pktools
2.6.7
Processing Kernel for geospatial data

program to filter raster images
Usage: pkfilter i input o output [f filter  perc value  srf file [srf file]* win wavelength [win wavelength]*  wout wavelength fwhm value [wout wavelength fwhm value]* win wavelength [win wavelength]*]
Options: [dx value [dy value]  dz value] [nodata value]
Advanced options: check table
This utility 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 multiband raster inputs. The kernel filter size can be set with the option dz (use odd values only).
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
Example: Filter input.tif in spatial domain with morphological dilation filter with kernel size 3x3.
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  SavitzkyGolay filter (check examples page!) 
percentile  calculate percentile value in window 
proportion  calculate proportion in windoww 
Example: Median filter in spatial domain
Example: Calculate statistical variance in spectral/temporal domain (single output band)
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
Example: Calculate discrete wavelet in spectral/temporal domain
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
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 (NESW) 
sobelyx  diagonal edge detection (NWSE) 
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
short
or long
options (both long=value
and long value
are supported)h
shows basic options only, long option help
shows all options short  long  type  default  description 

i  input  std::string  input image file  
o  output  std::string  Output image file  
f  filter  std::string  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 NESW),sobelyx (diagonal edge detection NWSE), 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)  
srf  srf  std::string  list of ASCII files containing spectral response functions (two columns: wavelength response)  
fwhm  fwhm  double  list of full width half to apply spectral filtering (fwhm band1 fwhm band2 ...)  
dx  dx  double  3  filter kernel size in x, use odd values only 
dy  dy  double  3  filter kernel size in y, use odd values only 
dz  dz  int  filter kernel size in z (spectral/temporal dimension), must be odd (example: 3).. Set dz>0 if 1D filter must be used in band domain  
nodata  nodata  double  nodata value(s) (used for smoothnodata filter)  
r  resamplingmethod  std::string  near  Resampling method for shifting operation (near: nearest neighbour, bilinear: bilinear interpolation). 
co  co  std::string  Creation option for output file. Multiple options can be specified.  
wt  wavelet  std::string  daubechies  wavelet type: daubechies,daubechies_centered, haar, haar_centered, bspline, bspline_centered 
wf  family  int  4  wavelet family (vanishing moment, see also http://www.gnu.org/software/gsl/manual/html_node/DWTInitialization.html) 
nl  nl  int  2  Number of leftward (past) data points used in SavitzkyGolay filter) 
nr  nr  int  2  Number of rightward (future) data points used in SavitzkyGolay filter) 
ld  ld  int  0  order of the derivative desired in SavitzkyGolay filter (e.g., ld=0 for smoothed function) 
m  m  int  2  order of the smoothing polynomial in SavitzkyGolay filter, also equal to the highest conserved moment; usual values are m = 2 or m = 4) 
class  class  short  class value(s) to use for density, erosion, dilation, openening and closing, thresholding  
t  threshold  double  0  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  tap  std::string  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  tapz  double  taps used for spectral filtering  
pad  pad  std::string  symmetric  Padding method for filtering (how to handle edge effects). Choose between: symmetric, replicate, circular, zero (pad with 0). 
win  wavelengthIn  double  list of wavelengths in input spectrum (win band1 win band2 ...)  
wout  wavelengthOut  double  list of wavelengths in output spectrum (wout band1 wout band2 ...)  
d  down  short  1  down sampling factor. Use value 1 for no downsampling). Use value n>1 for downsampling (aggregation) 
beta  beta  std::string  ASCII file with beta for each class transition in Markov Random Field  
interp  interp  std::string  akima  type of interpolation for spectral filtering (see http://www.gnu.org/software/gsl/manual/html_node/InterpolationTypes.html) 
ot  otype  std::string  Data type for output image ({Byte/Int16/UInt16/UInt32/Int32/Float32/Float64/CInt16/CInt32/CFloat32/CFloat64}). Empty string: inherit type from input image  
of  oformat  std::string  GTiff  Output image format (see also gdal_translate). 
ct  ct  std::string  color table (file with 5 columns: id R G B ALFA (0: transparent, 255: solid). Use none to ommit color table  
circ  circular  bool  false  circular disc kernel for dilation and erosion 
Some examples how to use pkfilter can be found here