From 62726a57149363ff02aad02172845121e6c1b239 Mon Sep 17 00:00:00 2001
From: CunrenLiang <56097947+CunrenLiang@users.noreply.github.com>
Date: Thu, 30 Apr 2020 23:43:41 -0700
Subject: [PATCH] update ALOS-2 ionospheric correction

---
 components/isceobj/Alos2Proc/runIonFilt.py  | 16 +++++++++++++---
 components/isceobj/Alos2Proc/runIonUwrap.py | 10 ++++++++++
 2 files changed, 23 insertions(+), 3 deletions(-)

diff --git a/components/isceobj/Alos2Proc/runIonFilt.py b/components/isceobj/Alos2Proc/runIonFilt.py
index 9c2ed5e..41c531d 100644
--- a/components/isceobj/Alos2Proc/runIonFilt.py
+++ b/components/isceobj/Alos2Proc/runIonFilt.py
@@ -80,11 +80,17 @@ def runIonFilt(self):
     cor[np.nonzero(cor<0)] = 0.0
     cor[np.nonzero(cor>1)] = 0.0
 
+    #remove water body
+    wbd = np.fromfile('wbd'+ml2+'.wbd', dtype=np.int8).reshape(length, width)
+    cor[np.nonzero(wbd==-1)] = 0.0
+
+    #remove small values
+    cor[np.nonzero(cor<corThresholdAdj)] = 0.0
+
     #compute ionosphere
     fl = SPEED_OF_LIGHT / self._insar.subbandRadarWavelength[0]
     fu = SPEED_OF_LIGHT / self._insar.subbandRadarWavelength[1]
     adjFlag = 1
-    cor[np.nonzero(cor<corThresholdAdj)] = 0.0
     ionos = computeIonosphere(lowerUnw, upperUnw, cor**corOrderAdj, fl, fu, adjFlag, 0)
 
     #dump ionosphere
@@ -131,13 +137,13 @@ def runIonFilt(self):
         # 1 is not good for low coherence case, changed to 20
         #corOrderFit = 1
         corOrderFit = 20
-        corOrderFilt = 20
+        corOrderFilt = 14
     else:
         #parameters for using lower/upper band coherence
         corfile = subbandPrefix[0]+ml2+'.cor'
         corThresholdFit = 0.4
         corOrderFit = 10
-        corOrderFilt = 10
+        corOrderFilt = 4
 
     #################################################
 
@@ -166,6 +172,10 @@ def runIonFilt(self):
     cor[np.nonzero(cor<0)] = 0.0
     cor[np.nonzero(cor>1)] = 0.0
 
+    #remove water body
+    wbd = np.fromfile('wbd'+ml2+'.wbd', dtype=np.int8).reshape(length, width)
+    cor[np.nonzero(wbd==-1)] = 0.0
+
     # #applying water body mask here
     # waterBodyFile = 'wbd'+ml2+'.wbd'
     # if os.path.isfile(waterBodyFile):
diff --git a/components/isceobj/Alos2Proc/runIonUwrap.py b/components/isceobj/Alos2Proc/runIonUwrap.py
index f9a35af..b8cb059 100644
--- a/components/isceobj/Alos2Proc/runIonUwrap.py
+++ b/components/isceobj/Alos2Proc/runIonUwrap.py
@@ -25,6 +25,7 @@ def runIonUwrap(self):
 
     masterTrack = self._insar.loadTrack(master=True)
     slaveTrack = self._insar.loadTrack(master=False)
+    wbdFile = os.path.abspath(self._insar.wbd)
 
     from isceobj.Alos2Proc.runIonSubband import defineIonDir
     ionDir = defineIonDir()
@@ -40,6 +41,7 @@ def runIonUwrap(self):
     ############################################################
     from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
     from contrib.alos2proc.alos2proc import look
+    from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
 
     ml2 = '_{}rlks_{}alks'.format(self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon, 
                               self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon)
@@ -69,6 +71,14 @@ def runIonUwrap(self):
         #         look(wbdOutFile, 'wbd'+ml2+'.wbd', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 0, 0, 1)
         #         create_xml('wbd'+ml2+'.wbd', width2, length2, 'byte')
 
+        #water body
+        if k == 0:
+            look(os.path.join(fullbandDir, self._insar.latitude), 'lat'+ml2+'.lat', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 3, 0, 1)
+            look(os.path.join(fullbandDir, self._insar.longitude), 'lon'+ml2+'.lon', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 3, 0, 1)
+            create_xml('lat'+ml2+'.lat', width2, length2, 'double')
+            create_xml('lon'+ml2+'.lon', width2, length2, 'double')
+            waterBodyRadar('lat'+ml2+'.lat', 'lon'+ml2+'.lon', wbdFile, 'wbd'+ml2+'.wbd')
+
 
     ############################################################
     # STEP 2. compute coherence