topo: call gdal2isce_xml.py inside runMultilook() if xml file missing

+ topo: merge runMultilookGdal() into runMultilook() with new argument "method" to control to use isce Looks module (averaging) or gdal_translate (extraction; default, same as before).

+ topo: call gdal2isce_xml.py so that xml file for multilooked data are always generate. This fix the warning message from gdal_translate: "Warning 1: Geotransform matrix has non rotational terms"

+ topo: skip multilooking if the data file has vrt/xml file missing, which sometimes happens to incLocal and shadowMask (don't know the cause yet; I used GPU version).

+ crossmul/resampleSlc: re-organize module import at the top of scripts

contrib/stack/stripmapStack/crossmul.py

@@ -1,12 +1,15 @@
 #!/usr/bin/env python3
-import isce
+
+
 import os
-import logging
-from components.stdproc.stdproc import crossmul
-import isceobj
-from iscesys.ImageUtil.ImageUtil import ImageUtil as IU
-import isceobj
 import argparse
+import logging
+
+import isce
+import isceobj
+from components.stdproc.stdproc import crossmul
+from iscesys.ImageUtil.ImageUtil import ImageUtil as IU
+
 
 def createParser():
 

contrib/stack/stripmapStack/resampleSlc.py

@@ -1,18 +1,19 @@
 #!/usr/bin/env python3
 
+import os
+import argparse
+import shelve
+import json
+import logging
+import numpy as np
+
 import isce
 import isceobj
 import stdproc
 from stdproc.stdproc import crossmul
-import numpy as np
-from isceobj.Util.Poly2D import Poly2D
-import argparse
-import os
-import shelve
-from iscesys.ImageUtil.ImageUtil import ImageUtil as IU
-import json
-import logging
 from isceobj.Util.decorators import use_api
+from isceobj.Util.Poly2D import Poly2D
+from iscesys.ImageUtil.ImageUtil import ImageUtil as IU
 
 def createParser():
     parser = argparse.ArgumentParser( description='Use polynomial offsets and create burst by burst interferograms')

contrib/stack/stripmapStack/topo.py

@@ -6,11 +6,12 @@ import shelve
 import datetime
 import shutil
 import numpy as np
+import gdal
 import isce
 import isceobj
 from isceobj.Constants import SPEED_OF_LIGHT
 from isceobj.Util.Poly2D import Poly2D
-from mroipac.looks.Looks import Looks
+
 
 def createParser():
     '''
@@ -49,12 +50,11 @@ class Dummy(object):
 
 def runTopoGPU(info, demImage, dop=None, nativedop=False, legendre=False):
 
-    from isceobj.Planet.Planet import Planet
-    from zerodop.GPUtopozero.GPUtopozero import PyTopozero
     from isceobj import Constants as CN
+    from isceobj.Planet.Planet import Planet
     from isceobj.Util.Poly2D import Poly2D
     from iscesys import DateTimeUtil as DTU
-
+    from zerodop.GPUtopozero.GPUtopozero import PyTopozero
 
     ## TODO GPU does not support shadow and layover and local inc file generation
     full = False
@@ -358,20 +358,29 @@ def runSimamp(outdir, hname='z.rdr'):
     return
 
 
-def runMultilook(in_dir, out_dir, alks, rlks):
-    print('generate multilooked geometry files with alks={} and rlks={}'.format(alks, rlks))
+def runMultilook(in_dir, out_dir, alks, rlks, in_ext='.rdr', out_ext='.rdr', method='gdal',
+                 fbase_list=['hgt', 'incLocal', 'lat', 'lon', 'los', 'shadowMask', 'waterMask']):
+    """
+    Multilook geometry files.
+    """
     from iscesys.Parsers.FileParserFactory import createFileParser
-    FP = createFileParser('xml')
+    from mroipac.looks.Looks import Looks
 
+    print('generate multilooked geometry files with alks={} and rlks={}'.format(alks, rlks))
+
+    # create 'geom_master' directory
     os.makedirs(out_dir, exist_ok=True)
 
-    for fbase in ['hgt', 'incLocal', 'lat', 'lon', 'los', 'shadowMask', 'waterMask']:
-        fname = '{}.rdr'.format(fbase)
-        in_file = os.path.join(in_dir, fname)
-        out_file = os.path.join(out_dir, fname)
+    # multilook files one by one
+    for fbase in fbase_list:
+        in_file = os.path.join(in_dir, '{}{}'.format(fbase, in_ext))
+        out_file = os.path.join(out_dir, '{}{}'.format(fbase, out_ext))
 
-        if os.path.isfile(in_file):
-            xmlProp = FP.parse(in_file+'.xml')[0]
+        if all(os.path.isfile(in_file+ext) for ext in ['','.vrt','.xml']):
+
+            # option 1 - Looks module (isce)
+            if method == 'isce':
+                xmlProp = createFileParser('xml').parse(in_file+'.xml')[0]
                 if('image_type' in xmlProp and xmlProp['image_type'] == 'dem'):
                     inImage = isceobj.createDemImage()
                 else:
@@ -387,29 +396,8 @@ def runMultilook(in_dir, out_dir, alks, rlks):
                 lkObj.setOutputFilename(out_file)
                 lkObj.looks()
 
-            # copy the full resolution xml/vrt file from ./merged/geom_master to ./geom_master
-            # to facilitate the number of looks extraction
-            # the file path inside .xml file is not, but should, updated
-            shutil.copy(in_file+'.xml', out_file+'.full.xml')
-            shutil.copy(in_file+'.vrt', out_file+'.full.vrt')
-
-    return out_dir
-
-
-def runMultilookGdal(in_dir, out_dir, alks, rlks, in_ext='.rdr', out_ext='.rdr',
-                     fbase_list=['hgt', 'incLocal', 'lat', 'lon', 'los', 'shadowMask', 'waterMask']):
-    print('generate multilooked geometry files with alks={} and rlks={}'.format(alks, rlks))
-    import gdal
-
-    # create 'geom_master' directory
-    os.makedirs(out_dir, exist_ok=True)
-
-    # multilook files one by one
-    for fbase in fbase_list:
-        in_file = os.path.join(in_dir, '{}{}'.format(fbase, in_ext))
-        out_file = os.path.join(out_dir, '{}{}'.format(fbase, out_ext))
-
-        if os.path.isfile(in_file):
+            # option 2 - gdal_translate (gdal)
+            elif method == 'gdal':
                 ds = gdal.Open(in_file, gdal.GA_ReadOnly)
                 in_wid = ds.RasterXSize
                 in_len = ds.RasterYSize
@@ -424,6 +412,15 @@ def runMultilookGdal(in_dir, out_dir, alks, rlks, in_ext='.rdr', out_ext='.rdr',
                 print(cmd)
                 os.system(cmd)
 
+                # generate ISCE .xml file
+                if not os.path.isfile(out_file+'.xml'):
+                    cmd = 'gdal2isce_xml.py -i {}.vrt'.format(out_file)
+                    print(cmd)
+                    os.system(cmd)
+
+            else:
+                raise ValueError('un-supported multilook method: {}'.format(method))
+
             # copy the full resolution xml/vrt file from ./merged/geom_master to ./geom_master
             # to facilitate the number of looks extraction
             # the file path inside .xml file is not, but should, updated
@@ -521,8 +518,7 @@ def main(iargs=None):
     # write multilooked geometry files in "geom_master" directory, same level as "Igrams"
     if inps.rlks * inps.rlks > 1:
         out_dir = os.path.join(os.path.dirname(os.path.dirname(info.outdir)), 'geom_master')
-        runMultilookGdal(in_dir=info.outdir, out_dir=out_dir, alks=inps.alks, rlks=inps.rlks)
-        #runMultilook(in_dir=info.outdir, out_dir=out_dir, alks=inps.alks, rlks=inps.rlks)
+        runMultilook(in_dir=info.outdir, out_dir=out_dir, alks=inps.alks, rlks=inps.rlks)
 
     return