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NAME

       X-GEN - imageform


SYNOPSIS

       [xgen] imageform [-pmbsrkdqv] [-x{val}] [-y{val}] [filenam]


DESCRIPTION

       "imageform"  reads  in  crystallographic detector images created in any
       format recognized by the X-GEN package and writes them out in  a  user-
       specified format.

              It  therefore  can  be  used to convert from one image format to
              another.

       If the user specifies an X-GEN-style USPLINE file  via  an  environment
       variable  (see  below),  it will correct the spatial distortions in the
       images before output.

              The formats that it knows how to read are:

       *      Siemens/Nicolet/Xentronics multiwire images

              (both the old PCS formats and the FRAMBO formats)

       *      San Diego Multiwire Systems images

       *      FAST images

       *      Bruker/Siemens 1k CCD images

       *      Bruker/Siemens 2k CCD images

       *      Bruker/Siemens Mosaic CCD images

       *      Mar image plate images

       *      R-Axis image plate images

       *      MacScience image plate images (2xxx and 3xxx)

       *      Argonne CCD images (all known formats)

       *      Fuji raw image plate images

       *      Mar CCD detector images (all sizes)

       Other formats may be added in the future.  The formats  that  it  knows
       how to output are:

       *      Siemens/Nicolet/Xentronics multiwire image format

       *      Bruker/Siemens FRAMBO/SMART format

       *      Mar image plate format

       *      R-Axis image plate format

       Thus  the  list  of output formats is somewhat shorter than the list of
       input formats.

              If the user requires the image to be spatially corrected before-
              hand,

       a file with name or environment variable USPLINE must be present.  This
       file should be the X-GEN-generated file  containing  the  mapping  from
       pixels to centimeters and vice versa. IMCA users employing this program
       to convert Mosaic CCD images from the IMCA-CAT Bruker system  into  Mar
       or  R-Axis  formats will receive a copy of the appropriate USPLINE file
       along with the executable of the program.  Thus if that file is  called
       mosaic.uca, then to run the program:

              % setenv USPLINE ./mosaic.uca
              % imageform [args...]

       If  the  user _is_ spatially correcting the images, the program can re-
       dimension the images; see below.

       This is one of the few X-GEN applications that exists as  a  standalone
       executable in addition to being available from within "xgen" itself.


OPTIONS

       -p     Output images in PCS format (an old Nicolet format).

       -m     Output  images  in  Mar image-plate format.  This is the default
              output format.

       -b     Output images in Bruker (FRAMBO / SMART)  8-bits-per-pixel  for-
              mat.

       -s     Output  images in Bruker (FRAMBO / SMART) 16-bits-per-pixel for-
              mat.

       -r     Output images in R-Axis format.

       -k     Keep the spatial properties of the input image.

       By default the spatial correction is applied before output; if the user
       does not want the spatial correction applied, this option will suppress
       the correction.

       -d     Do NOT delete the original image before  writing  out  the  con-
              verted  file.  Instead, rename the old version by appending ",0"
              to the end of the filename, unless <filename>,0 already  exists;
              in  that  case,  append ",1" to the end. If <filename>,1 already
              exists, use ",2", and so on, up through ",99".  The output file-
              name will be free of appendages.

       -q     Suppress  diagnostic outputs to stdout and to the logfile almost
              completely.

       -y{val}
              Redimension the detector's height from whatever the input was to
              {val}. This option is ignored  unless  spatial  corrections  are
              being applied, as described above.

       Processed Files:

              The program picks which files to process in any of three ways:

       *      If the user specifies one or more filenames in the command line,
              it will process ONLY the files named.

       *      If the user does not specify any files in the command line,  and
              there  exists  a  file with name or environment variable FRAMES,
              then it is consulted to  define  which  files  to  convert.  All
              images named in the FRAMES file will be converted.  Each line in
              the FRAMES file will look like

              43/data0/ahoward/83071c/data/83071c.0043

       i.e. the first five characters in the line are an index value  for  the
       image and the remainder is a filename.

       *      If  the user does not specify any files in the command line, and
              the FRAMES file does not exist, then all images in  the  current
              directory  will be converted.  A file is believed to be an image
              if its file extension (the portion of the filename following the
              last  period)  is  entirely  numeric,  is "image", "osc", "stl",
              "ipf", or "img", or is "_xy", where x and y are any two letters.
              Thus  83071c.0043,  george043.img,  fred._br, and mydata0387.stl
              will   all   be   converted;   135735_235,    135735.stu,    and
              goody123.0x3will  not.   These  _could_ be converted if they are
              explicitly named in a separate run of the imageform program.

       Other Files:

       XLOG   Diagnostic logfile.

       USPLINE
              Input pixel-to-centimeter conversion file.

       FRAMES Index of convertable images.


EXAMPLES

       setenv USPLINE mosaic.uca; imageform
              Convert all the images in a directory to MAR image-plate format

       setenv USPLINE mosaic.uca; imageform -r
              Convert all the images in a directory to R-Axis format

       imageform -k ikw.0043 ikw.0372 gru._br
              Convert images ikw.0043, ikw.0372, and gru._br into MAR  format,
              without correcting for spatial distortion

       imageform -kd ikw.0043 ikw.0372 gru._br
              Convert  images ikw.0043, ikw.0372, and gru._br into MAR format,
              without correcting for spatial distortion, and  preserving  (not
              deleting) the original images.

       Diagnostics

       Some  diagnostics  are written to a file with name or environment vari-
       able XLOG.  Similar diagnostics are written  to  the  standard  output.
       The  amount  of  information emitted can be increased or decreased with
       the -v and -q command-line options, respectively.

       Warnings

       Specifying non-equal values for "-x" and  "-y"  options  has  not  been
       tested.   That  is,  imageform  -x1200 -y1200 is known to work, whereas
       imageform -x1200 -y1500 might or might not work.


REPORTING BUGS

       Report bugs to Andy Howard at howard@iit.edu or 312-567-5881.


COPYRIGHT

       Copyright (C) 2002, Illinois Institute of  Technology.   See  the  file
       'LICENSE' for information on usage and redistribution of this file, and
       for a DISCLAIMER OF ALL WARRANTIES



Version 5.5.5                    October 2005                         X-GEN(1)

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