raw2mrc(1)                  General Commands Manual                 raw2mrc(1)



NAME
       raw2mrc - Create an MRC image stack from raw image data.

SYNOPSIS
       raw2mrc  [options]  raw_image_files...  MRC_output_file

DESCRIPTION
       raw2mrc can be used to create MRC image files from many types of raw
       binary image data.  Command line options are used to adjust the image
       size and to skip the input image header.  Several raw images can be
       combined into one file by listing all of their filenames before the
       name of the output file.

OPTIONS
       -x width
              Set the width of the image, the default value is 640 pixels.

       -y height
              Set the height of the input image, the default is 480 pixels.

       -z sections
              Set the number of sections in each input image file, the default
              is 1.

       -t type
              Set the type of input data, the default byte data.  The allowed
              types are byte, short, ushort, long, ulong, float, double, and
              rgb.  Where byte is 8-bit integer values, short is 16-bit signed
              values, ushort is 16-bit unsigned values, long is 32-bit signed
              values, ulong is 32-bit unsigned values, float and double are
              32-bit and 64-bit floating point values and rgb is three byte
              values--one for each color.

       -s     Swap input bytes.  Does not work for doubles.

       -o offset
              Set the offset value used at the beginning of the file, the
              default is 0.

       -oz offset
              Set the offset value used at the end of each section, the
              default offset is 0.

       -f     Flip the images around the X axis.

       -i     Produce an inverted output stack by both inverting the order in
              which files are processed and inverting the order of reading Z
              slices from each file.

       -iz    Invert the order of reading Z slices from each individual file.

       -d     Divide unsigned 16-bit values by 2, or divide any 32-bit inte-
              gers or 64-bit doubles being converted to 16 bits by 2.  The
              default for unsigned short values is to subtract 32767, which
              allows all unsigned short values to be stored as signed short
              integers in the MRC file of mode 1.  Use this option if you do
              not want negative numbers and do not care about the loss of pre-
              cision.  If the values in the input files are all less than
              32768, then specify that the input data are short rather than
              ushort.

       -u     Store unsigned 16-bit values without modification in an MRC file
              of mode 6; or store doubles in mode 6 if the -c option is given
              also.

       -c     Convert 32-bit integers or 64-bit doubles to 16-bit integers
              instead of to 32-bit floating-point numbers.  If the type is
              long, you can use this option alone if values are between -32768
              and 32767; or you can use the option with -d to divide by 2 if
              values are between -65536 and 65535.  If you specify the type as
              ulong, then by default 32767 will be subtracted from the input
              values, so that values from 0 to 65534 can be stored as -32767
              to 32767.  Again, -d can be used to divide by 2 instead, so that
              values from 0 to 65534 can be stored as 0 to 32767.  Also, -u
              can be used to store the numbers as unsigned integers in a file
              of mode 6. Thus, doubles with a range of 0 to 131070 can be
              stored as unsigned 16-bit values using all of -c, -d, and -u.

              If values in the input files are all less than 32768, then spec-
              ify the type as long instead of ulong.

       -p pixel
              Set the pixel spacing of the MRC file header to the given value,
              which should generally be a pixel size in Angstroms.  -pz pixel
              Set the Z pixel spacing of the MRC file header to the given
              value if it is different from the one given with the -p option.

FILES
       If the output file already exists, it will be made a backup file by
       adding ~ to its name.

AUTHORS
       Jim Kremer, David Mastronarde

SEE ALSO
       tif2mrc

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                4.10.10                         raw2mrc(1)