Ubuntu Manpage: dimfilter - Directional filtering of 2-D gridded files in the space (or time) domain

NAME

       dimfilter - Directional filtering of 2-D gridded files in the space (or time) domain

SYNOPSIS

       dimfilter      input_file.grd      -Ddistance_flag      -F<filtertype><width>[mode]     -Goutput_file.grd
       -N<filtertype><n_sectors> -Qcols [ -Ixinc[unit][=|+][/yinc[unit][=|+]] ] [ -Rwest/east/south/north[r] ] [
       -T ] [ -V ]

DESCRIPTION

dimfilter will filter a .grd file in the space (or time) domain by dividing the given filter circle into
n_sectors, applying one of the selected primary convolution or non-convolution filters to each sector,
and choosing the final outcome according to the selected secondary filter. It computes distances using
Cartesian or Spherical geometries. The output .grd file can optionally be generated as a sub-Region of
the input and/or with a new -I ncrement. In this way, one may have "extra space" in the input data so
that the edges will not be used and the output can be within one-half-width of the input edges. If the
filter is low-pass, then the output may be less frequently sampled than the input. -Q is for the error
analysis mode and only requires the total number of columns in the input file, which contains the
filtered depths. Finally, one should know that dimfilter will not produce a smooth output as other
spatial filters do because it returns a minimum median out of N medians of N sectors. The output can be
edgy unless the input data is noise-free. Thus, an additional filtering (e.g., Gaussian) to the DiM-
filtered data is generally recommended.

input_file.grd
The file of points to be filtered.

-D Distance flag tells how grid (x,y) relates to filter width as follows:

flag = 0: grid (x,y) same units as width, Cartesian distances.
flag = 1: grid (x,y) in degrees, width in kilometers, Cartesian distances.
flag = 2: grid (x,y) in degrees, width in km, dx scaled by cos(middle y), Cartesian distances.

The above options are fastest because they allow weight matrix to be computed only once. The next
three options are slower because they recompute weights for each latitude.

flag = 3: grid (x,y) in degrees, width in km, dx scaled by cosine(y), Cartesian distance
calculation.
flag = 4: grid (x,y) in degrees, width in km, Spherical distance calculation.

-F Sets the primary filter type. Choose among convolution and non-convolution filters. Append the
filter code followed by the full diameter width. Available convolution filters are:
(b) Boxcar: All weights are equal.
(c) Cosine Arch: Weights follow a cosine arch curve.
(g) Gaussian: Weights are given by the Gaussian function.
Non-convolution filters are:
(m) Median: Returns median value.
(p) Maximum likelihood probability (a mode estimator): Return modal value. If more than one mode
is found we return their average value. Append - or + to the filter width if you rather want to
return the smallest or largest of the modal values.

-N Sets the secondary filter type and the number of bow-tie sectors. n_sectors must be integer and
larger than 0. When n_sectors is set to 1, the secondary filter is not effective. Available
secondary filters are:
(l) Lower: Return the minimum of all filtered values.
(u) Upper: Return the maximum of all filtered values.
(a) Average: Return the mean of all filtered values.
(m) Median: Return the median of all filtered values.
(p) Mode: Return the mode of all filtered values.

-G output_file.grd is the output of the filter.

OPTIONS

       -I     x_inc  [and  optionally  y_inc]  is  the  output  Increment. Append m to indicate minutes, or c to
              indicate seconds.  If  the new x_inc, y_inc are NOT integer multiples of  the  old  ones  (in  the
              input data), filtering will be considerably slower.  [Default:  Same as input.]

       -R     west, east, south, and north defines the Region of the output points.  [Default:  Same as input.]

       -T     Toggle  the  node  registration for the output grid so as to become the opposite of the input grid
              [Default gives the same registration as the input grid].

       -Q     cols is the total number of columns in the input file.  For this mode, it expects to  read  depths
              consisted  of  several  columns. Each column represents a filtered grid with a filter width, which
              can be obtained by 'grd2xyz -Z'. The outcome will be median, MAD, and mean. So,  the  column  with
              the medians is used to generate the regional component and the column with the MADs to conduct the
              error analysis.

       -V     Selects verbose mode, which will send progress reports to stderr [Default runs "silently"].

GRID FILE FORMATS

By default GMT writes out grid as single precision floats in a COARDS-complaint netCDF file format.
However, GMT is able to produce grid files in many other commonly used grid file formats and also
facilitates so called "packing" of grids, writing out floating point data as 2- or 4-byte integers. To
specify the precision, scale and offset, the user should add the suffix =id[/scale/offset[/nan]], where
id is a two-letter identifier of the grid type and precision, and scale and offset are optional scale
factor and offset to be applied to all grid values, and nan is the value used to indicate missing data.
When reading grids, the format is generally automatically recognized. If not, the same suffix can be
added to input grid file names. See grdreformat(1) and Section 4.17 of the GMT Technical Reference and
Cookbook for more information.

When reading a netCDF file that contains multiple grids, GMT will read, by default, the first
2-dimensional grid that can find in that file. To coax GMT into reading another multi-dimensional
variable in the grid file, append ?varname to the file name, where varname is the name of the variable.
Note that you may need to escape the special meaning of ? in your shell program by putting a backslash in
front of it, or by placing the filename and suffix between quotes or double quotes. The ?varname suffix
can also be used for output grids to specify a variable name different from the default: "z". See
grdreformat(1) and Section 4.18 of the GMT Technical Reference and Cookbook for more information,
particularly on how to read splices of 3-, 4-, or 5-dimensional grids.

GEOGRAPHICAL AND TIME COORDINATES

       When  the  output grid type is netCDF, the coordinates will be labeled "longitude", "latitude", or "time"
       based on the attributes of the input data or grid (if any) or on the -f or -R options. For example,  both
       -f0x  -f1t  and  -R 90w/90e/0t/3t will result in a longitude/time grid. When the x, y, or z coordinate is
       time, it will be stored in the grid as relative time since epoch as specified by TIME_UNIT and TIME_EPOCH
       in the .gmtdefaults file or on the command line.  In addition, the unit attribute of  the  time  variable
       will indicate both this unit and epoch.

EXAMPLES

       Suppose  that  north_pacific_dbdb5.grd  is a file of 5 minute bathymetry from 140E to 260E and 0N to 50N,
       and you want to find the medians of values within a 300km radius (600km full width) of the output points,
       which you choose to be from 150E to 250E and 10N to 40N, and you want the output values every 0.5 degree.
       To prevent the medians from being biased by the sloping plane, you want to divide the filter circle  into
       6  sectors  and  to  choose  the lowest value among 6 medians. Using spherical distance calculations, you
       need:

       dimfilter north_pacific_dbdb5.grd -G filtered_pacific.grd -Fm600 -D 4 -N l6 -R150/250/10/40 -I 0.5 -V

       Suppose that cape_verde.grd is a file of 0.5 minute bathymetry from 32W to 15W and 8N  to  25N,  and  you
       want  to remove small-length-scale features in order to define a swell in an area extending from 27.5W to
       20.5W and 12.5N to 19.5N, and you want  the  output  value  every  2  minute.  Using  cartesian  distance
       calculations, you need:

       dimfilter cape_verde.grd -G t.grd -Fm220 -Nl8 -D 2 -R-27.5/-20.5/12.5/19.5 -I 2m -V
       grdfilter t.grd -G cape_swell.grd -Fg50 -D 2 -V

       Suppose  that you found a range of filter widths for a given area, and you filtered the given bathymetric
       data using the range of filter widths (e.g., f100.grd f110.grd f120.grd f130.grd), and you want to define
       a regional trend using the range of filter widths, and you want to obtain median absolute deviation (MAD)
       estimates at each data point, you need:

       grd2xyz f100.grd -Z > f100.d
       grd2xyz f110.grd -Z > f110.d
       grd2xyz f120.grd -Z > f120.d
       grd2xyz f130.grd -Z > f130.d
       paste f100.d f110.d f120.d f130.d > depths.d
       dimfilter depths.d -Q4 > output.z

LIMITATIONS

       When working with geographic (lat, lon) grids, all three convolution filters (boxcar,  cosine  arch,  and
       gaussian) will properly normalize the filter weights for the variation in gridbox size with latitude, and
       correctly  determine  which  nodes  are  needed  for  the  convolution when the filter "circle" crosses a
       periodic (0-360) boundary or contains a geographic pole.  However, the spatial filters,  such  as  median
       and  mode  filters,  do  not  use weights and thus should only be used on Cartesian grids (or at very low
       latitudes) only.  If you want to apply such spatial filters you should project your data to an equal-area
       projection and run dimfilter on the resulting Cartesian grid.

SCRIPT TEMPLATE

       The dim.template.sh is a skeleton shell script that can be used  to  set  up  a  complete  DiM  analysis,
       including the MAD analysis.

REFERENCE

       Kim,  S.-S.,  and  Wessel,  P.  (2008),  Directional Median Filtering for Regional-Residual Separation of
       Bathymetry, Geochem. Geophys. Geosyst., 9(Q03005), doi:10.1029/2007GC001850.