Merge pull request #25 from meyerls/dev

Dev

.github/workflows/python-package.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.7", "3.8", "3.9", "3.10" ]
+        python-version: ["3.8", "3.9", "3.10" ]
 
     steps:
       - uses: actions/checkout@v3
@@ -22,15 +22,10 @@ jobs:
           pip install pip==21.3.1
           pip install numpy --use-deprecated=legacy-resolver
           pip install charset_normalizer
-          git clone https://github.com/meyerls/mistree.git
-          cd mistree 
-          pip install -e .
-          cd ..
           pip install -r requirements.txt
           pip install .
-      #- name: 'Test PC Skeletor'
-      #  run: |
-      #    pytest .
-      #    ls -la
-      #    ls -la ${{ github.workspace }}
-      #    pwd
+      - name: 'Test PC Skeletor'
+        run: |
+          pwd
+          ls -la
+          pytest tests

.github/workflows/python-publish.yml

@@ -8,10 +8,10 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
         - uses: actions/checkout@master
-        - name: Set up Python 3.7
+        - name: Set up Python 3.8
           uses: actions/setup-python@v1
           with:
-              python-version: 3.7
+              python-version: 3.8
         - name: Install pypa/build
           run: python -m pip install build --user
         - name: Build a binary wheel and a source tarball

.gitignore

@@ -11,9 +11,13 @@ pc_skeletor.egg-info
 pc_skeletor/__pycache__/**
 pc_skeletor/tmp*
 
+# Output
+pc_skeletor/output*
 output
+
 __pycache__
 test/__pycache__
-
 test/__pycache__/**
-__pycache__/**
+__pycache__/**
+
+annotated_tree.py

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "mistree"]
+	path = third_party/mistree
+	url = https://github.com/meyerls/mistree.git

Readme.md

@@ -5,17 +5,17 @@
 <a href="https://github.com/meyerls/pc-skeletor/blob/main/LICENSE"><img alt="license" src="https://img.shields.io/github/license/meyerls/pc-skeletor"></a>
 <!--a href="https://github.com/meyerls/pc-skeletor/actions"><img alt="GitHub Workflow Status" src="https://img.shields.io/github/workflow/status/meyerls/pc-skeletor/Python%20package"></a-->
 
-**PC Skeletor** is a Python library for extracting a 1d skeleton from 3d point clouds using
+**PC Skeletor** is a Python library for extracting a curved skeleton from 3d point clouds using
 [Laplacian-Based Contraction](https://taiya.github.io/pubs/cao2010cloudcontr.pdf) and
 [Semantic Laplacian-Based Contraction](https://arxiv.org/abs/2304.04708).
 
 ## Abstract
-Standard Laplacian-based contraction (LBC) is prone to mal-contraction in cases where
+Basic Laplacian-based contraction (LBC) is prone to mal-contraction in cases where
 there is a significant disparity in diameter between trunk and branches. In such cases fine structures experience 
 an over-contraction and leading to a distortion of their topological characteristics. In addition, LBC shows a 
 topologically incorrect tree skeleton for trunk structures that have holes in the point cloud.In order to address 
 these topological artifacts, we introduce semantic Laplacian-based contraction (S-LBC). It integrates semantic 
-information of the point cloud into the contraction algorithm.
+information of the point cloud into the contraction algorithm to overcome these artifacts.
 
 
 <table>
@@ -35,7 +35,7 @@ information of the point cloud into the contraction algorithm.
 
 ### Installation
 
-First install [Python](https://www.python.org/downloads/) Version 3.7 or higher. The python package can be installed
+First install [Python](https://www.python.org/downloads/) Version 3.8 or higher. The python package can be installed
 via [PyPi](https://pypi.org/project/pc-skeletor/) using pip.
 
  ````sh
@@ -83,10 +83,10 @@ lbc = LBC(point_cloud=pcd,
           down_sample=0.008)
 lbc.extract_skeleton()
 lbc.extract_topology()
+
+# Debug/Visualization
 lbc.visualize()
-lbc.show_graph(lbc.skeleton_graph)
-lbc.show_graph(lbc.topology_graph)
-lbc.save('./output')
+lbc.export_results('./output')
 lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]),
             steps=300,
             output='./output')
@@ -103,10 +103,12 @@ s_lbc = SLBC(point_cloud={'trunk': pcd_trunk, 'branches': pcd_branch},
              debug=True)
 s_lbc.extract_skeleton()
 s_lbc.extract_topology()
+
+# Debug/Visualization
 s_lbc.visualize()
 s_lbc.show_graph(s_lbc.skeleton_graph)
 s_lbc.show_graph(s_lbc.topology_graph)
-s_lbc.save('./output')
+s_lbc.export_results('./output')
 s_lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
 ````
 

example_tree.py

@@ -22,9 +22,9 @@
     lbc.visualize()
     lbc.show_graph(lbc.skeleton_graph, fig_size=(30, 30))
     lbc.show_graph(lbc.topology_graph)
-    lbc.save('./output')
-    # lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=500, output='./output')
-    # lbc.animate_contracted_pcd(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
+    lbc.export_results('./output')
+    lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=500, output='./output_lbc')
+    #lbc.animate_contracted_pcd(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
     lbc.animate_topology(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
 
     # Semantic Laplacian-based Contraction
@@ -36,9 +36,9 @@
     s_lbc.extract_skeleton()
     s_lbc.extract_topology()
     s_lbc.visualize()
-    s_lbc.show_graph(lbc.skeleton_graph, fig_size=(30, 30))
-    s_lbc.show_graph(lbc.topology_graph)
-    s_lbc.save('./output')
-    #s_lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=500, output='./output')
+    s_lbc.show_graph(s_lbc.skeleton_graph, fig_size=(30, 30))
+    s_lbc.show_graph(s_lbc.topology_graph)
+    s_lbc.export_results('./output_slbc')
+    s_lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=500, output='./output')
     #s_lbc.animate_contracted_pcd(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
-    s_lbc.animate_topology(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
+    s_lbc.animate_topology(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output_slbc')

pc_skeletor/base.py

@@ -41,12 +41,26 @@ def __init__(self, verbose: bool = False, debug: bool = False):
         self.topology_graph: nx.Graph = nx.Graph()
 
     def extract_skeleton(self):
+        '''
+        Extract skeleton from point cloud
+
+        :return:
+        '''
         pass
 
     def extract_topology(self):
+        '''
+        Extract topology from point cloud
+
+        :return:
+        '''
         pass
 
-    def save(self, *args):
+    def process(self):
+        self.extract_topology()
+        self.extract_topology()
+
+    def export_results(self, *args):
         pass
 
     def show_graph(self, graph: networkx.Graph, pos: Union[np.ndarray, bool] = True, fig_size: tuple = (20, 20)):

pc_skeletor/laplacian.py

@@ -13,6 +13,7 @@
 import open3d.visualization as o3d
 import robust_laplacian
 import mistree as mist
+import networkx as nx
 
 # Own modules
 from pc_skeletor.download import *
@@ -29,8 +30,8 @@ def __init__(self,
                  algo_type: str,
                  point_cloud: Union[str, open3d.geometry.PointCloud, dict],
                  init_contraction: int,
-                 init_attraction: int,
-                 max_contraction: int,
+                 init_attraction: float,
+                 max_contraction: float,
                  max_attraction: int,
                  step_wise_contraction_amplification: Union[float, str],
                  termination_ratio: float,
@@ -58,16 +59,16 @@ def __init__(self,
 
         # Set or load point cloud to apply algorithm
         if isinstance(point_cloud, str):
-            self.pcd: o3d.geometry.PointCloud = load_pcd(filename=point_cloud, normalize=False)
+            self.pcd: o3d.geometry.PointCloud = load_pcd(filename=point_cloud)
         elif isinstance(point_cloud, dict):
             # Currently only two classes are supported!
             if isinstance(point_cloud['trunk'], str):
-                self.trunk: o3d.geometry.PointCloud = load_pcd(filename=point_cloud['trunk'], normalize=False)
+                self.trunk: o3d.geometry.PointCloud = load_pcd(filename=point_cloud['trunk'])
             else:
                 self.trunk: o3d.geometry.PointCloud = point_cloud['trunk']
 
             if isinstance(point_cloud['branches'], str):
-                self.branches: o3d.geometry.PointCloud = load_pcd(filename=point_cloud['branches'], normalize=False)
+                self.branches: o3d.geometry.PointCloud = load_pcd(filename=point_cloud['branches'])
             else:
                 self.branches: o3d.geometry.PointCloud = point_cloud['branches']
         elif isinstance(point_cloud, open3d.geometry.PointCloud):
@@ -181,7 +182,7 @@ def extract_skeleton(self):
         pcd_points_current = pcd_points
         while np.mean(M_list[-1]) / np.mean(M_list[0]) > self.param_termination_ratio:
             pbar.set_description(
-                "Current volume ratio {}. Contraction weights {}. Attraction weights {}. Progress {}".format(
+                "Volume ratio: {}. Contraction weights: {}. Attraction weights: {}. Progress {}".format(
                     volume_ratio, np.mean(laplacian_weights), np.mean(positional_weights), self.algo_type))
             logging.debug('Laplacian Weight: {}'.format(laplacian_weights))
             logging.debug('Mean Positional Weight: {}'.format(np.mean(positional_weights)))
@@ -294,22 +295,22 @@ def extract_topology(self):
 
         return self.topology
 
-    def save(self, output: str):
+    def export_results(self, output: str):
         os.makedirs(output, exist_ok=True)
         path_contracted_pcd = os.path.join(output, '01_point_cloud_contracted_{}'.format(self.algo_type) + '.ply')
         o3d.io.write_point_cloud(path_contracted_pcd, self.contracted_point_cloud)
 
         path_skeleton = os.path.join(output, '02_skeleton_{}'.format(self.algo_type) + '.ply')
-        o3d.io.write_point_cloud(path_skeleton, self.skeleton)
+        o3d.io.write_point_cloud(filename=path_skeleton, pointcloud=self.skeleton)
 
         path_topology = os.path.join(output, '03_topology_{}'.format(self.algo_type) + '.ply')
-        o3d.io.write_line_set(path_topology, self.topology)
+        o3d.io.write_line_set(filename=path_topology, line_set=self.topology)
 
         path_skeleton_graph = os.path.join(output, '04_skeleton_graph_{}'.format(self.algo_type) + '.gpickle')
-        nx.write_gpickle(self.skeleton_graph, path_skeleton_graph)
+        nx.write_gpickle(G=self.skeleton_graph, path=path_skeleton_graph)
 
         path_topology_graph = os.path.join(output, '05_topology_graph_{}'.format(self.algo_type) + '.gpickle')
-        nx.write_gpickle(self.skeleton_graph, path_topology_graph)
+        nx.write_gpickle(G=self.topology_graph, path=path_topology_graph)
 
 
 class LBC(LaplacianBasedContractionBase):
@@ -363,6 +364,18 @@ def __init__(self,
             o3d.visualization.draw_geometries([pcd], window_name="Default Point Cloud")
 
     def __least_squares_sparse(self, pcd_points, L, laplacian_weighting, positional_weighting):
+        """
+        Perform least squares sparse solving for the Laplacian-based contraction.
+
+        Args:
+            pcd_points: The input point cloud points.
+            L: The Laplacian matrix.
+            laplacian_weighting: The Laplacian weighting matrix.
+            positional_weighting: The positional weighting matrix.
+
+        Returns:
+            The contracted point cloud.
+        """
         # Define Weights
         WL = sparse.diags(laplacian_weighting)  # I * laplacian_weighting
         WH = sparse.diags(positional_weighting)
@@ -413,12 +426,12 @@ class SLBC(LaplacianBasedContractionBase):
 
     Our semantic skeletonization algorithm based on Laplacian-Based Contraction.
 
-    Paper: tbd
+    Paper: https://arxiv.org/abs/2304.04708
 
     """
 
     def __init__(self,
-                 point_cloud: Union[str, open3d.geometry.PointCloud],
+                 point_cloud: Union[str, dict],
                  semantic_weighting: float = 10.,
                  init_contraction: float = 1.,
                  init_attraction: float = 0.5,
@@ -463,6 +476,18 @@ def __init__(self,
             o3d.visualization.draw_geometries([self.pcd], window_name="Default Point Cloud")
 
     def __least_squares_sparse(self, pcd_points, L, laplacian_weighting, positional_weighting):
+        """
+        Perform least squares sparse solving for the Semantic Laplacian-Based Contraction (S-LBC).
+
+        Args:
+            pcd_points: The input point cloud points.
+            L: The Laplacian matrix.
+            laplacian_weighting: The Laplacian weighting matrix.
+            positional_weighting: The positional weighting matrix.
+
+        Returns:
+            The contracted point cloud.
+        """
         # Define Weights
         WL = sparse.diags(laplacian_weighting)  # I * laplacian_weighting
         WH = sparse.diags(positional_weighting)
@@ -483,6 +508,7 @@ def __least_squares_sparse(self, pcd_points, L, laplacian_weighting, positional_
         num_valid = np.arange(0, pcd_points.shape[0])[mask]
         S[rows, cols] = 1
 
+        # ToDo: Speed up!
         for i in num_valid:
             S[i, L[i].nonzero()[1]] = multiplier
 
@@ -531,22 +557,28 @@ def __least_squares_sparse(self, pcd_points, L, laplacian_weighting, positional_
     pcd_branch = o3d.io.read_point_cloud(branch_pcd_path)
     pcd = pcd_trunk + pcd_branch
 
+    # pcd = o3d.io.read_point_cloud("/home/luigi/Documents/reco/23_04_14/02/tree.ply")
     # Laplacian-based Contraction
-    lbc = LBC(point_cloud=pcd, down_sample=0.01)
-    lbc.extract_skeleton()
-    lbc.extract_topology()
-    lbc.show_graph(lbc.skeleton_graph)
-    lbc.show_graph(lbc.topology_graph)
-    lbc.visualize()
-    lbc.save('./output')
-    lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
-
-    # Semantic Laplacian-based Contraction
-    s_lbc = SLBC(point_cloud={'trunk': pcd_trunk, 'branches': pcd_branch}, semantic_weighting=10, down_sample=0.01)
-    s_lbc.extract_skeleton()
-    s_lbc.extract_topology()
-    s_lbc.show_graph(s_lbc.skeleton_graph)
-    s_lbc.show_graph(s_lbc.topology_graph)
-    s_lbc.visualize()
-    s_lbc.save('./output')
-    s_lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')
+    if False:
+        lbc = LBC(point_cloud=pcd, init_contraction=3.,
+                  init_attraction=0.6,
+                  max_contraction=2048,
+                  max_attraction=1024,
+                  down_sample=0.02)
+        lbc.extract_skeleton()
+        lbc.extract_topology()
+        lbc.show_graph(lbc.skeleton_graph)
+        lbc.show_graph(lbc.topology_graph)
+        lbc.visualize()
+        lbc.export_results('./output')
+    # lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output_1')
+    else:
+        # Semantic Laplacian-based Contraction
+        s_lbc = SLBC(point_cloud={'trunk': pcd_trunk, 'branches': pcd_branch}, semantic_weighting=10, down_sample=0.009)
+        s_lbc.extract_skeleton()
+        s_lbc.extract_topology()
+        s_lbc.show_graph(s_lbc.skeleton_graph)
+        s_lbc.show_graph(s_lbc.topology_graph)
+        s_lbc.visualize()
+        s_lbc.export_results('./output')
+        s_lbc.animate(init_rot=np.asarray([[1, 0, 0], [0, 0, 1], [0, 1, 0]]), steps=300, output='./output')

pyproject.toml

@@ -1,3 +1,3 @@
 [build-system]
 requires = ["setuptools>=42"]
-build-backend = "setuptools.build_meta"
+build-backend = "setuptools.build_meta"

requirements.txt

@@ -1,12 +1,13 @@
 numpy
-robust_laplacian
+robust_laplacian==0.2.4
 scipy
 matplotlib
-open3d
+open3d==0.16
 tqdm
 imageio
-networkx
+networkx==2.6.3
 charset-normalizer
-mistree==1.2.1
+#mistree==1.2.1
 pytest
-sniffio
+sniffio
+mistree @ git+https://github.com/meyerls/mistree.git