diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..129f92d
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+__pycache__
+build
+data
+results
+*.so
diff --git a/configs/config_abc.yaml b/configs/config_abc.yaml
new file mode 100644
index 0000000..6f5b525
--- /dev/null
+++ b/configs/config_abc.yaml
@@ -0,0 +1,11 @@
+dataset_name: ABC
+dataset_root: data/3d_shapes_abc_training
+
+manifold_points: 3000
+non_manifold_points: 2000
+iter_nbr: 600000
+training_random_rotation_x: 180
+training_random_rotation_y: 180
+training_random_rotation_z: 180
+
+val_interval: 5
diff --git a/configs/config_default.yaml b/configs/config_default.yaml
new file mode 100644
index 0000000..d5b9e0a
--- /dev/null
+++ b/configs/config_default.yaml
@@ -0,0 +1,45 @@
+experiment_name: null
+dataset_name: null
+dataset_root: null
+save_dir: 'results'
+train_split: 'training'
+val_split: 'validation'
+test_split: 'test'
+filter_name: null
+
+manifold_points: 2048
+non_manifold_points: 2048
+random_noise: null # 0.1
+normals: False
+
+#training
+training_random_scale: null # 0.1
+training_random_rotation_x: null # 180
+training_random_rotation_y: null # 180
+training_random_rotation_z: null # 180
+training_batch_size: 16
+training_iter_nbr: 100000
+training_lr_start: 0.001
+
+resume: false
+
+network_backbone: FKAConv
+network_latent_size: 32
+network_decoder: InterpAttentionKHeadsNet
+network_decoder_k: 64
+network_n_labels: 2
+
+device: "cuda"
+threads: 8
+log_mode: "no_log"
+logging: INFO
+
+val_num_mesh: null
+val_interval: 1
+
+
+
+
+
+
+
diff --git a/configs/config_shapenet.yaml b/configs/config_shapenet.yaml
new file mode 100644
index 0000000..472055f
--- /dev/null
+++ b/configs/config_shapenet.yaml
@@ -0,0 +1,8 @@
+dataset_name: ShapeNet
+dataset_root: data/ShapeNet
+
+manifold_points: 3000
+non_manifold_points: 2048
+random_noise: 0.005
+
+iter_nbr: 600000
diff --git a/configs/config_synthetic.yaml b/configs/config_synthetic.yaml
new file mode 100644
index 0000000..b25d6b8
--- /dev/null
+++ b/configs/config_synthetic.yaml
@@ -0,0 +1,12 @@
+dataset_name: SyntheticRooms
+dataset_root: data/synthetic_room_dataset
+
+manifold_points: 10000
+non_manifold_points: 2048
+random_noise: 0.005
+
+training_batch_size: 8
+iter_nbr: 600000
+
+val_interval: 5
+val_num_mesh: 20
\ No newline at end of file
diff --git a/datasets/__init__.py b/datasets/__init__.py
new file mode 100644
index 0000000..9552611
--- /dev/null
+++ b/datasets/__init__.py
@@ -0,0 +1,15 @@
+from .shapenet import ShapeNet
+
+from .synthetic_room import ShapeNetSyntheticRooms as SyntheticRooms
+
+from .scenenet import SceneNet
+from .scenenet import SceneNet as SceneNet20
+from .scenenet import SceneNet as SceneNet100
+from .scenenet import SceneNet as SceneNet500
+from .scenenet import SceneNet as SceneNet1000
+
+from .abc import ABCTrain as ABC
+from .abc_test import ABCTest, ABCTestNoiseFree, ABCTestExtraNoise
+from .real_world import RealWorld
+from .famous_test import FamousTest, FamousTestNoiseFree, FamousTestExtraNoisy, FamousTestSparse, FamousTestDense
+from .thingi10k_test import Thingi10kTest, Thingi10kTestNoiseFree, Thingi10kTestExtraNoisy, Thingi10kTestSparse, Thingi10kTestDense
diff --git a/datasets/abc.py b/datasets/abc.py
new file mode 100644
index 0000000..ba1fb48
--- /dev/null
+++ b/datasets/abc.py
@@ -0,0 +1,103 @@
+from torch_geometric.data import Dataset
+from lightconvpoint.datasets.data import Data
+import os
+import numpy as np
+import torch
+import logging
+
+
+class ABCTrain(Dataset):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, dataset_size=None, **kwargs):
+
+ super().__init__(root, transform, None)
+
+ logging.info(f"Dataset - ABC Training - {split} - {dataset_size}")
+
+
+ self.root = os.path.join(self.root, "abc_train")
+
+ self.filenames = []
+ if split in ["train", "training"]:
+ split_file = os.path.join(self.root, "trainset.txt")
+ elif split in ["val", "validation"]:
+ split_file = os.path.join(self.root, "valset.txt")
+ else:
+ raise ValueError("Unknown split")
+
+ with open(split_file) as f:
+ content = f.readlines()
+ content = [line.split("\n")[0] for line in content]
+ content = [os.path.join(self.root, "04_pts", line) for line in content]
+ self.filenames += content
+ self.filenames.sort()
+
+ if dataset_size is not None:
+ self.filenames = self.filenames[:dataset_size]
+
+ logging.info(f"Dataset - len {len(self.filenames)}")
+
+ def get_category(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ def get_object_name(self, f_id):
+ return self.filenames[f_id].split("/")[-1]
+
+ def get_class_name(self, f_id):
+ return self.metadata[self.get_category(f_id)]["name"]
+
+ @property
+ def raw_file_names(self):
+ return []
+
+ @property
+ def processed_file_names(self):
+ return []
+
+ def _download(self): # override _download to remove makedirs
+ pass
+
+ def download(self):
+ pass
+
+ def process(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+
+ def get_data_for_evaluation(self, idx):
+ filename = self.filenames[idx]
+ raise NotImplementedError
+ data_shape = np.load(os.path.join(filename, "pointcloud.npz"))
+ data_space = np.load(os.path.join(filename, "points.npz"))
+ return data_shape, data_space
+
+ def get(self, idx):
+ """Get item."""
+ filename = self.filenames[idx]
+
+ pts_shp = np.load(filename+".xyz.npy")
+
+ filename = filename.replace("04_pts", "05_query_pts")
+ pts_space = np.load(filename+".ply.npy")
+
+ filename = filename.replace("05_query_pts", "05_query_dist")
+ occupancies = np.load(filename+".ply.npy")
+ occupancies = (occupancies>0).astype(np.int64)
+
+ pts_shp = torch.tensor(pts_shp, dtype=torch.float)
+ pts_space = torch.tensor(pts_space, dtype=torch.float)
+ occupancies = torch.tensor(occupancies, dtype=torch.long)
+
+ data = Data(x = torch.ones_like(pts_shp),
+ shape_id=idx,
+ pos=pts_shp,
+ pos_non_manifold=pts_space, occupancies=occupancies, #
+ )
+
+ return data
\ No newline at end of file
diff --git a/datasets/abc_test.py b/datasets/abc_test.py
new file mode 100644
index 0000000..bc54ae5
--- /dev/null
+++ b/datasets/abc_test.py
@@ -0,0 +1,119 @@
+from torch_geometric.data import Dataset
+from lightconvpoint.datasets.data import Data
+import os
+import numpy as np
+import torch
+import glob
+import logging
+
+
+class ABCTest(Dataset):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, dataset_size=None, variant_directory="abc", **kwargs):
+ super().__init__(root, transform, None)
+
+ logging.info(f"Dataset - ABC Test - Test only - {dataset_size}")
+
+
+ self.root = os.path.join(self.root, variant_directory)
+
+ self.filenames = []
+ split_file = os.path.join(self.root, "testset.txt")
+
+ with open(split_file) as f:
+ content = f.readlines()
+ content = [line.split("\n")[0] for line in content]
+ content = [os.path.join(self.root, "04_pts", line) for line in content]
+ self.filenames += content
+ self.filenames.sort()
+
+ if dataset_size is not None:
+ self.filenames = self.filenames[:dataset_size]
+
+ logging.info(f"Dataset - len {len(self.filenames)}")
+
+ def get_category(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ def get_object_name(self, f_id):
+ return self.filenames[f_id].split("/")[-1]
+
+ def get_class_name(self, f_id):
+ return self.metadata[self.get_category(f_id)]["name"]
+
+ @property
+ def raw_file_names(self):
+ return []
+
+ @property
+ def processed_file_names(self):
+ return []
+
+ def _download(self): # override _download to remove makedirs
+ pass
+
+ def download(self):
+ pass
+
+ def process(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+
+ def get_data_for_evaluation(self, idx):
+ filename = self.filenames[idx]
+ raise NotImplementedError
+ data_shape = np.load(os.path.join(filename, "pointcloud.npz"))
+ data_space = np.load(os.path.join(filename, "points.npz"))
+ return data_shape, data_space
+
+ def get(self, idx):
+ """Get item."""
+ filename = self.filenames[idx]
+
+ pts_shp = np.load(filename+".xyz.npy")
+
+ # np.savetxt("/root/no_backup/test.xyz", np.concatenate([pts_space, occupancies[:,np.newaxis]], axis=1))
+ # exit()
+
+ pts_shp = torch.tensor(pts_shp, dtype=torch.float)
+ pts_space = torch.ones((1,3), dtype=torch.float)
+ occupancies = torch.ones((1,), dtype=torch.long)
+
+ data = Data(x = torch.ones_like(pts_shp),
+ shape_id=idx,
+ pos=pts_shp,
+ pos_non_manifold=pts_space, occupancies=occupancies, #
+ )
+
+ return data
+
+class ABCTestNoiseFree(ABCTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="abc_noisefree", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
+
+
+class ABCTestExtraNoise(ABCTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="abc_extra_noisy", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
diff --git a/datasets/famous_test.py b/datasets/famous_test.py
new file mode 100644
index 0000000..e223ba8
--- /dev/null
+++ b/datasets/famous_test.py
@@ -0,0 +1,139 @@
+from torch_geometric.data import Dataset
+from lightconvpoint.datasets.data import Data
+import os
+import numpy as np
+import torch
+import logging
+
+class FamousTest(Dataset):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="famous_original", dataset_size=None, **kwargs):
+
+ super().__init__(root, transform, None)
+
+ logging.info(f"Dataset - Famous Test - Test only - {dataset_size}")
+
+
+ self.root = os.path.join(self.root, variant_directory)
+
+ self.filenames = []
+ split_file = os.path.join(self.root, "testset.txt")
+
+ with open(split_file) as f:
+ content = f.readlines()
+ content = [line.split("\n")[0] for line in content]
+ content = [os.path.join(self.root, "04_pts", line) for line in content]
+ self.filenames += content
+ self.filenames.sort()
+
+ if dataset_size is not None:
+ self.filenames = self.filenames[:dataset_size]
+
+ logging.info(f"Dataset - len {len(self.filenames)}")
+
+ def get_category(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ def get_object_name(self, f_id):
+ return self.filenames[f_id].split("/")[-1]
+
+ def get_class_name(self, f_id):
+ return self.metadata[self.get_category(f_id)]["name"]
+
+ @property
+ def raw_file_names(self):
+ return []
+
+ @property
+ def processed_file_names(self):
+ return []
+
+ def _download(self): # override _download to remove makedirs
+ pass
+
+ def download(self):
+ pass
+
+ def process(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+
+ def get_data_for_evaluation(self, idx):
+ filename = self.filenames[idx]
+ raise NotImplementedError
+ data_shape = np.load(os.path.join(filename, "pointcloud.npz"))
+ data_space = np.load(os.path.join(filename, "points.npz"))
+ return data_shape, data_space
+
+ def get(self, idx):
+ """Get item."""
+ filename = self.filenames[idx]
+
+ pts_shp = np.load(filename+".xyz.npy")
+ pts_shp = torch.tensor(pts_shp, dtype=torch.float)
+ pts_space = torch.ones((1,3), dtype=torch.float)
+ occupancies = torch.ones((1,), dtype=torch.long)
+
+ data = Data(x = torch.ones_like(pts_shp),
+ shape_id=idx,
+ pos=pts_shp,
+ pos_non_manifold=pts_space, occupancies=occupancies, #
+ )
+
+ return data
+
+
+
+class FamousTestNoiseFree(FamousTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="famous_noisefree", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
+
+class FamousTestExtraNoisy(FamousTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="famous_extra_noisy", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
+
+class FamousTestSparse(FamousTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="famous_sparse", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
+
+class FamousTestDense(FamousTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="famous_dense", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
\ No newline at end of file
diff --git a/datasets/real_world.py b/datasets/real_world.py
new file mode 100644
index 0000000..091861f
--- /dev/null
+++ b/datasets/real_world.py
@@ -0,0 +1,89 @@
+from torch_geometric.data import Dataset
+from lightconvpoint.datasets.data import Data
+import os
+import numpy as np
+import torch
+import logging
+
+class RealWorld(Dataset):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, dataset_size=None, **kwargs):
+
+ super().__init__(root, transform, None)
+
+ logging.info(f"Dataset - Real World- {dataset_size}")
+
+
+ self.root = os.path.join(self.root, "real_world")
+
+ self.filenames = []
+ with open(os.path.join(self.root, "testset.txt")) as f:
+ content = f.readlines()
+ content = [line.split("\n")[0] for line in content]
+ content = [os.path.join(self.root, "03_meshes", line) for line in content]
+ self.filenames += content
+ self.filenames.sort()
+
+ if dataset_size is not None:
+ self.filenames = self.filenames[:dataset_size]
+
+ logging.info(f"Dataset - len {len(self.filenames)}")
+
+ def get_category(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ def get_object_name(self, f_id):
+ return self.filenames[f_id].split("/")[-1]
+
+ def get_class_name(self, f_id):
+ return self.metadata[self.get_category(f_id)]["name"]
+
+ @property
+ def raw_file_names(self):
+ return []
+
+ @property
+ def processed_file_names(self):
+ return []
+
+ def _download(self): # override _download to remove makedirs
+ pass
+
+ def download(self):
+ pass
+
+ def process(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+
+ def get_data_for_evaluation(self, idx):
+ filename = self.filenames[idx]
+ raise NotImplementedError
+ data_shape = np.load(os.path.join(filename, "pointcloud.npz"))
+ data_space = np.load(os.path.join(filename, "points.npz"))
+ return data_shape, data_space
+
+ def get(self, idx):
+ """Get item."""
+ filename = self.filenames[idx]
+
+ filename = filename.replace("03_meshes", "04_pts")
+ pts_shp = np.load(filename+".xyz.npy")
+
+ pts_shp = torch.tensor(pts_shp, dtype=torch.float32)
+
+ data = Data(x = torch.ones_like(pts_shp),
+ shape_id=idx,
+ pos=pts_shp,
+ normal=None,
+ pos_non_manifold=torch.zeros((1,3), dtype=torch.float32),
+ occupancies=None, #
+ )
+
+ return data
\ No newline at end of file
diff --git a/datasets/scenenet.py b/datasets/scenenet.py
new file mode 100644
index 0000000..27598e6
--- /dev/null
+++ b/datasets/scenenet.py
@@ -0,0 +1,123 @@
+import os
+import logging
+import torch
+from torch_geometric.data import Dataset, Data
+import importlib
+from pathlib import Path
+import numpy as np
+import trimesh
+
+class SceneNet(Dataset):
+
+
+ def __init__(self,
+ root,
+ train=True,
+ transform=None, split="training", filter_name=None, dataset_size=None,
+ point_density=None,
+ **kwargs):
+
+
+ super().__init__(root, transform, None)
+
+ logging.info("Dataset - SceneNet")
+
+ self.split = split
+ self.point_density = point_density
+
+ self.filenames = [
+ "1Bathroom/107_labels.obj.ply",
+ "1Bathroom/1_labels.obj.ply",
+ "1Bathroom/28_labels.obj.ply",
+ "1Bathroom/29_labels.obj.ply",
+ "1Bathroom/4_labels.obj.ply",
+ "1Bathroom/5_labels.obj.ply",
+ "1Bathroom/69_labels.obj.ply",
+ "1Bedroom/3_labels.obj.ply",
+ "1Bedroom/77_labels.obj.ply",
+ "1Bedroom/bedroom27.obj.ply",
+ "1Bedroom/bedroom_1.obj.ply",
+ "1Bedroom/bedroom_68.obj.ply",
+ "1Bedroom/bedroom_wenfagx.obj.ply",
+ "1Bedroom/bedroom_xpg.obj.ply",
+ "1Kitchen/1-14_labels.obj.ply",
+ "1Kitchen/102.obj.ply",
+ "1Kitchen/13_labels.obj.ply",
+ "1Kitchen/2.obj.ply",
+ "1Kitchen/35_labels.obj.ply",
+ "1Kitchen/kitchen_106_blender_name_and_mat.obj.ply",
+ "1Kitchen/kitchen_16_blender_name_and_mat.obj.ply",
+ "1Kitchen/kitchen_76_blender_name_and_mat.obj.ply",
+ "1Living-room/cnh_blender_name_and_mat.obj.ply",
+ "1Living-room/living_room_33.obj.ply",
+ "1Living-room/lr_kt7_blender_scene.obj.ply",
+ "1Living-room/pg_blender_name_and_mat.obj.ply",
+ "1Living-room/room_89_blender.obj.ply",
+ "1Living-room/room_89_blender_no_paintings.obj.ply",
+ "1Living-room/yoa_blender_name_mat.obj.ply",
+ "1Office/2_crazy3dfree_labels.obj.ply",
+ "1Office/2_hereisfree_labels.obj.ply",
+ "1Office/4_3dmodel777.obj.ply",
+ "1Office/4_hereisfree_labels.obj.ply",
+ "1Office/7_crazy3dfree_old_labels.obj.ply",
+ ]
+ self.filenames = [os.path.join(self.root, filename) for filename in self.filenames]
+ self.filenames.sort()
+
+ self.dataset_size = dataset_size
+ if self.dataset_size is not None:
+ self.filenames = self.filenames[:self.dataset_size]
+
+ logging.info(f"Dataset - len {len(self.filenames)}")
+
+ def _download(self): # override _download to remove makedirs
+ pass
+
+ def download(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+ def get_category(self, idx):
+ return self.filenames[idx].split("/")[-2]
+
+ def get_object_name(self, idx):
+ return self.filenames[idx].split("/")[-1]
+
+ def get_class_name(self, idx):
+ return "n/a"
+
+
+ def get_data_for_evaluation(self, idx):
+ raise NotImplementedError
+ scene = self.filenames[idx]
+ input_pointcloud = np.load(scene)
+ return input_pointcloud, None
+
+
+ def get(self, idx):
+ """Get item."""
+
+ # load the mesh
+ scene_filename = self.filenames[idx]
+
+ data = np.loadtxt(scene_filename+".xyz", dtype=np.float32)
+
+ pos = data[:,:3]
+ nls = data[:,3:]
+
+ pos = torch.tensor(pos, dtype=torch.float)
+ nls = torch.tensor(nls, dtype=torch.float)
+ pos_non_manifold = torch.zeros((1,3), dtype=torch.float)
+
+
+ data = Data(shape_id=idx, x=torch.ones_like(pos),
+ normal=nls,
+ pos=pos, pos_non_manifold=pos_non_manifold
+ )
+
+ return data
\ No newline at end of file
diff --git a/datasets/scenenet_sample.py b/datasets/scenenet_sample.py
new file mode 100644
index 0000000..4a40aa8
--- /dev/null
+++ b/datasets/scenenet_sample.py
@@ -0,0 +1,72 @@
+import os
+import subprocess
+import open3d as o3d
+import os
+import logging
+import torch
+from torch_geometric.data import Dataset, Data
+import importlib
+from pathlib import Path
+import numpy as np
+import trimesh
+
+point_density = 20
+data_dir = "data/SceneNet"
+target_dir = f"data/SceneNet{point_density}"
+
+filenames = [
+"1Bathroom/107_labels.obj.ply",
+"1Bathroom/1_labels.obj.ply",
+"1Bathroom/28_labels.obj.ply",
+"1Bathroom/29_labels.obj.ply",
+"1Bathroom/4_labels.obj.ply",
+"1Bathroom/5_labels.obj.ply",
+"1Bathroom/69_labels.obj.ply",
+"1Bedroom/3_labels.obj.ply",
+"1Bedroom/77_labels.obj.ply",
+"1Bedroom/bedroom27.obj.ply",
+"1Bedroom/bedroom_1.obj.ply",
+"1Bedroom/bedroom_68.obj.ply",
+"1Bedroom/bedroom_wenfagx.obj.ply",
+"1Bedroom/bedroom_xpg.obj.ply",
+"1Kitchen/1-14_labels.obj.ply",
+"1Kitchen/102.obj.ply",
+"1Kitchen/13_labels.obj.ply",
+"1Kitchen/2.obj.ply",
+"1Kitchen/35_labels.obj.ply",
+"1Kitchen/kitchen_106_blender_name_and_mat.obj.ply",
+"1Kitchen/kitchen_16_blender_name_and_mat.obj.ply",
+"1Kitchen/kitchen_76_blender_name_and_mat.obj.ply",
+"1Living-room/cnh_blender_name_and_mat.obj.ply",
+"1Living-room/living_room_33.obj.ply",
+"1Living-room/lr_kt7_blender_scene.obj.ply",
+"1Living-room/pg_blender_name_and_mat.obj.ply",
+"1Living-room/room_89_blender.obj.ply",
+"1Living-room/room_89_blender_no_paintings.obj.ply",
+"1Living-room/yoa_blender_name_mat.obj.ply",
+"1Office/2_crazy3dfree_labels.obj.ply",
+"1Office/2_hereisfree_labels.obj.ply",
+"1Office/4_3dmodel777.obj.ply",
+"1Office/4_hereisfree_labels.obj.ply",
+"1Office/7_crazy3dfree_old_labels.obj.ply",
+]
+
+for filename in filenames:
+
+ mesh = trimesh.load(os.path.join(data_dir, filename))
+ target_fname = os.path.join(target_dir, filename+".xyz")
+
+ area = mesh.area
+ n_points = int(area * point_density)
+
+ pos, face_index = trimesh.sample.sample_surface(mesh, n_points)
+ nls = mesh.face_normals[face_index]
+
+ pos = pos.astype(np.float16)
+ nls = pos.astype(np.float16)
+
+ pts = np.concatenate([pos, nls], axis=1)
+
+ # create the directory
+ os.makedirs(os.path.dirname(target_fname), exist_ok=True)
+ np.savetxt(target_fname, pts)
diff --git a/datasets/scenenet_watertight.py b/datasets/scenenet_watertight.py
new file mode 100644
index 0000000..8aad316
--- /dev/null
+++ b/datasets/scenenet_watertight.py
@@ -0,0 +1,66 @@
+import os
+import subprocess
+import open3d as o3d
+
+# processed using the code from https://github.com/hjwdzh/Manifold
+
+raw_data_dir="../downloadscenenet"
+manifold_code_dir="./"
+
+filenames =[
+"1Bathroom/107_labels.obj",
+"1Bathroom/1_labels.obj",
+"1Bathroom/28_labels.obj",
+"1Bathroom/29_labels.obj",
+"1Bathroom/4_labels.obj",
+"1Bathroom/5_labels.obj",
+"1Bathroom/69_labels.obj",
+"1Bedroom/3_labels.obj",
+"1Bedroom/77_labels.obj",
+"1Bedroom/bedroom27.obj"
+"1Bedroom/bedroom_1.obj",
+"1Bedroom/bedroom_68.obj",
+"1Bedroom/bedroom_wenfagx.obj",
+"1Bedroom/bedroom_xpg.obj",
+"1Kitchen/1-14_labels.obj",
+"1Kitchen/102.obj",
+"1Kitchen/13_labels.obj",
+"1Kitchen/2.obj",
+"1Kitchen/35_labels.obj",
+"1Kitchen/kitchen_106_blender_name_and_mat.obj",
+"1Kitchen/kitchen_16_blender_name_and_mat.obj",
+"1Kitchen/kitchen_76_blender_name_and_mat.obj",
+"1Living-room/cnh_blender_name_and_mat.obj",
+"1Living-room/living_room_33.obj",
+"1Living-room/lr_kt7_blender_scene.obj",
+"1Living-room/pg_blender_name_and_mat.obj",
+"1Living-room/room_89_blender.obj",
+"1Living-room/room_89_blender_no_paintings.obj",
+"1Living-room/yoa_blender_name_mat.obj",
+"1Office/2_crazy3dfree_labels.obj",
+"1Office/2_hereisfree_labels.obj",
+"1Office/4_3dmodel777.obj",
+"1Office/4_hereisfree_labels.obj",
+"1Office/7_crazy3dfree_labels.obj",
+]
+
+filenames = [os.path.join(raw_data_dir, filename) for filename in filenames]
+
+for filename in filenames:
+ print(filename)
+ fname = filename.split("/")
+ fname = fname[-2:]
+ os.makedirs(fname[0], exist_ok=True)
+ fname = os.path.join(fname[0], fname[1])
+
+ # watertight
+ subprocess.call([os.path.join(manifold_code_dir,"Manifold/build/manifold"),
+ filename, "tmp.obj", "500000"])
+
+ # mesh clean
+ mesh = o3d.io.read_triangle_mesh("tmp.obj")
+ mesh.remove_degenerate_triangles()
+ mesh.remove_duplicated_triangles()
+ mesh.remove_duplicated_vertices()
+
+ o3d.io.write_triangle_mesh(fname+".ply", mesh)
diff --git a/datasets/shapenet.py b/datasets/shapenet.py
new file mode 100644
index 0000000..24f5664
--- /dev/null
+++ b/datasets/shapenet.py
@@ -0,0 +1,181 @@
+from torch_geometric.data import Dataset
+from lightconvpoint.datasets.data import Data
+import os
+import numpy as np
+import torch
+import glob
+import logging
+
+class ShapeNet(Dataset):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, dataset_size=None, **kwargs):
+
+ super().__init__(root, transform, None)
+
+ logging.info(f"Dataset - ShapeNet- {dataset_size}")
+
+ self.split = split
+ self.filter_name = filter_name
+ self.filelists = []
+ self.num_non_manifold_points = num_non_manifold_points
+ if split in ["train", "training"]:
+ for path in glob.glob(os.path.join(self.root,"*/train.lst")):
+ self.filelists.append(path)
+ elif split in ["validation", "val"]:
+ for path in glob.glob(os.path.join(self.root,"*/val.lst")):
+ self.filelists.append(path)
+ elif split in ["trainVal", "trainingValidation", "training_validation"]:
+ for path in glob.glob(os.path.join(self.root,"*/train.lst")):
+ self.filelists.append(path)
+ for path in glob.glob(os.path.join(self.root,"*/val.lst")):
+ self.filelists.append(path)
+ elif split in ["test", "testing"]:
+ for path in glob.glob(os.path.join(self.root,"*/test.lst")):
+ self.filelists.append(path)
+ self.filelists.sort()
+
+ self.filenames = []
+
+ for flist in self.filelists:
+ with open(flist) as f:
+ dirname = os.path.dirname(flist)
+ content = f.readlines()
+ content = [line.split("\n")[0] for line in content]
+ content = [os.path.join(dirname, line) for line in content]
+ if dataset_size is not None:
+ content = content[:dataset_size]
+ self.filenames += content
+
+ if self.filter_name is not None:
+ logging.info(f"Dataset - filter {self.filter_name}")
+ fname_list = []
+ for fname in self.filenames:
+ if self.filter_name in fname:
+ fname_list.append(fname)
+ self.filenames = fname_list
+
+ fnames = []
+ for fname in self.filenames:
+ if os.path.exists(fname):
+ fnames.append(fname)
+ self.filenames = fnames
+
+ logging.info(f"Dataset - len {len(self.filenames)}")
+
+
+ self.metadata = {
+ "04256520": {
+ "id": "04256520",
+ "name": "sofa"
+ },
+ "02691156": {
+ "id": "02691156",
+ "name": "airplane"
+ },
+ "03636649": {
+ "id": "03636649",
+ "name": "lamp"
+ },
+ "04401088": {
+ "id": "04401088",
+ "name": "phone"
+ },
+ "04530566": {
+ "id": "04530566",
+ "name": "vessel"
+ },
+ "03691459": {
+ "id": "03691459",
+ "name": "speaker"
+ },
+ "03001627": {
+ "id": "03001627",
+ "name": "chair"
+ },
+ "02933112": {
+ "id": "02933112",
+ "name": "cabinet"
+ },
+ "04379243": {
+ "id": "04379243",
+ "name": "table"
+ },
+ "03211117": {
+ "id": "03211117",
+ "name": "display"
+ },
+ "02958343": {
+ "id": "02958343",
+ "name": "car"
+ },
+ "02828884": {
+ "id": "02828884",
+ "name": "bench"
+ },
+ "04090263": {
+ "id": "04090263",
+ "name": "rifle"
+ }
+ }
+
+
+ def get_category(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ def get_object_name(self, f_id):
+ return self.filenames[f_id].split("/")[-1]
+
+ def get_class_name(self, f_id):
+ return self.metadata[self.get_category(f_id)]["name"]
+
+ @property
+ def raw_file_names(self):
+ return []
+
+ @property
+ def processed_file_names(self):
+ return []
+
+ def _download(self): # override _download to remove makedirs
+ pass
+
+ def download(self):
+ pass
+
+ def process(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+
+ def get_data_for_evaluation(self, idx):
+ filename = self.filenames[idx]
+ data_shape = np.load(os.path.join(filename, "pointcloud.npz"))
+ data_space = np.load(os.path.join(filename, "points.npz"))
+ return data_shape, data_space
+
+ def get(self, idx):
+ """Get item."""
+ filename = self.filenames[idx]
+ manifold_data =np.load(os.path.join(filename, "pointcloud.npz"))
+ points_shape = manifold_data["points"]
+ normals_shape = manifold_data["normals"]
+ pts_shp = torch.tensor(points_shape, dtype=torch.float)
+ nls_shp = torch.tensor(normals_shape, dtype=torch.float)
+
+ points = np.load(os.path.join(filename, "points.npz"))
+ points_space = torch.tensor(points["points"], dtype=torch.float)
+ occupancies = torch.tensor(np.unpackbits(points['occupancies']), dtype=torch.long)
+
+ data = Data(x = torch.ones_like(pts_shp),
+ shape_id=idx,
+ pos=pts_shp,
+ normal=nls_shp,
+ pos_non_manifold=points_space, occupancies=occupancies, #
+ )
+
+ return data
\ No newline at end of file
diff --git a/datasets/synthetic_room.py b/datasets/synthetic_room.py
new file mode 100644
index 0000000..56d1f32
--- /dev/null
+++ b/datasets/synthetic_room.py
@@ -0,0 +1,145 @@
+import os
+import numpy as np
+import glob
+import torch
+from torch_geometric.data import Dataset
+from torch_geometric.data import Data
+import logging
+
+
+
+class ShapeNetSyntheticRooms(Dataset):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, dataset_size=None, **kwargs):
+
+ super().__init__(root, transform, None)
+
+ logging.info(f"ShapeNetSyntheticRoom")
+
+ input_directories = ["rooms_04", "rooms_05", "rooms_06", "rooms_07", "rooms_08"]
+ self.split = split
+ self.filter_name = filter_name
+ self.num_non_manifold_points = num_non_manifold_points
+
+ self.filenames = []
+ for input_directory in input_directories:
+ if self.split in ["training", "train"]:
+ split_file = ["train"]
+ elif self.split in ["test", "testing"]:
+ split_file = ["test"]
+ elif self.split in ["val", "validation"]:
+ split_file = ["val"]
+ elif self.split in ["trainval", "trainVal", "TrainVal"]:
+ split_file = ["train", "val"]
+ else:
+ raise ValueError(f"Wrong split value {self.split}")
+ for sp_file in split_file:
+ lines = open(os.path.join(self.root, input_directory, f"{sp_file}.lst")).readlines()
+ lines = [l.split("\n")[0] for l in lines]
+ lines = [os.path.join(self.root, input_directory, l) for l in lines]
+ self.filenames += lines
+
+ if dataset_size is not None:
+ self.filenames = self.filenames[:dataset_size]
+ logging.info(f"dataset len {len(self.filenames)}")
+
+
+
+ self.object_classes = ['04256520', '03636649', '03001627', '04379243', '02933112']
+ self.object_classes.sort()
+
+ self.class_corresp = {
+ 0: "outside",
+ 1: "ground",
+ 2: "wall",
+ 3:'02933112',
+ 4:'03001627',
+ 5: '03636649',
+ 6: '04256520',
+ 7: '04379243',
+ }
+
+ self.class_colors = {
+ 1: [100,100,100],
+ 2: [255,255,0],
+ 3: [255,0,0],
+ 4: [0,255,0],
+ 5: [0,0,255],
+ 6: [255,0,255],
+ 7: [0,255,255],
+ }
+
+ def get_category(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ def get_object_name(self, f_id):
+ return self.filenames[f_id].split("/")[-1]
+
+ def get_class_name(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ @property
+ def raw_file_names(self):
+ return []
+
+ @property
+ def processed_file_names(self):
+ return []
+
+ def _download(self):
+ pass
+
+ def download(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+ def get_data_for_evaluation(self, idx):
+ scene = self.filenames[idx]
+
+ input_pointcloud = glob.glob(os.path.join(scene, "pointcloud/*.npz"))
+ input_pointcloud = input_pointcloud[torch.randint(0,len(input_pointcloud),size=(1,)).item()]
+ input_pointcloud = np.load(input_pointcloud)
+
+ non_manifold_pc = glob.glob(os.path.join(scene, "points_iou/*.npz"))
+ non_manifold_pc = non_manifold_pc[torch.randint(0,len(non_manifold_pc),size=(1,)).item()]
+ non_manifold_pc = np.load(non_manifold_pc)
+
+ return input_pointcloud, non_manifold_pc
+
+ def get(self, idx):
+ """Get item."""
+
+ scene = self.filenames[idx]
+
+ manifold_data = glob.glob(os.path.join(scene, "pointcloud/*.npz"))
+ manifold_data = manifold_data[torch.randint(0,len(manifold_data),size=(1,)).item()]
+ manifold_data = np.load(manifold_data)
+ points_shape = manifold_data["points"]
+ normals_shape = manifold_data["normals"]
+ pts_shp = torch.tensor(points_shape, dtype=torch.float)
+ nls_shp = torch.tensor(normals_shape, dtype=torch.float)
+
+
+ non_manifold_data = glob.glob(os.path.join(scene, "points_iou/*.npz"))
+ non_manifold_data = non_manifold_data[torch.randint(0,len(non_manifold_data),size=(1,)).item()]
+ non_manifold_data = np.load(non_manifold_data)
+ points_space = torch.tensor(non_manifold_data["points"], dtype=torch.float)
+ occupancies = torch.tensor(np.unpackbits(non_manifold_data['occupancies']), dtype=torch.long)
+
+
+ data = Data(x = torch.ones_like(pts_shp),
+ shape_id=idx,
+ pos=pts_shp,
+ normal=nls_shp,
+ pos_non_manifold=points_space, occupancies=occupancies, #
+ )
+
+ return data
\ No newline at end of file
diff --git a/datasets/thingi10k_test.py b/datasets/thingi10k_test.py
new file mode 100644
index 0000000..7383db7
--- /dev/null
+++ b/datasets/thingi10k_test.py
@@ -0,0 +1,143 @@
+from torch_geometric.data import Dataset
+from lightconvpoint.datasets.data import Data
+import os
+import numpy as np
+import torch
+import logging
+
+class Thingi10kTest(Dataset):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="thingi10k_scans_original", dataset_size=None, **kwargs):
+
+ super().__init__(root, transform, None)
+
+ logging.info(f"Dataset - Thingi10k Test - Test only - {dataset_size}")
+
+
+ self.root = os.path.join(self.root, variant_directory)
+
+ self.filenames = []
+ split_file = os.path.join(self.root, "testset.txt")
+
+ with open(split_file) as f:
+ content = f.readlines()
+ content = [line.split("\n")[0] for line in content]
+ content = [os.path.join(self.root, "04_pts", line) for line in content]
+ self.filenames += content
+ self.filenames.sort()
+
+ if dataset_size is not None:
+ self.filenames = self.filenames[:dataset_size]
+
+ logging.info(f"Dataset - len {len(self.filenames)}")
+
+ def get_category(self, f_id):
+ return self.filenames[f_id].split("/")[-2]
+
+ def get_object_name(self, f_id):
+ return self.filenames[f_id].split("/")[-1]
+
+ def get_class_name(self, f_id):
+ return self.metadata[self.get_category(f_id)]["name"]
+
+ @property
+ def raw_file_names(self):
+ return []
+
+ @property
+ def processed_file_names(self):
+ return []
+
+ def _download(self): # override _download to remove makedirs
+ pass
+
+ def download(self):
+ pass
+
+ def process(self):
+ pass
+
+ def _process(self):
+ pass
+
+ def len(self):
+ return len(self.filenames)
+
+
+ def get_data_for_evaluation(self, idx):
+ filename = self.filenames[idx]
+ raise NotImplementedError
+ data_shape = np.load(os.path.join(filename, "pointcloud.npz"))
+ data_space = np.load(os.path.join(filename, "points.npz"))
+ return data_shape, data_space
+
+ def get(self, idx):
+ """Get item."""
+ filename = self.filenames[idx]
+
+ pts_shp = np.load(filename+".xyz.npy")
+
+ # np.savetxt("/root/no_backup/test.xyz", np.concatenate([pts_space, occupancies[:,np.newaxis]], axis=1))
+ # exit()
+
+ pts_shp = torch.tensor(pts_shp, dtype=torch.float)
+ pts_space = torch.ones((1,3), dtype=torch.float)
+ occupancies = torch.ones((1,), dtype=torch.long)
+
+ data = Data(x = torch.ones_like(pts_shp),
+ shape_id=idx,
+ pos=pts_shp,
+ pos_non_manifold=pts_space, occupancies=occupancies, #
+ )
+
+ return data
+
+
+
+class Thingi10kTestNoiseFree(Thingi10kTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="thingi10k_scans_noisefree", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
+
+class Thingi10kTestExtraNoisy(Thingi10kTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="thingi10k_scans_extra_noisy", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
+
+class Thingi10kTestSparse(Thingi10kTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="thingi10k_scans_sparse", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
+
+class Thingi10kTestDense(Thingi10kTest):
+
+ def __init__(self, root, split="training", transform=None, filter_name=None, num_non_manifold_points=2048, variant_directory="thingi10k_scans_dense", dataset_size=None, **kwargs):
+
+ super().__init__(root,
+ split=split,
+ transform=transform,
+ filter_name=filter_name,
+ num_non_manifold_points=num_non_manifold_points,
+ variant_directory=variant_directory,
+ dataset_size=dataset_size, **kwargs)
\ No newline at end of file
diff --git a/eval/eval_point2surf/__init__.py b/eval/eval_point2surf/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/eval/eval_point2surf/evaluation.py b/eval/eval_point2surf/evaluation.py
new file mode 100644
index 0000000..0f2ce3f
--- /dev/null
+++ b/eval/eval_point2surf/evaluation.py
@@ -0,0 +1,405 @@
+import numpy as np
+import os
+
+from .utils_mp import start_process_pool
+from .file_utils import make_dir_for_file
+
+
+def calc_accuracy(num_true, num_predictions):
+ if num_predictions == 0:
+ return float('NaN')
+ else:
+ return num_true / num_predictions
+
+
+def calc_precision(num_true_pos, num_false_pos):
+ if isinstance(num_true_pos, (int, float)) and isinstance(num_false_pos, (int, float)) and \
+ num_true_pos + num_false_pos == 0:
+ return float('NaN')
+ else:
+ return num_true_pos / (num_true_pos + num_false_pos)
+
+
+def calc_recall(num_true_pos, num_false_neg):
+ if isinstance(num_true_pos, (int, float)) and isinstance(num_false_neg, (int, float)) and \
+ num_true_pos + num_false_neg == 0:
+ return float('NaN')
+ else:
+ return num_true_pos / (num_true_pos + num_false_neg)
+
+
+def calc_f1(precision, recall):
+ if isinstance(precision, (int, float)) and isinstance(recall, (int, float)) and \
+ precision + recall == 0:
+ return float('NaN')
+ else:
+ return 2.0 * (precision * recall) / (precision + recall)
+
+
+def compare_predictions_binary_tensors(ground_truth, predicted, prediction_name):
+ """
+ :param ground_truth:
+ :param predicted:
+ :param prediction_name:
+ :return: res_dict, prec_per_patch
+ """
+
+ import torch
+
+ if ground_truth.shape != predicted.shape:
+ raise ValueError('The ground truth matrix and the predicted matrix have different sizes!')
+
+ if not isinstance(ground_truth, torch.Tensor) and not isinstance(predicted, torch.Tensor):
+ raise ValueError('Both matrices must be dense of type torch.tensor!')
+
+ ground_truth_int = (ground_truth > 0.0).to(dtype=torch.int32)
+ predicted_int = (predicted > 0.0).to(dtype=torch.int32)
+ res_dict = dict()
+ res_dict['comp_name'] = prediction_name
+
+ res_dict["predictions"] = float(torch.numel(ground_truth_int))
+ res_dict["pred_gt"] = float(torch.numel(ground_truth_int))
+ res_dict["positives"] = float(torch.nonzero(predicted_int).shape[0])
+ res_dict["pos_gt"] = float(torch.nonzero(ground_truth_int).shape[0])
+ res_dict["true_neg"] = res_dict["predictions"] - float(torch.nonzero(predicted_int + ground_truth_int).shape[0])
+ res_dict["negatives"] = res_dict["predictions"] - res_dict["positives"]
+ res_dict["neg_gt"] = res_dict["pred_gt"] - res_dict["pos_gt"]
+ true_pos = ((predicted_int + ground_truth_int) == 2).sum().to(dtype=torch.float32)
+ res_dict["true_pos"] = float(true_pos.sum())
+ res_dict["true"] = res_dict["true_pos"] + res_dict["true_neg"]
+ false_pos = ((predicted_int * 2 + ground_truth_int) == 2).sum().to(dtype=torch.float32)
+ res_dict["false_pos"] = float(false_pos.sum())
+ false_neg = ((predicted_int + 2 * ground_truth_int) == 2).sum().to(dtype=torch.float32)
+ res_dict["false_neg"] = float(false_neg.sum())
+ res_dict["false"] = res_dict["false_pos"] + res_dict["false_neg"]
+ res_dict["accuracy"] = calc_accuracy(res_dict["true"], res_dict["predictions"])
+ res_dict["precision"] = calc_precision(res_dict["true_pos"], res_dict["false_pos"])
+ res_dict["recall"] = calc_recall(res_dict["true_pos"], res_dict["false_neg"])
+ res_dict["f1_score"] = calc_f1(res_dict["precision"], res_dict["recall"])
+
+ return res_dict
+
+
+def eval_predictions(pred_path, gt_path, report_file=None, unsigned=False):
+ files = [f for f in os.listdir(pred_path) if os.path.isfile(os.path.join(pred_path, f)) and f[-4:] == '.npy']
+
+ results = []
+ for f in files:
+ gt_off_path = os.path.join(gt_path, f[:-8] + '.ply.npy')
+ rec_off_path = os.path.join(pred_path, f)
+
+ mat_gt = np.load(gt_off_path)
+ mat_rec = np.load(rec_off_path)
+
+ if unsigned:
+ mat_gt = np.abs(mat_gt)
+ mat_rec = np.abs(mat_rec)
+
+ gt_or_pred_nz = ((mat_rec != 0.0) + (mat_gt != 0.0)) > 0
+ l2 = (mat_rec - mat_gt)
+ l2_sq = l2 * l2
+ mse = l2_sq[gt_or_pred_nz].mean()
+
+ mat_gt_mean = mat_gt.mean()
+ mat_rec_mean = mat_rec.mean()
+ mat_gt_var = (mat_gt * mat_gt).mean() - mat_gt_mean * mat_gt_mean
+ mat_rec_var = (mat_rec * mat_rec).mean() - mat_rec_mean * mat_rec_mean
+
+ res_dict = {
+ 'file': f,
+ 'mse': mse,
+ 'mean_gt': mat_gt_mean,
+ 'mean_pred': mat_rec_mean,
+ 'var_gt': mat_gt_var,
+ 'var_pred': mat_rec_var,
+ }
+ results.append(res_dict)
+
+ print('compare_prediction: {} vs {}\n'.format(gt_path, pred_path))
+ lines = print_list_of_dicts(results, ['file', 'mse', 'mean_gt', 'mean_pred', 'var_gt', 'var_pred'], mode='csv')
+
+ if report_file is not None:
+ make_dir_for_file(report_file)
+ with open(report_file, 'w') as the_file:
+ for l in lines:
+ the_file.write(l + '\n')
+
+
+def print_list_of_dicts(comp_res, keys_to_print=None, mode='latex'):
+
+ if len(comp_res) == 0:
+ return 'WARNING: comp_res is empty'
+
+ if keys_to_print is None or len(keys_to_print) == 0:
+ keys_to_print = comp_res[0].keys()
+
+ def get_separator(i, length):
+ if mode == 'latex':
+ if i < length - 1:
+ return ' & '
+ else:
+ return ' \\\\'
+ elif mode == 'csv':
+ return ','
+
+ # key per line, mesh per column
+ #for key in keys_to_print:
+ # line = key + ' && '
+ # for i, d in enumerate(comp_res):
+ # if isinstance(d[key], str):
+ # line += d[key] + get_separator(i, len(keys_to_print))
+ # else:
+ # line += '{0:.3f}'.format(d[key]) + get_separator(i, len(keys_to_print))
+ # print(line)
+
+ # mesh per line, key per column
+ lines = []
+ # contents
+ for d in comp_res:
+ line = ''
+ for i, key in enumerate(keys_to_print):
+ if isinstance(d[key], str):
+ line += d[key][:10].replace('_', ' ').rjust(max(10, len(key))) + get_separator(i, len(keys_to_print))
+ else:
+ line += '{0:.5f}'.format(d[key]).rjust(max(10, len(key))) + get_separator(i, len(keys_to_print))
+ lines.append(line)
+
+ lines.sort()
+
+ # header
+ line = ''
+ for i, key in enumerate(keys_to_print):
+ line += key.replace('_', ' ').rjust(10) + get_separator(i, len(keys_to_print))
+ lines.insert(0, line)
+
+ for l in lines:
+ print(l)
+
+ return lines
+
+
+def visualize_patch(patch_pts_ps, patch_pts_ms, query_point_ps, pts_sub_sample_ms, query_point_ms,
+ file_path='debug/patch.ply'):
+
+ from .point_cloud import write_ply
+
+ def filter_padding(patch_pts, query_point):
+ query_point_repeated = np.repeat(np.expand_dims(np.array(query_point), axis=0), patch_pts.shape[0], axis=0)
+ same_points = patch_pts == query_point_repeated
+ non_padding_point_ids = np.sum(same_points, axis=1) != 3
+ return patch_pts[non_padding_point_ids]
+
+ patch_pts_ps = filter_padding(patch_pts_ps, query_point_ps)
+ if patch_pts_ms is not None:
+ patch_pts_ms = filter_padding(patch_pts_ms, query_point_ms)
+
+ query_point_ps = np.expand_dims(query_point_ps, axis=0) \
+ if len(query_point_ps.shape) < 2 else query_point_ps
+ query_point_ms = np.expand_dims(query_point_ms, axis=0) \
+ if len(query_point_ms.shape) < 2 else query_point_ms
+
+ pts = np.concatenate((patch_pts_ps, query_point_ps, pts_sub_sample_ms, query_point_ms), axis=0)
+ if patch_pts_ms is not None:
+ pts = np.concatenate((pts, patch_pts_ms), axis=0)
+
+ def repeat_color_for_points(color, points):
+ return np.repeat(np.expand_dims(np.array(color), axis=0), points.shape[0], axis=0)
+
+ colors_patch_pts_ps = repeat_color_for_points([0.0, 0.0, 1.0], patch_pts_ps)
+ colors_query_point_ps = repeat_color_for_points([1.0, 1.0, 0.0], query_point_ps)
+ colors_pts_sub_sample_ms = repeat_color_for_points([0.0, 1.0, 0.0], pts_sub_sample_ms)
+ colors_query_point_ms = repeat_color_for_points([1.0, 0.0, 1.0], query_point_ms)
+ colors = np.concatenate((colors_patch_pts_ps, colors_query_point_ps, colors_pts_sub_sample_ms,
+ colors_query_point_ms), axis=0)
+ if patch_pts_ms is not None:
+ colors_patch_pts_ms = repeat_color_for_points([1.0, 0.0, 0.0], patch_pts_ms)
+ colors = np.concatenate((colors, colors_patch_pts_ms), axis=0)
+
+ write_ply(file_path=file_path, points=pts, colors=colors)
+
+
+def _chamfer_distance_single_file(file_in, file_ref, samples_per_model, num_processes=1):
+ # http://graphics.stanford.edu/courses/cs468-17-spring/LectureSlides/L14%20-%203d%20deep%20learning%20on%20point%20cloud%20representation%20(analysis).pdf
+
+ import trimesh
+ import trimesh.sample
+ import sys
+ import scipy.spatial as spatial
+
+ def sample_mesh(mesh_file, num_samples):
+ try:
+ mesh = trimesh.load(mesh_file)
+ except:
+ return np.zeros((0, 3))
+ samples, face_indices = trimesh.sample.sample_surface_even(mesh, num_samples)
+ return samples
+
+ new_mesh_samples = sample_mesh(file_in, samples_per_model)
+ ref_mesh_samples = sample_mesh(file_ref, samples_per_model)
+
+ if new_mesh_samples.shape[0] == 0 or ref_mesh_samples.shape[0] == 0:
+ return file_in, file_ref, -1.0
+
+ leaf_size = 100
+ sys.setrecursionlimit(int(max(1000, round(new_mesh_samples.shape[0] / leaf_size))))
+ kdtree_new_mesh_samples = spatial.cKDTree(new_mesh_samples, leaf_size)
+ kdtree_ref_mesh_samples = spatial.cKDTree(ref_mesh_samples, leaf_size)
+
+ ref_new_dist, corr_new_ids = kdtree_new_mesh_samples.query(ref_mesh_samples, 1, n_jobs=num_processes)
+ new_ref_dist, corr_ref_ids = kdtree_ref_mesh_samples.query(new_mesh_samples, 1, n_jobs=num_processes)
+
+ ref_new_dist_sum = np.sum(ref_new_dist)
+ new_ref_dist_sum = np.sum(new_ref_dist)
+ chamfer_dist = ref_new_dist_sum + new_ref_dist_sum
+
+ return file_in, file_ref, chamfer_dist
+
+
+def _hausdorff_distance_directed_single_file(file_in, file_ref, samples_per_model):
+ import scipy.spatial as spatial
+ import trimesh
+ import trimesh.sample
+
+ def sample_mesh(mesh_file, num_samples):
+ try:
+ mesh = trimesh.load(mesh_file)
+ except:
+ return np.zeros((0, 3))
+ samples, face_indices = trimesh.sample.sample_surface_even(mesh, num_samples)
+ return samples
+
+ new_mesh_samples = sample_mesh(file_in, samples_per_model)
+ ref_mesh_samples = sample_mesh(file_ref, samples_per_model)
+
+ if new_mesh_samples.shape[0] == 0 or ref_mesh_samples.shape[0] == 0:
+ return file_in, file_ref, -1.0
+
+ dist, _, _ = spatial.distance.directed_hausdorff(new_mesh_samples, ref_mesh_samples)
+ return file_in, file_ref, dist
+
+
+def _hausdorff_distance_single_file(file_in, file_ref, samples_per_model):
+ import scipy.spatial as spatial
+ import trimesh
+ import trimesh.sample
+
+ def sample_mesh(mesh_file, num_samples):
+ try:
+ mesh = trimesh.load(mesh_file)
+ except:
+ return np.zeros((0, 3))
+ samples, face_indices = trimesh.sample.sample_surface_even(mesh, num_samples)
+ return samples
+
+ new_mesh_samples = sample_mesh(file_in, samples_per_model)
+ ref_mesh_samples = sample_mesh(file_ref, samples_per_model)
+
+ if new_mesh_samples.shape[0] == 0 or ref_mesh_samples.shape[0] == 0:
+ return file_in, file_ref, -1.0, -1.0, -1.0
+
+ dist_new_ref, _, _ = spatial.distance.directed_hausdorff(new_mesh_samples, ref_mesh_samples)
+ dist_ref_new, _, _ = spatial.distance.directed_hausdorff(ref_mesh_samples, new_mesh_samples)
+ dist = max(dist_new_ref, dist_ref_new)
+ return file_in, file_ref, dist_new_ref, dist_ref_new, dist
+
+
+def mesh_comparison(new_meshes_dir_abs, ref_meshes_dir_abs,
+ num_processes, report_name, samples_per_model=10000, dataset_file_abs=None):
+ if not os.path.isdir(new_meshes_dir_abs):
+ print('Warning: dir to check doesn\'t exist'.format(new_meshes_dir_abs))
+ return
+
+ new_mesh_files = [f for f in os.listdir(new_meshes_dir_abs)
+ if os.path.isfile(os.path.join(new_meshes_dir_abs, f))]
+ ref_mesh_files = [f for f in os.listdir(ref_meshes_dir_abs)
+ if os.path.isfile(os.path.join(ref_meshes_dir_abs, f))]
+
+ if dataset_file_abs is None:
+ mesh_files_to_compare_set = set(ref_mesh_files) # set for efficient search
+ else:
+ if not os.path.isfile(dataset_file_abs):
+ raise ValueError('File does not exist: {}'.format(dataset_file_abs))
+ with open(dataset_file_abs) as f:
+ mesh_files_to_compare_set = f.readlines()
+ mesh_files_to_compare_set = [f.replace('\n', '') + '.ply' for f in mesh_files_to_compare_set]
+ mesh_files_to_compare_set = [f.split('.')[0] for f in mesh_files_to_compare_set]
+ mesh_files_to_compare_set = set(mesh_files_to_compare_set)
+
+ # # skip if everything is unchanged
+ # new_mesh_files_abs = [os.path.join(new_meshes_dir_abs, f) for f in new_mesh_files]
+ # ref_mesh_files_abs = [os.path.join(ref_meshes_dir_abs, f) for f in ref_mesh_files]
+ # if not utils_files.call_necessary(new_mesh_files_abs + ref_mesh_files_abs, report_name):
+ # return
+
+ def ref_mesh_for_new_mesh(new_mesh_file: str, all_ref_meshes: list) -> list:
+ stem_new_mesh_file = new_mesh_file.split('.')[0]
+ ref_files = list(set([f for f in all_ref_meshes if f.split('.')[0] == stem_new_mesh_file]))
+ return ref_files
+
+ call_params = []
+ for fi, new_mesh_file in enumerate(new_mesh_files):
+ # if new_mesh_file.split('.')[0] in mesh_files_to_compare_set:
+ if new_mesh_file in mesh_files_to_compare_set:
+ new_mesh_file_abs = os.path.join(new_meshes_dir_abs, new_mesh_file)
+ ref_mesh_files_matching = ref_mesh_for_new_mesh(new_mesh_file, ref_mesh_files)
+ if len(ref_mesh_files_matching) > 0:
+ ref_mesh_file_abs = os.path.join(ref_meshes_dir_abs, ref_mesh_files_matching[0])
+ call_params.append((new_mesh_file_abs, ref_mesh_file_abs, samples_per_model))
+ if len(call_params) == 0:
+ raise ValueError('Results are empty!')
+ results_hausdorff = start_process_pool(_hausdorff_distance_single_file, call_params, num_processes)
+ results = [(r[0], r[1], str(r[2]), str(r[3]), str(r[4])) for r in results_hausdorff]
+
+ call_params = []
+ for fi, new_mesh_file in enumerate(new_mesh_files):
+ # if new_mesh_file.split('.')[0] in mesh_files_to_compare_set:
+ if new_mesh_file in mesh_files_to_compare_set:
+ new_mesh_file_abs = os.path.join(new_meshes_dir_abs, new_mesh_file)
+ ref_mesh_files_matching = ref_mesh_for_new_mesh(new_mesh_file, ref_mesh_files)
+ if len(ref_mesh_files_matching) > 0:
+ ref_mesh_file_abs = os.path.join(ref_meshes_dir_abs, ref_mesh_files_matching[0])
+ call_params.append((new_mesh_file_abs, ref_mesh_file_abs, samples_per_model))
+ results_chamfer = start_process_pool(_chamfer_distance_single_file, call_params, num_processes)
+ results = [r + (str(results_chamfer[ri][2]),) for ri, r in enumerate(results)]
+
+ # no reference but reconstruction
+ for fi, new_mesh_file in enumerate(new_mesh_files):
+ # if new_mesh_file.split('.')[0] not in mesh_files_to_compare_set:
+ if new_mesh_file not in mesh_files_to_compare_set:
+ if dataset_file_abs is None:
+ new_mesh_file_abs = os.path.join(new_meshes_dir_abs, new_mesh_file)
+ ref_mesh_files_matching = ref_mesh_for_new_mesh(new_mesh_file, ref_mesh_files)
+ if len(ref_mesh_files_matching) > 0:
+ reference_mesh_file_abs = os.path.join(ref_meshes_dir_abs, ref_mesh_files_matching[0])
+ results.append((new_mesh_file_abs, reference_mesh_file_abs, str(-2), str(-2), str(-2), str(-2)))
+ else:
+ # mesh_files_to_compare_set.remove(new_mesh_file.split('.')[0])
+ mesh_files_to_compare_set.remove(new_mesh_file)
+
+ # no reconstruction but reference
+ for ref_without_new_mesh in mesh_files_to_compare_set:
+ new_mesh_file_abs = os.path.join(new_meshes_dir_abs, ref_without_new_mesh)
+ reference_mesh_file_abs = os.path.join(ref_meshes_dir_abs, ref_without_new_mesh)
+ results.append((new_mesh_file_abs, reference_mesh_file_abs, str(-1), str(-1), str(-1), str(-1)))
+
+ # sort by file name
+ results = sorted(results, key=lambda x: x[0])
+
+ # compute the average of the scores
+ res = np.array([list(item[2:]) for item in results], dtype=np.float)
+ res = res.mean(axis=0)
+ res = ("mean", "mean", str(res[0]), str(res[1]), str(res[2]), str(res[3]))
+ results.append(res)
+
+
+ make_dir_for_file(report_name)
+ csv_lines = ['in mesh,ref mesh,Hausdorff dist new-ref,Hausdorff dist ref-new,Hausdorff dist,'
+ 'Chamfer dist(-1: no input; -2: no reference)']
+ csv_lines += [','.join(item) for item in results]
+ #csv_lines += ['=AVERAGE(E2:E41)']
+ csv_lines_str = '\n'.join(csv_lines)
+ with open(report_name, "w") as text_file:
+ text_file.write(csv_lines_str)
+
+
+
\ No newline at end of file
diff --git a/eval/eval_point2surf/file_utils.py b/eval/eval_point2surf/file_utils.py
new file mode 100644
index 0000000..8a60023
--- /dev/null
+++ b/eval/eval_point2surf/file_utils.py
@@ -0,0 +1,253 @@
+import numpy as np
+import os
+import scipy.sparse as sparse
+
+
+def filename_to_hash(file_path):
+ import hashlib
+ if not os.path.isfile(file_path):
+ raise ValueError('Path does not point to a file: {}'.format(file_path))
+ hash_input = os.path.basename(file_path).split('.')[0]
+ hash = int(hashlib.md5(hash_input.encode()).hexdigest(), 16) % (2**32 - 1)
+ return hash
+
+
+def load_npy_if_valid(filename, data_type, mmap_mode=None):
+ if not os.path.isfile(filename) or (os.path.isfile(filename + '.npy') and
+ (os.path.getmtime(filename + '.npy') > os.path.getmtime(filename))):
+ data = np.load(filename + '.npy', mmap_mode).astype(data_type)
+ else:
+ data = np.loadtxt(filename).astype(data_type)
+ np.save(filename + '.npy', data)
+ if os.path.isfile(filename + '.npy') and (os.path.getmtime(filename + '.npy') < os.path.getmtime(filename)):
+ print('Warning: \"' + filename + '\" is newer than \"' + filename + '.npy\". Loading \"' + filename + '\"')
+
+ return data
+
+
+def npz_to_txt(path_in, path_out, num_files=None):
+
+ files = [f for f in os.listdir(path_in) if os.path.isfile(os.path.join(path_in, f)) and f[-4:] == '.npz']
+
+ for fi, f in enumerate(files):
+ print('Converting npz to txt: ' + f)
+ npz_to_txt_file(file_npz_in=os.path.join(path_in, f), file_txt_out=os.path.join(path_out, f[:-4]))
+ if not num_files is None and fi >= num_files - 1:
+ break
+
+
+def npz_to_txt_file(file_npz_in, file_txt_out):
+
+ sparse_mat = sparse.load_npz(file_npz_in)
+
+ coo = sparse_mat.nonzero()
+ coo_x = coo[0]
+ coo_y = coo[1]
+
+ make_dir_for_file(file_txt_out)
+
+ with open(file_txt_out, 'w') as the_file:
+ for i in range(coo_x.shape[0]):
+ the_file.write(str(coo_x[i]) + ' ' + str(coo_y[i]) + ' ' + str(sparse_mat[coo_x[i], coo_y[i]]) + '\n')
+
+
+def txt_to_npz_file(file_txt_in, file_npz_out, dtype=None, size=None):
+ if dtype is None:
+ dtype={'names': ('i', 'j', 'val'),
+ 'formats': (np.uint32, np.uint32, np.float32)}
+ v_from, v_to, val = np.loadtxt(file_txt_in, unpack=True, dtype=dtype)
+ if size is None:
+ size = max(v_from.max(), v_to.max())
+ sparse_mat = sparse.coo_matrix((val, (v_from, v_to)), (size+1, size+1)).tocsr()
+ sparse.save_npz(file_npz_out, sparse_mat)
+
+
+def txt_to_npz(path, ending='.txt', dtype=None, size=None):
+
+ files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and f[-len(ending):] == ending]
+
+ for f in files:
+ file = os.path.join(path, f)
+ file_npz = file+'.npz'
+ print(file + ' to ' + file_npz)
+ txt_to_npz_file(file_txt_in=file, file_npz_out=file_npz, dtype=dtype, size=size)
+
+
+def txt_to_npy_file(file_txt_in, file_npy_out):
+ arr = np.loadtxt(file_txt_in, unpack=True)
+ arr = arr.transpose()[:, :3].astype(np.float32)
+ np.save(file_npy_out, arr)
+
+
+def txt_to_npy(path, ending='.txt'):
+ files = [f for f in os.listdir(path) if os.path.isfile(os.path.join(path, f)) and f[-len(ending):] == ending]
+
+ for f in files:
+ file = os.path.join(path, f)
+ file_npy = file + '.npy'
+ print(file + ' to ' + file_npy)
+ txt_to_npy_file(file_txt_in=file, file_npy_out=file_npy)
+
+
+def concat_txt_files(files_in, file_out):
+ lines_per_file = []
+ for fi, f in enumerate(files_in):
+ with open(f) as file:
+ new_lines = file.readlines()
+ new_lines = [l.replace(' \n', '') for l in new_lines]
+ lines_per_file.append(new_lines)
+
+ # assume same number of lines in all files
+ lines_output = []
+ for li in range(len(lines_per_file[0])):
+ lines = [f[li] for f in lines_per_file]
+ lines_output.append(' '.join(lines))
+
+ with open(file_out, "w+") as file:
+ file.writelines(lines_output)
+
+
+def concat_txt_dirs(ref_dir, ref_ending, dirs, endings_per_dir=('.txt',), out_dir='../concat/', out_ending='.txt'):
+
+ file_stems = [os.path.splitext(f)[0] for f in os.listdir(ref_dir)
+ if os.path.isfile(os.path.join(ref_dir, f)) and f[-len(ref_ending):] == ref_ending]
+ files = []
+ for fi, file_stem in enumerate(file_stems):
+ files.append([os.path.join(dir, file_stem + endings_per_dir[di]) for di, dir in enumerate(dirs)])
+
+ os.makedirs(out_dir, exist_ok=True)
+
+ for fi, f in enumerate(files):
+ file_out = os.path.join(out_dir, file_stems[fi] + out_ending)
+ if call_necessary(f, file_out):
+ print('concat {} to {}'.format(f, file_out))
+ concat_txt_files(files_in=f, file_out=file_out)
+
+
+def make_dir_for_file(file):
+ file_dir = os.path.dirname(file)
+ if file_dir != '':
+ if not os.path.exists(file_dir):
+ try:
+ os.makedirs(os.path.dirname(file))
+ except OSError as exc: # Guard against race condition
+ raise
+
+
+def load_npz(npz_file, mmap_mode=None):
+ try:
+ return sparse.load_npz(npz_file)
+ except:
+ # npz does not contain a sparse matrix but the data to construct one
+ geodesic_file = np.load(npz_file, mmap_mode)
+ data = geodesic_file['data']
+ col_ind = geodesic_file['col_ind']
+ row_ind = geodesic_file['row_ind']
+ shape = tuple(geodesic_file['shape'])
+ return sparse.csr_matrix((data, (row_ind, col_ind)), shape=shape)
+
+
+def path_leaf(path):
+ import ntpath
+ head, tail = ntpath.split(path)
+ return tail or ntpath.basename(head)
+
+
+def touch_files_in_dir(dir, extension=None):
+ import os
+ from pathlib import Path
+
+ files = [f for f in os.listdir(dir) if os.path.isfile(os.path.join(dir, f))]
+ if extension is not None:
+ files = [f for f in files if f[-len(extension):] == extension]
+ for fi, f in enumerate(files):
+ file_in_abs = os.path.join(dir, f)
+ Path(file_in_abs).touch()
+
+
+def copy_list_of_files_in_dir(dir_in, dir_out, file_list):
+ import os
+ import shutil
+
+ files = [f for f in os.listdir(dir_in) if os.path.isfile(os.path.join(dir_in, f))]
+ file_stems = [os.path.basename(f) for f in files]
+ file_stems = [f.split('.')[0] for f in file_stems]
+
+ if file_list is None:
+ files_to_copy_set = set(file_stems) # set for efficient search
+ else:
+ with open(file_list) as f:
+ files_to_copy_set = f.readlines()
+ files_to_copy_set = [f.replace('\n', '') for f in files_to_copy_set]
+ files_to_copy_set = [f.split('.')[0] for f in files_to_copy_set]
+ files_to_copy_set = set(files_to_copy_set)
+
+ os.makedirs(dir_out, exist_ok=True)
+
+ for fi, f in enumerate(files):
+ if file_stems[fi] in files_to_copy_set:
+ file_in_abs = os.path.join(dir_in, f)
+ file_out_abs = os.path.join(dir_out, f)
+ shutil.copyfile(src=file_in_abs, dst=file_out_abs)
+
+
+def call_necessary(file_in, file_out, min_file_size=0):
+ """
+ Check if all input files exist and at least one output file does not exist or is invalid.
+ :param file_in: list of str or str
+ :param file_out: list of str or str
+ :param min_file_size: int
+ :return:
+ """
+
+ if isinstance(file_in, str):
+ file_in = [file_in]
+ elif isinstance(file_in, list):
+ pass
+ else:
+ raise ValueError('Wrong input type')
+
+ if isinstance(file_out, str):
+ file_out = [file_out]
+ elif isinstance(file_out, list):
+ pass
+ else:
+ raise ValueError('Wrong output type')
+
+ inputs_missing = [f for f in file_in if not os.path.isfile(f)]
+ if len(inputs_missing) > 0:
+ print('WARNING: Input file are missing: {}'.format(inputs_missing))
+ return False
+
+ outputs_missing = [f for f in file_out if not os.path.isfile(f)]
+ if len(outputs_missing) > 0:
+ if len(outputs_missing) < len(file_out):
+ print("WARNING: Only some output files are missing: {}".format(outputs_missing))
+ return True
+
+ min_output_file_size = min([os.path.getsize(f) for f in file_out])
+ if min_output_file_size < min_file_size:
+ return True
+
+ oldest_input_file_mtime = max([os.path.getmtime(f) for f in file_in])
+ youngest_output_file_mtime = min([os.path.getmtime(f) for f in file_out])
+
+ if oldest_input_file_mtime >= youngest_output_file_mtime:
+ # debug
+ import time
+ input_file_mtime_arg_max = np.argmax(np.array([os.path.getmtime(f) for f in file_in]))
+ output_file_mtime_arg_min = np.argmin(np.array([os.path.getmtime(f) for f in file_out]))
+ input_file_mtime_max = time.strftime('%Y-%m-%d %H:%M:%S', time.gmtime(oldest_input_file_mtime))
+ output_file_mtime_min = time.strftime('%Y-%m-%d %H:%M:%S', time.gmtime(youngest_output_file_mtime))
+ print('Input file {} \nis newer than output file {}: \n{} >= {}'.format(
+ file_in[input_file_mtime_arg_max], file_out[output_file_mtime_arg_min],
+ input_file_mtime_max, output_file_mtime_min))
+ return True
+
+ return False
+
+
+def xyz_to_npy(file):
+ from .point_cloud import load_xyz
+ p = load_xyz(file)
+ np.save(file + '.npy', p)
\ No newline at end of file
diff --git a/eval/eval_point2surf/point_cloud.py b/eval/eval_point2surf/point_cloud.py
new file mode 100644
index 0000000..9c8f44c
--- /dev/null
+++ b/eval/eval_point2surf/point_cloud.py
@@ -0,0 +1,193 @@
+import numpy as np
+import scipy.spatial as spatial
+
+from .file_utils import make_dir_for_file
+
+
+def get_aabb(points: np.ndarray):
+ aabb_min = points.min(axis=0)
+ aabb_max = points.max(axis=0)
+ return aabb_min, aabb_max
+
+
+def load_xyz(file_path):
+ data = np.loadtxt(file_path).astype('float32')
+ nan_lines = np.isnan(data).any(axis=1)
+ num_nan_lines = np.sum(nan_lines)
+ if num_nan_lines > 0:
+ data = data[~nan_lines] # filter rows with nan values
+ print('Ignored {} points containing NaN coordinates in point cloud {}'.format(num_nan_lines, file_path))
+ return data
+
+
+def write_ply(file_path: str, points: np.ndarray, normals=None, colors=None):
+ """
+ Write point cloud file as .ply.
+ :param file_path:
+ :param points:
+ :param normals:
+ :param colors:
+ :return: None
+ """
+
+ import trimesh
+
+ assert(file_path.endswith('.ply'))
+
+ make_dir_for_file(file_path)
+
+ if points.shape == (3,):
+ points = np.expand_dims(points, axis=0)
+
+ if points.shape[0] == 3 and points.shape[1] != 3:
+ points = points.transpose([1, 0])
+
+ if colors is not None and colors.shape[0] == 3 and colors.shape[1] != 3:
+ colors = colors.transpose([1, 0])
+
+ if normals is not None and normals.shape[0] == 3 and normals.shape[1] != 3:
+ normals = normals.transpose([1, 0])
+
+ # convert 2d points to 3d
+ if points.shape[1] == 2:
+ vertices_2p5d = np.zeros((points.shape[0], 3))
+ vertices_2p5d[:, :2] = points
+ vertices_2p5d[:, 2] = 0.0
+ points = vertices_2p5d
+
+ mesh = trimesh.Trimesh(vertices=points, vertex_colors=colors, vertex_normals=normals)
+ mesh.export(file_path)
+
+
+def write_xyz(file_path, points: np.ndarray, normals=None, colors=None):
+ """
+ Write point cloud file.
+ :param file_path:
+ :param points:
+ :param normals:
+ :param colors:
+ :return: None
+ """
+
+ make_dir_for_file(file_path)
+
+ if points.shape == (3,):
+ points = np.expand_dims(points, axis=0)
+
+ if points.shape[0] == 3 and points.shape[1] != 3:
+ points = points.transpose([1, 0])
+
+ if colors is not None and colors.shape[0] == 3 and colors.shape[1] != 3:
+ colors = colors.transpose([1, 0])
+
+ if normals is not None and normals.shape[0] == 3 and normals.shape[1] != 3:
+ normals = normals.transpose([1, 0])
+
+ with open(file_path, 'w') as fp:
+
+ # convert 2d points to 3d
+ if points.shape[1] == 2:
+ vertices_2p5d = np.zeros((points.shape[0], 3))
+ vertices_2p5d[:, :2] = points
+ vertices_2p5d[:, 2] = 0.0
+ points = vertices_2p5d
+
+ # write points
+ # meshlab doesn't like colors, only using normals. try cloud compare instead.
+ for vi, v in enumerate(points):
+ line_vertex = str(v[0]) + " " + str(v[1]) + " " + str(v[2]) + " "
+ if normals is not None:
+ line_vertex += str(normals[vi][0]) + " " + str(normals[vi][1]) + " " + str(normals[vi][2]) + " "
+ if colors is not None:
+ line_vertex += str(colors[vi][0]) + " " + str(colors[vi][1]) + " " + str(colors[vi][2]) + " "
+ fp.write(line_vertex + "\n")
+
+
+def load_pcd(file_in):
+ # PCD: http://pointclouds.org/documentation/tutorials/pcd_file_format.php
+ # PCD RGB: http://docs.pointclouds.org/trunk/structpcl_1_1_r_g_b.html#a4ad91ab9726a3580e6dfc734ab77cd18
+
+ def read_header(lines_header):
+ header_info = dict()
+
+ def add_line_to_header_dict(header_dict, line, expected_field):
+ line_parts = line.split(sep=' ')
+ assert (line_parts[0] == expected_field), \
+ ('Warning: "' + expected_field + '" expected but not found in pcd header!')
+ header_dict[expected_field] = (' '.join(line_parts[1:])).replace('\n', '')
+
+ add_line_to_header_dict(header_info, lines_header[0], '#')
+ add_line_to_header_dict(header_info, lines_header[1], 'VERSION')
+ add_line_to_header_dict(header_info, lines_header[2], 'FIELDS')
+ add_line_to_header_dict(header_info, lines_header[3], 'SIZE')
+ add_line_to_header_dict(header_info, lines_header[4], 'TYPE')
+ add_line_to_header_dict(header_info, lines_header[5], 'COUNT')
+ add_line_to_header_dict(header_info, lines_header[6], 'WIDTH')
+ add_line_to_header_dict(header_info, lines_header[7], 'HEIGHT')
+ add_line_to_header_dict(header_info, lines_header[8], 'VIEWPOINT')
+ add_line_to_header_dict(header_info, lines_header[9], 'POINTS')
+ add_line_to_header_dict(header_info, lines_header[10], 'DATA')
+
+ # TODO: lift limitations
+ assert header_info['VERSION'] == '0.7'
+ assert header_info['FIELDS'] == 'x y z rgb label'
+ assert header_info['SIZE'] == '4 4 4 4 4'
+ assert header_info['TYPE'] == 'F F F F U'
+ assert header_info['COUNT'] == '1 1 1 1 1'
+ # assert header_info['HEIGHT'] == '1'
+ assert header_info['DATA'] == 'ascii'
+ # assert header_info['WIDTH'] == header_info['POINTS']
+
+ return header_info
+
+ f = open(file_in, "r")
+ f_lines = f.readlines()
+ f_lines_header = f_lines[:11]
+ f_lines_points = f_lines[11:]
+ header_info = read_header(f_lines_header)
+ header_info['_file_'] = file_in
+
+ num_points = int(header_info['POINTS'])
+ point_data_list_str_ = [l.split(sep=' ')[:3] for l in f_lines_points]
+ point_data_list = [[float(l[0]), float(l[1]), float(l[2])] for l in point_data_list_str_]
+
+ # filter nan points that appear through the blensor kinect sensor
+ point_data_list = [p for p in point_data_list if
+ (not np.isnan(p[0]) and not np.isnan(p[1]) and not np.isnan(p[2]))]
+
+ point_data = np.array(point_data_list)
+
+ f.close()
+
+ return point_data, header_info
+
+
+def get_patch_radius(grid_res, epsilon):
+ return (1.0 + epsilon) / grid_res
+
+
+def get_patch_kdtree(
+ kdtree: spatial.cKDTree, rng: np.random.RandomState,
+ query_point, patch_radius, points_per_patch, n_jobs):
+
+ if patch_radius <= 0.0:
+ pts_dists_ms, patch_pts_ids = kdtree.query(x=query_point, k=points_per_patch, n_jobs=n_jobs)
+ else:
+ patch_pts_ids = kdtree.query_ball_point(x=query_point, r=patch_radius, n_jobs=n_jobs)
+ patch_pts_ids = np.array(patch_pts_ids, dtype=np.int32)
+ point_count = patch_pts_ids.shape[0]
+
+ # if there are too many neighbors, pick a random subset
+ if point_count > points_per_patch:
+ patch_pts_ids = patch_pts_ids[rng.choice(np.arange(point_count), points_per_patch, replace=False)]
+
+ # pad with zeros
+ if point_count < points_per_patch:
+ missing_points = points_per_patch - point_count
+ padding = np.full((missing_points), -1, dtype=np.int32)
+ if point_count == 0:
+ patch_pts_ids = padding
+ else:
+ patch_pts_ids = np.concatenate((patch_pts_ids, padding), axis=0)
+
+ return patch_pts_ids
\ No newline at end of file
diff --git a/eval/eval_point2surf/utils_mp.py b/eval/eval_point2surf/utils_mp.py
new file mode 100644
index 0000000..dc4dd47
--- /dev/null
+++ b/eval/eval_point2surf/utils_mp.py
@@ -0,0 +1,37 @@
+import subprocess
+import multiprocessing
+
+
+def mp_worker(call):
+ """
+ Small function that starts a new thread with a system call. Used for thread pooling.
+ :param call:
+ :return:
+ """
+ call = call.split(' ')
+ verbose = call[-1] == '--verbose'
+ if verbose:
+ call = call[:-1]
+ subprocess.run(call)
+ else:
+ #subprocess.run(call, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) # suppress outputs
+ subprocess.run(call, stdout=subprocess.DEVNULL)
+
+
+def start_process_pool(worker_function, parameters, num_processes, timeout=None):
+
+ if len(parameters) > 0:
+ if num_processes <= 1:
+ print('Running loop for {} with {} calls on {} workers'.format(
+ str(worker_function), len(parameters), num_processes))
+ results = []
+ for c in parameters:
+ results.append(worker_function(*c))
+ return results
+ print('Running loop for {} with {} calls on {} subprocess workers'.format(
+ str(worker_function), len(parameters), num_processes))
+ with multiprocessing.Pool(processes=num_processes, maxtasksperchild=1) as pool:
+ results = pool.starmap(worker_function, parameters)
+ return results
+ else:
+ return None
\ No newline at end of file
diff --git a/eval/src/__init__.py b/eval/src/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/eval/src/common.py b/eval/src/common.py
new file mode 100644
index 0000000..ece0f2b
--- /dev/null
+++ b/eval/src/common.py
@@ -0,0 +1,301 @@
+import torch
+from eval.src.utils.libkdtree import KDTree
+import numpy as np
+
+
+def compute_iou(occ1, occ2):
+ ''' Computes the Intersection over Union (IoU) value for two sets of
+ occupancy values.
+ Args:
+ occ1 (tensor): first set of occupancy values
+ occ2 (tensor): second set of occupancy values
+ '''
+ occ1 = np.asarray(occ1)
+ occ2 = np.asarray(occ2)
+
+ # Put all data in second dimension
+ # Also works for 1-dimensional data
+ if occ1.ndim >= 2:
+ occ1 = occ1.reshape(occ1.shape[0], -1)
+ if occ2.ndim >= 2:
+ occ2 = occ2.reshape(occ2.shape[0], -1)
+
+ # Convert to boolean values
+ occ1 = (occ1 >= 0.5)
+ occ2 = (occ2 >= 0.5)
+
+ # Compute IOU
+ area_union = (occ1 | occ2).astype(np.float32).sum(axis=-1)
+ area_intersect = (occ1 & occ2).astype(np.float32).sum(axis=-1)
+
+ iou = (area_intersect / area_union)
+
+ return iou
+
+
+def chamfer_distance(points1, points2, use_kdtree=True, give_id=False):
+ ''' Returns the chamfer distance for the sets of points.
+ Args:
+ points1 (numpy array): first point set
+ points2 (numpy array): second point set
+ use_kdtree (bool): whether to use a kdtree
+ give_id (bool): whether to return the IDs of nearest points
+ '''
+ if use_kdtree:
+ return chamfer_distance_kdtree(points1, points2, give_id=give_id)
+ else:
+ return chamfer_distance_naive(points1, points2)
+
+
+def chamfer_distance_naive(points1, points2):
+ ''' Naive implementation of the Chamfer distance.
+ Args:
+ points1 (numpy array): first point set
+ points2 (numpy array): second point set
+ '''
+ assert(points1.size() == points2.size())
+ batch_size, T, _ = points1.size()
+
+ points1 = points1.view(batch_size, T, 1, 3)
+ points2 = points2.view(batch_size, 1, T, 3)
+
+ distances = (points1 - points2).pow(2).sum(-1)
+
+ chamfer1 = distances.min(dim=1)[0].mean(dim=1)
+ chamfer2 = distances.min(dim=2)[0].mean(dim=1)
+
+ chamfer = chamfer1 + chamfer2
+ return chamfer
+
+
+def chamfer_distance_kdtree(points1, points2, give_id=False):
+ ''' KD-tree based implementation of the Chamfer distance.
+ Args:
+ points1 (numpy array): first point set
+ points2 (numpy array): second point set
+ give_id (bool): whether to return the IDs of the nearest points
+ '''
+ # Points have size batch_size x T x 3
+ batch_size = points1.size(0)
+
+ # First convert points to numpy
+ points1_np = points1.detach().cpu().numpy()
+ points2_np = points2.detach().cpu().numpy()
+
+ # Get list of nearest neighbors indieces
+ idx_nn_12, _ = get_nearest_neighbors_indices_batch(points1_np, points2_np)
+ idx_nn_12 = torch.LongTensor(idx_nn_12).to(points1.device)
+ # Expands it as batch_size x 1 x 3
+ idx_nn_12_expand = idx_nn_12.view(batch_size, -1, 1).expand_as(points1)
+
+ # Get list of nearest neighbors indieces
+ idx_nn_21, _ = get_nearest_neighbors_indices_batch(points2_np, points1_np)
+ idx_nn_21 = torch.LongTensor(idx_nn_21).to(points1.device)
+ # Expands it as batch_size x T x 3
+ idx_nn_21_expand = idx_nn_21.view(batch_size, -1, 1).expand_as(points2)
+
+ # Compute nearest neighbors in points2 to points in points1
+ # points_12[i, j, k] = points2[i, idx_nn_12_expand[i, j, k], k]
+ points_12 = torch.gather(points2, dim=1, index=idx_nn_12_expand)
+
+ # Compute nearest neighbors in points1 to points in points2
+ # points_21[i, j, k] = points2[i, idx_nn_21_expand[i, j, k], k]
+ points_21 = torch.gather(points1, dim=1, index=idx_nn_21_expand)
+
+ # Compute chamfer distance
+ chamfer1 = (points1 - points_12).pow(2).sum(2).mean(1)
+ chamfer2 = (points2 - points_21).pow(2).sum(2).mean(1)
+
+ # Take sum
+ chamfer = chamfer1 + chamfer2
+
+ # If required, also return nearest neighbors
+ if give_id:
+ return chamfer1, chamfer2, idx_nn_12, idx_nn_21
+
+ return chamfer
+
+
+def get_nearest_neighbors_indices_batch(points_src, points_tgt, k=1):
+ ''' Returns the nearest neighbors for point sets batchwise.
+ Args:
+ points_src (numpy array): source points
+ points_tgt (numpy array): target points
+ k (int): number of nearest neighbors to return
+ '''
+ indices = []
+ distances = []
+
+ for (p1, p2) in zip(points_src, points_tgt):
+ kdtree = KDTree(p2)
+ dist, idx = kdtree.query(p1, k=k)
+ indices.append(idx)
+ distances.append(dist)
+
+ return indices, distances
+
+
+def normalize_imagenet(x):
+ ''' Normalize input images according to ImageNet standards.
+ Args:
+ x (tensor): input images
+ '''
+ x = x.clone()
+ x[:, 0] = (x[:, 0] - 0.485) / 0.229
+ x[:, 1] = (x[:, 1] - 0.456) / 0.224
+ x[:, 2] = (x[:, 2] - 0.406) / 0.225
+ return x
+
+
+def make_3d_grid(bb_min, bb_max, shape):
+ ''' Makes a 3D grid.
+ Args:
+ bb_min (tuple): bounding box minimum
+ bb_max (tuple): bounding box maximum
+ shape (tuple): output shape
+ '''
+ size = shape[0] * shape[1] * shape[2]
+
+ pxs = torch.linspace(bb_min[0], bb_max[0], shape[0])
+ pys = torch.linspace(bb_min[1], bb_max[1], shape[1])
+ pzs = torch.linspace(bb_min[2], bb_max[2], shape[2])
+
+ pxs = pxs.view(-1, 1, 1).expand(*shape).contiguous().view(size)
+ pys = pys.view(1, -1, 1).expand(*shape).contiguous().view(size)
+ pzs = pzs.view(1, 1, -1).expand(*shape).contiguous().view(size)
+ p = torch.stack([pxs, pys, pzs], dim=1)
+
+ return p
+
+
+def transform_points(points, transform):
+ ''' Transforms points with regard to passed camera information.
+ Args:
+ points (tensor): points tensor
+ transform (tensor): transformation matrices
+ '''
+ assert(points.size(2) == 3)
+ assert(transform.size(1) == 3)
+ assert(points.size(0) == transform.size(0))
+
+ if transform.size(2) == 4:
+ R = transform[:, :, :3]
+ t = transform[:, :, 3:]
+ points_out = points @ R.transpose(1, 2) + t.transpose(1, 2)
+ elif transform.size(2) == 3:
+ K = transform
+ points_out = points @ K.transpose(1, 2)
+
+ return points_out
+
+
+def b_inv(b_mat):
+ ''' Performs batch matrix inversion.
+ Arguments:
+ b_mat: the batch of matrices that should be inverted
+ '''
+
+ eye = b_mat.new_ones(b_mat.size(-1)).diag().expand_as(b_mat)
+ b_inv, _ = torch.gesv(eye, b_mat)
+ return b_inv
+
+
+def transform_points_back(points, transform):
+ ''' Inverts the transformation.
+ Args:
+ points (tensor): points tensor
+ transform (tensor): transformation matrices
+ '''
+ assert(points.size(2) == 3)
+ assert(transform.size(1) == 3)
+ assert(points.size(0) == transform.size(0))
+
+ if transform.size(2) == 4:
+ R = transform[:, :, :3]
+ t = transform[:, :, 3:]
+ points_out = points - t.transpose(1, 2)
+ points_out = points_out @ b_inv(R.transpose(1, 2))
+ elif transform.size(2) == 3:
+ K = transform
+ points_out = points @ b_inv(K.transpose(1, 2))
+
+ return points_out
+
+
+def project_to_camera(points, transform):
+ ''' Projects points to the camera plane.
+ Args:
+ points (tensor): points tensor
+ transform (tensor): transformation matrices
+ '''
+ p_camera = transform_points(points, transform)
+ p_camera = p_camera[..., :2] / p_camera[..., 2:]
+ return p_camera
+
+
+def get_camera_args(data, loc_field=None, scale_field=None, device=None):
+ ''' Returns dictionary of camera arguments.
+ Args:
+ data (dict): data dictionary
+ loc_field (str): name of location field
+ scale_field (str): name of scale field
+ device (device): pytorch device
+ '''
+ Rt = data['inputs.world_mat'].to(device)
+ K = data['inputs.camera_mat'].to(device)
+
+ if loc_field is not None:
+ loc = data[loc_field].to(device)
+ else:
+ loc = torch.zeros(K.size(0), 3, device=K.device, dtype=K.dtype)
+
+ if scale_field is not None:
+ scale = data[scale_field].to(device)
+ else:
+ scale = torch.zeros(K.size(0), device=K.device, dtype=K.dtype)
+
+ Rt = fix_Rt_camera(Rt, loc, scale)
+ K = fix_K_camera(K, img_size=137.)
+ kwargs = {'Rt': Rt, 'K': K}
+ return kwargs
+
+
+def fix_Rt_camera(Rt, loc, scale):
+ ''' Fixes Rt camera matrix.
+ Args:
+ Rt (tensor): Rt camera matrix
+ loc (tensor): location
+ scale (float): scale
+ '''
+ # Rt is B x 3 x 4
+ # loc is B x 3 and scale is B
+ batch_size = Rt.size(0)
+ R = Rt[:, :, :3]
+ t = Rt[:, :, 3:]
+
+ scale = scale.view(batch_size, 1, 1)
+ R_new = R * scale
+ t_new = t + R @ loc.unsqueeze(2)
+
+ Rt_new = torch.cat([R_new, t_new], dim=2)
+
+ assert(Rt_new.size() == (batch_size, 3, 4))
+ return Rt_new
+
+
+def fix_K_camera(K, img_size=137):
+ """Fix camera projection matrix.
+ This changes a camera projection matrix that maps to
+ [0, img_size] x [0, img_size] to one that maps to [-1, 1] x [-1, 1].
+ Args:
+ K (np.ndarray): Camera projection matrix.
+ img_size (float): Size of image plane K projects to.
+ """
+ # Unscale and recenter
+ scale_mat = torch.tensor([
+ [2./img_size, 0, -1],
+ [0, 2./img_size, -1],
+ [0, 0, 1.],
+ ], device=K.device, dtype=K.dtype)
+ K_new = scale_mat.view(1, 3, 3) @ K
+ return K_new
\ No newline at end of file
diff --git a/eval/src/eval.py b/eval/src/eval.py
new file mode 100644
index 0000000..e2341ae
--- /dev/null
+++ b/eval/src/eval.py
@@ -0,0 +1,213 @@
+import logging
+import numpy as np
+import trimesh
+# from scipy.spatial import cKDTree
+from eval.src.utils.libkdtree import KDTree
+from eval.src.utils.libmesh import check_mesh_contains
+from eval.src.common import compute_iou
+
+# Maximum values for bounding box [-0.5, 0.5]^3
+EMPTY_PCL_DICT = {
+ 'completeness': np.sqrt(3),
+ 'accuracy': np.sqrt(3),
+ 'completeness2': 3,
+ 'accuracy2': 3,
+ 'chamfer': 6,
+}
+
+EMPTY_PCL_DICT_NORMALS = {
+ 'normals completeness': -1.,
+ 'normals accuracy': -1.,
+ 'normals': -1.,
+}
+
+logger = logging.getLogger(__name__)
+
+
+class MeshEvaluator(object):
+ ''' Mesh evaluation class.
+ It handles the mesh evaluation process.
+ Args:
+ n_points (int): number of points to be used for evaluation
+ '''
+
+ def __init__(self, n_points=100000):
+ self.n_points = n_points
+
+ def eval_mesh(self, mesh, pointcloud_tgt, normals_tgt,
+ points_iou, occ_tgt, remove_wall=False):
+ ''' Evaluates a mesh.
+ Args:
+ mesh (trimesh): mesh which should be evaluated
+ pointcloud_tgt (numpy array): target point cloud
+ normals_tgt (numpy array): target normals
+ points_iou (numpy_array): points tensor for IoU evaluation
+ occ_tgt (numpy_array): GT occupancy values for IoU points
+ '''
+ if len(mesh.vertices) != 0 and len(mesh.faces) != 0:
+ if remove_wall: #! Remove walls and floors
+ pointcloud, idx = mesh.sample(2*self.n_points, return_index=True)
+ eps = 0.007
+ x_max, x_min = pointcloud_tgt[:, 0].max(), pointcloud_tgt[:, 0].min()
+ y_max, y_min = pointcloud_tgt[:, 1].max(), pointcloud_tgt[:, 1].min()
+ z_max, z_min = pointcloud_tgt[:, 2].max(), pointcloud_tgt[:, 2].min()
+
+ # add small offsets
+ x_max, x_min = x_max + eps, x_min - eps
+ y_max, y_min = y_max + eps, y_min - eps
+ z_max, z_min = z_max + eps, z_min - eps
+
+ mask_x = (pointcloud[:, 0] <= x_max) & (pointcloud[:, 0] >= x_min)
+ mask_y = (pointcloud[:, 1] >= y_min) # floor
+ mask_z = (pointcloud[:, 2] <= z_max) & (pointcloud[:, 2] >= z_min)
+
+ mask = mask_x & mask_y & mask_z
+ pointcloud_new = pointcloud[mask]
+ # Subsample
+ idx_new = np.random.randint(pointcloud_new.shape[0], size=self.n_points)
+ pointcloud = pointcloud_new[idx_new]
+ idx = idx[mask][idx_new]
+ else:
+ pointcloud, idx = mesh.sample(self.n_points, return_index=True)
+
+ pointcloud = pointcloud.astype(np.float32)
+ normals = mesh.face_normals[idx]
+ else:
+ pointcloud = np.empty((0, 3))
+ normals = np.empty((0, 3))
+
+ out_dict = self.eval_pointcloud(
+ pointcloud, pointcloud_tgt, normals, normals_tgt)
+
+
+ if (points_iou is not None) and (occ_tgt is not None) and len(mesh.vertices) != 0 and len(mesh.faces) != 0:
+ occ = check_mesh_contains(mesh, points_iou)
+ out_dict['iou'] = compute_iou(occ, occ_tgt)
+ else:
+ out_dict['iou'] = 0.
+
+ return out_dict
+
+ def eval_pointcloud(self, pointcloud, pointcloud_tgt,
+ normals=None, normals_tgt=None,
+ thresholds=np.linspace(1./1000, 1, 1000)):
+ ''' Evaluates a point cloud.
+ Args:
+ pointcloud (numpy array): predicted point cloud
+ pointcloud_tgt (numpy array): target point cloud
+ normals (numpy array): predicted normals
+ normals_tgt (numpy array): target normals
+ thresholds (numpy array): threshold values for the F-score calculation
+ '''
+ # Return maximum losses if pointcloud is empty
+ if pointcloud.shape[0] == 0:
+ logger.warn('Empty pointcloud / mesh detected!')
+ out_dict = EMPTY_PCL_DICT.copy()
+ if normals is not None and normals_tgt is not None:
+ out_dict.update(EMPTY_PCL_DICT_NORMALS)
+ return out_dict
+
+ pointcloud = np.asarray(pointcloud)
+ pointcloud_tgt = np.asarray(pointcloud_tgt)
+
+ # Completeness: how far are the points of the target point cloud
+ # from thre predicted point cloud
+ completeness, completeness_normals = distance_p2p(
+ pointcloud_tgt, normals_tgt, pointcloud, normals
+ )
+ recall = get_threshold_percentage(completeness, thresholds)
+ completeness2 = completeness**2
+
+ completeness = completeness.mean()
+ completeness2 = completeness2.mean()
+ completeness_normals = completeness_normals.mean()
+
+ # Accuracy: how far are th points of the predicted pointcloud
+ # from the target pointcloud
+ accuracy, accuracy_normals = distance_p2p(
+ pointcloud, normals, pointcloud_tgt, normals_tgt
+ )
+ precision = get_threshold_percentage(accuracy, thresholds)
+ accuracy2 = accuracy**2
+
+ accuracy = accuracy.mean()
+ accuracy2 = accuracy2.mean()
+ accuracy_normals = accuracy_normals.mean()
+
+ # Chamfer distance
+ chamferL2 = 0.5 * (completeness2 + accuracy2)
+ normals_correctness = (
+ 0.5 * completeness_normals + 0.5 * accuracy_normals
+ )
+ chamferL1 = 0.5 * (completeness + accuracy)
+
+ # F-Score
+ F = [
+ 2 * precision[i] * recall[i] / (precision[i] + recall[i])
+ for i in range(len(precision))
+ ]
+
+ out_dict = {
+ 'completeness': completeness,
+ 'accuracy': accuracy,
+ 'normals completeness': completeness_normals,
+ 'normals accuracy': accuracy_normals,
+ 'normals': normals_correctness,
+ 'completeness2': completeness2,
+ 'accuracy2': accuracy2,
+ 'chamfer-L2': chamferL2,
+ 'chamfer-L1': chamferL1,
+ 'f-score': F[9], # threshold = 1.0%
+ 'f-score-15': F[14], # threshold = 1.5%
+ 'f-score-20': F[19], # threshold = 2.0%
+ }
+
+ return out_dict
+
+
+def distance_p2p(points_src, normals_src, points_tgt, normals_tgt):
+ ''' Computes minimal distances of each point in points_src to points_tgt.
+ Args:
+ points_src (numpy array): source points
+ normals_src (numpy array): source normals
+ points_tgt (numpy array): target points
+ normals_tgt (numpy array): target normals
+ '''
+ kdtree = KDTree(points_tgt)
+ dist, idx = kdtree.query(points_src)
+
+ if normals_src is not None and normals_tgt is not None:
+ normals_src = \
+ normals_src / np.linalg.norm(normals_src, axis=-1, keepdims=True)
+ normals_tgt = \
+ normals_tgt / np.linalg.norm(normals_tgt, axis=-1, keepdims=True)
+
+ normals_dot_product = (normals_tgt[idx] * normals_src).sum(axis=-1)
+ # Handle normals that point into wrong direction gracefully
+ # (mostly due to mehtod not caring about this in generation)
+ normals_dot_product = np.abs(normals_dot_product)
+ else:
+ normals_dot_product = np.array(
+ [np.nan] * points_src.shape[0], dtype=np.float32)
+ return dist, normals_dot_product
+
+
+def distance_p2m(points, mesh):
+ ''' Compute minimal distances of each point in points to mesh.
+ Args:
+ points (numpy array): points array
+ mesh (trimesh): mesh
+ '''
+ _, dist, _ = trimesh.proximity.closest_point(mesh, points)
+ return dist
+
+def get_threshold_percentage(dist, thresholds):
+ ''' Evaluates a point cloud.
+ Args:
+ dist (numpy array): calculated distance
+ thresholds (numpy array): threshold values for the F-score calculation
+ '''
+ in_threshold = [
+ (dist <= t).mean() for t in thresholds
+ ]
+ return in_threshold
\ No newline at end of file
diff --git a/eval/src/utils/__init__.py b/eval/src/utils/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/eval/src/utils/binvox_rw.py b/eval/src/utils/binvox_rw.py
new file mode 100644
index 0000000..c9c11d6
--- /dev/null
+++ b/eval/src/utils/binvox_rw.py
@@ -0,0 +1,287 @@
+# Copyright (C) 2012 Daniel Maturana
+# This file is part of binvox-rw-py.
+#
+# binvox-rw-py is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# binvox-rw-py is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with binvox-rw-py. If not, see .
+#
+# Modified by Christopher B. Choy
+# for python 3 support
+
+"""
+Binvox to Numpy and back.
+
+
+>>> import numpy as np
+>>> import binvox_rw
+>>> with open('chair.binvox', 'rb') as f:
+... m1 = binvox_rw.read_as_3d_array(f)
+...
+>>> m1.dims
+[32, 32, 32]
+>>> m1.scale
+41.133000000000003
+>>> m1.translate
+[0.0, 0.0, 0.0]
+>>> with open('chair_out.binvox', 'wb') as f:
+... m1.write(f)
+...
+>>> with open('chair_out.binvox', 'rb') as f:
+... m2 = binvox_rw.read_as_3d_array(f)
+...
+>>> m1.dims==m2.dims
+True
+>>> m1.scale==m2.scale
+True
+>>> m1.translate==m2.translate
+True
+>>> np.all(m1.data==m2.data)
+True
+
+>>> with open('chair.binvox', 'rb') as f:
+... md = binvox_rw.read_as_3d_array(f)
+...
+>>> with open('chair.binvox', 'rb') as f:
+... ms = binvox_rw.read_as_coord_array(f)
+...
+>>> data_ds = binvox_rw.dense_to_sparse(md.data)
+>>> data_sd = binvox_rw.sparse_to_dense(ms.data, 32)
+>>> np.all(data_sd==md.data)
+True
+>>> # the ordering of elements returned by numpy.nonzero changes with axis
+>>> # ordering, so to compare for equality we first lexically sort the voxels.
+>>> np.all(ms.data[:, np.lexsort(ms.data)] == data_ds[:, np.lexsort(data_ds)])
+True
+"""
+
+import numpy as np
+
+class Voxels(object):
+ """ Holds a binvox model.
+ data is either a three-dimensional numpy boolean array (dense representation)
+ or a two-dimensional numpy float array (coordinate representation).
+
+ dims, translate and scale are the model metadata.
+
+ dims are the voxel dimensions, e.g. [32, 32, 32] for a 32x32x32 model.
+
+ scale and translate relate the voxels to the original model coordinates.
+
+ To translate voxel coordinates i, j, k to original coordinates x, y, z:
+
+ x_n = (i+.5)/dims[0]
+ y_n = (j+.5)/dims[1]
+ z_n = (k+.5)/dims[2]
+ x = scale*x_n + translate[0]
+ y = scale*y_n + translate[1]
+ z = scale*z_n + translate[2]
+
+ """
+
+ def __init__(self, data, dims, translate, scale, axis_order):
+ self.data = data
+ self.dims = dims
+ self.translate = translate
+ self.scale = scale
+ assert (axis_order in ('xzy', 'xyz'))
+ self.axis_order = axis_order
+
+ def clone(self):
+ data = self.data.copy()
+ dims = self.dims[:]
+ translate = self.translate[:]
+ return Voxels(data, dims, translate, self.scale, self.axis_order)
+
+ def write(self, fp):
+ write(self, fp)
+
+def read_header(fp):
+ """ Read binvox header. Mostly meant for internal use.
+ """
+ line = fp.readline().strip()
+ if not line.startswith(b'#binvox'):
+ raise IOError('Not a binvox file')
+ dims = [int(i) for i in fp.readline().strip().split(b' ')[1:]]
+ translate = [float(i) for i in fp.readline().strip().split(b' ')[1:]]
+ scale = [float(i) for i in fp.readline().strip().split(b' ')[1:]][0]
+ line = fp.readline()
+ return dims, translate, scale
+
+def read_as_3d_array(fp, fix_coords=True):
+ """ Read binary binvox format as array.
+
+ Returns the model with accompanying metadata.
+
+ Voxels are stored in a three-dimensional numpy array, which is simple and
+ direct, but may use a lot of memory for large models. (Storage requirements
+ are 8*(d^3) bytes, where d is the dimensions of the binvox model. Numpy
+ boolean arrays use a byte per element).
+
+ Doesn't do any checks on input except for the '#binvox' line.
+ """
+ dims, translate, scale = read_header(fp)
+ raw_data = np.frombuffer(fp.read(), dtype=np.uint8)
+ # if just using reshape() on the raw data:
+ # indexing the array as array[i,j,k], the indices map into the
+ # coords as:
+ # i -> x
+ # j -> z
+ # k -> y
+ # if fix_coords is true, then data is rearranged so that
+ # mapping is
+ # i -> x
+ # j -> y
+ # k -> z
+ values, counts = raw_data[::2], raw_data[1::2]
+ data = np.repeat(values, counts).astype(np.bool)
+ data = data.reshape(dims)
+ if fix_coords:
+ # xzy to xyz TODO the right thing
+ data = np.transpose(data, (0, 2, 1))
+ axis_order = 'xyz'
+ else:
+ axis_order = 'xzy'
+ return Voxels(data, dims, translate, scale, axis_order)
+
+
+def read_as_coord_array(fp, fix_coords=True):
+ """ Read binary binvox format as coordinates.
+
+ Returns binvox model with voxels in a "coordinate" representation, i.e. an
+ 3 x N array where N is the number of nonzero voxels. Each column
+ corresponds to a nonzero voxel and the 3 rows are the (x, z, y) coordinates
+ of the voxel. (The odd ordering is due to the way binvox format lays out
+ data). Note that coordinates refer to the binvox voxels, without any
+ scaling or translation.
+
+ Use this to save memory if your model is very sparse (mostly empty).
+
+ Doesn't do any checks on input except for the '#binvox' line.
+ """
+ dims, translate, scale = read_header(fp)
+ raw_data = np.frombuffer(fp.read(), dtype=np.uint8)
+
+ values, counts = raw_data[::2], raw_data[1::2]
+
+ sz = np.prod(dims)
+ index, end_index = 0, 0
+ end_indices = np.cumsum(counts)
+ indices = np.concatenate(([0], end_indices[:-1])).astype(end_indices.dtype)
+
+ values = values.astype(np.bool)
+ indices = indices[values]
+ end_indices = end_indices[values]
+
+ nz_voxels = []
+ for index, end_index in zip(indices, end_indices):
+ nz_voxels.extend(range(index, end_index))
+ nz_voxels = np.array(nz_voxels)
+ # TODO are these dims correct?
+ # according to docs,
+ # index = x * wxh + z * width + y; // wxh = width * height = d * d
+
+ x = nz_voxels / (dims[0]*dims[1])
+ zwpy = nz_voxels % (dims[0]*dims[1]) # z*w + y
+ z = zwpy / dims[0]
+ y = zwpy % dims[0]
+ if fix_coords:
+ data = np.vstack((x, y, z))
+ axis_order = 'xyz'
+ else:
+ data = np.vstack((x, z, y))
+ axis_order = 'xzy'
+
+ #return Voxels(data, dims, translate, scale, axis_order)
+ return Voxels(np.ascontiguousarray(data), dims, translate, scale, axis_order)
+
+def dense_to_sparse(voxel_data, dtype=np.int):
+ """ From dense representation to sparse (coordinate) representation.
+ No coordinate reordering.
+ """
+ if voxel_data.ndim!=3:
+ raise ValueError('voxel_data is wrong shape; should be 3D array.')
+ return np.asarray(np.nonzero(voxel_data), dtype)
+
+def sparse_to_dense(voxel_data, dims, dtype=np.bool):
+ if voxel_data.ndim!=2 or voxel_data.shape[0]!=3:
+ raise ValueError('voxel_data is wrong shape; should be 3xN array.')
+ if np.isscalar(dims):
+ dims = [dims]*3
+ dims = np.atleast_2d(dims).T
+ # truncate to integers
+ xyz = voxel_data.astype(np.int)
+ # discard voxels that fall outside dims
+ valid_ix = ~np.any((xyz < 0) | (xyz >= dims), 0)
+ xyz = xyz[:,valid_ix]
+ out = np.zeros(dims.flatten(), dtype=dtype)
+ out[tuple(xyz)] = True
+ return out
+
+#def get_linear_index(x, y, z, dims):
+ #""" Assuming xzy order. (y increasing fastest.
+ #TODO ensure this is right when dims are not all same
+ #"""
+ #return x*(dims[1]*dims[2]) + z*dims[1] + y
+
+def write(voxel_model, fp):
+ """ Write binary binvox format.
+
+ Note that when saving a model in sparse (coordinate) format, it is first
+ converted to dense format.
+
+ Doesn't check if the model is 'sane'.
+
+ """
+ if voxel_model.data.ndim==2:
+ # TODO avoid conversion to dense
+ dense_voxel_data = sparse_to_dense(voxel_model.data, voxel_model.dims)
+ else:
+ dense_voxel_data = voxel_model.data
+
+ fp.write('#binvox 1\n')
+ fp.write('dim '+' '.join(map(str, voxel_model.dims))+'\n')
+ fp.write('translate '+' '.join(map(str, voxel_model.translate))+'\n')
+ fp.write('scale '+str(voxel_model.scale)+'\n')
+ fp.write('data\n')
+ if not voxel_model.axis_order in ('xzy', 'xyz'):
+ raise ValueError('Unsupported voxel model axis order')
+
+ if voxel_model.axis_order=='xzy':
+ voxels_flat = dense_voxel_data.flatten()
+ elif voxel_model.axis_order=='xyz':
+ voxels_flat = np.transpose(dense_voxel_data, (0, 2, 1)).flatten()
+
+ # keep a sort of state machine for writing run length encoding
+ state = voxels_flat[0]
+ ctr = 0
+ for c in voxels_flat:
+ if c==state:
+ ctr += 1
+ # if ctr hits max, dump
+ if ctr==255:
+ fp.write(chr(state))
+ fp.write(chr(ctr))
+ ctr = 0
+ else:
+ # if switch state, dump
+ fp.write(chr(state))
+ fp.write(chr(ctr))
+ state = c
+ ctr = 1
+ # flush out remainders
+ if ctr > 0:
+ fp.write(chr(state))
+ fp.write(chr(ctr))
+
+if __name__ == '__main__':
+ import doctest
+ doctest.testmod()
diff --git a/eval/src/utils/icp.py b/eval/src/utils/icp.py
new file mode 100644
index 0000000..982b4d7
--- /dev/null
+++ b/eval/src/utils/icp.py
@@ -0,0 +1,121 @@
+import numpy as np
+from sklearn.neighbors import NearestNeighbors
+
+
+def best_fit_transform(A, B):
+ '''
+ Calculates the least-squares best-fit transform that maps corresponding
+ points A to B in m spatial dimensions
+ Input:
+ A: Nxm numpy array of corresponding points
+ B: Nxm numpy array of corresponding points
+ Returns:
+ T: (m+1)x(m+1) homogeneous transformation matrix that maps A on to B
+ R: mxm rotation matrix
+ t: mx1 translation vector
+ '''
+
+ assert A.shape == B.shape
+
+ # get number of dimensions
+ m = A.shape[1]
+
+ # translate points to their centroids
+ centroid_A = np.mean(A, axis=0)
+ centroid_B = np.mean(B, axis=0)
+ AA = A - centroid_A
+ BB = B - centroid_B
+
+ # rotation matrix
+ H = np.dot(AA.T, BB)
+ U, S, Vt = np.linalg.svd(H)
+ R = np.dot(Vt.T, U.T)
+
+ # special reflection case
+ if np.linalg.det(R) < 0:
+ Vt[m-1,:] *= -1
+ R = np.dot(Vt.T, U.T)
+
+ # translation
+ t = centroid_B.T - np.dot(R,centroid_A.T)
+
+ # homogeneous transformation
+ T = np.identity(m+1)
+ T[:m, :m] = R
+ T[:m, m] = t
+
+ return T, R, t
+
+
+def nearest_neighbor(src, dst):
+ '''
+ Find the nearest (Euclidean) neighbor in dst for each point in src
+ Input:
+ src: Nxm array of points
+ dst: Nxm array of points
+ Output:
+ distances: Euclidean distances of the nearest neighbor
+ indices: dst indices of the nearest neighbor
+ '''
+
+ assert src.shape == dst.shape
+
+ neigh = NearestNeighbors(n_neighbors=1)
+ neigh.fit(dst)
+ distances, indices = neigh.kneighbors(src, return_distance=True)
+ return distances.ravel(), indices.ravel()
+
+
+def icp(A, B, init_pose=None, max_iterations=20, tolerance=0.001):
+ '''
+ The Iterative Closest Point method: finds best-fit transform that maps
+ points A on to points B
+ Input:
+ A: Nxm numpy array of source mD points
+ B: Nxm numpy array of destination mD point
+ init_pose: (m+1)x(m+1) homogeneous transformation
+ max_iterations: exit algorithm after max_iterations
+ tolerance: convergence criteria
+ Output:
+ T: final homogeneous transformation that maps A on to B
+ distances: Euclidean distances (errors) of the nearest neighbor
+ i: number of iterations to converge
+ '''
+
+ assert A.shape == B.shape
+
+ # get number of dimensions
+ m = A.shape[1]
+
+ # make points homogeneous, copy them to maintain the originals
+ src = np.ones((m+1,A.shape[0]))
+ dst = np.ones((m+1,B.shape[0]))
+ src[:m,:] = np.copy(A.T)
+ dst[:m,:] = np.copy(B.T)
+
+ # apply the initial pose estimation
+ if init_pose is not None:
+ src = np.dot(init_pose, src)
+
+ prev_error = 0
+
+ for i in range(max_iterations):
+ # find the nearest neighbors between the current source and destination points
+ distances, indices = nearest_neighbor(src[:m,:].T, dst[:m,:].T)
+
+ # compute the transformation between the current source and nearest destination points
+ T,_,_ = best_fit_transform(src[:m,:].T, dst[:m,indices].T)
+
+ # update the current source
+ src = np.dot(T, src)
+
+ # check error
+ mean_error = np.mean(distances)
+ if np.abs(prev_error - mean_error) < tolerance:
+ break
+ prev_error = mean_error
+
+ # calculate final transformation
+ T,_,_ = best_fit_transform(A, src[:m,:].T)
+
+ return T, distances, i
diff --git a/eval/src/utils/io.py b/eval/src/utils/io.py
new file mode 100644
index 0000000..247b3b7
--- /dev/null
+++ b/eval/src/utils/io.py
@@ -0,0 +1,112 @@
+import os
+from plyfile import PlyElement, PlyData
+import numpy as np
+
+
+def export_pointcloud(vertices, out_file, as_text=True):
+ assert(vertices.shape[1] == 3)
+ vertices = vertices.astype(np.float32)
+ vertices = np.ascontiguousarray(vertices)
+ vector_dtype = [('x', 'f4'), ('y', 'f4'), ('z', 'f4')]
+ vertices = vertices.view(dtype=vector_dtype).flatten()
+ plyel = PlyElement.describe(vertices, 'vertex')
+ plydata = PlyData([plyel], text=as_text)
+ plydata.write(out_file)
+
+
+def load_pointcloud(in_file):
+ plydata = PlyData.read(in_file)
+ vertices = np.stack([
+ plydata['vertex']['x'],
+ plydata['vertex']['y'],
+ plydata['vertex']['z']
+ ], axis=1)
+ return vertices
+
+
+def read_off(file):
+ """
+ Reads vertices and faces from an off file.
+
+ :param file: path to file to read
+ :type file: str
+ :return: vertices and faces as lists of tuples
+ :rtype: [(float)], [(int)]
+ """
+
+ assert os.path.exists(file), 'file %s not found' % file
+
+ with open(file, 'r') as fp:
+ lines = fp.readlines()
+ lines = [line.strip() for line in lines]
+
+ # Fix for ModelNet bug were 'OFF' and the number of vertices and faces
+ # are all in the first line.
+ if len(lines[0]) > 3:
+ assert lines[0][:3] == 'OFF' or lines[0][:3] == 'off', \
+ 'invalid OFF file %s' % file
+
+ parts = lines[0][3:].split(' ')
+ assert len(parts) == 3
+
+ num_vertices = int(parts[0])
+ assert num_vertices > 0
+
+ num_faces = int(parts[1])
+ assert num_faces > 0
+
+ start_index = 1
+ # This is the regular case!
+ else:
+ assert lines[0] == 'OFF' or lines[0] == 'off', \
+ 'invalid OFF file %s' % file
+
+ parts = lines[1].split(' ')
+ assert len(parts) == 3
+
+ num_vertices = int(parts[0])
+ assert num_vertices > 0
+
+ num_faces = int(parts[1])
+ assert num_faces > 0
+
+ start_index = 2
+
+ vertices = []
+ for i in range(num_vertices):
+ vertex = lines[start_index + i].split(' ')
+ vertex = [float(point.strip()) for point in vertex if point != '']
+ assert len(vertex) == 3
+
+ vertices.append(vertex)
+
+ faces = []
+ for i in range(num_faces):
+ face = lines[start_index + num_vertices + i].split(' ')
+ face = [index.strip() for index in face if index != '']
+
+ # check to be sure
+ for index in face:
+ assert index != '', \
+ 'found empty vertex index: %s (%s)' \
+ % (lines[start_index + num_vertices + i], file)
+
+ face = [int(index) for index in face]
+
+ assert face[0] == len(face) - 1, \
+ 'face should have %d vertices but as %d (%s)' \
+ % (face[0], len(face) - 1, file)
+ assert face[0] == 3, \
+ 'only triangular meshes supported (%s)' % file
+ for index in face:
+ assert index >= 0 and index < num_vertices, \
+ 'vertex %d (of %d vertices) does not exist (%s)' \
+ % (index, num_vertices, file)
+
+ assert len(face) > 1
+
+ faces.append(face)
+
+ return vertices, faces
+
+ assert False, 'could not open %s' % file
diff --git a/eval/src/utils/libkdtree/.gitignore b/eval/src/utils/libkdtree/.gitignore
new file mode 100644
index 0000000..378eac2
--- /dev/null
+++ b/eval/src/utils/libkdtree/.gitignore
@@ -0,0 +1 @@
+build
diff --git a/eval/src/utils/libkdtree/LICENSE.txt b/eval/src/utils/libkdtree/LICENSE.txt
new file mode 100644
index 0000000..e3acbd5
--- /dev/null
+++ b/eval/src/utils/libkdtree/LICENSE.txt
@@ -0,0 +1,165 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007, 2015 Free Software Foundation, Inc.
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+ This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+ 0. Additional Definitions.
+
+ As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+ "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+ An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+ A "Combined Work" is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+ The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+ The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+ 1. Exception to Section 3 of the GNU GPL.
+
+ You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+ 2. Conveying Modified Versions.
+
+ If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+ a) under this License, provided that you make a good faith effort to
+ ensure that, in the event an Application does not supply the
+ function or data, the facility still operates, and performs
+ whatever part of its purpose remains meaningful, or
+
+ b) under the GNU GPL, with none of the additional permissions of
+ this License applicable to that copy.
+
+ 3. Object Code Incorporating Material from Library Header Files.
+
+ The object code form of an Application may incorporate material from
+a header file that is part of the Library. You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+ a) Give prominent notice with each copy of the object code that the
+ Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b) Accompany the object code with a copy of the GNU GPL and this license
+ document.
+
+ 4. Combined Works.
+
+ You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+ a) Give prominent notice with each copy of the Combined Work that
+ the Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b) Accompany the Combined Work with a copy of the GNU GPL and this license
+ document.
+
+ c) For a Combined Work that displays copyright notices during
+ execution, include the copyright notice for the Library among
+ these notices, as well as a reference directing the user to the
+ copies of the GNU GPL and this license document.
+
+ d) Do one of the following:
+
+ 0) Convey the Minimal Corresponding Source under the terms of this
+ License, and the Corresponding Application Code in a form
+ suitable for, and under terms that permit, the user to
+ recombine or relink the Application with a modified version of
+ the Linked Version to produce a modified Combined Work, in the
+ manner specified by section 6 of the GNU GPL for conveying
+ Corresponding Source.
+
+ 1) Use a suitable shared library mechanism for linking with the
+ Library. A suitable mechanism is one that (a) uses at run time
+ a copy of the Library already present on the user's computer
+ system, and (b) will operate properly with a modified version
+ of the Library that is interface-compatible with the Linked
+ Version.
+
+ e) Provide Installation Information, but only if you would otherwise
+ be required to provide such information under section 6 of the
+ GNU GPL, and only to the extent that such information is
+ necessary to install and execute a modified version of the
+ Combined Work produced by recombining or relinking the
+ Application with a modified version of the Linked Version. (If
+ you use option 4d0, the Installation Information must accompany
+ the Minimal Corresponding Source and Corresponding Application
+ Code. If you use option 4d1, you must provide the Installation
+ Information in the manner specified by section 6 of the GNU GPL
+ for conveying Corresponding Source.)
+
+ 5. Combined Libraries.
+
+ You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+ a) Accompany the combined library with a copy of the same work based
+ on the Library, uncombined with any other library facilities,
+ conveyed under the terms of this License.
+
+ b) Give prominent notice with the combined library that part of it
+ is a work based on the Library, and explaining where to find the
+ accompanying uncombined form of the same work.
+
+ 6. Revised Versions of the GNU Lesser General Public License.
+
+ The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+ If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
diff --git a/eval/src/utils/libkdtree/MANIFEST.in b/eval/src/utils/libkdtree/MANIFEST.in
new file mode 100644
index 0000000..0ff2a61
--- /dev/null
+++ b/eval/src/utils/libkdtree/MANIFEST.in
@@ -0,0 +1,2 @@
+exclude pykdtree/render_template.py
+include LICENSE.txt
diff --git a/eval/src/utils/libkdtree/README b/eval/src/utils/libkdtree/README
new file mode 100644
index 0000000..cb7001e
--- /dev/null
+++ b/eval/src/utils/libkdtree/README
@@ -0,0 +1,148 @@
+.. image:: https://travis-ci.org/storpipfugl/pykdtree.svg?branch=master
+ :target: https://travis-ci.org/storpipfugl/pykdtree
+.. image:: https://ci.appveyor.com/api/projects/status/ubo92368ktt2d25g/branch/master
+ :target: https://ci.appveyor.com/project/storpipfugl/pykdtree
+
+========
+pykdtree
+========
+
+Objective
+---------
+pykdtree is a kd-tree implementation for fast nearest neighbour search in Python.
+The aim is to be the fastest implementation around for common use cases (low dimensions and low number of neighbours) for both tree construction and queries.
+
+The implementation is based on scipy.spatial.cKDTree and libANN by combining the best features from both and focus on implementation efficiency.
+
+The interface is similar to that of scipy.spatial.cKDTree except only Euclidean distance measure is supported.
+
+Queries are optionally multithreaded using OpenMP.
+
+Installation
+------------
+Default build of pykdtree with OpenMP enabled queries using libgomp
+
+.. code-block:: bash
+
+ $ cd
+ $ python setup.py install
+
+If it fails with undefined compiler flags or you want to use another OpenMP implementation please modify setup.py at the indicated point to match your system.
+
+Building without OpenMP support is controlled by the USE_OMP environment variable
+
+.. code-block:: bash
+
+ $ cd
+ $ export USE_OMP=0
+ $ python setup.py install
+
+Note evironment variables are by default not exported when using sudo so in this case do
+
+.. code-block:: bash
+
+ $ USE_OMP=0 sudo -E python setup.py install
+
+Usage
+-----
+The usage of pykdtree is similar to scipy.spatial.cKDTree so for now refer to its documentation
+
+ >>> from pykdtree.kdtree import KDTree
+ >>> kd_tree = KDTree(data_pts)
+ >>> dist, idx = kd_tree.query(query_pts, k=8)
+
+The number of threads to be used in OpenMP enabled queries can be controlled with the standard OpenMP environment variable OMP_NUM_THREADS.
+
+The **leafsize** argument (number of data points per leaf) for the tree creation can be used to control the memory overhead of the kd-tree. pykdtree uses a default **leafsize=16**.
+Increasing **leafsize** will reduce the memory overhead and construction time but increase query time.
+
+pykdtree accepts data in double precision (numpy.float64) or single precision (numpy.float32) floating point. If data of another type is used an internal copy in double precision is made resulting in a memory overhead. If the kd-tree is constructed on single precision data the query points must be single precision as well.
+
+Benchmarks
+----------
+Comparison with scipy.spatial.cKDTree and libANN. This benchmark is on geospatial 3D data with 10053632 data points and 4276224 query points. The results are indexed relative to the construction time of scipy.spatial.cKDTree. A leafsize of 10 (scipy.spatial.cKDTree default) is used.
+
+Note: libANN is *not* thread safe. In this benchmark libANN is compiled with "-O3 -funroll-loops -ffast-math -fprefetch-loop-arrays" in order to achieve optimum performance.
+
+================== ===================== ====== ======== ==================
+Operation scipy.spatial.cKDTree libANN pykdtree pykdtree 4 threads
+------------------ --------------------- ------ -------- ------------------
+
+Construction 100 304 96 96
+
+query 1 neighbour 1267 294 223 70
+
+Total 1 neighbour 1367 598 319 166
+
+query 8 neighbours 2193 625 449 143
+
+Total 8 neighbours 2293 929 545 293
+================== ===================== ====== ======== ==================
+
+Looking at the combined construction and query this gives the following performance improvement relative to scipy.spatial.cKDTree
+
+========== ====== ======== ==================
+Neighbours libANN pykdtree pykdtree 4 threads
+---------- ------ -------- ------------------
+1 129% 329% 723%
+
+8 147% 320% 682%
+========== ====== ======== ==================
+
+Note: mileage will vary with the dataset at hand and computer architecture.
+
+Test
+----
+Run the unit tests using nosetest
+
+.. code-block:: bash
+
+ $ cd
+ $ python setup.py nosetests
+
+Installing on AppVeyor
+----------------------
+
+Pykdtree requires the "stdint.h" header file which is not available on certain
+versions of Windows or certain Windows compilers including those on the
+continuous integration platform AppVeyor. To get around this the header file(s)
+can be downloaded and placed in the correct "include" directory. This can
+be done by adding the `anaconda/missing-headers.ps1` script to your repository
+and running it the install step of `appveyor.yml`:
+
+ # install missing headers that aren't included with MSVC 2008
+ # https://github.com/omnia-md/conda-recipes/pull/524
+ - "powershell ./appveyor/missing-headers.ps1"
+
+In addition to this, AppVeyor does not support OpenMP so this feature must be
+turned off by adding the following to `appveyor.yml` in the
+`environment` section:
+
+ environment:
+ global:
+ # Don't build with openmp because it isn't supported in appveyor's compilers
+ USE_OMP: "0"
+
+Changelog
+---------
+v1.3.1 : Fix masking in the "query" method introduced in 1.3.0
+
+v1.3.0 : Keyword argument "mask" added to "query" method. OpenMP compilation now works for MS Visual Studio compiler
+
+v1.2.2 : Build process fixes
+
+v1.2.1 : Fixed OpenMP thread safety issue introduced in v1.2.0
+
+v1.2.0 : 64 and 32 bit MSVC Windows support added
+
+v1.1.1 : Same as v1.1 release due to incorrect pypi release
+
+v1.1 : Build process improvements. Add data attribute to kdtree class for scipy interface compatibility
+
+v1.0 : Switched license from GPLv3 to LGPLv3
+
+v0.3 : Avoid zipping of installed egg
+
+v0.2 : Reduced memory footprint. Can now handle single precision data internally avoiding copy conversion to double precision. Default leafsize changed from 10 to 16 as this reduces the memory footprint and makes it a cache line multiplum (negligible if any query performance observed in benchmarks). Reduced memory allocation for leaf nodes. Applied patch for building on OS X.
+
+v0.1 : Initial version.
diff --git a/eval/src/utils/libkdtree/README.rst b/eval/src/utils/libkdtree/README.rst
new file mode 100644
index 0000000..cb7001e
--- /dev/null
+++ b/eval/src/utils/libkdtree/README.rst
@@ -0,0 +1,148 @@
+.. image:: https://travis-ci.org/storpipfugl/pykdtree.svg?branch=master
+ :target: https://travis-ci.org/storpipfugl/pykdtree
+.. image:: https://ci.appveyor.com/api/projects/status/ubo92368ktt2d25g/branch/master
+ :target: https://ci.appveyor.com/project/storpipfugl/pykdtree
+
+========
+pykdtree
+========
+
+Objective
+---------
+pykdtree is a kd-tree implementation for fast nearest neighbour search in Python.
+The aim is to be the fastest implementation around for common use cases (low dimensions and low number of neighbours) for both tree construction and queries.
+
+The implementation is based on scipy.spatial.cKDTree and libANN by combining the best features from both and focus on implementation efficiency.
+
+The interface is similar to that of scipy.spatial.cKDTree except only Euclidean distance measure is supported.
+
+Queries are optionally multithreaded using OpenMP.
+
+Installation
+------------
+Default build of pykdtree with OpenMP enabled queries using libgomp
+
+.. code-block:: bash
+
+ $ cd
+ $ python setup.py install
+
+If it fails with undefined compiler flags or you want to use another OpenMP implementation please modify setup.py at the indicated point to match your system.
+
+Building without OpenMP support is controlled by the USE_OMP environment variable
+
+.. code-block:: bash
+
+ $ cd
+ $ export USE_OMP=0
+ $ python setup.py install
+
+Note evironment variables are by default not exported when using sudo so in this case do
+
+.. code-block:: bash
+
+ $ USE_OMP=0 sudo -E python setup.py install
+
+Usage
+-----
+The usage of pykdtree is similar to scipy.spatial.cKDTree so for now refer to its documentation
+
+ >>> from pykdtree.kdtree import KDTree
+ >>> kd_tree = KDTree(data_pts)
+ >>> dist, idx = kd_tree.query(query_pts, k=8)
+
+The number of threads to be used in OpenMP enabled queries can be controlled with the standard OpenMP environment variable OMP_NUM_THREADS.
+
+The **leafsize** argument (number of data points per leaf) for the tree creation can be used to control the memory overhead of the kd-tree. pykdtree uses a default **leafsize=16**.
+Increasing **leafsize** will reduce the memory overhead and construction time but increase query time.
+
+pykdtree accepts data in double precision (numpy.float64) or single precision (numpy.float32) floating point. If data of another type is used an internal copy in double precision is made resulting in a memory overhead. If the kd-tree is constructed on single precision data the query points must be single precision as well.
+
+Benchmarks
+----------
+Comparison with scipy.spatial.cKDTree and libANN. This benchmark is on geospatial 3D data with 10053632 data points and 4276224 query points. The results are indexed relative to the construction time of scipy.spatial.cKDTree. A leafsize of 10 (scipy.spatial.cKDTree default) is used.
+
+Note: libANN is *not* thread safe. In this benchmark libANN is compiled with "-O3 -funroll-loops -ffast-math -fprefetch-loop-arrays" in order to achieve optimum performance.
+
+================== ===================== ====== ======== ==================
+Operation scipy.spatial.cKDTree libANN pykdtree pykdtree 4 threads
+------------------ --------------------- ------ -------- ------------------
+
+Construction 100 304 96 96
+
+query 1 neighbour 1267 294 223 70
+
+Total 1 neighbour 1367 598 319 166
+
+query 8 neighbours 2193 625 449 143
+
+Total 8 neighbours 2293 929 545 293
+================== ===================== ====== ======== ==================
+
+Looking at the combined construction and query this gives the following performance improvement relative to scipy.spatial.cKDTree
+
+========== ====== ======== ==================
+Neighbours libANN pykdtree pykdtree 4 threads
+---------- ------ -------- ------------------
+1 129% 329% 723%
+
+8 147% 320% 682%
+========== ====== ======== ==================
+
+Note: mileage will vary with the dataset at hand and computer architecture.
+
+Test
+----
+Run the unit tests using nosetest
+
+.. code-block:: bash
+
+ $ cd
+ $ python setup.py nosetests
+
+Installing on AppVeyor
+----------------------
+
+Pykdtree requires the "stdint.h" header file which is not available on certain
+versions of Windows or certain Windows compilers including those on the
+continuous integration platform AppVeyor. To get around this the header file(s)
+can be downloaded and placed in the correct "include" directory. This can
+be done by adding the `anaconda/missing-headers.ps1` script to your repository
+and running it the install step of `appveyor.yml`:
+
+ # install missing headers that aren't included with MSVC 2008
+ # https://github.com/omnia-md/conda-recipes/pull/524
+ - "powershell ./appveyor/missing-headers.ps1"
+
+In addition to this, AppVeyor does not support OpenMP so this feature must be
+turned off by adding the following to `appveyor.yml` in the
+`environment` section:
+
+ environment:
+ global:
+ # Don't build with openmp because it isn't supported in appveyor's compilers
+ USE_OMP: "0"
+
+Changelog
+---------
+v1.3.1 : Fix masking in the "query" method introduced in 1.3.0
+
+v1.3.0 : Keyword argument "mask" added to "query" method. OpenMP compilation now works for MS Visual Studio compiler
+
+v1.2.2 : Build process fixes
+
+v1.2.1 : Fixed OpenMP thread safety issue introduced in v1.2.0
+
+v1.2.0 : 64 and 32 bit MSVC Windows support added
+
+v1.1.1 : Same as v1.1 release due to incorrect pypi release
+
+v1.1 : Build process improvements. Add data attribute to kdtree class for scipy interface compatibility
+
+v1.0 : Switched license from GPLv3 to LGPLv3
+
+v0.3 : Avoid zipping of installed egg
+
+v0.2 : Reduced memory footprint. Can now handle single precision data internally avoiding copy conversion to double precision. Default leafsize changed from 10 to 16 as this reduces the memory footprint and makes it a cache line multiplum (negligible if any query performance observed in benchmarks). Reduced memory allocation for leaf nodes. Applied patch for building on OS X.
+
+v0.1 : Initial version.
diff --git a/eval/src/utils/libkdtree/__init__.py b/eval/src/utils/libkdtree/__init__.py
new file mode 100644
index 0000000..cbd34df
--- /dev/null
+++ b/eval/src/utils/libkdtree/__init__.py
@@ -0,0 +1,6 @@
+from .pykdtree.kdtree import KDTree
+
+
+__all__ = [
+ KDTree
+]
diff --git a/eval/src/utils/libkdtree/pykdtree/__init__.py b/eval/src/utils/libkdtree/pykdtree/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/eval/src/utils/libkdtree/pykdtree/_kdtree_core.c b/eval/src/utils/libkdtree/pykdtree/_kdtree_core.c
new file mode 100644
index 0000000..aebb816
--- /dev/null
+++ b/eval/src/utils/libkdtree/pykdtree/_kdtree_core.c
@@ -0,0 +1,1417 @@
+/*
+pykdtree, Fast kd-tree implementation with OpenMP-enabled queries
+
+Copyright (C) 2013 - present Esben S. Nielsen
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+details.
+
+You should have received a copy of the GNU Lesser General Public License along
+with this program. If not, see .
+*/
+
+/*
+This kd-tree implementation is based on the scipy.spatial.cKDTree by
+Anne M. Archibald and libANN by David M. Mount and Sunil Arya.
+*/
+
+
+#include
+#include
+#include
+#include
+
+#define PA(i,d) (pa[no_dims * pidx[i] + d])
+#define PASWAP(a,b) { uint32_t tmp = pidx[a]; pidx[a] = pidx[b]; pidx[b] = tmp; }
+
+#ifdef _MSC_VER
+#define restrict __restrict
+#endif
+
+
+typedef struct
+{
+ float cut_val;
+ int8_t cut_dim;
+ uint32_t start_idx;
+ uint32_t n;
+ float cut_bounds_lv;
+ float cut_bounds_hv;
+ struct Node_float *left_child;
+ struct Node_float *right_child;
+} Node_float;
+
+typedef struct
+{
+ float *bbox;
+ int8_t no_dims;
+ uint32_t *pidx;
+ struct Node_float *root;
+} Tree_float;
+
+
+typedef struct
+{
+ double cut_val;
+ int8_t cut_dim;
+ uint32_t start_idx;
+ uint32_t n;
+ double cut_bounds_lv;
+ double cut_bounds_hv;
+ struct Node_double *left_child;
+ struct Node_double *right_child;
+} Node_double;
+
+typedef struct
+{
+ double *bbox;
+ int8_t no_dims;
+ uint32_t *pidx;
+ struct Node_double *root;
+} Tree_double;
+
+
+
+void insert_point_float(uint32_t *closest_idx, float *closest_dist, uint32_t pidx, float cur_dist, uint32_t k);
+void get_bounding_box_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, float *bbox);
+int partition_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *bbox, int8_t *cut_dim,
+ float *cut_val, uint32_t *n_lo);
+Tree_float* construct_tree_float(float *pa, int8_t no_dims, uint32_t n, uint32_t bsp);
+Node_float* construct_subtree_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, float *bbox);
+Node_float * create_node_float(uint32_t start_idx, uint32_t n, int is_leaf);
+void delete_subtree_float(Node_float *root);
+void delete_tree_float(Tree_float *tree);
+void print_tree_float(Node_float *root, int level);
+float calc_dist_float(float *point1_coord, float *point2_coord, int8_t no_dims);
+float get_cube_offset_float(int8_t dim, float *point_coord, float *bbox);
+float get_min_dist_float(float *point_coord, int8_t no_dims, float *bbox);
+void search_leaf_float(float *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *restrict point_coord,
+ uint32_t k, uint32_t *restrict closest_idx, float *restrict closest_dist);
+void search_leaf_float_mask(float *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *restrict point_coord,
+ uint32_t k, uint8_t *restrict mask, uint32_t *restrict closest_idx, float *restrict closest_dist);
+void search_splitnode_float(Node_float *root, float *pa, uint32_t *pidx, int8_t no_dims, float *point_coord,
+ float min_dist, uint32_t k, float distance_upper_bound, float eps_fac, uint8_t *mask, uint32_t * closest_idx, float *closest_dist);
+void search_tree_float(Tree_float *tree, float *pa, float *point_coords,
+ uint32_t num_points, uint32_t k, float distance_upper_bound,
+ float eps, uint8_t *mask, uint32_t *closest_idxs, float *closest_dists);
+
+
+void insert_point_double(uint32_t *closest_idx, double *closest_dist, uint32_t pidx, double cur_dist, uint32_t k);
+void get_bounding_box_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, double *bbox);
+int partition_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *bbox, int8_t *cut_dim,
+ double *cut_val, uint32_t *n_lo);
+Tree_double* construct_tree_double(double *pa, int8_t no_dims, uint32_t n, uint32_t bsp);
+Node_double* construct_subtree_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, double *bbox);
+Node_double * create_node_double(uint32_t start_idx, uint32_t n, int is_leaf);
+void delete_subtree_double(Node_double *root);
+void delete_tree_double(Tree_double *tree);
+void print_tree_double(Node_double *root, int level);
+double calc_dist_double(double *point1_coord, double *point2_coord, int8_t no_dims);
+double get_cube_offset_double(int8_t dim, double *point_coord, double *bbox);
+double get_min_dist_double(double *point_coord, int8_t no_dims, double *bbox);
+void search_leaf_double(double *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *restrict point_coord,
+ uint32_t k, uint32_t *restrict closest_idx, double *restrict closest_dist);
+void search_leaf_double_mask(double *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *restrict point_coord,
+ uint32_t k, uint8_t *restrict mask, uint32_t *restrict closest_idx, double *restrict closest_dist);
+void search_splitnode_double(Node_double *root, double *pa, uint32_t *pidx, int8_t no_dims, double *point_coord,
+ double min_dist, uint32_t k, double distance_upper_bound, double eps_fac, uint8_t *mask, uint32_t * closest_idx, double *closest_dist);
+void search_tree_double(Tree_double *tree, double *pa, double *point_coords,
+ uint32_t num_points, uint32_t k, double distance_upper_bound,
+ double eps, uint8_t *mask, uint32_t *closest_idxs, double *closest_dists);
+
+
+
+/************************************************
+Insert point into priority queue
+Params:
+ closest_idx : index queue
+ closest_dist : distance queue
+ pidx : permutation index of data points
+ cur_dist : distance to point inserted
+ k : number of neighbours
+************************************************/
+void insert_point_float(uint32_t *closest_idx, float *closest_dist, uint32_t pidx, float cur_dist, uint32_t k)
+{
+ int i;
+ for (i = k - 1; i > 0; i--)
+ {
+ if (closest_dist[i - 1] > cur_dist)
+ {
+ closest_dist[i] = closest_dist[i - 1];
+ closest_idx[i] = closest_idx[i - 1];
+ }
+ else
+ {
+ break;
+ }
+ }
+ closest_idx[i] = pidx;
+ closest_dist[i] = cur_dist;
+}
+
+/************************************************
+Get the bounding box of a set of points
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ n : number of points
+ bbox : bounding box (return)
+************************************************/
+void get_bounding_box_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, float *bbox)
+{
+ float cur;
+ int8_t bbox_idx, i, j;
+ uint32_t i2;
+
+ /* Use first data point to initialize */
+ for (i = 0; i < no_dims; i++)
+ {
+ bbox[2 * i] = bbox[2 * i + 1] = PA(0, i);
+ }
+
+ /* Update using rest of data points */
+ for (i2 = 1; i2 < n; i2++)
+ {
+ for (j = 0; j < no_dims; j++)
+ {
+ bbox_idx = 2 * j;
+ cur = PA(i2, j);
+ if (cur < bbox[bbox_idx])
+ {
+ bbox[bbox_idx] = cur;
+ }
+ else if (cur > bbox[bbox_idx + 1])
+ {
+ bbox[bbox_idx + 1] = cur;
+ }
+ }
+ }
+}
+
+/************************************************
+Partition a range of data points by manipulation the permutation index.
+The sliding midpoint rule is used for the partitioning.
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ start_idx : index of first data point to use
+ n : number of data points
+ bbox : bounding box of data points
+ cut_dim : dimension used for partition (return)
+ cut_val : value of cutting point (return)
+ n_lo : number of point below cutting plane (return)
+************************************************/
+int partition_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *bbox, int8_t *cut_dim, float *cut_val, uint32_t *n_lo)
+{
+ int8_t dim = 0, i;
+ uint32_t p, q, i2;
+ float size = 0, min_val, max_val, split, side_len, cur_val;
+ uint32_t end_idx = start_idx + n - 1;
+
+ /* Find largest bounding box side */
+ for (i = 0; i < no_dims; i++)
+ {
+ side_len = bbox[2 * i + 1] - bbox[2 * i];
+ if (side_len > size)
+ {
+ dim = i;
+ size = side_len;
+ }
+ }
+
+ min_val = bbox[2 * dim];
+ max_val = bbox[2 * dim + 1];
+
+ /* Check for zero length or inconsistent */
+ if (min_val >= max_val)
+ return 1;
+
+ /* Use middle for splitting */
+ split = (min_val + max_val) / 2;
+
+ /* Partition all data points around middle */
+ p = start_idx;
+ q = end_idx;
+ while (p <= q)
+ {
+ if (PA(p, dim) < split)
+ {
+ p++;
+ }
+ else if (PA(q, dim) >= split)
+ {
+ /* Guard for underflow */
+ if (q > 0)
+ {
+ q--;
+ }
+ else
+ {
+ break;
+ }
+ }
+ else
+ {
+ PASWAP(p, q);
+ p++;
+ q--;
+ }
+ }
+
+ /* Check for empty splits */
+ if (p == start_idx)
+ {
+ /* No points less than split.
+ Split at lowest point instead.
+ Minimum 1 point will be in lower box.
+ */
+
+ uint32_t j = start_idx;
+ split = PA(j, dim);
+ for (i2 = start_idx + 1; i2 <= end_idx; i2++)
+ {
+ /* Find lowest point */
+ cur_val = PA(i2, dim);
+ if (cur_val < split)
+ {
+ j = i2;
+ split = cur_val;
+ }
+ }
+ PASWAP(j, start_idx);
+ p = start_idx + 1;
+ }
+ else if (p == end_idx + 1)
+ {
+ /* No points greater than split.
+ Split at highest point instead.
+ Minimum 1 point will be in higher box.
+ */
+
+ uint32_t j = end_idx;
+ split = PA(j, dim);
+ for (i2 = start_idx; i2 < end_idx; i2++)
+ {
+ /* Find highest point */
+ cur_val = PA(i2, dim);
+ if (cur_val > split)
+ {
+ j = i2;
+ split = cur_val;
+ }
+ }
+ PASWAP(j, end_idx);
+ p = end_idx;
+ }
+
+ /* Set return values */
+ *cut_dim = dim;
+ *cut_val = split;
+ *n_lo = p - start_idx;
+ return 0;
+}
+
+/************************************************
+Construct a sub tree over a range of data points.
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ start_idx : index of first data point to use
+ n : number of data points
+ bsp : number of points per leaf
+ bbox : bounding box of set of data points
+************************************************/
+Node_float* construct_subtree_float(float *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, float *bbox)
+{
+ /* Create new node */
+ int is_leaf = (n <= bsp);
+ Node_float *root = create_node_float(start_idx, n, is_leaf);
+ int rval;
+ int8_t cut_dim;
+ uint32_t n_lo;
+ float cut_val, lv, hv;
+ if (is_leaf)
+ {
+ /* Make leaf node */
+ root->cut_dim = -1;
+ }
+ else
+ {
+ /* Make split node */
+ /* Partition data set and set node info */
+ rval = partition_float(pa, pidx, no_dims, start_idx, n, bbox, &cut_dim, &cut_val, &n_lo);
+ if (rval == 1)
+ {
+ root->cut_dim = -1;
+ return root;
+ }
+ root->cut_val = cut_val;
+ root->cut_dim = cut_dim;
+
+ /* Recurse on both subsets */
+ lv = bbox[2 * cut_dim];
+ hv = bbox[2 * cut_dim + 1];
+
+ /* Set bounds for cut dimension */
+ root->cut_bounds_lv = lv;
+ root->cut_bounds_hv = hv;
+
+ /* Update bounding box before call to lower subset and restore after */
+ bbox[2 * cut_dim + 1] = cut_val;
+ root->left_child = (struct Node_float *)construct_subtree_float(pa, pidx, no_dims, start_idx, n_lo, bsp, bbox);
+ bbox[2 * cut_dim + 1] = hv;
+
+ /* Update bounding box before call to higher subset and restore after */
+ bbox[2 * cut_dim] = cut_val;
+ root->right_child = (struct Node_float *)construct_subtree_float(pa, pidx, no_dims, start_idx + n_lo, n - n_lo, bsp, bbox);
+ bbox[2 * cut_dim] = lv;
+ }
+ return root;
+}
+
+/************************************************
+Construct a tree over data points.
+Params:
+ pa : data points
+ no_dims: number of dimensions
+ n : number of data points
+ bsp : number of points per leaf
+************************************************/
+Tree_float* construct_tree_float(float *pa, int8_t no_dims, uint32_t n, uint32_t bsp)
+{
+ Tree_float *tree = (Tree_float *)malloc(sizeof(Tree_float));
+ uint32_t i;
+ uint32_t *pidx;
+ float *bbox;
+
+ tree->no_dims = no_dims;
+
+ /* Initialize permutation array */
+ pidx = (uint32_t *)malloc(sizeof(uint32_t) * n);
+ for (i = 0; i < n; i++)
+ {
+ pidx[i] = i;
+ }
+
+ bbox = (float *)malloc(2 * sizeof(float) * no_dims);
+ get_bounding_box_float(pa, pidx, no_dims, n, bbox);
+ tree->bbox = bbox;
+
+ /* Construct subtree on full dataset */
+ tree->root = (struct Node_float *)construct_subtree_float(pa, pidx, no_dims, 0, n, bsp, bbox);
+
+ tree->pidx = pidx;
+ return tree;
+}
+
+/************************************************
+Create a tree node.
+Params:
+ start_idx : index of first data point to use
+ n : number of data points
+************************************************/
+Node_float* create_node_float(uint32_t start_idx, uint32_t n, int is_leaf)
+{
+ Node_float *new_node;
+ if (is_leaf)
+ {
+ /*
+ Allocate only the part of the struct that will be used in a leaf node.
+ This relies on the C99 specification of struct layout conservation and padding and
+ that dereferencing is never attempted for the node pointers in a leaf.
+ */
+ new_node = (Node_float *)malloc(sizeof(Node_float) - 2 * sizeof(Node_float *));
+ }
+ else
+ {
+ new_node = (Node_float *)malloc(sizeof(Node_float));
+ }
+ new_node->n = n;
+ new_node->start_idx = start_idx;
+ return new_node;
+}
+
+/************************************************
+Delete subtree
+Params:
+ root : root node of subtree to delete
+************************************************/
+void delete_subtree_float(Node_float *root)
+{
+ if (root->cut_dim != -1)
+ {
+ delete_subtree_float((Node_float *)root->left_child);
+ delete_subtree_float((Node_float *)root->right_child);
+ }
+ free(root);
+}
+
+/************************************************
+Delete tree
+Params:
+ tree : Tree struct of kd tree
+************************************************/
+void delete_tree_float(Tree_float *tree)
+{
+ delete_subtree_float((Node_float *)tree->root);
+ free(tree->bbox);
+ free(tree->pidx);
+ free(tree);
+}
+
+/************************************************
+Print
+************************************************/
+void print_tree_float(Node_float *root, int level)
+{
+ int i;
+ for (i = 0; i < level; i++)
+ {
+ printf(" ");
+ }
+ printf("(cut_val: %f, cut_dim: %i)\n", root->cut_val, root->cut_dim);
+ if (root->cut_dim != -1)
+ print_tree_float((Node_float *)root->left_child, level + 1);
+ if (root->cut_dim != -1)
+ print_tree_float((Node_float *)root->right_child, level + 1);
+}
+
+/************************************************
+Calculate squared cartesian distance between points
+Params:
+ point1_coord : point 1
+ point2_coord : point 2
+************************************************/
+float calc_dist_float(float *point1_coord, float *point2_coord, int8_t no_dims)
+{
+ /* Calculate squared distance */
+ float dist = 0, dim_dist;
+ int8_t i;
+ for (i = 0; i < no_dims; i++)
+ {
+ dim_dist = point2_coord[i] - point1_coord[i];
+ dist += dim_dist * dim_dist;
+ }
+ return dist;
+}
+
+/************************************************
+Get squared distance from point to cube in specified dimension
+Params:
+ dim : dimension
+ point_coord : cartesian coordinates of point
+ bbox : cube
+************************************************/
+float get_cube_offset_float(int8_t dim, float *point_coord, float *bbox)
+{
+ float dim_coord = point_coord[dim];
+
+ if (dim_coord < bbox[2 * dim])
+ {
+ /* Left of cube in dimension */
+ return dim_coord - bbox[2 * dim];
+ }
+ else if (dim_coord > bbox[2 * dim + 1])
+ {
+ /* Right of cube in dimension */
+ return dim_coord - bbox[2 * dim + 1];
+ }
+ else
+ {
+ /* Inside cube in dimension */
+ return 0.;
+ }
+}
+
+/************************************************
+Get minimum squared distance between point and cube.
+Params:
+ point_coord : cartesian coordinates of point
+ no_dims : number of dimensions
+ bbox : cube
+************************************************/
+float get_min_dist_float(float *point_coord, int8_t no_dims, float *bbox)
+{
+ float cube_offset = 0, cube_offset_dim;
+ int8_t i;
+
+ for (i = 0; i < no_dims; i++)
+ {
+ cube_offset_dim = get_cube_offset_float(i, point_coord, bbox);
+ cube_offset += cube_offset_dim * cube_offset_dim;
+ }
+
+ return cube_offset;
+}
+
+/************************************************
+Search a leaf node for closest point
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ start_idx : index of first data point to use
+ size : number of data points
+ point_coord : query point
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_leaf_float(float *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *restrict point_coord,
+ uint32_t k, uint32_t *restrict closest_idx, float *restrict closest_dist)
+{
+ float cur_dist;
+ uint32_t i;
+ /* Loop through all points in leaf */
+ for (i = 0; i < n; i++)
+ {
+ /* Get distance to query point */
+ cur_dist = calc_dist_float(&PA(start_idx + i, 0), point_coord, no_dims);
+ /* Update closest info if new point is closest so far*/
+ if (cur_dist < closest_dist[k - 1])
+ {
+ insert_point_float(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k);
+ }
+ }
+}
+
+
+/************************************************
+Search a leaf node for closest point with data point mask
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ start_idx : index of first data point to use
+ size : number of data points
+ point_coord : query point
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_leaf_float_mask(float *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, float *restrict point_coord,
+ uint32_t k, uint8_t *mask, uint32_t *restrict closest_idx, float *restrict closest_dist)
+{
+ float cur_dist;
+ uint32_t i;
+ /* Loop through all points in leaf */
+ for (i = 0; i < n; i++)
+ {
+ /* Is this point masked out? */
+ if (mask[pidx[start_idx + i]])
+ {
+ continue;
+ }
+ /* Get distance to query point */
+ cur_dist = calc_dist_float(&PA(start_idx + i, 0), point_coord, no_dims);
+ /* Update closest info if new point is closest so far*/
+ if (cur_dist < closest_dist[k - 1])
+ {
+ insert_point_float(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k);
+ }
+ }
+}
+
+/************************************************
+Search subtree for nearest to query point
+Params:
+ root : root node of subtree
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ point_coord : query point
+ min_dist : minumum distance to nearest neighbour
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_splitnode_float(Node_float *root, float *pa, uint32_t *pidx, int8_t no_dims, float *point_coord,
+ float min_dist, uint32_t k, float distance_upper_bound, float eps_fac, uint8_t *mask,
+ uint32_t *closest_idx, float *closest_dist)
+{
+ int8_t dim;
+ float dist_left, dist_right;
+ float new_offset;
+ float box_diff;
+
+ /* Skip if distance bound exeeded */
+ if (min_dist > distance_upper_bound)
+ {
+ return;
+ }
+
+ dim = root->cut_dim;
+
+ /* Handle leaf node */
+ if (dim == -1)
+ {
+ if (mask)
+ {
+ search_leaf_float_mask(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, mask, closest_idx, closest_dist);
+ }
+ else
+ {
+ search_leaf_float(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, closest_idx, closest_dist);
+ }
+ return;
+ }
+
+ /* Get distance to cutting plane */
+ new_offset = point_coord[dim] - root->cut_val;
+
+ if (new_offset < 0)
+ {
+ /* Left of cutting plane */
+ dist_left = min_dist;
+ if (dist_left < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search left subtree if minimum distance is below limit */
+ search_splitnode_float((Node_float *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+
+ /* Right of cutting plane. Update minimum distance.
+ See Algorithms for Fast Vector Quantization
+ Sunil Arya and David M. Mount. */
+ box_diff = root->cut_bounds_lv - point_coord[dim];
+ if (box_diff < 0)
+ {
+ box_diff = 0;
+ }
+ dist_right = min_dist - box_diff * box_diff + new_offset * new_offset;
+ if (dist_right < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search right subtree if minimum distance is below limit*/
+ search_splitnode_float((Node_float *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+ }
+ else
+ {
+ /* Right of cutting plane */
+ dist_right = min_dist;
+ if (dist_right < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search right subtree if minimum distance is below limit*/
+ search_splitnode_float((Node_float *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+
+ /* Left of cutting plane. Update minimum distance.
+ See Algorithms for Fast Vector Quantization
+ Sunil Arya and David M. Mount. */
+ box_diff = point_coord[dim] - root->cut_bounds_hv;
+ if (box_diff < 0)
+ {
+ box_diff = 0;
+ }
+ dist_left = min_dist - box_diff * box_diff + new_offset * new_offset;
+ if (dist_left < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search left subtree if minimum distance is below limit*/
+ search_splitnode_float((Node_float *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+ }
+}
+
+/************************************************
+Search for nearest neighbour for a set of query points
+Params:
+ tree : Tree struct of kd tree
+ pa : data points
+ pidx : permutation index of data points
+ point_coords : query points
+ num_points : number of query points
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_tree_float(Tree_float *tree, float *pa, float *point_coords,
+ uint32_t num_points, uint32_t k, float distance_upper_bound,
+ float eps, uint8_t *mask, uint32_t *closest_idxs, float *closest_dists)
+{
+ float min_dist;
+ float eps_fac = 1 / ((1 + eps) * (1 + eps));
+ int8_t no_dims = tree->no_dims;
+ float *bbox = tree->bbox;
+ uint32_t *pidx = tree->pidx;
+ uint32_t j = 0;
+#if defined(_MSC_VER) && defined(_OPENMP)
+ int32_t i = 0;
+ int32_t local_num_points = (int32_t) num_points;
+#else
+ uint32_t i;
+ uint32_t local_num_points = num_points;
+#endif
+ Node_float *root = (Node_float *)tree->root;
+
+ /* Queries are OpenMP enabled */
+ #pragma omp parallel
+ {
+ /* The low chunk size is important to avoid L2 cache trashing
+ for spatial coherent query datasets
+ */
+ #pragma omp for private(i, j) schedule(static, 100) nowait
+ for (i = 0; i < local_num_points; i++)
+ {
+ for (j = 0; j < k; j++)
+ {
+ closest_idxs[i * k + j] = UINT32_MAX;
+ closest_dists[i * k + j] = DBL_MAX;
+ }
+ min_dist = get_min_dist_float(point_coords + no_dims * i, no_dims, bbox);
+ search_splitnode_float(root, pa, pidx, no_dims, point_coords + no_dims * i, min_dist,
+ k, distance_upper_bound, eps_fac, mask, &closest_idxs[i * k], &closest_dists[i * k]);
+ }
+ }
+}
+
+/************************************************
+Insert point into priority queue
+Params:
+ closest_idx : index queue
+ closest_dist : distance queue
+ pidx : permutation index of data points
+ cur_dist : distance to point inserted
+ k : number of neighbours
+************************************************/
+void insert_point_double(uint32_t *closest_idx, double *closest_dist, uint32_t pidx, double cur_dist, uint32_t k)
+{
+ int i;
+ for (i = k - 1; i > 0; i--)
+ {
+ if (closest_dist[i - 1] > cur_dist)
+ {
+ closest_dist[i] = closest_dist[i - 1];
+ closest_idx[i] = closest_idx[i - 1];
+ }
+ else
+ {
+ break;
+ }
+ }
+ closest_idx[i] = pidx;
+ closest_dist[i] = cur_dist;
+}
+
+/************************************************
+Get the bounding box of a set of points
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ n : number of points
+ bbox : bounding box (return)
+************************************************/
+void get_bounding_box_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, double *bbox)
+{
+ double cur;
+ int8_t bbox_idx, i, j;
+ uint32_t i2;
+
+ /* Use first data point to initialize */
+ for (i = 0; i < no_dims; i++)
+ {
+ bbox[2 * i] = bbox[2 * i + 1] = PA(0, i);
+ }
+
+ /* Update using rest of data points */
+ for (i2 = 1; i2 < n; i2++)
+ {
+ for (j = 0; j < no_dims; j++)
+ {
+ bbox_idx = 2 * j;
+ cur = PA(i2, j);
+ if (cur < bbox[bbox_idx])
+ {
+ bbox[bbox_idx] = cur;
+ }
+ else if (cur > bbox[bbox_idx + 1])
+ {
+ bbox[bbox_idx + 1] = cur;
+ }
+ }
+ }
+}
+
+/************************************************
+Partition a range of data points by manipulation the permutation index.
+The sliding midpoint rule is used for the partitioning.
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ start_idx : index of first data point to use
+ n : number of data points
+ bbox : bounding box of data points
+ cut_dim : dimension used for partition (return)
+ cut_val : value of cutting point (return)
+ n_lo : number of point below cutting plane (return)
+************************************************/
+int partition_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *bbox, int8_t *cut_dim, double *cut_val, uint32_t *n_lo)
+{
+ int8_t dim = 0, i;
+ uint32_t p, q, i2;
+ double size = 0, min_val, max_val, split, side_len, cur_val;
+ uint32_t end_idx = start_idx + n - 1;
+
+ /* Find largest bounding box side */
+ for (i = 0; i < no_dims; i++)
+ {
+ side_len = bbox[2 * i + 1] - bbox[2 * i];
+ if (side_len > size)
+ {
+ dim = i;
+ size = side_len;
+ }
+ }
+
+ min_val = bbox[2 * dim];
+ max_val = bbox[2 * dim + 1];
+
+ /* Check for zero length or inconsistent */
+ if (min_val >= max_val)
+ return 1;
+
+ /* Use middle for splitting */
+ split = (min_val + max_val) / 2;
+
+ /* Partition all data points around middle */
+ p = start_idx;
+ q = end_idx;
+ while (p <= q)
+ {
+ if (PA(p, dim) < split)
+ {
+ p++;
+ }
+ else if (PA(q, dim) >= split)
+ {
+ /* Guard for underflow */
+ if (q > 0)
+ {
+ q--;
+ }
+ else
+ {
+ break;
+ }
+ }
+ else
+ {
+ PASWAP(p, q);
+ p++;
+ q--;
+ }
+ }
+
+ /* Check for empty splits */
+ if (p == start_idx)
+ {
+ /* No points less than split.
+ Split at lowest point instead.
+ Minimum 1 point will be in lower box.
+ */
+
+ uint32_t j = start_idx;
+ split = PA(j, dim);
+ for (i2 = start_idx + 1; i2 <= end_idx; i2++)
+ {
+ /* Find lowest point */
+ cur_val = PA(i2, dim);
+ if (cur_val < split)
+ {
+ j = i2;
+ split = cur_val;
+ }
+ }
+ PASWAP(j, start_idx);
+ p = start_idx + 1;
+ }
+ else if (p == end_idx + 1)
+ {
+ /* No points greater than split.
+ Split at highest point instead.
+ Minimum 1 point will be in higher box.
+ */
+
+ uint32_t j = end_idx;
+ split = PA(j, dim);
+ for (i2 = start_idx; i2 < end_idx; i2++)
+ {
+ /* Find highest point */
+ cur_val = PA(i2, dim);
+ if (cur_val > split)
+ {
+ j = i2;
+ split = cur_val;
+ }
+ }
+ PASWAP(j, end_idx);
+ p = end_idx;
+ }
+
+ /* Set return values */
+ *cut_dim = dim;
+ *cut_val = split;
+ *n_lo = p - start_idx;
+ return 0;
+}
+
+/************************************************
+Construct a sub tree over a range of data points.
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ start_idx : index of first data point to use
+ n : number of data points
+ bsp : number of points per leaf
+ bbox : bounding box of set of data points
+************************************************/
+Node_double* construct_subtree_double(double *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, double *bbox)
+{
+ /* Create new node */
+ int is_leaf = (n <= bsp);
+ Node_double *root = create_node_double(start_idx, n, is_leaf);
+ int rval;
+ int8_t cut_dim;
+ uint32_t n_lo;
+ double cut_val, lv, hv;
+ if (is_leaf)
+ {
+ /* Make leaf node */
+ root->cut_dim = -1;
+ }
+ else
+ {
+ /* Make split node */
+ /* Partition data set and set node info */
+ rval = partition_double(pa, pidx, no_dims, start_idx, n, bbox, &cut_dim, &cut_val, &n_lo);
+ if (rval == 1)
+ {
+ root->cut_dim = -1;
+ return root;
+ }
+ root->cut_val = cut_val;
+ root->cut_dim = cut_dim;
+
+ /* Recurse on both subsets */
+ lv = bbox[2 * cut_dim];
+ hv = bbox[2 * cut_dim + 1];
+
+ /* Set bounds for cut dimension */
+ root->cut_bounds_lv = lv;
+ root->cut_bounds_hv = hv;
+
+ /* Update bounding box before call to lower subset and restore after */
+ bbox[2 * cut_dim + 1] = cut_val;
+ root->left_child = (struct Node_double *)construct_subtree_double(pa, pidx, no_dims, start_idx, n_lo, bsp, bbox);
+ bbox[2 * cut_dim + 1] = hv;
+
+ /* Update bounding box before call to higher subset and restore after */
+ bbox[2 * cut_dim] = cut_val;
+ root->right_child = (struct Node_double *)construct_subtree_double(pa, pidx, no_dims, start_idx + n_lo, n - n_lo, bsp, bbox);
+ bbox[2 * cut_dim] = lv;
+ }
+ return root;
+}
+
+/************************************************
+Construct a tree over data points.
+Params:
+ pa : data points
+ no_dims: number of dimensions
+ n : number of data points
+ bsp : number of points per leaf
+************************************************/
+Tree_double* construct_tree_double(double *pa, int8_t no_dims, uint32_t n, uint32_t bsp)
+{
+ Tree_double *tree = (Tree_double *)malloc(sizeof(Tree_double));
+ uint32_t i;
+ uint32_t *pidx;
+ double *bbox;
+
+ tree->no_dims = no_dims;
+
+ /* Initialize permutation array */
+ pidx = (uint32_t *)malloc(sizeof(uint32_t) * n);
+ for (i = 0; i < n; i++)
+ {
+ pidx[i] = i;
+ }
+
+ bbox = (double *)malloc(2 * sizeof(double) * no_dims);
+ get_bounding_box_double(pa, pidx, no_dims, n, bbox);
+ tree->bbox = bbox;
+
+ /* Construct subtree on full dataset */
+ tree->root = (struct Node_double *)construct_subtree_double(pa, pidx, no_dims, 0, n, bsp, bbox);
+
+ tree->pidx = pidx;
+ return tree;
+}
+
+/************************************************
+Create a tree node.
+Params:
+ start_idx : index of first data point to use
+ n : number of data points
+************************************************/
+Node_double* create_node_double(uint32_t start_idx, uint32_t n, int is_leaf)
+{
+ Node_double *new_node;
+ if (is_leaf)
+ {
+ /*
+ Allocate only the part of the struct that will be used in a leaf node.
+ This relies on the C99 specification of struct layout conservation and padding and
+ that dereferencing is never attempted for the node pointers in a leaf.
+ */
+ new_node = (Node_double *)malloc(sizeof(Node_double) - 2 * sizeof(Node_double *));
+ }
+ else
+ {
+ new_node = (Node_double *)malloc(sizeof(Node_double));
+ }
+ new_node->n = n;
+ new_node->start_idx = start_idx;
+ return new_node;
+}
+
+/************************************************
+Delete subtree
+Params:
+ root : root node of subtree to delete
+************************************************/
+void delete_subtree_double(Node_double *root)
+{
+ if (root->cut_dim != -1)
+ {
+ delete_subtree_double((Node_double *)root->left_child);
+ delete_subtree_double((Node_double *)root->right_child);
+ }
+ free(root);
+}
+
+/************************************************
+Delete tree
+Params:
+ tree : Tree struct of kd tree
+************************************************/
+void delete_tree_double(Tree_double *tree)
+{
+ delete_subtree_double((Node_double *)tree->root);
+ free(tree->bbox);
+ free(tree->pidx);
+ free(tree);
+}
+
+/************************************************
+Print
+************************************************/
+void print_tree_double(Node_double *root, int level)
+{
+ int i;
+ for (i = 0; i < level; i++)
+ {
+ printf(" ");
+ }
+ printf("(cut_val: %f, cut_dim: %i)\n", root->cut_val, root->cut_dim);
+ if (root->cut_dim != -1)
+ print_tree_double((Node_double *)root->left_child, level + 1);
+ if (root->cut_dim != -1)
+ print_tree_double((Node_double *)root->right_child, level + 1);
+}
+
+/************************************************
+Calculate squared cartesian distance between points
+Params:
+ point1_coord : point 1
+ point2_coord : point 2
+************************************************/
+double calc_dist_double(double *point1_coord, double *point2_coord, int8_t no_dims)
+{
+ /* Calculate squared distance */
+ double dist = 0, dim_dist;
+ int8_t i;
+ for (i = 0; i < no_dims; i++)
+ {
+ dim_dist = point2_coord[i] - point1_coord[i];
+ dist += dim_dist * dim_dist;
+ }
+ return dist;
+}
+
+/************************************************
+Get squared distance from point to cube in specified dimension
+Params:
+ dim : dimension
+ point_coord : cartesian coordinates of point
+ bbox : cube
+************************************************/
+double get_cube_offset_double(int8_t dim, double *point_coord, double *bbox)
+{
+ double dim_coord = point_coord[dim];
+
+ if (dim_coord < bbox[2 * dim])
+ {
+ /* Left of cube in dimension */
+ return dim_coord - bbox[2 * dim];
+ }
+ else if (dim_coord > bbox[2 * dim + 1])
+ {
+ /* Right of cube in dimension */
+ return dim_coord - bbox[2 * dim + 1];
+ }
+ else
+ {
+ /* Inside cube in dimension */
+ return 0.;
+ }
+}
+
+/************************************************
+Get minimum squared distance between point and cube.
+Params:
+ point_coord : cartesian coordinates of point
+ no_dims : number of dimensions
+ bbox : cube
+************************************************/
+double get_min_dist_double(double *point_coord, int8_t no_dims, double *bbox)
+{
+ double cube_offset = 0, cube_offset_dim;
+ int8_t i;
+
+ for (i = 0; i < no_dims; i++)
+ {
+ cube_offset_dim = get_cube_offset_double(i, point_coord, bbox);
+ cube_offset += cube_offset_dim * cube_offset_dim;
+ }
+
+ return cube_offset;
+}
+
+/************************************************
+Search a leaf node for closest point
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ start_idx : index of first data point to use
+ size : number of data points
+ point_coord : query point
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_leaf_double(double *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *restrict point_coord,
+ uint32_t k, uint32_t *restrict closest_idx, double *restrict closest_dist)
+{
+ double cur_dist;
+ uint32_t i;
+ /* Loop through all points in leaf */
+ for (i = 0; i < n; i++)
+ {
+ /* Get distance to query point */
+ cur_dist = calc_dist_double(&PA(start_idx + i, 0), point_coord, no_dims);
+ /* Update closest info if new point is closest so far*/
+ if (cur_dist < closest_dist[k - 1])
+ {
+ insert_point_double(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k);
+ }
+ }
+}
+
+
+/************************************************
+Search a leaf node for closest point with data point mask
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ start_idx : index of first data point to use
+ size : number of data points
+ point_coord : query point
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_leaf_double_mask(double *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, double *restrict point_coord,
+ uint32_t k, uint8_t *mask, uint32_t *restrict closest_idx, double *restrict closest_dist)
+{
+ double cur_dist;
+ uint32_t i;
+ /* Loop through all points in leaf */
+ for (i = 0; i < n; i++)
+ {
+ /* Is this point masked out? */
+ if (mask[pidx[start_idx + i]])
+ {
+ continue;
+ }
+ /* Get distance to query point */
+ cur_dist = calc_dist_double(&PA(start_idx + i, 0), point_coord, no_dims);
+ /* Update closest info if new point is closest so far*/
+ if (cur_dist < closest_dist[k - 1])
+ {
+ insert_point_double(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k);
+ }
+ }
+}
+
+/************************************************
+Search subtree for nearest to query point
+Params:
+ root : root node of subtree
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ point_coord : query point
+ min_dist : minumum distance to nearest neighbour
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_splitnode_double(Node_double *root, double *pa, uint32_t *pidx, int8_t no_dims, double *point_coord,
+ double min_dist, uint32_t k, double distance_upper_bound, double eps_fac, uint8_t *mask,
+ uint32_t *closest_idx, double *closest_dist)
+{
+ int8_t dim;
+ double dist_left, dist_right;
+ double new_offset;
+ double box_diff;
+
+ /* Skip if distance bound exeeded */
+ if (min_dist > distance_upper_bound)
+ {
+ return;
+ }
+
+ dim = root->cut_dim;
+
+ /* Handle leaf node */
+ if (dim == -1)
+ {
+ if (mask)
+ {
+ search_leaf_double_mask(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, mask, closest_idx, closest_dist);
+ }
+ else
+ {
+ search_leaf_double(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, closest_idx, closest_dist);
+ }
+ return;
+ }
+
+ /* Get distance to cutting plane */
+ new_offset = point_coord[dim] - root->cut_val;
+
+ if (new_offset < 0)
+ {
+ /* Left of cutting plane */
+ dist_left = min_dist;
+ if (dist_left < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search left subtree if minimum distance is below limit */
+ search_splitnode_double((Node_double *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+
+ /* Right of cutting plane. Update minimum distance.
+ See Algorithms for Fast Vector Quantization
+ Sunil Arya and David M. Mount. */
+ box_diff = root->cut_bounds_lv - point_coord[dim];
+ if (box_diff < 0)
+ {
+ box_diff = 0;
+ }
+ dist_right = min_dist - box_diff * box_diff + new_offset * new_offset;
+ if (dist_right < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search right subtree if minimum distance is below limit*/
+ search_splitnode_double((Node_double *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+ }
+ else
+ {
+ /* Right of cutting plane */
+ dist_right = min_dist;
+ if (dist_right < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search right subtree if minimum distance is below limit*/
+ search_splitnode_double((Node_double *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+
+ /* Left of cutting plane. Update minimum distance.
+ See Algorithms for Fast Vector Quantization
+ Sunil Arya and David M. Mount. */
+ box_diff = point_coord[dim] - root->cut_bounds_hv;
+ if (box_diff < 0)
+ {
+ box_diff = 0;
+ }
+ dist_left = min_dist - box_diff * box_diff + new_offset * new_offset;
+ if (dist_left < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search left subtree if minimum distance is below limit*/
+ search_splitnode_double((Node_double *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+ }
+}
+
+/************************************************
+Search for nearest neighbour for a set of query points
+Params:
+ tree : Tree struct of kd tree
+ pa : data points
+ pidx : permutation index of data points
+ point_coords : query points
+ num_points : number of query points
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_tree_double(Tree_double *tree, double *pa, double *point_coords,
+ uint32_t num_points, uint32_t k, double distance_upper_bound,
+ double eps, uint8_t *mask, uint32_t *closest_idxs, double *closest_dists)
+{
+ double min_dist;
+ double eps_fac = 1 / ((1 + eps) * (1 + eps));
+ int8_t no_dims = tree->no_dims;
+ double *bbox = tree->bbox;
+ uint32_t *pidx = tree->pidx;
+ uint32_t j = 0;
+#if defined(_MSC_VER) && defined(_OPENMP)
+ int32_t i = 0;
+ int32_t local_num_points = (int32_t) num_points;
+#else
+ uint32_t i;
+ uint32_t local_num_points = num_points;
+#endif
+ Node_double *root = (Node_double *)tree->root;
+
+ /* Queries are OpenMP enabled */
+ #pragma omp parallel
+ {
+ /* The low chunk size is important to avoid L2 cache trashing
+ for spatial coherent query datasets
+ */
+ #pragma omp for private(i, j) schedule(static, 100) nowait
+ for (i = 0; i < local_num_points; i++)
+ {
+ for (j = 0; j < k; j++)
+ {
+ closest_idxs[i * k + j] = UINT32_MAX;
+ closest_dists[i * k + j] = DBL_MAX;
+ }
+ min_dist = get_min_dist_double(point_coords + no_dims * i, no_dims, bbox);
+ search_splitnode_double(root, pa, pidx, no_dims, point_coords + no_dims * i, min_dist,
+ k, distance_upper_bound, eps_fac, mask, &closest_idxs[i * k], &closest_dists[i * k]);
+ }
+ }
+}
diff --git a/eval/src/utils/libkdtree/pykdtree/_kdtree_core.c.mako b/eval/src/utils/libkdtree/pykdtree/_kdtree_core.c.mako
new file mode 100644
index 0000000..a8270f5
--- /dev/null
+++ b/eval/src/utils/libkdtree/pykdtree/_kdtree_core.c.mako
@@ -0,0 +1,734 @@
+/*
+pykdtree, Fast kd-tree implementation with OpenMP-enabled queries
+
+Copyright (C) 2013 - present Esben S. Nielsen
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU Lesser General Public License as published by the Free
+Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
+details.
+
+You should have received a copy of the GNU Lesser General Public License along
+with this program. If not, see .
+*/
+
+/*
+This kd-tree implementation is based on the scipy.spatial.cKDTree by
+Anne M. Archibald and libANN by David M. Mount and Sunil Arya.
+*/
+
+
+#include
+#include
+#include
+#include
+
+#define PA(i,d) (pa[no_dims * pidx[i] + d])
+#define PASWAP(a,b) { uint32_t tmp = pidx[a]; pidx[a] = pidx[b]; pidx[b] = tmp; }
+
+#ifdef _MSC_VER
+#define restrict __restrict
+#endif
+
+% for DTYPE in ['float', 'double']:
+
+typedef struct
+{
+ ${DTYPE} cut_val;
+ int8_t cut_dim;
+ uint32_t start_idx;
+ uint32_t n;
+ ${DTYPE} cut_bounds_lv;
+ ${DTYPE} cut_bounds_hv;
+ struct Node_${DTYPE} *left_child;
+ struct Node_${DTYPE} *right_child;
+} Node_${DTYPE};
+
+typedef struct
+{
+ ${DTYPE} *bbox;
+ int8_t no_dims;
+ uint32_t *pidx;
+ struct Node_${DTYPE} *root;
+} Tree_${DTYPE};
+
+% endfor
+
+% for DTYPE in ['float', 'double']:
+
+void insert_point_${DTYPE}(uint32_t *closest_idx, ${DTYPE} *closest_dist, uint32_t pidx, ${DTYPE} cur_dist, uint32_t k);
+void get_bounding_box_${DTYPE}(${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, ${DTYPE} *bbox);
+int partition_${DTYPE}(${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, ${DTYPE} *bbox, int8_t *cut_dim,
+ ${DTYPE} *cut_val, uint32_t *n_lo);
+Tree_${DTYPE}* construct_tree_${DTYPE}(${DTYPE} *pa, int8_t no_dims, uint32_t n, uint32_t bsp);
+Node_${DTYPE}* construct_subtree_${DTYPE}(${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, ${DTYPE} *bbox);
+Node_${DTYPE} * create_node_${DTYPE}(uint32_t start_idx, uint32_t n, int is_leaf);
+void delete_subtree_${DTYPE}(Node_${DTYPE} *root);
+void delete_tree_${DTYPE}(Tree_${DTYPE} *tree);
+void print_tree_${DTYPE}(Node_${DTYPE} *root, int level);
+${DTYPE} calc_dist_${DTYPE}(${DTYPE} *point1_coord, ${DTYPE} *point2_coord, int8_t no_dims);
+${DTYPE} get_cube_offset_${DTYPE}(int8_t dim, ${DTYPE} *point_coord, ${DTYPE} *bbox);
+${DTYPE} get_min_dist_${DTYPE}(${DTYPE} *point_coord, int8_t no_dims, ${DTYPE} *bbox);
+void search_leaf_${DTYPE}(${DTYPE} *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, ${DTYPE} *restrict point_coord,
+ uint32_t k, uint32_t *restrict closest_idx, ${DTYPE} *restrict closest_dist);
+void search_leaf_${DTYPE}_mask(${DTYPE} *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, ${DTYPE} *restrict point_coord,
+ uint32_t k, uint8_t *restrict mask, uint32_t *restrict closest_idx, ${DTYPE} *restrict closest_dist);
+void search_splitnode_${DTYPE}(Node_${DTYPE} *root, ${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, ${DTYPE} *point_coord,
+ ${DTYPE} min_dist, uint32_t k, ${DTYPE} distance_upper_bound, ${DTYPE} eps_fac, uint8_t *mask, uint32_t * closest_idx, ${DTYPE} *closest_dist);
+void search_tree_${DTYPE}(Tree_${DTYPE} *tree, ${DTYPE} *pa, ${DTYPE} *point_coords,
+ uint32_t num_points, uint32_t k, ${DTYPE} distance_upper_bound,
+ ${DTYPE} eps, uint8_t *mask, uint32_t *closest_idxs, ${DTYPE} *closest_dists);
+
+% endfor
+
+% for DTYPE in ['float', 'double']:
+
+/************************************************
+Insert point into priority queue
+Params:
+ closest_idx : index queue
+ closest_dist : distance queue
+ pidx : permutation index of data points
+ cur_dist : distance to point inserted
+ k : number of neighbours
+************************************************/
+void insert_point_${DTYPE}(uint32_t *closest_idx, ${DTYPE} *closest_dist, uint32_t pidx, ${DTYPE} cur_dist, uint32_t k)
+{
+ int i;
+ for (i = k - 1; i > 0; i--)
+ {
+ if (closest_dist[i - 1] > cur_dist)
+ {
+ closest_dist[i] = closest_dist[i - 1];
+ closest_idx[i] = closest_idx[i - 1];
+ }
+ else
+ {
+ break;
+ }
+ }
+ closest_idx[i] = pidx;
+ closest_dist[i] = cur_dist;
+}
+
+/************************************************
+Get the bounding box of a set of points
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ n : number of points
+ bbox : bounding box (return)
+************************************************/
+void get_bounding_box_${DTYPE}(${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, uint32_t n, ${DTYPE} *bbox)
+{
+ ${DTYPE} cur;
+ int8_t bbox_idx, i, j;
+ uint32_t i2;
+
+ /* Use first data point to initialize */
+ for (i = 0; i < no_dims; i++)
+ {
+ bbox[2 * i] = bbox[2 * i + 1] = PA(0, i);
+ }
+
+ /* Update using rest of data points */
+ for (i2 = 1; i2 < n; i2++)
+ {
+ for (j = 0; j < no_dims; j++)
+ {
+ bbox_idx = 2 * j;
+ cur = PA(i2, j);
+ if (cur < bbox[bbox_idx])
+ {
+ bbox[bbox_idx] = cur;
+ }
+ else if (cur > bbox[bbox_idx + 1])
+ {
+ bbox[bbox_idx + 1] = cur;
+ }
+ }
+ }
+}
+
+/************************************************
+Partition a range of data points by manipulation the permutation index.
+The sliding midpoint rule is used for the partitioning.
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ start_idx : index of first data point to use
+ n : number of data points
+ bbox : bounding box of data points
+ cut_dim : dimension used for partition (return)
+ cut_val : value of cutting point (return)
+ n_lo : number of point below cutting plane (return)
+************************************************/
+int partition_${DTYPE}(${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, ${DTYPE} *bbox, int8_t *cut_dim, ${DTYPE} *cut_val, uint32_t *n_lo)
+{
+ int8_t dim = 0, i;
+ uint32_t p, q, i2;
+ ${DTYPE} size = 0, min_val, max_val, split, side_len, cur_val;
+ uint32_t end_idx = start_idx + n - 1;
+
+ /* Find largest bounding box side */
+ for (i = 0; i < no_dims; i++)
+ {
+ side_len = bbox[2 * i + 1] - bbox[2 * i];
+ if (side_len > size)
+ {
+ dim = i;
+ size = side_len;
+ }
+ }
+
+ min_val = bbox[2 * dim];
+ max_val = bbox[2 * dim + 1];
+
+ /* Check for zero length or inconsistent */
+ if (min_val >= max_val)
+ return 1;
+
+ /* Use middle for splitting */
+ split = (min_val + max_val) / 2;
+
+ /* Partition all data points around middle */
+ p = start_idx;
+ q = end_idx;
+ while (p <= q)
+ {
+ if (PA(p, dim) < split)
+ {
+ p++;
+ }
+ else if (PA(q, dim) >= split)
+ {
+ /* Guard for underflow */
+ if (q > 0)
+ {
+ q--;
+ }
+ else
+ {
+ break;
+ }
+ }
+ else
+ {
+ PASWAP(p, q);
+ p++;
+ q--;
+ }
+ }
+
+ /* Check for empty splits */
+ if (p == start_idx)
+ {
+ /* No points less than split.
+ Split at lowest point instead.
+ Minimum 1 point will be in lower box.
+ */
+
+ uint32_t j = start_idx;
+ split = PA(j, dim);
+ for (i2 = start_idx + 1; i2 <= end_idx; i2++)
+ {
+ /* Find lowest point */
+ cur_val = PA(i2, dim);
+ if (cur_val < split)
+ {
+ j = i2;
+ split = cur_val;
+ }
+ }
+ PASWAP(j, start_idx);
+ p = start_idx + 1;
+ }
+ else if (p == end_idx + 1)
+ {
+ /* No points greater than split.
+ Split at highest point instead.
+ Minimum 1 point will be in higher box.
+ */
+
+ uint32_t j = end_idx;
+ split = PA(j, dim);
+ for (i2 = start_idx; i2 < end_idx; i2++)
+ {
+ /* Find highest point */
+ cur_val = PA(i2, dim);
+ if (cur_val > split)
+ {
+ j = i2;
+ split = cur_val;
+ }
+ }
+ PASWAP(j, end_idx);
+ p = end_idx;
+ }
+
+ /* Set return values */
+ *cut_dim = dim;
+ *cut_val = split;
+ *n_lo = p - start_idx;
+ return 0;
+}
+
+/************************************************
+Construct a sub tree over a range of data points.
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims: number of dimensions
+ start_idx : index of first data point to use
+ n : number of data points
+ bsp : number of points per leaf
+ bbox : bounding box of set of data points
+************************************************/
+Node_${DTYPE}* construct_subtree_${DTYPE}(${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, uint32_t bsp, ${DTYPE} *bbox)
+{
+ /* Create new node */
+ int is_leaf = (n <= bsp);
+ Node_${DTYPE} *root = create_node_${DTYPE}(start_idx, n, is_leaf);
+ int rval;
+ int8_t cut_dim;
+ uint32_t n_lo;
+ ${DTYPE} cut_val, lv, hv;
+ if (is_leaf)
+ {
+ /* Make leaf node */
+ root->cut_dim = -1;
+ }
+ else
+ {
+ /* Make split node */
+ /* Partition data set and set node info */
+ rval = partition_${DTYPE}(pa, pidx, no_dims, start_idx, n, bbox, &cut_dim, &cut_val, &n_lo);
+ if (rval == 1)
+ {
+ root->cut_dim = -1;
+ return root;
+ }
+ root->cut_val = cut_val;
+ root->cut_dim = cut_dim;
+
+ /* Recurse on both subsets */
+ lv = bbox[2 * cut_dim];
+ hv = bbox[2 * cut_dim + 1];
+
+ /* Set bounds for cut dimension */
+ root->cut_bounds_lv = lv;
+ root->cut_bounds_hv = hv;
+
+ /* Update bounding box before call to lower subset and restore after */
+ bbox[2 * cut_dim + 1] = cut_val;
+ root->left_child = (struct Node_${DTYPE} *)construct_subtree_${DTYPE}(pa, pidx, no_dims, start_idx, n_lo, bsp, bbox);
+ bbox[2 * cut_dim + 1] = hv;
+
+ /* Update bounding box before call to higher subset and restore after */
+ bbox[2 * cut_dim] = cut_val;
+ root->right_child = (struct Node_${DTYPE} *)construct_subtree_${DTYPE}(pa, pidx, no_dims, start_idx + n_lo, n - n_lo, bsp, bbox);
+ bbox[2 * cut_dim] = lv;
+ }
+ return root;
+}
+
+/************************************************
+Construct a tree over data points.
+Params:
+ pa : data points
+ no_dims: number of dimensions
+ n : number of data points
+ bsp : number of points per leaf
+************************************************/
+Tree_${DTYPE}* construct_tree_${DTYPE}(${DTYPE} *pa, int8_t no_dims, uint32_t n, uint32_t bsp)
+{
+ Tree_${DTYPE} *tree = (Tree_${DTYPE} *)malloc(sizeof(Tree_${DTYPE}));
+ uint32_t i;
+ uint32_t *pidx;
+ ${DTYPE} *bbox;
+
+ tree->no_dims = no_dims;
+
+ /* Initialize permutation array */
+ pidx = (uint32_t *)malloc(sizeof(uint32_t) * n);
+ for (i = 0; i < n; i++)
+ {
+ pidx[i] = i;
+ }
+
+ bbox = (${DTYPE} *)malloc(2 * sizeof(${DTYPE}) * no_dims);
+ get_bounding_box_${DTYPE}(pa, pidx, no_dims, n, bbox);
+ tree->bbox = bbox;
+
+ /* Construct subtree on full dataset */
+ tree->root = (struct Node_${DTYPE} *)construct_subtree_${DTYPE}(pa, pidx, no_dims, 0, n, bsp, bbox);
+
+ tree->pidx = pidx;
+ return tree;
+}
+
+/************************************************
+Create a tree node.
+Params:
+ start_idx : index of first data point to use
+ n : number of data points
+************************************************/
+Node_${DTYPE}* create_node_${DTYPE}(uint32_t start_idx, uint32_t n, int is_leaf)
+{
+ Node_${DTYPE} *new_node;
+ if (is_leaf)
+ {
+ /*
+ Allocate only the part of the struct that will be used in a leaf node.
+ This relies on the C99 specification of struct layout conservation and padding and
+ that dereferencing is never attempted for the node pointers in a leaf.
+ */
+ new_node = (Node_${DTYPE} *)malloc(sizeof(Node_${DTYPE}) - 2 * sizeof(Node_${DTYPE} *));
+ }
+ else
+ {
+ new_node = (Node_${DTYPE} *)malloc(sizeof(Node_${DTYPE}));
+ }
+ new_node->n = n;
+ new_node->start_idx = start_idx;
+ return new_node;
+}
+
+/************************************************
+Delete subtree
+Params:
+ root : root node of subtree to delete
+************************************************/
+void delete_subtree_${DTYPE}(Node_${DTYPE} *root)
+{
+ if (root->cut_dim != -1)
+ {
+ delete_subtree_${DTYPE}((Node_${DTYPE} *)root->left_child);
+ delete_subtree_${DTYPE}((Node_${DTYPE} *)root->right_child);
+ }
+ free(root);
+}
+
+/************************************************
+Delete tree
+Params:
+ tree : Tree struct of kd tree
+************************************************/
+void delete_tree_${DTYPE}(Tree_${DTYPE} *tree)
+{
+ delete_subtree_${DTYPE}((Node_${DTYPE} *)tree->root);
+ free(tree->bbox);
+ free(tree->pidx);
+ free(tree);
+}
+
+/************************************************
+Print
+************************************************/
+void print_tree_${DTYPE}(Node_${DTYPE} *root, int level)
+{
+ int i;
+ for (i = 0; i < level; i++)
+ {
+ printf(" ");
+ }
+ printf("(cut_val: %f, cut_dim: %i)\n", root->cut_val, root->cut_dim);
+ if (root->cut_dim != -1)
+ print_tree_${DTYPE}((Node_${DTYPE} *)root->left_child, level + 1);
+ if (root->cut_dim != -1)
+ print_tree_${DTYPE}((Node_${DTYPE} *)root->right_child, level + 1);
+}
+
+/************************************************
+Calculate squared cartesian distance between points
+Params:
+ point1_coord : point 1
+ point2_coord : point 2
+************************************************/
+${DTYPE} calc_dist_${DTYPE}(${DTYPE} *point1_coord, ${DTYPE} *point2_coord, int8_t no_dims)
+{
+ /* Calculate squared distance */
+ ${DTYPE} dist = 0, dim_dist;
+ int8_t i;
+ for (i = 0; i < no_dims; i++)
+ {
+ dim_dist = point2_coord[i] - point1_coord[i];
+ dist += dim_dist * dim_dist;
+ }
+ return dist;
+}
+
+/************************************************
+Get squared distance from point to cube in specified dimension
+Params:
+ dim : dimension
+ point_coord : cartesian coordinates of point
+ bbox : cube
+************************************************/
+${DTYPE} get_cube_offset_${DTYPE}(int8_t dim, ${DTYPE} *point_coord, ${DTYPE} *bbox)
+{
+ ${DTYPE} dim_coord = point_coord[dim];
+
+ if (dim_coord < bbox[2 * dim])
+ {
+ /* Left of cube in dimension */
+ return dim_coord - bbox[2 * dim];
+ }
+ else if (dim_coord > bbox[2 * dim + 1])
+ {
+ /* Right of cube in dimension */
+ return dim_coord - bbox[2 * dim + 1];
+ }
+ else
+ {
+ /* Inside cube in dimension */
+ return 0.;
+ }
+}
+
+/************************************************
+Get minimum squared distance between point and cube.
+Params:
+ point_coord : cartesian coordinates of point
+ no_dims : number of dimensions
+ bbox : cube
+************************************************/
+${DTYPE} get_min_dist_${DTYPE}(${DTYPE} *point_coord, int8_t no_dims, ${DTYPE} *bbox)
+{
+ ${DTYPE} cube_offset = 0, cube_offset_dim;
+ int8_t i;
+
+ for (i = 0; i < no_dims; i++)
+ {
+ cube_offset_dim = get_cube_offset_${DTYPE}(i, point_coord, bbox);
+ cube_offset += cube_offset_dim * cube_offset_dim;
+ }
+
+ return cube_offset;
+}
+
+/************************************************
+Search a leaf node for closest point
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ start_idx : index of first data point to use
+ size : number of data points
+ point_coord : query point
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_leaf_${DTYPE}(${DTYPE} *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, ${DTYPE} *restrict point_coord,
+ uint32_t k, uint32_t *restrict closest_idx, ${DTYPE} *restrict closest_dist)
+{
+ ${DTYPE} cur_dist;
+ uint32_t i;
+ /* Loop through all points in leaf */
+ for (i = 0; i < n; i++)
+ {
+ /* Get distance to query point */
+ cur_dist = calc_dist_${DTYPE}(&PA(start_idx + i, 0), point_coord, no_dims);
+ /* Update closest info if new point is closest so far*/
+ if (cur_dist < closest_dist[k - 1])
+ {
+ insert_point_${DTYPE}(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k);
+ }
+ }
+}
+
+
+/************************************************
+Search a leaf node for closest point with data point mask
+Params:
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ start_idx : index of first data point to use
+ size : number of data points
+ point_coord : query point
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_leaf_${DTYPE}_mask(${DTYPE} *restrict pa, uint32_t *restrict pidx, int8_t no_dims, uint32_t start_idx, uint32_t n, ${DTYPE} *restrict point_coord,
+ uint32_t k, uint8_t *mask, uint32_t *restrict closest_idx, ${DTYPE} *restrict closest_dist)
+{
+ ${DTYPE} cur_dist;
+ uint32_t i;
+ /* Loop through all points in leaf */
+ for (i = 0; i < n; i++)
+ {
+ /* Is this point masked out? */
+ if (mask[pidx[start_idx + i]])
+ {
+ continue;
+ }
+ /* Get distance to query point */
+ cur_dist = calc_dist_${DTYPE}(&PA(start_idx + i, 0), point_coord, no_dims);
+ /* Update closest info if new point is closest so far*/
+ if (cur_dist < closest_dist[k - 1])
+ {
+ insert_point_${DTYPE}(closest_idx, closest_dist, pidx[start_idx + i], cur_dist, k);
+ }
+ }
+}
+
+/************************************************
+Search subtree for nearest to query point
+Params:
+ root : root node of subtree
+ pa : data points
+ pidx : permutation index of data points
+ no_dims : number of dimensions
+ point_coord : query point
+ min_dist : minumum distance to nearest neighbour
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_splitnode_${DTYPE}(Node_${DTYPE} *root, ${DTYPE} *pa, uint32_t *pidx, int8_t no_dims, ${DTYPE} *point_coord,
+ ${DTYPE} min_dist, uint32_t k, ${DTYPE} distance_upper_bound, ${DTYPE} eps_fac, uint8_t *mask,
+ uint32_t *closest_idx, ${DTYPE} *closest_dist)
+{
+ int8_t dim;
+ ${DTYPE} dist_left, dist_right;
+ ${DTYPE} new_offset;
+ ${DTYPE} box_diff;
+
+ /* Skip if distance bound exeeded */
+ if (min_dist > distance_upper_bound)
+ {
+ return;
+ }
+
+ dim = root->cut_dim;
+
+ /* Handle leaf node */
+ if (dim == -1)
+ {
+ if (mask)
+ {
+ search_leaf_${DTYPE}_mask(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, mask, closest_idx, closest_dist);
+ }
+ else
+ {
+ search_leaf_${DTYPE}(pa, pidx, no_dims, root->start_idx, root->n, point_coord, k, closest_idx, closest_dist);
+ }
+ return;
+ }
+
+ /* Get distance to cutting plane */
+ new_offset = point_coord[dim] - root->cut_val;
+
+ if (new_offset < 0)
+ {
+ /* Left of cutting plane */
+ dist_left = min_dist;
+ if (dist_left < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search left subtree if minimum distance is below limit */
+ search_splitnode_${DTYPE}((Node_${DTYPE} *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+
+ /* Right of cutting plane. Update minimum distance.
+ See Algorithms for Fast Vector Quantization
+ Sunil Arya and David M. Mount. */
+ box_diff = root->cut_bounds_lv - point_coord[dim];
+ if (box_diff < 0)
+ {
+ box_diff = 0;
+ }
+ dist_right = min_dist - box_diff * box_diff + new_offset * new_offset;
+ if (dist_right < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search right subtree if minimum distance is below limit*/
+ search_splitnode_${DTYPE}((Node_${DTYPE} *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+ }
+ else
+ {
+ /* Right of cutting plane */
+ dist_right = min_dist;
+ if (dist_right < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search right subtree if minimum distance is below limit*/
+ search_splitnode_${DTYPE}((Node_${DTYPE} *)root->right_child, pa, pidx, no_dims, point_coord, dist_right, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+
+ /* Left of cutting plane. Update minimum distance.
+ See Algorithms for Fast Vector Quantization
+ Sunil Arya and David M. Mount. */
+ box_diff = point_coord[dim] - root->cut_bounds_hv;
+ if (box_diff < 0)
+ {
+ box_diff = 0;
+ }
+ dist_left = min_dist - box_diff * box_diff + new_offset * new_offset;
+ if (dist_left < closest_dist[k - 1] * eps_fac)
+ {
+ /* Search left subtree if minimum distance is below limit*/
+ search_splitnode_${DTYPE}((Node_${DTYPE} *)root->left_child, pa, pidx, no_dims, point_coord, dist_left, k, distance_upper_bound, eps_fac, mask, closest_idx, closest_dist);
+ }
+ }
+}
+
+/************************************************
+Search for nearest neighbour for a set of query points
+Params:
+ tree : Tree struct of kd tree
+ pa : data points
+ pidx : permutation index of data points
+ point_coords : query points
+ num_points : number of query points
+ mask : boolean array of invalid (True) and valid (False) data points
+ closest_idx : index of closest data point found (return)
+ closest_dist : distance to closest point (return)
+************************************************/
+void search_tree_${DTYPE}(Tree_${DTYPE} *tree, ${DTYPE} *pa, ${DTYPE} *point_coords,
+ uint32_t num_points, uint32_t k, ${DTYPE} distance_upper_bound,
+ ${DTYPE} eps, uint8_t *mask, uint32_t *closest_idxs, ${DTYPE} *closest_dists)
+{
+ ${DTYPE} min_dist;
+ ${DTYPE} eps_fac = 1 / ((1 + eps) * (1 + eps));
+ int8_t no_dims = tree->no_dims;
+ ${DTYPE} *bbox = tree->bbox;
+ uint32_t *pidx = tree->pidx;
+ uint32_t j = 0;
+#if defined(_MSC_VER) && defined(_OPENMP)
+ int32_t i = 0;
+ int32_t local_num_points = (int32_t) num_points;
+#else
+ uint32_t i;
+ uint32_t local_num_points = num_points;
+#endif
+ Node_${DTYPE} *root = (Node_${DTYPE} *)tree->root;
+
+ /* Queries are OpenMP enabled */
+ #pragma omp parallel
+ {
+ /* The low chunk size is important to avoid L2 cache trashing
+ for spatial coherent query datasets
+ */
+ #pragma omp for private(i, j) schedule(static, 100) nowait
+ for (i = 0; i < local_num_points; i++)
+ {
+ for (j = 0; j < k; j++)
+ {
+ closest_idxs[i * k + j] = UINT32_MAX;
+ closest_dists[i * k + j] = DBL_MAX;
+ }
+ min_dist = get_min_dist_${DTYPE}(point_coords + no_dims * i, no_dims, bbox);
+ search_splitnode_${DTYPE}(root, pa, pidx, no_dims, point_coords + no_dims * i, min_dist,
+ k, distance_upper_bound, eps_fac, mask, &closest_idxs[i * k], &closest_dists[i * k]);
+ }
+ }
+}
+% endfor
diff --git a/eval/src/utils/libkdtree/pykdtree/kdtree.c b/eval/src/utils/libkdtree/pykdtree/kdtree.c
new file mode 100644
index 0000000..895c0d2
--- /dev/null
+++ b/eval/src/utils/libkdtree/pykdtree/kdtree.c
@@ -0,0 +1,11350 @@
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+ #undef CYTHON_FAST_PYCALL
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+ unaryfunc am_await;
+ unaryfunc am_aiter;
+ unaryfunc am_anext;
+ } __Pyx_PyAsyncMethodsStruct;
+#endif
+#ifndef CYTHON_RESTRICT
+ #if defined(__GNUC__)
+ #define CYTHON_RESTRICT __restrict__
+ #elif defined(_MSC_VER) && _MSC_VER >= 1400
+ #define CYTHON_RESTRICT __restrict
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_RESTRICT restrict
+ #else
+ #define CYTHON_RESTRICT
+ #endif
+#endif
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+#ifndef CYTHON_MAYBE_UNUSED_VAR
+# if defined(__cplusplus)
+ template void CYTHON_MAYBE_UNUSED_VAR( const T& ) { }
+# else
+# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x)
+# endif
+#endif
+#ifndef CYTHON_NCP_UNUSED
+# if CYTHON_COMPILING_IN_CPYTHON
+# define CYTHON_NCP_UNUSED
+# else
+# define CYTHON_NCP_UNUSED CYTHON_UNUSED
+# endif
+#endif
+#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None)
+#ifdef _MSC_VER
+ #ifndef _MSC_STDINT_H_
+ #if _MSC_VER < 1300
+ typedef unsigned char uint8_t;
+ typedef unsigned int uint32_t;
+ #else
+ typedef unsigned __int8 uint8_t;
+ typedef unsigned __int32 uint32_t;
+ #endif
+ #endif
+#else
+ #include
+#endif
+#ifndef CYTHON_FALLTHROUGH
+ #if defined(__cplusplus) && __cplusplus >= 201103L
+ #if __has_cpp_attribute(fallthrough)
+ #define CYTHON_FALLTHROUGH [[fallthrough]]
+ #elif __has_cpp_attribute(clang::fallthrough)
+ #define CYTHON_FALLTHROUGH [[clang::fallthrough]]
+ #elif __has_cpp_attribute(gnu::fallthrough)
+ #define CYTHON_FALLTHROUGH [[gnu::fallthrough]]
+ #endif
+ #endif
+ #ifndef CYTHON_FALLTHROUGH
+ #if __has_attribute(fallthrough)
+ #define CYTHON_FALLTHROUGH __attribute__((fallthrough))
+ #else
+ #define CYTHON_FALLTHROUGH
+ #endif
+ #endif
+ #if defined(__clang__ ) && defined(__apple_build_version__)
+ #if __apple_build_version__ < 7000000
+ #undef CYTHON_FALLTHROUGH
+ #define CYTHON_FALLTHROUGH
+ #endif
+ #endif
+#endif
+
+#ifndef CYTHON_INLINE
+ #if defined(__clang__)
+ #define CYTHON_INLINE __inline__ __attribute__ ((__unused__))
+ #elif defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
+
+#if defined(WIN32) || defined(MS_WINDOWS)
+ #define _USE_MATH_DEFINES
+#endif
+#include
+#ifdef NAN
+#define __PYX_NAN() ((float) NAN)
+#else
+static CYTHON_INLINE float __PYX_NAN() {
+ float value;
+ memset(&value, 0xFF, sizeof(value));
+ return value;
+}
+#endif
+#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL)
+#define __Pyx_truncl trunc
+#else
+#define __Pyx_truncl truncl
+#endif
+
+
+#define __PYX_ERR(f_index, lineno, Ln_error) \
+{ \
+ __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \
+}
+
+#ifndef __PYX_EXTERN_C
+ #ifdef __cplusplus
+ #define __PYX_EXTERN_C extern "C"
+ #else
+ #define __PYX_EXTERN_C extern
+ #endif
+#endif
+
+#define __PYX_HAVE__pykdtree__kdtree
+#define __PYX_HAVE_API__pykdtree__kdtree
+#include
+#include
+#include "numpy/arrayobject.h"
+#include "numpy/ufuncobject.h"
+#include
+#ifdef _OPENMP
+#include
+#endif /* _OPENMP */
+
+#if defined(PYREX_WITHOUT_ASSERTIONS) && !defined(CYTHON_WITHOUT_ASSERTIONS)
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding;
+ const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
+
+#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
+#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
+#define __PYX_DEFAULT_STRING_ENCODING ""
+#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
+#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+#define __Pyx_uchar_cast(c) ((unsigned char)c)
+#define __Pyx_long_cast(x) ((long)x)
+#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\
+ (sizeof(type) < sizeof(Py_ssize_t)) ||\
+ (sizeof(type) > sizeof(Py_ssize_t) &&\
+ likely(v < (type)PY_SSIZE_T_MAX ||\
+ v == (type)PY_SSIZE_T_MAX) &&\
+ (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\
+ v == (type)PY_SSIZE_T_MIN))) ||\
+ (sizeof(type) == sizeof(Py_ssize_t) &&\
+ (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\
+ v == (type)PY_SSIZE_T_MAX))) )
+#if defined (__cplusplus) && __cplusplus >= 201103L
+ #include
+ #define __Pyx_sst_abs(value) std::abs(value)
+#elif SIZEOF_INT >= SIZEOF_SIZE_T
+ #define __Pyx_sst_abs(value) abs(value)
+#elif SIZEOF_LONG >= SIZEOF_SIZE_T
+ #define __Pyx_sst_abs(value) labs(value)
+#elif defined (_MSC_VER)
+ #define __Pyx_sst_abs(value) ((Py_ssize_t)_abs64(value))
+#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define __Pyx_sst_abs(value) llabs(value)
+#elif defined (__GNUC__)
+ #define __Pyx_sst_abs(value) __builtin_llabs(value)
+#else
+ #define __Pyx_sst_abs(value) ((value<0) ? -value : value)
+#endif
+static CYTHON_INLINE const char* __Pyx_PyObject_AsString(PyObject*);
+static CYTHON_INLINE const char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
+#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
+#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
+#define __Pyx_PyBytes_FromString PyBytes_FromString
+#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
+static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+#else
+ #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
+#endif
+#define __Pyx_PyBytes_AsWritableString(s) ((char*) PyBytes_AS_STRING(s))
+#define __Pyx_PyBytes_AsWritableSString(s) ((signed char*) PyBytes_AS_STRING(s))
+#define __Pyx_PyBytes_AsWritableUString(s) ((unsigned char*) PyBytes_AS_STRING(s))
+#define __Pyx_PyBytes_AsString(s) ((const char*) PyBytes_AS_STRING(s))
+#define __Pyx_PyBytes_AsSString(s) ((const signed char*) PyBytes_AS_STRING(s))
+#define __Pyx_PyBytes_AsUString(s) ((const unsigned char*) PyBytes_AS_STRING(s))
+#define __Pyx_PyObject_AsWritableString(s) ((char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsWritableSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsWritableUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsSString(s) ((const signed char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsUString(s) ((const unsigned char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s)
+#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s)
+#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s)
+#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s)
+#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s)
+static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) {
+ const Py_UNICODE *u_end = u;
+ while (*u_end++) ;
+ return (size_t)(u_end - u - 1);
+}
+#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
+#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
+#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
+#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj)
+#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None)
+#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False))
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x);
+#define __Pyx_PySequence_Tuple(obj)\
+ (likely(PyTuple_CheckExact(obj)) ? __Pyx_NewRef(obj) : PySequence_Tuple(obj))
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+#if CYTHON_ASSUME_SAFE_MACROS
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
+#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x))
+#else
+#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x))
+#endif
+#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x))
+#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+static int __Pyx_sys_getdefaultencoding_not_ascii;
+static int __Pyx_init_sys_getdefaultencoding_params(void) {
+ PyObject* sys;
+ PyObject* default_encoding = NULL;
+ PyObject* ascii_chars_u = NULL;
+ PyObject* ascii_chars_b = NULL;
+ const char* default_encoding_c;
+ sys = PyImport_ImportModule("sys");
+ if (!sys) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL);
+ Py_DECREF(sys);
+ if (!default_encoding) goto bad;
+ default_encoding_c = PyBytes_AsString(default_encoding);
+ if (!default_encoding_c) goto bad;
+ if (strcmp(default_encoding_c, "ascii") == 0) {
+ __Pyx_sys_getdefaultencoding_not_ascii = 0;
+ } else {
+ char ascii_chars[128];
+ int c;
+ for (c = 0; c < 128; c++) {
+ ascii_chars[c] = c;
+ }
+ __Pyx_sys_getdefaultencoding_not_ascii = 1;
+ ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
+ if (!ascii_chars_u) goto bad;
+ ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
+ if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
+ PyErr_Format(
+ PyExc_ValueError,
+ "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
+ default_encoding_c);
+ goto bad;
+ }
+ Py_DECREF(ascii_chars_u);
+ Py_DECREF(ascii_chars_b);
+ }
+ Py_DECREF(default_encoding);
+ return 0;
+bad:
+ Py_XDECREF(default_encoding);
+ Py_XDECREF(ascii_chars_u);
+ Py_XDECREF(ascii_chars_b);
+ return -1;
+}
+#endif
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
+#else
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+static char* __PYX_DEFAULT_STRING_ENCODING;
+static int __Pyx_init_sys_getdefaultencoding_params(void) {
+ PyObject* sys;
+ PyObject* default_encoding = NULL;
+ char* default_encoding_c;
+ sys = PyImport_ImportModule("sys");
+ if (!sys) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
+ Py_DECREF(sys);
+ if (!default_encoding) goto bad;
+ default_encoding_c = PyBytes_AsString(default_encoding);
+ if (!default_encoding_c) goto bad;
+ __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
+ if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
+ strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
+ Py_DECREF(default_encoding);
+ return 0;
+bad:
+ Py_XDECREF(default_encoding);
+ return -1;
+}
+#endif
+#endif
+
+
+/* Test for GCC > 2.95 */
+#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
+ #define likely(x) __builtin_expect(!!(x), 1)
+ #define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* !__GNUC__ or GCC < 2.95 */
+ #define likely(x) (x)
+ #define unlikely(x) (x)
+#endif /* __GNUC__ */
+static CYTHON_INLINE void __Pyx_pretend_to_initialize(void* ptr) { (void)ptr; }
+
+static PyObject *__pyx_m = NULL;
+static PyObject *__pyx_d;
+static PyObject *__pyx_b;
+static PyObject *__pyx_cython_runtime;
+static PyObject *__pyx_empty_tuple;
+static PyObject *__pyx_empty_bytes;
+static PyObject *__pyx_empty_unicode;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+
+/* Header.proto */
+#if !defined(CYTHON_CCOMPLEX)
+ #if defined(__cplusplus)
+ #define CYTHON_CCOMPLEX 1
+ #elif defined(_Complex_I)
+ #define CYTHON_CCOMPLEX 1
+ #else
+ #define CYTHON_CCOMPLEX 0
+ #endif
+#endif
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ #include
+ #else
+ #include
+ #endif
+#endif
+#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
+ #undef _Complex_I
+ #define _Complex_I 1.0fj
+#endif
+
+
+static const char *__pyx_f[] = {
+ "pykdtree/kdtree.pyx",
+ "stringsource",
+ "__init__.pxd",
+ "type.pxd",
+};
+/* BufferFormatStructs.proto */
+#define IS_UNSIGNED(type) (((type) -1) > 0)
+struct __Pyx_StructField_;
+#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
+typedef struct {
+ const char* name;
+ struct __Pyx_StructField_* fields;
+ size_t size;
+ size_t arraysize[8];
+ int ndim;
+ char typegroup;
+ char is_unsigned;
+ int flags;
+} __Pyx_TypeInfo;
+typedef struct __Pyx_StructField_ {
+ __Pyx_TypeInfo* type;
+ const char* name;
+ size_t offset;
+} __Pyx_StructField;
+typedef struct {
+ __Pyx_StructField* field;
+ size_t parent_offset;
+} __Pyx_BufFmt_StackElem;
+typedef struct {
+ __Pyx_StructField root;
+ __Pyx_BufFmt_StackElem* head;
+ size_t fmt_offset;
+ size_t new_count, enc_count;
+ size_t struct_alignment;
+ int is_complex;
+ char enc_type;
+ char new_packmode;
+ char enc_packmode;
+ char is_valid_array;
+} __Pyx_BufFmt_Context;
+
+/* NoFastGil.proto */
+#define __Pyx_PyGILState_Ensure PyGILState_Ensure
+#define __Pyx_PyGILState_Release PyGILState_Release
+#define __Pyx_FastGIL_Remember()
+#define __Pyx_FastGIL_Forget()
+#define __Pyx_FastGilFuncInit()
+
+/* ForceInitThreads.proto */
+#ifndef __PYX_FORCE_INIT_THREADS
+ #define __PYX_FORCE_INIT_THREADS 0
+#endif
+
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":743
+ * # in Cython to enable them only on the right systems.
+ *
+ * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
+ * ctypedef npy_int16 int16_t
+ * ctypedef npy_int32 int32_t
+ */
+typedef npy_int8 __pyx_t_5numpy_int8_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":744
+ *
+ * ctypedef npy_int8 int8_t
+ * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
+ * ctypedef npy_int32 int32_t
+ * ctypedef npy_int64 int64_t
+ */
+typedef npy_int16 __pyx_t_5numpy_int16_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":745
+ * ctypedef npy_int8 int8_t
+ * ctypedef npy_int16 int16_t
+ * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
+ * ctypedef npy_int64 int64_t
+ * #ctypedef npy_int96 int96_t
+ */
+typedef npy_int32 __pyx_t_5numpy_int32_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":746
+ * ctypedef npy_int16 int16_t
+ * ctypedef npy_int32 int32_t
+ * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
+ * #ctypedef npy_int96 int96_t
+ * #ctypedef npy_int128 int128_t
+ */
+typedef npy_int64 __pyx_t_5numpy_int64_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":750
+ * #ctypedef npy_int128 int128_t
+ *
+ * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
+ * ctypedef npy_uint16 uint16_t
+ * ctypedef npy_uint32 uint32_t
+ */
+typedef npy_uint8 __pyx_t_5numpy_uint8_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":751
+ *
+ * ctypedef npy_uint8 uint8_t
+ * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
+ * ctypedef npy_uint32 uint32_t
+ * ctypedef npy_uint64 uint64_t
+ */
+typedef npy_uint16 __pyx_t_5numpy_uint16_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":752
+ * ctypedef npy_uint8 uint8_t
+ * ctypedef npy_uint16 uint16_t
+ * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
+ * ctypedef npy_uint64 uint64_t
+ * #ctypedef npy_uint96 uint96_t
+ */
+typedef npy_uint32 __pyx_t_5numpy_uint32_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":753
+ * ctypedef npy_uint16 uint16_t
+ * ctypedef npy_uint32 uint32_t
+ * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
+ * #ctypedef npy_uint96 uint96_t
+ * #ctypedef npy_uint128 uint128_t
+ */
+typedef npy_uint64 __pyx_t_5numpy_uint64_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":757
+ * #ctypedef npy_uint128 uint128_t
+ *
+ * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
+ * ctypedef npy_float64 float64_t
+ * #ctypedef npy_float80 float80_t
+ */
+typedef npy_float32 __pyx_t_5numpy_float32_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":758
+ *
+ * ctypedef npy_float32 float32_t
+ * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
+ * #ctypedef npy_float80 float80_t
+ * #ctypedef npy_float128 float128_t
+ */
+typedef npy_float64 __pyx_t_5numpy_float64_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":767
+ * # The int types are mapped a bit surprising --
+ * # numpy.int corresponds to 'l' and numpy.long to 'q'
+ * ctypedef npy_long int_t # <<<<<<<<<<<<<<
+ * ctypedef npy_longlong long_t
+ * ctypedef npy_longlong longlong_t
+ */
+typedef npy_long __pyx_t_5numpy_int_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":768
+ * # numpy.int corresponds to 'l' and numpy.long to 'q'
+ * ctypedef npy_long int_t
+ * ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
+ * ctypedef npy_longlong longlong_t
+ *
+ */
+typedef npy_longlong __pyx_t_5numpy_long_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":769
+ * ctypedef npy_long int_t
+ * ctypedef npy_longlong long_t
+ * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_ulong uint_t
+ */
+typedef npy_longlong __pyx_t_5numpy_longlong_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":771
+ * ctypedef npy_longlong longlong_t
+ *
+ * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
+ * ctypedef npy_ulonglong ulong_t
+ * ctypedef npy_ulonglong ulonglong_t
+ */
+typedef npy_ulong __pyx_t_5numpy_uint_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":772
+ *
+ * ctypedef npy_ulong uint_t
+ * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
+ * ctypedef npy_ulonglong ulonglong_t
+ *
+ */
+typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":773
+ * ctypedef npy_ulong uint_t
+ * ctypedef npy_ulonglong ulong_t
+ * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_intp intp_t
+ */
+typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":775
+ * ctypedef npy_ulonglong ulonglong_t
+ *
+ * ctypedef npy_intp intp_t # <<<<<<<<<<<<<<
+ * ctypedef npy_uintp uintp_t
+ *
+ */
+typedef npy_intp __pyx_t_5numpy_intp_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":776
+ *
+ * ctypedef npy_intp intp_t
+ * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_double float_t
+ */
+typedef npy_uintp __pyx_t_5numpy_uintp_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":778
+ * ctypedef npy_uintp uintp_t
+ *
+ * ctypedef npy_double float_t # <<<<<<<<<<<<<<
+ * ctypedef npy_double double_t
+ * ctypedef npy_longdouble longdouble_t
+ */
+typedef npy_double __pyx_t_5numpy_float_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":779
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+ * ctypedef npy_longdouble longdouble_t
+ *
+ */
+typedef npy_double __pyx_t_5numpy_double_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":780
+ * ctypedef npy_double float_t
+ * ctypedef npy_double double_t
+ * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
+ *
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+ */
+typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
+/* Declarations.proto */
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ typedef ::std::complex< float > __pyx_t_float_complex;
+ #else
+ typedef float _Complex __pyx_t_float_complex;
+ #endif
+#else
+ typedef struct { float real, imag; } __pyx_t_float_complex;
+#endif
+static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float);
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+/* Declarations.proto */
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ typedef ::std::complex< double > __pyx_t_double_complex;
+ #else
+ typedef double _Complex __pyx_t_double_complex;
+ #endif
+#else
+ typedef struct { double real, imag; } __pyx_t_double_complex;
+#endif
+static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double);
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+struct __pyx_obj_8pykdtree_6kdtree_KDTree;
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+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":782
+ * ctypedef npy_longdouble longdouble_t
+ *
+ * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<<
+ * ctypedef npy_cdouble cdouble_t
+ * ctypedef npy_clongdouble clongdouble_t
+ */
+typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":783
+ *
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+ * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<<
+ * ctypedef npy_clongdouble clongdouble_t
+ *
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+typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":784
+ * ctypedef npy_cfloat cfloat_t
+ * ctypedef npy_cdouble cdouble_t
+ * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
+ *
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+ */
+typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
+
+/* "../../../anaconda/envs/polar2grid_py36/lib/python3.6/site-packages/Cython/Includes/numpy/__init__.pxd":786
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+ *
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+struct __pyx_t_8pykdtree_6kdtree_tree_float;
+struct __pyx_t_8pykdtree_6kdtree_node_double;
+struct __pyx_t_8pykdtree_6kdtree_tree_double;
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+struct __pyx_t_8pykdtree_6kdtree_node_float {
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+ uint32_t start_idx;
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+ struct __pyx_t_8pykdtree_6kdtree_node_float *left_child;
+ struct __pyx_t_8pykdtree_6kdtree_node_float *right_child;
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+ double cut_val;
+ int8_t cut_dim;
+ uint32_t start_idx;
+ uint32_t n;
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+ double cut_bounds_hv;
+ struct __pyx_t_8pykdtree_6kdtree_node_double *left_child;
+ struct __pyx_t_8pykdtree_6kdtree_node_double *right_child;
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+struct __pyx_t_8pykdtree_6kdtree_tree_double {
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+ * cdef extern void delete_tree_double(tree_double *kdtree)
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+ struct __pyx_t_8pykdtree_6kdtree_tree_float *_kdtree_float;
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+ #define __Pyx_RefNannyFinishContext()
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+ #define __Pyx_GOTREF(r)
+ #define __Pyx_GIVEREF(r)
+ #define __Pyx_XINCREF(r) Py_XINCREF(r)
+ #define __Pyx_XDECREF(r) Py_XDECREF(r)
+ #define __Pyx_XGOTREF(r)
+ #define __Pyx_XGIVEREF(r)
+#endif
+#define __Pyx_XDECREF_SET(r, v) do {\
+ PyObject *tmp = (PyObject *) r;\
+ r = v; __Pyx_XDECREF(tmp);\
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+#define __Pyx_DECREF_SET(r, v) do {\
+ PyObject *tmp = (PyObject *) r;\
+ r = v; __Pyx_DECREF(tmp);\
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+#define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0)
+#define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0)
+
+/* PyObjectGetAttrStr.proto */
+#if CYTHON_USE_TYPE_SLOTS
+static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) {
+ PyTypeObject* tp = Py_TYPE(obj);
+ if (likely(tp->tp_getattro))
+ return tp->tp_getattro(obj, attr_name);
+#if PY_MAJOR_VERSION < 3
+ if (likely(tp->tp_getattr))
+ return tp->tp_getattr(obj, PyString_AS_STRING(attr_name));
+#endif
+ return PyObject_GetAttr(obj, attr_name);
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+#else
+#define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n)
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+
+/* GetBuiltinName.proto */
+static PyObject *__Pyx_GetBuiltinName(PyObject *name);
+
+/* RaiseArgTupleInvalid.proto */
+static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact,
+ Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found);
+
+/* KeywordStringCheck.proto */
+static int __Pyx_CheckKeywordStrings(PyObject *kwdict, const char* function_name, int kw_allowed);
+
+/* RaiseDoubleKeywords.proto */
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
+
+/* ParseKeywords.proto */
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\
+ const char* function_name);
+
+/* ArgTypeTest.proto */
+#define __Pyx_ArgTypeTest(obj, type, none_allowed, name, exact)\
+ ((likely((Py_TYPE(obj) == type) | (none_allowed && (obj == Py_None)))) ? 1 :\
+ __Pyx__ArgTypeTest(obj, type, name, exact))
+static int __Pyx__ArgTypeTest(PyObject *obj, PyTypeObject *type, const char *name, int exact);
+
+/* PyObjectCall.proto */
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw);
+#else
+#define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw)
+#endif
+
+/* PyThreadStateGet.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate;
+#define __Pyx_PyThreadState_assign __pyx_tstate = __Pyx_PyThreadState_Current;
+#define __Pyx_PyErr_Occurred() __pyx_tstate->curexc_type
+#else
+#define __Pyx_PyThreadState_declare
+#define __Pyx_PyThreadState_assign
+#define __Pyx_PyErr_Occurred() PyErr_Occurred()
+#endif
+
+/* PyErrFetchRestore.proto */
+#if CYTHON_FAST_THREAD_STATE
+#define __Pyx_PyErr_Clear() __Pyx_ErrRestore(NULL, NULL, NULL)
+#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb)
+#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb)
+#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb)
+#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb)
+static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb);
+static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#if CYTHON_COMPILING_IN_CPYTHON
+#define __Pyx_PyErr_SetNone(exc) (Py_INCREF(exc), __Pyx_ErrRestore((exc), NULL, NULL))
+#else
+#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
+#endif
+#else
+#define __Pyx_PyErr_Clear() PyErr_Clear()
+#define __Pyx_PyErr_SetNone(exc) PyErr_SetNone(exc)
+#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb)
+#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb)
+#define __Pyx_ErrRestoreInState(tstate, type, value, tb) PyErr_Restore(type, value, tb)
+#define __Pyx_ErrFetchInState(tstate, type, value, tb) PyErr_Fetch(type, value, tb)
+#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb)
+#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb)
+#endif
+
+/* RaiseException.proto */
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
+
+/* GetModuleGlobalName.proto */
+static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name);
+
+/* PyCFunctionFastCall.proto */
+#if CYTHON_FAST_PYCCALL
+static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs);
+#else
+#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL)
+#endif
+
+/* PyFunctionFastCall.proto */
+#if CYTHON_FAST_PYCALL
+#define __Pyx_PyFunction_FastCall(func, args, nargs)\
+ __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL)
+#if 1 || PY_VERSION_HEX < 0x030600B1
+static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs);
+#else
+#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs)
+#endif
+#endif
+
+/* PyObjectCallMethO.proto */
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
+#endif
+
+/* PyObjectCallOneArg.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
+
+/* PyObjectCallNoArg.proto */
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func);
+#else
+#define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL)
+#endif
+
+/* ExtTypeTest.proto */
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
+
+/* IsLittleEndian.proto */
+static CYTHON_INLINE int __Pyx_Is_Little_Endian(void);
+
+/* BufferFormatCheck.proto */
+static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts);
+static void __Pyx_BufFmt_Init(__Pyx_BufFmt_Context* ctx,
+ __Pyx_BufFmt_StackElem* stack,
+ __Pyx_TypeInfo* type);
+
+/* BufferGetAndValidate.proto */
+#define __Pyx_GetBufferAndValidate(buf, obj, dtype, flags, nd, cast, stack)\
+ ((obj == Py_None || obj == NULL) ?\
+ (__Pyx_ZeroBuffer(buf), 0) :\
+ __Pyx__GetBufferAndValidate(buf, obj, dtype, flags, nd, cast, stack))
+static int __Pyx__GetBufferAndValidate(Py_buffer* buf, PyObject* obj,
+ __Pyx_TypeInfo* dtype, int flags, int nd, int cast, __Pyx_BufFmt_StackElem* stack);
+static void __Pyx_ZeroBuffer(Py_buffer* buf);
+static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info);
+static Py_ssize_t __Pyx_minusones[] = { -1, -1, -1, -1, -1, -1, -1, -1 };
+static Py_ssize_t __Pyx_zeros[] = { 0, 0, 0, 0, 0, 0, 0, 0 };
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+/* BufferFallbackError.proto */
+static void __Pyx_RaiseBufferFallbackError(void);
+
+/* DictGetItem.proto */
+#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY
+static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) {
+ PyObject *value;
+ value = PyDict_GetItemWithError(d, key);
+ if (unlikely(!value)) {
+ if (!PyErr_Occurred()) {
+ PyObject* args = PyTuple_Pack(1, key);
+ if (likely(args))
+ PyErr_SetObject(PyExc_KeyError, args);
+ Py_XDECREF(args);
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+ Py_INCREF(value);
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+}
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+ #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key)
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+/* RaiseTooManyValuesToUnpack.proto */
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+/* RaiseNeedMoreValuesToUnpack.proto */
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+/* RaiseNoneIterError.proto */
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
+
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+static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb)
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+#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb)
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+#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err)
+static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err);
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+#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err)
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+#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb)
+static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb);
+#else
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
+#endif
+
+/* SetupReduce.proto */
+static int __Pyx_setup_reduce(PyObject* type_obj);
+
+/* Import.proto */
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+
+/* CLineInTraceback.proto */
+#ifdef CYTHON_CLINE_IN_TRACEBACK
+#define __Pyx_CLineForTraceback(tstate, c_line) (((CYTHON_CLINE_IN_TRACEBACK)) ? c_line : 0)
+#else
+static int __Pyx_CLineForTraceback(PyThreadState *tstate, int c_line);
+#endif
+
+/* CodeObjectCache.proto */
+typedef struct {
+ PyCodeObject* code_object;
+ int code_line;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+
+/* AddTraceback.proto */
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename);
+
+/* BufferStructDeclare.proto */
+typedef struct {
+ Py_ssize_t shape, strides, suboffsets;
+} __Pyx_Buf_DimInfo;
+typedef struct {
+ size_t refcount;
+ Py_buffer pybuffer;
+} __Pyx_Buffer;
+typedef struct {
+ __Pyx_Buffer *rcbuffer;
+ char *data;
+ __Pyx_Buf_DimInfo diminfo[8];
+} __Pyx_LocalBuf_ND;
+
+#if PY_MAJOR_VERSION < 3
+ static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
+ static void __Pyx_ReleaseBuffer(Py_buffer *view);
+#else
+ #define __Pyx_GetBuffer PyObject_GetBuffer
+ #define __Pyx_ReleaseBuffer PyBuffer_Release
+#endif
+
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_uint32_t(uint32_t value);
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int8_t(int8_t value);
+
+/* RealImag.proto */
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ #define __Pyx_CREAL(z) ((z).real())
+ #define __Pyx_CIMAG(z) ((z).imag())
+ #else
+ #define __Pyx_CREAL(z) (__real__(z))
+ #define __Pyx_CIMAG(z) (__imag__(z))
+ #endif
+#else
+ #define __Pyx_CREAL(z) ((z).real)
+ #define __Pyx_CIMAG(z) ((z).imag)
+#endif
+#if defined(__cplusplus) && CYTHON_CCOMPLEX\
+ && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103)
+ #define __Pyx_SET_CREAL(z,x) ((z).real(x))
+ #define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
+#else
+ #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x)
+ #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y)
+#endif
+
+/* Arithmetic.proto */
+#if CYTHON_CCOMPLEX
+ #define __Pyx_c_eq_float(a, b) ((a)==(b))
+ #define __Pyx_c_sum_float(a, b) ((a)+(b))
+ #define __Pyx_c_diff_float(a, b) ((a)-(b))
+ #define __Pyx_c_prod_float(a, b) ((a)*(b))
+ #define __Pyx_c_quot_float(a, b) ((a)/(b))
+ #define __Pyx_c_neg_float(a) (-(a))
+ #ifdef __cplusplus
+ #define __Pyx_c_is_zero_float(z) ((z)==(float)0)
+ #define __Pyx_c_conj_float(z) (::std::conj(z))
+ #if 1
+ #define __Pyx_c_abs_float(z) (::std::abs(z))
+ #define __Pyx_c_pow_float(a, b) (::std::pow(a, b))
+ #endif
+ #else
+ #define __Pyx_c_is_zero_float(z) ((z)==0)
+ #define __Pyx_c_conj_float(z) (conjf(z))
+ #if 1
+ #define __Pyx_c_abs_float(z) (cabsf(z))
+ #define __Pyx_c_pow_float(a, b) (cpowf(a, b))
+ #endif
+ #endif
+#else
+ static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex);
+ #if 1
+ static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex);
+ #endif
+#endif
+
+/* Arithmetic.proto */
+#if CYTHON_CCOMPLEX
+ #define __Pyx_c_eq_double(a, b) ((a)==(b))
+ #define __Pyx_c_sum_double(a, b) ((a)+(b))
+ #define __Pyx_c_diff_double(a, b) ((a)-(b))
+ #define __Pyx_c_prod_double(a, b) ((a)*(b))
+ #define __Pyx_c_quot_double(a, b) ((a)/(b))
+ #define __Pyx_c_neg_double(a) (-(a))
+ #ifdef __cplusplus
+ #define __Pyx_c_is_zero_double(z) ((z)==(double)0)
+ #define __Pyx_c_conj_double(z) (::std::conj(z))
+ #if 1
+ #define __Pyx_c_abs_double(z) (::std::abs(z))
+ #define __Pyx_c_pow_double(a, b) (::std::pow(a, b))
+ #endif
+ #else
+ #define __Pyx_c_is_zero_double(z) ((z)==0)
+ #define __Pyx_c_conj_double(z) (conj(z))
+ #if 1
+ #define __Pyx_c_abs_double(z) (cabs(z))
+ #define __Pyx_c_pow_double(a, b) (cpow(a, b))
+ #endif
+ #endif
+#else
+ static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex);
+ #if 1
+ static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex);
+ #endif
+#endif
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value);
+
+/* CIntFromPy.proto */
+static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
+
+/* CIntFromPy.proto */
+static CYTHON_INLINE uint32_t __Pyx_PyInt_As_uint32_t(PyObject *);
+
+/* CIntToPy.proto */
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
+
+/* CIntFromPy.proto */
+static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
+
+/* FastTypeChecks.proto */
+#if CYTHON_COMPILING_IN_CPYTHON
+#define __Pyx_TypeCheck(obj, type) __Pyx_IsSubtype(Py_TYPE(obj), (PyTypeObject *)type)
+static CYTHON_INLINE int __Pyx_IsSubtype(PyTypeObject *a, PyTypeObject *b);
+static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches(PyObject *err, PyObject *type);
+static CYTHON_INLINE int __Pyx_PyErr_GivenExceptionMatches2(PyObject *err, PyObject *type1, PyObject *type2);
+#else
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+#define __Pyx_PyErr_GivenExceptionMatches(err, type) PyErr_GivenExceptionMatches(err, type)
+#define __Pyx_PyErr_GivenExceptionMatches2(err, type1, type2) (PyErr_GivenExceptionMatches(err, type1) || PyErr_GivenExceptionMatches(err, type2))
+#endif
+
+/* CheckBinaryVersion.proto */
+static int __Pyx_check_binary_version(void);
+
+/* PyIdentifierFromString.proto */
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
+
+/* ModuleImport.proto */
+static PyObject *__Pyx_ImportModule(const char *name);
+
+/* TypeImport.proto */
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);
+
+/* InitStrings.proto */
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
+
+
+/* Module declarations from 'cpython.buffer' */
+
+/* Module declarations from 'libc.string' */
+
+/* Module declarations from 'libc.stdio' */
+
+/* Module declarations from '__builtin__' */
+
+/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
+
+/* Module declarations from 'cpython' */
+
+/* Module declarations from 'cpython.object' */
+
+/* Module declarations from 'cpython.ref' */
+
+/* Module declarations from 'cpython.mem' */
+
+/* Module declarations from 'numpy' */
+
+/* Module declarations from 'numpy' */
+static PyTypeObject *__pyx_ptype_5numpy_dtype = 0;
+static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
+static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0;
+static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0;
+static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
+static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/
+
+/* Module declarations from 'libc.stdint' */
+
+/* Module declarations from 'cython' */
+
+/* Module declarations from 'pykdtree.kdtree' */
+static PyTypeObject *__pyx_ptype_8pykdtree_6kdtree_KDTree = 0;
+__PYX_EXTERN_C DL_IMPORT(struct __pyx_t_8pykdtree_6kdtree_tree_float) *construct_tree_float(float *, int8_t, uint32_t, uint32_t); /*proto*/
+__PYX_EXTERN_C DL_IMPORT(void) search_tree_float(struct __pyx_t_8pykdtree_6kdtree_tree_float *, float *, float *, uint32_t, uint32_t, float, float, uint8_t *, uint32_t *, float *); /*proto*/
+__PYX_EXTERN_C DL_IMPORT(void) delete_tree_float(struct __pyx_t_8pykdtree_6kdtree_tree_float *); /*proto*/
+__PYX_EXTERN_C DL_IMPORT(struct __pyx_t_8pykdtree_6kdtree_tree_double) *construct_tree_double(double *, int8_t, uint32_t, uint32_t); /*proto*/
+__PYX_EXTERN_C DL_IMPORT(void) search_tree_double(struct __pyx_t_8pykdtree_6kdtree_tree_double *, double *, double *, uint32_t, uint32_t, double, double, uint8_t *, uint32_t *, double *); /*proto*/
+__PYX_EXTERN_C DL_IMPORT(void) delete_tree_double(struct __pyx_t_8pykdtree_6kdtree_tree_double *); /*proto*/
+static __Pyx_TypeInfo __Pyx_TypeInfo_float = { "float", NULL, sizeof(float), { 0 }, 0, 'R', 0, 0 };
+static __Pyx_TypeInfo __Pyx_TypeInfo_double = { "double", NULL, sizeof(double), { 0 }, 0, 'R', 0, 0 };
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn_uint32_t = { "uint32_t", NULL, sizeof(uint32_t), { 0 }, 0, IS_UNSIGNED(uint32_t) ? 'U' : 'I', IS_UNSIGNED(uint32_t), 0 };
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn___pyx_t_5numpy_uint8_t = { "uint8_t", NULL, sizeof(__pyx_t_5numpy_uint8_t), { 0 }, 0, IS_UNSIGNED(__pyx_t_5numpy_uint8_t) ? 'U' : 'I', IS_UNSIGNED(__pyx_t_5numpy_uint8_t), 0 };
+#define __Pyx_MODULE_NAME "pykdtree.kdtree"
+extern int __pyx_module_is_main_pykdtree__kdtree;
+int __pyx_module_is_main_pykdtree__kdtree = 0;
+
+/* Implementation of 'pykdtree.kdtree' */
+static PyObject *__pyx_builtin_ValueError;
+static PyObject *__pyx_builtin_TypeError;
+static PyObject *__pyx_builtin_range;
+static PyObject *__pyx_builtin_RuntimeError;
+static PyObject *__pyx_builtin_ImportError;
+static const char __pyx_k_k[] = "k";
+static const char __pyx_k_np[] = "np";
+static const char __pyx_k_Inf[] = "Inf";
+static const char __pyx_k_eps[] = "eps";
+static const char __pyx_k_max[] = "max";
+static const char __pyx_k_main[] = "__main__";
+static const char __pyx_k_mask[] = "mask";
+static const char __pyx_k_name[] = "__name__";
+static const char __pyx_k_size[] = "size";
+static const char __pyx_k_sqrt[] = "sqrt";
+static const char __pyx_k_test[] = "__test__";
+static const char __pyx_k_dtype[] = "dtype";
+static const char __pyx_k_empty[] = "empty";
+static const char __pyx_k_finfo[] = "finfo";
+static const char __pyx_k_numpy[] = "numpy";
+static const char __pyx_k_range[] = "range";
+static const char __pyx_k_ravel[] = "ravel";
+static const char __pyx_k_uint8[] = "uint8";
+static const char __pyx_k_import[] = "__import__";
+static const char __pyx_k_reduce[] = "__reduce__";
+static const char __pyx_k_uint32[] = "uint32";
+static const char __pyx_k_float32[] = "float32";
+static const char __pyx_k_float64[] = "float64";
+static const char __pyx_k_reshape[] = "reshape";
+static const char __pyx_k_data_pts[] = "data_pts";
+static const char __pyx_k_getstate[] = "__getstate__";
+static const char __pyx_k_leafsize[] = "leafsize";
+static const char __pyx_k_setstate[] = "__setstate__";
+static const char __pyx_k_TypeError[] = "TypeError";
+static const char __pyx_k_query_pts[] = "query_pts";
+static const char __pyx_k_reduce_ex[] = "__reduce_ex__";
+static const char __pyx_k_sqr_dists[] = "sqr_dists";
+static const char __pyx_k_ValueError[] = "ValueError";
+static const char __pyx_k_ImportError[] = "ImportError";
+static const char __pyx_k_RuntimeError[] = "RuntimeError";
+static const char __pyx_k_reduce_cython[] = "__reduce_cython__";
+static const char __pyx_k_setstate_cython[] = "__setstate_cython__";
+static const char __pyx_k_ascontiguousarray[] = "ascontiguousarray";
+static const char __pyx_k_cline_in_traceback[] = "cline_in_traceback";
+static const char __pyx_k_distance_upper_bound[] = "distance_upper_bound";
+static const char __pyx_k_eps_must_be_non_negative[] = "eps must be non-negative";
+static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
+static const char __pyx_k_Data_and_query_points_must_have[] = "Data and query points must have same dimensions";
+static const char __pyx_k_Mask_must_have_the_same_size_as[] = "Mask must have the same size as data points";
+static const char __pyx_k_Type_mismatch_query_points_must[] = "Type mismatch. query points must be of type float32 when data points are of type float32";
+static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import";
+static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
+static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
+static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported";
+static const char __pyx_k_Number_of_neighbours_must_be_gre[] = "Number of neighbours must be greater than zero";
+static const char __pyx_k_distance_upper_bound_must_be_non[] = "distance_upper_bound must be non negative";
+static const char __pyx_k_leafsize_must_be_greater_than_ze[] = "leafsize must be greater than zero";
+static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous";
+static const char __pyx_k_no_default___reduce___due_to_non[] = "no default __reduce__ due to non-trivial __cinit__";
+static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import";
+static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short.";
+static PyObject *__pyx_kp_s_Data_and_query_points_must_have;
+static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
+static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
+static PyObject *__pyx_n_s_ImportError;
+static PyObject *__pyx_n_s_Inf;
+static PyObject *__pyx_kp_s_Mask_must_have_the_same_size_as;
+static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
+static PyObject *__pyx_kp_s_Number_of_neighbours_must_be_gre;
+static PyObject *__pyx_n_s_RuntimeError;
+static PyObject *__pyx_n_s_TypeError;
+static PyObject *__pyx_kp_s_Type_mismatch_query_points_must;
+static PyObject *__pyx_n_s_ValueError;
+static PyObject *__pyx_n_s_ascontiguousarray;
+static PyObject *__pyx_n_s_cline_in_traceback;
+static PyObject *__pyx_n_s_data_pts;
+static PyObject *__pyx_n_s_distance_upper_bound;
+static PyObject *__pyx_kp_s_distance_upper_bound_must_be_non;
+static PyObject *__pyx_n_s_dtype;
+static PyObject *__pyx_n_s_empty;
+static PyObject *__pyx_n_s_eps;
+static PyObject *__pyx_kp_s_eps_must_be_non_negative;
+static PyObject *__pyx_n_s_finfo;
+static PyObject *__pyx_n_s_float32;
+static PyObject *__pyx_n_s_float64;
+static PyObject *__pyx_n_s_getstate;
+static PyObject *__pyx_n_s_import;
+static PyObject *__pyx_n_s_k;
+static PyObject *__pyx_n_s_leafsize;
+static PyObject *__pyx_kp_s_leafsize_must_be_greater_than_ze;
+static PyObject *__pyx_n_s_main;
+static PyObject *__pyx_n_s_mask;
+static PyObject *__pyx_n_s_max;
+static PyObject *__pyx_n_s_name;
+static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
+static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
+static PyObject *__pyx_kp_s_no_default___reduce___due_to_non;
+static PyObject *__pyx_n_s_np;
+static PyObject *__pyx_n_s_numpy;
+static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to;
+static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor;
+static PyObject *__pyx_n_s_query_pts;
+static PyObject *__pyx_n_s_range;
+static PyObject *__pyx_n_s_ravel;
+static PyObject *__pyx_n_s_reduce;
+static PyObject *__pyx_n_s_reduce_cython;
+static PyObject *__pyx_n_s_reduce_ex;
+static PyObject *__pyx_n_s_reshape;
+static PyObject *__pyx_n_s_setstate;
+static PyObject *__pyx_n_s_setstate_cython;
+static PyObject *__pyx_n_s_size;
+static PyObject *__pyx_n_s_sqr_dists;
+static PyObject *__pyx_n_s_sqrt;
+static PyObject *__pyx_n_s_test;
+static PyObject *__pyx_n_s_uint32;
+static PyObject *__pyx_n_s_uint8;
+static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
+static int __pyx_pf_8pykdtree_6kdtree_6KDTree___cinit__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */
+static int __pyx_pf_8pykdtree_6kdtree_6KDTree_2__init__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self, PyArrayObject *__pyx_v_data_pts, int __pyx_v_leafsize); /* proto */
+static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_4query(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self, PyArrayObject *__pyx_v_query_pts, PyObject *__pyx_v_k, PyObject *__pyx_v_eps, PyObject *__pyx_v_distance_upper_bound, PyObject *__pyx_v_sqr_dists, PyObject *__pyx_v_mask); /* proto */
+static void __pyx_pf_8pykdtree_6kdtree_6KDTree_6__dealloc__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_8data_pts___get__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_4data___get__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_8pykdtree_6kdtree_6KDTree_1n___get__(struct __pyx_obj_8pykdtree_6kdtree_KDTree *__pyx_v_self); /* proto */
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