Apply Savitzky-Golay filter to an ENVI BIL file

apply_savgol_filter.py

#!/usr/bin/env python
"""
Apply Savitzky-Golay filter to an ENVI BIL file

Uses scipy

http://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.savgol_filter.html

And arsf_envi_reader (available from: https://github.com/pmlrsg/arsf_tools)

Dan Clewley
16/06/2016

"""

from __future__ import print_function
import argparse
from scipy import signal

from arsf_envi_reader import numpy_bin_reader
from arsf_envi_reader import envi_header

POLY_ORDER = 3
WINDOW_SIZE = 7

if __name__ == "__main__":
   parser = argparse.ArgumentParser()
   parser.add_argument("inputimage", nargs=1,
                       type=str, help="Input image")
   parser.add_argument("outputimage", nargs=1,
                       type=str, help="Output image")
   args = parser.parse_args()

   # Open input file
   in_data = numpy_bin_reader.BilReader(args.inputimage[0])

   # Open file for output
   out_file = open(args.outputimage[0], "wb")

   for i, line in enumerate(in_data):
      print(" Line {0}/{1}".format(str(i).zfill(len(str(in_data.lines))),
                                   in_data.lines), end="\r")
      # Apply filter
      out_line = signal.savgol_filter(line,
                                      WINDOW_SIZE, POLY_ORDER,
                                      axis=0)
      # Remove negative values
      out_line[out_line < 0] = 0
      # Set output to the same as input
      out_line = out_line.astype(line.dtype)
      out_line.tofile(out_file)

   print(" Line {0}/{0}".format(in_data.lines), end="\n")

   # Copy header
   envi_header.write_envi_header(args.outputimage[0] + ".hdr",
                                 in_data.get_hdr_dict())

   # Close files
   out_file.close()
   in_data = None