diff --git a/main.py b/main.py
index 1fae7ec0421f8cf5238310abc9fa8356e217b15c..8ef5c8a435cb817d75a4ff05db38869041101514 100644
--- a/main.py
+++ b/main.py
@@ -23,8 +23,6 @@ from download_gedi import download_gedi
## GET CONSTANTS
CWD = os.getcwd()
-print("current working directory...")
-print(CWD)
## Function to return beam dataframe with some meta data
def get_beam_gdf(beam,l1b_ds,l2a_ds):
@@ -106,9 +104,9 @@ if __name__ == '__main__':
l2a_basename = os.path.basename(l2a_url)
# Read in domain polys and allom data
- domain_poly_fp = os.path.join(CWD, "./NEON_Domains/NEON_Domains.shp")
+ domain_poly_fp = os.path.join(CWD, "NEON_Domains/NEON_Domains.shp")
domain_polys = gpd.read_file(domain_poly_fp)
- allom_fp = os.path.join(CWD, "./NEON-DOMAINS-HSE-edited.csv")
+ allom_fp = os.path.join(CWD, "NEON-DOMAINS-HSE-edited.csv")
allom_df = pd.read_csv(allom_fp)
diff --git a/notebooks/run-gedi-biomass.ipynb b/notebooks/run-gedi-biomass.ipynb
index 18131e181ab32e3080d585e230c4931d47ffd557..21f618883f0d6c598d3aeb0d0531a27c03ea219e 100644
--- a/notebooks/run-gedi-biomass.ipynb
+++ b/notebooks/run-gedi-biomass.ipynb
@@ -97,7 +97,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "[{'job_id': '973bf65b-2305-441d-87eb-32b6e91e1c43', 'status': 'Accepted', 'machine_type': None, 'architecture': None, 'machine_memory_size': None, 'directory_size': None, 'operating_system': None, 'job_start_time': None, 'job_end_time': None, 'job_duration_seconds': None, 'cpu_usage': None, 'cache_usage': None, 'mem_usage': None, 'max_mem_usage': None, 'swap_usage': None, 'read_io_stats': None, 'write_io_stats': None, 'sync_io_stats': None, 'async_io_stats': None, 'total_io_stats': None, 'error_details': None, 'response_code': 200, 'outputs': []}]\n"
+ "[{'job_id': 'ba87642f-df6e-47f5-b509-0d94ca990b2d', 'status': 'Accepted', 'machine_type': None, 'architecture': None, 'machine_memory_size': None, 'directory_size': None, 'operating_system': None, 'job_start_time': None, 'job_end_time': None, 'job_duration_seconds': None, 'cpu_usage': None, 'cache_usage': None, 'mem_usage': None, 'max_mem_usage': None, 'swap_usage': None, 'read_io_stats': None, 'write_io_stats': None, 'sync_io_stats': None, 'async_io_stats': None, 'total_io_stats': None, 'error_details': None, 'response_code': 200, 'outputs': []}]\n"
]
}
],
@@ -116,7 +116,7 @@
"output_type": "stream",
"text": [
"Accepted\n",
- "973bf65b-2305-441d-87eb-32b6e91e1c43\n"
+ "ba87642f-df6e-47f5-b509-0d94ca990b2d\n"
]
}
],
@@ -130,7 +130,7 @@
},
{
"cell_type": "code",
- "execution_count": 13,
+ "execution_count": 5,
"id": "2018077f-9640-4e70-bd01-a9d939b3626a",
"metadata": {},
"outputs": [
@@ -139,7 +139,7 @@
"output_type": "stream",
"text": [
"Failed\n",
- "973bf65b-2305-441d-87eb-32b6e91e1c43\n"
+ "ba87642f-df6e-47f5-b509-0d94ca990b2d\n"
]
}
],
@@ -153,7 +153,7 @@
},
{
"cell_type": "code",
- "execution_count": 14,
+ "execution_count": 6,
"id": "873e9ea7-d6cb-4bb9-b082-5bffb4026615",
"metadata": {},
"outputs": [
@@ -161,7 +161,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "['http://maap-ops-workspace.s3-website-us-west-2.amazonaws.com/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/973bf65b-2305-441d-87eb-32b6e91e1c43', 's3://s3-us-west-2.amazonaws.com:80/maap-ops-workspace/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/973bf65b-2305-441d-87eb-32b6e91e1c43', 'https://s3.console.aws.amazon.com/s3/buckets/maap-ops-workspace/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/973bf65b-2305-441d-87eb-32b6e91e1c43/?region=us-east-1&tab=overview', '+ export HOME=/root\\n+ HOME=/root\\n+ exec /docker-stats-on-exit-shim _docker_stats.json /app/dps_wrapper.sh /app/biomass-gedi-conus/run.sh \\'https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\\n\\' https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\\n+ /app/biomass-gedi-conus/run.sh \\'https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\\n\\' https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\\nMatplotlib created a temporary cache directory at /tmp/matplotlib-rr0rwtpl because the default path (/root/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\\nFontconfig error: No writable cache directories\\nTraceback (most recent call last):\\n File \"fiona/ogrext.pyx\", line 136, in fiona.ogrext.gdal_open_vector\\n File \"fiona/_err.pyx\", line 291, in fiona._err.exc_wrap_pointer\\nfiona._err.CPLE_OpenFailedError: ./NEON_Domains/NEON_Domains.shp: No such file or directory\\n\\nDuring handling of the above exception, another exception occurred:\\n\\nTraceback (most recent call last):\\n File \"/app/biomass-gedi-conus/main.py\", line 104, in <module>\\n domain_polys = gpd.read_file(\"./NEON_Domains/NEON_Domains.shp\")\\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/geopandas/io/file.py\", line 281, in _read_file\\n return _read_file_fiona(\\n ^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/geopandas/io/file.py\", line 322, in _read_file_fiona\\n with reader(path_or_bytes, **kwargs) as features:\\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/env.py\", line 457, in wrapper\\n return f(*args, **kwds)\\n ^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/__init__.py\", line 292, in open\\n colxn = Collection(\\n ^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/collection.py\", line 243, in __init__\\n self.session.start(self, **kwargs)\\n File \"fiona/ogrext.pyx\", line 588, in fiona.ogrext.Session.start\\n File \"fiona/ogrext.pyx\", line 143, in fiona.ogrext.gdal_open_vector\\nfiona.errors.DriverError: ./NEON_Domains/NEON_Domains.shp: No such file or directory\\n+ cp _stderr.txt _alt_traceback.txt\\n']\n"
+ "['http://maap-ops-workspace.s3-website-us-west-2.amazonaws.com/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/ba87642f-df6e-47f5-b509-0d94ca990b2d', 's3://s3-us-west-2.amazonaws.com:80/maap-ops-workspace/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/ba87642f-df6e-47f5-b509-0d94ca990b2d', 'https://s3.console.aws.amazon.com/s3/buckets/maap-ops-workspace/dataset/triaged_job/arojas_biomass_gedi_conus/master/2023/09/27/ba87642f-df6e-47f5-b509-0d94ca990b2d/?region=us-east-1&tab=overview', '+ export HOME=/root\\n+ HOME=/root\\n+ exec /docker-stats-on-exit-shim _docker_stats.json /app/dps_wrapper.sh /app/biomass-gedi-conus/run.sh \\'https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\\n\\' https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\\n+ /app/biomass-gedi-conus/run.sh \\'https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI01_B.002/2021.05.31/GEDI01_B_2021151223415_O13976_02_T00676_02_005_02_V002.h5\\n\\' https://e4ftl01.cr.usgs.gov//GEDI_L1_L2/GEDI/GEDI02_A.002/2021.05.31/GEDI02_A_2021151223415_O13976_02_T00676_02_003_02_V002.h5\\nMatplotlib created a temporary cache directory at /tmp/matplotlib-ej7h32oy because the default path (/root/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\\nFontconfig error: No writable cache directories\\nTraceback (most recent call last):\\n File \"fiona/ogrext.pyx\", line 136, in fiona.ogrext.gdal_open_vector\\n File \"fiona/_err.pyx\", line 291, in fiona._err.exc_wrap_pointer\\nfiona._err.CPLE_OpenFailedError: /data/work/jobs/2023/09/27/04/01/job-arojas_biomass_gedi_conus__master-20230927T035526.152033Z/./NEON_Domains/NEON_Domains.shp: No such file or directory\\n\\nDuring handling of the above exception, another exception occurred:\\n\\nTraceback (most recent call last):\\n File \"/app/biomass-gedi-conus/main.py\", line 110, in <module>\\n domain_polys = gpd.read_file(domain_poly_fp)\\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/geopandas/io/file.py\", line 281, in _read_file\\n return _read_file_fiona(\\n ^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/geopandas/io/file.py\", line 322, in _read_file_fiona\\n with reader(path_or_bytes, **kwargs) as features:\\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/env.py\", line 457, in wrapper\\n return f(*args, **kwds)\\n ^^^^^^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/__init__.py\", line 292, in open\\n colxn = Collection(\\n ^^^^^^^^^^^\\n File \"/opt/conda/envs/osgeo-env/lib/python3.11/site-packages/fiona/collection.py\", line 243, in __init__\\n self.session.start(self, **kwargs)\\n File \"fiona/ogrext.pyx\", line 588, in fiona.ogrext.Session.start\\n File \"fiona/ogrext.pyx\", line 143, in fiona.ogrext.gdal_open_vector\\nfiona.errors.DriverError: /data/work/jobs/2023/09/27/04/01/job-arojas_biomass_gedi_conus__master-20230927T035526.152033Z/./NEON_Domains/NEON_Domains.shp: No such file or directory\\n+ cp _stderr.txt _alt_traceback.txt\\n']\n"
]
}
],
diff --git a/run.sh b/run.sh
index dc438ff32083f0481d935e178d39e3e132deb7cc..1572e6a553d2e666712b9b5d2425ef8893ffed27 100644
--- a/run.sh
+++ b/run.sh
@@ -5,13 +5,11 @@ basedir=$( cd "$(dirname "$0")" ; pwd -P)
# Activate environment that was created in the builed-env.sh file
source activate osgeo-env
-# view contents of where thi file is
-echo viewing contents of run.sh folder...
-ls
+
# Create output dir
OUTPUTDIR="${PWD}/output"
mkdir -p ${OUTPUTDIR}
-# INPUT_FILE=$(ls -d *.txt)
+# INPUT_FILES
L1B_URL=$1
L2A_URL=$2 # e.g. GEDI01_B or GEDI02_A
# YR=$3