ign-pdal-tools 1.7.3__py3-none-any.whl → 1.7.5__py3-none-any.whl

{ign_pdal_tools-1.7.3.dist-info → ign_pdal_tools-1.7.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ign-pdal-tools
-Version: 1.7.3
+Version: 1.7.5
 Summary: Library for common LAS files manipulation with PDAL
 Author-email: Guillaume Liegard <guillaume.liegard@ign.fr>
 Description-Content-Type: text/markdown
@@ -87,6 +87,11 @@ By default, `xcoord` and `ycoord` are given in kilometers and the shape of the t
 `readers.las: Global encoding WKT flag not set for point format 6 - 10.` which is due to TerraSolid
 malformed LAS output for LAS1.4 files with point format 6 to 10.
 
+## Add points in Las
+
+[add_points_in_las.py](pdaltools/add_points_in_las.py): add points from some vector files (ex: shp, geojson, ...) inside Las. New points will have X,Y and Z coordinates. Other attributes values given by  the initial las file are null (ex: classification at 0). These others attributes could be forced by using the '--dimensions/-d' option in the command line (ex : 'add_points_in_las.py -i myLas.las -g myPoints.json -d classification=64' - points will have their classification set to 64). The dimension should be present in the initial las ; this is not allowed to add new dimension.
+
+
 # Dev / Build
 
 ## Contribute

ign_pdal_tools-1.7.5.dist-info/RECORD

@@ -0,0 +1,17 @@
+pdaltools/_version.py,sha256=Jr3d2rnNzq-ZLSjZiEMdSSozTrU6AhKJLKOvXK3-0H0,74
+pdaltools/add_points_in_las.py,sha256=TGbt5JUkszjmbQiA2LCUntsjz6A8DHb7QPIXGDuEgWA,3643
+pdaltools/color.py,sha256=PSdtMMdsapOtgzojdnaKVx6IxbKOaN2xP9mScAbCGm0,8629
+pdaltools/las_add_buffer.py,sha256=sBpTywlfsHHS8KuCUa-eydB2hylshEvjrMQt5TrqXb8,11275
+pdaltools/las_clip.py,sha256=GvEOYu8RXV68e35kU8i42GwSkbo4P9TvmS6rkrdPmFM,1034
+pdaltools/las_info.py,sha256=cVVsOrtwgyOpI093PuXNhs2N7BJIdfW0BgxxRb-XqyQ,8096
+pdaltools/las_merge.py,sha256=tcFVueV9X9nNEaoAl5zCduY5DETlBg63MAgP2SuKiNo,4121
+pdaltools/las_remove_dimensions.py,sha256=u_3VfkabkN_Y3eDLdJwCLVGpondvIx0f0v0RdFDoAFw,1792
+pdaltools/pcd_info.py,sha256=NIAH5KGikVDQLlbCcw9FuaPqe20UZvRfkHsDZd5kmZA,3210
+pdaltools/replace_attribute_in_las.py,sha256=po1F-fi8s7iilqKWaryW4JRbsmdMOUe0yGvG3AEKxtk,4771
+pdaltools/standardize_format.py,sha256=gqm2GJbtDkT4k4oC_NX2LIPh9R2BLh4sMHLKYgfKrMc,3973
+pdaltools/unlock_file.py,sha256=pIThdWMNkTph0xgJVVRaM1o9aUMQhM6804PscScB3JI,1963
+ign_pdal_tools-1.7.5.dist-info/LICENSE.md,sha256=iVzCFZTUXeiqP8bP474iuWZiWO_kDCD4SPh1Wiw125Y,1120
+ign_pdal_tools-1.7.5.dist-info/METADATA,sha256=EqDhgZ2NEpoOr7Whk2RefX9emt_M05l7MGotTplcgkE,5722
+ign_pdal_tools-1.7.5.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+ign_pdal_tools-1.7.5.dist-info/top_level.txt,sha256=KvGW0ZzqQbhCKzB5_Tp_buWMZyIgiO2M2krWF_ecOZc,10
+ign_pdal_tools-1.7.5.dist-info/RECORD,,

{ign_pdal_tools-1.7.3.dist-info → ign_pdal_tools-1.7.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (74.0.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pdaltools/_version.py

@@ -1,4 +1,4 @@
-__version__ = "1.7.3"
+__version__ = "1.7.5"
 
 
 if __name__ == "__main__":

pdaltools/add_points_in_las.py

@@ -0,0 +1,104 @@
+import argparse
+
+import geopandas
+import numpy as np
+import pdal
+
+from pdaltools.las_info import get_writer_parameters_from_reader_metadata, las_info_metadata, get_bounds_from_header_info
+
+
+def extract_points_from_geo(input_geo: str):
+    file = open(input_geo)
+    df = geopandas.read_file(file)
+    return df.get_coordinates(ignore_index=True, include_z=True)
+
+def point_in_bound(bound_minx, bound_maxx, bound_miny, bound_maxy, pt_x, pt_y):
+    return pt_x >= bound_minx and  pt_x <= bound_maxx and pt_y >= bound_miny and  pt_y <= bound_maxy
+
+def add_points_in_las(input_las: str, input_geo: str, output_las: str, inside_las: bool, values_dimensions: {}):
+    points_geo = extract_points_from_geo(input_geo)
+    pipeline = pdal.Pipeline() | pdal.Reader.las(input_las)
+    pipeline.execute()
+    points_las = pipeline.arrays[0]
+    dimensions = list(points_las.dtype.fields.keys())
+
+    if inside_las:
+        mtd = las_info_metadata(input_las)
+        bound_minx, bound_maxx, bound_miny, bound_maxy = get_bounds_from_header_info(mtd)
+
+    for i in points_geo.index:
+        if inside_las :
+            if not point_in_bound(bound_minx, bound_maxx, bound_miny, bound_maxy, points_geo["x"][i], points_geo["y"][i]):
+                continue
+        pt_las = np.empty(1, dtype=points_las.dtype)
+        pt_las[0][dimensions.index("X")] = points_geo["x"][i]
+        pt_las[0][dimensions.index("Y")] = points_geo["y"][i]
+        pt_las[0][dimensions.index("Z")] = points_geo["z"][i]
+        for val in values_dimensions:
+            pt_las[0][dimensions.index(val)] = values_dimensions[val]
+        points_las = np.append(points_las, pt_las, axis=0)
+
+    params = get_writer_parameters_from_reader_metadata(pipeline.metadata)
+    pipeline_end = pdal.Pipeline(arrays=[points_las])
+    pipeline_end |= pdal.Writer.las(output_las, forward="all", **params)
+    pipeline_end.execute()
+
+
+def parse_args():
+    parser = argparse.ArgumentParser("Add points from geometry file in a las/laz file.")
+    parser.add_argument("--input_file", "-i", type=str, help="Las/Laz input file")
+    parser.add_argument("--output_file", "-o", type=str, help="Las/Laz output file.")
+    parser.add_argument("--input_geo_file", "-g", type=str, help="Geometry input file.")
+    parser.add_argument("--inside_las", "-l", type=str, help="Keep points only inside the las boundary.")
+    parser.add_argument(
+        "--dimensions",
+        "-d",
+        metavar="KEY=VALUE",
+        nargs="+",
+        help="Set a number of key-value pairs corresponding to value "
+        "needed in points added in the output las; key should be included in the input las.",
+    )
+    return parser.parse_args()
+
+
+def is_nature(value, nature):
+    if value is None:
+        return False
+    try:
+        nature(value)
+        return True
+    except:
+        return False
+
+
+def parse_var(s):
+    items = s.split("=")
+    key = items[0].strip()
+    if len(items) > 1:
+        value = "=".join(items[1:])
+        if is_nature(value, int):
+            value = int(value)
+        elif is_nature(value, float):
+            value = float(value)
+    return (key, value)
+
+
+def parse_vars(items):
+    d = {}
+    if items:
+        for item in items:
+            key, value = parse_var(item)
+            d[key] = value
+    return d
+
+
+if __name__ == "__main__":
+    args = parse_args()
+    added_dimensions = parse_vars(args.dimensions)
+    add_points_in_las(
+        input_las=args.input_file,
+        input_geo=args.input_geo_file,
+        output_las=args.input_file if args.output_file is None else args.output_file,
+        inside_las=args.inside_las,
+        values_dimensions=added_dimensions,
+    )

pdaltools/color.py

@@ -69,11 +69,11 @@ def is_image_white(filename: str):
 def download_image_from_geoplateforme(
     proj, layer, minx, miny, maxx, maxy, pixel_per_meter, outfile, timeout, check_images
 ):
-    # Give single-point clouds a width/height of at least one pixel to have valid BBOX and SIZE
-    if minx == maxx:
-        maxx = minx + 1 / pixel_per_meter
-    if miny == maxy:
-        maxy = miny + 1 / pixel_per_meter
+    # Force a 1-pixel margin in the east and south borders
+    # to make sure that no point of the pointcloud is on the limit of the last pixel
+    # to prevent interpolation issues
+    maxx = maxx + 1 / pixel_per_meter
+    miny = miny - 1 / pixel_per_meter
 
     # for layer in layers:
     URL_GPP = "https://data.geopf.fr/wms-r/wms?"
@@ -136,22 +136,26 @@ def color(
 
     tmp_ortho = None
     if color_rvb_enabled:
-        tmp_ortho = tempfile.NamedTemporaryFile()
+        tmp_ortho = tempfile.NamedTemporaryFile(suffix="_rvb.tif")
         download_image_from_geoplateforme_retrying(
             proj, stream_RGB, minx, miny, maxx, maxy, pixel_per_meter, tmp_ortho.name, timeout_second, check_images
         )
-
+        # Warning: the initial color is multiplied by 256 despite its initial 8-bits encoding
+        # which turns it to a 0 to 255*256 range.
+        # It is kept this way because of other dependencies that have been tuned to fit this range
         pipeline |= pdal.Filter.colorization(
             raster=tmp_ortho.name, dimensions="Red:1:256.0, Green:2:256.0, Blue:3:256.0"
         )
 
     tmp_ortho_irc = None
     if color_ir_enabled:
-        tmp_ortho_irc = tempfile.NamedTemporaryFile()
+        tmp_ortho_irc = tempfile.NamedTemporaryFile(suffix="_irc.tif")
         download_image_from_geoplateforme_retrying(
             proj, stream_IRC, minx, miny, maxx, maxy, pixel_per_meter, tmp_ortho_irc.name, timeout_second, check_images
         )
-
+        # Warning: the initial color is multiplied by 256 despite its initial 8-bits encoding
+        # which turns it to a 0 to 255*256 range.
+        # It is kept this way because of other dependencies that have been tuned to fit this range
         pipeline |= pdal.Filter.colorization(raster=tmp_ortho_irc.name, dimensions="Infrared:1:256.0")
 
     pipeline |= pdal.Writer.las(

pdaltools/las_info.py

@@ -6,6 +6,8 @@ from typing import Dict, Tuple
 import osgeo.osr as osr
 import pdal
 
+from pdaltools.pcd_info import infer_tile_origin
+
 osr.UseExceptions()
 
 
@@ -17,13 +19,37 @@ def las_info_metadata(filename: str):
     return metadata
 
 
-def get_bounds_from_header_info(metadata):
+def get_bounds_from_header_info(metadata: Dict) -> Tuple[float, float, float, float]:
+    """Get bounds from metadata that has been extracted previously from the header of a las file
+
+    Args:
+        metadata (str): Dictonary containing metadata from a las file (as extracted with pipeline.quickinfo)
+
+    Returns:
+        Tuple[float, float, float, float]: minx, maxx, miny, maxy
+    """
     bounds = metadata["bounds"]
     minx, maxx, miny, maxy = bounds["minx"], bounds["maxx"], bounds["miny"], bounds["maxy"]
 
     return minx, maxx, miny, maxy
 
 
+def get_tile_origin_using_header_info(filename: str, tile_width: int = 1000) -> Tuple[int, int]:
+    """ "Get las file theoretical origin (xmin, ymax) for a data that originates from a square tesselation/tiling
+    using the tesselation tile width only, directly from its path
+    Args:
+        filename (str): path to the las file
+        tile_width (int, optional): Tesselation tile width (in meters). Defaults to 1000.
+
+    Returns:
+        Tuple[int, int]: (origin_x, origin_y) tile origin coordinates = theoretical (xmin, ymax)
+    """
+    metadata = las_info_metadata(filename)
+    minx, maxx, miny, maxy = get_bounds_from_header_info(metadata)
+
+    return infer_tile_origin(minx, maxx, miny, maxy, tile_width)
+
+
 def get_epsg_from_header_info(metadata):
     if "srs" not in metadata.keys():
         raise RuntimeError("EPSG could not be inferred from metadata: No 'srs' key in metadata.")

pdaltools/las_remove_dimensions.py

@@ -1,9 +1,9 @@
 import argparse
-import os
 
 import pdal
 from pdaltools.las_info import get_writer_parameters_from_reader_metadata
 
+
 def remove_dimensions_from_las(input_las: str, dimensions: [str], output_las: str):
     """
     export new las without some dimensions
@@ -43,7 +43,7 @@ def parse_args():
         required=True,
         nargs="+",
         help="The dimension we would like to remove from the point cloud file ; be aware to not remove mandatory "
-             "dimensions of las"
+        "dimensions of las",
     )
 
     return parser.parse_args()

pdaltools/pcd_info.py

@@ -5,14 +5,52 @@ from typing import Tuple
 import numpy as np
 
 
+def infer_tile_origin(minx: float, maxx: float, miny: float, maxy: float, tile_width: int) -> Tuple[int, int]:
+    """Get point cloud theoretical origin (xmin, ymax) for a data that originates from a square tesselation/tiling
+    using the tesselation tile width only, based on the min/max values
+
+    Edge values are supposed to be included in the tile
+
+    Args:
+        minx (float): point cloud min x value
+        maxx (float): point cloud max x value
+        miny (float): point cloud min y value
+        maxy (float): point cloud max y value
+        tile_width (int): tile width in meters
+
+    Raises:
+        ValueError: In case the min and max values do not belong to the same tile
+
+    Returns:
+        Tuple[int, int]: (origin_x, origin_y) tile origin coordinates = theoretical (xmin, ymax)
+    """
+
+    minx_tile_index = np.floor(minx / tile_width)
+    maxx_tile_index = np.floor(maxx / tile_width) if maxx % tile_width != 0 else np.floor(maxx / tile_width) - 1
+    miny_tile_index = np.ceil(miny / tile_width) if miny % tile_width != 0 else np.floor(miny / tile_width) + 1
+    maxy_tile_index = np.ceil(maxy / tile_width)
+
+    if maxx_tile_index == minx_tile_index and maxy_tile_index == miny_tile_index:
+        origin_x = minx_tile_index * tile_width
+        origin_y = maxy_tile_index * tile_width
+        return origin_x, origin_y
+    else:
+        raise ValueError(
+            f"Min values (x={minx} and y={miny}) do not belong to the same theoretical tile as"
+            f"max values (x={maxx} and y={maxy})."
+        )
+
+
 def get_pointcloud_origin_from_tile_width(
     points: np.ndarray, tile_width: int = 1000, buffer_size: float = 0
 ) -> Tuple[int, int]:
     """Get point cloud theoretical origin (xmin, ymax) for a data that originates from a square tesselation/tiling
-    using the tesselation tile width only.
+    using the tesselation tile width only, based on the point cloud as a np.ndarray
 
     Edge values are supposed to be included in the tile
 
+    In case buffer_size is provided, the origin will be calculated on an "original" tile, supposing that
+    there has been a buffer added to the input tile.
 
     Args:
         points (np.ndarray): numpy array with the tile points
@@ -20,27 +58,19 @@ def get_pointcloud_origin_from_tile_width(
         buffer_size (float, optional): Optional buffer around the tile. Defaults to 0.
 
     Raises:
-        ValueError: Raise an error when the bounding box of the tile is not included in a tile
+        ValueError: Raise an error when the initial tile is smaller than the buffer (in this case, we cannot find the
+        origin (it can be either in the buffer or in the tile))
 
     Returns:
         Tuple[int, int]: (origin_x, origin_y) origin coordinates
     """
     # Extract coordinates xmin, xmax, ymin and ymax of the original tile without buffer
-    x_min, y_min = np.min(points[:, :2], axis=0) + buffer_size
-    x_max, y_max = np.max(points[:, :2], axis=0) - buffer_size
-
-    # Calculate the tiles to which x, y bounds belong
-    tile_x_min = np.floor(x_min / tile_width)
-    tile_x_max = np.floor(x_max / tile_width) if x_max % tile_width != 0 else np.floor(x_max / tile_width) - 1
-    tile_y_min = np.ceil(y_min / tile_width) if y_min % tile_width != 0 else np.floor(y_min / tile_width) + 1
-    tile_y_max = np.ceil(y_max / tile_width)
-
-    if not (tile_x_max - tile_x_min) and not (tile_y_max - tile_y_min):
-        origin_x = tile_x_min * tile_width
-        origin_y = tile_y_max * tile_width
-        return origin_x, origin_y
-    else:
+    minx, miny = np.min(points[:, :2], axis=0) + buffer_size
+    maxx, maxy = np.max(points[:, :2], axis=0) - buffer_size
+
+    if maxx < minx or maxy < miny:
         raise ValueError(
-            f"Min values (x={x_min} and y={y_min}) do not belong to the same theoretical tile as"
-            f"max values (x={x_max} and y={y_max})."
+            "Cannot find pointcloud origin as the pointcloud width or height is smaller than buffer width"
         )
+
+    return infer_tile_origin(minx, maxx, miny, maxy, tile_width)

pdaltools/standardize_format.py

@@ -10,14 +10,16 @@
 
 import argparse
 import os
+import platform
 import subprocess as sp
 import tempfile
-from typing import Dict
+from typing import Dict, List
 
 import pdal
 
 from pdaltools.unlock_file import copy_and_hack_decorator
 
+# Standard parameters to pass to the pdal writer
 STANDARD_PARAMETERS = dict(
     major_version="1",
     minor_version="4",  # Laz format version (pdal always write in 1.x format)
@@ -43,6 +45,13 @@ def parse_args():
         "--record_format", choices=[6, 8], type=int, help="Record format: 6 (no color) or 8 (4 color channels)"
     )
     parser.add_argument("--projection", default="EPSG:2154", type=str, help="Projection, eg. EPSG:2154")
+    parser.add_argument(
+        "--class_points_removed",
+        default=[],
+        nargs="*",
+        type=str,
+        help="List of classes number. Points of this classes will be removed from the file",
+    )
     parser.add_argument(
         "--extra_dims",
         default=[],
@@ -51,7 +60,6 @@ def parse_args():
         help="List of extra dims to keep in the output (default=[], use 'all' to keep all extra dims), "
         "extra_dims must be specified with their type (see pdal.writers.las documentation, eg 'dim1=double')",
     )
-
     return parser.parse_args()
 
 
@@ -61,20 +69,28 @@ def get_writer_parameters(new_parameters: Dict) -> Dict:
     override the standard ones
     """
     params = STANDARD_PARAMETERS | new_parameters
-
     return params
 
 
-def rewrite_with_pdal(input_file: str, output_file: str, params_from_parser: Dict) -> None:
-    # Update parameters with command line values
+def rewrite_with_pdal(
+    input_file: str, output_file: str, params_from_parser: Dict, classes_to_remove: List = []
+) -> None:
     params = get_writer_parameters(params_from_parser)
-    pipeline = pdal.Reader.las(input_file)
+    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()
 
 
 def exec_las2las(input_file: str, output_file: str):
-    r = sp.run(["las2las", "-i", input_file, "-o", output_file], stderr=sp.PIPE, stdout=sp.PIPE)
+    if platform.processor() == "arm" and platform.architecture()[0] == "64bit":
+        las2las = "las2las64"
+    else:
+        las2las = "las2las"
+    r = sp.run([las2las, "-i", input_file, "-o", output_file], stderr=sp.PIPE, stdout=sp.PIPE)
     if r.returncode == 1:
         msg = r.stderr.decode()
         print(msg)
@@ -86,14 +102,18 @@ def exec_las2las(input_file: str, output_file: str):
 
 
 @copy_and_hack_decorator
-def standardize(input_file: str, output_file: str, params_from_parser: Dict) -> None:
+def standardize(input_file: str, output_file: str, params_from_parser: Dict, class_points_removed: []) -> None:
     filename = os.path.basename(output_file)
     with tempfile.NamedTemporaryFile(suffix=filename) as tmp:
-        rewrite_with_pdal(input_file, tmp.name, params_from_parser)
+        rewrite_with_pdal(input_file, tmp.name, params_from_parser, class_points_removed)
         exec_las2las(tmp.name, output_file)
 
 
 if __name__ == "__main__":
     args = parse_args()
-    params_from_parser = dict(dataformat_id=args.record_format, a_srs=args.projection, extra_dims=args.extra_dims)
-    standardize(args.input_file, args.output_file, params_from_parser)
+    params_from_parser = dict(
+        dataformat_id=args.record_format,
+        a_srs=args.projection,
+        extra_dims=args.extra_dims,
+    )
+    standardize(args.input_file, args.output_file, params_from_parser, args.class_points_removed)

ign_pdal_tools-1.7.3.dist-info/RECORD

@@ -1,16 +0,0 @@
-pdaltools/_version.py,sha256=CIj6_M9SXht6CUH70oDuQQl4_AP2fggn-8tFZbGL0AY,74
-pdaltools/color.py,sha256=7U-SThIKqrfE1xXXnFqpbIhmZEqna29nRiyLW8l8Y1c,8075
-pdaltools/las_add_buffer.py,sha256=sBpTywlfsHHS8KuCUa-eydB2hylshEvjrMQt5TrqXb8,11275
-pdaltools/las_clip.py,sha256=GvEOYu8RXV68e35kU8i42GwSkbo4P9TvmS6rkrdPmFM,1034
-pdaltools/las_info.py,sha256=RE-UBdEUXqKvSrMV3mOlvE_16mhum7bw-p-ERu5bGOc,6979
-pdaltools/las_merge.py,sha256=tcFVueV9X9nNEaoAl5zCduY5DETlBg63MAgP2SuKiNo,4121
-pdaltools/las_remove_dimensions.py,sha256=0zhv9LBvlL69TLmXTJlRQcUBOaBmCRZEQU2Qadx27aM,1805
-pdaltools/pcd_info.py,sha256=d7ukCEdOFBQqaFp3HYM2MNbKDl1hdxUVHI9vSu9jN-M,1897
-pdaltools/replace_attribute_in_las.py,sha256=po1F-fi8s7iilqKWaryW4JRbsmdMOUe0yGvG3AEKxtk,4771
-pdaltools/standardize_format.py,sha256=lUzrjWY22WfxT_2zLtxuXbmWgiAvjy9o7fBXWsAZmDg,3240
-pdaltools/unlock_file.py,sha256=pIThdWMNkTph0xgJVVRaM1o9aUMQhM6804PscScB3JI,1963
-ign_pdal_tools-1.7.3.dist-info/LICENSE.md,sha256=iVzCFZTUXeiqP8bP474iuWZiWO_kDCD4SPh1Wiw125Y,1120
-ign_pdal_tools-1.7.3.dist-info/METADATA,sha256=PfhYtt73bGGZxehInuRGdzwfhfW_1UxMO7K3CrPlDL0,5112
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