modifymdocs(1)              General Commands Manual             modifymdocs(1)



NAME
       modifymdocs - Reorder mdoc file by tilt angle and/or replace dose or
       size information

SYNOPSIS
       modifymdocs [options] inputFile outputFile

DESCRIPTION
       Modifymdocs can change entries in the ".mdoc" file (metadata autodoc)
       file associated with an image file and can reorder the file so that the
       sections are in order by tilt angle.  The entries in an ".mdoc" file
       produced by SerialEM are documented here:
          https://bio3d.colorado.edu/SerialEM/hlp/html/about_formats.htm#meta-
       data

       Some of the operations that Modifymdocs does correspond to what Align-
       frames(1) does when it produces an adjusted ".mdoc" file matching the
       tilt series of aligned frames that it produces.  Modifymdocs can rear-
       range the sections in the ".mdoc" so that are in order by tilt angle.
       It can insert or modify the dose information in the file so that it has
       correct values and can be used for dose weighting in IMOD.  It can also
       change the binning and pixel size entries in the output file, similar
       to what Alignframes does.  It is potentially useful for 1) inserting
       dose information into an ".mdoc" file lacking it, prior to running
       Alignframes; 2) getting a reordered ".mdoc" file from a file in
       order by original acquisition when aligning with other software; 3)
       fixing dose information or other entries in faulty ".mdoc" files pro-
       vided by acquisition software other than SerialEM.

OPTIONS
       Modifymdocs 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 (-i) OR -InputFile      File name
              Name of input .mdoc file to modify

       -output (-ou) OR -OutputFile   File name
              Name of modified .mdoc file to write

       -order (-or) OR -OrderToProduce     Integer
              Enter 1 to reorder file with tilt angles from negative to posi-
              tive, -1 to reorder from positive to negative, or 0 not to
              reorder file (the default).

       -dose (-d) OR -ElectronDosePerImage      Floating point
              Electron dose applied to each image in electrons per square
              Angstrom. The value will replace existing dose information, if
              any, and PriorRecordDose entries will be inserted based on the
              time information in the file (TimeStamp or DateTime entries).
              If there are no such entries, the mdoc is assumed to be in order
              by time of acquisition.

       -binning (-b) OR -BinningToScaleTo       Floating point
              A new binning value to replace the existing Binning entries in
              the .mdoc file.  PixelSpacing and ImageSize entries will be
              scaled by the ratio of new to old binnings, although the Image-
              Size may not match the larger size actually obtained in camera
              frames.

       -pixel (-pi) OR -PixelSpacingToSet       Floating point
              Pixel size in Angstroms to set in the output file; this replaces
              existing PixelSpacing entries and overrides the pixel siz ethat
              would be produced by scaling for a new binning.

       -param (-pa) OR -ParameterFile      Parameter file
              Read parameter entries from file

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

       -StandardInput
              Read parameter entries from standard input


AUTHOR
       David Mastronarde

SEE ALSO
       alignframes

BUGS
       Email bug reports to mast at colorado dot edu.



                                                                modifymdocs(1)