NAME¶
pkfilter - program to filter raster images
SYNOPSIS¶
pkfilter
-i input -o output [
-f filter |
-srf file [
-srf file]... |
-fwhm
value [
-fwhm value]... ] [
options] [
advanced
options]
DESCRIPTION¶
pkfilter implements spatial and spectral filtering for raster data. In
the spatial domain (X, Y), the filter typically involves a rectangular
convolution kernel (moving window). To avoid image shifting, the size of the
window should be odd (3, 5, 7, ...). You can set the window sizes in X and Y
directions separately with the options
-dx and
-dy. A circular
kernel (disc) is applied if option
-circ is set. An overview of the
supported filters (option
-f|
--filter) is given below. You can
create customized filters by defining your own filter taps (multiplicative
elements of the filter kernel) via an ascii file (option
-tap). In the
spectral/temporal domain (Z) you can filter multi-band raster inputs. The
kernel filter size can be set with the option
-dz (use odd values
only).
FILTERS IN SPATIAL (DX, DY) AND SPECTRAL/TEMPORAL (DZ) DOMAIN¶
The number of output bands equals number of input bands
| Filter |
Description |
| dilate |
morphological dilation |
| erode |
morphological erosion |
| close |
morpholigical closing (dilate+erode) |
| open |
morpholigical opening (erode+dilate) |
| smoothnodata values |
smooth nodata values (set --nodata option!) |
Example: "Smooth" (interpolate) nodata in spectral/temporal domain (
-dz 1), using a linear interpolation
pkfilter -i input.tif -o smoothed.tif -dz 1 -f smoothnodata -interp linear
Example: Filter
input.tif in spatial domain with morphological dilation
filter with kernel size 3x3.
pkfilter -i input.tif -o dilated.tif -dx 3 -dy 3 -f dilate
In case of moving window, the number of output bands equals number of input
bands. In case dz=1, the single output band is calculated as the result of the
statistical function applied to all bands.
| Filter |
Description |
| nvalid |
report number of valid (not nodata) values in window |
| median |
perform a median filter in spatial (dx, dy) or spectral/temporal (dz)
domain |
| var |
calculate variance in window |
| min |
calculate minimum in window |
| max |
calculate maximum in window |
| sum |
calculate sum in window |
| mean |
calculate mean in window |
| stdev |
calculate standard deviation in window |
| savgolay |
Savitzky-Golay filter (check examples page!) |
| percentile |
calculate percentile value in window |
| proportion |
calculate proportion in window |
Example: Median filter in spatial domain
pkfilter -i input.tif -o median.tif -dx 3 -dy 3 -f median
Example: Calculate statistical variance in spectral/temporal domain (single
output band)
pkfilter -i input.tif -o var.tif -dz 1 -f var
WAVELET FILTERS¶
The number of output bands equals number of input bands
| Filter |
Description |
| dwt |
discrete wavelet transform |
| dwti |
discrete inverse wavelet transform |
| dwt_cut |
discrete wavelet + inverse transform, using threshold option to cut
percentile of coefficients |
Example: Calculate discrete wavelet in spatial domain
pkfilter -i lena.tif -o lena_dwt.tif -f dwt
Example: Calculate discrete wavelet in spectral/temporal domain
pkfilter -i timeseries.tif -o dwt.tif -f dwt -dz 1
The number of output bands equals number of input bands
| Filter |
Description |
| dwt_cut_from |
discrete wavelet + inverse transform, setting all high frequence
coefficients to zero (scale >= threshold) |
Example: Calculate low frequency time series based on discrete wavelet + inverse
transform in spectral/temporal domain, retaining only coefficients until scale
3.
pkfilter -i timeseries.tif -o lowfrequency.tif -f dwt_cut_from -dz 1 -t 4
FILTERS IN SPATIAL DOMAIN ONLY (DX, DY > 1 AND ODD).¶
The number of output bands equals number of input bands.
| Filter |
Description |
| mrf |
Markov random field |
| ismin |
pixel is minimum? |
| ismax |
pixel is maximum? |
| shift |
perform a pixel shift in spatial window |
| scramble |
scramble pixels in a spatial window |
| mode (majority voting) |
perform a majority voring (set --class option) |
| sobelx |
horizontal edge detection |
| sobely |
vertical edge detection |
| sobelxy |
diagonal edge detection (NE-SW) |
| sobelyx |
diagonal edge detection (NW-SE) |
| countid |
count digital numbers in window |
| order |
rank pixels in order |
| density |
calculated the density |
| homog |
central pixel must be identical to all other pixels within window |
| heterog |
central pixel must be different than all other pixels within window |
| sauvola |
Sauvola's thresholding method |
Example: Sobel edge detection in horizontal direction
pkfilter -i lena.tif -o sobelx.tif -f solbelx -dx 5 -dy 5
OPTIONS¶
- -i filename, --input filename
- input image
- -o filename, --output filename
- output classification image
- -f filter, --filter filter
- filter function (nvalid, median, var, min, max, sum, mean, dilate, erode,
close, open, homog (central pixel must be identical to all other pixels
within window), heterog (central pixel must be different than all other
pixels within window), sobelx (horizontal edge detection), sobely
(vertical edge detection), sobelxy (diagonal edge detection NE-SW),sobelyx
(diagonal edge detection NW-SE), density, countid, mode (majority voting,
only for classes), smoothnodata (smooth nodata values only) values, ismin,
ismax, order (rank pixels in order), stdev, mrf, dwt, dwti, dwt_cut,
dwt_cut_from, scramble, shift, savgolay, percentile, proportion)
- -dx value, --dx value
- filter kernel size in x, use odd values only
- -dy value, --dy value
- filter kernel size in y, use odd values only
- -dz value, --dz value
- filter kernel size in z (band or spectral dimension), must be odd
(example: 3). Set dz>0 if 1-D filter must be used in band domain
- -nodata value, --nodata value
- nodata value(s) (used for smoothnodata filter)
- -v level, --verbose level
- verbose mode if > 0
Advanced options
- -circ, --circular
- circular disc kernel for dilation and erosion
- -r method, --resampling-method method
- Resampling method for shifting operation (near: nearest neighbour,
bilinear: bi-linear interpolation).
- -co option, --co option
- Creation option for output file. Multiple options can be specified.
- -wt type, --wavelet type
- wavelet type: daubechies,daubechies_centered, haar, haar_centered,
bspline, bspline_centered
- -wf family, --wf family
- wavelet family (vanishing moment, see also
http://www.gnu.org/software/gsl/manual/html_node/DWT-Initialization.html)
- -class value, --class value
- class value(s) to use for density, erosion, dilation, openening and
closing, thresholding
- -t threshold, --threshold threshold
- threshold value(s) to use for threshold filter (one for each class), or
threshold to cut for dwt_cut (use 0 to keep all) or dwt_cut_from, or sigma
for shift
- -tap filename, --tap filename
- text file containing taps used for spatial filtering (from ul to lr). Use
dimX and dimY to specify tap dimensions in x and y. Leave empty for not
using taps
- -tapz value, --tapz value
- taps used for spectral filtering
- -pad method, --pad method
- Padding method for filtering (how to handle edge effects). Choose between:
symmetric, replicate, circular, constant (pad with 0).
- -fwhm value, --fwhm value
- list of full width half to apply spectral filtering ( -fwhm
band1 -fwhm band2 ...)
- -srf filename, --srf filename
- list of ASCII files containing spectral response functions (two columns:
wavelength response)
- -win col, --wavelengthIn col
- column number of input ASCII file containing wavelengths
- -wout value, --wavelengthOut value
- list of wavelengths in output spectrum ( -wout band1
-wout band2 ...)
- -down value, --down value
- down sampling factor. Use value 1 for no downsampling). Use value n>1
for downsampling (aggregation)
- -beta filename, --beta filename
- ASCII file with beta for each class transition in Markov Random Field
- -eps value, --eps value
- error marging for linear feature
- -l1, --l1
- obtain longest object length for linear feature
- -a1, --a1
- obtain angle found for longest object length for linear feature
- -a2, --a2
- obtain angle found for shortest object length for linear feature
- -interp type, --interp type
- type of interpolation for spectral filtering (see
http://www.gnu.org/software/gsl/manual/html_node/Interpolation-Types.html)
- -ot type, --otype type
- Data type for output image ({Byte / Int16 / UInt16 / UInt32 / Int32 /
Float32 / Float64 / CInt16 / CInt32 / CFloat32 / CFloat64}). Empty string:
inherit type from input image
- -of GDALformat, --oformat GDALformat
- Output image format (see also gdal_translate(1)).
- -ct filename, --ct filename
- color table (file with 5 columns: id R G B ALFA (0: transparent, 255:
solid)). Use none to ommit color table
EXAMPLE¶
Filtering in spatial domain
Filter input.tif with morphological dilation filter. Use a circular kernel
(instead of rectangular) of size 3x3.
pkfilter -i input.tif -o filter.tif -dx 3 -dy 3 -f dilate -circ
Similar to previous example, but consider only values of 255 for filtering
operation. Typical usage: dilate cloud values in input image that are flagged
as 255
pkfilter -i input.tif -o filter.tif -dx 3 -dy 3 -class 255 -f dilate -circ
Filtering in spectral/temporal domain
Calculate the median value for each pixel, calculated on a moving window of
width 3 (
-dz 3) over all input bands. The output raster dataset
will contain as many bands as the input raster dataset.
pkfilter -i input.tif -o filter_stdev.tif -dz 3 -f median
No moving window (
-dz 1). Calculate the standard deviation for
each pixel, calculated on all input bands. The output raster dataset will
contain a single band only.
pkfilter -i input.tif -o filter_stdev.tif -dz 1 -f stdev
"Smooth" (interpolate) nodata in spectral/temporal domain (
-dz
1), using a linear interpolation. The following interpolation types are
supported: akima (default), linear, polynomial, cspline, cspline_periodic,
akima_periodic (please check gsl
⟨http://www.gnu.org/software/gsl/manual/html_node/Interpolation-Types.html⟩
page for more information on the interpolation types).
pkfilter -i input.tif -o input_smoothed.tif -dz 1 -f smoothnodata -interp linear
