model2point(1) General Commands Manual model2point(1)
NAME
model2point - converts model file to point file
SYNOPSIS
model2point [options] model_file point_file
DESCRIPTION
Model2point will convert an IMOD or WIMP model file to a list of points
with integer or floating point coordinates. Each point will be written
on a separate line, and the coordinates may be written either with no
information about which object or contour the point came from, or with
contour numbers, or with object numbers.
Model2point and the companion program, Point2model, provide a more
simple, but less versatile, way of converting data from and to an IMOD
model than the Ascii format that can be output by Imodinfo.
Prior to IMOD 4.10.35, Model2point put out integer coordinates by
default, but it now puts out floating point values by default. Thus,
the -float option is no longer needed, unless the environment variable
MODEL2POINT_INTEGERS is set to revert to the old behavior.
OPTIONS
Model2point uses the PIP package for input (see the manual page for
pip). The following options can be specified either as command line
arguments (with the -) or one per line in a command file or parameter
file (without the -). Options can be abbreviated to unique letters;
the currently valid abbreviations for short names are shown in paren-
theses.
-input (-inp) OR -InputFile File name
Input model file. If this option is not entered, the first non-
option argument will be used for the input file.
-output (-ou) OR -OutputFile File name
Output text file for points. If this option is not entered, the
second non-option argument will be used for the output file.
-float (-fl) OR -FloatingPoint
Output model coordinates as floating point; otherwise the near-
est integer value is output. Floating point output is the
default unless the environment variable MODEL2POINT_INTEGERS is
set to any value. This entry is still useful for overriding the
environment variable setting.
-integer (-int) OR -IntegerOutput
Output model coordinates by taking the nearest integer instead
of outputting floating point numbers, which is the default
behavior. This option cannot be entered with -float.
-scaled (-s) OR -ScaledCoordinates
Output coordinates in the model coordinate system, scaled by the
original image pixel size in Angstroms and offset by origin val-
ues. The default is to output index coordinates corresponding
to the pixel coordinates in the image.
-object (-ob) OR -ObjectAndContour
Output object and contour numbers for each point (numbered from
1)
-contour (-c) OR -Contour
Output contour number for each point (numbered from 1)
-zero (-ze) OR -NumberedFromZero
Output object and contour numbers starting from 0 instead of 1
-zcoord (-zc) OR -ZCoordinatesFromZero
Output Z coordinates that are 0 instead of -0.5 at the bottom of
the volume. In IMOD models, integer Z values are defined as
being located in the middle of a pixel in Z, which makes model
coordinates range from -0.5 to NZ - 0.5 for a volume of NZ
slices. With this option, the point coordinates will be shifted
so that they range from 0 to NZ, i.e., so that their fractional
parts actually correspond to their fractional positions within
the pixels in Z.
-values (-v) OR -ValuesInLastColumn Integer
Enter 1 to output general point values as the last number on
each line, after the Z coordinate, or -1 to output general con-
tour values for the first point in each contour. A point file
with either format can be read back in by Point2model, pro-
vided that the -values option is given to that program. When a
point or contour has no stored value, a value of 0 will be out-
put, unless a different value is specified with the -fill
option.
-fill (-fi) OR -FillValue Floating point
Value to output when contour/point has no stored value (default
0)
-help (-h) OR -usage
Print help output.
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde, 4/23/95
Converted to PIP, added output options
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 model2point(1)