model2point

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 (-sc) 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.
 -sizes (-si) OR -PointSizes
 Output the point sizes for individual points, placing them after
 the Z coordinate on each line. If a point has no non-default
 size defined, or a contour has no point sizes for any of its
 points, then the 3D sphere size of the object will be used.
 -times (-t) OR -TimesForContours
 Output a time index for each contour, on the first line for that
 contour. This index will appear after the Z coordinate, or
 after the point size if any, and before a contour or point
 value. If there are no time indexes, 0 will be output.
 -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)
 -mesh (-m) OR -MeshVertexCoordinates Integer
 Output mesh vertex coordinates instead of contours points; enter
 1 for output only from objects with no contours, or 2 for output
 from all objects with meshes. Output will be floating point
 regardless of whether the -integer option is entered or
 MODEL2POINT_INTEGERS is set. Use the -object option to output
 object numbers before the coordinates. The output is also
 affected by the -zero and -zcoord options.
 -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 5.2.0 model2point(1)