multifiltsetup(1)           General Commands Manual          multifiltsetup(1)



NAME
       multifiltsetup - Test multiple reconstruction filter values on a sub-
       volume

SYNOPSIS
       multifiltsetup  options  tilt_com_file_name

DESCRIPTION
       Multifiltsetup produces command files for reconstructing a defined
       region of a tomogram with a series of values for one of the types of
       radial filters in Tilt.  Four kinds of filters can be varied, but
       only one kind can be changed on any given run.

       Two filters providing an alternative form for the ramp function, the
       SIRT-like filter and "exact filters", can be varied with:
         -fake    List of iteration values
         -exact   List of "object sizes"
       The two alternative high-frequency filtering options, the standard
       Gaussian filter and the Hamming-like filter, can be varied with:
         -cutoff   List of cutoffs and/or -falloff  List of falloffs
         -hamming  List of start frequencies

       The behavior and requirements when varying the Gaussian filter are com-
       plicated because there are two parameters.  The rules are these:
         1) If both -cutoff and -falloff are entered, either both must have
       the same number of frequencies listed, or one must have only a single
       value.
         2) If -falloff is entered but not -cutoff, a fixed cutoff for all
       runs is taken from the "RADIAL" entry in the input command file.
         3) If -falloff is entered with multiple values and -cutoff with one
       value, that cutoff is used for all of the runs
         4) If -cutoff is entered but not -falloff, a fixed ratio of falloff
       to cutoff is taken from the ratio of the falloff and cutoff values of
       the "RADIAL" entry in the input command file.
         5) If -cutoff is entered with multiple values and -falloff with one
       value, a fixed ratio of falloff to cutoff is taken from the ratio of
       the entered falloff value and the first cutoff.
         6) If -cutoff is entered with multiple values and a falloff is not
       entered for each, then the falloff values will all be this fixed ratio
       times their respective cutoff values.
       This scaling will not work if the first cutoff is 0, or if the falloff
       is 0.

       For example, if -cutoff is entered as "0.1,0.2,0.3", no -falloff is
       entered, and the "RADIAL" entry in the file is "0.35 0.035", then the
       ratio will be 0.035 / 0.35 = 0.1 and the falloffs will be 0.01, 0.02,
       and 0.03.  If -falloff is entered with just "0.02", the ratio will be
       0.02 / 0.1 = 0.2 and the falloffs will be 0.02, 0.04, and 0.06.

       Unless options are entered to specify a subvolume, the default is to
       reconstruction the full area with the same thickness.

OPTIONS
       Multifiltsetup 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.

       -com (-co) OR -CommandFile     File name
              Command file for reconstruction, which can be entered with or
              without its extension of ".com".  If this option is not entered,
              a non-option argument is used for the command file.

       -fake (-fak) OR -FakeSIRTiterations      List of integer ranges
              List of iteration numbers for runs with SIRT-like filtering.
              Ranges are allowed.  An entry for "ExactFilterSize" will be
              removed from the command file and the high-frequency filtering
              option will be retained.

       -exact (-e) OR -ExactObjectSizes    List of integer ranges
              List of "object sizes" for runs with "exact filters".  Ranges
              are allowed.  An entry for "FakeSIRTiterations" will be will be
              removed from the command file and the high-frequency filtering
              option will be retained.

       -hamming (-ha) OR -HammingLikeStarts     Multiple floats
              Set of starting frequencies, in reciprocal pixels (0 - 0.5) for
              a Hamming-like filter.  An entry for "RADIAL" will be removed
              from the command file and any options about the initial form of
              the filter will be retained.

       -cutoffs (-cu) OR -GaussianCutoffs       Multiple floats
              Set of frequencies for the cutoff of the standard Gaussian fil-
              ter, in reciprocal pixels (0 - 0.5).  See the rules above for
              how the cutoff and falloff vary when this option does not have
              the same number of entries as the -falloff option.

       -falloffs (-fal) OR -GaussianFalloffs    Multiple floats
              Set of frequencies for the falloff of the standard Gaussian fil-
              ter, in reciprocal pixels (0 - 0.5).

       -width (-w) OR -WidthInX       Integer
              Width of tomograms to build, in unbinned pixels.  The default is
              to do the whole extent in X.  An existing "WIDTH" entry in the
              command file will be replaced or removed.

       -ysize (-ysi) OR -SizeInY      Integer
              Size in Y (the Y dimension of the aligned stack) of tomograms to
              build, in unbinned pixels.  The default is to do the whole
              extent in Y.  An existing "SLICE" entry in the command file will
              be replaced or removed.

       -thick (-t) OR -ThicknessInZ   Integer
              Thickness of tomograms to make, in unbinned pixels.  The default
              is to use the "THICKNESS" entry in the command file.

       -xshift (-x) OR -ShiftInX      Floating point
              Shift of tomograms in X, in unbinned pixels.  For this and the
              other shift entries, a positive shift will bring an area at neg-
              ative offset to the center.  The default is 0 shift; an existing
              "SHIFT" entry in the command file will be replaced or removed.

       -yshift (-ysh) OR -ShiftInY    Integer
              Shift of tomograms in Y (the Y dimension of the aligned stack),
              in unbinned pixels. The default is 0 shift.

       -zshift (-z) OR -ShiftInDepth       Floating point
              Shift of tomograms in Z (the depth dimension), in unbinned pix-
              els.  The default is to use the Z shift value from the "SHIFT"
              entry in the command file, if any.

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

       -StandardInput
              Read parameter entries from standard input


FILES
       The command files are named "tilt_mulfil-*.com" for an input file
       "tilt.com", "tilt_mulfila-*.com" for "tilta.com", etc.  For -fake and
       -exact options, they produce tomograms "setname_slfinnn.mrc" and "set-
       name_efosnnn.mrc", where "setname" is the root name of the data set and
       "nnn" is the iteration number or object size, respectively, and all
       files in a run will be 2, 3, or 4 digits with leading zeros as needed.
       For the -hamming option, the tomograms are "setname_hlfs0.xxx.mrc"
       where "0.xxx" is the starting frequency to 3 decimal places.  When
       varying the Gaussian filter, the tomogram names contain both the cutoff
       and falloff as "setname_gfc0.xxx-f0.xxx.mrc".

AUTHOR
       David Mastronarde

SEE ALSO
       tilt, proceschunks(1)

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                4.12.35                  multifiltsetup(1)