MaskAndFilter: more ploting options
+ plot the evolution of offset after each step to better check the changes by masking, filling and filtering operations. + plot both azimuth and range offset in one figure and move the plotting to the end after file writing + update file path in xml file so that script can work even if the files are moved. + convert SNR nan value to zero before used as the mask, to avoid warning message + add the following options to customize the plot - add -v and --v-snr option to change the display range for offset and SNR - add --figsize and --save option + suppress the DEBUG message from matplotlib + remove obsolete getShape() and resampleOffset() + update IML module import + adjust indentationLT1AB
Zhang Yunjun
parent
3f82b2cfe9
commit
7644bf8c93
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@ -4,52 +4,80 @@
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# Copyright 2016
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#
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import numpy as np
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import argparse
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import os
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import isce
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import isceobj
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import argparse
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import numpy as np
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from scipy import ndimage
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import matplotlib.pyplot as plt
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import gdal
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from gdalconst import GA_ReadOnly
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from scipy import ndimage
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# suppress the DEBUG message
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import logging
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mpl_logger = logging.getLogger('matplotlib')
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mpl_logger.setLevel(logging.WARNING)
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import isce
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import isceobj
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from isceobj.Util.ImageUtil import ImageLib as IML
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GDAL2NUMPY_DATATYPE = {
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1 : np.uint8,
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2 : np.uint16,
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3 : np.int16,
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4 : np.uint32,
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5 : np.int32,
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6 : np.float32,
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7 : np.float64,
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10: np.complex64,
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11: np.complex128,
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1 : np.uint8,
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2 : np.uint16,
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3 : np.int16,
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4 : np.uint32,
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5 : np.int32,
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6 : np.float32,
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7 : np.float64,
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10: np.complex64,
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11: np.complex128,
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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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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='filters the densOffset, oversamples it and adds back to the geometry offset')
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parser = argparse.ArgumentParser(description='Mask and filter the densOffset',
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formatter_class=argparse.RawTextHelpFormatter,
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epilog=EXAMPLE)
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parser.add_argument('-d', '--dense_offset', dest='denseOffset', type=str, required=True,
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help='The dense offsets file obtained from cross correlation or any other approach')
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parser.add_argument('-s', '--snr', dest='snr', type=str, required=True,
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help='The SNR of the dense offsets obtained from cross correlation or any other approach')
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parser.add_argument('-n', '--filter_size', dest='filterSize', type=int, default=8,
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help='The size of the median filter')
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help='Size of the median filter (default: %(default)s).')
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parser.add_argument('-t', '--snr_threshold', dest='snrThreshold', type=float, default=5,
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help='The snr threshold used to mask the offset')
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help='Min SNR used in the offset (default: %(default)s).')
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# output
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parser.add_argument('-A', '--output_azimuth_offset', dest='outAzimuth', type=str, default='filtAzimuth.off',
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help='The azimuth offsets after rubber sheeting')
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help='File name of the azimuth offsets after rubber sheeting (default: %(default)s).')
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parser.add_argument('-R', '--output_range_offset', dest='outRange', type=str, default='filtRange.off',
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help='The range offsets after rubber sheeting')
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help='File name of the range offsets after rubber sheeting (default: %(default)s).')
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parser.add_argument('-o', '--output_directory', dest='outDir', type=str, default='./',
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help='Output directory')
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parser.add_argument('-p', '--plot', dest='plot', action='store_true', default=False,
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help='plot the offsets before and after masking and filtering')
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help='Output directory (default: %(default)s).')
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# plot
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plot = parser.add_argument_group('plot')
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plot.add_argument('-p', '--plot', dest='plot', action='store_true', default=False,
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help='plot the offsets before and after masking and filtering')
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plot.add_argument('-v', dest='vlim', nargs=2, type=float, default=(-0.05, 0.05),
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help='display range for offset (default: %(default)s).')
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plot.add_argument('--v-snr', dest='vlim_snr', nargs=2, type=float, default=(0, 100),
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help='display range for offset SNR (default: %(default)s).')
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plot.add_argument('--figsize', dest='figsize', nargs=2, type=float, default=(18, 5),
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help='figure size in inch (default: %(default)s).')
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plot.add_argument('--save', dest='fig_name', type=str, default=None,
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help='save figure as file')
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return parser
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@ -58,7 +86,7 @@ def cmdLineParse(iargs = None):
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return parser.parse_args(args=iargs)
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def read(file, processor='ISCE' , bands=None , dataType=None):
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def read(file, processor='ISCE', bands=None, dataType=None):
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''' raeder based on GDAL.
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Args:
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@ -73,10 +101,13 @@ def read(file, processor='ISCE' , bands=None , dataType=None):
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Returns:
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* data : A numpy array with dimensions : number_of_bands * length * width
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'''
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# generate ENVI hdr file and fix the file path in xml
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file = os.path.abspath(file)
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if processor == 'ISCE':
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cmd = 'isce2gis.py envi -i ' + file
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os.system(cmd)
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img, dataname, metaname = IML.loadImage(file)
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img.filename = file
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img.setAccessMode('READ')
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img.renderHdr()
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dataset = gdal.Open(file,GA_ReadOnly)
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@ -97,23 +128,22 @@ def read(file, processor='ISCE' , bands=None , dataType=None):
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# Fill the array with the Raster bands
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idx=0
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for i in bands:
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band=dataset.GetRasterBand(i)
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data[idx,:,:] = band.ReadAsArray()
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idx+=1
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band=dataset.GetRasterBand(i)
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data[idx,:,:] = band.ReadAsArray()
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idx+=1
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dataset = None
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return data
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def write(raster, fileName, nbands, bandType):
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############
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# Create the file
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driver = gdal.GetDriverByName( 'ENVI' )
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dst_ds = driver.Create(fileName, raster.shape[1], raster.shape[0], nbands, bandType )
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dst_ds.GetRasterBand(1).WriteArray( raster, 0 ,0 )
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dst_ds = None
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return
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def fill(data, invalid=None):
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"""
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@ -132,40 +162,46 @@ def fill(data, invalid=None):
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if invalid is None: invalid = np.isnan(data)
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ind = ndimage.distance_transform_edt(invalid,
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return_distances=False,
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return_indices=True)
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return_distances=False,
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return_indices=True)
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return data[tuple(ind)]
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def mask_filter(inps, band, outName, plot=False):
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#masking and Filtering
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Offset = read(inps.denseOffset, bands=band)
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Offset = Offset[0,:,:]
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def mask_filter(inps, band, outName):
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"""masking and Filtering"""
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# read offset
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offset = read(inps.denseOffset, bands=band)
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offset = offset[0,:,:]
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# read SNR
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snr = read(inps.snr, bands=[1])
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snr = snr[0,:,:]
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snr[np.isnan(snr)] = 0
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# Masking the dense offsets based on SNR
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print ('masking the dense offsets with SNR threshold: ', inps.snrThreshold)
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Offset[snr<inps.snrThreshold] = 0
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# mask the offset based on SNR
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print('masking the dense offsets with SNR threshold: {}'.format(inps.snrThreshold))
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offset1 = np.array(offset)
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offset1[snr < inps.snrThreshold] = np.nan
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############
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Offset[snr<inps.snrThreshold]=np.nan
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Offset = fill(Offset)
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############
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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 the masked offsets
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print ('Filtering with median filter with size : ', inps.filterSize)
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Offset = ndimage.median_filter(Offset, size=inps.filterSize)
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length, width = Offset.shape
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# median filtering
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print('filtering with median filter with size : ', 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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# writing the masked and filtered offsets to a file
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print ('writing masked and filtered offsets to: ', outName)
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write(Offset, outName, 1, 6)
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# write data to file
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print('writing masked and filtered offsets to: ', outName)
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write(offset3, outName, 1, 6)
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# write the xml file
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# write the xml/vrt/hdr file
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img = isceobj.createImage()
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img.setFilename(outName)
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img.setWidth(width)
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img.setLength(length)
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img.setAccessMode('READ')
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img.bands = 1
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img.dataType = 'FLOAT'
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@ -175,103 +211,72 @@ def mask_filter(inps, band, outName, plot=False):
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img.renderVRT()
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#img.finalizeImage()
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################################
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if plot:
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import matplotlib.pyplot as plt
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fig = plt.figure()
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return [snr, offset, offset1, offset2, offset3]
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ax=fig.add_subplot(1,2,1)
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# cax=ax.imshow(azOffset[800:,:], vmin=-2, vmax=4)
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cax=ax.imshow(Offset, vmin=-2, vmax=4)
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ax.set_title('''Offset''')
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ax=fig.add_subplot(1,2,2)
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#ax.imshow(azOffset_filt[800:,:], vmin=-2, vmax=4)
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ax.imshow(Offset_filt, vmin=-2, vmax=4)
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ax.set_title('''Offset filt''')
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plt.show()
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def getShape(file):
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dataset = gdal.Open(file,GA_ReadOnly)
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return dataset.RasterYSize, dataset.RasterXSize
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def plot_mask_and_filtering(az_list, rg_list, inps=None):
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def resampleOffset(maskedFiltOffset, geometryOffset, resampledOffset, outName):
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length, width = getShape(geometryOffset)
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print('oversampling the filtered and masked offsets to the width and length:', width, ' ', length )
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cmd = 'gdal_translate -of ENVI -outsize ' + str(width) + ' ' + str(length) + ' ' + maskedFiltOffset + ' ' + resampledOffset
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os.system(cmd)
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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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img = isceobj.createImage()
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img.setFilename(resampledOffset)
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img.setWidth(width)
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img.setAccessMode('READ')
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img.bands = 1
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img.dataType = 'FLOAT'
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img.scheme = 'BIP'
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#img.createImage()
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img.renderHdr()
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img.renderVRT()
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#img.finalizeImage()
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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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axs[0,0].set_title('SNR', fontsize=12)
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print ('Adding the dense offsets to the geometry offsets. Output: ', outName)
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cmd = "imageMath.py -e='a+b' -o " + outName + " -t float --a=" + geometryOffset + " --b=" + resampledOffset
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os.system(cmd)
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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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# plot offset
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for i in range(1,len(az_list)):
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im1 = axs[0,i].imshow(az_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
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im1 = axs[1,i].imshow(rg_list[i], vmin=inps.vlim[0], vmax=inps.vlim[1], cmap='jet')
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axs[0,i].set_title(titles[i], fontsize=12)
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fig.tight_layout()
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# colorbar
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fig.subplots_adjust(bottom=0.15)
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cax0 = fig.add_axes([0.09, 0.1, 0.08, 0.015])
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cbar0 = plt.colorbar(im0, cax=cax0, orientation='horizontal')
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cax0.yaxis.set_ticks_position('left')
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#fig.subplots_adjust(right=0.93)
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cax1 = fig.add_axes([0.57, 0.1, 0.08, 0.015])
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cbar1 = plt.colorbar(im1, cax=cax1, orientation='horizontal')
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cbar1.set_label('pixel', fontsize=12)
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# save figure to file
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if inps.fig_name is not None:
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inps.fig_name = os.path.abspath(inps.fig_name)
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print('save figure to file {}'.format(inps.fig_name))
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plt.savefig(inps.fig_name, bbox_inches='tight', transparent=True, dpi=300)
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plt.show()
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return
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def main(iargs=None):
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inps = cmdLineParse(iargs)
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#######################
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# working on the azimuth offsets
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#######################
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#cmd = 'isce2gis.py envi -i ' + inps.geometryAzimuthOffset
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#os.system(cmd)
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if not os.path.exists(inps.outDir):
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os.makedirs(inps.outDir)
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inps = cmdLineParse(iargs)
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#######################
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# masking the dense offsets based on SNR and median filter the masked offsets
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maskedFiltOffset = os.path.join(inps.outDir, inps.outAzimuth)
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mask_filter(inps, band=[1], outName = maskedFiltOffset, plot=inps.plot)
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if not os.path.exists(inps.outDir):
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os.makedirs(inps.outD)
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cmd = 'isce2gis.py envi -i ' + maskedFiltOffset
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os.system(cmd)
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#######################
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# resampling the masked and filtered dense offsets to the same
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# grid size of the geometry offsets and adding back to the
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# geometry offsets
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# outAzimuth = os.path.join(inps.outDir, inps.outAzimuth)
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#######################
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# masking the dense offsets based on SNR and median filter the masked offs
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# resampledDenseOffset = os.path.join(inps.outDir, 'filtAzOff_resampled.bil')
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# resampleOffset(maskedFiltOffset, inps.geometryAzimuthOffset, resampledDenseOffset, outAzimuth)
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#######################
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#######################
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# working on the range offsets
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#######################
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#cmd = 'isce2gis.py envi -i ' + inps.geometryRangeOffset
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#os.system(cmd)
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if not os.path.exists(inps.outDir):
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os.makedirs(inps.outDir)
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#######################
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# masking the dense offsets based on SNR and median filter the masked offsets
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# azimuth offsets
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inps.outAzimuth = os.path.join(inps.outDir, inps.outAzimuth)
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az_list = mask_filter(inps, band=[1], outName=inps.outAzimuth)
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maskedFiltOffset = os.path.join(inps.outDir, inps.outRange)
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mask_filter(inps, band=[2], outName = maskedFiltOffset, plot=inps.plot)
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# range offsets
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inps.outRange = os.path.join(inps.outDir, inps.outRange)
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rg_list = mask_filter(inps, band=[2], outName=inps.outRange)
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cmd = 'isce2gis.py envi -i ' + maskedFiltOffset
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os.system(cmd)
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#######################
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# resampling the masked and filtered dense offsets to the same grid size of the geometry offsets
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#outRange = os.path.join(inps.outDir, inps.outRange)
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#resampledDenseOffset = os.path.join(inps.outDir, 'filtRngOff_resampled.bil')
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#resampleOffset(maskedFiltOffset, inps.geometryRangeOffset, resampledDenseOffset, outRange)
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# plot result
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if inps.plot:
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plot_mask_and_filtering(az_list, rg_list, inps)
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return
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if __name__ == '__main__':
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