colornewst(1)                                                    colornewst(1)



NAME
       colornewst - Run Newstack command on a color file

SYNOPSIS
       colornewst  [options]  input_file  output_file

DESCRIPTION
       Colornewst is a Python script to run Newstack operations on a color
       file by splitting the file into components with "clip splitrgb", run-
       ning Newstack, and recombining the components with "clip joinrgb".
       Most options to Newstack can be included, but not -fileinlist,
       -fileoutlist, -split, -replace, -numout, -skip, -blank, -onexform,
       -exclude, -input, or -output.
        There must be only one input file and one output file, specified as
       the last
        two arguments on the command line.  If placing options in a command
       file or
        script, always use at least three letters for the Newstack options.

       The input file can be any type readable by IMOD programs generally,
       namely  MRC, TIFF, HDF, or JPEG.  The output file will be an MRC file,
       unless the environment variable IMOD_OUTPUT_FORMAT is set to TIFF, HDF,
       or JPEG.  The latter will work only for single-image byte or RGB files,
       not stacks or other data modes; in the latter cases the output will be
       MRC despite the variable setting.  See the imodenv man page for
       other environment variables to control compression type and quality
       when getting TIFF or JPEG files in this way.  If the input file is a
       TIFF file, you can use the -cntiff option to tell the program to con-
       vert the input file to an MRC file with Tif2mrc using no options,
       and convert the processed MRC file to TIFF with Mrc2tif using the -s
       option.  If any more complicated conversions are desired, run the con-
       versions separately with the desired options.

       If the input file is gray-scale instead of color, Newstack will be
       run directly on it with the given options.

       Colornewst itself takes the following options, which cannot be abbrevi-
       ated.  These options can be intermixed with the Newstack options.
       Two leading dashes are accepted, just as for the Newstack options.

       -cntiff
              Convert the input file from TIFF to MRC with Tif2mrc, process
              it, and convert the processed file to TIFF.  By default, TIFF
              files will be read by Newstack and an MRC file will be pro-
              duced.

       -cntempdir dir
              Path to directory to use for temporary files, namely the red,
              green, and blue components produced by "clip splitrgb" and files
              for each component processed by Newstack.  The default is the
              standard temporary directory for IMOD commands.

       -cnmaxtemp #
              Maximum amount of space to use in the temporary directory, in
              megabytes (floating point values allowed).  The default is 1024.
              When processing the whole file at once would require more than
              this amount of space, the program will process the file in
              chunks.

       -cnverbose
              Pass on the printed output from running Newstack and the TIFF
              conversion programs, if any.  The default is for this output to
              be swallowed.

FILES
       Temporary files are named starting with "colornewst.PID" and removed at
       the end, if there is an error, or if the program is interrupted with
       Ctrl-C.  If the output file exists, it is turned into a backup file by
       appending "~" to the name unless the environment variable
       IMOD_NO_IMAGE_BACKUP is set.

AUTHOR
       David Mastronarde

SEE ALSO
       newstack, clip, tif2mrc, mrc2tif

BUGS
       Email bug reports to mast at colorado dot edu.




IMOD                                 4.9.5                       colornewst(1)