Merge pull request #244 from ASFHyP3/develop

Release v2.1.0

CHANGELOG.md

@@ -6,6 +6,14 @@ 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).
 
+## [2.1.0]
+### Added
+- The ability for the `insar_tops_burst` workflow to support processing multiple bursts as one SLC.
+
+### Changed
+- The interface for `insar_tops_burst` so that it takes `--reference` and `--secondary` granule lists. The positional `granules` argument is now optional and deprecated.
+- Moved HyP3 product packaging functionality out of `insar_tops_burst.py` and to a new `packaging.py` so that both `insar_tops` and `insar_tops_burst` can use it.
+
 ## [2.0.0]
 ### Changed
 - Orbit files are now retrieved using the [s1-orbits](https://github.com/ASFHyP3/sentinel1-orbits-py) library.

README.md

@@ -8,22 +8,32 @@ The HyP3-ISCE2 plugin provides a set of workflows to process SAR satellite data
 ## Usage
 The HyP3-ISCE2 plugin provides a set of workflows (accessible directly in Python or via a CLI) that can be used to process SAR data using ISCE2. The workflows currently included in this plugin are:
 
-- `insar_tops`: A workflow for creating full-SLC Sentinel-1 geocoded unwrapped interferogram using ISCE2's TOPS processing workflow 
-- `insar_tops_burst`: A workflow for creating single-burst Sentinel-1 geocoded unwrapped interferogram using ISCE2's TOPS processing workflow 
+- `insar_stripmap`: A workflow for creating ALOS-1 geocoded unwrapped interferogram using ISCE2's Stripmap processing workflow
+- `insar_tops`: A workflow for creating full-SLC Sentinel-1 geocoded unwrapped interferogram using ISCE2's TOPS processing workflow
+- `insar_tops_burst`: A workflow for creating burst-based Sentinel-1 geocoded unwrapped interferogram using ISCE2's TOPS processing workflow
 ---
 
 To run a workflow, simply run `python -m hyp3_isce2 ++process [WORKFLOW_NAME] [WORKFLOW_ARGS]`. For example, to run the `insar_tops_burst` workflow:
 
 ```
 python -m hyp3_isce2 ++process insar_tops_burst \
-  S1_136231_IW2_20200604T022312_VV_7C85-BURST \
-  S1_136231_IW2_20200616T022313_VV_5D11-BURST \
+  --reference S1_136231_IW2_20200604T022312_VV_7C85-BURST \
+  --secondary S1_136231_IW2_20200616T022313_VV_5D11-BURST \
   --looks 20x4 \
   --apply-water-mask True
 ```
 
-This command will create a Sentinel-1 interferogram that contains a deformation signal related to a 
-2020 Iranian earthquake. 
+and, for multiple burst pairs:
+
+```
+python -m hyp3_isce2 ++process insar_tops_burst \
+  --reference S1_136231_IW2_20200604T022312_VV_7C85-BURST S1_136232_IW2_20200604T022315_VV_7C85-BURST \
+  --secondary S1_136231_IW2_20200616T022313_VV_5D11-BURST S1_136232_IW2_20200616T022316_VV_5D11-BURST \
+  --looks 20x4 \
+  --apply-water-mask True
+```
+
+These commands will both create a Sentinel-1 interferogram that contains a deformation signal related to a 2020 Iranian earthquake.
 
 ### Product Merging Utility Usage
 **This feature is under active development and is subject to change!**

environment.yml

@@ -14,6 +14,7 @@ dependencies:
   - asf_search>=6.4.0
   - gdal
   - opencv
+  - burst2safe
   # For packaging, and testing
   - flake8
   - flake8-import-order

pyproject.toml

@@ -29,6 +29,7 @@ dependencies = [
   "gdal",
   "hyp3lib>=3,<4",
   "s1_orbits",
+  "burst2safe"
   # Conda-forge only dependencies are listed below
   # "opencv",
   # "isce2>=2.6.3",

src/hyp3_isce2/burst.py

@@ -7,8 +7,7 @@
 from dataclasses import dataclass
 from datetime import datetime, timedelta
 from pathlib import Path
-from secrets import token_hex
-from typing import Iterator, List, Optional, Tuple, Union
+from typing import Iterable, Iterator, List, Optional, Tuple, Union
 
 import asf_search
 import numpy as np
@@ -345,45 +344,6 @@ def download_bursts(param_list: Iterator[BurstParams]) -> List[BurstMetadata]:
     return bursts
 
 
-def get_product_name(reference_scene: str, secondary_scene: str, pixel_spacing: int) -> str:
-    """Get the name of the interferogram product.
-
-    Args:
-        reference_scene: The reference burst name.
-        secondary_scene: The secondary burst name.
-        pixel_spacing: The spacing of the pixels in the output image.
-
-    Returns:
-        The name of the interferogram product.
-    """
-
-    reference_split = reference_scene.split('_')
-    secondary_split = secondary_scene.split('_')
-
-    platform = reference_split[0]
-    burst_id = reference_split[1]
-    image_plus_swath = reference_split[2]
-    reference_date = reference_split[3][0:8]
-    secondary_date = secondary_split[3][0:8]
-    polarization = reference_split[4]
-    product_type = 'INT'
-    pixel_spacing = str(int(pixel_spacing))
-    product_id = token_hex(2).upper()
-
-    return '_'.join(
-        [
-            platform,
-            burst_id,
-            image_plus_swath,
-            reference_date,
-            secondary_date,
-            polarization,
-            product_type + pixel_spacing,
-            product_id,
-        ]
-    )
-
-
 def get_burst_params(scene_name: str) -> BurstParams:
     results = asf_search.search(product_list=[scene_name])
 
@@ -400,35 +360,47 @@ def get_burst_params(scene_name: str) -> BurstParams:
     )
 
 
-def validate_bursts(reference_scene: str, secondary_scene: str) -> None:
+def validate_bursts(reference: Union[str, Iterable[str]], secondary: Union[str, Iterable[str]]) -> None:
     """Check whether the reference and secondary bursts are valid.
 
     Args:
-        reference_scene: The reference burst name.
-        secondary_scene: The secondary burst name.
-
-    Returns:
-        None
+        reference: Reference granule(s)
+        secondary: Secondary granule(s)
     """
-    ref_split = reference_scene.split('_')
-    sec_split = secondary_scene.split('_')
+    if isinstance(reference, str):
+        reference = [reference]
+    if isinstance(secondary, str):
+        secondary = [secondary]
+
+    if len(reference) < 1 or len(secondary) < 1:
+        raise ValueError('Must include at least 1 reference and 1 secondary burst')
+    if len(reference) != len(secondary):
+        raise ValueError('Must have the same number of reference and secondary bursts')
+
+    ref_num_swath_pol = sorted(g.split('_')[1] + '_' + g.split('_')[2] + '_' + g.split('_')[4] for g in reference)
+    sec_num_swath_pol = sorted(g.split('_')[1] + '_' + g.split('_')[2] + '_' + g.split('_')[4] for g in secondary)
+    if ref_num_swath_pol != sec_num_swath_pol:
+        msg = 'The reference and secondary burst ID sets do not match.\n'
+        msg += f'    Reference IDs: {ref_num_swath_pol}\n'
+        msg += f'    Secondary IDs: {sec_num_swath_pol}'
+        raise ValueError(msg)
+
+    pols = list(set(g.split('_')[4] for g in reference + secondary))
 
-    ref_burst_id = ref_split[1]
-    sec_burst_id = sec_split[1]
+    if len(pols) > 1:
+        raise ValueError(f'All bursts must have a single polarization. Polarizations present: {" ".join(pols)}')
 
-    ref_polarization = ref_split[4]
-    sec_polarization = sec_split[4]
+    if pols[0] not in ['VV', 'HH']:
+        raise ValueError(f'{pols[0]} polarization is not currently supported, only VV and HH.')
 
-    if ref_burst_id != sec_burst_id:
-        raise ValueError(f'The reference and secondary burst IDs are not the same: {ref_burst_id} and {sec_burst_id}.')
+    ref_dates = list(set(g.split('_')[3][:8] for g in reference))
+    sec_dates = list(set(g.split('_')[3][:8] for g in secondary))
 
-    if ref_polarization != sec_polarization:
-        raise ValueError(
-            f'The reference and secondary polarizations are not the same: {ref_polarization} and {sec_polarization}.'
-        )
+    if len(ref_dates) > 1 or len(sec_dates) > 1:
+        raise ValueError('Reference granules must be from one date and secondary granules must be another.')
 
-    if ref_polarization != 'VV' and ref_polarization != 'HH':
-        raise ValueError(f'{ref_polarization} polarization is not currently supported, only VV and HH.')
+    if ref_dates[0] >= sec_dates[0]:
+        raise ValueError('Reference granules must be older than secondary granules.')
 
 
 def load_burst_position(swath_xml_path: str, burst_number: int) -> BurstPosition:
@@ -572,7 +544,7 @@ def safely_multilook(
     if subset_to_valid:
         last_line = position.first_valid_line + position.n_valid_lines
         last_sample = position.first_valid_sample + position.n_valid_samples
-        mask[position.first_valid_line: last_line, position.first_valid_sample: last_sample] = identity_value
+        mask[position.first_valid_line:last_line, position.first_valid_sample:last_sample] = identity_value
     else:
         mask[:, :] = identity_value
 

src/hyp3_isce2/insar_stripmap.py

@@ -23,7 +23,7 @@
 log = logging.getLogger(__name__)
 
 
-def insar_stripmap(user: str, password: str, reference_scene: str, secondary_scene: str) -> Path:
+def insar_stripmap(reference_scene: str, secondary_scene: str) -> Path:
     """Create a Stripmap interferogram
 
     Args:
@@ -35,12 +35,22 @@ def insar_stripmap(user: str, password: str, reference_scene: str, secondary_sce
     Returns:
         Path to the output files
     """
-    session = asf_search.ASFSession().auth_with_creds(user, password)
-
-    reference_product, secondary_product = asf_search.search(
+    scenes = sorted([reference_scene, secondary_scene])
+    print(scenes)
+    reference_scene = scenes[0]
+    secondary_scene = scenes[1]
+    products = asf_search.search(
         granule_list=[reference_scene, secondary_scene],
-        processingLevel=asf_search.L1_0,
+        processingLevel="L1.0",
     )
+
+    if products[0].properties['sceneName'] == reference_scene:
+        reference_product = products[0]
+        secondary_product = products[1]
+    else:
+        reference_product = products[1]
+        secondary_product = products[0]
+
     assert reference_product.properties['sceneName'] == reference_scene
     assert secondary_product.properties['sceneName'] == secondary_scene
     products = (reference_product, secondary_product)
@@ -51,7 +61,7 @@ def insar_stripmap(user: str, password: str, reference_scene: str, secondary_sce
     dem_path = download_dem_for_isce2(insar_roi, dem_name='glo_30', dem_dir=Path('dem'), buffer=0)
 
     urls = [product.properties['url'] for product in products]
-    asf_search.download_urls(urls=urls, path=os.getcwd(), session=session, processes=2)
+    asf_search.download_urls(urls=urls, path=os.getcwd(), processes=2)
 
     zip_paths = [product.properties['fileName'] for product in products]
     for zip_path in zip_paths:
@@ -93,7 +103,7 @@ def insar_stripmap(user: str, password: str, reference_scene: str, secondary_sce
 
 def get_product_file(product: asf_search.ASFProduct, file_prefix: str) -> str:
     paths = glob.glob(str(Path(product.properties['fileID']) / f'{file_prefix}*'))
-    assert len(paths) == 1
+    assert len(paths) > 0
     return paths[0]
 
 
@@ -104,10 +114,8 @@ def main():
 
     parser.add_argument('--bucket', help='AWS S3 bucket HyP3 for upload the final product(s)')
     parser.add_argument('--bucket-prefix', default='', help='Add a bucket prefix to product(s)')
-    parser.add_argument('--username', type=str, required=True)
-    parser.add_argument('--password', type=str, required=True)
-    parser.add_argument('--reference-scene', type=str, required=True)
-    parser.add_argument('--secondary-scene', type=str, required=True)
+    parser.add_argument('--reference', type=str, required=True)
+    parser.add_argument('--secondary', type=str, required=True)
 
     args = parser.parse_args()
 
@@ -117,10 +125,8 @@ def main():
     log.info('Begin InSAR Stripmap run')
 
     product_dir = insar_stripmap(
-        user=args.username,
-        password=args.password,
-        reference_scene=args.reference_scene,
-        secondary_scene=args.secondary_scene,
+        reference_scene=args.reference,
+        secondary_scene=args.secondary,
     )
 
     log.info('InSAR Stripmap run completed successfully')