raw2mrc(1) General Commands Manual raw2mrc(1)
NAME
raw2mrc - Create an MRC image stack from raw image data.
SYNOPSIS
raw2mrc [options] raw_image_files... MRC_output_file
DESCRIPTION
raw2mrc can be used to create MRC image stacks from many types of raw
binary image data. Command line options are used to specify the image
size and to skip the input image header. Several raw images can be
combined into one file by listing all of their filenames before the
name of the output file, or providing them with multiple entries of the
-input option. The environment variable IMOD_OUTPUT_FORMAT can be set
to produced TIFF or HDF output.
OPTIONS
Raw2mrc uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-input (-in) OR -InputFile File name
Input image file. Input files may also be entered after all
arguments on the command line. Files entered with this option
will be processed before files at the end of the command line,
if any. (Successive entries accumulate)
-output (-ou) OR -OutputFile File name
Output image file. If this entry is omitted, the last non-
option argument will be used for the output filename; otherwise,
all non-option arguments will be used as input filenames.
-x OR -XSize Integer
Set the width of the image; this entry is required
-y OR -YSize Integer
Set the height of the input image; this entry is required
-z OR -SectionsPerFile Integer
Set the number of sections in each input image file, the default
is 1.
-t OR -DataType Text string
Set the type of input data; the default is byte data. The
allowed types are byte, short, ushort, long, ulong, float, dou-
ble, and rgb. Where byte is 8-bit integer values, short is
16-bit signed values, ushort is 16-bit unsigned values, long is
32-bit signed values, ulong is 32-bit unsigned values, float and
double are 32-bit and 64-bit floating point values and rgb is
three byte values--one for each color.
-s OR -SwapBytes
Swap input bytes. Does not work for doubles.
-o OR -OffsetToImageData Integer
Set the offset value used at the beginning of the file, the
default is 0.
-oz OR -SkipBetweenSections Integer
Set the offset value used at the end of each section, the
default offset is 0.
-f OR -FlipInY
Flip the images around the X axis.
-i OR -InvertInZ
Produce an inverted output stack by both inverting the order in
which files are processed and inverting the order of reading Z
slices from each file.
-iz OR -ReadInvertedInZ
Invert the order of reading Z slices from each individual file.
-d OR -DivideBy2
Divide unsigned 16-bit values by 2, or divide any 32-bit inte-
gers or 64-bit doubles being converted to 16 bits by 2. The
default for unsigned short values is to subtract 32767, which
allows all unsigned short values to be stored as signed short
integers in the MRC file of mode 1. Use this option if you do
not want negative numbers and do not care about the loss of pre-
cision. If the values in the input files are all less than
32768, then specify that the input data are short rather than
ushort.
-u OR -UnsignedOutput
Store unsigned 16-bit values without modification in an MRC file
of mode 6; or store doubles in mode 6 if the -c option is given
also.
-c OR -ConvertTo16BitInt
Convert 32-bit integers or 64-bit doubles to 16-bit integers
instead of to 32-bit floating-point numbers. If the type is
long, you can use this option alone if values are between -32768
and 32767; or you can use the option with .B -d to divide by 2
if values are between -65536 and 65535. If you specify the type
as ulong, then by default 32767 will be subtracted from the
input values, so that values from 0 to 65534 can be stored as
-32767 to 32767. Again, .B -d can be used to divide by 2
instead, so that values from 0 to 65534 can be stored as 0 to
32767. Also, .B -u can be used to store the numbers as unsigned
integers in a file of mode 6. Thus, doubles with a range of 0 to
131070 can be stored as unsigned 16-bit values using all of -c,
-d, and -u. If values in the input files are all less than
32768, then specify the type as long instead of ulong.
-p OR -PixelSpacing Floating point
Set the pixel spacing of the MRC file header to the given value,
which should generally be a pixel size in Angstroms.
-pz OR -ZPixelSpacing Floating point
Set the Z pixel spacing of the MRC file header to the given
value if it is different from the one given with the .B -p
option.
-help (-h) OR -Usage
Print help output
-StandardInput
Read parameter entries from standard input
FILES
If the output file already exists, it will be made a backup file by
adding ~ to its name.
AUTHORS
Jim Kremer, David Mastronarde
SEE ALSO
tif2mrc
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.12.61 raw2mrc(1)