imodjoin(1) General Commands Manual imodjoin(1)
NAME
imodjoin - Combine two or more IMOD models into one.
SYNOPSIS
imodjoin [options] model_1 [-o list] model_2 [[-o list] model_3 ...]
out_model
DESCRIPTION
Combines the contents of two or more models, or a subset of the objects
from them, into a single model. With no options, the program will pro-
duce a model with all of the objects from the first model, followed by
all of the objects from the second model, then all of the objects from
any additional models.
The program will transform models if necessary to bring them to a com-
mon coordinate system, using image reference information stored in the
model. The most common case requiring this is when the models have
last been loaded on different subsets of the same image file. The
default assumption is that the models were loaded on either the same
image file or image files with congruent coordinate systems. For exam-
ple, an image file produced by Trimvol or Rotatevol has its
header entries adjusted so that its coordinate system is congruent with
that of the original image file. Squeezevol also produces a file
with a congruent coordinate system. When joining models coming from
such files, the program will take all coordinate differences between
the models into account: shifts, rotations, and scaling. This is not
always appropriate, so the -d option is available to indicate that mod-
els came from different volumes. Some examples of different or non-
congruent volumes are tomograms from serial sections, single and dual-
axis tomograms of the same specimen, and two files of the same volume
in which Y and Z are flipped. In such cases, the program will simply
shift each model, if necessary, to undo the effects of being loaded
onto a subset of its respective image file; it will also scale all mod-
els to a common scale unless the -s option is given. The resulting
model will be given image reference information so that it will display
correctly on the volume that the first model came from, unless a spe-
cific image file is identified with the -i option, in which case the
reference information will match that image.
The program will give a warning when it does not find adequate image
reference information in the models. Despite these warnings, the join-
ing should work as long as the models are based on the same image
stack, or on image stacks with similar coordinate systems (e.g., iden-
tical pixel spacings and origins). The warnings could be avoided by
loading the model together with a relevant image file into 3dmod and
resaving the model.
OPTIONS
All options except for -o must be entered before the first input model;
-o may be entered before each input model.
-o list of objects
This option can be used before a model file to specify a list of
objects that should be taken from that file. Each list of
objects can consist of comma-separated ranges of numbers, for
example 1-3,6-9,13,15.
-r list of objects
This option can be used to replace the listed objects in the
first model with objects from the second model. In this case,
the -o option cannot be used for the first model; the output
model will have the same number and ordering of objects as the
first model, with the specified ones replaced. This option can
be used only with two input models. If no -o option is used for
the second model, the objects in the list for the first model
will be replaced by objects 1, 2, 3, etc. from the second model.
If the -o option is used for the second model, then each of the
objects in the replacement list for the first model will be
replaced by the corresponding object in the list for the second
model.
-c Change colors of the objects being added to the first model. If
objects are being added without replacement, then they will be
changed to the colors automatically assigned to new objects. If
objects are replacing ones in the first model, then they will be
given the same color as the respective objects that they are
replacing. Without this option, objects will retain their orig-
inal colors, which is especially annoying when there are just
one or two objects from each model.
-d Models are from different volumes rather than from the same vol-
ume or volumes with congruent coordinate systems (see above).
-i filename
With this option, the header information in the given image file
will be taken as the reference for all models, and the resulting
model will display correctly on this image file. Otherwise, the
first model is taken as the reference. This option implies -d.
-s Do not adjust for scale (pixel spacing) differences between mod-
els from different volumes. This option might be appropriate
either if the pixel size differences in the image file headers
do not accurately reflect different scalings between the images,
or if the scale differences are being handled separately, such
as by an alignment transformation.
-f Retain (or restore) the original Y-Z flipped state of each
model. Without this option, the program will put all models
into the same flipped state before joining. This option would
be appropriate if one model was built on a tomogram that was not
flipped (and thus is loaded into 3dmod with flipping) and
another model was built on a flipped tomogram (no flipping
needed in 3dmod).
-n Do not transform models at all. This option will prevent all of
the behavior described above.
AUTHORS
Jim Kremer and David Mastronarde
SEE ALSO
3dmod, imodextract
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.12.61 imodjoin(1)