Merge pull request #82 from gshiroma/rtc_update_2024

Changes for v1.0.2

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v3.2.0
+    hooks:
+    -   id: check-added-large-files

Docker/Dockerfile

@@ -2,7 +2,7 @@ FROM oraclelinux:8
 
 LABEL author="OPERA ADT" \
     description="RTC cal/val release R4" \
-    version="1.0.1-final"
+    version="1.0.2-final"
 
 RUN yum -y update &&\
     yum -y install curl &&\

Docker/environment.yml

@@ -10,6 +10,6 @@ dependencies:
   - pyre>=1.11.2
 
   - scipy!=1.10.0
-  - isce3>=0.15.0
+  - isce3==0.15.0
   # Workaround for the issue with `libabseil` (09/11/2023)
   - libabseil=20230125.3

Docker/requirements.txt

@@ -21,4 +21,4 @@ setuptools
 shapely
 yamale
 backoff
-isce3>=0.14.0
+isce3==0.15.0

build_docker_image.sh

@@ -2,7 +2,7 @@
 
 REPO=opera
 IMAGE=rtc
-TAG=final_1.0.1
+TAG=final_1.0.2
 
 echo "IMAGE is $REPO/$IMAGE:$TAG"
 

src/rtc/core.py

@@ -83,7 +83,15 @@ def save_as_cog(filename, scratch_dir='.', logger=None,
         logger = logging.getLogger('rtc_s1')
 
     logger.info('        COG step 1: add overviews')
-    gdal_ds = gdal.Open(filename, gdal.GA_Update)
+
+    # open GeoTIFF file in update mode
+    try:
+        gdal_ds = gdal.Open(filename, gdal.GA_Update)
+    except RuntimeError:
+        # fix for GDAL >= 3.8
+        gdal_ds = gdal.OpenEx(filename, gdal.GA_Update,
+                              open_options=["IGNORE_COG_LAYOUT_BREAK=YES"])
+
     gdal_dtype = gdal_ds.GetRasterBand(1).DataType
     dtype_name = gdal.GetDataTypeName(gdal_dtype).lower()
 

src/rtc/h5_prep.py

@@ -415,6 +415,13 @@ def get_metadata_dict(product_id: str,
         # If the DEM description is not provided, use DEM source
         dem_file_description = os.path.basename(cfg_in.dem)
 
+    # reformat burst ID to URL data access format used by ASF
+    # (e.g., from "t018_038602_iw2" to "T018-038602-iw2")
+    burst_id_asf = str(burst_in.burst_id).upper().replace('_', '-')
+
+    # create substring "{end_date}"
+    end_date_str = burst_in.sensing_stop.strftime('%Y-%m-%d')
+
     # source data access (URL or DOI)
     source_data_access = cfg_in.groups.input_file_group.source_data_access
     if not source_data_access:
@@ -424,12 +431,20 @@ def get_metadata_dict(product_id: str,
     product_data_access = cfg_in.groups.product_group.product_data_access
     if not product_data_access:
         product_data_access = '(NOT PROVIDED)'
+    else:
+        # replace "{burst_id}"" and "{end_date}" substrings
+        product_data_access = product_data_access.format(
+            burst_id=burst_id_asf, end_date=end_date_str)
 
     # static layers data access (URL or DOI)
     static_layers_data_access = \
         cfg_in.groups.product_group.static_layers_data_access
     if not static_layers_data_access:
         static_layers_data_access = '(NOT PROVIDED)'
+    else:
+        # replace "{burst_id}"" and "{end_date}" substrings
+        static_layers_data_access = static_layers_data_access.format(
+            burst_id=burst_id_asf, end_date=end_date_str)
 
     # platform ID
     if burst_in.platform_id == 'S1A':

src/rtc/mosaic_geobursts.py

@@ -623,13 +623,13 @@ def mosaic_single_output_file(list_rtc_images, list_nlooks, mosaic_filename,
 
     for i_band in range(num_bands):
         gdal_band = raster_out.GetRasterBand(i_band+1)
-        gdal_band.WriteArray(arr_numerator[i_band])
         gdal_band.SetDescription(description_list[i_band])
         if ctable is not None:
             gdal_band.SetRasterColorTable(ctable)
             gdal_band.SetRasterColorInterpretation(gdal.GCI_PaletteIndex)
         if no_data_value is not None:
             gdal_band.SetNoDataValue(no_data_value)
+        gdal_band.WriteArray(arr_numerator[i_band])
 
     band_ds = None
     reference_raster = None
@@ -710,12 +710,12 @@ def mosaic_multiple_output_files(
 
         # for i_band in range(num_bands):
         band_out = raster_out.GetRasterBand(1)
-        band_out.WriteArray(arr_numerator[i_band])
         if ctable is not None:
             band_out.SetRasterColorTable(ctable)
             band_out.SetRasterColorInterpretation(gdal.GCI_PaletteIndex)
         if no_data_value is not None:
             band_out.SetNoDataValue(no_data_value)
+        band_out.WriteArray(arr_numerator[i_band])
 
     band_ds = None
     reference_raster = None

src/rtc/rtc_s1_single_job.py

@@ -822,13 +822,13 @@ def set_mask_fill_value_and_ctable(mask_file, reference_file):
     mask_gdal_band = mask_gdal_ds.GetRasterBand(1)
     mask_array = mask_gdal_band.ReadAsArray()
     mask_array[(np.isnan(ref_array)) & (mask_array == 0)] = 255
-    mask_gdal_band.WriteArray(mask_array)
     mask_gdal_band.SetNoDataValue(255)
 
     mask_ctable.SetColorEntry(255, (0, 0, 0, 0))
     mask_gdal_band.SetRasterColorTable(mask_ctable)
     mask_gdal_band.SetRasterColorInterpretation(
         gdal.GCI_PaletteIndex)
+    mask_gdal_band.WriteArray(mask_array)
 
     del mask_gdal_band
     del mask_gdal_ds

src/rtc/version.py

@@ -1 +1 @@
-VERSION='1.0.1'
+VERSION='1.0.2'