edmont(1)                   General Commands Manual                  edmont(1)

       edmont - to edit, combine, split apart, bin, and restack montages

       edmont  [options]  input_file(s)  output_file

       Edmont is a general montage editor than can be used to extract a subset
       of a montage, combine multiple montaged files or split a montage into
       multiple files, rescale images to a common range or mean of density,
       and  bin the montage pieces.

       If there are piece coordinates in the extended header of the image
       file, the program will transfer those coordinates to the output file.
       These coordinates can be used instead of ones from a piece list file.
       If one wishes to have sections numbered sequentially from zero, or the
       X and Y coordinates of an extracted subset of pieces shifted to start
       at zero, the coordinates in the header of the output file will be modi-
       fied appropriately.

       The general requirement when combining multiple montages is that they
       all have the same image size and overlap between adjacent pieces, and
       that they all fit on the same regular grid of positions.  They may have
       different numbers of pieces in each direction, and pieces at different
       locations; indeed, it is possible to assemble a montage from different
       files containing laterally adjacent pieces.

       If floating is not selected, data are rescaled uniformly, if necessary,
       to fit a new output data mode.  Specifically, data will be rescaled
       when going between byte and signed or unsigned integer modes, but only
       by the difference in data range between input and output modes.  Use
       the -1 floating option to have the data scaled to fill the data range
       instead.  If the input file has real data (mode 2) that is not confined
       to the range of the output mode, then you must specify one of the three
       kinds of floating to avoid truncating the data.

       Edmont uses the PIP package for input exclusively (see the manual page
       for pip).  The following options can be specified either as command
       line arguments (with the -) or one per line in a command file or param-
       eter file (without the -).  Options can be abbreviated to unique let-
       ters; the currently valid abbreviations for short names are shown in

       -imin (-imi) OR -ImageInputFile     File name
              Montaged image input file.  If there is more than one non-option
              argument, all except the last one are also taken as image input
              files, following any files entered with this option.  (Succes-
              sive entries accumulate)

       -plin (-pli) OR -PieceListInput     File name
              File with list of piece coordinates for image input file.  This
              file may be omitted if the image file has piece coordinates in
              its header, but if this entry is made for any image file, there
              must be an entry for each image file.  However, a filename of
              "none" can be entered if some image files have coordinates in
              the header and some do not.  (Successive entries accumulate)

       -imout (-imo) OR -ImageOutputFile   File name
              Output file for montaged images.  If there are any non-option
              arguments, the last one is also taken as an output image file,
              following any filenames entered with this option.  (Successive
              entries accumulate)

       -plout (-plo) OR -PieceListOutput   File name
              File for list of coordinates of pieces in output image file.
              This entry may be omitted if the coordinates are being placed in
              the image header, but is required if there are input piece list
              files.  (Successive entries accumulate)

       -mdoc (-md) OR -UseMdocFiles
              This option allows data about each image section in metadata
              autodoc (.mdoc) files to be transferred and managed much as data
              in the extended header of an MRC file are.  With it selected,
              the program will search for a matching .mdoc file for each input
              file that is not HDF, and create a matching .mdoc file for each
              output file that is not HDF.  (A matching file is one with .mdoc
              appended to the image filename, as SerialEM creates).  Metadata
              about each image slice in ZValue sections will be transferred
              between autodocs and the ZValue will be renumbered appropri-
              ately.  Thus, data can be transferred from one .mdoc to another,
              if input and output files are MRC; from an .mdoc into the
              attributes of an HDF file if input is MRC and output is HDF; or
              from HDF attributes into an .mdoc if input is HDF and output is
              MRC.  When input and output are both HDF, attributes are trans-
              ferred automatically.

       -secs (-se) OR -SectionsToRead      List of integer ranges
              List of sections to read from an input file, numbered from 0.
              Ranges may be entered (e.g., 1-3,5,8), and / may be used to
              specify all sections in the file.  If multiple lists are
              entered, each one will be applied to the respective input file.
              If no list is entered for a file, all sections will be read.
              Note that montages can have missing sections, and a list that
              includes such missing sections will generate an error.  (Succes-
              sive entries accumulate)

       -fromone (-fr) OR -NumberedFromOne
              With this option section numbers entered with the -secs option
              are numbered from 1 instead of 0.

       -numout (-n) OR -NumberToOutput     Multiple integers
              Number of sections to write to each output file, when there are
              multiple output files.  These numbers may be listed in sequence
              in one entry, or in several entries.  If there is one output
              file per section being written, then one section will be written
              to each file and this entry is not needed.  (Successive entries

       -mode (-mo) OR -ModeToOutput   Integer
              The storage mode of the output file; 0 for byte, 1 for 16-bit
              signed integer, 6 for 16-bit unsigned integer, 2 for 32-bit
              floating point, or 12 for 16-bit floating point.  The default is
              the mode of the first input file, although the default mode of
              floating point output for MRC files is governed by the value of
              environment variable IMOD_WRITE_FLOATS_16BIT.  Mode 12 is
              allowed only if the output format is MRC.

       -xminmax (-xm) OR -XMinAndMax       Two integers
              Minimum and maximum X coordinates to include in output.  Any
              piece containing pixels within this range will be included in
              the output.  Thus, you need to pick coordinates that are far
              enough away from the edges of a piece to exclude overlapping
              pieces that you do not want.

       -yminmax (-ym) OR -YMinAndMax       Two integers
              Minimum and maximum Y coordinates to include in output.  Any
              piece containing pixels within this range will be included in
              the output.

       -xframes (-xf) OR -XFrameMinAndMax       Two integers
              Starting and ending frames in X to include in the output.
              Frames are numbered from one for the leftmost frame in any of
              the input files, up to the rightmost frame in any of the input

       -yframes (-yf) OR -YFrameMinAndMax       Two integers
              Starting and ending frames in Y to include in the output.
              Frames are numbered from 1 for the bottommost frame of any input
              file, up to the topmost frame in any input file.

       -float (-fl) OR -FloatDensities     Integer
              Adjust densities of sections individually or together.  Enter 1
              for each section to fill the data range, 2 to scale sections to
              common mean and standard deviation, or -1 to scale all sections
              by the same factors to fill the data range.  The latter scaling
              occurs only when changing from one fixed point mode (0, 1, or 6)
              to another.  It is most useful when converting from an integer
              to a byte mode, because otherwise the data will fill only the
              fraction of the byte range that they occupy in the integer

       -bin (-b) OR -BinByFactor      Integer
              Use binning to reduce images in size by the given factor.
              Because coordinates are kept as integers, binning may not pro-
              duce exactly the same spacing between pieces as in the original
              data.  This is not a problem if the data are still to be
              blended, since Blendmont can adjust for any shifts induced by
              the binning.  However, if data are already blended, the pieces
              will not be precisely aligned unless both the original image
              size and overlap are evenly divisible by the the binning.  Use
              Reducemont for binning if this is not the case.

       -exclude (-e) OR -ExclusionModel    File name
              Model file with points on pieces to exclude from output.  This
              option allows you to remove bad pieces from a montage.  To make
              a model, set the object type to scattered points and turn on a
              symbol display so that you can see the points.  Place points
              near the middle of the unwanted pieces.  A point must be in the
              region outside the overlap zones, if overlap is less that one
              quarter of the piece size, or within the central half of the
              piece if overlap is higher than that.  If overlap is high, you
              will have to anticipate where the entire piece is located in the
              3dmod display, since pieces are generally overlaid on two sides
              by overlapping pieces that occur later in the image file.  All
              points in the model will be used as exclusion points.

       -renumber (-r) OR -RenumberZFromZero
              Renumber Z values to be sequential and start at zero.  This
              option can be used to close up gaps from missing sections or to
              shift the Z values of a subset stack down to start at zero.  It
              is required if you are combining two montages that have pieces
              at the same coordinates.

       -shift (-sh) OR -ShiftXYToZero
              Adjust X and Y piece coordinates to start at zero.  If the data
              are going into multiple output files, the coordinates of the
              entire collection of output sections will start at zero, but the
              coordinates in any one file may not start at zero.  To achieve
              other shifts of piece coordinates, use Edpiecepoint.

       -param (-pa) OR -ParameterFile      Parameter file
              Read parameter entries as keyword-value pairs from a parameter

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

              Read parameter entries from standard input.

       Written by David Mastronarde, 5/9/89
       1999: added ability to knock out pieces.
       1/3/00: made it handle extra header data, made scaling logic more
       like NEWSTACK and made sure it could handle negative integers.
       10/24/00: made it actually use coordinates in header and renumber
       sections sequentially.
       7/2/10: Converted to PIP, used memory allocation, added many error checks,
       default section lists, binning, shifting, subsetting by frame number, and
       more flexibility in assembling montages.

       blendmont, newstack, reducemont

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.32                          edmont(1)