extracttilts(1) General Commands Manual extracttilts(1)
NAME
extracttilts - Extract tilt angles or other info from image or metadata
file
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. The program can also extract angles stored as attributes
in an HDF file, or from an ".idoc" file saved by SerialEM. Enter an
option to extract one of the other kinds of information available.
In addition to extracting data stored in the extended header of an MRC
image file, 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. Information for which
no specific option is provided can be extracted by providing the name
of the information with the -key option. The program can also extract
attributes that are present for each section in an HDF file, either
with one of the specific options or by name.
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, An image file name is required unless the -other
option is entered.
-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. Thus, you do not supply the name of the .mdoc file
when you use this option. As of IMOD 4.8.7, the program will
look for such a file automatically if the requested values are
not present in the image file header. Thus, this option is no
longer necessary except for forcing the program to ignore values
in the header and access the .mdoc file first.
-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. Use this
option if the .mdoc file name does not start with the input
image file name, or if the image file is not available. If you
do omit an image input file and want an output file, you must
specify it with -output instead of as a non-option argument.
-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 script-
ing, which range from 0 to 1 and differ by a scaling factor from
the percent C2 readout in the Tecnai user interface. On the
JEOL, they correspond to the percent C3 readout shown in Seri-
alEM.
-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.
-mintilt (-mi) OR -MinimumTiltAndStartAngle
Output the minimum tilt angle and the view number at which it
-fixed (-f) OR -FixedDoseForInfoFile Floating point
Produce a dose information file to be used in dose weighting,
based on the fixed dose per image entered here and the image
time stamps in the image file. The input image file must be
derived from FEI software and have an extended header in the new
style (FEI1 type).
-aretomo (-ar) OR -DoseFileForAreTomo
Make a dose weighting file where each line lists the tilt angle
and the cumulative prior dose, a format accepted by AreTomo.
This option can be used either when there is an .mdoc file from
which cumulative doses can be obtained or deduced, or when mak-
ing a dose weighting file from an FEI file with the -fixed
option.
-prior (-pr) OR -PriorDose Floating point
Prior accumulated dose to assume when producing a dose informa-
tion file with the -fixed option.
-camera (-c) OR -CameraExposure
Extract camera exposure time, in seconds, from metadata file.
-pixel (-pi) 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.
-key (-k) OR -KeyName Text string
Complete name of item to extract from a metadata file or HDF
file. The item will be extracted and printed as a string, so it
can consist of string rather than numeric values.
-attrib (-at) OR -AttributesInHDFfile
Output all attributes in an HDF file to a file in the autodoc
format. Metadata for each image will appear in sections of the
file starting
-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 (-al) 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
EXAMPLES
Some of these examples mention HDF files. Currently the only way to
get information originating in SerialEM into an HDF file is to create
the HDF file from the image stack and .mdoc file. This command works
if SerialEM created a metadata file "rootname.mrc.mdoc":
newstack -mdoc rootname.mrc rootname.hdf
Extract tilt angles from an MRC or HDF file into a file:
extracttilts rootname.st rootname.tlt
Extract magnifications from an MRC or HDF file to the terminal:
extracttilts -mag rootname.st
Extract exposure times from an MRC or HDF file to the terminal (for an
MRC file, rootname.st.mdoc must exist):
extracttilts -camera rootname.st
Extract defocus values for an MRC file that has been renamed to the
terminal
extracttilts -defocus -other rootname.st.mdoc rootname_orig.st
extracttilts -defocus -other rootname.st.mdoc
Extract defocus values for an MRC file that has been renamed to a file
extracttilts -defocus -other rootname.st.mdoc -out rootname.defocus
Extract acquisition times from an MRC file or HDF file to the terminal
extracttilts -key DateTime rootname.st
HISTORY
Written by David Mastronarde, 1999
Converted for PIP input and to get other information, 3/17/04
Access to HDF files and automatic access to mdoc file, 6/5/14
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 extracttilts(1)