imodsetvalues(1) General Commands Manual imodsetvalues(1)
NAME
imodsetvalues - store per point or per contour values in an IMOD model.
SYNOPSIS
imodsetvalues [options] -values values_file input_model output_model
DESCRIPTION
Store or modify per point or per contour values in an IMOD model, and
configure the views to display these values in pseudo-color. Input file
values-file specifies the (possibly floating point) values to be stored
and their desired location in the model. Three different modes of oper-
ation are supported, depending on the number of columns in the values
file.
1) If only a single numeric column is present, that column represents
the values to be stored. In this case the number of lines / entries in
the values file, must exactly match the total number of points in the
model. Values will be stored sequentially from the first point in the
first contour of the first object, to the last point in the last con-
tour of the last object. Similar behavior can also be obtained using a
selected column from a multi-column values file using the "skip" option
described below.
2) If exactly 3 comma-separated columns are present, the first two col-
umns must be integer values and will be taken as 1-based object and
contour numbers, respectively, while the third (possibly floating
point) column, represents the value to be stored for the specified
object / contour.
3) Finally, if exactly 4 comma-separated columns are present, the first
3 columns will be interpreted as 1-based object, contour, and point
numbers, and the final column as the value to be stored for the speci-
fied object / contour / point.
Each object modified by imodsetvalues will automatically have its mini-
mum and maximum values updated to reflect the range of values stored in
that object. The resulting default pseudo-color display will stretch
the color map used from <min> to <max> independently for each object.
Intensity rather than pseudo-color display is also possible, but must
be manually selected in 3dmod. Additionally, user-defined color maps
can also be specified using the -cm option to 3dmod.
Manual specification of the pseudo-coloring range, rather than auto-
scaling is desirable in some cases. (For example, you may wish to dis-
play multiple objects or contours on a common scale with known limits).
This can be accomplished by specifying an optional min/max file using
the -minMax (or equivalent -MinMaxFile) option. Each line of the
min/max file must contain 3 comma-separated values: an integer object
number, followed by (possibly floating point) minimum and maximum val-
ues for that object. Minimum / maximum values can be specified for any
valid object, not just those effected by the values file. In fact, when
a min/max file is specified (and only then), the values file can
optionally be empty.
OPTIONS
Imodsetvalues 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.
-values (-v) OR -ValueFile File name
Input file containing values to be stored in the model.
-input (-i) OR -InputFile File name
Input model file to clone. If this option is not entered, the
first non-option argument will be used for the input file.
-output (-o) OR -OutputFile File name
Name to give the output model. If this option is not entered,
the second non-option argument will be used.
-column (-c) OR -ColumnNumber Integer
Specify a particular column in a multi-column values file which
contains the values to associate with each point in the model.
The result is equivalent to having constructed a single-column
values file containing only these entries.
-minMax (-m) OR -MinMaxFile File name
Input file giving the minimum and maximum values for pseudo-col-
oring specific objects.
-skip (-s) OR -SkipLines Integer
Number of lines to ignore at beginning of the values file. Use-
ful for skipping over header / comment lines.
-help (-h) OR -usage
Print help output
AUTHOR
John Heumann <heumannj at colorado dot edu>
SEE ALSO
3dmod
IMOD 4.11.0 imodsetvalues(1)