forked from kilianv/CoastSat_WRL
major updates
Kilian Vos
6 years ago
parent
2e3b90316f
commit
a0b49c7dcf
@ -0,0 +1,62 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<kml xmlns="http://www.opengis.net/kml/2.2">
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<Document>
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<name>NARRA</name>
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<LineStyle>
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</PolyStyle>
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<BalloonStyle>
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<text><![CDATA[<h3>$[name]</h3>]]></text>
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<BalloonStyle>
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<text><![CDATA[<h3>$[name]</h3>]]></text>
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<coordinates>
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151.2957545,-33.7012561,0
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151.297557,-33.7388075,0
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151.312234,-33.7390216,0
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151.311204,-33.701399,0
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151.2957545,-33.7012561,0
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</Document>
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</kml>
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@ -0,0 +1,540 @@
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#!/usr/bin/env python
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###############################################################################
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# $Id$
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#
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# Project: InSAR Peppers
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# Purpose: Module to extract data from many rasters into one output.
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# Author: Frank Warmerdam, warmerdam@pobox.com
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#
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###############################################################################
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# Copyright (c) 2000, Atlantis Scientific Inc. (www.atlsci.com)
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# Copyright (c) 2009-2011, Even Rouault <even dot rouault at mines-paris dot org>
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#
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# This library is free software; you can redistribute it and/or
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# modify it under the terms of the GNU Library General Public
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# License as published by the Free Software Foundation; either
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# version 2 of the License, or (at your option) any later version.
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#
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# This library is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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# Library General Public License for more details.
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#
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# You should have received a copy of the GNU Library General Public
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# License along with this library; if not, write to the
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# Free Software Foundation, Inc., 59 Temple Place - Suite 330,
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# Boston, MA 02111-1307, USA.
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###############################################################################
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# changes 29Apr2011
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# If the input image is a multi-band one, use all the channels in
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# building the stack.
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# anssi.pekkarinen@fao.org
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import math
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import sys
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import time
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from osgeo import gdal
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try:
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progress = gdal.TermProgress_nocb
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except:
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progress = gdal.TermProgress
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__version__ = '$id$'[5:-1]
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verbose = 0
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quiet = 0
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# =============================================================================
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def raster_copy( s_fh, s_xoff, s_yoff, s_xsize, s_ysize, s_band_n,
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t_fh, t_xoff, t_yoff, t_xsize, t_ysize, t_band_n,
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nodata=None ):
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if verbose != 0:
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print('Copy %d,%d,%d,%d to %d,%d,%d,%d.'
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% (s_xoff, s_yoff, s_xsize, s_ysize,
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t_xoff, t_yoff, t_xsize, t_ysize ))
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if nodata is not None:
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return raster_copy_with_nodata(
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s_fh, s_xoff, s_yoff, s_xsize, s_ysize, s_band_n,
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t_fh, t_xoff, t_yoff, t_xsize, t_ysize, t_band_n,
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nodata )
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s_band = s_fh.GetRasterBand( s_band_n )
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m_band = None
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# Works only in binary mode and doesn't take into account
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# intermediate transparency values for compositing.
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if s_band.GetMaskFlags() != gdal.GMF_ALL_VALID:
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m_band = s_band.GetMaskBand()
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elif s_band.GetColorInterpretation() == gdal.GCI_AlphaBand:
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m_band = s_band
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if m_band is not None:
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return raster_copy_with_mask(
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s_fh, s_xoff, s_yoff, s_xsize, s_ysize, s_band_n,
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t_fh, t_xoff, t_yoff, t_xsize, t_ysize, t_band_n,
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m_band )
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s_band = s_fh.GetRasterBand( s_band_n )
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t_band = t_fh.GetRasterBand( t_band_n )
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data = s_band.ReadRaster( s_xoff, s_yoff, s_xsize, s_ysize,
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t_xsize, t_ysize, t_band.DataType )
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t_band.WriteRaster( t_xoff, t_yoff, t_xsize, t_ysize,
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data, t_xsize, t_ysize, t_band.DataType )
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return 0
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# =============================================================================
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def raster_copy_with_nodata( s_fh, s_xoff, s_yoff, s_xsize, s_ysize, s_band_n,
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t_fh, t_xoff, t_yoff, t_xsize, t_ysize, t_band_n,
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nodata ):
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try:
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import numpy as Numeric
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except ImportError:
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import Numeric
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s_band = s_fh.GetRasterBand( s_band_n )
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t_band = t_fh.GetRasterBand( t_band_n )
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data_src = s_band.ReadAsArray( s_xoff, s_yoff, s_xsize, s_ysize,
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t_xsize, t_ysize )
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data_dst = t_band.ReadAsArray( t_xoff, t_yoff, t_xsize, t_ysize )
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nodata_test = Numeric.equal(data_src,nodata)
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to_write = Numeric.choose( nodata_test, (data_src, data_dst) )
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t_band.WriteArray( to_write, t_xoff, t_yoff )
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return 0
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# =============================================================================
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def raster_copy_with_mask( s_fh, s_xoff, s_yoff, s_xsize, s_ysize, s_band_n,
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t_fh, t_xoff, t_yoff, t_xsize, t_ysize, t_band_n,
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m_band ):
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try:
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import numpy as Numeric
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except ImportError:
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import Numeric
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s_band = s_fh.GetRasterBand( s_band_n )
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t_band = t_fh.GetRasterBand( t_band_n )
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data_src = s_band.ReadAsArray( s_xoff, s_yoff, s_xsize, s_ysize,
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t_xsize, t_ysize )
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data_mask = m_band.ReadAsArray( s_xoff, s_yoff, s_xsize, s_ysize,
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t_xsize, t_ysize )
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data_dst = t_band.ReadAsArray( t_xoff, t_yoff, t_xsize, t_ysize )
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mask_test = Numeric.equal(data_mask, 0)
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to_write = Numeric.choose( mask_test, (data_src, data_dst) )
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t_band.WriteArray( to_write, t_xoff, t_yoff )
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return 0
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# =============================================================================
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def names_to_fileinfos( names ):
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"""
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Translate a list of GDAL filenames, into file_info objects.
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names -- list of valid GDAL dataset names.
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Returns a list of file_info objects. There may be less file_info objects
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than names if some of the names could not be opened as GDAL files.
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"""
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file_infos = []
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for name in names:
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fi = file_info()
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if fi.init_from_name( name ) == 1:
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file_infos.append( fi )
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return file_infos
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# *****************************************************************************
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class file_info:
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"""A class holding information about a GDAL file."""
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def init_from_name(self, filename):
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"""
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Initialize file_info from filename
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filename -- Name of file to read.
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Returns 1 on success or 0 if the file can't be opened.
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"""
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fh = gdal.Open( filename )
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if fh is None:
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return 0
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self.filename = filename
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self.bands = fh.RasterCount
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self.xsize = fh.RasterXSize
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self.ysize = fh.RasterYSize
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self.band_type = fh.GetRasterBand(1).DataType
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self.projection = fh.GetProjection()
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self.geotransform = fh.GetGeoTransform()
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self.ulx = self.geotransform[0]
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self.uly = self.geotransform[3]
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self.lrx = self.ulx + self.geotransform[1] * self.xsize
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self.lry = self.uly + self.geotransform[5] * self.ysize
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ct = fh.GetRasterBand(1).GetRasterColorTable()
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if ct is not None:
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self.ct = ct.Clone()
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else:
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self.ct = None
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return 1
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def report( self ):
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print('Filename: '+ self.filename)
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print('File Size: %dx%dx%d'
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% (self.xsize, self.ysize, self.bands))
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print('Pixel Size: %f x %f'
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% (self.geotransform[1],self.geotransform[5]))
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print('UL:(%f,%f) LR:(%f,%f)'
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% (self.ulx,self.uly,self.lrx,self.lry))
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def copy_into( self, t_fh, s_band = 1, t_band = 1, nodata_arg=None ):
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"""
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Copy this files image into target file.
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This method will compute the overlap area of the file_info objects
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file, and the target gdal.Dataset object, and copy the image data
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for the common window area. It is assumed that the files are in
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a compatible projection ... no checking or warping is done. However,
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if the destination file is a different resolution, or different
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image pixel type, the appropriate resampling and conversions will
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be done (using normal GDAL promotion/demotion rules).
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t_fh -- gdal.Dataset object for the file into which some or all
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of this file may be copied.
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Returns 1 on success (or if nothing needs to be copied), and zero one
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failure.
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"""
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t_geotransform = t_fh.GetGeoTransform()
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t_ulx = t_geotransform[0]
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t_uly = t_geotransform[3]
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t_lrx = t_geotransform[0] + t_fh.RasterXSize * t_geotransform[1]
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t_lry = t_geotransform[3] + t_fh.RasterYSize * t_geotransform[5]
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# figure out intersection region
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tgw_ulx = max(t_ulx,self.ulx)
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tgw_lrx = min(t_lrx,self.lrx)
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if t_geotransform[5] < 0:
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tgw_uly = min(t_uly,self.uly)
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tgw_lry = max(t_lry,self.lry)
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else:
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tgw_uly = max(t_uly,self.uly)
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tgw_lry = min(t_lry,self.lry)
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# do they even intersect?
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if tgw_ulx >= tgw_lrx:
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return 1
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if t_geotransform[5] < 0 and tgw_uly <= tgw_lry:
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return 1
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if t_geotransform[5] > 0 and tgw_uly >= tgw_lry:
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return 1
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# compute target window in pixel coordinates.
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tw_xoff = int((tgw_ulx - t_geotransform[0]) / t_geotransform[1] + 0.1)
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tw_yoff = int((tgw_uly - t_geotransform[3]) / t_geotransform[5] + 0.1)
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tw_xsize = int((tgw_lrx - t_geotransform[0])/t_geotransform[1] + 0.5) \
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- tw_xoff
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tw_ysize = int((tgw_lry - t_geotransform[3])/t_geotransform[5] + 0.5) \
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- tw_yoff
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if tw_xsize < 1 or tw_ysize < 1:
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return 1
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# Compute source window in pixel coordinates.
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sw_xoff = int((tgw_ulx - self.geotransform[0]) / self.geotransform[1])
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sw_yoff = int((tgw_uly - self.geotransform[3]) / self.geotransform[5])
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sw_xsize = int((tgw_lrx - self.geotransform[0]) \
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/ self.geotransform[1] + 0.5) - sw_xoff
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sw_ysize = int((tgw_lry - self.geotransform[3]) \
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/ self.geotransform[5] + 0.5) - sw_yoff
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if sw_xsize < 1 or sw_ysize < 1:
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return 1
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# Open the source file, and copy the selected region.
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s_fh = gdal.Open( self.filename )
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return raster_copy( s_fh, sw_xoff, sw_yoff, sw_xsize, sw_ysize, s_band,
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t_fh, tw_xoff, tw_yoff, tw_xsize, tw_ysize, t_band,
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nodata_arg )
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# =============================================================================
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def Usage():
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print('Usage: gdal_merge.py [-o out_filename] [-of out_format] [-co NAME=VALUE]*')
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print(' [-ps pixelsize_x pixelsize_y] [-tap] [-separate] [-q] [-v] [-pct]')
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print(' [-ul_lr ulx uly lrx lry] [-init "value [value...]"]')
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print(' [-n nodata_value] [-a_nodata output_nodata_value]')
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print(' [-ot datatype] [-createonly] input_files')
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print(' [--help-general]')
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print('')
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# =============================================================================
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#
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# Program mainline.
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#
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|
||||||
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def main( argv=None ):
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||||||
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global verbose, quiet
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verbose = 0
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quiet = 0
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||||||
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names = []
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||||||
|
format = 'GTiff'
|
||||||
|
out_file = 'out.tif'
|
||||||
|
|
||||||
|
ulx = None
|
||||||
|
psize_x = None
|
||||||
|
separate = 0
|
||||||
|
copy_pct = 0
|
||||||
|
nodata = None
|
||||||
|
a_nodata = None
|
||||||
|
create_options = []
|
||||||
|
pre_init = []
|
||||||
|
band_type = None
|
||||||
|
createonly = 0
|
||||||
|
bTargetAlignedPixels = False
|
||||||
|
start_time = time.time()
|
||||||
|
|
||||||
|
gdal.AllRegister()
|
||||||
|
if argv is None:
|
||||||
|
argv = sys.argv
|
||||||
|
argv = gdal.GeneralCmdLineProcessor( argv )
|
||||||
|
if argv is None:
|
||||||
|
sys.exit( 0 )
|
||||||
|
|
||||||
|
# Parse command line arguments.
|
||||||
|
i = 1
|
||||||
|
while i < len(argv):
|
||||||
|
arg = argv[i]
|
||||||
|
|
||||||
|
if arg == '-o':
|
||||||
|
i = i + 1
|
||||||
|
out_file = argv[i]
|
||||||
|
|
||||||
|
elif arg == '-v':
|
||||||
|
verbose = 1
|
||||||
|
|
||||||
|
elif arg == '-q' or arg == '-quiet':
|
||||||
|
quiet = 1
|
||||||
|
|
||||||
|
elif arg == '-createonly':
|
||||||
|
createonly = 1
|
||||||
|
|
||||||
|
elif arg == '-separate':
|
||||||
|
separate = 1
|
||||||
|
|
||||||
|
elif arg == '-seperate':
|
||||||
|
separate = 1
|
||||||
|
|
||||||
|
elif arg == '-pct':
|
||||||
|
copy_pct = 1
|
||||||
|
|
||||||
|
elif arg == '-ot':
|
||||||
|
i = i + 1
|
||||||
|
band_type = gdal.GetDataTypeByName( argv[i] )
|
||||||
|
if band_type == gdal.GDT_Unknown:
|
||||||
|
print('Unknown GDAL data type: %s' % argv[i])
|
||||||
|
sys.exit( 1 )
|
||||||
|
|
||||||
|
elif arg == '-init':
|
||||||
|
i = i + 1
|
||||||
|
str_pre_init = argv[i].split()
|
||||||
|
for x in str_pre_init:
|
||||||
|
pre_init.append(float(x))
|
||||||
|
|
||||||
|
elif arg == '-n':
|
||||||
|
i = i + 1
|
||||||
|
nodata = float(argv[i])
|
||||||
|
|
||||||
|
elif arg == '-a_nodata':
|
||||||
|
i = i + 1
|
||||||
|
a_nodata = float(argv[i])
|
||||||
|
|
||||||
|
elif arg == '-f':
|
||||||
|
# for backward compatibility.
|
||||||
|
i = i + 1
|
||||||
|
format = argv[i]
|
||||||
|
|
||||||
|
elif arg == '-of':
|
||||||
|
i = i + 1
|
||||||
|
format = argv[i]
|
||||||
|
|
||||||
|
elif arg == '-co':
|
||||||
|
i = i + 1
|
||||||
|
create_options.append( argv[i] )
|
||||||
|
|
||||||
|
elif arg == '-ps':
|
||||||
|
psize_x = float(argv[i+1])
|
||||||
|
psize_y = -1 * abs(float(argv[i+2]))
|
||||||
|
i = i + 2
|
||||||
|
|
||||||
|
elif arg == '-tap':
|
||||||
|
bTargetAlignedPixels = True
|
||||||
|
|
||||||
|
elif arg == '-ul_lr':
|
||||||
|
ulx = float(argv[i+1])
|
||||||
|
uly = float(argv[i+2])
|
||||||
|
lrx = float(argv[i+3])
|
||||||
|
lry = float(argv[i+4])
|
||||||
|
i = i + 4
|
||||||
|
|
||||||
|
elif arg[:1] == '-':
|
||||||
|
print('Unrecognized command option: %s' % arg)
|
||||||
|
Usage()
|
||||||
|
sys.exit( 1 )
|
||||||
|
|
||||||
|
else:
|
||||||
|
names.append(arg)
|
||||||
|
|
||||||
|
i = i + 1
|
||||||
|
|
||||||
|
if len(names) == 0:
|
||||||
|
print('No input files selected.')
|
||||||
|
Usage()
|
||||||
|
sys.exit( 1 )
|
||||||
|
|
||||||
|
Driver = gdal.GetDriverByName(format)
|
||||||
|
if Driver is None:
|
||||||
|
print('Format driver %s not found, pick a supported driver.' % format)
|
||||||
|
sys.exit( 1 )
|
||||||
|
|
||||||
|
DriverMD = Driver.GetMetadata()
|
||||||
|
if 'DCAP_CREATE' not in DriverMD:
|
||||||
|
print('Format driver %s does not support creation and piecewise writing.\nPlease select a format that does, such as GTiff (the default) or HFA (Erdas Imagine).' % format)
|
||||||
|
sys.exit( 1 )
|
||||||
|
|
||||||
|
# Collect information on all the source files.
|
||||||
|
file_infos = names_to_fileinfos( names )
|
||||||
|
|
||||||
|
if ulx is None:
|
||||||
|
ulx = file_infos[0].ulx
|
||||||
|
uly = file_infos[0].uly
|
||||||
|
lrx = file_infos[0].lrx
|
||||||
|
lry = file_infos[0].lry
|
||||||
|
|
||||||
|
for fi in file_infos:
|
||||||
|
ulx = min(ulx, fi.ulx)
|
||||||
|
uly = max(uly, fi.uly)
|
||||||
|
lrx = max(lrx, fi.lrx)
|
||||||
|
lry = min(lry, fi.lry)
|
||||||
|
|
||||||
|
if psize_x is None:
|
||||||
|
psize_x = file_infos[0].geotransform[1]
|
||||||
|
psize_y = file_infos[0].geotransform[5]
|
||||||
|
|
||||||
|
if band_type is None:
|
||||||
|
band_type = file_infos[0].band_type
|
||||||
|
|
||||||
|
# Try opening as an existing file.
|
||||||
|
gdal.PushErrorHandler( 'CPLQuietErrorHandler' )
|
||||||
|
t_fh = gdal.Open( out_file, gdal.GA_Update )
|
||||||
|
gdal.PopErrorHandler()
|
||||||
|
|
||||||
|
# Create output file if it does not already exist.
|
||||||
|
if t_fh is None:
|
||||||
|
|
||||||
|
if bTargetAlignedPixels:
|
||||||
|
ulx = math.floor(ulx / psize_x) * psize_x
|
||||||
|
lrx = math.ceil(lrx / psize_x) * psize_x
|
||||||
|
lry = math.floor(lry / -psize_y) * -psize_y
|
||||||
|
uly = math.ceil(uly / -psize_y) * -psize_y
|
||||||
|
|
||||||
|
geotransform = [ulx, psize_x, 0, uly, 0, psize_y]
|
||||||
|
|
||||||
|
xsize = int((lrx - ulx) / geotransform[1] + 0.5)
|
||||||
|
ysize = int((lry - uly) / geotransform[5] + 0.5)
|
||||||
|
|
||||||
|
|
||||||
|
if separate != 0:
|
||||||
|
bands=0
|
||||||
|
|
||||||
|
for fi in file_infos:
|
||||||
|
bands=bands + fi.bands
|
||||||
|
else:
|
||||||
|
bands = file_infos[0].bands
|
||||||
|
|
||||||
|
|
||||||
|
t_fh = Driver.Create( out_file, xsize, ysize, bands,
|
||||||
|
band_type, create_options )
|
||||||
|
if t_fh is None:
|
||||||
|
print('Creation failed, terminating gdal_merge.')
|
||||||
|
sys.exit( 1 )
|
||||||
|
|
||||||
|
t_fh.SetGeoTransform( geotransform )
|
||||||
|
t_fh.SetProjection( file_infos[0].projection )
|
||||||
|
|
||||||
|
if copy_pct:
|
||||||
|
t_fh.GetRasterBand(1).SetRasterColorTable(file_infos[0].ct)
|
||||||
|
else:
|
||||||
|
if separate != 0:
|
||||||
|
bands=0
|
||||||
|
for fi in file_infos:
|
||||||
|
bands=bands + fi.bands
|
||||||
|
if t_fh.RasterCount < bands :
|
||||||
|
print('Existing output file has less bands than the input files. You should delete it before. Terminating gdal_merge.')
|
||||||
|
sys.exit( 1 )
|
||||||
|
else:
|
||||||
|
bands = min(file_infos[0].bands,t_fh.RasterCount)
|
||||||
|
|
||||||
|
# Do we need to set nodata value ?
|
||||||
|
if a_nodata is not None:
|
||||||
|
for i in range(t_fh.RasterCount):
|
||||||
|
t_fh.GetRasterBand(i+1).SetNoDataValue(a_nodata)
|
||||||
|
|
||||||
|
# Do we need to pre-initialize the whole mosaic file to some value?
|
||||||
|
if pre_init is not None:
|
||||||
|
if t_fh.RasterCount <= len(pre_init):
|
||||||
|
for i in range(t_fh.RasterCount):
|
||||||
|
t_fh.GetRasterBand(i+1).Fill( pre_init[i] )
|
||||||
|
elif len(pre_init) == 1:
|
||||||
|
for i in range(t_fh.RasterCount):
|
||||||
|
t_fh.GetRasterBand(i+1).Fill( pre_init[0] )
|
||||||
|
|
||||||
|
# Copy data from source files into output file.
|
||||||
|
t_band = 1
|
||||||
|
|
||||||
|
if quiet == 0 and verbose == 0:
|
||||||
|
progress( 0.0 )
|
||||||
|
fi_processed = 0
|
||||||
|
|
||||||
|
for fi in file_infos:
|
||||||
|
if createonly != 0:
|
||||||
|
continue
|
||||||
|
|
||||||
|
if verbose != 0:
|
||||||
|
print("")
|
||||||
|
print("Processing file %5d of %5d, %6.3f%% completed in %d minutes."
|
||||||
|
% (fi_processed+1,len(file_infos),
|
||||||
|
fi_processed * 100.0 / len(file_infos),
|
||||||
|
int(round((time.time() - start_time)/60.0)) ))
|
||||||
|
fi.report()
|
||||||
|
|
||||||
|
if separate == 0 :
|
||||||
|
for band in range(1, bands+1):
|
||||||
|
fi.copy_into( t_fh, band, band, nodata )
|
||||||
|
else:
|
||||||
|
for band in range(1, fi.bands+1):
|
||||||
|
fi.copy_into( t_fh, band, t_band, nodata )
|
||||||
|
t_band = t_band+1
|
||||||
|
|
||||||
|
fi_processed = fi_processed+1
|
||||||
|
if quiet == 0 and verbose == 0:
|
||||||
|
progress( fi_processed / float(len(file_infos)) )
|
||||||
|
|
||||||
|
# Force file to be closed.
|
||||||
|
t_fh = None
|
||||||
|
|
||||||
|
if __name__ == '__main__':
|
||||||
|
sys.exit(main())
|
||||||
@ -0,0 +1,285 @@
|
|||||||
|
#==========================================================#
|
||||||
|
# Create a classifier for satellite images
|
||||||
|
#==========================================================#
|
||||||
|
|
||||||
|
# load modules
|
||||||
|
import os
|
||||||
|
import pickle
|
||||||
|
import warnings
|
||||||
|
import numpy as np
|
||||||
|
import matplotlib.cm as cm
|
||||||
|
warnings.filterwarnings("ignore")
|
||||||
|
import matplotlib.pyplot as plt
|
||||||
|
from pylab import ginput
|
||||||
|
|
||||||
|
import SDS_download, SDS_preprocess, SDS_shoreline, SDS_tools, SDS_classification
|
||||||
|
|
||||||
|
filepath_sites = os.path.join(os.getcwd(), 'polygons')
|
||||||
|
sites = os.listdir(filepath_sites)
|
||||||
|
|
||||||
|
for site in sites:
|
||||||
|
|
||||||
|
polygon = SDS_tools.coords_from_kml(os.path.join(filepath_sites,site))
|
||||||
|
|
||||||
|
# load Sentinel-2 images
|
||||||
|
inputs = {
|
||||||
|
'polygon': polygon,
|
||||||
|
'dates': ['2016-10-01', '2016-11-01'],
|
||||||
|
'sat_list': ['S2'],
|
||||||
|
'sitename': site[:site.find('.')]
|
||||||
|
}
|
||||||
|
|
||||||
|
satname = inputs['sat_list'][0]
|
||||||
|
|
||||||
|
metadata = SDS_download.get_images(inputs)
|
||||||
|
metadata = SDS_download.remove_cloudy_images(metadata,inputs,0.2)
|
||||||
|
filepath = os.path.join(os.getcwd(), 'data', inputs['sitename'])
|
||||||
|
with open(os.path.join(filepath, inputs['sitename'] + '_metadata_' + satname + '.pkl'), 'wb') as f:
|
||||||
|
pickle.dump(metadata, f)
|
||||||
|
#with open(os.path.join(filepath, inputs['sitename'] + '_metadata_' + satname + '.pkl'), 'rb') as f:
|
||||||
|
# metadata = pickle.load(f)
|
||||||
|
|
||||||
|
# settings needed to run the shoreline extraction
|
||||||
|
settings = {
|
||||||
|
|
||||||
|
# general parameters:
|
||||||
|
'cloud_thresh': 0.1, # threshold on maximum cloud cover
|
||||||
|
'output_epsg': 28356, # epsg code of spatial reference system desired for the output
|
||||||
|
|
||||||
|
# shoreline detection parameters:
|
||||||
|
'min_beach_size': 20, # minimum number of connected pixels for a beach
|
||||||
|
'buffer_size': 7, # radius (in pixels) of disk for buffer around sandy pixels
|
||||||
|
'min_length_sl': 200, # minimum length of shoreline perimeter to be kept
|
||||||
|
'max_dist_ref': 100, # max distance (in meters) allowed from a reference shoreline
|
||||||
|
|
||||||
|
# quality control:
|
||||||
|
'check_detection': True, # if True, shows each shoreline detection and lets the user
|
||||||
|
# decide which ones are correct and which ones are false due to
|
||||||
|
# the presence of clouds
|
||||||
|
# also add the inputs
|
||||||
|
'inputs': inputs
|
||||||
|
}
|
||||||
|
# preprocess images (cloud masking, pansharpening/down-sampling)
|
||||||
|
SDS_preprocess.preprocess_all_images(metadata, settings)
|
||||||
|
|
||||||
|
training_data = dict([])
|
||||||
|
training_data['sand'] = dict([])
|
||||||
|
training_data['swash'] = dict([])
|
||||||
|
training_data['water'] = dict([])
|
||||||
|
training_data['land'] = dict([])
|
||||||
|
|
||||||
|
# read images
|
||||||
|
filepath = SDS_tools.get_filepath(inputs,satname)
|
||||||
|
filenames = metadata[satname]['filenames']
|
||||||
|
|
||||||
|
for i in range(len(filenames)):
|
||||||
|
|
||||||
|
fn = SDS_tools.get_filenames(filenames[i],filepath,satname)
|
||||||
|
im_ms, georef, cloud_mask, im20, imQA = SDS_preprocess.preprocess_single(fn,satname)
|
||||||
|
|
||||||
|
nrow = im_ms.shape[0]
|
||||||
|
ncol = im_ms.shape[1]
|
||||||
|
|
||||||
|
im_RGB = SDS_preprocess.rescale_image_intensity(im_ms[:,:,[2,1,0]], cloud_mask, 99.9)
|
||||||
|
plt.figure()
|
||||||
|
mng = plt.get_current_fig_manager()
|
||||||
|
mng.window.showMaximized()
|
||||||
|
plt.imshow(im_RGB)
|
||||||
|
plt.axis('off')
|
||||||
|
|
||||||
|
# Digitize sandy pixels
|
||||||
|
plt.title('Digitize SAND pixels', fontweight='bold', fontsize=15)
|
||||||
|
pt = ginput(n=1000, timeout=100000, show_clicks=True)
|
||||||
|
|
||||||
|
if len(pt) > 0:
|
||||||
|
pt = np.round(pt).astype(int)
|
||||||
|
im_sand = np.zeros((nrow,ncol))
|
||||||
|
for k in range(len(pt)):
|
||||||
|
im_sand[pt[k,1],pt[k,0]] = 1
|
||||||
|
im_RGB[pt[k,1],pt[k,0],0] = 1
|
||||||
|
im_RGB[pt[k,1],pt[k,0],1] = 0
|
||||||
|
im_RGB[pt[k,1],pt[k,0],2] = 0
|
||||||
|
im_sand = im_sand.astype(bool)
|
||||||
|
features = SDS_classification.calculate_features(im_ms, cloud_mask, im_sand)
|
||||||
|
else:
|
||||||
|
im_sand = np.zeros((nrow,ncol)).astype(bool)
|
||||||
|
features = []
|
||||||
|
training_data['sand'][filenames[i]] = {'pixels':im_sand,'features':features}
|
||||||
|
|
||||||
|
# Digitize swash pixels
|
||||||
|
plt.title('Digitize SWASH pixels', fontweight='bold', fontsize=15)
|
||||||
|
plt.draw()
|
||||||
|
pt = ginput(n=1000, timeout=100000, show_clicks=True)
|
||||||
|
|
||||||
|
if len(pt) > 0:
|
||||||
|
pt = np.round(pt).astype(int)
|
||||||
|
im_swash = np.zeros((nrow,ncol))
|
||||||
|
for k in range(len(pt)):
|
||||||
|
im_swash[pt[k,1],pt[k,0]] = 1
|
||||||
|
im_RGB[pt[k,1],pt[k,0],0] = 0
|
||||||
|
im_RGB[pt[k,1],pt[k,0],1] = 1
|
||||||
|
im_RGB[pt[k,1],pt[k,0],2] = 0
|
||||||
|
im_swash = im_swash.astype(bool)
|
||||||
|
features = SDS_classification.calculate_features(im_ms, cloud_mask, im_swash)
|
||||||
|
else:
|
||||||
|
im_swash = np.zeros((nrow,ncol)).astype(bool)
|
||||||
|
features = []
|
||||||
|
training_data['swash'][filenames[i]] = {'pixels':im_swash,'features':features}
|
||||||
|
|
||||||
|
# Digitize rectangle containig water pixels
|
||||||
|
plt.title('Click 2 points to draw a rectange in the WATER', fontweight='bold', fontsize=15)
|
||||||
|
plt.draw()
|
||||||
|
pt = ginput(n=2, timeout=100000, show_clicks=True)
|
||||||
|
if len(pt) > 0:
|
||||||
|
pt = np.round(pt).astype(int)
|
||||||
|
idx_row = np.arange(np.min(pt[:,1]),np.max(pt[:,1])+1,1)
|
||||||
|
idx_col = np.arange(np.min(pt[:,0]),np.max(pt[:,0])+1,1)
|
||||||
|
xx, yy = np.meshgrid(idx_row,idx_col, indexing='ij')
|
||||||
|
rows = xx.reshape(xx.shape[0]*xx.shape[1])
|
||||||
|
cols = yy.reshape(yy.shape[0]*yy.shape[1])
|
||||||
|
im_water = np.zeros((nrow,ncol)).astype(bool)
|
||||||
|
for k in range(len(rows)):
|
||||||
|
im_water[rows[k],cols[k]] = 1
|
||||||
|
im_RGB[rows[k],cols[k],0] = 0
|
||||||
|
im_RGB[rows[k],cols[k],1] = 0
|
||||||
|
im_RGB[rows[k],cols[k],2] = 1
|
||||||
|
im_water = im_water.astype(bool)
|
||||||
|
features = SDS_classification.calculate_features(im_ms, cloud_mask, im_water)
|
||||||
|
else:
|
||||||
|
im_water = np.zeros((nrow,ncol)).astype(bool)
|
||||||
|
features = []
|
||||||
|
training_data['water'][filenames[i]] = {'pixels':im_water,'features':features}
|
||||||
|
|
||||||
|
# Digitize rectangle containig land pixels
|
||||||
|
plt.title('Click 2 points to draw a rectange in the LAND', fontweight='bold', fontsize=15)
|
||||||
|
plt.draw()
|
||||||
|
pt = ginput(n=2, timeout=100000, show_clicks=True)
|
||||||
|
plt.close()
|
||||||
|
if len(pt) > 0:
|
||||||
|
pt = np.round(pt).astype(int)
|
||||||
|
idx_row = np.arange(np.min(pt[:,1]),np.max(pt[:,1])+1,1)
|
||||||
|
idx_col = np.arange(np.min(pt[:,0]),np.max(pt[:,0])+1,1)
|
||||||
|
xx, yy = np.meshgrid(idx_row,idx_col, indexing='ij')
|
||||||
|
rows = xx.reshape(xx.shape[0]*xx.shape[1])
|
||||||
|
cols = yy.reshape(yy.shape[0]*yy.shape[1])
|
||||||
|
im_land = np.zeros((nrow,ncol)).astype(bool)
|
||||||
|
for k in range(len(rows)):
|
||||||
|
im_land[rows[k],cols[k]] = 1
|
||||||
|
im_RGB[rows[k],cols[k],0] = 1
|
||||||
|
im_RGB[rows[k],cols[k],1] = 1
|
||||||
|
im_RGB[rows[k],cols[k],2] = 0
|
||||||
|
im_land = im_land.astype(bool)
|
||||||
|
features = SDS_classification.calculate_features(im_ms, cloud_mask, im_land)
|
||||||
|
else:
|
||||||
|
im_land = np.zeros((nrow,ncol)).astype(bool)
|
||||||
|
features = []
|
||||||
|
training_data['land'][filenames[i]] = {'pixels':im_land,'features':features}
|
||||||
|
|
||||||
|
plt.figure()
|
||||||
|
plt.title('Classified image')
|
||||||
|
plt.imshow(im_RGB)
|
||||||
|
|
||||||
|
# save training data for each site
|
||||||
|
filepath = os.path.join(os.getcwd(), 'data', inputs['sitename'])
|
||||||
|
with open(os.path.join(filepath, inputs['sitename'] + '_training_' + satname + '.pkl'), 'wb') as f:
|
||||||
|
pickle.dump(training_data, f)
|
||||||
|
#%%
|
||||||
|
|
||||||
|
## load Landsat 5 images
|
||||||
|
#inputs = {
|
||||||
|
# 'polygon': polygon,
|
||||||
|
# 'dates': ['1987-01-01', '1988-01-01'],
|
||||||
|
# 'sat_list': ['L5'],
|
||||||
|
# 'sitename': site[:site.find('.')]
|
||||||
|
# }
|
||||||
|
#metadata = SDS_download.get_images(inputs)
|
||||||
|
#
|
||||||
|
## load Landsat 7 images
|
||||||
|
#inputs = {
|
||||||
|
# 'polygon': polygon,
|
||||||
|
# 'dates': ['2001-01-01', '2002-01-01'],
|
||||||
|
# 'sat_list': ['L7'],
|
||||||
|
# 'sitename': site[:site.find('.')]
|
||||||
|
# }
|
||||||
|
#metadata = SDS_download.get_images(inputs)
|
||||||
|
#
|
||||||
|
## load Landsat 8 images
|
||||||
|
#inputs = {
|
||||||
|
# 'polygon': polygon,
|
||||||
|
# 'dates': ['2014-01-01', '2015-01-01'],
|
||||||
|
# 'sat_list': ['L8'],
|
||||||
|
# 'sitename': site[:site.find('.')]
|
||||||
|
# }
|
||||||
|
#metadata = SDS_download.get_images(inputs)
|
||||||
|
|
||||||
|
|
||||||
|
#%% clean the Landsat collections
|
||||||
|
|
||||||
|
#import ee
|
||||||
|
#from datetime import datetime, timedelta
|
||||||
|
#import pytz
|
||||||
|
#import copy
|
||||||
|
#ee.Initialize()
|
||||||
|
#site = sites[0]
|
||||||
|
#dates = ['2017-12-01', '2017-12-25']
|
||||||
|
#polygon = SDS_tools.coords_from_kml(os.path.join(filepath_sites,site))
|
||||||
|
## Landsat collection
|
||||||
|
#input_col = ee.ImageCollection('LANDSAT/LC08/C01/T1_RT_TOA')
|
||||||
|
## filter by location and dates
|
||||||
|
#flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(inputs['dates'][0],inputs['dates'][1])
|
||||||
|
## get all images in the filtered collection
|
||||||
|
#im_all = flt_col.getInfo().get('features')
|
||||||
|
#cloud_cover = [_['properties']['CLOUD_COVER'] for _ in im_all]
|
||||||
|
#if np.any([_ > 90 for _ in cloud_cover]):
|
||||||
|
# idx_delete = np.where([_ > 90 for _ in cloud_cover])[0]
|
||||||
|
# im_all_cloud = [x for k,x in enumerate(im_all) if k not in idx_delete]
|
||||||
|
|
||||||
|
|
||||||
|
#%% clean the S2 collection
|
||||||
|
|
||||||
|
#import ee
|
||||||
|
#from datetime import datetime, timedelta
|
||||||
|
#import pytz
|
||||||
|
#import copy
|
||||||
|
#ee.Initialize()
|
||||||
|
## Sentinel2 collection
|
||||||
|
#input_col = ee.ImageCollection('COPERNICUS/S2')
|
||||||
|
## filter by location and dates
|
||||||
|
#flt_col = input_col.filterBounds(ee.Geometry.Polygon(polygon)).filterDate(inputs['dates'][0],inputs['dates'][1])
|
||||||
|
## get all images in the filtered collection
|
||||||
|
#im_all = flt_col.getInfo().get('features')
|
||||||
|
#
|
||||||
|
## remove duplicates (there are many in S2 collection)
|
||||||
|
## timestamps
|
||||||
|
#timestamps = [datetime.fromtimestamp(_['properties']['system:time_start']/1000, tz=pytz.utc) for _ in im_all]
|
||||||
|
## utm zones
|
||||||
|
#utm_zones = np.array([int(_['bands'][0]['crs'][5:]) for _ in im_all])
|
||||||
|
#utm_zone_selected = np.max(np.unique(utm_zones))
|
||||||
|
#idx_all = np.arange(0,len(im_all),1)
|
||||||
|
#idx_covered = np.ones(len(im_all)).astype(bool)
|
||||||
|
#idx_delete = []
|
||||||
|
#i = 0
|
||||||
|
#while 1:
|
||||||
|
# same_time = np.abs([(timestamps[i]-_).total_seconds() for _ in timestamps]) < 60*60*24
|
||||||
|
# idx_same_time = np.where(same_time)[0]
|
||||||
|
# same_utm = utm_zones == utm_zone_selected
|
||||||
|
# idx_temp = np.where([same_time[j] == True and same_utm[j] == False for j in idx_all])[0]
|
||||||
|
# idx_keep = idx_same_time[[_ not in idx_temp for _ in idx_same_time ]]
|
||||||
|
# if len(idx_keep) > 2: # if more than 2 images with same date and same utm, drop the last one
|
||||||
|
# idx_temp = np.append(idx_temp,idx_keep[-1])
|
||||||
|
# for j in idx_temp:
|
||||||
|
# idx_delete.append(j)
|
||||||
|
# idx_covered[idx_same_time] = False
|
||||||
|
# if np.any(idx_covered):
|
||||||
|
# i = np.where(idx_covered)[0][0]
|
||||||
|
# else:
|
||||||
|
# break
|
||||||
|
#im_all_updated = [x for k,x in enumerate(im_all) if k not in idx_delete]
|
||||||
|
#
|
||||||
|
## remove very cloudy images (>90% cloud)
|
||||||
|
#cloud_cover = [_['properties']['CLOUDY_PIXEL_PERCENTAGE'] for _ in im_all_updated]
|
||||||
|
#if np.any([_ > 90 for _ in cloud_cover]):
|
||||||
|
# idx_delete = np.where([_ > 90 for _ in cloud_cover])[0]
|
||||||
|
# im_all_cloud = [x for k,x in enumerate(im_all_updated) if k not in idx_delete]
|
||||||
|
|
||||||
|
|
||||||
Loading…
Reference in New Issue