finddistort(1) General Commands Manual finddistort(1)
NAME
finddistort - Solves for image distortion field from overlapping images
SYNOPSIS
finddistort [options] input_file output_rootname
DESCRIPTION
Finddistort analyzes overlapping images and solves for the underlying
image distortion field. The basis for the analysis is the fact that
after two overlapping images are shifted into best registration, the
remaining image displacement at a particular point in the overlap zone
is the difference between the distortion vectors at two locations in
the original images. The optimal input for this analysis is a set of 4
pairs of overlapping images. Each pair would overlap over a little
more than 50% of their area. The two paired images would be displaced
from each other horizontally, vertically, and on 45 and 135 degree
diagonals for the 4 kinds of pairs. With this arrangement, the differ-
ent pairs provide largely independent rather than redundant informa-
tion, and the amount of data about image displacements is about twice
as numerous as the number of vectors of the image distortion field to
be solved for; thus a robust solution can be obtained.
The program operates as follows. First, each pair of images is cross-
correlated with a large amount of padding to find the overall displace-
ment. This is done by running Tiltxcorr. Next, this overall dis-
placement is applied to align the two images where they overlap, then
the local displacements are found at a grid of locations in the overlap
zone, using the same subroutines that Blendmont uses to find "edge
functions". The spacing of this grid is specified by the GridSpacing
option. Linear equations are set up relating data interpolated from
this grid (at a spacing set by the DataSpacing option) to the unknown
vectors of the underlying distortion field. These unknowns are located
on a grid at yet another spacing (set by the FieldSpacing option), and
making this spacing larger than the data spacing makes the equations
even more overdetermined. The program solves these equations to find
an initial distortion field.
Once there is a distortion field, the procedure is iterated, except
that the images are undistorted before being correlated to find the
overall displacement. However, this procedure will not converge to a
unique solution unless the distortion field is modified by another
operation at each step, because it is possible to change the overall
displacement between overlapping images and stretch the distortion
field to compensate. Thus, every time a field is solved for, any net
stretch in the field is removed to preduce a stretch-free distortion
field. With this step, the iterations converge to a stable solution
for the stretch-free distortion field. This distortion field is output
to a file rootname.nosidf after each iteration.
The stretch in the distortion field can be determined from the trans-
formation needed to align two images of the same field rotated by an
angle near 90 degrees. When such a transformation is supplied, the
program computes the implied stretch in the projection process, and
then introduces this stretch into the distortion field. Whether or not
this transformation is given, the final field is output into root-
name.idf.
Other temporary files produced are: rootname.xcxf with the shifts for
one image pair, output by Tiltxcorr; rootname.tmpxf with root-
name.rawxf with the initial shifts between paired images; rootname.udxf
with the shifts between undistorted imaged; rootname.udst with the
undistorted images.
OPTIONS
Finddistort uses the PIP package for input exclusively (see the manual
page for pip). The following options can be specified either as
command line arguments (with the -) or one per line in a command file
or parameter file (without the -). Options can be abbreviated to
unique letters; the currently valid abbreviations for short names are
shown in parentheses.
-input (-inp) OR -InputFile File name
Input image file with distortion pairs. If this option is not
entered, the first non-option argument will be taken as the
input file name.
-output (-o) OR -OutputRoot File name
Root name for output files. If this option is not entered, the
second non-option argument will be used as the root name.
-pairs (-pai) OR -PairsToAnalyze List of integer ranges
List of images to analyze in pairs; for example 0-7 if sections
0 and 1, 2 and 3, 4 and 5, and 6 and 7 are all image pairs. The
default is to assume that all images in the file form successive
pairs. Sections are numbered from 0.
-binning (-bi) OR -ImageBinning Integer
Binning of images on the CCD camera (default 2)
-field (-f) OR -FieldSpacing Integer
Pixel spacing for output distortion field (default 40)
-data (-d) OR -DataSpacing Integer
Pixel spacing for data used to solve linear equations for the
distortion field. This spacing should be about half of the
spacing for the output field. The default is 20.
-grid (-g) OR -GridSpacing Integer
Pixel spacing for grid on which displacements will be measured
in the overlap zones between paired images (default 16).
-box (-bo) OR -BoxSize Integer
Size of box used to measure local displacements. Boxes of this
size will be correlated between the two images at every position
on the grid. The default is 24. This value should be increased
if the solution is noisy.
-indent (-ind) OR -GridIndent Integer
Amount to indent the boxes in the grid of displacements from the
edge of the overlap zone. The default is 4 pixels; this vakue
can be dropped to 2 for larger than default boxes.
-iterations (-it) OR -Iterations Integer
Maximum number of iterations when solving equations
-usexf (-use) OR -UseOldTransforms
Use existing transforms instead of running Tiltxcorr on the
first iteration; these transforms are stored in the file root-
name.rawxf when Tiltxcorr is run on the first iteration.
-strfile (-s) OR -StretchFile File name
File with transformation that aligns two 90-degree rotated
images of the same area. This transformation is used to deter-
mine the absolute stretch in the distortion field.
-patch (-pat) OR -PatchOutput
Output a patch file to convert to a model with patch2imod. The
patch file will be named rootname.patch.
-coverage (-c) OR -CoverageImage File name
Name of file in which to place an image representing the amount
of data available for solving each vector. This is image is
based on the sum of the coefficients for each distortion vec-
tors, normalized so that the mean sum will equal the ratio of
total measurements to unknowns (rows to columns in the data
matrix). To get a true representation of the amount of nonre-
dundant coverage of each field position, use -data to set the
data spacing the same as the field spacing.
-redirect (-r) OR -RedirectOutput Text string
String for redirecting output from Tiltxcorr and Newstack. The
default is "> /dev/null", which will not work in Windows. A
valid Windows path must be entered; "> xcorr.tmp" would work.
-multr (-m) OR -SolveWithMultr
Use matrix inversion instead of iterative method to solve equa-
tions.
-param (-par) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output.
-StandardInput
Read parameter entries from standard input.
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 finddistort(1)