius2
tooltip = Sigma for Gaussian rolloff below low frequency cutoff and above
high frequency cutoff
manpage = Sigma value for the Gaussian rolloff below and above the cutoff
frequencies specified by FilterRadius1 and FilterRadius2
[Field = FilterAfterBinning]
short = after
type = B
usage = Apply the Fourier filter after binning data
tooltip =
manpage = Apply the Fourier filter after binning data. This will be much
faster, but it may introduce aliased noise from the higher frequencies in the
original data unless antialiased reduction is used. The radius and sigma
values represent frequencies in the binned image, not the original image.
If antialias reduction is not used, the default is to filter before binning,
in which case the high frequencies can be removed before binning; if
antialiasing is used, the filtering always happens after reduction and this
option is redundant.
[Field = SobelFilter]
short = sobel
type = B
usage = Apply edge-detecting Sobel filter to images
tooltip =
manpage = Apply edge-detecting Sobel filter to both images. This filter will
be applied after binning and filtering if any.
[Field = FloatOption]
short = float
type = I
usage = 0 to float to range, 1 to mean and SD, -1 not to float intensities
tooltip =
manpage = 0 to float images to have the same range, 1 to float them to have
the same mean and standard deviation, or -1 to leave intensities alone. Only
pixels within the range being analyzed will be considered when determining the
scaling. The default is 1.
[Field = CorrelationCoefficient]
short = ccc
type = B
usage = Compute correlation coefficient instead of image difference
tooltip =
manpage = Compute the standard cross-correlation coefficient instead of
difference between images. The difference measure that is minimized will
be 1 minus the CCC, but the CCC itself is printed in the trace and final
output. It takes < 5% more time to compute the CCC.
[Field = LocalPatchSize]
short = local
type = I
usage = Size of square subareas within which to compute SD of difference or CCC
tooltip =
manpage = Size of square subareas (patches) within which to compute a measure
of image difference, in pixels before binning, if any. The image will be
divided into patches of this size and the measure will be computed separately
within each patch; then a weighted average will be formed, weighted by the
number of pixels actually available for comparison within each patch. If
image difference is being computed, the measure will be the standard deviation
of the difference; otherwise the correlation coefficient is computed. Patches
with less than half the full number of pixels will be pooled with the nearest
patches containing enough pixels. This option should prevent the need for low
frequency filtering, which would increase execution time by roughly 10%.
Patch sizes on the order of 1/20 to 1/10 of the image size should be effective.
[Field = LinearInterpolation]
short = linear
type = B
usage = Use linear interpolation instead of nearest pixel
tooltip =
manpage = Use linear interpolation instead of nearest pixel interpolation when
computing image differences or correlation coefficients.
[Field = DistanceMeasure]
short = distance
type = B
usage = Use distance instead of difference or correlation measure
tooltip =
manpage =
[Field = NearestDistance]
short = near
type = I
usage = Distance to search to eliminate redundant points, 0 not to
tooltip =
manpage = Distance to search to eliminate redundant points, or 0 not to
search, when using the distance measure. The default is 0 for # of pixels <
240*180, 1 if # of pixels is between 240*180 and 480*360, 2 if # of pixels >
480*360.
[Field = RadiusToSearch]
short = radius
type = F
usage = Radius to search for matching pixels
tooltip =
manpage = Radius to search for matching pixels when using the distance
measure. The default is 4 if binning by 2, or 5 if not.
[Field = DensityDifference]
short = density
type = F
usage = Maximum density difference for match as a fraction of the range
tooltip =
manpage = Maximum density difference that constitutes a match when using the
distance measure, as a fraction of the density range. The default is 0.05.
[Field = PercentileRanges]
short = percent
type = FA
usage = Lower and upper limits of percentile ranges to match
tooltip =
manpage = Lower and upper limits of percentile ranges to match. The default
is to have two ranges, i.e., 0,8,92,100, for images less than 320*240, scaling
down to 5% ranges as image size increases from 320*240 to 640*480.
[Field = CoarseTolerances]
short = coarse
type = FP
usage = Fractional tolerances in difference and parameters for initial search
tooltip =
manpage = Fractional tolerances in difference and parameters for the initial
search. Enter 0,0 to skip the initial search. The default values are 0.005
and 0.2 of the basic step size.
[Field = FinalTolerances]
short = final
type = FP
usage = Fractional tolerances in difference and parameters for final search
tooltip =
manpage = Fractional tolerances in difference and parameters for the final or
only search. The default values are 0.0005 and 0.02 of the basic step size,
or 0.001 and 0.04 for images no bigger than 128 by 128.
[Field = StepSizeFactor]
short = step
type = F
usage = Factor for initial step size (default 2)
tooltip =
manpage = Factor to multiply basic step size by to get initial step size. The
default is 2.
[Field = TraceOutput]
short = trace
type = I
usage = 1 for output at each step, 2 for output at new minima
tooltip =
manpage =
[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 =