colornewst(1)               General Commands Manual              colornewst(1)

       colornewst - Run Newstack command on a color file

       colornewst  [options]  input_file  output_file

       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 output file, and
       unless the -cnfiles is used there must be only one input file.  Input
       and output files must be specified as the last arguments on the command
       line, not with options.  To use multiple input files, which will be
       stacked together, place the -cnfiles option after all other options,
       before the first input file.  There are several restrictions when using
       multiple input files:
         1) The output file must still be the last file on the command line.
         2) The input files must all be the same size in X, Y, and Z, and be
       either all gray-scale or all color.
         3) If files are indeed color, lists of sections to process or line
       numbers for transforms to use cannot be entered because Clip and
       Newstack would need different lists.  If all files are gray scale,
       the section lists must apply to each of the individual files if -cntiff
       is not used, but to the whole stack of sections if -cntiff is used.
         4) The -cntiff option cannot be used if the files have more than one
         5) Processing will not be broken into chunks, and the default direc-
       tory for intermediate files will be set to the current directory.  The
       -cnmaxtemp option cannot be entered to limit the size of intermediate
       files.  A different temporary directory can be set with -cntempdir but
       you must make sure that there is enough space there.

       If placing options in a command file or script, always use at least
       three letters for the Newstack options.

       The input file(s) 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 can be abbrevi-
       ated.  These options can be intermixed with the Newstack options,
       except for the -cnfiles option, which must be just before the file-
       names.  Two leading dashes are accepted, just as for the Newstack

              Multiple input files are listed just after this option.  See the
              restrictions above.

              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.  If there are multiple input files, they must all be sin-
              gle-section files.

       -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, unless there are
              multiple input files.

       -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, unless there are multiple input files.

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

       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.

       David Mastronarde

       newstack, clip, tif2mrc, mrc2tif

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.57                      colornewst(1)