Merge branch 'master' into cmake

.circleci/config.yml

@@ -143,7 +143,7 @@ jobs:
           name: Install dependencies
           command: |
             apk add --no-cache \
-              python-dev py-pip bash pigz build-base libffi-dev openssl-dev
+              python3-dev py3-pip bash pigz build-base libffi-dev openssl-dev
             pip install \
               docker-compose awscli
       - run:
@@ -170,7 +170,7 @@ jobs:
           name: Install dependencies
           command: |
             apk add --no-cache \
-              python-dev py-pip bash pigz build-base libffi-dev openssl-dev
+              python3-dev py3-pip bash pigz build-base libffi-dev openssl-dev
             pip install \
               docker-compose awscli
       - run:
@@ -196,7 +196,7 @@ jobs:
           name: Install dependencies
           command: |
             apk add --no-cache \
-              python-dev py-pip bash pigz build-base libffi-dev openssl-dev
+              python3-dev py3-pip bash pigz build-base libffi-dev openssl-dev
             pip install \
               docker-compose awscli
       - run:

components/isceobj/Alos2Proc/runPreprocessor.py

@@ -494,6 +494,10 @@ def runPreprocessor(self):
         mvel = np.array(masterSV.getVelocity())
         sxyz = np.array(slaveSV.getPosition())
 
+        #to fix abrupt change near zero in baseline grid. JUN-05-2020
+        mvelunit = mvel / np.linalg.norm(mvel)
+        sxyz = sxyz - np.dot ( sxyz-mxyz, mvelunit) * mvelunit
+
         aa = np.linalg.norm(sxyz-mxyz)
         costheta = (x[1]*x[1] + aa*aa - slvrng*slvrng)/(2.*x[1]*aa)
 

components/isceobj/Alos2burstProc/runPreprocessor.py

@@ -417,6 +417,10 @@ def runPreprocessor(self):
         mvel = np.array(masterSV.getVelocity())
         sxyz = np.array(slaveSV.getPosition())
 
+        #to fix abrupt change near zero in baseline grid. JUN-05-2020
+        mvelunit = mvel / np.linalg.norm(mvel)
+        sxyz = sxyz - np.dot ( sxyz-mxyz, mvelunit) * mvelunit
+
         aa = np.linalg.norm(sxyz-mxyz)
         costheta = (x[1]*x[1] + aa*aa - slvrng*slvrng)/(2.*x[1]*aa)
 

components/isceobj/TopsProc/runComputeBaseline.py

@@ -77,6 +77,8 @@ def runComputeBaseline(self):
                     mxyz = np.array(masterSV.getPosition())
                     mvel = np.array(masterSV.getVelocity())
                     sxyz = np.array(slaveSV.getPosition())
+                    mvelunit = mvel / np.linalg.norm(mvel)
+                    sxyz = sxyz - np.dot ( sxyz-mxyz, mvelunit) * mvelunit
 
                     aa = np.linalg.norm(sxyz-mxyz)
                     costheta = (rng*rng + aa*aa - slvrng*slvrng)/(2.*rng*aa)

components/zerodop/baseline/Baseline.py

@@ -103,6 +103,8 @@ class Baseline(Component):
             mxyz = np.array(masterSV.getPosition())
             mvel = np.array(masterSV.getVelocity())
             sxyz = np.array(slaveSV.getPosition())
+            mvelunit = mvel / np.linalg.norm(mvel)
+            sxyz = sxyz - np.dot ( sxyz-mxyz, mvelunit) * mvelunit
 
             aa = np.linalg.norm(sxyz-mxyz)
 

contrib/stack/topsStack/Stack.py

@@ -912,7 +912,8 @@ class sentinelSLC(object):
 
         self.SNWE=[min(lats),max(lats),min(lons),max(lons)]
 
-    def get_orbit(self, orbitDir, workDir):
+    def get_orbit(self, orbitDir, workDir, margin=60.0):
+        margin = datetime.timedelta(seconds=margin)
         datefmt = "%Y%m%dT%H%M%S"
         orbit_files = glob.glob(os.path.join(orbitDir,  self.platform + '*.EOF'))
         if len(orbit_files) == 0:
@@ -922,10 +923,10 @@ class sentinelSLC(object):
         for orbit in orbit_files:
            orbit = os.path.basename(orbit)
            fields = orbit.split('_')
-           orbit_start_date_time = datetime.datetime.strptime(fields[6].replace('V',''), datefmt)
+           orbit_start_date_time = datetime.datetime.strptime(fields[6].replace('V',''), datefmt) + margin
-           orbit_stop_date_time = datetime.datetime.strptime(fields[7].replace('.EOF',''), datefmt)
+           orbit_stop_date_time = datetime.datetime.strptime(fields[7].replace('.EOF',''), datefmt) - margin
 
-           if self.start_date_time > orbit_start_date_time and self.start_date_time < orbit_stop_date_time:
+           if self.start_date_time >= orbit_start_date_time and self.stop_date_time < orbit_stop_date_time:
                self.orbit = os.path.join(orbitDir,orbit)
                self.orbitType = 'precise'
                match = True
@@ -944,7 +945,7 @@ class sentinelSLC(object):
               fields = os.path.basename(orbitFile).split('_')
               orbit_start_date_time = datetime.datetime.strptime(fields[6].replace('V',''), datefmt)
               orbit_stop_date_time = datetime.datetime.strptime(fields[7].replace('.EOF',''), datefmt)
-              if self.start_date_time > orbit_start_date_time and self.start_date_time < orbit_stop_date_time:
+              if self.start_date_time >= orbit_start_date_time and self.stop_date_time < orbit_stop_date_time:
                   print ("restituted orbit already exists.")
                   self.orbit =  orbitFile
                   self.orbitType = 'restituted'

contrib/stack/topsStack/fetchOrbit.py

@@ -38,9 +38,11 @@ def FileToTimeStamp(safename):
     '''
     safename = os.path.basename(safename)
     fields = safename.split('_')
+    sstamp = []  # sstamp for getting SAFE file start time, not needed for orbit file timestamps
 
     try:
         tstamp = datetime.datetime.strptime(fields[-4], datefmt)
+        sstamp = datetime.datetime.strptime(fields[-5], datefmt)
     except: 
         p = re.compile(r'(?<=_)\d{8}')  
         dt2 = p.search(safename).group() 
@@ -48,7 +50,7 @@ def FileToTimeStamp(safename):
 
     satName = fields[0]
 
-    return tstamp, satName
+    return tstamp, satName, sstamp
 
 
 class MyHTMLParser(HTMLParser):
@@ -144,7 +146,7 @@ if __name__ == '__main__':
 
     inps = cmdLineParse()
 
-    fileTS, satName = FileToTimeStamp(inps.input)
+    fileTS, satName, fileTSStart = FileToTimeStamp(inps.input)
     print('Reference time: ', fileTS)
     print('Satellite name: ', satName)
     
@@ -198,7 +200,7 @@ if __name__ == '__main__':
                 for result in results:
                     tbef, taft, mission = fileToRange(os.path.basename(result))
 
-                    if (tbef <= fileTS) and (taft >= fileTS):
+                    if (tbef <= fileTSStart) and (taft >= fileTS):
                         datestr2 = FileToTimeStamp(result)[0].strftime(queryfmt2) 
                         match = (server2 + spec[1].replace('aux_', '').upper() +
                                  '/' +datestr2+ result + '.EOF')

contrib/stack/topsStack/s1a_isce_utils.py

@@ -193,6 +193,12 @@ def adjustCommonValidRegion(master,slave):
     master.firstValidLine = max(master.firstValidLine, slave.firstValidLine)
     master.firstValidSample = max(master.firstValidSample, slave.firstValidSample)
 
+    #set to 0 to avoid negative values
+    if master.firstValidLine<0:
+        master.firstValidLine=0
+    if master.firstValidSample<0:
+        master.firstValidSample=0
+
     master.numValidLines = igram_lastValidLine - master.firstValidLine + 1
     master.numValidSamples = igram_lastValidSample - master.firstValidSample + 1
 

defaults/logging/logging.conf

@@ -21,7 +21,8 @@ propagate=0
 class=handlers.RotatingFileHandler
 formatter=simpleFormatter
 # Filename, file mode, maximum file size in bytes,number of backups to keep
-args=('isce.log','a',1048576,5)
+# encoding, delay
+args=('isce.log','a',1048576,5,None,True)
 
 [handler_consoleHandler]
 class=StreamHandler

examples/input_files/alos2/alos2_tutorial.txt

@@ -92,7 +92,15 @@ in the data. Normally we only process HH polarization, so you can only extract H
 zip files to save space. If you want to process other polarizations, extract those polarization instead.
 
 2. DEM and water body
-If you only process one InSAR pair, there is no need to download DEM and water body. The program will
+
+You MUST FIRST have an account to download DEM and water body, no matter you download them manually or let 
+the program download them automatically. See
+https://github.com/isce-framework/isce2#notes-on-digital-elevation-models
+or
+https://github.com/isce-framework/isce2
+for more details.
+
+If you only process one InSAR pair, there is no need to download DEM and water body manually. The program will
 do it for you. However, if you want to process a stack of interferograms, we recommend downloading DEM
 and water body by yourself and set the parameters in the input file; otherwise, the program will download
 DEM and water body each time it processes a pair. See input file on how to download DEM and water