From c44a86b0fb8a09ef82bab4aa4273a75e137f97a1 Mon Sep 17 00:00:00 2001
From: Maciej Wielgosz <maciej.wielgosz@nibio.no>
Date: Fri, 7 Jul 2023 15:52:07 +0200
Subject: [PATCH] update for /home/datasciencefolder mapping in the oracle
cloud
---
Dockerfile | 9 ++++++---
check_list.info | 8 +++++++-
d_run.sh | 5 +++--
helpers/clean_oracle_log_from_timestemp.py | 23 ++++++++++++++++++++++
run_oracle_wrapper_local.py | 8 ++++++--
5 files changed, 45 insertions(+), 8 deletions(-)
create mode 100644 helpers/clean_oracle_log_from_timestemp.py
diff --git a/Dockerfile b/Dockerfile
index a3b9d19..a4a661e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -37,14 +37,17 @@ RUN pip install parse oci ocifs
COPY requirements.txt app/requirements.txt
RUN pip install --no-cache -r app/requirements.txt
-COPY . /app
+# COPY . /app
+# WORKDIR /app
-WORKDIR /app
+COPY . /home/datascience/app
+WORKDIR /home/datascience/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_local.py"]
+# ENTRYPOINT ["/miniconda/bin/conda", "run", "-n", "pdal-env", "python", "/app/run_oracle_wrapper_local.py"]
+ENTRYPOINT ["/miniconda/bin/conda", "run", "-n", "pdal-env", "python", "/home/datascience/app/run_oracle_wrapper_local.py"]
diff --git a/check_list.info b/check_list.info
index a2df05e..a5ae4cc 100644
--- a/check_list.info
+++ b/check_list.info
@@ -1,4 +1,10 @@
Dockerfile - set correct oracle wrapper
+
+# core steps
build.sh
run_oracle_wrapper.py or run_oracle_wrapper_local.py -> pick a right mode (DEBUG or not)
-config.yaml -> pick segmentation or instance segmentation
\ No newline at end of file
+config.yaml -> pick segmentation or instance segmentation
+
+# pushing docker
+docker tag nibio/pc-geoslam-oracle-inst-seg:latest fra.ocir.io/axqlz2potslu/nibio/pc-geoslam-oracle-inst-seg
+docker push fra.ocir.io/axqlz2potslu/nibio/pc-geoslam-oracle-sem-seg
\ No newline at end of file
diff --git a/d_run.sh b/d_run.sh
index 0897181..1199955 100644
--- a/d_run.sh
+++ b/d_run.sh
@@ -6,8 +6,9 @@ echo "Running the container"
# docker run --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_oracle,target=/app/local_folder_oracle \
- nibio/pc-geoslam-oracle
+ --mount type=bind,source=/home/nibio/mutable-outside-world/code/oracle_deploy/instance_segmentation_classic/local_folder_oracle,target=/home/datascience/app/local_folder_oracle \
+ --mount type=bind,source=/home/nibio/mutable-outside-world/code/oracle_deploy/instance_segmentation_classic/local_folder_oracle_hard,target=/home/datascience/app/local_folder_oracle_hard \
+ nibio/pc-geoslam-oracle > test_oracle.log 2>&1
diff --git a/helpers/clean_oracle_log_from_timestemp.py b/helpers/clean_oracle_log_from_timestemp.py
new file mode 100644
index 0000000..9610601
--- /dev/null
+++ b/helpers/clean_oracle_log_from_timestemp.py
@@ -0,0 +1,23 @@
+import sys
+
+def remove_prefix(lines):
+ processed_lines = [line.split(' - ', 1)[1] if ' - ' in line else line for line in lines]
+ return processed_lines
+
+def process_file(input_filename, output_filename):
+ with open(input_filename, 'r') as input_file:
+ data = input_file.read()
+ lines = data.split('\n')
+ processed_lines = remove_prefix(lines)
+ processed_data = '\n'.join(processed_lines)
+ with open(output_filename, 'w') as output_file:
+ output_file.write(processed_data)
+
+if __name__ == '__main__':
+ if len(sys.argv) < 3:
+ print("Please provide both input and output filenames as command-line arguments.")
+ else:
+ input_filename = sys.argv[1]
+ output_filename = sys.argv[2]
+ process_file(input_filename, output_filename)
+ print(f"Processed data saved to {output_filename}.")
diff --git a/run_oracle_wrapper_local.py b/run_oracle_wrapper_local.py
index 83f9049..f23d69b 100644
--- a/run_oracle_wrapper_local.py
+++ b/run_oracle_wrapper_local.py
@@ -20,8 +20,12 @@ def run_oracle_wrapper(path_to_config_file):
# read system environment variables
if DEBUG_MODE:
- input_location = "local_folder_oracle/las_files/"
- output_location = "local_folder_oracle/results/"
+ input_location = "local_folder_oracle_hard/las_files/"
+ output_location = "local_folder_oracle_hard/results/"
+
+ # input_location = "local_folder_oracle/las_files/"
+ # output_location = "local_folder_oracle/results/"
+
# remove content of the output folder if it exists
if os.path.exists(output_location):
shutil.rmtree(output_location, ignore_errors=True)
--
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