Merge pull request #166 from IGNF/dev

nlenglet-ign · web-flow · commit 05d44097639a · 2025-10-22T14:02:39.000+02:00
v 1.15.6
diff --git a/.github/workflows/cicd_light_windows.yml b/.github/workflows/cicd_light_windows.yml
@@ -0,0 +1,37 @@
+name: cicd_light_windows
+
+on:
+  # Run tests for non-draft pull request on dev
+  pull_request:
+    branches:
+      - dev
+
+
+jobs:
+  test_light_windows:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [windows-latest]
+    permissions:
+        contents: read
+        packages: write
+
+    steps:
+      - name: Checkout branch
+        uses: actions/checkout@v4
+
+      # See https://github.com/marketplace/actions/setup-micromamba
+      - name: setup-micromamba
+        uses: mamba-org/setup-micromamba@v1.9.0
+        with:
+          micromamba-version: '1.5.8-0'  # temporary fix as setup-mircomamba hangs with later mamba version
+          environment-file: environment.yml
+          environment-name: pdaltools  # activate the environment
+          cache-environment: true
+          cache-downloads: true
+          generate-run-shell: true
+
+      - name: Run tests with pytest
+        shell: cmd
+        run: micromamba run -n pdaltools python -m pytest ./test -s --log-cli-level DEBUG -m "not geopf"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,6 @@
+# 1.15.6
+- [fix] fix use of tempory file in windows
+
 # 1.15.5
 - [optimization] replace_area_plointcloud: select polygons in replace_area that intersect target LAS.
   - make the normal case faster
diff --git a/environment.yml b/environment.yml
@@ -2,7 +2,7 @@ name: pdaltools
 channels:
   - conda-forge
 dependencies:
-  - python=3.11.*
+  - python=3.12.*
   - numpy
   - conda-forge:pdal>=2.9.*
   - conda-forge:python-pdal>=3.4
diff --git a/pdaltools/_version.py b/pdaltools/_version.py
@@ -1,4 +1,4 @@
-__version__ = "1.15.5"
+__version__ = "1.15.6"
 
 
 if __name__ == "__main__":
diff --git a/pdaltools/add_points_in_pointcloud.py b/pdaltools/add_points_in_pointcloud.py
@@ -156,7 +156,7 @@ def add_points_to_las(
     new_points.z = z_coords.astype(new_points.z.dtype)
     new_points.classification = classes.astype(new_points.classification.dtype)
 
-    with tempfile.NamedTemporaryFile(suffix="_new_points.las") as tmp:
+    with tempfile.NamedTemporaryFile(suffix="_new_points.las", delete_on_close=False) as tmp:
         with laspy.open(tmp.name, mode="w", header=header) as las_file:
             las_file.write_points(new_points)
 
diff --git a/pdaltools/color.py b/pdaltools/color.py
@@ -101,7 +101,7 @@ def color(
 
     tmp_ortho = None
     if color_rvb_enabled:
-        tmp_ortho = tempfile.NamedTemporaryFile(suffix="_rvb.tif")
+        tmp_ortho = tempfile.NamedTemporaryFile(suffix="_rvb.tif", delete_on_close=False)
         download_image(
             proj,
             stream_RGB,
@@ -124,7 +124,7 @@ def color(
 
     tmp_ortho_irc = None
     if color_ir_enabled:
-        tmp_ortho_irc = tempfile.NamedTemporaryFile(suffix="_irc.tif")
+        tmp_ortho_irc = tempfile.NamedTemporaryFile(suffix="_irc.tif", delete_on_close=False)
         download_image(
             proj,
             stream_IRC,
diff --git a/pdaltools/create_random_laz.py b/pdaltools/create_random_laz.py
@@ -1,10 +1,11 @@
-import numpy as np
-import laspy
-from pathlib import Path
 import argparse
-from pyproj import CRS
+from pathlib import Path
 from typing import List, Tuple
 
+import laspy
+import numpy as np
+from pyproj import CRS
+
 
 def create_random_laz(
     output_file: str,
@@ -27,7 +28,7 @@ def create_random_laz(
                 (default: (650000, 6810000) ; around Paris)
         extra_dims: List of tuples (dimension_name, dimension_type) where type can be:
                    'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64'
-        classifications: Optional list of classification values. 
+        classifications: Optional list of classification values.
     """
 
     # Create a new point cloud
@@ -103,7 +104,6 @@ def create_random_laz(
 
 
 def test_output_file(result: dict, output_file: str):
-
     # Validate output file path
     output_path = Path(output_file)
     if not output_path.exists():
@@ -126,12 +126,14 @@ def parse_args():
     )
     parser.add_argument("--crs", type=int, default=2154, help="Projection code")
     parser.add_argument(
-        "--center", type=float, nargs=2, default=[650000.0, 6810000.0],
-        help="Center coordinates (x y) of the area to generate points in (space-separated)"
+        "--center",
+        type=float,
+        nargs=2,
+        default=[650000.0, 6810000.0],
+        help="Center coordinates (x y) of the area to generate points in (space-separated)",
     )
     parser.add_argument(
-        "--classifications", type=int, nargs='+',
-        help="List of classification values (space-separated)"
+        "--classifications", type=int, nargs="+", help="List of classification values (space-separated)"
     )
     return parser.parse_args()
 
@@ -145,19 +147,13 @@ def main():
 
     # Parse center
     center = tuple(args.center[:2])  # Only take first 2 values if more are provided
-    
+
     # Parse classifications if provided
     classifications = args.classifications
 
     # Call create_random_laz
     result = create_random_laz(
-        args.output_file, 
-        args.point_format, 
-        args.num_points, 
-        args.crs, 
-        center, 
-        extra_dims,
-        classifications
+        args.output_file, args.point_format, args.num_points, args.crs, center, extra_dims, classifications
     )
 
     # Test output file
diff --git a/pdaltools/download_image.py b/pdaltools/download_image.py
@@ -185,7 +185,7 @@ def download_image(proj, layer, minx, miny, maxx, maxy, pixel_per_meter, outfile
                 tmp_gpg_ortho.append(cells_ortho_paths)
 
         # merge the cells
-        with tempfile.NamedTemporaryFile(suffix="_gpf.vrt") as tmp_vrt:
+        with tempfile.NamedTemporaryFile(suffix="_gpf.vrt", delete_on_close=False) as tmp_vrt:
             gdal.BuildVRT(tmp_vrt.name, tmp_gpg_ortho)
             gdal.Translate(outfile, tmp_vrt.name)
 
diff --git a/pdaltools/las_add_buffer.py b/pdaltools/las_add_buffer.py
@@ -153,7 +153,7 @@ def remove_points_from_buffer(input_file: str, output_file: str):
         input_file (str): path to the input file containing the "is_in_original" dimension
         output_file (str): path to the output_file
     """
-    with tempfile.NamedTemporaryFile(suffix="_with_additional_dim.las") as tmp_las:
+    with tempfile.NamedTemporaryFile(suffix="_with_additional_dim.las", delete_on_close=False) as tmp_las:
         pipeline = pdal.Pipeline() | pdal.Reader.las(input_file)
         pipeline |= pdal.Filter.range(limits=f"{ORIGINAL_TILE_TAG}[1:1]")
         pipeline |= pdal.Writer.las(filename=tmp_las.name, forward="all", extra_dims="all")
@@ -217,8 +217,8 @@ def wrapper(*args, **kwargs):
                 )
 
             with (
-                tempfile.NamedTemporaryFile(suffix="_buffered_input.laz", dir=".") as buf_in,
-                tempfile.NamedTemporaryFile(suffix="_buffered_output.laz", dir=".") as buf_out,
+                tempfile.NamedTemporaryFile(suffix="_buffered_input.laz", dir=".", delete_on_close=False) as buf_in,
+                tempfile.NamedTemporaryFile(suffix="_buffered_output.laz", dir=".", delete_on_close=False) as buf_out,
             ):
                 create_las_with_buffer(
                     Path(input_file).parent,
diff --git a/pdaltools/las_comparison.py b/pdaltools/las_comparison.py
@@ -1,9 +1,10 @@
-import laspy
-from pathlib import Path
-import numpy as np
 import argparse
+from pathlib import Path
 from typing import Tuple
 
+import laspy
+import numpy as np
+
 
 def compare_las_dimensions(file1: Path, file2: Path, dimensions: list = None) -> Tuple[bool, int, float]:
     """
diff --git a/pdaltools/las_rename_dimension.py b/pdaltools/las_rename_dimension.py
@@ -6,11 +6,13 @@
 
 import argparse
 import logging
-import pdal
 import sys
 from pathlib import Path
-from pdaltools.las_remove_dimensions import remove_dimensions_from_points
+
+import pdal
+
 from pdaltools.las_info import las_info_metadata
+from pdaltools.las_remove_dimensions import remove_dimensions_from_points
 
 
 def rename_dimension(input_file: str, output_file: str, old_dims: list[str], new_dims: list[str]):
diff --git a/pdaltools/replace_area_in_pointcloud.py b/pdaltools/replace_area_in_pointcloud.py
@@ -271,7 +271,7 @@ def replace_area(
     points = pipeline.execute()
 
     end = time.time()
-    print(f"Step 3: merge: { points }, points in {end-t3:.2f} seconds")
+    print(f"Step 3: merge: {points}, points in {end-t3:.2f} seconds")
     print("all steps done in ", f"{end-start:.2f}", " seconds")
 
 
diff --git a/pdaltools/standardize_format.py b/pdaltools/standardize_format.py
@@ -9,13 +9,14 @@
 """
 
 import argparse
+import os
 import tempfile
 from typing import Dict, List
 
 import pdal
 
-from pdaltools.unlock_file import copy_and_hack_decorator
 from pdaltools.las_rename_dimension import rename_dimension
+from pdaltools.unlock_file import copy_and_hack_decorator
 
 # Standard parameters to pass to the pdal writer
 STANDARD_PARAMETERS = dict(
@@ -76,34 +77,50 @@ def get_writer_parameters(new_parameters: Dict) -> Dict:
     params = STANDARD_PARAMETERS | new_parameters
     return params
 
+
 @copy_and_hack_decorator
 def standardize(
-    input_file: str, output_file: str, params_from_parser: Dict, classes_to_remove: List = [], rename_dims: List = []
+    input_file: str, 
+    output_file: str, 
+    params_from_parser: Dict, 
+    classes_to_remove: List = [], 
+    rename_dims: List = []
 ) -> None:
+    """
+    Standardize a LAS/LAZ file with improved error handling and resource management.
+    
+    Args:
+        input_file: Input file path
+        output_file: Output file path
+        params_from_parser: Parameters for the PDAL writer
+        classes_to_remove: List of classification classes to remove
+        rename_dims: List of dimension names to rename (pairs of old_name, new_name)
+    """
     params = get_writer_parameters(params_from_parser)
-
-    # Create temporary file for dimension renaming if needed
-    if rename_dims:
-        with tempfile.NamedTemporaryFile(suffix=".laz", delete=False) as tmp_file:
-            tmp_file_name = tmp_file.name
-
-            # Rename dimensions
-            old_dims = rename_dims[::2]
-            new_dims = rename_dims[1::2]
-            rename_dimension(input_file, tmp_file_name, old_dims, new_dims)
-
-            # Use renamed file as input
-            input_file = tmp_file_name
-    else:
-        tmp_file_name = input_file
-
-    pipeline = pdal.Pipeline()
-    pipeline |= pdal.Reader.las(tmp_file_name)
-    if classes_to_remove:
-        expression = "&&".join([f"Classification != {c}" for c in classes_to_remove])
-        pipeline |= pdal.Filter.expression(expression=expression)
-    pipeline |= pdal.Writer(filename=output_file, forward="all", **params)
-    pipeline.execute()
+    tmp_file_name = None
+
+    try:
+        # Create temporary file for dimension renaming if needed
+        if rename_dims:
+            with tempfile.NamedTemporaryFile(suffix=".laz", delete=False) as tmp_file:
+                tmp_file_name = tmp_file.name
+                old_dims = rename_dims[::2]
+                new_dims = rename_dims[1::2]
+                rename_dimension(input_file, tmp_file_name, old_dims, new_dims)
+                input_file = tmp_file_name
+
+        pipeline = pdal.Pipeline()
+        pipeline |= pdal.Reader.las(input_file)
+        if classes_to_remove:
+            expression = "&&".join([f"Classification != {c}" for c in classes_to_remove])
+            pipeline |= pdal.Filter.expression(expression=expression)
+        pipeline |= pdal.Writer(filename=output_file, forward="all", **params)
+        pipeline.execute()
+
+    finally:
+        # Clean up temporary file
+        if tmp_file_name and os.path.exists(tmp_file_name):
+            os.remove(tmp_file_name)
 
 
 def main():
diff --git a/pdaltools/unlock_file.py b/pdaltools/unlock_file.py
@@ -39,10 +39,9 @@ def newfn(*args, **kwargs):
             if "readers.las: Global encoding WKT flag not set for point format 6 - 10." in str(e):
                 args = list(args)
                 in_file = args[0]
-                with tempfile.NamedTemporaryFile(suffix=os.path.splitext(in_file)[-1]) as tmp:
+                with tempfile.NamedTemporaryFile(suffix=os.path.splitext(in_file)[-1], delete_on_close=False) as tmp:
                     copy_and_hack_input_file(in_file, tmp.name)
                     args[0] = tmp.name
-
                     return func(*args, **kwargs)
 
             else:
diff --git a/test/test_add_points_in_pointcloud.py b/test/test_add_points_in_pointcloud.py
@@ -1,10 +1,12 @@
 import inspect
 import os
+import tempfile
 from pathlib import Path
 
 import geopandas as gpd
 import laspy
 import numpy as np
+import pdal
 import pytest
 from shapely.geometry import LineString, MultiPoint, Point
 
@@ -424,3 +426,49 @@ def test_parse_args():
     parsed_args_keys = args.__dict__.keys()
     main_parameters = inspect.signature(add_points_in_pointcloud.add_points_from_geometry_to_las).parameters.keys()
     assert set(parsed_args_keys) == set(main_parameters)
+
+
+def test_namedtemporaryfile_delete_on_close_false():
+    """Test that NamedTemporaryFile could be used on windows in the context with delete_on_close=False"""
+    temp_file_path = None
+
+    with tempfile.NamedTemporaryFile(suffix="_test.las", delete_on_close=False) as tmp:
+        temp_file_path = tmp.name
+        # Verify that the file exists during the context
+        assert os.path.exists(temp_file_path)
+
+        # Write some data to the temporary file
+        with open(temp_file_path, "w") as f:
+            f.write("test data")
+        f.close()
+
+    # Verify that the file still exists after exiting the context
+    assert not os.path.exists(
+        temp_file_path
+    ), f"Temporary file {temp_file_path} should not exist oustside the context with delete_on_close=False"
+
+
+def test_namedtemporaryfile_delete_false_with_pdal():
+    """Test that NamedTemporaryFile could be used on windows in the context
+    with delete_on_close=False and some pdal operations"""
+
+    def read_las(input_las, tmp):
+        pipeline = pdal.Pipeline()
+        pipeline |= pdal.Reader.las(filename=input_las)
+        pipeline |= pdal.Writer.las(filename=tmp.name, forward="all", extra_dims="all")
+        pipeline.execute()
+
+    input_las = os.path.join(TEST_PATH, "data/crop_duplicate.laz")
+    temp_file_path = None
+    with tempfile.NamedTemporaryFile(suffix="_test.las", delete_on_close=False) as tmp:
+        temp_file_path = tmp.name
+        read_las(input_las, tmp)
+        pipeline = pdal.Pipeline()
+        pipeline |= pdal.Reader.las(filename=tmp.name)
+        pipeline.execute()
+        assert os.path.exists(tmp.name)
+
+    # Verify that the file still exists after exiting the context
+    assert not os.path.exists(
+        temp_file_path
+    ), f"Temporary file {temp_file_path} should not exist oustside the context with delete_on_close=False"
diff --git a/test/test_create_random_laz.py b/test/test_create_random_laz.py
diff --git a/test/test_las_comparison.py b/test/test_las_comparison.py
diff --git a/test/test_las_remove_dimensions.py b/test/test_las_remove_dimensions.py
diff --git a/test/test_las_rename_dimension.py b/test/test_las_rename_dimension.py
diff --git a/test/test_pdal.py b/test/test_pdal.py
diff --git a/test/test_standardize_format.py b/test/test_standardize_format.py

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-__version__ = "1.15.5"`
	`1`	`+__version__ = "1.15.6"`
`2`	`2`
`3`	`3`
`4`	`4`	`if __name__ == "__main__":`