Merge pull request #47 from hfattahi/master

adding UAVSAR_HDF5_SLC Sensor

applications/make_raw.py

@@ -167,7 +167,7 @@ class make_raw(Component, FrameMixin):
 
         startHeight = sv0.calculateHeight(ellipsoid)
         midHeight = sv1.calculateHeight(ellipsoid)
-        if 'uav' in self.sensor.family.lower():
+        if ('uav' in self.sensor.family.lower()) and (hasattr(self.sensor, 'platformHeight')):
             self.spacecraftHeight = self.sensor.platformHeight
         else:
             self.spacecraftHeight = startHeight

components/isceobj/Sensor/UAVSAR_HDF5_SLC.py

@@ -0,0 +1,325 @@
+#!/usr/bin/env python3
+
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# Copyright 2013 California Institute of Technology. ALL RIGHTS RESERVED.
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+# http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# 
+# United States Government Sponsorship acknowledged. This software is subject to
+# U.S. export control laws and regulations and has been classified as 'EAR99 NLR'
+# (No [Export] License Required except when exporting to an embargoed country,
+# end user, or in support of a prohibited end use). By downloading this software,
+# the user agrees to comply with all applicable U.S. export laws and regulations.
+# The user has the responsibility to obtain export licenses, or other export
+# authority as may be required before exporting this software to any 'EAR99'
+# embargoed foreign country or citizen of those countries.
+#
+# Author: Heresh Fattahi
+#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+
+
+
+import datetime
+import logging
+try:
+    import h5py
+except ImportError:
+    raise ImportError(
+            "Python module h5py is required to process COSMO-SkyMed data"
+            )
+
+import isceobj
+from isceobj.Scene.Frame import Frame
+from isceobj.Orbit.Orbit import StateVector
+from isceobj.Planet.Planet import Planet
+from isceobj.Planet.AstronomicalHandbook import Const
+from isceobj.Sensor import cosar
+from iscesys.DateTimeUtil.DateTimeUtil import DateTimeUtil as DTU
+from isceobj.Sensor import tkfunc,createAuxFile
+from iscesys.Component.Component import Component
+from isceobj.Constants import SPEED_OF_LIGHT
+
+HDF5 = Component.Parameter(
+    'hdf5',
+    public_name='HDF5',
+    default=None,
+    type=str,
+    mandatory=True,
+    intent='input',
+    doc='UAVSAR slc input file in HDF5 format'
+)
+
+FREQUENCY = Component.Parameter(
+    'frequency',
+    public_name='FREQUENCY',
+    default='frequencyA',
+    type=str,
+    mandatory=True,
+    intent='input',
+    doc='frequency band of the UAVSAR slc file to be processed (frequencyA or frequencyB)'
+)
+
+POLARIZATION = Component.Parameter(
+    'polarization',
+    public_name='POLARIZATION',
+    default='HH',
+    type=str,
+    mandatory=True,
+    intent='input',
+    doc='polarization channel of the UAVSAR slc file to be processed'
+)
+
+from .Sensor import Sensor
+class UAVSAR_HDF5_SLC(Sensor):
+    """
+    A class representing a Level1Product meta data.
+    Level1Product(hdf5=h5filename) will parse the hdf5
+    file and produce an object with attributes for metadata.
+    """
+    parameter_list = (HDF5,
+                      FREQUENCY,
+                      POLARIZATION) + Sensor.parameter_list
+
+    logging_name = 'isce.Sensor.UAVSAR_HDF5_SLC'
+    family = 'uavsar_hdf5_slc'
+
+    def __init__(self,family='',name=''):# , frequency='frequencyA', polarization='HH'):
+        super(UAVSAR_HDF5_SLC,self).__init__(family if family else  self.__class__.family, name=name)
+        self.frame = Frame()
+        self.frame.configure()
+        # Some extra processing parameters unique to UAVSAR HDF5 SLC (currently)
+        self.dopplerRangeTime = []
+        self.dopplerAzimuthTime = []
+        self.azimuthRefTime = None
+        self.rangeRefTime = None
+        self.rangeFirstTime = None
+        self.rangeLastTime = None
+        #self.frequency = frequency
+        #self.polarization = polarization
+
+        self.lookMap = {'right': -1,
+                        'left': 1}
+        return
+
+    def __getstate__(self):
+        d = dict(self.__dict__)
+        del d['logger']
+        return d
+
+    def __setstate__(self,d):
+        self.__dict__.update(d)
+        self.logger = logging.getLogger('isce.Sensor.UAVSAR_HDF5_SLC')
+        return
+
+
+    def getFrame(self):
+        return self.frame
+
+    def parse(self):
+        try:
+            fp = h5py.File(self.hdf5,'r')
+        except Exception as strerr:
+            self.logger.error("IOError: %s" % strerr)
+            return None
+
+        self.populateMetadata(fp)
+        fp.close()
+
+    def populateMetadata(self, file):
+        """
+            Populate our Metadata objects
+        """
+
+        self._populatePlatform(file)
+        self._populateInstrument(file)
+        self._populateFrame(file)
+        self._populateOrbit(file)
+        
+
+    def _populatePlatform(self, file):
+        platform = self.frame.getInstrument().getPlatform()
+
+        platform.setMission(file['/science/LSAR/identification'].get('missionId')[()].decode('utf-8'))
+        platform.setPointingDirection(self.lookMap[file['/science/LSAR/identification'].get('lookDirection')[()].decode('utf-8')])
+        platform.setPlanet(Planet(pname="Earth"))
+
+        # We are not using this value anywhere. Let's fix it for now.
+        platform.setAntennaLength(12.0)
+
+    def _populateInstrument(self, file):
+        instrument = self.frame.getInstrument()
+
+        rangePixelSize = file['/science/LSAR/SLC/swaths/' + self.frequency + '/slantRangeSpacing'][()]
+        wvl = SPEED_OF_LIGHT/file['/science/LSAR/SLC/swaths/' + self.frequency + '/processedCenterFrequency'][()]
+        instrument.setRadarWavelength(wvl)
+        instrument.setPulseRepetitionFrequency(1.0/file['/science/LSAR/SLC/swaths/zeroDopplerTimeSpacing'][()])
+        rangePixelSize = file['/science/LSAR/SLC/swaths/' + self.frequency + '/slantRangeSpacing'][()]
+        instrument.setRangePixelSize(rangePixelSize)
+
+        # Chrip slope and length only are used in the split spectrum workflow to compute the bandwidth.
+        # Therefore fixing it to 1.0 won't breack anything
+        Chirp_slope = 1.0
+        rangeBandwidth = file['/science/LSAR/SLC/swaths/' + self.frequency + '/processedRangeBandwidth'][()]
+        Chirp_length = rangeBandwidth/Chirp_slope
+        instrument.setPulseLength(Chirp_length)
+        instrument.setChirpSlope(Chirp_slope)
+        rangeSamplingFrequency = SPEED_OF_LIGHT/2./rangePixelSize
+        instrument.setRangeSamplingRate(rangeSamplingFrequency)
+
+        incangle = 0.0
+        instrument.setIncidenceAngle(incangle)
+
+
+    def _populateFrame(self, file):
+
+        slantRange = file['/science/LSAR/SLC/swaths/' + self.frequency + '/slantRange'][0]
+        self.frame.setStartingRange(slantRange)
+
+        referenceUTC = file['/science/LSAR/SLC/swaths/zeroDopplerTime'].attrs['units'].decode('utf-8')
+        referenceUTC = referenceUTC.replace('seconds since ','')
+        referenceUTC = datetime.datetime.strptime(referenceUTC,'%Y-%m-%d %H:%M:%S')
+
+        relStart = file['/science/LSAR/SLC/swaths/zeroDopplerTime'][0]
+        relEnd = file['/science/LSAR/SLC/swaths/zeroDopplerTime'][-1]
+        relMid = 0.5*(relStart + relEnd)
+
+        sensingStart = self._combineDateTime(referenceUTC, relStart)
+        sensingStop = self._combineDateTime(referenceUTC, relEnd)
+        sensingMid = self._combineDateTime(referenceUTC, relMid)
+
+
+        self.frame.setPassDirection(file['/science/LSAR/identification'].get('orbitPassDirection')[()].decode('utf-8'))  
+        self.frame.setOrbitNumber(file['/science/LSAR/identification'].get('trackNumber')[()])
+        self.frame.setProcessingFacility('JPL')
+        self.frame.setProcessingSoftwareVersion(file['/science/LSAR/SLC/metadata/processingInformation/algorithms'].get('ISCEVersion')[()].decode('utf-8'))
+        self.frame.setPolarization(self.polarization)
+        self.frame.setNumberOfLines(file['/science/LSAR/SLC/swaths/' + self.frequency + '/' + self.polarization].shape[0])
+        self.frame.setNumberOfSamples(file['/science/LSAR/SLC/swaths/' + self.frequency + '/' + self.polarization].shape[1])
+        self.frame.setSensingStart(sensingStart)
+        self.frame.setSensingMid(sensingMid)
+        self.frame.setSensingStop(sensingStop)
+
+        rangePixelSize = self.frame.instrument.rangePixelSize
+        farRange = slantRange +  (self.frame.getNumberOfSamples()-1)*rangePixelSize
+        self.frame.setFarRange(farRange)
+
+    def _populateOrbit(self,file):
+        orbit = self.frame.getOrbit()
+
+        orbit.setReferenceFrame('ECR')
+        orbit.setOrbitSource('Header')
+
+        referenceUTC = file['/science/LSAR/SLC/swaths/zeroDopplerTime'].attrs['units'].decode('utf-8')
+        referenceUTC = referenceUTC.replace('seconds since ','')
+        t0 = datetime.datetime.strptime(referenceUTC,'%Y-%m-%d %H:%M:%S')
+        t = file['/science/LSAR/SLC/metadata/orbit/time']
+        position = file['/science/LSAR/SLC/metadata/orbit/position']
+        velocity = file['/science/LSAR/SLC/metadata/orbit/velocity']
+
+        for i in range(len(position)):
+            vec = StateVector()
+            dt = t0 + datetime.timedelta(seconds=t[i])
+            vec.setTime(dt)
+            vec.setPosition([position[i,0],position[i,1],position[i,2]])
+            vec.setVelocity([velocity[i,0],velocity[i,1],velocity[i,2]])
+            orbit.addStateVector(vec)
+
+
+    def extractImage(self):
+
+        import numpy as np
+        import h5py
+
+        self.parse()
+        
+        fid = h5py.File(self.hdf5, 'r')
+        ds = fid['/science/LSAR/SLC/swaths/' + self.frequency + '/' + self.polarization]
+        nLines = ds.shape[0]
+
+        with open(self.output, 'wb') as fout:
+            for ii in range(nLines):
+                ds[ii,:].astype(np.complex64).tofile(fout)
+
+        fid.close()
+  
+        slcImage = isceobj.createSlcImage()
+        slcImage.setFilename(self.output)
+        slcImage.setXmin(0)
+        slcImage.setXmax(self.frame.getNumberOfSamples())
+        slcImage.setWidth(self.frame.getNumberOfSamples())
+        slcImage.setAccessMode('r')
+        slcImage.renderHdr()
+        self.frame.setImage(slcImage)
+
+
+    def _parseNanoSecondTimeStamp(self,timestamp):
+        """
+            Parse a date-time string with nanosecond precision and return a datetime object
+        """
+        dateTime,nanoSeconds = timestamp.decode('utf-8').split('.')
+        microsec = float(nanoSeconds)*1e-3
+        dt = datetime.datetime.strptime(dateTime,'%Y-%m-%d %H:%M:%S')
+        dt = dt + datetime.timedelta(microseconds=microsec)
+        return dt
+
+    def _combineDateTime(self,dobj, secsstr):
+        '''Takes the date from dobj and time from secs to spit out a date time object.
+        '''
+        sec = float(secsstr)
+        dt = datetime.timedelta(seconds = sec)
+        return dobj + dt
+
+    def extractDoppler(self):
+        """
+        Return the doppler centroid as defined in the HDF5 file.
+        """
+
+        import h5py
+        from scipy.interpolate import UnivariateSpline
+        import numpy as np
+
+        h5 = h5py.File(self.hdf5,'r')
+
+        # extract the 2D LUT of Doppler and choose only one range line as the data duplicates for other range lines
+        dop = h5['/science/LSAR/SLC/metadata/processingInformation/parameters/' + self.frequency + '/dopplerCentroid'][0,:]
+        rng = h5['/science/LSAR/SLC/metadata/processingInformation/parameters/slantRange']
+
+        # extract the slant range of the image grid
+        imgRng = h5['/science/LSAR/SLC/swaths/' + self.frequency + '/slantRange']
+
+        # use only part of the slant range that closely covers image ranges and ignore the rest
+        ind0 = np.argmin(np.abs(rng-imgRng[0])) - 1
+        ind0 = np.max([0,ind0])
+        ind1 = np.argmin(np.abs(rng-imgRng[-1])) + 1
+        ind1 = np.min([ind1, rng.shape[0]])
+
+        dop = dop[ind0:ind1]
+        rng = rng[ind0:ind1]
+
+        f = UnivariateSpline(rng, dop)
+        imgDop = f(imgRng)
+
+        dr = imgRng[1]-imgRng[0]
+        pix = (imgRng - imgRng[0])/dr
+        fit = np.polyfit(pix, imgDop, 41)
+
+        self.frame._dopplerVsPixel = list(fit[::-1])
+
+        ####insarApp style (doesn't get used for stripmapApp). A fixed Doppler at the middle of the scene
+        quadratic = {}
+        quadratic['a'] = imgDop[int(imgDop.shape[0]/2)]/self.frame.getInstrument().getPulseRepetitionFrequency()
+        quadratic['b'] = 0.
+        quadratic['c'] = 0.
+
+        return quadratic

components/isceobj/Sensor/__init__.py

@@ -97,6 +97,7 @@ createERS_ENVISAT = partial(factory_template, 'ERS_EnviSAT')
 createERS_EnviSAT_SLC = partial(factory_template, 'ERS_EnviSAT_SLC')
 createSICD_RGZERO = partial(factory_template, 'SICD_RGZERO')
 createICEYE_SLC = partial(factory_template, 'ICEYE_SLC')
+createUAVSAR_Hdf5_SLC = partial(factory_template, 'UAVSAR_HDF5_SLC')
 
 SENSORS = {'ALOS' : createALOS,
            'ALOS_SLC' : createALOS_SLC,
@@ -121,7 +122,8 @@ SENSORS = {'ALOS' : createALOS,
            'ERS_ENVISAT' : createERS_ENVISAT,
            'ERS_ENVISAT_SLC' : createERS_EnviSAT_SLC,
            'SICD_RGZERO' : createSICD_RGZERO,
-           'ICEYE_SLC' : createICEYE_SLC}
+           'ICEYE_SLC' : createICEYE_SLC,
+           'UAVSAR_HDF5_SLC' : createUAVSAR_Hdf5_SLC}
 
 #These are experimental and can be added in as they become ready
 #           'JERS': createJERS,

components/isceobj/StripmapProc/Factories.py

@@ -52,7 +52,7 @@ def isRawSensor(sensor):
     '''
     Check if input data is raw / slc.
     '''
-    if str(sensor).lower() in ["terrasarx","cosmo_skymed_slc","radarsat2",'tandemx', 'kompsat5','risat1_slc','sentinel1', 'alos2','ers_slc','alos_slc','envisat_slc', 'uavsar_rpi','ers_envisat_slc','sicd_rgzero', 'iceye_slc']:
+    if str(sensor).lower() in ["terrasarx","cosmo_skymed_slc","radarsat2",'tandemx', 'kompsat5','risat1_slc','sentinel1', 'alos2','ers_slc','alos_slc','envisat_slc', 'uavsar_rpi','ers_envisat_slc','sicd_rgzero', 'iceye_slc', 'uavsar_hdf5_slc']:
         return False
     else:
         return True
@@ -63,7 +63,7 @@ def isZeroDopplerSLC(sensor):
     Check if SLC is zero doppler / native doppler.
     '''
 
-    if str(sensor).lower() in ["terrasarx","cosmo_skymed_slc","radarsat2",'tandemx', 'kompsat5','risat1_slc','sentinel1', 'alos2','ers_slc','envisat_slc','ers_envisat_slc','sicd_rgzero', 'iceye_slc']:
+    if str(sensor).lower() in ["terrasarx","cosmo_skymed_slc","radarsat2",'tandemx', 'kompsat5','risat1_slc','sentinel1', 'alos2','ers_slc','envisat_slc','ers_envisat_slc','sicd_rgzero', 'iceye_slc', 'uavsar_hdf5_slc']:
         return True
     elif sensor.lower() in ['alos_slc', 'uavsar_rpi']:
         return False
@@ -76,7 +76,7 @@ def getDopplerMethod(sensor):
     Return appropriate doppler method based on user input.
     '''
 
-    if str(sensor).lower() in ["terrasarx","cosmo_skymed_slc","radarsat2",'tandemx', 'kompsat5','risat1_slc','sentinel1', 'alos2','ers_slc','alos_slc','envisat_slc', 'uavsar_rpi','cosmo_skymed','ers_envisat_slc','sicd_rgzero', 'iceye_slc']:
+    if str(sensor).lower() in ["terrasarx","cosmo_skymed_slc","radarsat2",'tandemx', 'kompsat5','risat1_slc','sentinel1', 'alos2','ers_slc','alos_slc','envisat_slc', 'uavsar_rpi','cosmo_skymed','ers_envisat_slc','sicd_rgzero', 'iceye_slc', 'uavsar_hdf5_slc']:
         res =  'useDEFAULT'
     else:
         res =  'useDOPIQ'