changes in .py file's Path

Indonesia_Countrybased_90thPct/.ipynb_checkpoints/ClippingAlgo-checkpoint.py

 import sys
 import argparse
 import subprocess
-# Even though for this example we dont require the python gdal client, we import it to ensure gdal is installed
-from osgeo import gdal
-
-
-def gdal_translate(input_filename, output_filename, reduction_percent):
-    gdal_cmd = ["gdal_translate", "-outsize", f"{reduction_percent}%", f"{reduction_percent}%",
-                input_filename, output_filename]
-    proc = subprocess.Popen(gdal_cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
-    out, err = proc.communicate()
-    print(out)
-    return proc.returncode, output_filename
-
-
-def env_check():
-    # Include any code here that might need to check for the correct env setup.
-    print("Installed GDAL Version: " + gdal.__version__)
-
-
-if __name__ == "__main__":
-    parse = argparse.ArgumentParser(description="Runs gdal_translate -outsize to reduce input size by n%")
-    parse.add_argument("--input_file", help="Input file to use", required=True)
-    parse.add_argument("--output_file", help="Output file to write", required=True)
-    parse.add_argument("--outsize", help="Reduction size", required=True)
-    args = parse.parse_args()
-    env_check()
-    exit_code, output = gdal_translate(args.input_file, args.output_file, args.outsize)
-    if exit_code != 0:
-        print(f"gdal_translate failed with a non-zero exit code: {exit_code}")
-        exit(exit_code)
+import geopandas as gpd
+import gdal
+
+# Define file paths
+aoi_file = '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Input/Indonesia.shp'
+input_gpkg1 = '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Input/merged_L4AIndonesia_Subsets.gpkg'
+output_gpkg1 = '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Output/merged_L4AIndonesia_Subsets_Clipped.gpkg'
+
+# Define chunk size
+chunk_size = 1000
+
+# Read AOI shapefile
+aoi = gpd.read_file(aoi_file)
+
+# Initialize a list to store clipped chunks
+clipped_chunks = []
+
+# Process input GeoPackage files in chunks
+for chunk in gpd.read_file(input_gpkg1, chunksize=chunk_size):
+    # Reproject AOI to match CRS of current chunk
+    aoi_reprojected = aoi.to_crs(chunk.crs)
+    
+    # Clip current chunk based on AOI
+    clipped_chunk = gpd.clip(chunk, aoi_reprojected)
+    
+    # Append clipped chunk to the list
+    clipped_chunks.append(clipped_chunk)
+
+# Concatenate clipped chunks into a single GeoDataFrame
+clipped_gdf1 = gpd.GeoDataFrame(pd.concat(clipped_chunks, ignore_index=True), crs=chunk.crs)
+
+# Save the clipped GeoPackage file
+clipped_gdf1.to_file(output_gpkg1, driver='GPKG')
+
+print("Clipping completed and saved to GeoPackage file.")
+

Indonesia_Countrybased_90thPct/.ipynb_checkpoints/check_versions-checkpoint.py

+import gdal
+import fiona
+import geopandas
+
+print(f"GDAL version: {gdal.__version__}")
+print(f"Fiona version: {fiona.__version__}")
+print(f"GeoPandas version: {geopandas.__version__}")
\ No newline at end of file

Indonesia_Countrybased_90thPct/.ipynb_checkpoints/output-checkpoint.txt

+Traceback (most recent call last):
+  File "fiona/ogrext.pyx", line 136, in fiona.ogrext.gdal_open_vector
+  File "fiona/_err.pyx", line 291, in fiona._err.exc_wrap_pointer
+fiona._err.CPLE_OpenFailedError: '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Input/merged_L4AIndonesia_Subsets.gpkg' not recognized as a supported file format.
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/ClippingAlgo.py", line 21, in <module>
+    for chunk in gpd.read_file(input_gpkg1, chunksize=chunk_size):
+  File "/opt/conda/envs/vanilla/lib/python3.10/site-packages/geopandas/io/file.py", line 297, in _read_file
+    return _read_file_fiona(
+  File "/opt/conda/envs/vanilla/lib/python3.10/site-packages/geopandas/io/file.py", line 338, in _read_file_fiona
+    with reader(path_or_bytes, **kwargs) as features:
+  File "/opt/conda/envs/vanilla/lib/python3.10/site-packages/fiona/env.py", line 457, in wrapper
+    return f(*args, **kwds)
+  File "/opt/conda/envs/vanilla/lib/python3.10/site-packages/fiona/__init__.py", line 292, in open
+    colxn = Collection(
+  File "/opt/conda/envs/vanilla/lib/python3.10/site-packages/fiona/collection.py", line 243, in __init__
+    self.session.start(self, **kwargs)
+  File "fiona/ogrext.pyx", line 588, in fiona.ogrext.Session.start
+  File "fiona/ogrext.pyx", line 143, in fiona.ogrext.gdal_open_vector
+fiona.errors.DriverError: '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Input/merged_L4AIndonesia_Subsets.gpkg' not recognized as a supported file format.

Indonesia_Countrybased_90thPct/ClippingAlgo.py

@@ -2,11 +2,12 @@ import sys
 import argparse
 import subprocess
 import geopandas as gpd
+import gdal
 
 # Define file paths
-aoi_file = '/projects/Indonesia_Countrybased_90thPct/Input/Indonesia.shp'
-input_gpkg1 = '/projects/Indonesia_Countrybased_90thPct/Input/merged_L4AIndonesia_Subsets.gpkg'
-output_gpkg1 = '/projects/Indonesia_Countrybased_90thPct/Output/merged_L4AIndonesia_Subsets_Clipped.gpkg'
+aoi_file = '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Input/Indonesia.shp'
+input_gpkg1 = '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Input/merged_L4AIndonesia_Subsets.gpkg'
+output_gpkg1 = '/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/Output/merged_L4AIndonesia_Subsets_Clipped.gpkg'
 
 # Define chunk size
 chunk_size = 1000

Indonesia_Countrybased_90thPct/check_versions.py

+import gdal
+import fiona
+import geopandas
+
+print(f"GDAL version: {gdal.__version__}")
+print(f"Fiona version: {fiona.__version__}")
+print(f"GeoPandas version: {geopandas.__version__}")
\ No newline at end of file

Indonesia_Countrybased_90thPct/output.txt

+Traceback (most recent call last):
+  File "/projects/indonesiahotspots/Indonesia_Countrybased_90thPct/ClippingAlgo.py", line 5, in <module>
+    import gdal
+ModuleNotFoundError: No module named 'gdal'