Merge pull request #104 from IGNF/replace_name_dimension

rename dimension

Author: alavenant

CHANGELOG.md

@@ -1,4 +1,5 @@
 - custom PDAL: fix CI for cicd_full (build docker image with custom PDAL, and skip custom PDAL test for local pytest)
+- las_rename_dimension: new tool to rename one or many dimensions
 
 # 1.9.1
 - las_add_points_to_pointcloud: Fix add points to LAS (use PDAL instead of Laspy)

pdaltools/count_occurences/count_occurences_for_attribute.py

@@ -1,5 +1,5 @@
 """Count occurences of each value of a given attribute in a set of pointclouds.
-Eg. to count points of each class in classified point clouds """
+Eg. to count points of each class in classified point clouds"""
 
 import argparse
 import json

pdaltools/las_remove_dimensions.py

@@ -5,22 +5,36 @@
 from pdaltools.las_info import get_writer_parameters_from_reader_metadata
 
 
-def remove_dimensions_from_las(input_las: str, dimensions: [str], output_las: str):
+def remove_dimensions_from_points(points, metadata, dimensions: [str], output_las: str):
     """
     export new las without some dimensions
     """
-    pipeline = pdal.Pipeline() | pdal.Reader.las(input_las)
-    pipeline.execute()
-    points = pipeline.arrays[0]
+
+    mandatory_dimensions = ["X", "Y", "Z", "x", "y", "z"]
+    output_dimensions_test = [dim for dim in dimensions if dim not in mandatory_dimensions]
+    assert len(output_dimensions_test) == len(
+        dimensions
+    ), "All dimensions to remove must not be mandatory dimensions (X,Y,Z,x,y,z)"
+
     input_dimensions = list(points.dtype.fields.keys())
     output_dimensions = [dim for dim in input_dimensions if dim not in dimensions]
     points_pruned = points[output_dimensions]
-    params = get_writer_parameters_from_reader_metadata(pipeline.metadata)
+    params = get_writer_parameters_from_reader_metadata(metadata)
     pipeline_end = pdal.Pipeline(arrays=[points_pruned])
     pipeline_end |= pdal.Writer.las(output_las, forward="all", **params)
     pipeline_end.execute()
 
 
+def remove_dimensions_from_las(input_las: str, dimensions: [str], output_las: str):
+    """
+    export new las without some dimensions
+    """
+    pipeline = pdal.Pipeline() | pdal.Reader.las(input_las)
+    pipeline.execute()
+    points = pipeline.arrays[0]
+    remove_dimensions_from_points(points, pipeline.metadata, dimensions, output_las)
+
+
 def parse_args():
     parser = argparse.ArgumentParser("Remove dimensions from las")
     parser.add_argument(

pdaltools/las_rename_dimension.py

@@ -0,0 +1,79 @@
+"""
+Rename dimensions in a LAS file using PDAL's Python API.
+
+This script allows renaming dimensions in a LAS file while preserving all other data.
+"""
+
+import argparse
+import pdal
+import sys
+from pathlib import Path
+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]):
+    """
+Rename one or multiple dimensions in a LAS file using PDAL.
+
+Args:
+    input_file: Path to the input LAS file
+    output_file: Path to save the output LAS file
+    old_dims: List of names of dimensions to rename
+    new_dims: List of new names for the dimensions
+"""
+
+    # Validate dimensions
+    if len(old_dims) != len(new_dims):
+        raise ValueError("Number of old dimensions must match number of new dimensions")
+
+    mandatory_dimensions = ['X', 'Y', 'Z', 'x', 'y', 'z']
+    for dim in new_dims:
+        if dim in mandatory_dimensions:
+            raise ValueError(f"New dimension {dim} cannot be a mandatory dimension (X,Y,Z,x,y,z)")
+
+    pipeline = pdal.Pipeline() | pdal.Reader.las(input_file)
+    for old, new in zip(old_dims, new_dims):
+        pipeline |= pdal.Filter.ferry(dimensions=f"{old} => {new}")
+    pipeline |= pdal.Writer.las(output_file)
+    pipeline.execute()
+    points = pipeline.arrays[0]
+
+    # Remove old dimensions
+    remove_dimensions_from_points(points, pipeline.metadata, old_dims, output_file)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Rename dimensions in a LAS file")
+    parser.add_argument("input_file", help="Input LAS file")
+    parser.add_argument("output_file", help="Output LAS file")
+    parser.add_argument(
+        "--old-dims",
+        nargs="+",
+        required=True,
+        help="Names of dimensions to rename (can specify multiple)",
+    )
+    parser.add_argument(
+        "--new-dims",
+        nargs="+",
+        required=True,
+        help="New names for the dimensions (must match --old-dims count)",
+    )
+
+    args = parser.parse_args()
+    
+    # Validate input file
+    input_path = Path(args.input_file)
+    if not input_path.exists():
+        print(f"Error: Input file {args.input_file} does not exist", file=sys.stderr)
+        sys.exit(1)
+    
+    # Validate output file
+    output_path = Path(args.output_file)
+    if output_path.exists():
+        print(f"Warning: Output file {args.output_file} already exists. It will be overwritten.")
+    
+    rename_dimension(args.input_file, args.output_file, args.old_dims, args.new_dims)
+
+
+if __name__ == "__main__":
+    main()

pdaltools/unlock_file.py

@@ -1,5 +1,4 @@
-"""Tools to handle malformed las/laz files
-    """
+"""Tools to handle malformed las/laz files"""
 
 # https://gis.stackexchange.com/questions/413191/python-pdal-error-reading-format-1-4-las-file-readers-las-error-global-enco
 

test/test_las_rename_dimension.py

@@ -0,0 +1,159 @@
+import os
+import pytest
+import tempfile
+import numpy as np
+import laspy
+import sys
+from pdaltools.las_rename_dimension import rename_dimension, main
+from pyproj import CRS
+
+def create_test_las_file():
+    """Create a temporary LAS file with test data."""
+    with tempfile.NamedTemporaryFile(suffix='.las', delete=False) as tmp_file:
+        # Create a LAS file with some test points
+        header = laspy.LasHeader(point_format=3, version="1.4")
+        header.add_extra_dim(laspy.ExtraBytesParams(name="test_dim", type=np.float32))
+        header.add_extra_dim(laspy.ExtraBytesParams(name="test_dim2", type=np.int32))
+        
+        las = laspy.LasData(header)
+
+        crs_pyproj = CRS.from_string("epsg:4326")
+        las.header.add_crs(crs_pyproj)
+
+        # Add some test points
+        las.x = np.array([1.0, 2.0, 3.0])
+        las.y = np.array([4.0, 5.0, 6.0])
+        las.z = np.array([7.0, 8.0, 9.0])
+        las.test_dim = np.array([10.0, 11.0, 12.0])
+        las.test_dim2 = np.array([12, 13, 14])
+        
+        las.write(tmp_file.name)
+        return tmp_file.name
+
+def test_rename_dimension():
+    """Test renaming a dimension in a LAS file."""
+    # Create a temporary input LAS file
+    input_file = create_test_las_file()
+    
+    # Create temporary output file
+    with tempfile.NamedTemporaryFile(suffix='.las', delete=False) as tmp_file:
+        output_file = tmp_file.name
+    
+    try:
+        # Rename dimension using direct function call
+        rename_dimension(input_file, output_file, ["test_dim", "test_dim2"], ["new_test_dim", "new_test_dim2"])
+        
+        # Verify the dimension was renamed
+        with laspy.open(output_file) as las_file:
+            las = las_file.read()
+            assert "new_test_dim" in las.point_format.dimension_names
+            assert "test_dim" not in las.point_format.dimension_names
+            assert "new_test_dim2" in las.point_format.dimension_names
+            assert "test_dim2" not in las.point_format.dimension_names
+            
+            # Verify the data is preserved
+            np.testing.assert_array_equal(las.x, [1.0, 2.0, 3.0])
+            np.testing.assert_array_equal(las.y, [4.0, 5.0, 6.0])
+            np.testing.assert_array_equal(las.z, [7.0, 8.0, 9.0])
+            np.testing.assert_array_equal(las["new_test_dim"], [10.0, 11.0, 12.0])
+            np.testing.assert_array_equal(las["new_test_dim2"], [12, 13, 14])
+    finally:
+        # Clean up temporary files
+        try:
+            os.unlink(input_file)
+            os.unlink(output_file)
+        except:
+            pass
+
+def test_rename_nonexistent_dimension():
+    """Test attempting to rename a dimension that doesn't exist."""
+    input_file = create_test_las_file()
+    
+    with tempfile.NamedTemporaryFile(suffix='.las', delete=False) as tmp_file:
+        output_file = tmp_file.name
+    
+    try:
+        with pytest.raises(RuntimeError):
+            rename_dimension(input_file, output_file, ["nonexistent_dim"], ["new_dim"])
+    finally:
+        os.unlink(input_file)
+        os.unlink(output_file)
+
+def test_rename_to_existing_dimension():
+    """Test attempting to rename to an existing dimension."""
+    input_file = create_test_las_file()
+    
+    with tempfile.NamedTemporaryFile(suffix='.las', delete=False) as tmp_file:
+        output_file = tmp_file.name
+    
+    try:
+        with pytest.raises(ValueError):
+            rename_dimension(input_file, output_file, ["test_dim"], ["x"])
+    finally:
+        os.unlink(input_file)
+        os.unlink(output_file)
+
+def test_rename_dimension_case_sensitive():
+    """Test that dimension renaming is case-sensitive."""
+    input_file = create_test_las_file()
+    
+    with tempfile.NamedTemporaryFile(suffix='.las', delete=False) as tmp_file:
+        output_file = tmp_file.name
+    
+    try:
+        with pytest.raises(RuntimeError):
+            rename_dimension(input_file, output_file, ["TEST_DIM"], ["new_dim"])
+    finally:
+        os.unlink(input_file)
+        os.unlink(output_file)
+
+
+def test_rename_dimension_main():
+    """Test renaming dimensions using the main() function."""
+    # Create a temporary input LAS file
+    input_file = create_test_las_file()
+    
+    # Create temporary output file
+    with tempfile.NamedTemporaryFile(suffix='.las', delete=False) as tmp_file:
+        output_file = tmp_file.name
+    
+    try:
+        # Save original sys.argv
+        original_argv = sys.argv
+        
+        # Mock command-line arguments
+        sys.argv = [
+            "las_rename_dimension.py",  # script name
+            input_file,
+            output_file,
+            "--old-dims", "test_dim", "test_dim2",
+            "--new-dims", "new_test_dim", "new_test_dim2"
+        ]
+        
+        # Call main() function
+        main()
+        
+        # Restore original sys.argv
+        sys.argv = original_argv
+        
+        # Verify the dimension was renamed
+        with laspy.open(output_file) as las_file:
+            las = las_file.read()
+            assert "new_test_dim" in las.point_format.dimension_names
+            assert "test_dim" not in las.point_format.dimension_names
+            assert "new_test_dim2" in las.point_format.dimension_names
+            assert "test_dim2" not in las.point_format.dimension_names
+            
+            # Verify the data is preserved
+            np.testing.assert_array_equal(las.x, [1.0, 2.0, 3.0])
+            np.testing.assert_array_equal(las.y, [4.0, 5.0, 6.0])
+            np.testing.assert_array_equal(las.z, [7.0, 8.0, 9.0])
+            np.testing.assert_array_equal(las["new_test_dim"], [10.0, 11.0, 12.0])
+            np.testing.assert_array_equal(las["new_test_dim2"], [12, 13, 14])
+    finally:
+        # Clean up temporary files
+        try:
+            os.unlink(input_file)
+            os.unlink(output_file)
+        except:
+            pass