xyzproj(1)                  General Commands Manual                 xyzproj(1)

       xyzproj - to project volume at a series of tilts around the X, Y, or Z

       xyzproj  [options]  input_file  output_file

       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

       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 of 6 for signed or unsigned
              integer, 2 or 12 for 32-bit or 16-bit floats).  The default is
              mode 1 for input mode 0 or 1; the default mode of floating point
              output with float input for MRC files is governed by the value
              of environment variable IMOD_WRITE_FLOATS_16BIT.  Mode 12 is
              allowed only if the output format is MRC.

       -width (-w) OR -WidthToOutput       Integer
              Width of output file (default is same as width of input coordi-

       -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

       -param (-p) OR -ParameterFile       Parameter file
              Read parameter entries as keyword-value pairs from a parameter

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard 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.

       Written by David Mastronarde  10/13/89
       Converted to PIP, 6/19/06

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.60                         xyzproj(1)