raw2mrc(1)                                                          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 and rgb.
              Where byte is 8-bit integer values, short is 16-bit signed val-
              ues, ushort is 16-bit unsigned values, long is 32-bit signed
              values, ulong is 32-bit unsigned values, float is a 32-bit
              floating point value and rgb is three byte values--one for each
              color.

       -s     Swap input bytes.

       -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 or any 32-bit values 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, which is a non-standard mode that may not be
              completely supported.

       -c     Convert 32-bit integers to 16-bit integers instead of to float-
              ing 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 num-
              bers as unsigned integers in a file of mode 6.  If values in the
              input files are all less than 32768, then specify 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, tomrc(1), frommrc(1), mrcv(1)

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                          raw2mrc(1)