Fix ply (#1829)

* Create README.md for fix_ply

* Create fix_ply.py

* Update fix_ply.py to match current

* Update README.md to match Jaime's description

* Add more description

contrib/fix_ply/README.md

@@ -0,0 +1,19 @@
+# Fix Ply
+
+Use to translate a modified ply into a compatible format for subsequent steps in ODM. Via Jaime Chacoff, https://community.opendronemap.org/t/edited-point-cloud-with-cloudcompare-wont-rerun-from-odm-meshing/21449/6
+
+The basic idea is to process through ODM until the point cloud is created, use a 3rd party tool, like CloudCompare to edit the point cloud, and then continue processing in OpenDroneMap.
+
+This useful bit of python will convert the PLY exported from CloudCompare back into a compatible format for continued processing in OpenDroneMap.
+
+1. Run project in WebODM and add this to your settings: `end-with: odm-filterpoints`
+1. Once complete, go to your NodeODM container and copy `/var/www/data/[Task ID]/odm-filterpoints` directory
+1. Open CloudCompare and from `odm-filterpoints` directory you've copied, open `point_cloud.ply`
+1. In the box that pops up, add a scalar field `vertex - views`
+1. To see the actual colours again - select the point cloud, then in properties change colours from "Scalar field" to "RGB"
+1. Make your changes to the point cloud
+1. Compute normals (Edit > Normals > Compute)
+1. Save PLY file as ASCII
+1. Run Python file above to fix PLY file and convert to binary
+1. Copy `odm_filterpoints` directory (or just `point_cloud.ply`) back into NodeODM container
+1. Restart project in WebODM "From Meshing" (don't forget to edit settings to remove `end-with: odm-filterpoints` or it's not going to do anything).

contrib/fix_ply/fix_ply.py

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+import os
+import logging
+from plyfile import PlyData, PlyElement
+import numpy as np
+
+# Configure logging
+logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')
+
+def pcd_ascii_to_binary_ply(ply_file: str, binary_ply: str) -> None:
+    """Converts ASCII PLY to binary, ensuring 'views' is present and of type uchar.
+       Raises ValueError if neither 'scalar_views' nor 'views' is found.
+    """
+
+    try:
+        logging.info(f"Reading ASCII PLY file: {ply_file}")
+        ply_data: PlyData = PlyData.read(ply_file)
+    except FileNotFoundError:
+        logging.error(f"File not found: {ply_file}")
+        return
+    except Exception as e:
+        logging.error(f"Error reading PLY file: {e}")
+        return
+
+    new_elements: list[PlyElement] = []
+
+    for element in ply_data.elements:
+        new_data = element.data.copy()
+
+        if 'scalar_views' in element.data.dtype.names:
+            new_data['views'] = new_data['scalar_views'].astype('u1')
+            del new_data['scalar_views']
+        elif 'views' in element.data.dtype.names:
+            new_data['views'] = new_data['views'].astype('u1')
+        else:
+            raise ValueError(f"Neither 'scalar_views' nor 'views' found - did you import them when opened the file in CloudCompare?")
+
+
+        new_element = PlyElement.describe(new_data, element.name)
+        new_elements.append(new_element)
+
+    new_ply_data = PlyData(new_elements, text=False)
+
+    try:
+        logging.info(f"Writing binary PLY file: {binary_ply}")
+        new_ply_data.write(binary_ply)
+    except Exception as e:
+        logging.error(f"Error writing PLY file: {e}")
+        return
+
+    logging.info("PLY conversion complete.")
+
+
+if __name__ == '__main__':
+
+    # Parameters
+    base: str = os.path.dirname(os.path.abspath(__file__))
+    ply_file: str = os.path.join(base, 'point_cloud_ascii.ply')
+    binary_ply_file: str = os.path.join(base, 'point_cloud.ply')
+
+    if not os.path.exists(ply_file):
+        logging.error(f"Input file not found: {ply_file}")
+        exit(1) # Exit with error code
+
+    try:
+        pcd_ascii_to_binary_ply(ply_file, binary_ply_file)
+    except ValueError as e:
+        logging.error(f"PLY conversion failed: {e}")
+        exit(1) # Exit with error code to indicate failure