imodtrans(1) imodtrans(1)
NAME
imodtrans - Transform an IMOD model file.
SYNOPSIS
imodtrans [options] <input model> <output model>
DESCRIPTION
Applies transformations to an IMOD model and copies the result to a new
IMOD model. The transformations can be specified in three different
ways: 1) as translations, rotations, and scaling factors; 2) as a list
of 2-D transformations in a file, one for each section, such as are
produced by Midas and Xfalign; 3) as a single 3-D transformation
in a file, such as are produced by Solvematch. When the transforma-
tion is specified by individual components, they are applied in the
order that they are entered, and any option can be entered more than
once. If you want your rotations to match those applied by the Slicer
in 3dmod or by Rotatevol, specify rotations around Z, then Y,
then X.
If you plan to display the transformed model on a different image file
from the one that it was built on, the program will not be able to
translate the model to the correct location unless it knows the dimen-
sions of the other image file. If these dimensions differ from those
of the original image file, enter them with the -n option.
For 3-D transformations, however they are specified, all contour points
are transformed, as well as all mesh points, surface normals, and clip-
ping planes. The mesh is transformed because contours that have been
rotated out of the X/Y plane cannot currently be remeshed. For 2-D
transformations, only contour points are transformed, so clipping
planes are not preserved and the model will have to be remeshed. How-
ever, if a single 2D transformation is applied to the whole model it is
converted to a 3D transformation and the entire model is properly
transformed.
The program can also manipulate the flipped state of the model in Y and
Z either by actually flipping the Y and Z coordinates, or by simply
toggling the flag that indicates whether the model was loaded on data
that were flipped in 3dmod. Either way may be used after flipping a
volume with "clip flipyz" to change a model built on the unflipped vol-
ume so that it will load onto the flipped volume. In addition, the
model can be transformed to match a particular image file, just the
same as if it were loaded onto that file in 3dmod. The order of opera-
tions is: flipping, then transforming to match an image file, then
transforming either via transformations in a file or via the entered
options.
Options
-tx <value>
-ty <value>
-tz <value>
The -tx, -ty and -tz options can be used to translate the model
in the particular direction by the given floating point value,
in pixels.
-sx <value>
-sy <value>
-sz <value>
The -sx, -sy and -sz options can be used to scale the model in
the particular dimension by the given floating point value.
-rx <value>
-ry <value>
-rz <value>
The -rx, -ry and -rz options can be used to rotate the model
about the particular axis by the given value in degrees.
-2 <transform file>
Transform the model in 2-D sections using the given transform
file as input. One line is expected per section, and slices at
Z values greater than the number of lines will not be trans-
formed, unless the -l option is given to apply one transform to
the whole model. This option is useful for transforming a model
to match an image stack that has been aligned with Xfalign or
Midas. This option cannot be entered with the translation,
scaling, or rotation options, or with -3.
-l <line #>
Transform the whole model with the single 2D transformation at
the given line number in the transform file entered with -2.
Lines are numbered from 0.
-3 <transform file>
Transform the model with the single 3-D transformation in the
given file. The format of the file is to have 3 lines, each
with 4 numbers, the coefficients for multiplying the old X, Y,
and Z coordinates and a translation value. The first, second,
and third lines are for computing new X, Y, and Z coordinates,
respectively. This option cannot be entered with the transla-
tion, scaling, or rotation options, or with -2.
-n <NX,NY,NZ>
Specify the dimensions of the image file on which the model is
to be displayed, if these dimensions are not the same as for the
image file on which the model was originally built. This entry
is needed to have the model translated to the correct location
when image file sizes differ.
-z Apply Z-scaling to the model, using the Z-scale from the model
header, before transforming the model. The transformed model
will then be descaled in Z so that it will display correctly
with the same Z-scale. This option would be needed to retain
the shape of a Z-scaled model, but it would probably prevent it
from matching a transformed image file.
-f If the model was last displayed on images loaded into 3dmod with
Y and Z flipped, use this option to apply the transformation to
the flipped coordinates. The default is to apply the transfor-
mation to native, unflipped coordinates, which will work with
transformations obtained from Solvematch.
-i <image file>
Transform the model coordinates as if the model were being
loaded into 3dmod together with the given image file.
-Y Exchange Y and Z coordinates in the model file, without changing
the flag indicating the model's flip state.
-T Toggle the flag indicating the model's flip state, without actu-
ally flipping the data.
AUTHOR
Jim Kremer and David Mastronarde
SEE ALSO
midas, xfalign, solvematch, matchvol, rotatevol,
clip, 3dmod
BUGS
Email bug reports to mast at colorado dot edu.
BL3DEMC 3.11.2 imodtrans(1)