xyzproj

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 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-
 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 5.2.0 xyzproj(1)