Added downsample_snapu factory to TopsProc/Factories.py
Added runner run_downsample_unwrapper.py to TopsProc added donwsample_unwraper module to contrib git commit -mLT1AB
giangi
parent
c5e086f16c
commit
6d3811ec11
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@ -50,7 +50,9 @@ def createUnwrapper(other, do_unwrap = None, unwrapperName = None,
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elif unwrapperName.lower() == 'snaphu':
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from .runUnwrapSnaphu import runUnwrap
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elif unwrapperName.lower() == 'snaphu_mcf':
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from .runUnwrapSnaphu import runUnwrapMcf as runUnwrap
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from .runUnwrapSnaphu import runUnwrap
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elif unwrapperName.lower() == 'downsample_snaphu':
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from .run_downsample_unwrapper import runUnwrap
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elif unwrapperName.lower() == 'icu':
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from .runUnwrapIcu import runUnwrap
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elif unwrapperName.lower() == 'grass':
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@ -40,6 +40,6 @@ project = 'TopsProc'
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install = os.path.join(envisceobj['PRJ_SCONS_INSTALL'],package,project)
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listFiles = ['__init__.py', 'Factories.py', 'TopsProc.py', 'runPreprocessor.py', 'runComputeBaseline.py', 'runVerifyDEM.py', 'runTopo.py', 'runSubsetOverlaps.py', 'runCoarseOffsets.py', 'runCoarseResamp.py', 'runOverlapIfg.py', 'runPrepESD.py', 'runESD.py', 'runRangeCoreg.py', 'runFineOffsets.py', 'runFineResamp.py', 'runBurstIfg.py', 'runMergeBursts.py', 'runFilter.py', 'runUnwrapGrass.py', 'runUnwrapIcu.py', 'runUnwrapSnaphu.py', 'runGeocode.py', 'runMergeSLCs.py', 'runDenseOffsets.py', 'runOffsetFilter.py', 'runOffsetGeocode.py', 'runCropOffsetGeo.py', 'runUnwrap2Stage.py', 'VRTManager.py', 'runVerifyGeocodeDEM.py', 'runIon.py']
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listFiles = ['__init__.py', 'run_downsample_unwrapper.py','Factories.py', 'TopsProc.py', 'runPreprocessor.py', 'runComputeBaseline.py', 'runVerifyDEM.py', 'runTopo.py', 'runSubsetOverlaps.py', 'runCoarseOffsets.py', 'runCoarseResamp.py', 'runOverlapIfg.py', 'runPrepESD.py', 'runESD.py', 'runRangeCoreg.py', 'runFineOffsets.py', 'runFineResamp.py', 'runBurstIfg.py', 'runMergeBursts.py', 'runFilter.py', 'runUnwrapGrass.py', 'runUnwrapIcu.py', 'runUnwrapSnaphu.py', 'runGeocode.py', 'runMergeSLCs.py', 'runDenseOffsets.py', 'runOffsetFilter.py', 'runOffsetGeocode.py', 'runCropOffsetGeo.py', 'runUnwrap2Stage.py', 'VRTManager.py', 'runVerifyGeocodeDEM.py', 'runIon.py']
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envisceobj.Install(install,listFiles)
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envisceobj.Alias('install',install)
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@ -0,0 +1,33 @@
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import sys
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import isceobj
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import os
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from isceobj.TopsProc.runUnwrapSnaphu import runUnwrapMcf
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from contrib.downsample_unwrapper.downsample_unwrapper import DownsampleUnwrapper
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def runUnwrap(self,costMode = None,initMethod = None, defomax = None, initOnly = None):
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#generate inputs from insar obj
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inps = {
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"flat_name":self._insar.filtFilename,
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"unw_name":self._insar.unwrappedIntFilename,
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"cor_name":self._insar.coherenceFilename,
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"range_looks":self.numberRangeLooks,
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"azimuth_looks":self.numberAzimuthLooks,
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"data_dir":self._insar.mergedDirname
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}
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du = DownsampleUnwrapper(inps)
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#modify the filenames so it uses the downsampled versions
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self._insar.filtFilename = du._dflat_name
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self._insar.unwrappedIntFilename = du._dunw_name
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self._insar.coherenceFilename = du._dcor_name
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self.numberRangeLooks = int(du._resamp*du._range_looks)
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self.numberAzimuthLooks = int(du._resamp*du._azimuth_looks)
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du.downsample_images(du._ddir,du._flat_name,du._cor_name,du._resamp)
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runUnwrapMcf(self)
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du.upsample_unw(du._ddir,du._flat_name,du._dunw_name,du._dccomp_name,upsamp=du._resamp,filt_sizes=(3,4))
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#put back the original values
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self._insar.filtFilename = du._flat_name
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self._insar.unwrappedIntFilename = du._unw_name
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self._insar.coherenceFilename = du._cor_name
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self.numberRangeLooks = int(du._range_looks)
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self.numberAzimuthLooks = int(du._azimuth_looks)
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@ -65,6 +65,8 @@ frameUtils = os.path.join('frameUtils','SConscript')
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SConscript(frameUtils)
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unwUtils = os.path.join('UnwrapComp','SConscript')
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SConscript(unwUtils)
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downsample_unwrapper = os.path.join('downsample_unwrapper','SConscript')
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SConscript(downsample_unwrapper)
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if 'MOTIFLIBPATH' in envcontrib.Dictionary():
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mdx = os.path.join('mdx','SConscript')
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@ -0,0 +1,35 @@
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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#
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# Giangi Sacco
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# NASA Jet Propulsion Laboratory
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# California Institute of Technology
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# (c) 2019 All Rights Reserved
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#
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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#!/usr/bin/env python
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import os
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Import('envcontrib')
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envDSU = envcontrib.Clone()
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project = 'downsample_unwrapper'
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package = envDSU['PACKAGE']
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envDSU['PROJECT'] = project
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Export('envDSU')
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initFile = '__init__.py'
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if not os.path.exists(initFile):
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fout = open(initFile,"w")
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fout.write("#!/usr/bin/env python")
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fout.close()
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install = os.path.join(envDSU['PRJ_SCONS_INSTALL'],package,project)
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helpList,installHelp = envDSU['HELP_BUILDER'](envDSU,'__init__.py',install)
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envDSU.Install(installHelp,helpList)
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envDSU.Alias('install',installHelp)
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listFiles = ['downsample_unwrapper.py','run_unwrap_snaphu.py',initFile]
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envDSU.Install(install,listFiles)
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envDSU.Alias('install',install)
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@ -0,0 +1 @@
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#!/usr/bin/env python
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@ -0,0 +1,173 @@
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import sys
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import isceobj
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import os
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import json
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import numpy as np
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from scipy.ndimage import zoom,gaussian_filter
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from .run_unwrap_snaphu import runUnwrap
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from iscesys.Component.Component import Component
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class DownsampleUnwrapper(Component):
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def __init__(self,inps):
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self._dtype_map = {'cfloat':np.complex64,'float':np.float32,'byte':np.uint8}
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self._ddir = inps['data_dir']
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self._resamp = inps['resamp'] if 'resamp' in inps else 2
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self._cor_name = inps['cor_name'] if 'cor_name' in inps else 'phsig.cor'
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self._unw_name = inps['unw_name'] if 'unw_name' in inps else 'filt_topophase.flat'
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self._flat_name = inps['flat_name'] if 'flat_name' in inps else 'filt_topophase.unw'
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self._ccomp_name = self._unw_name + '.conncomp'
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self._dcor_name = '{0:s}_{1:d}x{1:d}.cor'.format(self._cor_name.replace('.cor',''),self._resamp)
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self._dunw_name = '{0:s}_{1:d}x{1:d}.unw'.format(self._unw_name.replace('.unw',''),self._resamp)
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self._dflat_name = '{0:s}_{1:d}x{1:d}.flat'.format(self._flat_name.replace('.flat',''),self._resamp)
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self._dccomp_name = self._dunw_name + '.conncomp'
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self._earth_radius = inps['earth_radius'] if 'earth_radius' in inps else 6371000
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self._altitude = inps['altitude'] if 'altitude' in inps else 800000
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self._wavelength = inps['wavelength'] if 'wavelength' in inps else 0
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self._azimuth_looks = inps['azimuth_looks']
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self._range_looks = inps['range_looks']
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self._remove_downsampled = True if 'remove_downsampled' in inps else False
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def get_isce_image(self,itype,fname,width,length):
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if itype == 'flat':
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im = isceobj.createIntImage()
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else:
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im = isceobj.createImage()
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im.dataType = 'FLOAT'
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if itype == 'unw':
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im.bands = 2
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im.scheme = 'BIL'
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elif itype == 'ccomp':
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im.dataType = 'BYTE'
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im.filename = fname
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im.extraFilename = fname + '.vrt'
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im.width = width
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im.length = length
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return im
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def save_image(self,ddir,fname,img,itype):
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dname = os.path.join(ddir,fname)
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im = self.get_isce_image(itype,dname,img.shape[-1],img.shape[0])
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img.astype(self._dtype_map[im.dataType.lower()]).tofile(dname)
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im.dump(dname + '.xml')
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def remove_downsampled(self,ddir,flat,unw,phsig,ccomp):
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try:
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#subprocess keeps changing API. just use system
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cmd = 'rm -rf {}* {}* {}* {}*'.format(os.path.join(ddir,flat),os.path.join(ddir,unw),os.path.join(ddir,phsig),os.path.join(ddir,ccomp))
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os.system(cmd)
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except Exception as e:
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print(e)
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def downsample_images(self,ddir,flat,phsig,resamp):
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img,im = self.load_image(ddir,flat)
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_,co = self.load_image(ddir,phsig)
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ims = []
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cos = []
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width = img.width
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length = img.length
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width -= width%resamp
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length -= length%resamp
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for i in range(resamp):
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for j in range(resamp):
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ims.append(im[i:length:resamp,j:width:resamp])
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cos.append(co[i:length:resamp,j:width:resamp])
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ims = np.array(ims).transpose([1,2,0])
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cos = np.array(cos).transpose([1,2,0])
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nims = ims.mean(2)
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ncos = cos.mean(2)
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self.save_image(ddir, self._dcor_name,ncos,'cor')
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self.save_image(ddir, self._dflat_name,nims,'flat')
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def load_image(self,ddir,fname):
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img = isceobj.createImage()
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img.load(os.path.join(ddir,fname + '.xml'))
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dtype = self._dtype_map[img.dataType.lower()]
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width = img.getWidth()
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length = img.getLength()
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im = np.fromfile(os.path.join(ddir,fname),dtype)
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if img.bands == 1:
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im = im.reshape([length,width])
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else:#the other option is the unw which is 2 bands BIL
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im = im.reshape([length,img.bands,width])
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return img,im
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def upsample_unw(self,ddir,flat,unw,ccomp,upsamp=2,filt_sizes=(3,4)):
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_,dunw = self.load_image(ddir,unw)
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_,flati = self.load_image(ddir,flat)
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_,dccomp = self.load_image(ddir,ccomp)
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uccomp = zoom(dccomp,upsamp)
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uccomp = np.round(uccomp).astype(np.uint8)
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ph_unw = dunw[:,1,:]
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amp = np.abs(flati)
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ph_flat = np.angle(flati)
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uph_unw = zoom(ph_unw,upsamp)
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uph_size = uph_unw.shape
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ph_size = ph_flat.shape
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if uph_size[0] != ph_size[0] or uph_size[0] != ph_size[1]:
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#the lost one pixel during downsampling/upsampling
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nunw = np.zeros(ph_flat.shape)
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nunw[:uph_size[0],:uph_size[1]] = uph_unw
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if ph_size[1] > uph_size[1]:
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nunw[-1,:-1] = uph_unw[-1,:]
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if ph_size[0] > uph_size[0]:
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nunw[:-1,-1] = uph_unw[:,-1]
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uph_unw = nunw
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funw = self.filter_image(uph_unw,ph_flat,filt_sizes)
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ifunw = np.round((funw - ph_flat)/(2*np.pi)).astype(np.int16)
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funw = ph_flat + 2*np.pi*ifunw
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unw_out = np.stack([amp,funw],0).transpose([1,0,2])
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self.save_image(ddir,self._unw_name,unw_out,'unw')
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self.save_image(ddir,self._ccomp_name,uccomp,'ccomp')
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if self._remove_downsampled:
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self.remove_downsampled(ddir, self._dflat_name,self._dunw_name,self._dccomp_name,self._dccomp_name)
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def filter_image(self,unw,wrp,filt_sizes):
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im0 = np.round((unw - wrp)/(2*np.pi))
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img = wrp + 2*np.pi*im0
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for filter in filt_sizes:
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if not isinstance(filter,tuple):
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filter = (filter,filter)
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img = gaussian_filter(img,filter,0)
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return wrp + 2*np.pi*np.round((img - wrp)/(2*np.pi))
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def run_snaphu(self):
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range_looks = int(self._range_looks*self._resamp)
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azimuth_looks = int(self._azimuth_looks*self._resamp)
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inps_json = {'flat_name':self._dflat_name,'unw_name':self._dunw_name,
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'cor_name':self._dcor_name,'wavelength':self._wavelength,
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'range_looks':range_looks,'azimuth_looks':azimuth_looks,
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'earth_radius':self._earth_radius,'altitude':self._altitude}
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runUnwrap(inps_json)
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def main(inps):
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"""
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Run the unwrapper with downsampling
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inputs:
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inps = dictionary with the following key,value
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{
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"flat_name":"filt_topophase.flat",
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"unw_name":"filt_topophase.unw",
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"cor_name":"phsig.cor",
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"range_looks":7,
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"azimuth_looks":3,
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"wavelength":0.05546576,
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"resamp":2,
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"data_dir":'./'
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}
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The range and azimuth looks are w.r.t the original image.
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"""
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du = DownsampleUnwrapper(inps)
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#du.downsample_images(du._ddir,du._flat_name,du._cor_name,du._resamp)
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#du.run_snaphu()
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du.upsample_unw(du._ddir,du._flat_name,du._dunw_name,du._dccomp_name,upsamp=du._resamp,filt_sizes=(3,4))
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if __name__ == '__main__':
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inp_json = sys.argv[1]
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ddir = sys.argv[2]
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inps = json.load(open(inp_json))
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inps['data_dir'] = ddir
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main(inps)
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@ -0,0 +1,91 @@
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#
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# Author: Piyush Agram
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# Copyright 2016
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#
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import sys
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import isceobj
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from contrib.Snaphu.Snaphu import Snaphu
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from isceobj.Constants import SPEED_OF_LIGHT
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from isceobj.Planet.Planet import Planet
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import os
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import json
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def runUnwrap(inps_json):
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costMode = 'SMOOTH'
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initMethod = 'MCF'
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defomax = 2.0
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initOnly = True
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if isinstance(inps_json,str):
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inps = json.load(open(inps_json))
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elif isinstance(inps_json,dict):
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inps = inps_json
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else:
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print('Expecting a json filename or a dictionary')
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raise ValueError
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wrapName = inps['flat_name']
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unwrapName = inps['unw_name']
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img = isceobj.createImage()
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img.load(wrapName + '.xml')
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width = img.getWidth()
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earthRadius = inps['earth_radius']
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altitude = inps['altitude']
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corrfile = inps['cor_name']
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rangeLooks = inps['range_looks']
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azimuthLooks = inps['azimuth_looks']
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wavelength = inps['wavelength']
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azfact = 0.8
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rngfact = 0.8
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corrLooks = rangeLooks * azimuthLooks/(azfact*rngfact)
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maxComponents = 20
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snp = Snaphu()
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snp.setInitOnly(initOnly)
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snp.setInput(wrapName)
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snp.setOutput(unwrapName)
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snp.setWidth(width)
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snp.setCostMode(costMode)
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snp.setEarthRadius(earthRadius)
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snp.setWavelength(wavelength)
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snp.setAltitude(altitude)
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snp.setCorrfile(corrfile)
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snp.setInitMethod(initMethod)
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snp.setCorrLooks(corrLooks)
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snp.setMaxComponents(maxComponents)
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snp.setDefoMaxCycles(defomax)
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snp.setRangeLooks(rangeLooks)
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snp.setAzimuthLooks(azimuthLooks)
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snp.setCorFileFormat('FLOAT_DATA')
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snp.prepare()
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snp.unwrap()
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######Render XML
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outImage = isceobj.Image.createUnwImage()
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outImage.setFilename(unwrapName)
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outImage.setWidth(width)
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outImage.setAccessMode('read')
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outImage.renderVRT()
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outImage.createImage()
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outImage.finalizeImage()
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outImage.renderHdr()
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#####Check if connected components was created
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if snp.dumpConnectedComponents:
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connImage = isceobj.Image.createImage()
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connImage.setFilename(unwrapName+'.conncomp')
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#At least one can query for the name used
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connImage.setWidth(width)
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connImage.setAccessMode('read')
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connImage.setDataType('BYTE')
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connImage.renderVRT()
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connImage.createImage()
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connImage.finalizeImage()
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connImage.renderHdr()
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return
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def main(inps):
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runUnwrap(inps)
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if __name__ == '__main__':
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sys.exit(main(sys.argv[1]))
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