imodchopconts(1) General Commands Manual imodchopconts(1)
NAME
imodchopconts - Chop up contours in IMOD model based on length or color
SYNOPSIS
imodchopconts [options] input_model output_model
DESCRIPTION
This program will chop contours into pieces in two different ways. In
one mode, it will produce contours with equal numbers of points, and
with a specified amount of overlap between the pieces. This mode of
operation has two main uses: 1) Breaking up the contours produced by
patch tracking with Tiltxcorr into overlapping pieces, which can
give a better fit in Tiltalign. 2) Splitting up scattered point
contours so that there is one point per contour. However, it could
also be used to split up contours into other lengths, with or without
overlap. In its other mode of operation, the program will break con-
tours apart at fine-grained color changes between points, and put the
new contours into separate surfaces or separate objects. Whole con-
tours that are a different color because of a fine-grained contour
color property will also be sorted into different surfaces or objects.
The color can thus be changed at the surface or object level for all
contour segments of the same color, which is otherwise difficult.
Breaking contours apart in this way also allows quantitative analysis
to be done on separately colored segments by programs that do not take
account of fine-grained color changes.
Specifying positive numbers for the -length and -overlap options here
has exactly the same effect as providing those two numbers to the
-length option of Tiltxcorr.
When doing length-base chopping, fine grained information at the point
level will be preserved in the newly created contours. Fine-grained
information for an individual contour will be transferred to each of
the new contours derived from it. Surface-level fine-grained informa-
tion will also be preserved unless the -surfaces option is given.
When doing color-based chopping, all line segments will be appear with
their original colors for open or closed contour objects. This
requires a duplication of points at the contour endpoints. However,
there is no such duplication of points for scattered point objects.
Fine grained information will be preserved during color-based chopping
to the extent that it makes sense. Specifically, fine-grained proper-
ties at all three levels (point, contour, or surface) will be preserved
in the new contours, except for color. The color is not lost, but is
incorporated into the surface or object to which the derived contours
are assigned and is thus removed as a fine-grained property. Contour
level fine-grained properties are transferred from the original contour
to each contour derived from it. Surface level information is trans-
ferred differently depending on whether contours are assigned to sur-
faces or objects. In the latter case, the derived contours have the
same surface number as the original one, and all non-color surface
information is copied to each new object. When derived contours are
assigned to new surfaces, surface information that applies to the orig-
inal contour is duplicated for the new surfaces.
If for some reason your model has surface-level fine-grained data, it
will probably be preferable to split contours into new objects, to
avoid a proliferation of surfaces.
OPTIONS
Imodchopconts uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-input (-i) OR -InputModel File name
Name of input model file. If this option is not entered, the
first non-option argument will be taken as the input file.
-output (-ou) OR -OutputModel File name
Name of output model file. If this option is not entered, the
second non-option argument will be taken as the output file.
-length (-l) OR -LengthOfPieces Integer
The length of the new contours, i.e., the number of points to
put in each. The actual length can be affected by the entry for
-overlap. If -1 is entered and the -number option is not, the
length will be the default for breaking up contours from patch
tracking in Etomo, which is the Z size in the model divided by
5, but no less than 16. The default if neither this option nor
-number is entered is to leave contours as they are. Unless
this option is entered with a -1, it cannot be entered with
-number.
-overlap (-ov) OR -MinimumOverlap Integer
The minimum number of points overlapping between pieces. If the
minimum overlap is 0 or positive, then all new contours will be
given the same number of points, but both the overlap and the
number of contours will vary depending on the length of the
original contour. Enter -1 to enforce zero overlap between con-
tours and have the contours broken into variable lengths, typi-
cally less than the specified length. The default is 4, unless
1 is entered for -length, in which case the default is 0.
-number (-n) OR -NumberOfPieces Integer
This option provides an alternative way to specify how to chop
up contours. The maximum number of points in any contour to be
processed will be divided by the given number to determine the
number of points to require in each new contour. This option
cannot be entered if -length is entered with a value greater
than 0.
-surfaces (-s) OR -AssignSurfaces
Give each new contour a surface number equal to the number of
the contour from which it came. This will replace any existing
surface numbers and invalidate any fine-grained information that
applies to surfaces.
-colors (-c) OR -BreakAtColors Integer
Break contours at fine-grained color changes, assigning them to
new surfaces or new objects with the appropriate color if 1 or 2
is entered, respectively. None of the options related to
length-based chopping (-length, -overlap, -number, or -surfaces)
may be entered with this option. See above for details.
-objects (-ob) OR -ObjectsToDo List of integer ranges
List of objects to chop up, a comma-separate list of ranges.
The default is to chop up all objects.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
AUTHOR
David Mastronarde
SEE ALSO
tiltxcorr
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 imodchopconts(1)