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.