selfalign

selfalign(1) General Commands Manual selfalign(1)
NAME
 selfalign - Realign model based on fits to trajectories
SYNOPSIS
 selfalign options root_name|input_file output_file
DESCRIPTION
 selfalign will refine the alignment of a model of fibers that progress
 through the Z-dimension, such as microtubules modeled through serial
 sections, using the trajectories in the model. This provides a way of
 smoothing a model without disrupting the spacings between fibers in a
 section, which would happen if trajectories were smoothed independently
 with mtsmooth. selfalign works by first running xfmodel to
 obtain transformations relating each section to the previous one (f
 transforms). The kind of transformation can be specified with the -t
 option, e.g., full linear, rotations and translations only, etc. If
 there are few fibers, it is appropriate to reduce the complexity of
 transformations being solved for. In addition, one can specify the
 range of sections in the model over which to solve for transformations,
 and thus exclude regions near the ends of the model that have few
 fibers. If sections are excluded at the start or end of the model,
 selfalign supplies transforms for those sections by replicating the
 first or last transform actually solved for, respectively. This pre-
 vents artifacts when local fits are made to the trends in the trans-
 forms. The f transforms are converted to g transforms using xftoxg,
 using fitting parameters that can be adjusted with the -l and -o
 options. The self-aligned model is produced by running imodtrans.
 The program can be run with either one or two arguments after the
 options. Use one argument to specify a root filename. The program
 then assumes that the input model is root_name.mod and generates an
 output model named root_name.selfmod. Alternatively, use two arguments
 to specify the full names of the input and output models. In this
 case, the root name for the other files is assumed to be the name of
 the input model with any extension removed.
OPTIONS
 Run selfalign with no arguments to get a usage statement listing the
 default values of the parameters.
 -s list
 Solve for transformations over the range of sections given in
 list. A single range (e.g., 3-32) will give best results. The
 default is to solve over the whole extent of the model.
 -l extent
 Do local fits to transformation parameters over the number of
 sections given in extent. This parameter is used in running
 xftoxg.
 -o order
 Set the polynomial order for the local fits to order. This
 parameter is also used in running xftoxg.
 -t type
 Specify the type of transformations to solve for; set type to 0
 for general linear transforms, 2 for translations only, 3 for
 rotations and translations, or 4 for magnifications, rotations
 and translations.
 -i file
 Specify the name of the image stack upon which the model was
 built. If no file is entered, the default is the root name of
 the model with extension .ali. If such an image file is not
 available, the program will extract the needed information about
 image dimensions from the header of the model, and assume that
 this will adequately represent the information that could be
 extracted from the image file header.
FILES
 In addition to the self-aligned model, the program creates files with
 the f transforms (root_name.selfxf) and the g transforms
 (root_name.selfxg). If any of the output files already exists a backup
 of the original is created with the ~ extension.
AUTHOR
 David Mastronarde <mast at colorado dot edu>
SEE ALSO
 xfmodel, xftoxg, imodtrans
IMOD 5.2.0 selfalign(1)