From b08adc43a115f585d911db9ec2fe5517b95c0664 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Fri, 14 Jun 2024 12:48:46 -0800
Subject: [PATCH 01/23] No need to provide ESA credentials arguments for
 s1_correction workflow; just use netrc or env vars

---
 src/hyp3_autorift/s1_correction.py | 2 --
 src/hyp3_autorift/s1_isce2.py      | 6 +-----
 2 files changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/hyp3_autorift/s1_correction.py b/src/hyp3_autorift/s1_correction.py
index dc5995a1..8b8d4338 100644
--- a/src/hyp3_autorift/s1_correction.py
+++ b/src/hyp3_autorift/s1_correction.py
@@ -16,8 +16,6 @@ def main():
     )
     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('--esa-username', default=None, help="Username for ESA's Copernicus Data Space Ecosystem")
-    parser.add_argument('--esa-password', default=None, help="Password for ESA's Copernicus Data Space Ecosystem")
     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. '
diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index c1b2ee97..5127fb59 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -5,7 +5,6 @@
 import textwrap
 from datetime import timedelta
 from pathlib import Path
-from typing import Optional
 
 import numpy as np
 from hyp3lib.fetch import download_file
@@ -93,8 +92,6 @@ def generate_correction_data(
     scene: str,
     buffer: int = 0,
     parameter_file: str = DEFAULT_PARAMETER_FILE,
-    esa_username: Optional[str] = None,
-    esa_password: Optional[str] = None,
 ):
     from hyp3_autorift.vend.testGeogrid_ISCE import loadParsedata, runGeogrid
     scene_path = Path(f'{scene}.zip')
@@ -105,8 +102,7 @@ def generate_correction_data(
     orbits = Path('Orbits').resolve()
     orbits.mkdir(parents=True, exist_ok=True)
 
-    if (esa_username is None) or (esa_password is None):
-        esa_username, esa_password = get_esa_credentials()
+    esa_username, esa_password = get_esa_credentials()
 
     state_vec, oribit_provider = downloadSentinelOrbitFile(
         scene, directory=str(orbits), esa_credentials=(esa_username, esa_password)

From 9ca9fbf06f94df5c57d3a104877af6beb47c58a0 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 17 Jun 2024 16:07:07 +0000
Subject: [PATCH 02/23] Bump ASFHyP3/actions from 0.11.0 to 0.11.1

Bumps [ASFHyP3/actions](https://github.com/asfhyp3/actions) from 0.11.0 to 0.11.1.
- [Release notes](https://github.com/asfhyp3/actions/releases)
- [Changelog](https://github.com/ASFHyP3/actions/blob/develop/CHANGELOG.md)
- [Commits](https://github.com/asfhyp3/actions/compare/v0.11.0...v0.11.1)

---
updated-dependencies:
- dependency-name: ASFHyP3/actions
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/changelog.yml                | 2 +-
 .github/workflows/create-jira-issue.yml        | 2 +-
 .github/workflows/labeled-pr.yml               | 2 +-
 .github/workflows/release-template-comment.yml | 2 +-
 .github/workflows/release.yml                  | 2 +-
 .github/workflows/static-analysis.yml          | 4 ++--
 .github/workflows/tag-version.yml              | 2 +-
 .github/workflows/test-and-build.yml           | 6 +++---
 8 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index 3ce6f429..6b6bbdaa 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -13,6 +13,6 @@ on:
 
 jobs:
   call-changelog-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.11.1
     secrets:
       USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/create-jira-issue.yml b/.github/workflows/create-jira-issue.yml
index 0b69efec..129ff5f1 100644
--- a/.github/workflows/create-jira-issue.yml
+++ b/.github/workflows/create-jira-issue.yml
@@ -6,7 +6,7 @@ on:
 
 jobs:
   call-create-jira-issue-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.11.1
     secrets:
       JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
       JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}
diff --git a/.github/workflows/labeled-pr.yml b/.github/workflows/labeled-pr.yml
index 66ba502e..3ba21604 100644
--- a/.github/workflows/labeled-pr.yml
+++ b/.github/workflows/labeled-pr.yml
@@ -12,4 +12,4 @@ on:
 
 jobs:
   call-labeled-pr-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.11.1
diff --git a/.github/workflows/release-template-comment.yml b/.github/workflows/release-template-comment.yml
index cae89e6f..01d20589 100644
--- a/.github/workflows/release-template-comment.yml
+++ b/.github/workflows/release-template-comment.yml
@@ -7,6 +7,6 @@ on:
 
 jobs:
   call-release-checklist-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.11.1
     secrets:
       USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index c8fed248..f04a3669 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -7,7 +7,7 @@ on:
 
 jobs:
   call-release-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.11.1
     with:
       release_prefix: HyP3 autoRIFT
     secrets:
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 3b07f93b..6e006ab8 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -4,10 +4,10 @@ on: push
 
 jobs:
   call-flake8-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-flake8.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-flake8.yml@v0.11.1
     with:
       local_package_names: hyp3_autorift
       excludes: src/hyp3_autorift/vend
 
   call-secrets-analysis-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.11.1
diff --git a/.github/workflows/tag-version.yml b/.github/workflows/tag-version.yml
index 4714c1f1..7bc79246 100644
--- a/.github/workflows/tag-version.yml
+++ b/.github/workflows/tag-version.yml
@@ -7,6 +7,6 @@ on:
 
 jobs:
   call-bump-version-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.11.1
     secrets:
       USER_TOKEN: ${{ secrets.TOOLS_BOT_PAK }}
diff --git a/.github/workflows/test-and-build.yml b/.github/workflows/test-and-build.yml
index cee1a1e2..cfc16752 100644
--- a/.github/workflows/test-and-build.yml
+++ b/.github/workflows/test-and-build.yml
@@ -12,18 +12,18 @@ on:
 
 jobs:
   call-pytest-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.11.1
     with:
       local_package_name: hyp3_autorift
       python_versions: >-
         ["3.9"]
 
   call-version-info-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.11.1
 
   call-docker-ghcr-workflow:
     needs: call-version-info-workflow
-    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.11.0
+    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.11.1
     with:
       version_tag: ${{ needs.call-version-info-workflow.outputs.version_tag }}
     secrets:

From 3119c017dbdf13588857ebcd87c99773e39a7a6e Mon Sep 17 00:00:00 2001
From: Jake Herrmann <jtherrmann@alaska.edu>
Date: Mon, 17 Jun 2024 09:20:10 -0800
Subject: [PATCH 03/23] Update .github/workflows/changelog.yml

---
 .github/workflows/changelog.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index 6b6bbdaa..6047ddb1 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -14,5 +14,3 @@ on:
 jobs:
   call-changelog-check-workflow:
     uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.11.1
-    secrets:
-      USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}

From 9c868f708167c100b69aaf1a85ed391df33cbbe1 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Mon, 17 Jun 2024 12:46:31 -0800
Subject: [PATCH 04/23] update utils load geospatial to return srs info

---
 src/hyp3_autorift/process.py | 2 +-
 src/hyp3_autorift/utils.py   | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/src/hyp3_autorift/process.py b/src/hyp3_autorift/process.py
index 38f5d9f8..0ff7b60d 100644
--- a/src/hyp3_autorift/process.py
+++ b/src/hyp3_autorift/process.py
@@ -242,7 +242,7 @@ def apply_wallis_nodata_fill_filter(array: np.ndarray, nodata: int) -> Tuple[np.
 
 
 def _apply_filter_function(image_path: str, filter_function: Callable) -> Tuple[str, Optional[str]]:
-    image_array, image_transform, image_projection, image_nodata = utils.load_geospatial(image_path)
+    image_array, image_transform, image_projection, _, image_nodata = utils.load_geospatial(image_path)
     image_array = image_array.astype(np.float32)
 
     image_filtered, zero_mask = filter_function(image_array, image_nodata)
diff --git a/src/hyp3_autorift/utils.py b/src/hyp3_autorift/utils.py
index a36a80a4..f2c58e85 100644
--- a/src/hyp3_autorift/utils.py
+++ b/src/hyp3_autorift/utils.py
@@ -125,10 +125,13 @@ def load_geospatial(infile: str, band: int = 1):
 
     data = ds.GetRasterBand(band).ReadAsArray()
     nodata = ds.GetRasterBand(band).GetNoDataValue()
-    projection = ds.GetProjection()
+
     transform = ds.GetGeoTransform()
+    projection = ds.GetProjection()
+    srs = ds.GetSpatialRef()
+
     del ds
-    return data, transform, projection, nodata
+    return data, transform, projection, srs, nodata
 
 
 def write_geospatial(outfile: str, data, transform, projection, nodata,

From f51ad18ab75de2d22877205d2150954e32795a88 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Tue, 18 Jun 2024 14:01:02 -0800
Subject: [PATCH 05/23] Create M conversion matricies netCDF as part of S1
 correction workflow

---
 src/hyp3_autorift/s1_correction.py |   3 +-
 src/hyp3_autorift/s1_isce2.py      | 166 ++++++++++++++++++++++++++++-
 2 files changed, 166 insertions(+), 3 deletions(-)

diff --git a/src/hyp3_autorift/s1_correction.py b/src/hyp3_autorift/s1_correction.py
index 8b8d4338..fd785566 100644
--- a/src/hyp3_autorift/s1_correction.py
+++ b/src/hyp3_autorift/s1_correction.py
@@ -23,8 +23,9 @@ def main():
     parser.add_argument('granule', help='Reference granule to process')
     args = parser.parse_args()
 
-    _ = generate_correction_data(args.granule, buffer=args.buffer)
+    _, conversion_nc = generate_correction_data(args.granule, buffer=args.buffer)
 
     if args.bucket:
+        upload_file_to_s3(conversion_nc, args.bucket, args.bucket_prefix)
         for geotiff in Path.cwd().glob('*.tif'):
             upload_file_to_s3(geotiff, args.bucket, args.bucket_prefix)
diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index 5127fb59..f1e0fd46 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -1,15 +1,17 @@
 import copy
+import json
 import logging
 import os
 import sys
 import textwrap
-from datetime import timedelta
+from datetime import datetime, timedelta
 from pathlib import Path
 
 import numpy as np
 from hyp3lib.fetch import download_file
 from hyp3lib.get_orb import downloadSentinelOrbitFile
 from hyp3lib.scene import get_download_url
+from netCDF4 import Dataset
 from osgeo import gdal
 
 from hyp3_autorift import geometry, utils
@@ -88,6 +90,164 @@ def process_sentinel1_with_isce2(reference, secondary, parameter_file):
     return netcdf_file
 
 
+def write_conversion_file(*, file_name, srs, epsg, tran, x, y, M11, M12, dr_2_vr_factor, ChunkSize,
+                          NoDataValue=-32767) -> Path:
+
+    # FIXME: what else needs to be added to the nextCDF file
+    nc_outfile = Dataset(file_name, 'w', clobber=True, format='NETCDF4')
+
+    nc_outfile.setncattr('GDAL_AREA_OR_POINT', 'Area')
+    nc_outfile.setncattr('Conventions', 'CF-1.8')
+    nc_outfile.setncattr('date_created', datetime.now().strftime("%d-%b-%Y %H:%M:%S"))
+    nc_outfile.setncattr('title', 'autoRIFT S1 Corrections')
+    # nc_outfile.setncattr('autoRIFT_software_version', 'FIXME')
+    # nc_outfile.setncattr('autoRIFT_parameter_file', 'FIXME')
+
+    nc_outfile.createDimension('x', len(x))
+    nc_outfile.createDimension('y', len(y))
+
+    var = nc_outfile.createVariable('x', np.dtype('float64'), 'x', fill_value=None)
+    var.setncattr('standard_name', 'projection_x_coordinate')
+    var.setncattr('description', 'x coordinate of projection')
+    var.setncattr('units', 'm')
+    var[:] = x
+
+    var = nc_outfile.createVariable('y', np.dtype('float64'), 'y', fill_value=None)
+    var.setncattr('standard_name', 'projection_y_coordinate')
+    var.setncattr('description', 'y coordinate of projection')
+    var.setncattr('units', 'm')
+    var[:] = y
+
+    mapping_var_name = 'mapping'
+    var = nc_outfile.createVariable(mapping_var_name, 'U1', (), fill_value=None)
+    if srs.GetAttrValue('PROJECTION') == 'Polar_Stereographic':
+        var.setncattr('grid_mapping_name', 'polar_stereographic')
+        var.setncattr('straight_vertical_longitude_from_pole', srs.GetProjParm('central_meridian'))
+        var.setncattr('false_easting', srs.GetProjParm('false_easting'))
+        var.setncattr('false_northing', srs.GetProjParm('false_northing'))
+        var.setncattr('latitude_of_projection_origin', np.sign(srs.GetProjParm('latitude_of_origin')) * 90.0)
+        var.setncattr('latitude_of_origin', srs.GetProjParm('latitude_of_origin'))
+        var.setncattr('semi_major_axis', float(srs.GetAttrValue('GEOGCS|SPHEROID', 1)))
+        var.setncattr('scale_factor_at_projection_origin', 1)
+        var.setncattr('inverse_flattening', float(srs.GetAttrValue('GEOGCS|SPHEROID', 2)))
+        var.setncattr('spatial_ref', srs.ExportToWkt())
+        var.setncattr('crs_wkt', srs.ExportToWkt())
+        var.setncattr('proj4text', srs.ExportToProj4())
+        var.setncattr('spatial_epsg', epsg)
+        var.setncattr('GeoTransform', ' '.join(str(x) for x in tran))
+
+    elif srs.GetAttrValue('PROJECTION') == 'Transverse_Mercator':
+        var.setncattr('grid_mapping_name', 'universal_transverse_mercator')
+        zone = epsg - np.floor(epsg / 100) * 100
+        var.setncattr('utm_zone_number', zone)
+        var.setncattr('longitude_of_central_meridian', srs.GetProjParm('central_meridian'))
+        var.setncattr('false_easting', srs.GetProjParm('false_easting'))
+        var.setncattr('false_northing', srs.GetProjParm('false_northing'))
+        var.setncattr('latitude_of_projection_origin', srs.GetProjParm('latitude_of_origin'))
+        var.setncattr('semi_major_axis', float(srs.GetAttrValue('GEOGCS|SPHEROID', 1)))
+        var.setncattr('scale_factor_at_central_meridian', srs.GetProjParm('scale_factor'))
+        var.setncattr('inverse_flattening', float(srs.GetAttrValue('GEOGCS|SPHEROID', 2)))
+        var.setncattr('spatial_ref', srs.ExportToWkt())
+        var.setncattr('crs_wkt', srs.ExportToWkt())
+        var.setncattr('proj4text', srs.ExportToProj4())
+        var.setncattr('spatial_epsg', epsg)
+        var.setncattr('GeoTransform', ' '.join(str(x) for x in tran))
+    else:
+        raise Exception('Projection {0} not recognized for this program'.format(srs.GetAttrValue('PROJECTION')))
+
+    var = nc_outfile.createVariable('M11', np.dtype('float32'), ('y', 'x'), fill_value=NoDataValue,
+                                    zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
+    var.setncattr('standard_name', 'conversion_matrix_element_11')
+    var.setncattr(
+        'description',
+        'conversion matrix element (1st row, 1st column) that can be multiplied with vx to give range pixel '
+        'displacement dr (see Eq. A18 in https://www.mdpi.com/2072-4292/13/4/749)'
+    )
+    var.setncattr('units', 'pixel/(meter/year)')
+    var.setncattr('grid_mapping', mapping_var_name)
+    var.setncattr('dr_to_vr_factor', dr_2_vr_factor)
+    var.setncattr('dr_to_vr_factor_description', 'multiplicative factor that converts slant range '
+                                                 'pixel displacement dr to slant range velocity vr')
+    var[:] = M11
+
+    var = nc_outfile.createVariable('M12', np.dtype('float32'), ('y', 'x'), fill_value=NoDataValue,
+                                    zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
+    var.setncattr('standard_name', 'conversion_matrix_element_12')
+    var.setncattr(
+        'description',
+        'conversion matrix element (1st row, 2nd column) that can be multiplied with vy to give range pixel '
+        'displacement dr (see Eq. A18 in https://www.mdpi.com/2072-4292/13/4/749)'
+    )
+    var.setncattr('units', 'pixel/(meter/year)')
+    var.setncattr('grid_mapping', mapping_var_name)
+    var.setncattr('dr_to_vr_factor', dr_2_vr_factor)
+    var.setncattr('dr_to_vr_factor_description',
+                  'multiplicative factor that converts slant range pixel displacement dr to slant range velocity vr')
+    var[:] = M12
+
+    return Path(nc_outfile.filepath())
+
+
+def create_conversion_matrices(
+        *,
+        scene: str,
+        grid_location: str = 'window_location.tif',
+        search_range: str = 'window_search_range.tif',
+        offset2vx: str = 'window_rdr_off2vel_x_vec.tif',
+        offset2vy: str = 'window_rdr_off2vel_y_vec.tif',
+        scale_factor: str = 'window_scale_factor.tif',
+        epsg: int = 4326,
+        **kwargs,  # noqa: consume kwargs we don't care about for convenience
+) -> Path:
+    xGrid, tran, _, srs, nodata = utils.load_geospatial(grid_location, band=1)
+    yGrid, _, _, _, _ = utils.load_geospatial(grid_location, band=2)
+
+    offset2vy_1, _, _, _, _ = utils.load_geospatial(offset2vy, band=1)
+    offset2vy_1[offset2vy_1 == nodata] = np.nan
+
+    offset2vy_2, _, _, _, _ = utils.load_geospatial(offset2vy, band=2)
+    offset2vy_2[offset2vy_2 == nodata] = np.nan
+
+    offset2vx_1, _, _, _, _ = utils.load_geospatial(offset2vx, band=1)
+    offset2vx_1[offset2vx_1 == nodata] = np.nan
+
+    offset2vx_2, _, _, _, _ = utils.load_geospatial(offset2vx, band=2)
+    offset2vx_2[offset2vx_2 == nodata] = np.nan
+
+    offset2vr, _, _, _, _ = utils.load_geospatial(offset2vx, band=3)
+    offset2vr[offset2vr == nodata] = np.nan
+
+    scale_factor_1, _, _, _, _ = utils.load_geospatial(scale_factor, band=1)
+    scale_factor_1[scale_factor_1 == nodata] = np.nan
+
+    scale_factor_2, _, _, _, _ = utils.load_geospatial(scale_factor, band=2)
+    scale_factor_2[scale_factor_2 == nodata] = np.nan
+
+    SRx0, _, _, _, _ = utils.load_geospatial(search_range, band=1)
+    SRx0 = SRx0.astype('float32')
+    SRx0[SRx0 == nodata] = np.nan
+
+    dimidY, dimidX = xGrid.shape
+
+    y = np.arange(tran[3], tran[3] + tran[5] * dimidY, tran[5])
+    x = np.arange(tran[0], tran[0] + tran[1] * dimidX, tran[1])
+
+    M11 = offset2vy_2 / (offset2vx_1 * offset2vy_2 - offset2vx_2 * offset2vy_1) / scale_factor_1
+    M12 = -offset2vx_2 / (offset2vx_1 * offset2vy_2 - offset2vx_2 * offset2vy_1) / scale_factor_1
+
+    dr_2_vr_factor = np.median(offset2vr[np.logical_not(np.isnan(offset2vr))])
+
+    chunk_lines = np.min([np.ceil(8192 / dimidY) * 128, dimidY])
+    ChunkSize = [chunk_lines, dimidX]
+
+    conversion_nc = write_conversion_file(
+        file_name=f'{scene}_conversion_matrices.nc', srs=srs, epsg=epsg, tran=tran, x=x, y=y, M11=M11, M12=M12,
+        dr_2_vr_factor=dr_2_vr_factor, ChunkSize=ChunkSize
+    )
+
+    return conversion_nc
+
+
 def generate_correction_data(
     scene: str,
     buffer: int = 0,
@@ -127,7 +287,9 @@ def generate_correction_data(
 
     geogrid_info = runGeogrid(reference_meta, secondary_meta, epsg=parameter_info['epsg'], **parameter_info['geogrid'])
 
-    return geogrid_info
+    conversion_nc = create_conversion_matrices(scene=scene, epsg=parameter_info['epsg'], **parameter_info['autorift'])
+
+    return geogrid_info, conversion_nc
 
 
 class SysArgvManager:

From 06e4d8370d973bbc8b4c38f0c6e1689860e6ad0d Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Tue, 18 Jun 2024 14:04:47 -0800
Subject: [PATCH 06/23] tweaks

---
 src/hyp3_autorift/s1_isce2.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index f1e0fd46..cc6f3f1f 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -1,5 +1,4 @@
 import copy
-import json
 import logging
 import os
 import sys
@@ -90,8 +89,8 @@ def process_sentinel1_with_isce2(reference, secondary, parameter_file):
     return netcdf_file
 
 
-def write_conversion_file(*, file_name, srs, epsg, tran, x, y, M11, M12, dr_2_vr_factor, ChunkSize,
-                          NoDataValue=-32767) -> Path:
+def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr_2_vr_factor, ChunkSize,
+                          NoDataValue=-32767) -> str:
 
     # FIXME: what else needs to be added to the nextCDF file
     nc_outfile = Dataset(file_name, 'w', clobber=True, format='NETCDF4')
@@ -185,7 +184,7 @@ def write_conversion_file(*, file_name, srs, epsg, tran, x, y, M11, M12, dr_2_vr
                   'multiplicative factor that converts slant range pixel displacement dr to slant range velocity vr')
     var[:] = M12
 
-    return Path(nc_outfile.filepath())
+    return file_name
 
 
 def create_conversion_matrices(
@@ -198,7 +197,7 @@ def create_conversion_matrices(
         scale_factor: str = 'window_scale_factor.tif',
         epsg: int = 4326,
         **kwargs,  # noqa: consume kwargs we don't care about for convenience
-) -> Path:
+) -> str:
     xGrid, tran, _, srs, nodata = utils.load_geospatial(grid_location, band=1)
     yGrid, _, _, _, _ = utils.load_geospatial(grid_location, band=2)
 
@@ -252,7 +251,7 @@ def generate_correction_data(
     scene: str,
     buffer: int = 0,
     parameter_file: str = DEFAULT_PARAMETER_FILE,
-):
+) -> (dict, str):
     from hyp3_autorift.vend.testGeogrid_ISCE import loadParsedata, runGeogrid
     scene_path = Path(f'{scene}.zip')
     if not scene_path.exists():

From 7d2dcbfd40421404f82988e50a5860cd8de624f0 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Tue, 18 Jun 2024 14:07:11 -0800
Subject: [PATCH 07/23] Add changelog

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9c60d4c4..07a7fb62 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,10 @@ 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).
 
 
+## [ 0.18.0]
+### Added
+* The Sentinel-1 correction workflow will now calculate and write the M11/M12 conversion matrices to a netCDF file.
+
 ## [0.17.0]
 ## Changed
 * In preparation for a major update, the Sentinel-1 processing workflow has been isolated to a new `hyp3_autorift.s1_isce2` module. 

From 97ba71edd19069a62656ba8459278fd5f4688cec Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Tue, 18 Jun 2024 16:06:21 -0800
Subject: [PATCH 08/23] Register all gdal drivers b/c Geogrid :rolling_eyes:

---
 src/hyp3_autorift/s1_isce2.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index cc6f3f1f..5e486a62 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -286,6 +286,10 @@ def generate_correction_data(
 
     geogrid_info = runGeogrid(reference_meta, secondary_meta, epsg=parameter_info['epsg'], **parameter_info['geogrid'])
 
+    # NOTE: After Geogrid is run, all drivers are no longer registered.
+    #       I've got no idea why, or if there are other affects...
+    gdal.AllRegister()
+
     conversion_nc = create_conversion_matrices(scene=scene, epsg=parameter_info['epsg'], **parameter_info['autorift'])
 
     return geogrid_info, conversion_nc

From c25fb8a20c8637a7403fc5eebeb352c05e0d6e7e Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 11:36:05 -0800
Subject: [PATCH 09/23] Apply suggestions from code review

Co-authored-by: Jake Herrmann <jtherrmann@alaska.edu>
---
 CHANGELOG.md                  | 2 +-
 src/hyp3_autorift/s1_isce2.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 07a7fb62..de56d257 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,7 +7,7 @@ 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).
 
 
-## [ 0.18.0]
+## [0.18.0]
 ### Added
 * The Sentinel-1 correction workflow will now calculate and write the M11/M12 conversion matrices to a netCDF file.
 
diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index 5e486a62..343cb3e0 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -92,7 +92,7 @@ def process_sentinel1_with_isce2(reference, secondary, parameter_file):
 def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr_2_vr_factor, ChunkSize,
                           NoDataValue=-32767) -> str:
 
-    # FIXME: what else needs to be added to the nextCDF file
+    # FIXME: what else needs to be added to the netCDF file
     nc_outfile = Dataset(file_name, 'w', clobber=True, format='NETCDF4')
 
     nc_outfile.setncattr('GDAL_AREA_OR_POINT', 'Area')

From c43310f06eefa05a383684d1b9499bddfece4eeb Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 13:59:03 -0800
Subject: [PATCH 10/23] add missing netcdf attributes and use correct nan for
 floats

---
 src/hyp3_autorift/s1_isce2.py | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index 343cb3e0..d673f602 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -7,6 +7,7 @@
 from pathlib import Path
 
 import numpy as np
+from autoRIFT import __version__ as version
 from hyp3lib.fetch import download_file
 from hyp3lib.get_orb import downloadSentinelOrbitFile
 from hyp3lib.scene import get_download_url
@@ -90,7 +91,7 @@ def process_sentinel1_with_isce2(reference, secondary, parameter_file):
 
 
 def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr_2_vr_factor, ChunkSize,
-                          NoDataValue=-32767) -> str:
+                          NoDataValue=np.nan, parameter_file: str) -> str:
 
     # FIXME: what else needs to be added to the netCDF file
     nc_outfile = Dataset(file_name, 'w', clobber=True, format='NETCDF4')
@@ -99,8 +100,8 @@ def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr
     nc_outfile.setncattr('Conventions', 'CF-1.8')
     nc_outfile.setncattr('date_created', datetime.now().strftime("%d-%b-%Y %H:%M:%S"))
     nc_outfile.setncattr('title', 'autoRIFT S1 Corrections')
-    # nc_outfile.setncattr('autoRIFT_software_version', 'FIXME')
-    # nc_outfile.setncattr('autoRIFT_parameter_file', 'FIXME')
+    nc_outfile.setncattr('autoRIFT_software_version', version)
+    nc_outfile.setncattr('autoRIFT_parameter_file', parameter_file)
 
     nc_outfile.createDimension('x', len(x))
     nc_outfile.createDimension('y', len(y))
@@ -196,6 +197,7 @@ def create_conversion_matrices(
         offset2vy: str = 'window_rdr_off2vel_y_vec.tif',
         scale_factor: str = 'window_scale_factor.tif',
         epsg: int = 4326,
+        parameter_file: str = DEFAULT_PARAMETER_FILE,
         **kwargs,  # noqa: consume kwargs we don't care about for convenience
 ) -> str:
     xGrid, tran, _, srs, nodata = utils.load_geospatial(grid_location, band=1)
@@ -241,7 +243,7 @@ def create_conversion_matrices(
 
     conversion_nc = write_conversion_file(
         file_name=f'{scene}_conversion_matrices.nc', srs=srs, epsg=epsg, tran=tran, x=x, y=y, M11=M11, M12=M12,
-        dr_2_vr_factor=dr_2_vr_factor, ChunkSize=ChunkSize
+        dr_2_vr_factor=dr_2_vr_factor, ChunkSize=ChunkSize, parameter_file=parameter_file,
     )
 
     return conversion_nc
@@ -290,7 +292,9 @@ def generate_correction_data(
     #       I've got no idea why, or if there are other affects...
     gdal.AllRegister()
 
-    conversion_nc = create_conversion_matrices(scene=scene, epsg=parameter_info['epsg'], **parameter_info['autorift'])
+    conversion_nc = create_conversion_matrices(
+        scene=scene, epsg=parameter_info['epsg'], parameter_file=parameter_file, **parameter_info['autorift']
+    )
 
     return geogrid_info, conversion_nc
 

From 4aaa993b372030c5fe5106783d82a147af70c0bd Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 14:00:29 -0800
Subject: [PATCH 11/23] drop fixme

---
 src/hyp3_autorift/s1_isce2.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index d673f602..c6416b3c 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -93,7 +93,6 @@ def process_sentinel1_with_isce2(reference, secondary, parameter_file):
 def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr_2_vr_factor, ChunkSize,
                           NoDataValue=np.nan, parameter_file: str) -> str:
 
-    # FIXME: what else needs to be added to the netCDF file
     nc_outfile = Dataset(file_name, 'w', clobber=True, format='NETCDF4')
 
     nc_outfile.setncattr('GDAL_AREA_OR_POINT', 'Area')

From 407efc9584983375d9c15c0557cb5f0987c6a3b8 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 14:19:17 -0800
Subject: [PATCH 12/23] just use float64 everywhere; add type hints

---
 src/hyp3_autorift/s1_isce2.py | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index c6416b3c..d4fc0f50 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -3,6 +3,7 @@
 import os
 import sys
 import textwrap
+from typing import List
 from datetime import datetime, timedelta
 from pathlib import Path
 
@@ -12,7 +13,7 @@
 from hyp3lib.get_orb import downloadSentinelOrbitFile
 from hyp3lib.scene import get_download_url
 from netCDF4 import Dataset
-from osgeo import gdal
+from osgeo import gdal, osr
 
 from hyp3_autorift import geometry, utils
 from hyp3_autorift.process import DEFAULT_PARAMETER_FILE
@@ -90,8 +91,21 @@ def process_sentinel1_with_isce2(reference, secondary, parameter_file):
     return netcdf_file
 
 
-def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr_2_vr_factor, ChunkSize,
-                          NoDataValue=np.nan, parameter_file: str) -> str:
+def write_conversion_file(
+        *,
+        file_name: str,
+        srs: osr.SpatialReference,
+        epsg: int,
+        tran: List[float],
+        x: np.ndarray,
+        y: np.ndarray,
+        M11: np.ndarray,
+        M12: np.ndarray,
+        dr_2_vr_factor: float,
+        ChunkSize: List[int],
+        NoDataValue=np.nan,
+        parameter_file: str
+) -> str:
 
     nc_outfile = Dataset(file_name, 'w', clobber=True, format='NETCDF4')
 
@@ -154,7 +168,7 @@ def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr
     else:
         raise Exception('Projection {0} not recognized for this program'.format(srs.GetAttrValue('PROJECTION')))
 
-    var = nc_outfile.createVariable('M11', np.dtype('float32'), ('y', 'x'), fill_value=NoDataValue,
+    var = nc_outfile.createVariable('M11', np.dtype('float64'), ('y', 'x'), fill_value=NoDataValue,
                                     zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
     var.setncattr('standard_name', 'conversion_matrix_element_11')
     var.setncattr(
@@ -169,7 +183,7 @@ def write_conversion_file(*, file_name: str, srs, epsg, tran, x, y, M11, M12, dr
                                                  'pixel displacement dr to slant range velocity vr')
     var[:] = M11
 
-    var = nc_outfile.createVariable('M12', np.dtype('float32'), ('y', 'x'), fill_value=NoDataValue,
+    var = nc_outfile.createVariable('M12', np.dtype('float64'), ('y', 'x'), fill_value=NoDataValue,
                                     zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
     var.setncattr('standard_name', 'conversion_matrix_element_12')
     var.setncattr(
@@ -224,7 +238,7 @@ def create_conversion_matrices(
     scale_factor_2[scale_factor_2 == nodata] = np.nan
 
     SRx0, _, _, _, _ = utils.load_geospatial(search_range, band=1)
-    SRx0 = SRx0.astype('float32')
+    SRx0 = SRx0.astype('float64')
     SRx0[SRx0 == nodata] = np.nan
 
     dimidY, dimidX = xGrid.shape

From 2aa993d22746ee8d48764452423b8844e6c9808b Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 14:22:08 -0800
Subject: [PATCH 13/23] Apply suggestions from code review

Co-authored-by: Jake Herrmann <jtherrmann@alaska.edu>
---
 src/hyp3_autorift/s1_isce2.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index d4fc0f50..20252846 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -166,7 +166,7 @@ def write_conversion_file(
         var.setncattr('spatial_epsg', epsg)
         var.setncattr('GeoTransform', ' '.join(str(x) for x in tran))
     else:
-        raise Exception('Projection {0} not recognized for this program'.format(srs.GetAttrValue('PROJECTION')))
+        raise Exception(f'Projection {srs.GetAttrValue('PROJECTION')} not recognized for this program')
 
     var = nc_outfile.createVariable('M11', np.dtype('float64'), ('y', 'x'), fill_value=NoDataValue,
                                     zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
@@ -211,7 +211,7 @@ def create_conversion_matrices(
         scale_factor: str = 'window_scale_factor.tif',
         epsg: int = 4326,
         parameter_file: str = DEFAULT_PARAMETER_FILE,
-        **kwargs,  # noqa: consume kwargs we don't care about for convenience
+        **kwargs,
 ) -> str:
     xGrid, tran, _, srs, nodata = utils.load_geospatial(grid_location, band=1)
     yGrid, _, _, _, _ = utils.load_geospatial(grid_location, band=2)
@@ -302,7 +302,7 @@ def generate_correction_data(
     geogrid_info = runGeogrid(reference_meta, secondary_meta, epsg=parameter_info['epsg'], **parameter_info['geogrid'])
 
     # NOTE: After Geogrid is run, all drivers are no longer registered.
-    #       I've got no idea why, or if there are other affects...
+    #       I've got no idea why, or if there are other effects...
     gdal.AllRegister()
 
     conversion_nc = create_conversion_matrices(

From df02c09a6234e68613453149d519cf7ebbb3e95e Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 14:24:32 -0800
Subject: [PATCH 14/23] lint

---
 src/hyp3_autorift/s1_isce2.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index 20252846..23176878 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -3,8 +3,8 @@
 import os
 import sys
 import textwrap
-from typing import List
 from datetime import datetime, timedelta
+from typing import List
 from pathlib import Path
 
 import numpy as np

From 066cea7000e48b62193d8b6f3036814704937e7a Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 14:25:35 -0800
Subject: [PATCH 15/23] fix f string

---
 src/hyp3_autorift/s1_isce2.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index 23176878..999b63b1 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -166,7 +166,7 @@ def write_conversion_file(
         var.setncattr('spatial_epsg', epsg)
         var.setncattr('GeoTransform', ' '.join(str(x) for x in tran))
     else:
-        raise Exception(f'Projection {srs.GetAttrValue('PROJECTION')} not recognized for this program')
+        raise Exception(f'Projection {srs.GetAttrValue("PROJECTION")} not recognized for this program')
 
     var = nc_outfile.createVariable('M11', np.dtype('float64'), ('y', 'x'), fill_value=NoDataValue,
                                     zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)

From 2162174fe99781c2da7c6f547fea4d22ffefb384 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Wed, 19 Jun 2024 14:26:43 -0800
Subject: [PATCH 16/23] import order

---
 src/hyp3_autorift/s1_isce2.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index 999b63b1..7895abba 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -4,8 +4,8 @@
 import sys
 import textwrap
 from datetime import datetime, timedelta
-from typing import List
 from pathlib import Path
+from typing import List
 
 import numpy as np
 from autoRIFT import __version__ as version

From 6fa18e4fb9d992974876b8a3e8e46fca1a4f031b Mon Sep 17 00:00:00 2001
From: Andrew Player <andrewplayer3@gmail.com>
Date: Wed, 26 Jun 2024 14:56:35 -0500
Subject: [PATCH 17/23] dropped support for python 3.8

---
 CHANGELOG.md    | 3 +++
 environment.yml | 2 +-
 pyproject.toml  | 4 +---
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index de56d257..9b165e26 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 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).
 
+## [0.19.0]
+### Removed
+* Support for Python 3.8 has been dropped.
 
 ## [0.18.0]
 ### Added
diff --git a/environment.yml b/environment.yml
index 0afab498..3fb87871 100644
--- a/environment.yml
+++ b/environment.yml
@@ -6,7 +6,7 @@ channels:
 dependencies:
   - boto3
   - botocore
-  - python>=3.8,<3.10  # Top pin to fix ISCE2 incompatibility: https://github.com/isce-framework/isce2/issues/458
+  - python>=3.9,<3.10  # Top pin to fix ISCE2 incompatibility: https://github.com/isce-framework/isce2/issues/458
   - pip
   # For packaging, and testing
   - build
diff --git a/pyproject.toml b/pyproject.toml
index 2032aa16..878d283b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "hyp3_autorift"
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 authors = [
     {name="ASF APD/Tools Team", email="uaf-asf-apd@alaska.edu"},
 ]
@@ -17,9 +17,7 @@ classifiers=[
     "Natural Language :: English",
     "Operating System :: OS Independent",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
 ]
 dependencies = [
     'boto3',

From 98abf66e29248968d97392b5c72d8a45a6c4dbee Mon Sep 17 00:00:00 2001
From: Jake Herrmann <jtherrmann@alaska.edu>
Date: Thu, 27 Jun 2024 10:03:52 -0800
Subject: [PATCH 18/23] Update CHANGELOG.md

---
 CHANGELOG.md | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9b165e26..23a65519 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,13 +6,11 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 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).
 
-## [0.19.0]
-### Removed
-* Support for Python 3.8 has been dropped.
-
 ## [0.18.0]
 ### Added
 * The Sentinel-1 correction workflow will now calculate and write the M11/M12 conversion matrices to a netCDF file.
+### Removed
+* Support for Python 3.8 has been dropped.
 
 ## [0.17.0]
 ## Changed

From 0dec0d79ecfc28ed2683f5446ff764efde3ec459 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 1 Jul 2024 16:49:05 +0000
Subject: [PATCH 19/23] Bump ASFHyP3/actions from 0.11.1 to 0.11.2

Bumps [ASFHyP3/actions](https://github.com/asfhyp3/actions) from 0.11.1 to 0.11.2.
- [Release notes](https://github.com/asfhyp3/actions/releases)
- [Changelog](https://github.com/ASFHyP3/actions/blob/develop/CHANGELOG.md)
- [Commits](https://github.com/asfhyp3/actions/compare/v0.11.1...v0.11.2)

---
updated-dependencies:
- dependency-name: ASFHyP3/actions
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/changelog.yml                | 2 +-
 .github/workflows/create-jira-issue.yml        | 2 +-
 .github/workflows/labeled-pr.yml               | 2 +-
 .github/workflows/release-template-comment.yml | 2 +-
 .github/workflows/release.yml                  | 2 +-
 .github/workflows/static-analysis.yml          | 4 ++--
 .github/workflows/tag-version.yml              | 2 +-
 .github/workflows/test-and-build.yml           | 6 +++---
 8 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/changelog.yml b/.github/workflows/changelog.yml
index 6047ddb1..7740de9e 100644
--- a/.github/workflows/changelog.yml
+++ b/.github/workflows/changelog.yml
@@ -13,4 +13,4 @@ on:
 
 jobs:
   call-changelog-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-changelog-check.yml@v0.11.2
diff --git a/.github/workflows/create-jira-issue.yml b/.github/workflows/create-jira-issue.yml
index 129ff5f1..99489d50 100644
--- a/.github/workflows/create-jira-issue.yml
+++ b/.github/workflows/create-jira-issue.yml
@@ -6,7 +6,7 @@ on:
 
 jobs:
   call-create-jira-issue-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-create-jira-issue.yml@v0.11.2
     secrets:
       JIRA_BASE_URL: ${{ secrets.JIRA_BASE_URL }}
       JIRA_USER_EMAIL: ${{ secrets.JIRA_USER_EMAIL }}
diff --git a/.github/workflows/labeled-pr.yml b/.github/workflows/labeled-pr.yml
index 3ba21604..f89f3e3b 100644
--- a/.github/workflows/labeled-pr.yml
+++ b/.github/workflows/labeled-pr.yml
@@ -12,4 +12,4 @@ on:
 
 jobs:
   call-labeled-pr-check-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-labeled-pr-check.yml@v0.11.2
diff --git a/.github/workflows/release-template-comment.yml b/.github/workflows/release-template-comment.yml
index 01d20589..dd3650ce 100644
--- a/.github/workflows/release-template-comment.yml
+++ b/.github/workflows/release-template-comment.yml
@@ -7,6 +7,6 @@ on:
 
 jobs:
   call-release-checklist-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-release-checklist-comment.yml@v0.11.2
     secrets:
       USER_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index f04a3669..784648ef 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -7,7 +7,7 @@ on:
 
 jobs:
   call-release-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-release.yml@v0.11.2
     with:
       release_prefix: HyP3 autoRIFT
     secrets:
diff --git a/.github/workflows/static-analysis.yml b/.github/workflows/static-analysis.yml
index 6e006ab8..c7f96d1e 100644
--- a/.github/workflows/static-analysis.yml
+++ b/.github/workflows/static-analysis.yml
@@ -4,10 +4,10 @@ on: push
 
 jobs:
   call-flake8-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-flake8.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-flake8.yml@v0.11.2
     with:
       local_package_names: hyp3_autorift
       excludes: src/hyp3_autorift/vend
 
   call-secrets-analysis-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-secrets-analysis.yml@v0.11.2
diff --git a/.github/workflows/tag-version.yml b/.github/workflows/tag-version.yml
index 7bc79246..3b94479b 100644
--- a/.github/workflows/tag-version.yml
+++ b/.github/workflows/tag-version.yml
@@ -7,6 +7,6 @@ on:
 
 jobs:
   call-bump-version-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-bump-version.yml@v0.11.2
     secrets:
       USER_TOKEN: ${{ secrets.TOOLS_BOT_PAK }}
diff --git a/.github/workflows/test-and-build.yml b/.github/workflows/test-and-build.yml
index cfc16752..984878d6 100644
--- a/.github/workflows/test-and-build.yml
+++ b/.github/workflows/test-and-build.yml
@@ -12,18 +12,18 @@ on:
 
 jobs:
   call-pytest-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-pytest.yml@v0.11.2
     with:
       local_package_name: hyp3_autorift
       python_versions: >-
         ["3.9"]
 
   call-version-info-workflow:
-    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.11.2
 
   call-docker-ghcr-workflow:
     needs: call-version-info-workflow
-    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.11.1
+    uses: ASFHyP3/actions/.github/workflows/reusable-docker-ghcr.yml@v0.11.2
     with:
       version_tag: ${{ needs.call-version-info-workflow.outputs.version_tag }}
     secrets:

From 52c2b84a4918315e8087e8e122da2d6256d58c4f Mon Sep 17 00:00:00 2001
From: Jake Herrmann <jtherrmann@alaska.edu>
Date: Mon, 1 Jul 2024 10:39:05 -0800
Subject: [PATCH 20/23] Update .github/workflows/test-and-build.yml

---
 .github/workflows/test-and-build.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test-and-build.yml b/.github/workflows/test-and-build.yml
index 984878d6..f23e4baf 100644
--- a/.github/workflows/test-and-build.yml
+++ b/.github/workflows/test-and-build.yml
@@ -20,6 +20,8 @@ jobs:
 
   call-version-info-workflow:
     uses: ASFHyP3/actions/.github/workflows/reusable-version-info.yml@v0.11.2
+    with:
+      python_version: '3.9'
 
   call-docker-ghcr-workflow:
     needs: call-version-info-workflow

From abea71933aacad91f5270fa0130a1476f75fd31d Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Tue, 2 Jul 2024 20:18:04 -0800
Subject: [PATCH 21/23] switch to writing ints; drop unused

---
 src/hyp3_autorift/s1_isce2.py | 47 +++++++++++++++++++++++------------
 1 file changed, 31 insertions(+), 16 deletions(-)

diff --git a/src/hyp3_autorift/s1_isce2.py b/src/hyp3_autorift/s1_isce2.py
index 7895abba..58c873ac 100644
--- a/src/hyp3_autorift/s1_isce2.py
+++ b/src/hyp3_autorift/s1_isce2.py
@@ -103,7 +103,8 @@ def write_conversion_file(
         M12: np.ndarray,
         dr_2_vr_factor: float,
         ChunkSize: List[int],
-        NoDataValue=np.nan,
+        NoDataValue: int = -32767,
+        noDataMask: np.ndarray,
         parameter_file: str
 ) -> str:
 
@@ -168,7 +169,7 @@ def write_conversion_file(
     else:
         raise Exception(f'Projection {srs.GetAttrValue("PROJECTION")} not recognized for this program')
 
-    var = nc_outfile.createVariable('M11', np.dtype('float64'), ('y', 'x'), fill_value=NoDataValue,
+    var = nc_outfile.createVariable('M11', np.dtype('int16'), ('y', 'x'), fill_value=NoDataValue,
                                     zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
     var.setncattr('standard_name', 'conversion_matrix_element_11')
     var.setncattr(
@@ -181,9 +182,20 @@ def write_conversion_file(
     var.setncattr('dr_to_vr_factor', dr_2_vr_factor)
     var.setncattr('dr_to_vr_factor_description', 'multiplicative factor that converts slant range '
                                                  'pixel displacement dr to slant range velocity vr')
+
+    x1 = np.nanmin(M11[:])
+    x2 = np.nanmax(M11[:])
+    y1 = -50
+    y2 = 50
+
+    C = [(y2 - y1) / (x2 - x1), y1 - x1 * (y2 - y1) / (x2 - x1)]
+    var.setncattr('scale_factor', np.float32(1 / C[0]))
+    var.setncattr('add_offset', np.float32(-C[1] / C[0]))
+
+    M11[noDataMask] = NoDataValue * np.float32(1 / C[0]) + np.float32(-C[1] / C[0])
     var[:] = M11
 
-    var = nc_outfile.createVariable('M12', np.dtype('float64'), ('y', 'x'), fill_value=NoDataValue,
+    var = nc_outfile.createVariable('M12', np.dtype('int16'), ('y', 'x'), fill_value=NoDataValue,
                                     zlib=True, complevel=2, shuffle=True, chunksizes=ChunkSize)
     var.setncattr('standard_name', 'conversion_matrix_element_12')
     var.setncattr(
@@ -196,6 +208,17 @@ def write_conversion_file(
     var.setncattr('dr_to_vr_factor', dr_2_vr_factor)
     var.setncattr('dr_to_vr_factor_description',
                   'multiplicative factor that converts slant range pixel displacement dr to slant range velocity vr')
+
+    x1 = np.nanmin(M12[:])
+    x2 = np.nanmax(M12[:])
+    y1 = -50
+    y2 = 50
+
+    C = [(y2 - y1) / (x2 - x1), y1 - x1 * (y2 - y1) / (x2 - x1)]
+    var.setncattr('scale_factor', np.float32(1 / C[0]))
+    var.setncattr('add_offset', np.float32(-C[1] / C[0]))
+
+    M12[noDataMask] = NoDataValue * np.float32(1 / C[0]) + np.float32(-C[1] / C[0])
     var[:] = M12
 
     return file_name
@@ -205,7 +228,6 @@ def create_conversion_matrices(
         *,
         scene: str,
         grid_location: str = 'window_location.tif',
-        search_range: str = 'window_search_range.tif',
         offset2vx: str = 'window_rdr_off2vel_x_vec.tif',
         offset2vy: str = 'window_rdr_off2vel_y_vec.tif',
         scale_factor: str = 'window_scale_factor.tif',
@@ -214,7 +236,6 @@ def create_conversion_matrices(
         **kwargs,
 ) -> str:
     xGrid, tran, _, srs, nodata = utils.load_geospatial(grid_location, band=1)
-    yGrid, _, _, _, _ = utils.load_geospatial(grid_location, band=2)
 
     offset2vy_1, _, _, _, _ = utils.load_geospatial(offset2vy, band=1)
     offset2vy_1[offset2vy_1 == nodata] = np.nan
@@ -234,29 +255,23 @@ def create_conversion_matrices(
     scale_factor_1, _, _, _, _ = utils.load_geospatial(scale_factor, band=1)
     scale_factor_1[scale_factor_1 == nodata] = np.nan
 
-    scale_factor_2, _, _, _, _ = utils.load_geospatial(scale_factor, band=2)
-    scale_factor_2[scale_factor_2 == nodata] = np.nan
-
-    SRx0, _, _, _, _ = utils.load_geospatial(search_range, band=1)
-    SRx0 = SRx0.astype('float64')
-    SRx0[SRx0 == nodata] = np.nan
-
     dimidY, dimidX = xGrid.shape
+    noDataMask = xGrid == nodata
 
     y = np.arange(tran[3], tran[3] + tran[5] * dimidY, tran[5])
     x = np.arange(tran[0], tran[0] + tran[1] * dimidX, tran[1])
 
+    chunk_lines = np.min([np.ceil(8192 / dimidY) * 128, dimidY])
+    ChunkSize = [chunk_lines, dimidX]
+
     M11 = offset2vy_2 / (offset2vx_1 * offset2vy_2 - offset2vx_2 * offset2vy_1) / scale_factor_1
     M12 = -offset2vx_2 / (offset2vx_1 * offset2vy_2 - offset2vx_2 * offset2vy_1) / scale_factor_1
 
     dr_2_vr_factor = np.median(offset2vr[np.logical_not(np.isnan(offset2vr))])
 
-    chunk_lines = np.min([np.ceil(8192 / dimidY) * 128, dimidY])
-    ChunkSize = [chunk_lines, dimidX]
-
     conversion_nc = write_conversion_file(
         file_name=f'{scene}_conversion_matrices.nc', srs=srs, epsg=epsg, tran=tran, x=x, y=y, M11=M11, M12=M12,
-        dr_2_vr_factor=dr_2_vr_factor, ChunkSize=ChunkSize, parameter_file=parameter_file,
+        dr_2_vr_factor=dr_2_vr_factor, ChunkSize=ChunkSize, noDataMask=noDataMask, parameter_file=parameter_file,
     )
 
     return conversion_nc

From 0670524bccf82e515392d3b317a02e0510243b31 Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Tue, 2 Jul 2024 22:12:57 -0800
Subject: [PATCH 22/23] Ensure are encoding attributes are carried over when
 cropping

---
 src/hyp3_autorift/crop.py | 27 +++++++--------------------
 1 file changed, 7 insertions(+), 20 deletions(-)

diff --git a/src/hyp3_autorift/crop.py b/src/hyp3_autorift/crop.py
index 4e14ab6a..58a725dc 100644
--- a/src/hyp3_autorift/crop.py
+++ b/src/hyp3_autorift/crop.py
@@ -36,22 +36,7 @@
 import pyproj
 import xarray as xr
 
-
-ENCODING_TEMPLATE = {
-        'interp_mask':      {'_FillValue': 0.0, 'dtype': 'ubyte', "zlib": True, "complevel": 2, "shuffle": True},
-        'chip_size_height': {'_FillValue': 0.0, 'dtype': 'ushort', "zlib": True, "complevel": 2, "shuffle": True},
-        'chip_size_width':  {'_FillValue': 0.0, 'dtype': 'ushort', "zlib": True, "complevel": 2, "shuffle": True},
-        'M11': {'_FillValue': -32767, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'M12': {'_FillValue': -32767, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'v':                {'_FillValue': -32767.0, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'vx':               {'_FillValue': -32767.0, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'vy':               {'_FillValue': -32767.0, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'v_error': {'_FillValue': -32767.0, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'va': {'_FillValue': -32767.0, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'vr': {'_FillValue': -32767.0, 'dtype': 'short', "zlib": True, "complevel": 2, "shuffle": True},
-        'x':                {'_FillValue': None},
-        'y':                {'_FillValue': None}
-    }
+ENCODING_ATTRS = ['_FillValue', 'dtype', "zlib", "complevel", "shuffle", 'add_offset', 'scale_factor']
 
 
 def crop_netcdf_product(netcdf_file: Path) -> Path:
@@ -114,10 +99,12 @@ def crop_netcdf_product(netcdf_file: Path) -> Path:
         chunk_lines = np.min([np.ceil(8192 / dims['y']) * 128, dims['y']])
         two_dim_chunks_settings = (chunk_lines, dims['x'])
 
-        encoding = ENCODING_TEMPLATE.copy()
-        if not netcdf_file.name.startswith('S1'):
-            for radar_variable in ['M11', 'M12', 'va', 'vr']:
-                del encoding[radar_variable]
+        encoding = {}
+        for variable in ds.data_vars.keys():
+            if variable in ['img_pair_info', 'mapping']:
+                continue
+            attributes = {attr: ds[variable].encoding[attr] for attr in ENCODING_ATTRS if attr in ds[variable].encoding}
+            encoding[variable] = attributes
 
         for _, attributes in encoding.items():
             if attributes['_FillValue'] is not None:

From e050c21088ba405ded817044cf321eb00f0e010d Mon Sep 17 00:00:00 2001
From: Joseph H Kennedy <me@jhkennedy.org>
Date: Tue, 2 Jul 2024 22:16:12 -0800
Subject: [PATCH 23/23] add changelog

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 23a65519..1ad1b937 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,10 @@ and uses [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 ## [0.18.0]
 ### Added
 * The Sentinel-1 correction workflow will now calculate and write the M11/M12 conversion matrices to a netCDF file.
+
+### Fixed
+* `hyp3_autorift.crop` will now preserve the `add_offset` and `scale_factor` encoding attributes for all variables, and in particular, for the M11/M12 conversion matrices. 
+
 ### Removed
 * Support for Python 3.8 has been dropped.