Merge pull request #21 from ASFHyP3/bugfix

HOTFIX: browse and ISCE version bugfixes

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).
 
+## [0.1.1](https://github.com/ASFHyP3/hyp3-autorift/compare/v0.1.0...v0.1.1)
+
+### Added
+* Browse and thumbnail images are now created and uploaded for hyp3v2
+
+### Fixes
+* Restrict ISCE version to 2.4.0 which includes autoRIFT 1.0.6
+
 ## [0.1.0](https://github.com/ASFHyP3/hyp3-autorift/compare/v0.0.0...v0.1.0)
 
 Initial release of hyp3-autorift, a HyP3 plugin for feature tracking processing

conda-env.yml

@@ -15,9 +15,10 @@ dependencies:
   - wheel
   # For running
   - hyp3lib=1.5
-  - isce2>=2.4
+  - isce2=2.4.0
   - importlib_metadata
   - numpy
+  - pillow
   - psycopg2  # missing hyp3proclib dep
   - requests
   - scikit-image  # missing autoRIFT dep

hyp3_autorift/__main__.py

@@ -11,6 +11,7 @@
 from mimetypes import guess_type
 
 import boto3
+from PIL import Image
 from hyp3proclib import (
     build_output_name_pair,
     earlier_granule_first,
@@ -49,6 +50,16 @@ def entry():
 
 
 # v2 functions
+def create_thumbnail(input_image, size=(100, 100)):
+    filename, ext = os.path.splitext(input_image)
+    thumbnail_name = f'{filename}_thumb{ext}'
+
+    output_image = Image.open(input_image)
+    output_image.thumbnail(size)
+    output_image.save(thumbnail_name)
+    return thumbnail_name
+
+
 def write_netrc_file(username, password):
     netrc_file = os.path.join(os.environ['HOME'], '.netrc')
     if os.path.isfile(netrc_file):
@@ -110,9 +121,16 @@ def main_v2():
     product_name = f'{outname}.nc'
     netcdf_file = glob.glob('*nc')[0]
     os.rename(netcdf_file, product_name)
+    browse_name = f'{outname}.png'
+    browse_file = glob.glob('*.png')[0]
+    os.rename(browse_file, browse_name)
 
     if args.bucket:
         upload_file_to_s3(product_name, 'product', args.bucket, args.bucket_prefix)
+        upload_file_to_s3(browse_name, 'browse', args.bucket, args.bucket_prefix)
+        thumbnail_name = create_thumbnail(browse_name)
+        upload_file_to_s3(thumbnail_name, 'thumbnail', args.bucket, args.bucket_prefix)
+# End v2 functions
 
 
 def hyp3_process(cfg, n):
@@ -139,10 +157,6 @@ def hyp3_process(cfg, n):
         out_name = build_output_name_pair(g1, g2, cfg['workdir'], cfg['suffix'])
         log.info(f'Output name: {out_name}')
 
-        # TODO:
-        #  * browse images
-        #  * citation
-        #  * phase_png (?)
         if extra_arg_is(cfg, 'intermediate_files', 'no'):
             product_glob = os.path.join(cfg['workdir'], cfg['ftd'], '*.nc')
             netcdf_files = glob.glob(product_glob)

hyp3_autorift/process.py

@@ -10,9 +10,12 @@
 import shutil
 from pathlib import Path
 
+import numpy as np
 from hyp3lib.execute import execute
 from hyp3lib.file_subroutines import mkdir_p
 from hyp3lib.get_orb import downloadSentinelOrbitFile
+from hyp3lib.makeAsfBrowse import makeAsfBrowse
+from osgeo import gdal
 
 from hyp3_autorift import geometry
 from hyp3_autorift import io
@@ -22,10 +25,18 @@
 _PRODUCT_LIST = [
     'offset.tif',
     'velocity.tif',
+    'velocity_browse.tif',
+    'velocity_browse.kmz',
+    'velocity_browse.png',
+    'velocity_browse.png.aux.xml',
+    'window_chip_size_max.tif',
+    'window_chip_size_min.tif',
     'window_location.tif',
     'window_offset.tif',
     'window_rdr_off2vel_x_vec.tif',
     'window_rdr_off2vel_y_vec.tif',
+    'window_search_range.tif',
+    'window_stable_surface_mask.tif',
 ]
 
 
@@ -124,6 +135,25 @@ def process(reference, secondary, download=False, polarization='hh', orbits=None
               f' -csmax window_chip_size_max.tif -nc S'
         execute(cmd, logfile=f, uselogging=True)
 
+    velocity_tif = gdal.Open('velocity.tif')
+    x_velocity = np.ma.masked_invalid(velocity_tif.GetRasterBand(1).ReadAsArray())
+    y_velocity = np.ma.masked_invalid(velocity_tif.GetRasterBand(2).ReadAsArray())
+    velocity = np.sqrt(x_velocity**2 + y_velocity**2)
+
+    browse_file = Path('velocity_browse.tif')
+    driver = gdal.GetDriverByName('GTiff')
+    browse_tif = driver.Create(
+        str(browse_file), velocity.shape[1], velocity.shape[0], 1, gdal.GDT_Byte, ['COMPRESS=LZW']
+    )
+    browse_tif.SetProjection(velocity_tif.GetProjection())
+    browse_tif.SetGeoTransform(velocity_tif.GetGeoTransform())
+    velocity_band = browse_tif.GetRasterBand(1)
+    velocity_band.WriteArray(velocity)
+
+    del velocity_band, browse_tif, velocity_tif
+
+    makeAsfBrowse(str(browse_file), browse_file.stem)
+
     if product:
         mkdir_p(product_dir)
         for f in _PRODUCT_LIST:

setup.py

@@ -40,6 +40,7 @@
         'hyp3lib==1.5',
         'hyp3proclib',
         'importlib_metadata',
+        'pillow',
         'numpy',
         'scipy',
     ],