DragonFly On-Line Manual Pages
DIMFILTER(1) Generic Mapping Tools DIMFILTER(1)
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.
SEE ALSO
GMT(1), grdfilter(1)
GMT 4.5.14 1 Nov 2015 DIMFILTER(1)