xyzproj(1) General Commands Manual xyzproj(1)
NAME
xyzproj - to project volume at a series of tilts around the X, Y, or Z
axis
SYNOPSIS
xyzproj [options] input_file output_file
DESCRIPTION
This program will compute projections of a 3-dimensional block of an
image file at a series of tilts around either the X, the Y or the Z
axis. The block may be any arbitrary subset of the image file. In
addition to projecting a fixed block of data, it can project a rectan-
gle of data in each X/Y image plane that is aligned with the angle of
projection, which is useful for common line analysis.
A projection along a ray line is simply the average of the pixels in
the block along that line. However, rather than taking the values of
the pixels that lie near the ray, interpolation is used to sample den-
sity at points evenly spaced at one pixel intervals along the ray.
When the -series option is entered to indicate that the input images
are a tilt series, the program operates differently. It automatically
produces projections at angles around the Z axis, i.e., within the
plane of each image. The projections are within a rectangular box that
is rotated so its sides are parallel to the projection rays. The size
of the box is constrained so that it is completely within the image
area on the zero-degree view, or within the area specified by the
-xminmax and -yminmax options. In addition, the box will be made
smaller in the direction of projection for images at higher tilts by
the cosine of the tilt angle, so that it will contain approximately the
same image features in the different images being projected at a given
angle. This tilt foreshortening can be suppressed with the -full
option.
OPTIONS
Xyzproj uses the PIP package for input (see the manual page for pip)
and can still take sequential input interactively. 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 parentheses.
-input (-inp) OR -InputFile File name
Input image file to project. If this option is not entered, the
first non-option argument will be used for the input file.
-output (-o) OR -OutputFile File name
Output file for projection. If this option is not entered, the
second non-option argument will be used for the output file.
-axis (-ax) OR -AxisToTiltAround Text string
Axis to tilt around (X, Y, or Z)
-xminmax (-x) OR -XMinAndMax Two integers
Starting and ending X index coordinates of block to project
(numbered from 0). The default is the whole extent in X.
-yminmax (-y) OR -YMinAndMax Two integers
Starting and ending Y index coordinates of block to project
(numbered from 0). The default is the whole extent in Y.
-zminmax (-z) OR -ZMinAndMax Two integers
Starting and ending Z index coordinates of block to project
(numbered from 0). The default is the whole extent in Z.
-angles (-an) OR -StartEndIncAngle Three floats
Starting, ending, and increment tilt angle. Enter the same
value for starting and ending angle to get only one image. When
input images are not from a tilt series, projection angles must
be entered with either this option, -tiltfile, or -tangles.
-tiltfile (-ti) OR -TiltFile File name
File with tilt angles to project at, or for input images from a
tilt series. Use this option if tilt angles in degrees are in a
file, one per line.
-adjust (-adj) OR -AdjustFileAngles File name
Value to add to angles read in from file
-tangles (-ta) OR -TiltAngles Multiple floats
Use this option to enter the individual tilt angles in degrees,
either to project at or for input images from a tilt series.
(Successive entries accumulate)
-mode (-m) OR -ModeToOutput Integer
Mode of output file (0 for byte, 1 for integer, 2 for real).
The default is mode 1 for input mode 0 or 1, mode 2 for input
mode 2.
-width (-w) OR -WidthToOutput Integer
Width of output file (default is same as width of input coordi-
nates)
-addmult (-add) OR -AddThenMultiply Two floats
Factors to add then multiply by (default 0,1)
-fill (-fil) OR -FillValue Floating point
Value to fill empty areas with (default is mean)
-constant (-c) OR -ConstantScaling
Scale all projection sums by the same amount, by dividing by the
thickness of the slab being projected. The default is to divide
each projection sum by the number of pixels along the projection
ray. Constant scaling is more appropriate when projecting a
largely empty volume.
-ray (-r) OR -UseRayIntersections
Compute projections from areas of intersection between rays and
pixels, instead of by interpolating between sets of 4 pixels
along each ray. Each pixel is intersected by one to 3 rays.
The fraction of area in each intersection is computed and that
fraction of the pixel's value is added to the respective ray.
This may give a more accurate result than interpolating, partic-
ularly when projecting model data.
-series (-s) OR -InputIsTiltSeries
The input file is a tilt series and will be treated as described
above. The angles of the tilt series must be entered with
either -tiltfile, -first and -increment, or -tangles.
-first (-fir) OR -FirstTiltAngle Floating point
Tilt angle of first view, in degrees, for images from a tilt
series. Use this option together with -increment. Both of
these options may only be entered with -series.
-increment (-inc) OR -TiltIncrement Floating point
Increment between tilt angles, in degrees, for input images from
a tilt series. Use this option together with -first.
-full (-fu) OR -FullAreaAtTilt
Use this option to keep the projection box the same size on all
images of a tilt series, rather than making it smaller at higher
tilt. The box will thus include new material at each higher
tilt.
-param (-p) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
INTERACTIVE INPUT
If there are no command-line arguments, Xyzproj takes sequential input
the old way, with the following entries:
Input image file
Output image file
Index coordinates (with numbering starting from 0 in X, Y and Z) of the
starting and ending X, Y then Z coordinates of the block. The default
is the whole image file. The Z coordinates may be entered in inverted
order (e.g. 56,34) and should be so entered if the input stack is a
tomogram that was built in inverted order.
Axis to tilt around for projections. Enter X, Y or Z. The Z axis
passes perpendicular to the sections in the file.
Starting tilt angle, ending tilt angle, and increment to apply between
these limits. All angles are allowed.
Width (x dimension) of the output images. An appropriate default may
be selected with /
Data mode for output file.
Scaling factors to apply to the average pixel values: a factor to be
added to the values, then a factor to multiply by after the addition.
The default is 0,1, for no scaling.
Value to fill parts of the output image that have no points in the
block projecting to them The scaling factors are applied to this
value. The default is the mean of the input file.
The user must determine the proper scaling in order to output data most
efficiently (mode 0). The user must also set the header information
properly to get the coordinate system to correspond to that of the
input image file. This program does not set up the header to indicate
that the output file is a tilt series.
HISTORY
Written by David Mastronarde 10/13/89
Converted to PIP, 6/19/06
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 xyzproj(1)