initial commit of GCOV pipeline for ADE use

environment.yml

@@ -1,10 +1,13 @@
 name: sar2-d2
 channels:
   - conda-forge
-  - nodefaults
+  - nodefaults  # force everything to come from conda-forge channel
 dependencies:
-  - isce3
+  - isce3=0.24.1  # R4.0.4 delivery
   - python >=3.12
+  - pip:
+      - git+https://github.com/MAAP-Project/maap-py.git
+  - sardem  # to download and crop the SRTM DEM
 
 # # Used by conda lock
 # platforms:

nasa/run.sh

@@ -7,33 +7,41 @@ input_dir="${PWD}/input"
 output_dir="${PWD}/output"
 
 if [[ $# == 0 || "$1" == "-h" ]]; then
-    echo "usage: nasa/run.sh [-h] CALIBRATION_FILE LEFT BOTTOM RIGHT TOP
+    echo "usage: nasa/run.sh [-h] INPUT_FILE LEFT BOTTOM RIGHT TOP INPUT_PRODUCT_TYPE OUTPUT_PRODUCT_TYPE GCOV_POSTING
 
 SAR2-D2: Synthetic Aperture Radar Remote Disturbance Detector
 
 positional arguments:
-  CALIBRATION_FILE      path to calibration file
-  LEFT                  left longitude of your desired bounding box
-  BOTTOM                bottom latitude of your desired bounding box
-  RIGHT                 right longitude of your desired bounding box
-  TOP                   top latitude of your desired bounding box
-
-options:
-  -h, --help            show this help message and exit"
+  INPUT_FILE            path to input file
+  LEFT                  left longitude of bounding box of the input file
+  BOTTOM                bottom latitude of the input file
+  RIGHT                 right longitude of the input file
+  TOP                   top latitude of the input file
+  INPUT_PRODUCT_TYPE    Product type of the input file. One of: 'alos1', 'l0b', 'rslc'.
+                        Will be processed through the ALOS1->L0B->RSLC->GCOV pipeline,
+                        ending with type specified by `out_type`.
+  OUTPUT_PRODUCT_TYPE   Product type of the output file. One of: 'l0b', 'rslc', 'gcov'.
+                        In combination with `in_type`, determines which processing steps
+                        occur.
+  GCOV_POSTING          Posting for pixel spacing for GCOV (square pixels). Must be
+                        in units of EPSG 4326 (same as DEM and bbox coordinates)."
     exit 1
 fi
 
 if test -d "${input_dir}"; then
     # RUNNING IN DPS
     #
     # There is an `input` sub-directory of the current working directory, so assume the
-    # calibration file is the sole file within the `input` sub-directory that the DPS
+    # input file is the sole file within the `input` sub-directory that the DPS
     # automatically downloaded for us, based upon the URL given as the value of the
-    # calibration_file job input.
+    # in_file job input.
     ls -l "${input_dir}" >&2
 
-    calibration_file="$(ls "${input_dir}"/*)"
+    in_file="$(ls "${input_dir}"/*)"
     bbox="$1"
+    in_type="$2"
+    out_type="$3"
+    posting="$4"
 else
     # RUNNING IN DEVELOPMENT ENVIRONMENT
     #
@@ -42,21 +50,27 @@ else
     # non-DPS environment, where there is no `input` directory since the DPS creates
     # the `input` directory.  In this case, we must pass a path to a "local" file,
     # which can be a path to a file in a shared bucket in the ADE.
-    calibration_file="$1"
+    in_file="$1"
 
-    if [[ $# -eq 5 ]]; then
+    if [[ $# -eq 8 ]]; then
         # Allow us to pass the coordinates as individual arguments, so we don't need to
         # remember to put quotes around them:
         #
         #   nasa/run.sh path/to/calibration-file LEFT BOTTOM RIGHT TOP
         #
         bbox="$2 $3 $4 $5"
+        in_type="$6"
+        out_type="$7"
+        posting="$8"        
     else
         # Also allow us to put quotes around the 4 coordinates:
         #
         #   nasa/run.sh path/to/calibration-file "LEFT BOTTOM RIGHT TOP"
         #
         bbox="$2"
+        in_type="$3"
+        out_type="$4"
+        posting="$5"
     fi
 fi
 
@@ -67,7 +81,15 @@ fi
 # arguments.
 
 # shellcheck disable=SC2086
-"${basedir}"/bin/conda/run.sh python "${basedir}/sar2_d2/cli.py" \
-    --calibration-file "${calibration_file}" \
+"${basedir}"/bin/conda/run.sh python "${basedir}/src/alos1_2_gcov/alos1_to_gcov.py" \
+    --in-file "${in_file}" \
     --bbox ${bbox} \
-    --output-dir "${output_dir}"
+    --out-dir "${output_dir}" \
+    --in_type "${in_type}" \
+    --out_type "${out_type}" \
+    --gcov_posting "${posting}" \
+    # --dem /projects/alos1-dist/sar2-d2/nasa/output/dem.tif
+
+
+
+