imodsetvalues(1)            General Commands Manual           imodsetvalues(1)

       imodsetvalues - store per point or per contour values in an IMOD model.

       imodsetvalues [options] -values values_file  input_model  output_model

       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

       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.

       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

       John Heumann  <heumannj at colorado dot edu>


IMOD                                4.10.22                   imodsetvalues(1)