edmont
edmont(1) General Commands Manual edmont(1)
NAME
edmont - to edit, combine, split apart, bin, and restack montages
SYNOPSIS
edmont [options] input_file(s) output_file
DESCRIPTION
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.
OPTIONS
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
parentheses.
-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
accumulate)
-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
files.
-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
range.
-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
file.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
HISTORY
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.
SEE ALSO
blendmont, newstack, reducemont
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.2.0 edmont(1)