trimvol(1)                                                          trimvol(1)



NAME
       trimvol - Trim a volume and scale it to bytes.

SYNOPSIS
       trimvol [options] <input file>  <output file>

DESCRIPTION
       Trimvol provides a command-line interface to the programs Findcon-
       trast(1) and Newstack, for copying a selected portion of an MRC
       image volume into a new file, with automatic scaling to bytes.  There
       are options for specifying the volume to be extracted, and for control-
       ling the scaling to bytes.  There is also an option to scale floating
       point numbers to integers.  By default, coordinates are numbered from
       1.

       If you use the -sz or -s option, then Findcontrast will be run on
       the specified sections.  By default, regions within 10% of the lateral
       borders of each section are omitted, but a different region can be set
       with -sx and -sy.  A scaling is chosen which saturates the intensities
       of one pixel per slice, on average, at the dark and the light end.  If
       you use -sz then coordinates specified with these options will be
       treated as coming from a flipped volume only if the -f option is
       entered.  If you use -s then coordinates will always be taken as coming
       from a flipped volume.

       By default, the origin of the output file will be adjusted so that a
       model built on the input volume will display correctly on the output
       file.  This will even work for a volume rotated with -rx but not for
       one flipped with -yz.  This adjustment can be turned off with the -k
       option.


   Options
       You can enter only one of -c, -s, -sz or -mm.  Similarly, you cannot
       enter both -x and -nx, both -y and -ny, or both -z and -nz.  You can
       also enter only one of -sz and -s and only one of -yz and -rx.

       -x <X0,X1>
              Copy pixels in X between X0 and X1, inclusive.

       -y <Y0,Y1>
              Copy pixels in Y between Y0 and Y1, inclusive.

       -z <Z0,Z1>
              Copy pixels in Z between Z0 and Z1, inclusive.

       -nx <size>
              Copy "size" pixels in the X dimension, centered on the middle in
              X.

       -ny <size>
              Copy "size" pixels in the Y dimension, centered on the middle in
              Y.

       -nz <size>
              Copy "size" pixels in the Z dimension, centered on the middle in
              Z.

       -sz <S0,S1>
              Scale to bytes, determining the optimal scaling to bytes by ana-
              lyzing intensities from sections S0 to S1, inclusive.  Coordi-
              nates are treated as coming from a flipped volume only if the -f
              option is given.  Slices are numbered from 1 regardless of
              whether the -i option is used.

       -s <S0,S1>
              Scale to bytes, determining the optimal scaling to bytes by ana-
              lyzing intensities from sections S0 to S1, inclusive, in a
              flipped volume (legacy behavior).

       -sx <X0,X1>

       -sy <Y0,Y1>
              Analyze the region from X0 to X1 in X, or from Y0 to Y1 in Y,
              inclusive, in determining the scaling to bytes.

       -c <black,white>
              Scale to bytes, with relative intensities between "black" and
              "white" (on a scale of 0 to 255) stretched to occupy the full
              range of byte values.

       -mm <min,max>
              Scale to integers (mode 1), so that the current minimum and max-
              imum of the file would be scaled to the given values of minimum
              and maximum.  Newstack is run with the -scale option and the
              entered values.  This option would be used to scale from mode 2
              (floating point) to mode 1.

       -yz    Flip Y and Z in the output volume by first creating a temporary
              trimmed volume with newstack then running "clip flipyz" on this
              volume to create the final output file.

       -rx    Rotate the output volume by -90 degrees around the X axis, by
              first creating a temporary trimmed volume with newstack then
              running "clip rotx" on this volume to create the final output
              file.  The slices will look the same as with the -yz option but
              rotating instead of flipping will preserve the handedness of
              structures.

       -i     Interpret -x, -y, -z, -sx, and -sy entries as index coordinates
              numbered from 0, rather than as 3dmod coordinates numbered from
              1.

       -f     Interpret -y, -z, -ny, -nz, -sy, and -sz entries as referring to
              a flipped volume, with Y and Z transposed.

       -k     Keep the origin the same in the output from Newstack instead
              of passing it the -origin option to adjust the origin for the
              location of the subvolume being created.  This option can be
              used to reproduce a volume created with earlier versions of
              IMOD.

       -P     Output process ID.

FILES
       If the output file already exists a backup image of the original is
       created with the ~ extension.

AUTHOR
       David Mastronarde  <mast at colorado dot edu>

SEE ALSO
       newstack, findcontrast



BL3DEMC                             3.13.2                          trimvol(1)