Merge pull request #375 from KRiedmiller/cyl_radii_type

Cyl radii type

jupyter/4dobc-creation.ipynb

@@ -124,7 +124,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "analysis.m3c2 = py4dgeo.M3C2(cyl_radii=[2.0], normal_radii=[2.0])"
+    "analysis.m3c2 = py4dgeo.M3C2(cyl_radius=2.0, normal_radii=[2.0])"
    ]
   },
   {
@@ -258,7 +258,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

jupyter/customization.ipynb

@@ -120,9 +120,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "DirectionAlgorithm(\n",
-    "    epochs=(epoch1, epoch2), corepoints=corepoints, cyl_radii=(5.0,)\n",
-    ").run()"
+    "DirectionAlgorithm(epochs=(epoch1, epoch2), corepoints=corepoints, cyl_radius=5.0).run()"
    ]
   },
   {
@@ -188,7 +186,7 @@
     "CallbackAlgorithm(\n",
     "    epochs=(epoch1, epoch2),\n",
     "    corepoints=corepoints,\n",
-    "    cyl_radii=(2.0,),\n",
+    "    cyl_radius=2.0,\n",
     "    normal_radii=(1.0, 2.0),\n",
     ").run()"
    ]
@@ -221,7 +219,7 @@
     "PythonFallbackM3C2(\n",
     "    epochs=(epoch1, epoch2),\n",
     "    corepoints=corepoints,\n",
-    "    cyl_radii=(2.0,),\n",
+    "    cyl_radius=2.0,\n",
     "    normal_radii=(1.0, 2.0),\n",
     ").run()"
    ]
@@ -267,7 +265,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.6"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

jupyter/m3c2.ipynb

@@ -83,7 +83,7 @@
     "m3c2 = py4dgeo.M3C2(\n",
     "    epochs=(epoch1, epoch2),\n",
     "    corepoints=corepoints,\n",
-    "    cyl_radii=(2.0,),\n",
+    "    cyl_radius=2.0,\n",
     "    normal_radii=[0.5, 1.0, 2.0],\n",
     ")\n",
     "\n",
@@ -209,7 +209,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.12"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

jupyter/m3c2ep.ipynb

@@ -188,7 +188,7 @@
     "    epochs=(epoch1, epoch2),\n",
     "    corepoints=corepoints,\n",
     "    normal_radii=(0.5, 1.0, 2.0),\n",
-    "    cyl_radii=(0.5,),\n",
+    "    cyl_radius=0.5,\n",
     "    max_distance=3.0,\n",
     "    Cxx=Cxx,\n",
     "    tfM=tfM,\n",
@@ -364,7 +364,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.4"
+   "version": "3.12.3"
   }
  },
  "nbformat": 4,

src/py4dgeo/cloudcompare.py

@@ -5,7 +5,7 @@
     "normalscale": "normal_radii",
     "registrationerror": "reg_error",
     "searchdepth": "max_distance",
-    "searchscale": "cyl_radii",
+    "searchscale": "cyl_radius",
     "usemedian": "robust_aggr",
 }
 
@@ -21,10 +21,8 @@ def __init__(self, **params):
         # Apply changes that are not a mere renaming
 
         # Scale parameters are diameters in CloudCompare and radii in py4dgeo
-        if "cyl_radii" in py4dgeo_params:
-            py4dgeo_params["cyl_radii"] = tuple(
-                0.5 * r for r in py4dgeo_params["cyl_radii"]
-            )
+        if "cyl_radius" in py4dgeo_params:
+            py4dgeo_params["cyl_radius"] = py4dgeo_params["cyl_radius"] * 0.5
         if "normal_radii" in py4dgeo_params:
             py4dgeo_params["normal_radii"] = tuple(
                 0.5 * r for r in py4dgeo_params["normal_radii"]

src/py4dgeo/m3c2.py

@@ -1,3 +1,4 @@
+from ast import List
 from py4dgeo.epoch import Epoch, as_epoch
 from py4dgeo.util import (
     as_double_precision,
@@ -22,16 +23,18 @@
 class M3C2LikeAlgorithm(abc.ABC):
     def __init__(
         self,
-        epochs: typing.Tuple[Epoch, ...] = None,
-        corepoints: np.ndarray = None,
-        cyl_radii: typing.List[float] = None,
+        epochs: typing.Optional[typing.Tuple[Epoch, ...]] = None,
+        corepoints: typing.Optional[np.ndarray] = None,
+        cyl_radii: typing.Optional[List] = None,
+        cyl_radius: typing.Optional[float] = None,
         max_distance: float = 0.0,
         registration_error: float = 0.0,
         robust_aggr: bool = False,
     ):
         self.epochs = epochs
         self.corepoints = corepoints
         self.cyl_radii = cyl_radii
+        self.cyl_radius = cyl_radius
         self.max_distance = max_distance
         self.registration_error = registration_error
         self.robust_aggr = robust_aggr
@@ -72,9 +75,19 @@ def directions(self):
     def calculate_distances(self, epoch1, epoch2):
         """Calculate the distances between two epochs"""
 
-        if self.cyl_radii is None or len(self.cyl_radii) != 1:
+        if isinstance(self.cyl_radii, typing.Iterable):
+            logger.warning(
+                "DEPRECATION: use cyl_radius instead of cyl_radii. In a future version, cyl_radii will be removed!"
+            )
+            if len(self.cyl_radii) != 1:
+                Py4DGeoError("cyl_radii must be a list containing a single float!")
+            elif self.cyl_radius is None:
+                self.cyl_radius = self.cyl_radii[0]
+            self.cyl_radii = None
+
+        if self.cyl_radius is None:
             raise Py4DGeoError(
-                f"{self.name} requires exactly one cylinder radius to be given"
+                f"{self.name} requires exactly one cylinder radius to be given as a float."
             )
 
         # Ensure that the KDTree data structures have been built. This is no-op
@@ -85,7 +98,7 @@ def calculate_distances(self, epoch1, epoch2):
 
         distances, uncertainties = _py4dgeo.compute_distances(
             self.corepoints,
-            self.cyl_radii[0],
+            self.cyl_radius,
             epoch1,
             epoch2,
             self.directions(),

src/py4dgeo/m3c2ep.py

@@ -56,7 +56,7 @@ def calculate_distances(self, epoch1, epoch2):
         print(self.name + " running")
         """Calculate the distances between two epochs"""
 
-        if self.cyl_radii is None or len(self.cyl_radii) != 1:
+        if not isinstance(self.cyl_radius, float):
             raise Py4DGeoError(
                 f"{self.name} requires exactly one cylinder radius to be given"
             )
@@ -71,7 +71,7 @@ def calculate_distances(self, epoch1, epoch2):
 
         # set default M3C2Meta
         M3C2Meta = {"searchrad": 0.5, "maxdist": 3, "minneigh": 5, "maxneigh": 100000}
-        M3C2Meta["searchrad"] = self.cyl_radii[0]
+        M3C2Meta["searchrad"] = self.cyl_radius
         M3C2Meta["maxdist"] = self.max_distance
 
         M3C2Meta["spInfos"] = [epoch1.scanpos_info, epoch2.scanpos_info]

tests/python/test_cloudcompare.py

@@ -11,15 +11,17 @@ def test_cloudcompare_m3c2(epochs):
     m3c2 = M3C2(
         epochs=(epoch1, epoch2),
         corepoints=epoch1.cloud,
-        cyl_radii=(1.6,),
-        normal_radii=(1.1,),
+        cyl_radius=1.6,
+        normal_radii=[
+            1.1,
+        ],
     )
 
     # Instantiate Cloud compare variant
     cc_m3c2 = CloudCompareM3C2(
         epochs=(epoch1, epoch2),
         corepoints=epoch1.cloud,
-        searchscale=(3.2,),
+        searchscale=3.2,
         normalscale=(2.2,),
     )
 

tests/python/test_fallback.py

@@ -45,7 +45,7 @@ def callback_workingset_finder(self):
     pym3c2 = CxxTestM3C2(
         epochs=epochs,
         corepoints=epochs[0].cloud,
-        cyl_radii=(3.0,),
+        cyl_radius=3.0,
         normal_radii=(2.0,),
         max_distance=6.0,
     )
@@ -54,7 +54,7 @@ def callback_workingset_finder(self):
     m3c2 = PythonTestM3C2(
         epochs=epochs,
         corepoints=epochs[0].cloud,
-        cyl_radii=(3.0,),
+        cyl_radius=3.0,
         normal_radii=(2.0,),
         max_distance=6.0,
     )
@@ -65,12 +65,12 @@ def callback_workingset_finder(self):
 def test_python_fallback_m3c2(epochs):
     # Instantiate a fallback M3C2 instance
     pym3c2 = PythonFallbackM3C2(
-        epochs=epochs, corepoints=epochs[0].cloud, cyl_radii=(3.0,), normal_radii=(2.0,)
+        epochs=epochs, corepoints=epochs[0].cloud, cyl_radius=3.0, normal_radii=(2.0,)
     )
 
     # And a regular C++ based one
     m3c2 = M3C2(
-        epochs=epochs, corepoints=epochs[0].cloud, cyl_radii=(3.0,), normal_radii=(2.0,)
+        epochs=epochs, corepoints=epochs[0].cloud, cyl_radius=3.0, normal_radii=(2.0,)
     )
 
     compare_algorithms(m3c2, pym3c2)
@@ -87,7 +87,7 @@ def callback(*args):
 
     # Instantiate it
     m3c2 = ExcM3C2(
-        epochs=epochs, corepoints=epochs[0].cloud, cyl_radii=(3.0,), normal_radii=(2.0,)
+        epochs=epochs, corepoints=epochs[0].cloud, cyl_radius=3.0, normal_radii=(2.0,)
     )
 
     # Running it should throw the proper exception despite taking a detour

tests/python/test_m3c2.py

@@ -7,16 +7,15 @@
 @pytest.mark.parametrize("robust_aggr", (True, False))
 def test_m3c2(epochs, robust_aggr):
     epoch1, epoch2 = epochs
-
     # Try with wrong number of epochs
     with pytest.raises(Py4DGeoError):
-        M3C2(epochs=(epoch1,), corepoints=epoch1.cloud, cyl_radii=(1.0,))
+        M3C2(epochs=(epoch1,), corepoints=epoch1.cloud, cyl_radius=1.0)
 
     # Instantiate an M3C2 instance
     m3c2 = M3C2(
         epochs=(epoch1, epoch2),
         corepoints=epoch1.cloud,
-        cyl_radii=(3.0,),
+        cyl_radius=3.0,
         normal_radii=(2.0,),
         robust_aggr=robust_aggr,
     )
@@ -28,7 +27,7 @@ def test_m3c2(epochs, robust_aggr):
     distances, uncertainties = M3C2(
         epochs=(epoch1, epoch1),
         corepoints=epoch1.cloud,
-        cyl_radii=(3.0,),
+        cyl_radius=3.0,
         normal_radii=(2.0,),
         robust_aggr=robust_aggr,
     ).run()
@@ -43,7 +42,7 @@ def test_minimal_m3c2(epochs):
     m3c2 = M3C2(
         epochs=(epoch1, epoch2),
         corepoints=epoch1.cloud,
-        cyl_radii=(3.0,),
+        cyl_radius=3.0,
         normal_radii=(2.0,),
     )
 
@@ -57,7 +56,7 @@ def test_registration_error(epochs):
     m3c2 = M3C2(
         epochs=(epoch1, epoch1),
         corepoints=epoch1.cloud,
-        cyl_radii=(3.0,),
+        cyl_radius=3.0,
         normal_radii=(2.0,),
         registration_error=1.0,
     )
@@ -73,7 +72,7 @@ def test_external_normals(epochs):
     d, u = M3C2(
         epochs=(epoch1, epoch2),
         corepoints=epoch1.cloud,
-        cyl_radii=(3.0,),
+        cyl_radius=3.0,
         normal_radii=(2.0,),
         corepoint_normals=np.array([[0, 0, 1]]),
     ).run()
@@ -82,7 +81,7 @@ def test_external_normals(epochs):
         d, u = M3C2(
             epochs=(epoch1, epoch2),
             corepoints=epoch1.cloud,
-            cyl_radii=(3.0,),
+            cyl_radius=3.0,
             normal_radii=(2.0,),
             corepoint_normals=np.array([[0, 0, 1], [0, 0, 1]]),
         ).run()

tests/python/test_m3c2ep.py

@@ -18,7 +18,7 @@ def test_m3c2ep(epochs_m3c2ep, Cxx, tfM, redPoint, scanpos_info):
         epochs=(epoch1, epoch2),
         corepoints=corepoints,
         normal_radii=(0.5, 1.0, 2.0),
-        cyl_radii=(0.5,),
+        cyl_radius=0.5,
         max_distance=3.0,
         Cxx=Cxx,
         tfM=tfM,
@@ -60,7 +60,7 @@ def test_m3c2ep_external_normals(epochs_m3c2ep, Cxx, tfM, redPoint, scanpos_info
             epochs=(epoch1, epoch2),
             corepoints=corepoints,
             corepoint_normals=np.array([[0, 0, 1], [0, 0, 1]]),
-            cyl_radii=(0.5,),
+            cyl_radius=0.5,
             max_distance=3.0,
             Cxx=Cxx,
             tfM=tfM,
@@ -72,7 +72,7 @@ def test_m3c2ep_external_normals(epochs_m3c2ep, Cxx, tfM, redPoint, scanpos_info
         epochs=(epoch1, epoch2),
         corepoints=corepoints,
         normal_radii=(0.5, 1.0, 2.0),
-        cyl_radii=(0.5,),
+        cyl_radius=0.5,
         max_distance=3.0,
         Cxx=Cxx,
         tfM=tfM,
@@ -85,7 +85,7 @@ def test_m3c2ep_external_normals(epochs_m3c2ep, Cxx, tfM, redPoint, scanpos_info
         epochs=(epoch1, epoch2),
         corepoints=corepoints,
         corepoint_normals=corepoint_normals,
-        cyl_radii=(0.5,),
+        cyl_radius=0.5,
         max_distance=3.0,
         Cxx=Cxx,
         tfM=tfM,
@@ -100,7 +100,7 @@ def test_m3c2ep_external_normals(epochs_m3c2ep, Cxx, tfM, redPoint, scanpos_info
         epochs=(epoch1, epoch2),
         corepoints=corepoints,
         corepoint_normals=corepoint_normals,
-        cyl_radii=(0.5,),
+        cyl_radius=0.5,
         max_distance=3.0,
         Cxx=Cxx,
         tfM=tfM,
@@ -153,7 +153,7 @@ def test_m3c2ep_write_las(epochs_m3c2ep, Cxx, tfM, redPoint, scanpos_info):
         epochs=(epoch1, epoch2),
         corepoints=corepoints,
         normal_radii=(0.5, 1.0, 2.0),
-        cyl_radii=(0.5,),
+        cyl_radius=0.5,
         max_distance=3.0,
         Cxx=Cxx,
         tfM=tfM,

tests/python/test_segmentation.py

@@ -47,7 +47,7 @@ def test_construct_from_epochs(epochs, tmp_path):
     m3c2 = M3C2(
         epochs=(ref_epoch, epoch1),
         corepoints=ref_epoch.cloud,
-        cyl_radii=[2.0],
+        cyl_radius=2.0,
         normal_radii=[2.0],
     )