mrc2tif(1) mrc2tif(1)
NAME
mrc2tif - Create one or more TIFF image files from an MRC image file.
SYNOPSIS
mrc2tif [-s] <mrc file> <tiff file root name>
DESCRIPTION
mrc2tif usually creates a series of TIFF files with the prefix <tiff
root name> and with the suffix .nnn.tif, where nnn is the z number.
Byte, signed and unsigned 16-bit integer, float, and RGB color files
(modes 0, 1, 6, 2, 16) can be converted. The data will be written in
the same mode as in the input file by default, but there are options
that allow the integer and float modes to be scaled to bytes; the same
options allow scaling of byte and RGB values. If the input file has
only one section, then the output file will simply be the <tiff root
name> with no suffix added.
When the output mode is integer or float, the TIFF file will contain
the minimum and maximum value for the data in the file. When a TIFF
stack is created, each image will have the same overall minimum and
maximum, rather than values specific to that image. This way, 3dmod
will be able to read in the data with proper scaling. However, Photo-
shop pays no attention to these values when displaying integer data, so
when the integer data have a relatively small range, the image will
initially appear black or very dark. The simplest solution for this
problem is to apply the scaling options described next.
When either the -S or the -C option is entered, integer and floating
point data will be scaled to bytes and any values outside the range of
0 to 255 will be truncated. If the input data is already in bytes
(either byte data or RGB data), these options will cause the data to be
scaled, and values outside the range truncated. To have the range of
the input data mapped into the full range of byte data, just enter "-C
0,255". To have a subset of the input range mapped to 0 to 255, either
enter the limits of the subset of the range directly with the -S
option, or adjust the contrast in 3dmod to give the desired expan-
sion of the dynamic range for that subset of the image data, and enter
the contrast settings withs the -C option.
If the program is run with version 4 of the TIFF library, it will write
files bigger than 4 GB in the BigTIFF format, and continue to write
smaller files in classical TIFF format. Running with version 3 of the
TIFF library, it will write valid files up to 4 GB, although the
library cannot read such files if they are bigger than 2 GB. In Linux,
it is not necessary to have the program built against the version 4
library; the standard distributed program will run with this library,
provided that libtiff.so.3 is a link to the version 4 library and is
located in a directory on the LD_LIBRARY_PATH. For example, if the
directory with the version 4 library is on LD_LIBRARY_PATH, you can
make a link in that directory with:
ln -s libtiff.so.5 libtiff.so.3
Options
-s Create a single output file, a TIFF stack with all of the sec-
tions in the input file.
-c <value>
Compress the data with the type of compression indicated. The
most useful compression types are LZW (value 5), Zip or Deflate
(value 8), and JPEG (value 7). For these types, the value can
be given as a text string: "lzw", "zip", or "jpeg". On Linux,
see "man libtiff" for other numeric values that can be entered.
Not all of these options will be available on all operating sys-
tems.
-q <value>
Set the quality for JPEG or ZIP compression. For JPEG the qual-
ity ranges from 0 to 100 with a default of 75; higher numbers
preserve more information but with less compression. For ZIP,
which is a lossless compression, the quality factor ranges from
1 to 9 with a default of 6 and specifies a tradeoff between
speed and amount of compression, with higher numbers giving
somewhat more compression for more computational time.
-S <min,min>
Specify an initial intensity scaling that will scale "min" to 0
and "max" to 255, just as is achieved with the -s options to
3dmod and mrcbyte.
-C <black,white>
Specify intensity scaling to match the scaling achieved with the
given black and white contrast settings in 3dmod, with the -c
option to mrcbyte, or the "-contrast" option to newstack. If
both -S and -C are entered, the final scaling will be the prod-
uct of these two scalings. If -S is entered alone, the
black/white values are 0/255 (no scaling for contrast). If -C
is entered alone, the initial scaling will be from the minimum
in the input file to 0, and from the maximum in the file to 255.
If you have integer data and you want to convert it to bytes
-t <value>
Set the criterion for processing each image in strips to the
given value in megabytes (fractional values are allowed). Whole
images will be read in, processed, and saved as a unit if they
are less than this criterion (default 100 MB). Above the crite-
rion, images will be read, processed, and saved in strips, with
much lower memory requirements.
-o Use old IMOD code instead of libtiff for writing the files (for
testing purposes).
AUTHORS
Jim Kremer, David Mastronarde
SEE ALSO
clip, newstack
BUGS
Complex and long integer data modes are not supported.
Email bug reports to mast at colorado dot edu.
BL3DEMC 4.5.6 mrc2tif(1)