ign-pdal-tools 1.15.1__tar.gz → 1.15.3__tar.gz

{ign_pdal_tools-1.15.1 → ign_pdal_tools-1.15.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ign-pdal-tools
-Version: 1.15.1
+Version: 1.15.3
 Summary: Library for common LAS files manipulation with PDAL
 Author-email: Guillaume Liegard <guillaume.liegard@ign.fr>
 Description-Content-Type: text/markdown

{ign_pdal_tools-1.15.1 → ign_pdal_tools-1.15.3}/ign_pdal_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ign-pdal-tools
-Version: 1.15.1
+Version: 1.15.3
 Summary: Library for common LAS files manipulation with PDAL
 Author-email: Guillaume Liegard <guillaume.liegard@ign.fr>
 Description-Content-Type: text/markdown

{ign_pdal_tools-1.15.1 → ign_pdal_tools-1.15.3}/pdaltools/_version.py

@@ -1,4 +1,4 @@
-__version__ = "1.15.1"
+__version__ = "1.15.3"
 
 
 if __name__ == "__main__":

{ign_pdal_tools-1.15.1 → ign_pdal_tools-1.15.3}/pdaltools/add_points_in_pointcloud.py

@@ -6,6 +6,7 @@ import geopandas as gpd
 import laspy
 import numpy as np
 import pdal
+from shapely import set_precision
 from shapely.geometry import MultiPoint, Point, box
 
 from pdaltools.las_info import get_epsg_from_las, get_tile_bbox
@@ -327,6 +328,10 @@ def add_points_from_geometry_to_las(
     # Clip points from GeoJSON by LIDAR tile
     points_clipped = clip_3d_points_to_tile(points_gdf, input_las, spatial_ref, tile_width)
 
+    # Remove duplicate points (due to precision issue) - las file have centrimetric precision
+    points_clipped.geometry = set_precision(points_clipped.geometry, grid_size=0.01)
+    points_clipped = points_clipped.drop_duplicates()
+
     # Add points by LIDAR tile and save the result
     add_points_to_las(points_clipped, input_las, output_las, spatial_ref, virtual_points_classes)
 

{ign_pdal_tools-1.15.1 → ign_pdal_tools-1.15.3}/pdaltools/replace_area_in_pointcloud.py

@@ -33,13 +33,14 @@ def argument_parser():
         help="path of the source digital surface model (DSM), used to generate source points",
     )
     from_DSM.add_argument(
-        "--source_ground_area",
+        "--source_ground_mask",
         "-g",
         required=True,
         type=str,
         help=(
-            "area of the ground, used to intersect source cloud. "
-            "(shapefile, geojson or other format readable by GDAL)"
+            "ground mask, a raster file used to filter source cloud. "
+            "Pixel with value > 0 is considered as ground, and define the source cloud we keep. "
+            "(tif or other raster format readable by GDAL)"
         ),
     )
     from_DSM.add_argument(
@@ -65,7 +66,7 @@ def add_common_options(parser):
         "-r",
         required=True,
         type=str,
-        help="area to replace (shapefile, geojson or other format readable by GDAL)",
+        help="area to replace (shapefile, geojson or other vector format readable by GDAL)",
     )
     parser.add_argument("--output_cloud", "-o", required=True, type=str, help="output cloud file")
 
@@ -84,7 +85,7 @@ def from_DSM_func(args):
     replace_area(
         target_cloud=args.target_cloud,
         pipeline_source=pipeline_read_from_DSM(
-            dsm=args.source_dsm, ground_area=args.source_ground_area, classification=args.source_classification
+            dsm=args.source_dsm, ground_mask=args.source_ground_mask, classification=args.source_classification
         ),
         replacement_area=args.replacement_area,
         output_cloud=args.output_cloud,
@@ -101,27 +102,35 @@ def get_writer_params(input_file):
 
 
 def pipeline_read_from_cloud(filename):
+    print("source cloud: ", filename)
     pipeline_source = pdal.Pipeline()
     pipeline_source |= pdal.Reader.las(filename=filename)
     return pipeline_source
 
 
-def pipeline_read_from_DSM(dsm, ground_area, classification):
+def pipeline_read_from_DSM(dsm, ground_mask, classification):
+    print("DSM: ", dsm)
+    print("ground_mask: ", ground_mask)
+    print("classification: ", classification)
+
     # get nodata value
     ds = gdal.Open(dsm)
     band = ds.GetRasterBand(1)
     nodata_value = band.GetNoDataValue()
+    print("DSM: nodata:", nodata_value)
     ds.Close()
 
     pipeline = pdal.Pipeline()
     pipeline |= pdal.Reader.gdal(filename=dsm, header="Z")
-    pipeline |= pdal.Filter.expression(expression=f"Z != {nodata_value}")
 
-    pipeline |= pdal.Filter.ferry(dimensions="=> geometryFid")
-    pipeline |= pdal.Filter.assign(assignment="geometryFid[:]=-1")
-    pipeline |= pdal.Filter.overlay(column="fid", dimension="geometryFid", datasource=ground_area)
+    if nodata_value is not None:  # nodata_value may be None and cause bugs
+        pipeline |= pdal.Filter.expression(expression=f"Z != {nodata_value}")
+
+    pipeline |= pdal.Filter.ferry(dimensions="=> ground")
+    pipeline |= pdal.Filter.assign(assignment="ground[:]=-1")
+    pipeline |= pdal.Filter.colorization(dimensions="ground:1:1.0", raster=ground_mask)
     # Keep only points in the area
-    pipeline |= pdal.Filter.expression(expression="geometryFid>=0")
+    pipeline |= pdal.Filter.expression(expression="ground>0")
 
     # assign class
     pipeline |= pdal.Filter.ferry(dimensions="=>Classification")
@@ -133,6 +142,11 @@ def pipeline_read_from_DSM(dsm, ground_area, classification):
 def replace_area(
     target_cloud, pipeline_source, replacement_area, output_cloud, source_pdal_filter="", target_pdal_filter=""
 ):
+    print("target cloud: ", target_cloud)
+    print("replacement area: ", replacement_area)
+    print("output cloud: ", output_cloud)
+    print("source pdal filter: ", source_pdal_filter)
+    print("target pdal filter: ", target_pdal_filter)
     crops = []
     # pipeline to read target_cloud and remove points inside the polygon
     pipeline_target = pdal.Pipeline()

{ign_pdal_tools-1.15.1 → ign_pdal_tools-1.15.3}/test/test_add_points_in_pointcloud.py

@@ -109,7 +109,7 @@ def test_add_points_to_las(input_file, epsg, input_points_2d, expected_nb_points
     metadata_out = las_info_metadata(OUTPUT_FILE)
     output_dimensions = metadata_out["dimensions"]
 
-    assert input_dimensions == output_dimensions # All dimension should be preserve
+    assert input_dimensions == output_dimensions  # All dimension should be preserve
 
     point_count = compute_count_one_file(OUTPUT_FILE)["68"]
     assert point_count == expected_nb_points  # Add all points from geojson
@@ -261,7 +261,7 @@ def test_generate_3d_points_from_lines(lines_gdf, spacing, altitude_column, expe
             INPUT_PCD,
             INPUT_LIGNES_2D_GEOJSON,
             "EPSG:2154",
-            678,
+            677,
             0.25,
             "RecupZ",
         ),  # should add only lines (.GeoJSON) within tile extend
@@ -269,16 +269,16 @@ def test_generate_3d_points_from_lines(lines_gdf, spacing, altitude_column, expe
             INPUT_PCD,
             INPUT_LIGNES_SHAPE,
             "EPSG:2154",
-            678,
+            677,
             0.25,
             "RecupZ",
         ),  # should add only lines (.shp) within tile extend
-        (INPUT_PCD, INPUT_LIGNES_SHAPE, None, 678, 0.25, "RecupZ"),  # Should work with or with an input epsg
+        (INPUT_PCD, INPUT_LIGNES_SHAPE, None, 677, 0.25, "RecupZ"),  # Should work with or with an input epsg
         (
             INPUT_PCD,
             INPUT_LIGNES_3D_GEOJSON,
             None,
-            678,
+            677,
             0.25,
             None,
         ),  # Should work with or without an input epsg and without altitude_column
@@ -353,6 +353,52 @@ def test_add_points_from_geometry_to_las_nok(input_file, input_points, epsg, spa
         )
 
 
+@pytest.mark.parametrize(
+    "spacing",
+    [
+        0.1,
+        0.01,
+        0.001,
+        0.25,
+        0.5,
+        1,
+    ],
+)
+def test_add_points_from_geometry_to_las_no_dupplicate(spacing):
+    # there should have no duplicate in final las
+
+    input_las_file = os.path.join(TEST_PATH, "data/crop_duplicate.laz")
+    input_geo_file = os.path.join(TEST_PATH, "data/crop_duplicate.geojson")
+
+    add_points_in_pointcloud.add_points_from_geometry_to_las(
+        input_geo_file, input_las_file, OUTPUT_FILE, 68, "EPSG:2154", 1000, spacing, None
+    )
+    assert Path(OUTPUT_FILE).exists()  # check output exists
+
+    las = laspy.read(OUTPUT_FILE)
+
+    # Get all points with classification 68
+    class_68_points = las.points[las.classification == 68]
+    num_class_68_points = len(class_68_points)
+
+    # Print some information
+    print(f"Total points in file: {len(las.points)}")
+    print(f"Points with class 68: {num_class_68_points}")
+
+    # Verify we have some points with class 68
+    assert num_class_68_points > 0, "Expected to find points with class 68"
+
+    # Check for duplicate points (same X, Y, Z coordinates)
+    points_array = np.column_stack((class_68_points.x, class_68_points.y, class_68_points.z))
+    unique_points = np.unique(points_array, axis=0)
+
+    print(f"Number of unique points: {len(unique_points)}")
+    print(f"Number of total points: {len(points_array)}")
+
+    # Verify no duplicates
+    assert len(unique_points) == len(points_array), "Found duplicate points in class 68"
+
+
 def test_parse_args():
     # sanity check for arguments parsing
     args = add_points_in_pointcloud.parse_args(

{ign_pdal_tools-1.15.1 → ign_pdal_tools-1.15.3}/test/test_replace_area_in_pointcloud.py

@@ -30,7 +30,7 @@ SOURCE_CLOUD = os.path.join(INPUT_DIR, "source_cloud_crop.laz")
 
 # source may be a digital surface model
 SOURCE_DSM = os.path.join(INPUT_DIR, "DSM.tif")
-SOURCE_GROUND_AREA = os.path.join(INPUT_DIR, "ground_area.geojson")
+SOURCE_GROUND_MASK = os.path.join(INPUT_DIR, "ground_mask.tif")
 SOURCE_CLASSIF = 68
 
 TMP_EXTRA_DIMS = os.path.join(TMP_PATH, "input_with_extra_dims")
@@ -285,7 +285,7 @@ def test_replace_area_with_no_output_point_with_extra_dims():
 def test_pipeline_read_from_DSM():
     cloud_from_DSM = os.path.join(TMP_PATH, "las_from_DSM.laz")
 
-    pipeline = pipeline_read_from_DSM(dsm=SOURCE_DSM, ground_area=SOURCE_GROUND_AREA, classification=SOURCE_CLASSIF)
+    pipeline = pipeline_read_from_DSM(dsm=SOURCE_DSM, ground_mask=SOURCE_GROUND_MASK, classification=SOURCE_CLASSIF)
     pipeline |= pdal.Writer.las(cloud_from_DSM, forward="all", extra_dims="all")
     pipeline.execute()
 
@@ -326,9 +326,10 @@ def test_main_from_cloud_with_filter():
 
 
 def test_main_from_DSM():
-    output_file = os.path.join(TMP_PATH, "output_main_from_cloud.laz")
+    output_file = os.path.join(TMP_PATH, "main_from_DSM", "output_main_from_DSM.laz")
+    os.makedirs(os.path.dirname(output_file))
     cmd = (
-        f"from_DSM -d {SOURCE_DSM} -g {SOURCE_GROUND_AREA} -c {SOURCE_CLASSIF} -t {TARGET_CLOUD} -r {REPLACE_AREA}"
+        f"from_DSM -d {SOURCE_DSM} -g {SOURCE_GROUND_MASK} -c {SOURCE_CLASSIF} -t {TARGET_CLOUD} -r {REPLACE_AREA}"
         f" -o {output_file}"
     ).split()
     args = argument_parser().parse_args(cmd)