point2model
point2model(1) General Commands Manual point2model(1)
NAME
point2model - Convert point listing to IMOD model file
SYNOPSIS
point2model [options] point_file model_file
DESCRIPTION
Point2model will convert a text file with a simple list of 3D point
coordinates, one per line, to an IMOD model. The file can be in one of
four forms: each line consisting of X and Y coordinates, where a Z of 0
will be assumed; each line consisting of X, Y, and Z coordinates; each
line having a contour number followed by the X, Y, Z coordinates; or
each line having an object number and a contour number followed by the
X, Y, Z coordinates. The objects and contours can be numbered from
either 1 or 0. The last three forms correspond to the different forms
that can be output by the companion program, Model2point. In each
of these three cases, a general value can be present after the coordi-
nates for every point or for the first point in a contour. When con-
tour numbers are not contained in the file, there are options to place
points into different contours based on the number of points or their Z
values.
In addition to options for processing the coordinates, there are sev-
eral options for setting properties of the model or objects. These are
provided to save having to edit a model in 3dmod, a convenience that
becomes significant when models are produced repeatedly at the command
line or by a script. Other such options could be added easily.
If you intend to take the model directly into a processing program like
Tiltalign, Beadtrack, or Ccderaser, without resaving it from
3dmod, you need to use the -image option so that coordinates will be
treated correctly.
OPTIONS
Point2model 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 (-in) OR -InputFile File name
Input text file with points. 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 file for model. If this option is not entered, the sec-
ond non-option argument will be used for the output file.
-open (-op) OR -OpenContours
The default is to make all objects be closed contour type. This
option and -scat can be used to make all objects be open or
scattered, respectively.
-scat (-sc) OR -ScatteredPoints
Make objects be scattered point type
-number (-nu) OR -PointsPerContour Integer
Maximum number of points per contour. The default is to put all
points into one contour. This option is not allowed if the
point file has contour numbers.
-planar (-pl) OR -PlanarContours
Start a new contour at each new Z value encountered when reading
sequentially through the lines of input. This option is not
allowed if the point file has contour numbers.
-zero (-ze) OR -NumberedFromZero
Objects and contours are numbered from 0 instead of 1
-zcoord (-zc) OR -ZCoordinatesFromZero
Z coordinates of points 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. Use this option if the point coordinates range from 0
to NZ instead, i.e., if the fractional part of a Z coordinate
corresponds to its fractional position within a pixel in Z.
-sizes (-si) OR -PointSizes
Each line has an individual point size (radius) after the Z
coordinate. Values and sizes can both be present.
-default (-d) OR -SetAsDefaultSize
If individual point sizes are present and the size for a point
matches the default size for the object entered with the -sphere
option, store a size of -1 so that it will continue to have the
default size if that is later changed. Otherwise, the value
itself will be stored for the point.
-values (-va) OR -ValuesInLastColumn Integer
Use this option to indicate that lines have a general value at
the end, after the Z coordinate. Enter 1 to have the value
stored as a point value, or -1 to have the value stored as a
contour value. With point values, a value must appear on every
line. With contour values, the first point in each contour must
have a value, and values on later points in a contour will be
ignored and need not be present. Note that if a file has values
and this option is not given, the coordinates will NOT be read
correctly unless the file has both object and contour numbers,
because the program will think that the X coordinate is a con-
tour number.
-flags (-f) OR -DisplayFlags Integer
This entry is a sum of flags controlling display options, cur-
rently including just 1 to turn on the option to "Show stored
values" in the Model View Edit Objects Values panel, and 2 to
turn on the option for false color.
-times (-ti) OR -TimesForContours
Use this option to indicate that contours have time indexes.
These indexes should appear after point sizes, if any, just for
the first point in a contour. If there are point or contour
values, the time should be before the value.
-circle (-ci) OR -CircleSize Integer
Turn on display of circles of this size (radius) at each point.
If the points form open contours that progress through Z, this
option will let you see them in the Zap window of 3dmod without
having to edit the object.
-sphere (-sp) OR -SphereRadius Integer
Turn on display of spheres of this radius at each point. Use
this option to see scattered points in 3dmod without having to
edit the object.
-width (-w) OR -LineWidthIn2D Integer
Line width for the object in 2D displays like the Zap window.
This sets the same line width as in the 3dmod Edit Object Type
dialog.
-thick (-th) OR -LineThicknessIn3D Integer
Line width for the object in the Model View display. This sets
the same value as the 3D line width in the Line panel of the
3dmod Model View Edit Objects dialog.
-color (-co) OR -ColorOfObject Three integers
Color to make an object; enter red, green, and blue values rang-
ing from 0 to 255. To assign colors to multiple objects, enter
this option multiple times. (Successive entries accumulate)
-name (-na) OR -NameOfObject Text string
Name to give an object; enter a text string, enclosed in quotes
if it contains spaces. To assign names to multiple objects,
enter this option multiple times. (Successive entries accumu-
late)
-image (-im) OR -ImageForCoordinates File name
Make the model's coordinate system match this image file. This
is not needed for loading the model onto this image in 3dmod,
but will allow the model to be used together with this image
file in various programs (e.g., Beadtrack) without having to
load it into 3dmod and save it. As of IMOD 4.10.30, this entry
also sets the pixel size in the model header.
-volume (-vo) OR -VolumeSizeXYZ Three integers
Size of a volume in X, Y, and Z to store in the "max" fields of
the model header. Correct max values are needed for some opera-
tions such as rotation in Imodtrans. By default, the program
stores max values that are a few pixels past the actual data, or
the size of an image file if one is entered with -image. This
entry overrides a size from such an image file.
-pixel (-pi) OR -PixelSpacingOfImage Three floats
Set the reference scaling information of the model to the given
X, Y, and Z scale factors, which would correspond to the pixel
spacing in an image file header. The entry together with -ori-
gin provides an alternative to the -image option, so -image can-
not be used together with -pixel or -origin. Like -image, these
entries are not needed for loading the model into 3dmod together
with an image file of the same scaling, but would be useful for
loading into 3dmod with an image at a different binning, or for
use in other programs that require the scaling to be correct.
As of IMOD 4.10.30, this entry also sets the pixel size in the
model header.
-origin (-or) OR -OriginOfImage Three floats
Set the reference information of the model to the given X, Y,
and Z translations, which would correspond to the origin in an
image file header.
-modpix (-m) OR -ModelPixelSize Floating point
Pixel size to assign to model header, in nanometers. This
option can be entered along with -image or -pixel and overrides
the pixel size in the image file header or entered with -pixel,
respectively.
-zscale (-zs) OR -ZScaleOfModel Floating point
Z scale to assign to the model, corresponding to the value set
in the 3dmod Model Header and Model View Edir Controls dialogs.
This Z-scale is separate from the pixel spacing in Z and is used
for display, quantitative measurements, and determination of the
normals to the surface.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
AUTHOR
David Mastronarde (mast at colorado dot edu)
SEE ALSO
model2point
IMOD 5.2.0 point2model(1)