KEYWORD
     single_file swap_bytes output_file prefix extension

DESCRIPTION
     This application takes a Priism file and converts it
     into one or more files in Spider's native format.
     The conversion is direct: no scaling or transformation
     of the data values occurs.

     mrc2spi has the standard set of Priism controls for
     selecting a subset of the Priism file to convert.
     For the conversion, the key choice that has to be
     made is whether to convert each section in the input
     into a separate file or to place the sections one
     after the other in one file.  When you want to
     generate multiple output files, the "Prefix" and
     "Extension" fields control the output file names.
     When you want to generate a single output file,
     the name in the "Output file" field will be the
     name of the file generated.  By default, mrc2spi
     will generate a file using the native byte ordering
     for the operating system and machine where you run
     mrc2spi.  To generate a file with the non-native
     byte ordering, turn on the "swap bytes" toggle
     button.

     The current version of mrc2spi has several limitations:

     1) mrc2spi will not convert complex-valued data, for
        instance the result of a forward Fourier transform.
     2) mrc2spi will only convert the first wavelength and
        time point that you select.  It ignores all other
        wavelengths and time points.
     3) For EM tomographic series, mrc2spi does not write
        the tilt angles from the extended header to the
        Spider file.
     4) mrc2spi does not carry over the origin and tilt
        angles in the Priism header to the Spider file.
     5) Because Web uses a different convention than Priism
        does when displaying images, the display in Web of
        a file converted with mrc2spi is flipped in y
        compared to the original file displayed in Priism.

     mrc2spi accepts the command-line arguments described
     in Region.hlp.  In addition, it has the following
     options:

         -out=n
             Causes mrc2spi to generate a single Spider file
             named n.  If you specify both -out and -prefix
             options on the command line, whichever such
             option that appears last takes precedence.

         -prefix=p
             Causes mrc2spi to generate a numbered series
             of Spider files.  The file names for the
             numbered series will all start with the prefix,
             p.    If you specify both -out and -prefix
             options on the command line, whichever such
             option that appears last takes precedence.

         -ext=e
             Sets the extension mrc2spi will use when
             generating file names in a numbered series.
             By default, mrc2spi uses .spi as the extension.

         -swab
             Causes mrc2spi to generate files with the
             non-native byte ordering.  By default, mrc2spi
             generates files with the native byte ordering.

     The example below extracts a 160 x 160 x 160 region
     from a.dat and writes it to a.spi in the non-native
     byte ordering.

         mrc2spi a.dat -x=0:159 -y=0:159 -z=0:159 -out=a.spi \
             -swab

     The example below saves the data from b.dat as a
     numbered series of Spider files.

          mrc2spi /home/eric/data/b.dat \
               -prefix=/home/eric/data/b_ -ext=.spi

single_file
     The output of mrc2spi can be a single file with the
     sections appearing one after the other or multiple
     files with one section per file.  To generate one
     file with mrc2spi, turn on the "Single file" toggle
     button and enter the name of the file to generate
     in the "Output file" field.  To generate multiple
     files, turn off the "Single file" toggle button,
     enter the file name prefix (the directory name and
     leading part of the file name) in the "Prefix" field,
     and enter the file name extension (by default it is
     .spi) in the "Extension" field.  The names of the
     files will consist of the prefix followed by the
     section number written as a base ten integer with
     a fixed number of digits and then the extension.
     The section numbers will range from one to the
     number of sections selected.  If the number of
     sections selected is less than 1000, the section
     number will be written as three digits.  If the
     number of sections selected is greater than or equal
     to 1000, the section number will be written as n
     digits where n< is the number of digits necessary
     to express the number of selected sections as a base
     10 integer.

swap_bytes
     By default, mrc2spi generates Spider files in the
     native byte ordering for the machine and operating
     system where you run mrc2spi.  To generate a file
     with the non-native byte ordering, turn on the
     "swap bytes" toggle button.

output_file
     When the "Single file" toggle button is on, mrc2spi
     converts the input file to a single Spider file
     whose name is shown in the "Output file" field.

prefix
     When the "Single file" toggle button is off, mrc2spi
     converts the input file to a numbered series of
     Spider files.  The file names for the numbered
     series will all start with whatever is entered in
     the "Prefix" field.  Normally, the prefix would be
     something like

         /home/eric/data/cent_2005_10_12_a_

     It would contain the directory where the files would
     be written, /home/eric/data/, followed by something
     to identify the data set, cent_2005_10_12_a.

extension
     When the "Single file" toggle button is off, mrc2spi
     converts the input file to a numbered series of
     Spider files.  The file names for the number series
     will all end with whatever is entered in the
     "Extension" field.  By default, the extension is .spi.