xyzproj(1)                                                          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 input images are a tilt series and any one of the options are
       entered to provide the tilt angles for each image (e.g., -tiltfile),
       the program operates differently.  It automatically produces projec-
       tions 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 fore-
       shortening 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.

       -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 (-ad) 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.

       -tiltfile (-ti) OR -TiltFile   File name
              File with tilt angles for input images from a tilt series.  Use
              this option if tilt angles are in a file, one per line.

       -first (-fir) OR -FirstTiltAngle    Floating point
              Tilt angle of first view, in degrees, for images from a tilt
              series.  Use this option together with TiltIncrement.

       -increment (-inc) OR -TiltIncrement      Floating point
              Increment between tilt angles, in degrees, for input images from
              a tilt series.  Use this option together with FirstTiltAngle.

       -tangles (-ta) OR -TiltAngles       Multiple floats
              Use this option to enter the tilt angles for each view individu-
              ally, in degrees, for input images from a tilt series.  (Succes-
              sive entries accumulate)

       -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.



BL3DEMC                              4.7.3                          xyzproj(1)