IGNF · yoann-apel · Jan 8, 2025 · Jan 8, 2025 · Dec 18, 2024 · Dec 20, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,7 @@
+# v0.1.1
+- Mise à jour du ReadMe
+- Dans la fonction extract_points_skeleton, les fichiers las n'ont plus besoin d'être dans un sous-dossier `pointcloud`
+
 # v0.1.0
 - Correction du bug au moment de la jonction entre les parties du squelette qui créait des
 interpolations imprévues entre des extrémités de branches qui ne devraient pas être reliées.

diff --git a/Dockerfile b/Dockerfile
@@ -1,19 +1,31 @@
-FROM mambaorg/micromamba:latest
+FROM mambaorg/micromamba:latest AS mamba_pdal
+COPY environment.yml /environment.yml
+COPY requirements.txt /requirements.txt
 
+# Using USER root seems to fix permission issues when building mamba environment with pip packages
 USER root
-
 WORKDIR /lidro
 
-# # Set up the Conda environment: cf https://github.com/mamba-org/micromamba-docker
-COPY environment.yml /tmp/env.yaml
-COPY requirements.txt /tmp/requirements.txt
-RUN chown $MAMBA_USER:$MAMBA_USER /tmp/env.yaml
-RUN micromamba install -y -n base -f /tmp/env.yaml && \
-    micromamba clean --all --yes
+RUN micromamba env create -n lidro -f /environment.yml
+
+
+FROM debian:bullseye-slim
+
+# install PDAL
+COPY --from=mamba_pdal /opt/conda/envs/lidro/bin/pdal /opt/conda/envs/lidro/bin/pdal
+COPY --from=mamba_pdal /opt/conda/envs/lidro/bin/python /opt/conda/envs/lidro/bin/python
+COPY --from=mamba_pdal /opt/conda/envs/lidro/lib/ /opt/conda/envs/lidro/lib/
+COPY --from=mamba_pdal /opt/conda/envs/lidro/ssl /opt/conda/envs/lidro/ssl
+COPY --from=mamba_pdal /opt/conda/envs/lidro/share/proj/proj.db /opt/conda/envs/lidro/share/proj/proj.db
+
+ENV PATH=$PATH:/opt/conda/envs/lidro/bin/
+ENV PROJ_LIB=/opt/conda/envs/lidro/share/proj/
 
 ENV ENV=base
 ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
+WORKDIR /lidro
+
 COPY lidro lidro
 COPY configs configs
 COPY test test
diff --git a/README.md b/README.md
diff --git a/data b/data
diff --git a/images/alerte_squelette.png b/images/alerte_squelette.png
diff --git a/images/correction_alerte_squelette.png b/images/correction_alerte_squelette.png
diff --git a/images/correction_manuelle_masque_hydro.jpg b/images/correction_manuelle_masque_hydro.jpg
diff --git a/images/cuvettes_artefects.jpg b/images/cuvettes_artefects.jpg
diff --git a/images/decoupage_masque_fusionne.jpg b/images/decoupage_masque_fusionne.jpg
diff --git a/images/extraction_n_points_squelette.jpg b/images/extraction_n_points_squelette.jpg
diff --git a/images/masque_hydro_dalles.jpg b/images/masque_hydro_dalles.jpg
diff --git a/images/masque_hydro_merge.jpg b/images/masque_hydro_merge.jpg
diff --git a/images/mnt_avant_apres.jpg b/images/mnt_avant_apres.jpg
diff --git a/images/nettoyage_squelette.jpg b/images/nettoyage_squelette.jpg
diff --git a/images/points_virtuels.jpg b/images/points_virtuels.jpg
diff --git a/images/squelette_hydro.jpg b/images/squelette_hydro.jpg
diff --git a/lidro/_version.py b/lidro/_version.py
@@ -1,4 +1,4 @@
-__version__ = "0.1.0"
+__version__ = "0.1.1"
 
 if __name__ == "__main__":
     print(__version__)
diff --git a/lidro/create_virtual_point/vectors/extract_points_around_skeleton.py b/lidro/create_virtual_point/vectors/extract_points_around_skeleton.py
@@ -8,7 +8,7 @@
 
 import geopandas as gpd
 import pandas as pd
-from pdaltools.las_info import las_get_xy_bounds
+from lidro.las_info import las_get_xy_bounds
 from shapely.geometry import Point
 
 from lidro.create_virtual_point.pointcloud.crop_las import (
@@ -45,9 +45,8 @@ def extract_points_around_skeleton_points_one_tile(
         k (int): the number of nearest neighbors to find
     """
     # Step 1 : Crop filtered pointcloud by Mask Hydro with buffer
-    input_dir_points = os.path.join(input_dir, "pointcloud")
     tilename = os.path.splitext(filename)[0]  # filename to the LAS file
-    input_pointcloud = os.path.join(input_dir_points, filename)  # path to the LAS file
+    input_pointcloud = os.path.join(input_dir, filename)  # path to the LAS file
     logging.info(f"\nCroping filtered pointcloud by Mask Hydro with buffer for tile : {tilename}")
     # Croping filtered pointcloud by Mask Hydro with buffer for tile
     points_clip = read_filter_and_crop_pointcloud(input_pointcloud, str(input_mask_hydro_buffer), classes)

diff --git a/test/create_virtual_point/vectors/test_extract_points_around_skeleton.py b/test/create_virtual_point/vectors/test_extract_points_around_skeleton.py
@@ -11,7 +11,7 @@
 )
 
 TMP_PATH = Path("./tmp/create_virtual_point/vectors/extract_points_around_skeleton")
-INPUT_DIR = Path("./data/tile_0830_6291")
+INPUT_DIR = Path("./data/tile_0830_6291/pointcloud")
 MASK_HYDRO = "./data/tile_0830_6291/mask_hydro_merge/MaskHydro_merge.geojson"
 POINTS_SKELETON = "./data/tile_0830_6291/skeleton/points_along_skeleton.geojson"
 OUTPUT_GEOJSON = TMP_PATH / "Semis_2021_0830_6291_LA93_IGN69_points_skeleton.geojson"

diff --git a/test/test_main_extract_points_from_skeleton.py b/test/test_main_extract_points_from_skeleton.py
@@ -18,7 +18,7 @@ def setup_module(module):
 def test_main_run_okay():
 
     cmd = f"""python -m lidro.main_extract_points_from_skeleton \
-        io.input_dir={INPUT_DIR}\
+        io.input_dir={INPUT_DIR}/pointcloud \
         io.input_filename=Semis_2021_0830_6291_LA93_IGN69.laz \
         io.input_mask_hydro="{INPUT_DIR}/mask_hydro_merge/MaskHydro_merge.geojson"\
         io.input_skeleton="{INPUT_DIR}/skeleton/skeleton_hydro.geojson"\
@@ -28,7 +28,7 @@ def test_main_run_okay():
 
 
 def test_main_extract_points_skeleton_input_file():
-    input_dir = INPUT_DIR
+    input_dir = INPUT_DIR / "pointcloud"
     output_dir = OUTPUT_DIR / "main_extract_points_skeleton_input_file"
     input_filename = "Semis_2021_0830_6291_LA93_IGN69.laz"
     input_mask_hydro = INPUT_DIR / "mask_hydro_merge/MaskHydro_merge.geojson"
@@ -111,7 +111,7 @@ def test_main_extract_points_skeleton_fail_wrong_input_dir():
 
 
 def test_main_extract_points_skeleton_fail_no_output_dir():
-    input_dir = INPUT_DIR
+    input_dir = INPUT_DIR / "pointcloud"
     input_mask_hydro = INPUT_DIR / "mask_hydro_merge/MaskHydro_merge.geojson"
     input_skeleton = INPUT_DIR / "skeleton/skeleton_hydro.geojson"
     distances_meters = 5
@@ -137,7 +137,7 @@ def test_main_extract_points_skeleton_fail_no_output_dir():
 
 
 def test_main_extract_points_skeleton_fail_no_input_mask_hydro():
-    input_dir = INPUT_DIR
+    input_dir = INPUT_DIR / "pointcloud"
     output_dir = OUTPUT_DIR / "main_no_input_dir"
     input_skeleton = INPUT_DIR / "skeleton/skeleton_hydro.geojson"
     distances_meters = 5
@@ -163,7 +163,7 @@ def test_main_extract_points_skeleton_fail_no_input_mask_hydro():
 
 
 def test_main_extract_points_skeleton_fail_no_input_skeleton():
-    input_dir = INPUT_DIR
+    input_dir = INPUT_DIR / "pointcloud"
     output_dir = OUTPUT_DIR / "main_no_input_dir"
     input_mask_hydro = INPUT_DIR / "mask_hydro_merge/MaskHydro_merge.geojson"
     distances_meters = 5