extracttilts(1)                                                extracttilts(1)



NAME
       extracttilts - Extract tilt angles or other info from image file header

SYNOPSIS
       extracttilts  [option] input_image_file [output_file]

DESCRIPTION
       Extracttilts will extract one kind of information from the header of an
       image file, if it is present, and produce a file with a list of the
       values.  The default behavior is to extract tilt angles; these can be
       extracted from headers in the Agard/FEI format or from headers produced
       by SerialEM.  Enter an option to extract one of the other kinds of
       information written by SerialEM.

       In addition to extracting data stored in the image file header, the
       program can extract from a metadata file written by SerialEM in the
       autodoc format.  A wider range of information can be stored in such a
       file than in the header.  The metadata file must have the same number
       of sections as the image file.

OPTIONS
       Extracttilts uses the PIP package for input (see the manual page for
       pip). Thus, the following 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 (-inp) OR -InputFile    File name
              Image file with header information to extract.  If this option
              is not entered, the first non-option argument will be taken as
              the input file.

       -output (-ou) OR -OutputFile   File name
              Output file for header values.  If this option is not entered,
              the second non-option argument will be taken as the output file.
              If no output file is given, the values are printed to standard
              output.

       -mdoc (-md) OR -MdocMetadataFile
              Obtain values from a metadata file named with the name of the
              input file plus '.mdoc', instead of from the extended header of
              the image file.  A file with this name is generated by SerialEM
              when an option is selected to save extra information in a meta-
              data file.

       -other (-ot) OR -OtherMetadataFile       File name
              Obtain values from the metadata file with the given name,
              instead of from the extended header of the image file.

       -tilts (-t) OR -TiltAngles
              Extract tilt angles from header or metadata file (the default
              behavior).  The angles are in degrees.

       -stage (-s) OR -StagePositions
              Extract stage positions from header or metadata file.  The posi-
              tions are in microns.

       -mag (-ma) OR -Magnifications
              Extract magnifications from header or metadata file.

       -intensities (-int) OR -Intensities
              Extract intensities from header or metadata file.  On the Tec-
              nai, these are the intensity values reported by Tecnai
              scripting, which range from 0 to 1 and differ by a scaling fac-
              tor from the percent C2 readout in the Tecnai user interface.
              On the JEOL, they correspond to the percent C3 readout shown in
              SerialEM.

       -exp (-e) OR -ExposureDose
              Extract incident dose on specimen during camera exposure,
              referred to as exposure dose in SerialEM.  The units are elec-
              trons per square Angstrom.

       -camera (-c) OR -CameraExposure
              Extract camera exposure time, in seconds, from metadata file.

       -pixel (-p) OR -PixelSpacing
              Extract pixel size in Angstroms from metadata file

       -defocus (-d) OR -Defocus
              Extract defocus in microns from metadata file.  The value is the
              focus readout of the microscope, not the defocus measured by
              autofocusing.

       -warn (-w) OR -WarnIfTiltsSuspicious
              When extracting tilt angles, warn if more than half of them are
              near zero or any are bigger than 95 degrees.

       -all (-a) OR -AllPieces
              Extract the selected item for all pieces of a montage.  The
              default is to output the value for the last piece of the montage
              at each Z value.

       -help (-h) OR -usage
              Print help output

       -StandardInput
              Read parameter entries from standard input.

       If the program is started with no command line arguments, it reverts to
       interactive input with the following entries:

       Image file with tilt information
       Output file for tilt angles, or Return to print to standard output


HISTORY
       Written by David Mastronarde, 1999
       Converted for PIP input and to get other information, 3/17/04

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                     extracttilts(1)