cuDenseOffsets: expose --raw-osf and --corr-win-size option
contrib/PyCuAmpcor/cuDenseOffsets.py: + expose --raw-over-samp-factor option to change the raw data oversampling factor with default of 2 + expose --corr-win-size option, which by default, is calculated automatically based on the search window size and raw oversampling factor + change the namespace key for the oversampling factor of correlation surface from 'oversample' to 'corr_oversample' to avoid ambiguity, the cmd option name is still the same, thus no different in the user side. + use vrt file for master / slave slc data loading folllowing https://github.com/isce-framework/isce2/pull/78 + re-organize createParse() for readability + add example to argparse help stripmapStack/MaskAndFilter.py: + fix a bug introduced in #https://github.com/isce-framework/isce2/pull/112 + add example usage to help message + mask pixels with SNR == 0, for plotting only without touching data files + show input parameter in the figure title + show percentage after SNR thresholding + add interpolation for matplotlib while plotting topsStack/grossOffsets: move obsolete basemap import from the top to the related commented code blockLT1AB
Zhang Yunjun
piyushrpt
parent
aaa6efebad
commit
90d578fa5d
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@ -2,21 +2,32 @@
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# Author: Minyan Zhong, Lijun Zhu
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import argparse
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import os
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import argparse
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import numpy as np
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import isce
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import isceobj
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from isceobj.Util.decorators import use_api
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import numpy as np
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from contrib.PyCuAmpcor.PyCuAmpcor import PyCuAmpcor
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EXAMPLE = '''example
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cuDenseOffsets.py -m ./merged/SLC/20151120/20151120.slc.full -s ./merged/SLC/20151214/20151214.slc.full
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--masterxml ./master/IW1.xml --outprefix ./merged/offsets/20151120_20151214/offset
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--ww 256 --wh 256 --oo 32 --kw 300 --kh 100 --nwac 100 --nwdc 1 --sw 8 --sh 8 --gpuid 2
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'''
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def createParser():
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'''
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Command line parser.
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'''
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parser = argparse.ArgumentParser( description='Generate offset field between two Sentinel slc')
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parser = argparse.ArgumentParser(description='Generate offset field between two Sentinel slc',
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formatter_class=argparse.RawTextHelpFormatter,
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epilog=EXAMPLE)
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parser.add_argument('-m','--master', type=str, dest='master', required=True,
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help='Master image')
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parser.add_argument('-s', '--slave',type=str, dest='slave', required=True,
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@ -27,83 +38,90 @@ def createParser():
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help='Longitude')
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parser.add_argument('--los',type=str, dest='los', required=False,
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help='Line of Sight')
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parser.add_argument('--masterxml',type=str, dest='masterxml', required=False,
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help='Master Image Xml File')
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parser.add_argument('-x', '--masterxml',type=str, dest='masterxml', required=False,
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help='Master Image XML File')
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parser.add_argument('--op','--outprefix','--output-prefix', type=str, dest='outprefix',
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default='offset', required=True,
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help='Output prefix, default: offset.')
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parser.add_argument('--os','--outsuffix', type=str, dest='outsuffix', default='',
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help='Output suffix, default:.')
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parser.add_argument('--ww', type=int, dest='winwidth', default=64,
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help='Window Width')
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help='Window width (default: %(default)s).')
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parser.add_argument('--wh', type=int, dest='winhgt', default=64,
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help='Window height')
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parser.add_argument('--sw', type=int, dest='srcwidth', default=20,
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help='Search window width')
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parser.add_argument('--sh', type=int, dest='srchgt', default=20,
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help='Search window height')
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help='Window height (default: %(default)s).')
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parser.add_argument('--sw', type=int, dest='srcwidth', default=20, choices=range(8, 33),
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help='Search window width (default: %(default)s).')
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parser.add_argument('--sh', type=int, dest='srchgt', default=20, choices=range(8, 33),
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help='Search window height (default: %(default)s).')
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parser.add_argument('--mm', type=int, dest='margin', default=50,
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help='Margin')
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help='Margin (default: %(default)s).')
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parser.add_argument('--kw', type=int, dest='skipwidth', default=64,
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help='Skip across')
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help='Skip across (default: %(default)s).')
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parser.add_argument('--kh', type=int, dest='skiphgt', default=64,
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help='Skip down')
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help='Skip down (default: %(default)s).')
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parser.add_argument('--raw-osf','--raw-over-samp-factor', type=int, dest='raw_oversample',
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default=2, choices=range(2,5),
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help='raw data oversampling factor (default: %(default)s).')
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gross = parser.add_argument_group('Initial gross offset')
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gross.add_argument('-g','--gross', type=int, dest='gross', default=0,
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help='Use gross offset or not')
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gross.add_argument('--aa', type=int, dest='azshift', default=0,
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help='Gross azimuth offset (default: %(default)s).')
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gross.add_argument('--rr', type=int, dest='rgshift', default=0,
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help='Gross range offset (default: %(default)s).')
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corr = parser.add_argument_group('Correlation surface')
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corr.add_argument('--corr-win-size', type=int, dest='corr_win_size', default=-1,
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help='Zoom-in window size of the correlation surface for oversampling (default: %(default)s).')
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corr.add_argument('--corr-osf', '--oo', '--corr-over-samp-factor', type=int, dest='corr_oversample', default=32,
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help = 'Oversampling factor of the zoom-in correlation surface (default: %(default)s).')
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parser.add_argument('--nwa', type=int, dest='numWinAcross', default=-1,
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help='Number of Window Across')
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help='Number of window across (default: %(default)s).')
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parser.add_argument('--nwd', type=int, dest='numWinDown', default=-1,
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help='Number of Window Down')
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help='Number of window down (default: %(default)s).')
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parser.add_argument('--nwac', type=int, dest='numWinAcrossInChunk', default=1,
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help='Number of Window Across in Chunk')
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help='Number of window across in chunk (default: %(default)s).')
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parser.add_argument('--nwdc', type=int, dest='numWinDownInChunk', default=1,
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help='Number of Window Down in Chunk')
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help='Number of window down in chunk (default: %(default)s).')
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parser.add_argument('-r', '--redo', dest='redo', action='store_true',
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help='To redo by force (ignore the existing offset fields).')
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parser.add_argument('-op','--outprefix', type=str, dest='outprefix', default='dense_ampcor', required=True,
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help='Output prefix')
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parser.add_argument('--drmp', '--deramp', dest='deramp', type=int, default=0,
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help='deramp method (0: mag, 1: complex) (default: %(default)s).')
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parser.add_argument('-os','--outsuffix', type=str, dest='outsuffix',default='dense_ampcor',
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help='Output suffix')
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parser.add_argument('-g','--gross', type=int, dest='gross', default=0,
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help='Use gross offset or not')
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parser.add_argument('--aa', type=int, dest='azshift', default=0,
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help='Gross azimuth offset')
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parser.add_argument('--rr', type=int, dest='rgshift', default=0,
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help='Gross range offset')
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parser.add_argument('--oo', type=int, dest='oversample', default=32,
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help = 'Oversampling factor')
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parser.add_argument('-r', '--redo', dest='redo', type=int, default=0
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, help='To redo or not')
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parser.add_argument('-drmp', '--deramp', dest='deramp', type=int, default=0
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, help='deramp method (0: mag, 1: complex)')
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parser.add_argument('-gid', '--gpuid', dest='gpuid', type=int, default=-1
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, help='GPU ID')
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parser.add_argument('--gpuid', '--gid', '--gpu-id', dest='gpuid', type=int, default=-1,
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help='GPU ID (default: %(default)s).')
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return parser
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def cmdLineParse(iargs = None):
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parser = createParser()
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inps = parser.parse_args(args=iargs)
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return inps
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@use_api
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def estimateOffsetField(master, slave, inps=None):
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import pathlib
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###Loading the slave image object
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sim = isceobj.createSlcImage()
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sim.load(pathlib.Path(slave).with_suffix('.xml'))
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sim.load(slave+'.xml')
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sim.setAccessMode('READ')
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sim.createImage()
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###Loading the master image object
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sar = isceobj.createSlcImage()
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sar.load(pathlib.Path(master).with_suffix('.xml'))
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sar.load(master+'.xml')
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sar.setAccessMode('READ')
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sar.createImage()
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@ -114,16 +132,16 @@ def estimateOffsetField(master, slave, inps=None):
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objOffset.algorithm = 0
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objOffset.deviceID = inps.gpuid # -1:let system find the best GPU
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objOffset.nStreams = 1 #cudaStreams
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objOffset.nStreams = 2 #cudaStreams
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objOffset.derampMethod = inps.deramp
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print('deramp method (0 for magnitude, 1 for complex): ', objOffset.derampMethod)
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objOffset.masterImageName = master
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objOffset.masterImageName = master+'.vrt'
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objOffset.masterImageHeight = length
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objOffset.masterImageWidth = width
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objOffset.slaveImageName = slave
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objOffset.slaveImageName = slave+'.vrt'
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objOffset.slaveImageHeight = length
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objOffset.slaveImageWidth = width
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print("image length:",length)
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print("image width:",width)
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@ -132,39 +150,50 @@ def estimateOffsetField(master, slave, inps=None):
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if (inps.numWinDown != -1):
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objOffset.numberWindowDown = inps.numWinDown
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if (inps.numWinAcross != -1):
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objOffset.numberWindowAcross = inps.numWinAcross
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print("offset field length: ",objOffset.numberWindowDown)
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print("offset field width: ",objOffset.numberWindowAcross)
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# window size
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objOffset.windowSizeHeight = inps.winhgt
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objOffset.windowSizeWidth = inps.winwidth
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print('cross correlation window size: {} by {}'.format(objOffset.windowSizeHeight, objOffset.windowSizeWidth))
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# search range
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objOffset.halfSearchRangeDown = inps.srchgt
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objOffset.halfSearchRangeAcross = inps.srcwidth
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print('half search range: {} by {}'.format(inps.srchgt, inps.srcwidth))
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# starting pixel
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objOffset.masterStartPixelDownStatic = inps.margin
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objOffset.masterStartPixelAcrossStatic = inps.margin
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# skip size
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# skip/step size
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objOffset.skipSampleDown = inps.skiphgt
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objOffset.skipSampleAcross = inps.skipwidth
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print('search step: {} by {}'.format(inps.skiphgt, inps.skipwidth))
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# oversample raw data (SLC)
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objOffset.rawDataOversamplingFactor = inps.raw_oversample
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print('raw data oversampling factor:', inps.raw_oversample)
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# correlation surface
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if inps.corr_win_size == -1:
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corr_win_size_orig = min(inps.srchgt, inps.srcwidth) * inps.raw_oversample + 1
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inps.corr_win_size = np.power(2, int(np.log2(corr_win_size_orig)))
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objOffset.corrSurfaceZoomInWindow = inps.corr_win_size
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print('correlation surface zoom-in window size:', inps.corr_win_size)
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# oversampling
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objOffset.corrSufaceOverSamplingMethod = 0
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objOffset.corrSurfaceOverSamplingFactor = inps.oversample
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objOffset.corrSurfaceOverSamplingFactor = inps.corr_oversample
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print('correlation surface oversampling factor:', inps.corr_oversample)
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# output filenames
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objOffset.offsetImageName = str(inps.outprefix) + str(inps.outsuffix) + '.bip'
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objOffset.grossOffsetImageName = str(inps.outprefix) + str(inps.outsuffix) + '_gross.bip'
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objOffset.snrImageName = str(inps.outprefix) + str(inps.outsuffix) + '_snr.bip'
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objOffset.covImageName = str(inps.outprefix) + str(inps.outsuffix) + '_cov.bip'
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print("offsetfield: ",objOffset.offsetImageName)
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print("gross offsetfield: ",objOffset.grossOffsetImageName)
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print("snr: ",objOffset.snrImageName)
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@ -175,17 +204,17 @@ def estimateOffsetField(master, slave, inps=None):
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snrImageName = objOffset.snrImageName.decode('utf8')
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covImageName = objOffset.covImageName.decode('utf8')
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if os.path.exists(offsetImageName) and inps.redo==0:
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print(offsetImageName)
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print(inps.redo)
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if os.path.exists(offsetImageName) and not inps.redo:
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print('offsetfield file exists')
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exit()
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return 0
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# generic control
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objOffset.numberWindowDownInChunk = inps.numWinDownInChunk
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objOffset.numberWindowAcrossInChunk = inps.numWinAcrossInChunk
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objOffset.useMmap = 0
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objOffset.mmapSize = 8
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objOffset.setupParams()
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## Set Gross Offset ###
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@ -194,11 +223,13 @@ def estimateOffsetField(master, slave, inps=None):
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print("By default, the gross offsets are zero")
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print("You can override the default values here")
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objOffset.setConstantGrossOffset(0, 0)
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else:
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print("Set varying grossOffset")
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print("By default, the gross offsets are zero")
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print("You can override the default grossDown and grossAcross arrays here")
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objOffset.setVaryingGrossOffset(np.zeros(shape=grossDown.shape,dtype=np.int32), np.zeros(shape=grossAcross.shape,dtype=np.int32))
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objOffset.setVaryingGrossOffset(np.zeros(shape=grossDown.shape,dtype=np.int32),
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np.zeros(shape=grossAcross.shape,dtype=np.int32))
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# check
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objOffset.checkPixelInImageRange()
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@ -207,7 +238,6 @@ def estimateOffsetField(master, slave, inps=None):
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print('Running PyCuAmpcor')
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objOffset.runAmpcor()
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print('Finished')
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sar.finalizeImage()
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@ -257,17 +287,19 @@ def estimateOffsetField(master, slave, inps=None):
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covImg.setAccessMode('read')
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covImg.renderHdr()
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return 0
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return
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def main(iargs=None):
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inps = cmdLineParse(iargs)
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outDir = os.path.dirname(inps.outprefix)
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print(inps.outprefix)
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if not os.path.exists(outDir):
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os.makedirs(outDir)
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os.makedirs(outDir, exist_ok=True)
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estimateOffsetField(inps.master, inps.slave, inps)
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return
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if __name__ == '__main__':
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@ -35,6 +35,13 @@ GDAL2NUMPY_DATATYPE = {
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}
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EXAMPLE = '''example:
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MaskAndFilter.py -d offset.bip -s offset_snr.bip
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MaskAndFilter.py -d offset.bip -s offset_snr.bip --plot
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'''
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EXAMPLE = '''example:
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MaskAndFilter.py -d offset.bip -s offset_snr.bip
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MaskAndFilter.py -d offset.bip -s offset_snr.bip --plot
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@ -184,17 +191,21 @@ def mask_filter(inps, band, outName):
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offset1 = np.array(offset)
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offset1[snr < inps.snrThreshold] = np.nan
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# percentage of masked out pixels among all non-zero SNR pixels
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perc = np.sum(snr >= inps.snrThreshold) / np.sum(snr > 0)
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print('percentage of pixels with SNR >= {} among pixels with SNR > 0: {:.0%}'.format(inps.snrThreshold, perc))
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# fill the hole in offset with nearest data
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print('fill the masked out region with nearest data')
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offset2 = fill(offset1)
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# median filtering
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print('filtering with median filter with size : ', inps.filterSize)
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print('filtering with median filter with size: {}'.format(inps.filterSize))
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offset3 = ndimage.median_filter(offset2, size=inps.filterSize)
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length, width = offset3.shape
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# write data to file
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print('writing masked and filtered offsets to: ', outName)
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print('writing masked and filtered offsets to: {}'.format(outName))
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write(offset3, outName, 1, 6)
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# write the xml/vrt/hdr file
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@ -216,33 +227,55 @@ def mask_filter(inps, band, outName):
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def plot_mask_and_filtering(az_list, rg_list, inps=None):
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print('-'*30)
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print('plotting mask and filtering result ...')
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print('mask pixels with SNR == 0 (for plotting ONLY; data files are untouched)')
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snr = az_list[0]
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for i in range(1, len(az_list)):
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az_list[i][snr == 0] = np.nan
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rg_list[i][snr == 0] = np.nan
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# percentage of masked out pixels among all non-zero SNR pixels
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perc = np.sum(snr >= inps.snrThreshold) / np.sum(snr > 0)
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print('percentage of pixels with SNR >= {} among pixels with SNR > 0: {:.0%}'.format(inps.snrThreshold, perc))
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fig, axs = plt.subplots(nrows=2, ncols=5, figsize=inps.figsize, sharex=True, sharey=True)
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titles = ['SNR', 'offset', 'offset (mask)', 'offset (mask/fill)', 'offset (mask/fill/filter)']
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titles = ['SNR',
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'offset',
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'offset (mask {} - {:.0%} remain)'.format(inps.snrThreshold, perc),
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'offset (mask {} / fill)'.format(inps.snrThreshold),
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'offset (mask {} / fill / filter {})'.format(inps.snrThreshold, inps.filterSize)]
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# plot SNR
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im0 = axs[0,0].imshow(az_list[0], vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu')
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im0 = axs[1,0].imshow(rg_list[0], vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu')
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kwargs = dict(vmin=inps.vlim_snr[0], vmax=inps.vlim_snr[1], cmap='RdBu', interpolation='nearest')
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im0 = axs[0,0].imshow(snr, **kwargs)
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im0 = axs[1,0].imshow(snr, **kwargs)
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axs[0,0].set_title('SNR', fontsize=12)
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print('SNR data range: [{}, {}]'.format(np.nanmin(snr), np.nanmax(snr)))
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||||
|
||||
# label
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axs[0,0].set_ylabel('azimuth', fontsize=12)
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||||
axs[1,0].set_ylabel('range', fontsize=12)
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||||
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||||
# plot offset
|
||||
kwargs = dict(vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet', interpolation='nearest')
|
||||
for i in range(1,len(az_list)):
|
||||
im1 = axs[0,i].imshow(az_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
|
||||
im1 = axs[1,i].imshow(rg_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
|
||||
im1 = axs[0,i].imshow(az_list[i], **kwargs)
|
||||
im1 = axs[1,i].imshow(rg_list[i], **kwargs)
|
||||
axs[0,i].set_title(titles[i], fontsize=12)
|
||||
print('{} data range'.format(titles[i]))
|
||||
print('azimuth offset: [{:.3f}, {:.3f}]'.format(np.nanmin(az_list[i]), np.nanmax(az_list[i])))
|
||||
print('range offset: [{:.3f}, {:.3f}]'.format(np.nanmin(rg_list[i]), np.nanmax(rg_list[i])))
|
||||
fig.tight_layout()
|
||||
|
||||
# colorbar
|
||||
fig.subplots_adjust(bottom=0.15)
|
||||
cax0 = fig.add_axes([0.09, 0.1, 0.08, 0.015])
|
||||
cax0 = fig.add_axes([0.08, 0.1, 0.08, 0.015])
|
||||
cbar0 = plt.colorbar(im0, cax=cax0, orientation='horizontal')
|
||||
cax0.yaxis.set_ticks_position('left')
|
||||
|
||||
#fig.subplots_adjust(right=0.93)
|
||||
cax1 = fig.add_axes([0.57, 0.1, 0.08, 0.015])
|
||||
cax1 = fig.add_axes([0.60, 0.1, 0.15, 0.015])
|
||||
cbar1 = plt.colorbar(im1, cax=cax1, orientation='horizontal')
|
||||
cbar1.set_label('pixel', fontsize=12)
|
||||
|
||||
|
|
@ -259,7 +292,7 @@ def main(iargs=None):
|
|||
|
||||
inps = cmdLineParse(iargs)
|
||||
|
||||
os.makedirs(inps.outD, exist_ok=True)
|
||||
os.makedirs(inps.outDir, exist_ok=True)
|
||||
|
||||
#######################
|
||||
# masking the dense offsets based on SNR and median filter the masked offs
|
||||
|
|
@ -283,4 +316,3 @@ if __name__ == '__main__':
|
|||
Main driver.
|
||||
'''
|
||||
main()
|
||||
|
||||
|
|
|
|||
|
|
@ -11,13 +11,13 @@ import isceobj
|
|||
from iscesys.Component.ProductManager import ProductManager as PM
|
||||
import numpy as np
|
||||
from netCDF4 import Dataset
|
||||
from mpl_toolkits.basemap import Basemap
|
||||
import gdal
|
||||
|
||||
from scipy.interpolate import interp2d, griddata
|
||||
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
|
||||
class grossOffsets:
|
||||
|
||||
def __init__(self):
|
||||
|
|
@ -116,6 +116,7 @@ class grossOffsets:
|
|||
|
||||
#x,y = np.meshgrid(self.x0,self.y0)
|
||||
|
||||
#from mpl_toolkits.basemap import Basemap
|
||||
#self.AntVeloDataMap = Basemap(width=5600000,height=5600000,\
|
||||
# resolution='l',projection='stere',\
|
||||
# lat_ts=-71,lat_0=-90,lon_0=0)
|
||||
|
|
|
|||
Loading…
Reference in New Issue