From 6383b4097a7828a546ecc7a9a7749050d28fb01a Mon Sep 17 00:00:00 2001
From: Maciej Wielgosz <maciej.wielgosz@nibio.no>
Date: Tue, 23 May 2023 09:23:32 +0200
Subject: [PATCH] fixes for orcale deploy e.g. tiling center
---
Dockerfile | 2 --
config/config.yaml | 8 ++++----
d_run.sh | 9 +++++++++
nibio_preprocessing/tiling.py | 4 +++-
requirements.txt | Bin 2166 -> 2192 bytes
run_bash_scripts/sem_seg_sean.sh | 2 +-
6 files changed, 17 insertions(+), 8 deletions(-)
create mode 100644 d_run.sh
diff --git a/Dockerfile b/Dockerfile
index 23a4071..db1c725 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -44,6 +44,4 @@ WORKDIR /app
ENTRYPOINT ["/miniconda/bin/conda", "run", "-n", "pdal-env", "python", "/app/run_oracle_wrapper.py"]
-# CMD ["--help" ]
-
diff --git a/config/config.yaml b/config/config.yaml
index 3bba841..f3ef2f2 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -1,9 +1,9 @@
general:
- input_folder: './local_input_folder'
- output_folder: './local_output_folder'
+ input_folder: 'local_input_folder'
+ output_folder: 'local_output_folder'
clean_output_folder: false
run_sematic_segmentation: true
- run_instance_segmentation: false
+ run_instance_segmentation: true
label_formats:
label_for_instances_in_gt: 'treeID'
label_for_instances_in_predicted: 'instance_nr'
@@ -13,7 +13,7 @@ semantic_segmentation_params:
batch_size : 5 # batch size for inference
tile_size: 10 # tile size in meters
min_density: 100 # minimum density of points in a tile(used for removing small tiles)
- remove_small_tiles: 1 # 1: remove small tiles, 0: not remove small tiles
+ remove_small_tiles: 0 # 1: remove small tiles, 0: not remove small tiles
instance_segmentation_params:
instance_segmentation_script: './run_bash_scripts/tls.sh'
n_tiles: 3
diff --git a/d_run.sh b/d_run.sh
new file mode 100644
index 0000000..4feaeb6
--- /dev/null
+++ b/d_run.sh
@@ -0,0 +1,9 @@
+
+docker container rm test_oracle
+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
+
+
diff --git a/nibio_preprocessing/tiling.py b/nibio_preprocessing/tiling.py
index b9186ef..f113426 100644
--- a/nibio_preprocessing/tiling.py
+++ b/nibio_preprocessing/tiling.py
@@ -44,7 +44,9 @@ class Tiling:
{
"type":"filters.splitter",
"length":str(self.tile_size),
- "buffer":str(self.tile_buffer)
+ "buffer":str(self.tile_buffer),
+ "origin_x":"0.0",
+ "origin_y":"0.0"
},
{
"type":"writers.ply",
diff --git a/requirements.txt b/requirements.txt
index 9e761f979fd0727e61cbb3784f62c165ce705528..347f9ab5365df5006e3750b50d7661017fd907c9 100644
GIT binary patch
delta 34
mcmew+FhOub8HZFlLn=c)Ljgk~Lmop4Ln1>l11|#?7y|&G;RetE
delta 7
OcmbOr_)TC#83zCiZvxf;
diff --git a/run_bash_scripts/sem_seg_sean.sh b/run_bash_scripts/sem_seg_sean.sh
index b431eaa..3c598c5 100755
--- a/run_bash_scripts/sem_seg_sean.sh
+++ b/run_bash_scripts/sem_seg_sean.sh
@@ -3,7 +3,7 @@
############################ parameters #################################################
# General parameters
CLEAR_INPUT_FOLDER=1 # 1: clear input folder, 0: not clear input folder
-CONDA_ENV="pdal-env-1" # conda environment for running the pipeline
+CONDA_ENV="pdal-env" # conda environment for running the pipeline
# Parameters for the semetnic segmentation
data_folder="" # path to the folder containing the data
--
GitLab