From f7f0113603cdc898af9bf088a8df2a4ff83629a3 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Thu, 25 May 2023 11:42:54 -0800
Subject: [PATCH 01/12] Apply nasa-jpl/autoRIFT#78

---
 hyp3_autorift/vend/testGeogrid_ISCE.py | 61 ++++++++++++++++++++++++--
 1 file changed, 57 insertions(+), 4 deletions(-)

diff --git a/hyp3_autorift/vend/testGeogrid_ISCE.py b/hyp3_autorift/vend/testGeogrid_ISCE.py
index e79a7fe2..ddf55859 100755
--- a/hyp3_autorift/vend/testGeogrid_ISCE.py
+++ b/hyp3_autorift/vend/testGeogrid_ISCE.py
@@ -68,6 +68,10 @@ def cmdLineParse():
             help='Input stable surface mask')
     parser.add_argument('-fo', '--flag_optical', dest='optical_flag', type=bool, required=False, default=0,
             help='flag for reading optical data (e.g. Landsat): use 1 for on and 0 (default) for off')
+    parser.add_argument('-b', '--buffer', dest='buffer', type=bool, required=False, default=0,
+            help='buffer to add to the starting/end range accounting for all passes from the same relative orbit')
+    parser.add_argument('-p', '--parse', dest='parse', action='store_true',
+            default=False, help='Parse the SAFE zip file to get radar image and orbit metadata; no need to run ISCE')
 
     return parser.parse_args()
 
@@ -114,7 +118,7 @@ def getMergedOrbit(product):
     return orb
 
 
-def loadMetadata(indir):
+def loadMetadata(indir,buffer=0):
     '''
     Input file.
     '''
@@ -136,12 +140,57 @@ def loadMetadata(indir):
     info.prf = 1.0 / frames[0].bursts[0].azimuthTimeInterval
     info.rangePixelSize = frames[0].bursts[0].rangePixelSize
     info.lookSide = -1
+        
+    info.startingRange -= buffer * info.rangePixelSize
+    info.farRange += buffer * info.rangePixelSize
+    
     info.numberOfLines = int( np.round( (info.sensingStop - info.sensingStart).total_seconds() * info.prf)) + 1
-    info.numberOfSamples = int( np.round( (info.farRange - info.startingRange)/info.rangePixelSize)) + 1
+    info.numberOfSamples = int( np.round( (info.farRange - info.startingRange)/info.rangePixelSize)) + 1  + 2 * buffer
     info.orbit = getMergedOrbit(frames)
 
     return info
 
+def loadParsedata(indir,buffer=0):
+    '''
+    Input file.
+    '''
+    import os
+    import numpy as np
+    import isce
+    from isceobj.Sensor.TOPS.Sentinel1 import Sentinel1
+    
+
+    frames = []
+    for swath in range(1,4):
+        rdr=Sentinel1()
+        rdr.configure()
+#        rdr.safe=['./S1A_IW_SLC__1SDH_20180401T100057_20180401T100124_021272_024972_8CAF.zip']
+        rdr.safe=[indir]
+        rdr.output='reference'
+        rdr.orbitDir='/Users/yanglei/orbit/S1A/precise'
+        rdr.auxDir='/Users/yanglei/orbit/S1A/aux'
+        rdr.swathNumber=swath
+        rdr.polarization='hh'
+        rdr.parse()
+        frames.append(rdr.product)
+    
+    info = Dummy()
+    info.sensingStart = min([x.sensingStart for x in frames])
+    info.sensingStop = max([x.sensingStop for x in frames])
+    info.startingRange = min([x.startingRange for x in frames])
+    info.farRange = max([x.farRange for x in frames])
+    info.prf = 1.0 / frames[0].bursts[0].azimuthTimeInterval
+    info.rangePixelSize = frames[0].bursts[0].rangePixelSize
+    info.lookSide = -1
+    
+    info.startingRange -= buffer * info.rangePixelSize
+    info.farRange += buffer * info.rangePixelSize
+    
+    info.numberOfLines = int( np.round( (info.sensingStop - info.sensingStart).total_seconds() * info.prf)) + 1
+    info.numberOfSamples = int( np.round( (info.farRange - info.startingRange)/info.rangePixelSize)) + 1 + 2 * buffer
+    info.orbit = getMergedOrbit(frames)
+    
+    return info
 
 def coregisterLoadMetadataOptical(indir_m, indir_s, **kwargs):
     '''
@@ -390,8 +439,12 @@ def main():
         metadata_m, metadata_s = coregisterLoadMetadataOptical(inps.indir_m, inps.indir_s)
         runGeogridOptical(metadata_m, metadata_s, inps.demfile, inps.dhdxfile, inps.dhdyfile, inps.vxfile, inps.vyfile, inps.srxfile, inps.sryfile, inps.csminxfile, inps.csminyfile, inps.csmaxxfile, inps.csmaxyfile, inps.ssmfile)
     else:
-        metadata_m = loadMetadata(inps.indir_m)
-        metadata_s = loadMetadata(inps.indir_s)
+        if inps.parse:
+            metadata_m = loadParsedata(inps.indir_m,inps.buffer)
+            metadata_s = loadParsedata(inps.indir_s,inps.buffer)
+        else:
+            metadata_m = loadMetadata(inps.indir_m,inps.buffer)
+            metadata_s = loadMetadata(inps.indir_s,inps.buffer)
         runGeogrid(metadata_m, metadata_s, inps.demfile, inps.dhdxfile, inps.dhdyfile, inps.vxfile, inps.vyfile, inps.srxfile, inps.sryfile, inps.csminxfile, inps.csminyfile, inps.csmaxxfile, inps.csmaxyfile, inps.ssmfile)
 
 

From 5af781ee241f83fd17c8e23de231c55ded4225a5 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Thu, 25 May 2023 17:13:33 -0800
Subject: [PATCH 02/12] Initial workflow that runs through

---
 hyp3_autorift/__main__.py              | 64 +++++++------------------
 hyp3_autorift/process.py               | 58 ++++++++++++++++++-----
 hyp3_autorift/s1_correction.py         | 65 ++++++++++++++++++++++++++
 hyp3_autorift/vend/testGeogrid_ISCE.py |  6 +--
 setup.py                               |  4 +-
 5 files changed, 133 insertions(+), 64 deletions(-)
 create mode 100644 hyp3_autorift/s1_correction.py

diff --git a/hyp3_autorift/__main__.py b/hyp3_autorift/__main__.py
index 022f9f13..01f98008 100644
--- a/hyp3_autorift/__main__.py
+++ b/hyp3_autorift/__main__.py
@@ -2,63 +2,33 @@
 AutoRIFT processing for HyP3
 """
 
-import os
-from argparse import ArgumentParser
-
-from hyp3lib.aws import upload_file_to_s3
-from hyp3lib.fetch import write_credentials_to_netrc_file
-from hyp3lib.image import create_thumbnail
-
-from hyp3_autorift.process import DEFAULT_PARAMETER_FILE, get_datetime, process
-
-
-def check_earthdata_credentials(username, password):
-    if username is None:
-        username = os.getenv('EARTHDATA_USERNAME')
 
-    if password is None:
-        password = os.getenv('EARTHDATA_PASSWORD')
-
-    return username, password
+import argparse
+import os
+import sys
+from importlib.metadata import entry_points
 
 
 def main():
-    parser = ArgumentParser()
-    parser.add_argument('--username', help='NASA Earthdata Login username for fetching Sentinel-1 scenes')
-    parser.add_argument('--password', help='NASA Earthdata Login password for fetching Sentinel-1 scenes')
-    parser.add_argument('--bucket', help='AWS bucket to upload product files to')
-    parser.add_argument('--bucket-prefix', default='', help='AWS prefix (location in bucket) to add to product files')
-    parser.add_argument('--parameter-file', default=DEFAULT_PARAMETER_FILE,
-                        help='Shapefile for determining the correct search parameters by '
-                             'geographic location. '
-                             'Path to shapefile must be understood by GDAL')
-    parser.add_argument('--naming-scheme', default='ITS_LIVE_OD', choices=['ITS_LIVE_OD', 'ITS_LIVE_PROD', 'ASF'],
-                        help='Naming scheme to use for product files')
-    parser.add_argument('--omp-num-threads', type=int, help='The number of OpenMP threads to use for parallel regions')
-    parser.add_argument('granules', type=str.split, nargs='+',
-                        help='Granule pair to process')
-    args = parser.parse_args()
-    username, password = check_earthdata_credentials(args.username, args.password)
+    parser = argparse.ArgumentParser(prefix_chars='+', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser.add_argument(
+        '++process', choices=['hyp3_autorift', 's1_correction'], default='hyp3_autorift',
+        help='Select the console_script entrypoint to use'  # console_script entrypoints are specified in `setup.py`
+    )
+    parser.add_argument('++omp-num-threads', type=int, help='The number of OpenMP threads to use for parallel regions')
 
-    args.granules = [item for sublist in args.granules for item in sublist]
-    if len(args.granules) != 2:
-        parser.error('Must provide exactly two granules')
+    args, unknowns = parser.parse_known_args()
 
     if args.omp_num_threads:
         os.environ['OMP_NUM_THREADS'] = str(args.omp_num_threads)
 
-    if username and password:
-        write_credentials_to_netrc_file(username, password)
-
-    g1, g2 = sorted(args.granules, key=get_datetime)
-
-    product_file, browse_file = process(g1, g2, parameter_file=args.parameter_file, naming_scheme=args.naming_scheme)
+    eps = entry_points()['console_scripts']
+    (process_entry_point,) = {process for process in eps if process.name == args.process}
 
-    if args.bucket:
-        upload_file_to_s3(product_file, args.bucket, args.bucket_prefix)
-        upload_file_to_s3(browse_file, args.bucket, args.bucket_prefix)
-        thumbnail_file = create_thumbnail(browse_file)
-        upload_file_to_s3(thumbnail_file, args.bucket, args.bucket_prefix)
+    sys.argv = [args.process, *unknowns]
+    sys.exit(
+        process_entry_point.load()()
+    )
 
 
 if __name__ == '__main__':
diff --git a/hyp3_autorift/process.py b/hyp3_autorift/process.py
index ddb03830..6e9c8d57 100644
--- a/hyp3_autorift/process.py
+++ b/hyp3_autorift/process.py
@@ -17,8 +17,10 @@
 import botocore.exceptions
 import numpy as np
 import requests
-from hyp3lib.fetch import download_file
+from hyp3lib.aws import upload_file_to_s3
+from hyp3lib.fetch import download_file, write_credentials_to_netrc_file
 from hyp3lib.get_orb import downloadSentinelOrbitFile
+from hyp3lib.image import create_thumbnail
 from hyp3lib.scene import get_download_url
 from netCDF4 import Dataset
 from osgeo import gdal
@@ -331,7 +333,7 @@ def process(reference: str, secondary: str, parameter_file: str = DEFAULT_PARAME
     secondary_path = None
     reference_metadata = None
     secondary_metadata = None
-    reference_zero_path = None
+    rcdeference_zero_path = None
     secondary_zero_path = None
     reference_state_vec = None
     secondary_state_vec = None
@@ -492,20 +494,52 @@ def process(reference: str, secondary: str, parameter_file: str = DEFAULT_PARAME
     return product_file, browse_file
 
 
+def check_earthdata_credentials(username, password):
+    if username is None:
+        username = os.getenv('EARTHDATA_USERNAME')
+
+    if password is None:
+        password = os.getenv('EARTHDATA_PASSWORD')
+
+    return username, password
+
+
 def main():
-    """Main entrypoint"""
     parser = argparse.ArgumentParser(
-        prog=os.path.basename(__file__),
-        description=__doc__,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
     )
-    parser.add_argument('reference', type=os.path.abspath,
-                        help='Reference Sentinel-1, Sentinel-2, or Landsat-8 Collection 2 scene')
-    parser.add_argument('secondary', type=os.path.abspath,
-                        help='Secondary Sentinel-1, Sentinel-2, or Landsat-8 Collection 2 scene')
+    parser.add_argument('--username', help='NASA Earthdata Login username for fetching Sentinel-1 scenes')
+    parser.add_argument('--password', help='NASA Earthdata Login password for fetching Sentinel-1 scenes')
+    parser.add_argument('--bucket', help='AWS bucket to upload product files to')
+    parser.add_argument('--bucket-prefix', default='', help='AWS prefix (location in bucket) to add to product files')
+    parser.add_argument('--parameter-file', default=DEFAULT_PARAMETER_FILE,
+                        help='Shapefile for determining the correct search parameters by geographic location. '
+                             'Path to shapefile must be understood by GDAL')
+    parser.add_argument('--naming-scheme', default='ITS_LIVE_OD', choices=['ITS_LIVE_OD', 'ITS_LIVE_PROD', 'ASF'],
+                        help='Naming scheme to use for product files')
+    parser.add_argument('--omp-num-threads', type=int, help='The number of OpenMP threads to use for parallel regions')
+    parser.add_argument('granules', type=str.split, nargs='+',
+                        help='Granule pair to process')
     args = parser.parse_args()
+    username, password = check_earthdata_credentials(args.username, args.password)
+
+    args.granules = [item for sublist in args.granules for item in sublist]
+    if len(args.granules) != 2:
+        parser.error('Must provide exactly two granules')
+
+    if args.omp_num_threads:
+        os.environ['OMP_NUM_THREADS'] = str(args.omp_num_threads)
+
+    if username and password:
+        write_credentials_to_netrc_file(username, password)
+
+    g1, g2 = sorted(args.granules, key=get_datetime)
 
-    process(**args.__dict__)
+    product_file, browse_file = process(g1, g2, parameter_file=args.parameter_file, naming_scheme=args.naming_scheme)
 
+    if args.bucket:
+        upload_file_to_s3(product_file, args.bucket, args.bucket_prefix)
+        upload_file_to_s3(browse_file, args.bucket, args.bucket_prefix)
+        thumbnail_file = create_thumbnail(browse_file)
+        upload_file_to_s3(thumbnail_file, args.bucket, args.bucket_prefix)
 
-if __name__ == "__main__":
-    main()
diff --git a/hyp3_autorift/s1_correction.py b/hyp3_autorift/s1_correction.py
new file mode 100644
index 00000000..bc5ea33a
--- /dev/null
+++ b/hyp3_autorift/s1_correction.py
@@ -0,0 +1,65 @@
+import argparse
+import logging
+from pathlib import Path
+
+from hyp3lib.aws import upload_file_to_s3
+from hyp3lib.fetch import download_file, write_credentials_to_netrc_file
+from hyp3lib.get_orb import downloadSentinelOrbitFile
+from hyp3lib.scene import get_download_url
+
+from hyp3_autorift import geometry, io
+from hyp3_autorift.process import DEFAULT_PARAMETER_FILE, check_earthdata_credentials, get_s1_primary_polarization
+from hyp3_autorift.vend.testGeogrid_ISCE import loadParsedata, runGeogrid
+log = logging.getLogger(__name__)
+
+
+def generate_correction_data(scene: str, buffer: int = 0, parameter_file: str = DEFAULT_PARAMETER_FILE):
+    scene_path = Path(f'{scene}.zip')
+    if not scene_path.exists():
+        scene_url = get_download_url(scene)
+        scene_path = download_file(scene_url, chunk_size=5242880)
+
+    orbits = Path('Orbits').resolve()
+    orbits.mkdir(parents=True, exist_ok=True)
+    state_vec, oribit_provider = downloadSentinelOrbitFile(scene, directory=str(orbits))
+    log.info(f'Downloaded orbit file {state_vec} from {oribit_provider}')
+
+    polarization = get_s1_primary_polarization(scene)
+    lat_limits, lon_limits = geometry.bounding_box(f'{scene}.zip', polarization=polarization, orbits=orbits)
+
+    scene_poly = geometry.polygon_from_bbox(x_limits=lat_limits, y_limits=lon_limits)
+    parameter_info = io.find_jpl_parameter_info(scene_poly, parameter_file)
+
+    isce_dem = geometry.prep_isce_dem(parameter_info['geogrid']['dem'], lat_limits, lon_limits)
+    io.format_tops_xml(scene, scene, polarization, isce_dem, orbits)
+
+    scene_meta = loadParsedata(str(scene_path), orbit_dir=orbits, aux_dir=orbits, buffer=buffer)
+    geogrid_info = runGeogrid(scene_meta, scene_meta, epsg=parameter_info['epsg'], **parameter_info['geogrid'])
+
+    return geogrid_info
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    parser.add_argument('--username', help='NASA Earthdata Login username for fetching Sentinel-1 scenes')
+    parser.add_argument('--password', help='NASA Earthdata Login password for fetching Sentinel-1 scenes')
+    parser.add_argument('--bucket', help='AWS bucket to upload product files to')
+    parser.add_argument('--bucket-prefix', default='', help='AWS prefix (location in bucket) to add to product files')
+    parser.add_argument('--buffer', type=int, default=0, help='Number of pixels to buffer each edge of the input scene')
+    parser.add_argument('--parameter-file', default=DEFAULT_PARAMETER_FILE,
+                        help='Shapefile for determining the correct search parameters by geographic location. '
+                             'Path to shapefile must be understood by GDAL')
+    parser.add_argument('granule', help='Reference granule to process')
+    args = parser.parse_args()
+
+    username, password = check_earthdata_credentials(args.username, args.password)
+    if username and password:
+        write_credentials_to_netrc_file(username, password)
+
+    _ = generate_correction_data(args.granule, buffer=args.buffer)
+
+    if args.bucket:
+        for geotiff in Path.cwd().glob('*.tif'):
+            upload_file_to_s3(geotiff, args.bucket, args.bucket_prefix)
diff --git a/hyp3_autorift/vend/testGeogrid_ISCE.py b/hyp3_autorift/vend/testGeogrid_ISCE.py
index ddf55859..a20f7a95 100755
--- a/hyp3_autorift/vend/testGeogrid_ISCE.py
+++ b/hyp3_autorift/vend/testGeogrid_ISCE.py
@@ -150,7 +150,7 @@ def loadMetadata(indir,buffer=0):
 
     return info
 
-def loadParsedata(indir,buffer=0):
+def loadParsedata(indir, orbit_dir, aux_dir, buffer=0):
     '''
     Input file.
     '''
@@ -167,8 +167,8 @@ def loadParsedata(indir,buffer=0):
 #        rdr.safe=['./S1A_IW_SLC__1SDH_20180401T100057_20180401T100124_021272_024972_8CAF.zip']
         rdr.safe=[indir]
         rdr.output='reference'
-        rdr.orbitDir='/Users/yanglei/orbit/S1A/precise'
-        rdr.auxDir='/Users/yanglei/orbit/S1A/aux'
+        rdr.orbitDir=orbit_dir
+        rdr.auxDir=aux_dir
         rdr.swathNumber=swath
         rdr.polarization='hh'
         rdr.parse()
diff --git a/setup.py b/setup.py
index 14a0524c..d923cc8f 100644
--- a/setup.py
+++ b/setup.py
@@ -62,8 +62,8 @@
     packages=find_packages(),
 
     entry_points={'console_scripts': [
-        'hyp3_autorift = hyp3_autorift.__main__:main',
-        'autorift_proc_pair = hyp3_autorift.process:main',
+        'hyp3_autorift = hyp3_autorift.process:main',
+        's1_correction = hyp3_autorift.s1_correction:main'
         ]
     },
 

From 3f1d1441ea01f6a98c03ec45e3952ee03baca5cb Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 26 May 2023 11:43:48 -0800
Subject: [PATCH 03/12] Move opt-num-threads to __main__

---
 hyp3_autorift/process.py | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/hyp3_autorift/process.py b/hyp3_autorift/process.py
index 6e9c8d57..308318d8 100644
--- a/hyp3_autorift/process.py
+++ b/hyp3_autorift/process.py
@@ -517,7 +517,6 @@ def main():
                              'Path to shapefile must be understood by GDAL')
     parser.add_argument('--naming-scheme', default='ITS_LIVE_OD', choices=['ITS_LIVE_OD', 'ITS_LIVE_PROD', 'ASF'],
                         help='Naming scheme to use for product files')
-    parser.add_argument('--omp-num-threads', type=int, help='The number of OpenMP threads to use for parallel regions')
     parser.add_argument('granules', type=str.split, nargs='+',
                         help='Granule pair to process')
     args = parser.parse_args()
@@ -527,9 +526,6 @@ def main():
     if len(args.granules) != 2:
         parser.error('Must provide exactly two granules')
 
-    if args.omp_num_threads:
-        os.environ['OMP_NUM_THREADS'] = str(args.omp_num_threads)
-
     if username and password:
         write_credentials_to_netrc_file(username, password)
 

From cdcc2420b0e421ec813aad3166df64c171c0ef0f Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 26 May 2023 11:48:16 -0800
Subject: [PATCH 04/12] move earthdata login handling to __main__

---
 hyp3_autorift/__main__.py      | 12 ++++++++++++
 hyp3_autorift/process.py       |  8 +-------
 hyp3_autorift/s1_correction.py | 10 ++--------
 3 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/hyp3_autorift/__main__.py b/hyp3_autorift/__main__.py
index 01f98008..b49e65bf 100644
--- a/hyp3_autorift/__main__.py
+++ b/hyp3_autorift/__main__.py
@@ -6,7 +6,11 @@
 import argparse
 import os
 import sys
+import warnings
 from importlib.metadata import entry_points
+from pathlib import Path
+
+from hyp3lib.fetch import write_credentials_to_netrc_file
 
 
 def main():
@@ -22,6 +26,14 @@ def main():
     if args.omp_num_threads:
         os.environ['OMP_NUM_THREADS'] = str(args.omp_num_threads)
 
+    username = os.getenv('EARTHDATA_USERNAME')
+    password = os.getenv('EARTHDATA_PASSWORD')
+    if username and password:
+        write_credentials_to_netrc_file(username, password, append=False)
+
+    if not (Path.home() / '.netrc').exists():
+        warnings.warn('Earthdata credentials must be present as environment variables, or in your netrc.', UserWarning)
+
     eps = entry_points()['console_scripts']
     (process_entry_point,) = {process for process in eps if process.name == args.process}
 
diff --git a/hyp3_autorift/process.py b/hyp3_autorift/process.py
index 308318d8..c5c7ab4c 100644
--- a/hyp3_autorift/process.py
+++ b/hyp3_autorift/process.py
@@ -18,7 +18,7 @@
 import numpy as np
 import requests
 from hyp3lib.aws import upload_file_to_s3
-from hyp3lib.fetch import download_file, write_credentials_to_netrc_file
+from hyp3lib.fetch import download_file
 from hyp3lib.get_orb import downloadSentinelOrbitFile
 from hyp3lib.image import create_thumbnail
 from hyp3lib.scene import get_download_url
@@ -508,8 +508,6 @@ def main():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter
     )
-    parser.add_argument('--username', help='NASA Earthdata Login username for fetching Sentinel-1 scenes')
-    parser.add_argument('--password', help='NASA Earthdata Login password for fetching Sentinel-1 scenes')
     parser.add_argument('--bucket', help='AWS bucket to upload product files to')
     parser.add_argument('--bucket-prefix', default='', help='AWS prefix (location in bucket) to add to product files')
     parser.add_argument('--parameter-file', default=DEFAULT_PARAMETER_FILE,
@@ -520,15 +518,11 @@ def main():
     parser.add_argument('granules', type=str.split, nargs='+',
                         help='Granule pair to process')
     args = parser.parse_args()
-    username, password = check_earthdata_credentials(args.username, args.password)
 
     args.granules = [item for sublist in args.granules for item in sublist]
     if len(args.granules) != 2:
         parser.error('Must provide exactly two granules')
 
-    if username and password:
-        write_credentials_to_netrc_file(username, password)
-
     g1, g2 = sorted(args.granules, key=get_datetime)
 
     product_file, browse_file = process(g1, g2, parameter_file=args.parameter_file, naming_scheme=args.naming_scheme)
diff --git a/hyp3_autorift/s1_correction.py b/hyp3_autorift/s1_correction.py
index bc5ea33a..7c5bdced 100644
--- a/hyp3_autorift/s1_correction.py
+++ b/hyp3_autorift/s1_correction.py
@@ -3,12 +3,12 @@
 from pathlib import Path
 
 from hyp3lib.aws import upload_file_to_s3
-from hyp3lib.fetch import download_file, write_credentials_to_netrc_file
+from hyp3lib.fetch import download_file
 from hyp3lib.get_orb import downloadSentinelOrbitFile
 from hyp3lib.scene import get_download_url
 
 from hyp3_autorift import geometry, io
-from hyp3_autorift.process import DEFAULT_PARAMETER_FILE, check_earthdata_credentials, get_s1_primary_polarization
+from hyp3_autorift.process import DEFAULT_PARAMETER_FILE, get_s1_primary_polarization
 from hyp3_autorift.vend.testGeogrid_ISCE import loadParsedata, runGeogrid
 log = logging.getLogger(__name__)
 
@@ -43,8 +43,6 @@ def main():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter
     )
-    parser.add_argument('--username', help='NASA Earthdata Login username for fetching Sentinel-1 scenes')
-    parser.add_argument('--password', help='NASA Earthdata Login password for fetching Sentinel-1 scenes')
     parser.add_argument('--bucket', help='AWS bucket to upload product files to')
     parser.add_argument('--bucket-prefix', default='', help='AWS prefix (location in bucket) to add to product files')
     parser.add_argument('--buffer', type=int, default=0, help='Number of pixels to buffer each edge of the input scene')
@@ -54,10 +52,6 @@ def main():
     parser.add_argument('granule', help='Reference granule to process')
     args = parser.parse_args()
 
-    username, password = check_earthdata_credentials(args.username, args.password)
-    if username and password:
-        write_credentials_to_netrc_file(username, password)
-
     _ = generate_correction_data(args.granule, buffer=args.buffer)
 
     if args.bucket:

From fe5b4f67ca843aee08070895deea8b6fe542f9ed Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 26 May 2023 11:51:17 -0800
Subject: [PATCH 05/12] fix lint,typos

---
 hyp3_autorift/process.py                     |  3 +-
 hyp3_autorift/vend/nasa-jpl_autorift_78.diff | 98 ++++++++++++++++++++
 2 files changed, 99 insertions(+), 2 deletions(-)
 create mode 100644 hyp3_autorift/vend/nasa-jpl_autorift_78.diff

diff --git a/hyp3_autorift/process.py b/hyp3_autorift/process.py
index c5c7ab4c..159c4652 100644
--- a/hyp3_autorift/process.py
+++ b/hyp3_autorift/process.py
@@ -333,7 +333,7 @@ def process(reference: str, secondary: str, parameter_file: str = DEFAULT_PARAME
     secondary_path = None
     reference_metadata = None
     secondary_metadata = None
-    rcdeference_zero_path = None
+    reference_zero_path = None
     secondary_zero_path = None
     reference_state_vec = None
     secondary_state_vec = None
@@ -532,4 +532,3 @@ def main():
         upload_file_to_s3(browse_file, args.bucket, args.bucket_prefix)
         thumbnail_file = create_thumbnail(browse_file)
         upload_file_to_s3(thumbnail_file, args.bucket, args.bucket_prefix)
-
diff --git a/hyp3_autorift/vend/nasa-jpl_autorift_78.diff b/hyp3_autorift/vend/nasa-jpl_autorift_78.diff
new file mode 100644
index 00000000..67800c13
--- /dev/null
+++ b/hyp3_autorift/vend/nasa-jpl_autorift_78.diff
@@ -0,0 +1,98 @@
+diff --git a/testGeogrid_ISCE.py b/testGeogrid_ISCE.py
+index 22ecdcf..bc9cb06 100755
+--- a/testGeogrid_ISCE.py
++++ b/testGeogrid_ISCE.py
+@@ -67,6 +67,10 @@ def cmdLineParse():
+             help='Input stable surface mask')
+     parser.add_argument('-fo', '--flag_optical', dest='optical_flag', type=bool, required=False, default=0,
+             help='flag for reading optical data (e.g. Landsat): use 1 for on and 0 (default) for off')
++    parser.add_argument('-b', '--buffer', dest='buffer', type=bool, required=False, default=0,
++            help='buffer to add to the starting/end range accounting for all passes from the same relative orbit')
++    parser.add_argument('-p', '--parse', dest='parse', action='store_true',
++            default=False, help='Parse the SAFE zip file to get radar image and orbit metadata; no need to run ISCE')
+ 
+     return parser.parse_args()
+ 
+@@ -113,7 +117,7 @@ def getMergedOrbit(product):
+     return orb
+ 
+ 
+-def loadMetadata(indir):
++def loadMetadata(indir,buffer=0):
+     '''
+     Input file.
+     '''
+@@ -135,12 +139,57 @@ def loadMetadata(indir):
+     info.prf = 1.0 / frames[0].bursts[0].azimuthTimeInterval
+     info.rangePixelSize = frames[0].bursts[0].rangePixelSize
+     info.lookSide = -1
++        
++    info.startingRange -= buffer * info.rangePixelSize
++    info.farRange += buffer * info.rangePixelSize
++    
+     info.numberOfLines = int( np.round( (info.sensingStop - info.sensingStart).total_seconds() * info.prf)) + 1
+-    info.numberOfSamples = int( np.round( (info.farRange - info.startingRange)/info.rangePixelSize)) + 1
++    info.numberOfSamples = int( np.round( (info.farRange - info.startingRange)/info.rangePixelSize)) + 1  + 2 * buffer
+     info.orbit = getMergedOrbit(frames)
+ 
+     return info
+ 
++def loadParsedata(indir,buffer=0):
++    '''
++    Input file.
++    '''
++    import os
++    import numpy as np
++    import isce
++    from isceobj.Sensor.TOPS.Sentinel1 import Sentinel1
++    
++
++    frames = []
++    for swath in range(1,4):
++        rdr=Sentinel1()
++        rdr.configure()
++#        rdr.safe=['./S1A_IW_SLC__1SDH_20180401T100057_20180401T100124_021272_024972_8CAF.zip']
++        rdr.safe=[indir]
++        rdr.output='reference'
++        rdr.orbitDir='/Users/yanglei/orbit/S1A/precise'
++        rdr.auxDir='/Users/yanglei/orbit/S1A/aux'
++        rdr.swathNumber=swath
++        rdr.polarization='hh'
++        rdr.parse()
++        frames.append(rdr.product)
++    
++    info = Dummy()
++    info.sensingStart = min([x.sensingStart for x in frames])
++    info.sensingStop = max([x.sensingStop for x in frames])
++    info.startingRange = min([x.startingRange for x in frames])
++    info.farRange = max([x.farRange for x in frames])
++    info.prf = 1.0 / frames[0].bursts[0].azimuthTimeInterval
++    info.rangePixelSize = frames[0].bursts[0].rangePixelSize
++    info.lookSide = -1
++    
++    info.startingRange -= buffer * info.rangePixelSize
++    info.farRange += buffer * info.rangePixelSize
++    
++    info.numberOfLines = int( np.round( (info.sensingStop - info.sensingStart).total_seconds() * info.prf)) + 1
++    info.numberOfSamples = int( np.round( (info.farRange - info.startingRange)/info.rangePixelSize)) + 1 + 2 * buffer
++    info.orbit = getMergedOrbit(frames)
++    
++    return info
+ 
+ def coregisterLoadMetadataOptical(indir_m, indir_s):
+     '''
+@@ -383,8 +432,12 @@ def main():
+         metadata_m, metadata_s = coregisterLoadMetadataOptical(inps.indir_m, inps.indir_s)
+         runGeogridOptical(metadata_m, metadata_s, inps.demfile, inps.dhdxfile, inps.dhdyfile, inps.vxfile, inps.vyfile, inps.srxfile, inps.sryfile, inps.csminxfile, inps.csminyfile, inps.csmaxxfile, inps.csmaxyfile, inps.ssmfile)
+     else:
+-        metadata_m = loadMetadata(inps.indir_m)
+-        metadata_s = loadMetadata(inps.indir_s)
++        if inps.parse:
++            metadata_m = loadParsedata(inps.indir_m,inps.buffer)
++            metadata_s = loadParsedata(inps.indir_s,inps.buffer)
++        else:
++            metadata_m = loadMetadata(inps.indir_m,inps.buffer)
++            metadata_s = loadMetadata(inps.indir_s,inps.buffer)
+         runGeogrid(metadata_m, metadata_s, inps.demfile, inps.dhdxfile, inps.dhdyfile, inps.vxfile, inps.vyfile, inps.srxfile, inps.sryfile, inps.csminxfile, inps.csminyfile, inps.csmaxxfile, inps.csmaxyfile, inps.ssmfile)
+ 
+ 

From 392c30a15a8cdf898f55f37614663ca90d0e587f Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 26 May 2023 11:55:57 -0800
Subject: [PATCH 06/12] fix tests

---
 tests/test_entrypoints.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_entrypoints.py b/tests/test_entrypoints.py
index 41e2147f..fa5a1834 100644
--- a/tests/test_entrypoints.py
+++ b/tests/test_entrypoints.py
@@ -4,5 +4,5 @@ def test_hyp3_autorift(script_runner):
 
 
 def test_autorift_proc_pair(script_runner):
-    ret = script_runner.run('autorift_proc_pair', '-h')
+    ret = script_runner.run('s1_correction', '-h')
     assert ret.success

From 81a91a255589f8647b5809895160031f1b609c24 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 26 May 2023 11:57:14 -0800
Subject: [PATCH 07/12] drop unused fn

---
 hyp3_autorift/process.py | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/hyp3_autorift/process.py b/hyp3_autorift/process.py
index 159c4652..0138d688 100644
--- a/hyp3_autorift/process.py
+++ b/hyp3_autorift/process.py
@@ -494,16 +494,6 @@ def process(reference: str, secondary: str, parameter_file: str = DEFAULT_PARAME
     return product_file, browse_file
 
 
-def check_earthdata_credentials(username, password):
-    if username is None:
-        username = os.getenv('EARTHDATA_USERNAME')
-
-    if password is None:
-        password = os.getenv('EARTHDATA_PASSWORD')
-
-    return username, password
-
-
 def main():
     parser = argparse.ArgumentParser(
         formatter_class=argparse.ArgumentDefaultsHelpFormatter

From 538ca5c8cba66dbc617aa7fdb9717449f531df09 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 26 May 2023 11:58:51 -0800
Subject: [PATCH 08/12] lint

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index d923cc8f..5fd55996 100644
--- a/setup.py
+++ b/setup.py
@@ -63,7 +63,7 @@
 
     entry_points={'console_scripts': [
         'hyp3_autorift = hyp3_autorift.process:main',
-        's1_correction = hyp3_autorift.s1_correction:main'
+        's1_correction = hyp3_autorift.s1_correction:main',
         ]
     },
 

From 09e882e0d07b79e4186eb8397761189cf4b360df Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 9 Jun 2023 17:33:55 -0800
Subject: [PATCH 09/12] Use reference as secondary but with a fixed (false) dt
 to preven divide by zero errors

---
 hyp3_autorift/s1_correction.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/hyp3_autorift/s1_correction.py b/hyp3_autorift/s1_correction.py
index 7c5bdced..aea57113 100644
--- a/hyp3_autorift/s1_correction.py
+++ b/hyp3_autorift/s1_correction.py
@@ -1,5 +1,7 @@
 import argparse
+import copy
 import logging
+from datetime import timedelta
 from pathlib import Path
 
 from hyp3lib.aws import upload_file_to_s3
@@ -33,8 +35,14 @@ def generate_correction_data(scene: str, buffer: int = 0, parameter_file: str =
     isce_dem = geometry.prep_isce_dem(parameter_info['geogrid']['dem'], lat_limits, lon_limits)
     io.format_tops_xml(scene, scene, polarization, isce_dem, orbits)
 
-    scene_meta = loadParsedata(str(scene_path), orbit_dir=orbits, aux_dir=orbits, buffer=buffer)
-    geogrid_info = runGeogrid(scene_meta, scene_meta, epsg=parameter_info['epsg'], **parameter_info['geogrid'])
+    reference_meta = loadParsedata(str(scene_path), orbit_dir=orbits, aux_dir=orbits, buffer=buffer)
+
+    secondary_meta = copy.deepcopy(reference_meta)
+    spoof_dt = timedelta(days=1)
+    secondary_meta.sensingStart += spoof_dt
+    secondary_meta.sensingStop += spoof_dt
+
+    geogrid_info = runGeogrid(reference_meta, secondary_meta, epsg=parameter_info['epsg'], **parameter_info['geogrid'])
 
     return geogrid_info
 

From fe047d30298b43588abe5f7df2ec8e37f3f92a37 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 9 Jun 2023 19:38:38 -0800
Subject: [PATCH 10/12] state changes for release

---
 CHANGELOG.md                                     | 16 ++++++++++++++++
 ...autorift_78.diff => CHANGES-UPSTREAM-78.diff} |  0
 2 files changed, 16 insertions(+)
 rename hyp3_autorift/vend/{nasa-jpl_autorift_78.diff => CHANGES-UPSTREAM-78.diff} (100%)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b0ace898..b8e8ac45 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,22 @@ and this project adheres to [PEP 440](https://www.python.org/dev/peps/pep-0440/)
 and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 
+## [0.11.0]
+
+### Added
+* `hyp3_autorift`'s main entrypoint now accepts `++process` arguments to support multiple workflows
+  * `++process hyp3_autorift` (default) will run the same autoRIFT pair processing workflow
+  * `++process s1_correction` will run a Geogrid-only workflow to create the GeoTIFFs necessary to correct a 
+    scale-projection issue in polar-sterographic products generated from Sentinel-1 pairs that were created using 
+    HyP3 autoRIFT versions < 0.9.0, which was released November 2, 2022
+  
+### Changed
+* Patch [nasa-jpl/autorift#78](hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff) was applied from upstream to support the
+  Sentinel-1 correction workflow
+
+### Removed
+* The unused `autorift_proc_pair` console script entrypoint was removed
+
 ## [0.10.5]
 
 ### Fixed
diff --git a/hyp3_autorift/vend/nasa-jpl_autorift_78.diff b/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff
similarity index 100%
rename from hyp3_autorift/vend/nasa-jpl_autorift_78.diff
rename to hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff

From 0b0876e0367b3fa5b69c1ed9c05f7aa347caa059 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 9 Jun 2023 19:39:53 -0800
Subject: [PATCH 11/12] cleanup changes diff

---
 hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff b/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff
index 67800c13..2a13dc87 100644
--- a/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff
+++ b/hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff
@@ -1,7 +1,6 @@
-diff --git a/testGeogrid_ISCE.py b/testGeogrid_ISCE.py
-index 22ecdcf..bc9cb06 100755
---- a/testGeogrid_ISCE.py
-+++ b/testGeogrid_ISCE.py
+diff --git testGeogrid_ISCE.py testGeogrid_ISCE.py
+--- testGeogrid_ISCE.py
++++ testGeogrid_ISCE.py
 @@ -67,6 +67,10 @@ def cmdLineParse():
              help='Input stable surface mask')
      parser.add_argument('-fo', '--flag_optical', dest='optical_flag', type=bool, required=False, default=0,

From 12baaece4dd13791b8e2a5482648c1e3a55df235 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 9 Jun 2023 19:46:10 -0800
Subject: [PATCH 12/12] finish stating changes for release

---
 CHANGELOG.md                 | 6 +++---
 hyp3_autorift/vend/README.md | 4 ++++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b8e8ac45..a97425b7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,9 +12,9 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ### Added
 * `hyp3_autorift`'s main entrypoint now accepts `++process` arguments to support multiple workflows
   * `++process hyp3_autorift` (default) will run the same autoRIFT pair processing workflow
-  * `++process s1_correction` will run a Geogrid-only workflow to create the GeoTIFFs necessary to correct a 
-    scale-projection issue in polar-sterographic products generated from Sentinel-1 pairs that were created using 
-    HyP3 autoRIFT versions < 0.9.0, which was released November 2, 2022
+  * `++process s1_correction` will run a Geogrid-only workflow to create the GeoTIFFs necessary for correcting the
+    scale-projection issue in polar-sterographic products generated from Sentinel-1 pairs that were created using HyP3
+    autoRIFT versions < 0.9.0, which was released November 2, 2022
   
 ### Changed
 * Patch [nasa-jpl/autorift#78](hyp3_autorift/vend/CHANGES-UPSTREAM-78.diff) was applied from upstream to support the
diff --git a/hyp3_autorift/vend/README.md b/hyp3_autorift/vend/README.md
index 5bbd28c6..d79d58e9 100644
--- a/hyp3_autorift/vend/README.md
+++ b/hyp3_autorift/vend/README.md
@@ -60,3 +60,7 @@ We've replaced it  with `hyp3_autorift.io.get_topsinsar_config`.
    to fix the `noDataMask` used for the search range and %-valid pixel calculations. Unfortunately, this bug exists
    upstream but this fix is dependent on changes in (4) which are not easily applied upstream. Therefore, these changes
    are *not* expected to be applied upstream to `nasa-jpl/autoRIFT` without a significant refactor upstream.
+8. The changes listed in `CHANGES-UPSTREAM-78.diff` were applied from upstream ([nasa-jpl/autorift#78](https://github.com/nasa-jpl/autorift/pull/78))
+   in [ASFHyP3/hyp3-autorift#218](https://github.com/ASFHyP3/hyp3-autorift/pull/218) to run a Geogrid-only workflow to
+   create the GeoTIFFs necessary for correcting the scale-projection issue in polar-sterographic products generated
+   from Sentinel-1 pairs that were created using HyP3 autoRIFT versions < 0.9.0, which was released November 2, 2022