dimfilter(1) GMT dimfilter(1)
NAME
dimfilter - Directional filtering of 2-D gridded files in the space (or
time) domain
SYNOPSIS
dimfilter input_file.nc -Ddistance_flag
-Fxwidth[mode] -Goutput_file.nc
-Nxsectors [ -Qcols ] [ -Iincrement ] [ -Rregion ] [ -T ] [
-V[level] ] [ -fflags ]
Note: No space is allowed between the option flag and the associated
arguments.
DESCRIPTION
dimfilter will filter a .nc 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 fil-
ter. It computes distances using Cartesian or Spherical geometries.
The output .nc file can optionally be generated as a subregion of the
input and/or with a new -Increment. In this way, one may have aextra
spacea in the input data so that there will be no edge effects for the
output grid. 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 rough unless the input data is noise-free. Thus, an additional fil-
tering (e.g., Gaussian via grdfilter) of the DiM-filtered data is gen-
erally recommended.
REQUIRED ARGUMENTS
input_file.nc
The data grid to be filtered.
-Ddistance_flag
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.
-Fxwidth[mode]
Sets the primary filter type. Choose among convolution and
non-convolution filters. Append the filter code x 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.
-Nxsectors
Sets the secondary filter type x and the number of bow-tie sec-
tors. sectors must be integer and larger than 0. When 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.
-Goutput_file.nc
output_file.nc is the output of the filter.
OPTIONAL ARGUMENTS
-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 registra-
tion as the input grid].
-Qcols cols is the total number of columns in the input text table
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 is used to conduct the error analysis.
-V[level] (more a|)
Select verbosity level [c].
-f[i|o]colinfo (more a|)
Specify data types of input and/or output columns.
-^ or just -
Print a short message about the syntax of the command, then
exits (NOTE: on Windows just use -).
-+ or just +
Print an extensive usage (help) message, including the explana-
tion of any module-specific option (but not the GMT common
options), then exits.
-? or no arguments
Print a complete usage (help) message, including the explanation
of all options, then exits.
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 apackinga of grids, writing out floating point
data as 1- or 2-byte integers. (more a|)
GEOGRAPHICAL AND TIME COORDINATES
When the output grid type is netCDF, the coordinates will be labeled
alongitudea, alatitudea, or atimea 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 -R90w/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 gmt.conf 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.nc 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 spheri-
cal distance calculations, you need:
gmt dimfilter north_pacific_dbdb5.nc -Gfiltered_pacific.nc -Fm600 -D4 \
-Nl6 -R150/250/10/40 -I0.5 -V
Suppose that cape_verde.nc is a file of 0.5 minute bathymetry from 32W
to 15W and 8N to 25N, and you want to remove small-length-scale fea-
tures 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:
gmt dimfilter cape_verde.nc -Gt.nc -Fm220 -Nl8 -D2 -R-27.5/-20.5/12.5/19.5 -I2m -V
gmt grdfilter t.nc -Gcape_swell.nc -Fg50 -D2 -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.nc f110.nc f120.nc f130.nc), 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.
Then, you will need to do:
gmt grd2xyz f100.nc -Z > f100.d
gmt grd2xyz f110.nc -Z > f110.d
gmt grd2xyz f120.nc -Z > f120.d
gmt grd2xyz f130.nc -Z > f130.d
paste f100.d f110.d f120.d f130.d > depths.d
gmt 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 acirclea crosses a periodic (0-360) boundary or contains a geo-
graphic 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 spa-
tial 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)
COPYRIGHT
2017, P. Wessel, W. H. F. Smith, R. Scharroo, J. Luis, and F. Wobbe
5.4.2 Jun 24, 2017 dimfilter(1)
gmt5 5.4.2 - Generated Wed Jun 28 15:17:35 CDT 2017