update for prod oracle folder mapping -> to be tested on the oracle

Dockerfile

@@ -41,7 +41,10 @@ COPY . /app
 
 WORKDIR /app
 
-ENTRYPOINT ["/miniconda/bin/conda", "run", "-n", "pdal-env", "python", "/app/run_oracle_wrapper.py"]
+# ENTRYPOINT ["/miniconda/bin/conda", "run", "-n", "pdal-env", "python", "/app/run_oracle_wrapper.py"]
+
+ENTRYPOINT ["/miniconda/bin/conda", "run", "-n", "pdal-env", "python", "/app/run_oracle_wrapper_local.py"]
+
 
 
 

check_list.info

+Dockerfile - set correct oracle wrapper
+build.sh
+run_oracle_wrapper.py or run_oracle_wrapper_local.py -> set paths
+config.yaml -> pick segmentation or instance segmentation
\ No newline at end of file

config/config.yaml

@@ -3,7 +3,7 @@ general:
   output_folder: 'local_output_folder'
   clean_output_folder: false
   run_sematic_segmentation: true
-  run_instance_segmentation: true
+  run_instance_segmentation: false
 label_formats:
   label_for_instances_in_gt: 'treeID'
   label_for_instances_in_predicted: 'instance_nr'

d_run.sh

@@ -4,6 +4,10 @@ docker image rm nibio/pc-geoslam-oracle
 ./build.sh
 echo "Running the container"
 # docker run --gpus all --name test_oracle nibio/pc-geoslam-oracle
-docker run -it --gpus all --name test_oracle nibio/pc-geoslam-oracle
+docker run -it --gpus all \
+    --name test_oracle \
+    --mount type=bind,source=/home/nibio/mutable-outside-world/code/oracle_deploy/instance_segmentation_classic/local_folder_out/las_files,target=/app/local_folder_out/las_files \
+    nibio/pc-geoslam-oracle
+
 
 

run_oracle_wrapper_local.py

+# This is the the file to be run on the oracle cloud
+
+import oci
+import argparse
+import os
+import io
+import shutil
+import yaml
+
+from run import main
+
+def run_oracle_wrapper(path_to_config_file):
+
+    # read the config file from config folder
+    with open(path_to_config_file) as f:
+        config_flow_params = yaml.load(f, Loader=yaml.FullLoader)
+
+    # read system environment variables
+    # input_location = os.environ['OBJ_INPUT_LOCATION']
+    # output_location = os.environ['OBJ_OUTPUT_LOCATION']
+
+    # remap the input and output locations
+    # input_location = input_location.replace("@axqlz2potslu", "").replace("oci://", "/mnt/")
+    # output_location = output_location.replace("@axqlz2potslu", "").replace("oci://", "/mnt/")
+
+    input_location = "local_folder_in/las_files/"
+    output_location = "local_folder_out/las_files/"
+
+    # copy files from input_location to the input folder
+    shutil.copytree(input_location, config_flow_params['general']['input_folder'])
+
+    # run the main function
+    main(path_to_config_file)
+
+    # instance segmentation is set to true
+    if config_flow_params['general']['run_instance_segmentation']:
+        path_to_the_output_folder = os.path.join(config_flow_params['general']['output_folder'], 'instance_segmented_point_clouds_with_ground')
+    else:
+        path_to_the_output_folder = config_flow_params['general']['output_folder']
+
+    # zip the files in path_to_the_output_folder
+    zip_file_name  = 'results'
+    shutil.make_archive(zip_file_name, 'zip', path_to_the_output_folder) # this will be done in the current folder
+    shutil.copy('results.zip', path_to_the_output_folder)
+
+    # copy the zip file and other files to the output location
+    for filename in os.listdir(path_to_the_output_folder):
+        src_file = os.path.join(path_to_the_output_folder, filename)
+        dst_file = os.path.join(output_location, filename)
+        shutil.copy(src_file, dst_file)
+
+if __name__ == '__main__':
+    # use argparse to get the path to the config file
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--path_to_config_file", type=str, default="./config/config.yaml")
+    args = parser.parse_args()
+
+    # run the main function
+    print('Running the main function in run_oracle_wrapper.py')
+    run_oracle_wrapper(args.path_to_config_file)
+