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custom_dataset.py
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custom_dataset.py
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from typing import Dict, List, Optional, Tuple
from pathlib import Path
from os import path
import warnings
import json
import numpy as np
import glob
import h5py
import pandas as pd
import collections
from torch.utils.data.dataset import Dataset
import os
import torch
from PIL import Image
from util import torch_center_and_normalize, sort_jointly, load_obj, load_text
# from torch._six import container_abcs, string_classes, int_classes
import trimesh
import math
from pytorch3d.structures import Meshes
from pytorch3d.renderer.mesh import Textures
def rotation_matrix(axis, theta, in_degrees=True):
"""
Return the rotation matrix associated with counterclockwise rotation about
the given axis by theta radians.
"""
if in_degrees:
theta = math.radians(theta)
axis = np.asarray(axis)
axis = axis / math.sqrt(np.dot(axis, axis))
a = math.cos(theta / 2.0)
b, c, d = -axis * math.sin(theta / 2.0)
aa, bb, cc, dd = a * a, b * b, c * c, d * d
bc, ad, ac, ab, bd, cd = b * c, a * d, a * c, a * b, b * d, c * d
return np.array([[aa + bb - cc - dd, 2 * (bc + ad), 2 * (bd - ac)],
[2 * (bc - ad), aa + cc - bb - dd, 2 * (cd + ab)],
[2 * (bd + ac), 2 * (cd - ab), aa + dd - bb - cc]])
class ModelNet40(Dataset):
def find_classes(self, dir):
classes = [d for d in os.listdir(
dir) if os.path.isdir(os.path.join(dir, d))]
classes.sort()
class_to_idx = {classes[i]: i for i in range(len(classes))}
return classes, class_to_idx
def __init__(self, data_dir, split, nb_points=2048, simplified_mesh=False, cleaned_mesh=False, dset_norm=2, return_points_saved=False, is_rotated=False):
self.y = []
self.data_list = []
self.split = split
self.nb_points = nb_points
self.data_dir = data_dir
self.simplified_mesh = simplified_mesh
self.cleaned_mesh = cleaned_mesh
self.dset_norm = dset_norm
self.return_points_sampled = not return_points_saved
self.return_points_saved = return_points_saved
self.initial_angle = -90
self.classes, self.class_to_idx = self.find_classes(self.data_dir)
self.is_rotated = is_rotated
for label in os.listdir(self.data_dir):
for item in os.listdir(self.data_dir + '/' + label + '/' + self.split):
if item.endswith(".off"):
self.y.append(self.class_to_idx[label])
self.data_list.append(
self.data_dir + '/' + label + '/' + self.split + '/' + item)
self.simplified_data_list = [file_name.replace(
".off", "_SMPLER.obj") for file_name in self.data_list if file_name[-4::] == ".off"]
self.points_list = [file_name.replace(
".off", "POINTS.pkl") for file_name in self.data_list if file_name[-4::] == ".off"]
self.data_list, self.simplified_data_list, self.y, self.points_list = sort_jointly(
[self.data_list, self.simplified_data_list, self.y, self.points_list], dim=0)
if self.is_rotated:
df = pd.read_csv(os.path.join(
self.data_dir, "..", "rotated_modelnet_{}.csv".format(self.split)), sep=",")
self.rotations_list = [df[df.mesh_path.isin([x])].to_dict(
"list") for x in self.data_list]
self.correction_factors = [1]*len(self.data_list)
if self.cleaned_mesh:
fault_mesh_list = load_text(os.path.join(
self.data_dir, "..", "{}_faults.txt".format(self.split)))
fault_mesh_list = [int(x) for x in fault_mesh_list]
for x in fault_mesh_list:
self.correction_factors[x] = -1
def __getitem__(self, index):
if not self.simplified_mesh:
threeobject = trimesh.load(self.data_list[index])
else:
threeobject = trimesh.load(self.simplified_data_list[index])
if not self.is_rotated:
angle = self.initial_angle
rot_axis = [1, 0, 0]
else:
angle = self.rotations_list[index]["rot_theta"][0]
rot_axis = [self.rotations_list[index]["rot_x"]
[0], self.rotations_list[index]["rot_y"][0], self.rotations_list[index]["rot_z"][0]]
verts = np.array(threeobject.vertices.data.tolist())
faces = np.array(threeobject.faces.data.tolist())
if self.correction_factors[index] == -1 and self.cleaned_mesh and self.simplified_mesh:
faces[:, 0], faces[:, 2] = faces[:, 2], faces[:, 0]
verts = rotation_matrix(rot_axis, angle).dot(verts.T).T
verts = torch_center_and_normalize(torch.from_numpy(
verts).to(torch.float), p=self.dset_norm)
faces = torch.from_numpy(faces)
verts_rgb = torch.ones_like(verts)[None]
textures = Textures(verts_rgb=verts_rgb)
mesh = Meshes(
verts=[verts],
faces=[faces],
textures=textures
)
points = None
if self.return_points_sampled or self.return_points_saved:
if self.return_points_sampled:
points = threeobject.sample(self.nb_points, False)
else:
points = load_obj(self.points_list[index])
points = torch.from_numpy(rotation_matrix(
rot_axis, angle).dot(points.T).T).to(torch.float)
points = torch_center_and_normalize(points, p=self.dset_norm)
return self.y[index], mesh, points
def __len__(self):
return len(self.y)
def collate_fn(batch):
r"""Puts each data field into a tensor with outer dimension batch size"""
elem = batch[0]
elem_type = type(elem)
if isinstance(elem, torch.Tensor):
out = None
if torch.utils.data.get_worker_info() is not None:
numel = sum([x.numel() for x in batch])
storage = elem.storage()._new_shared(numel)
out = elem.new(storage)
return torch.stack(batch, 0, out=out)
elif elem_type.__module__ == 'pytorch3d.structures.meshes':
return batch
elif elem_type.__module__ == 'numpy' and elem_type.__name__ != 'str_' \
and elem_type.__name__ != 'string_':
if elem_type.__name__ == 'ndarray' or elem_type.__name__ == 'memmap':
return collate_fn([torch.as_tensor(b) for b in batch])
elif elem.shape == ():
return torch.as_tensor(batch)
elif isinstance(elem, float):
return torch.tensor(batch, dtype=torch.float64)
elif isinstance(elem, (int)):
return torch.tensor(batch)
elif isinstance(elem, (str, bytes)):
return batch
elif isinstance(elem, collections.abc.Mapping):
return {key: collate_fn([d[key] for d in batch]) for key in elem}
elif isinstance(elem, tuple) and hasattr(elem, '_fields'):
return elem_type(*(collate_fn(samples) for samples in zip(*batch)))
elif isinstance(elem, collections.abc.Sequence):
it = iter(batch)
elem_size = len(next(it))
if not all(len(elem) == elem_size for elem in it):
raise RuntimeError(
'each element in list of batch should be of equal size')
transposed = zip(*batch)
return [collate_fn(samples) for samples in transposed]
class ShapeNetBase(torch.utils.data.Dataset):
"""
'ShapeNetBase' implements a base Dataset for ShapeNet and R2N2 with helper methods.
It is not intended to be used on its own as a Dataset for a Dataloader. Both __init__
and __getitem__ need to be implemented.
"""
def __init__(self):
"""
Set up lists of synset_ids and model_ids.
"""
self.synset_ids = []
self.model_ids = []
self.synset_inv = {}
self.synset_start_idxs = {}
self.synset_num_models = {}
self.shapenet_dir = ""
self.model_dir = "model.obj"
self.load_textures = True
self.texture_resolution = 4
def __len__(self):
"""
Return number of total models in the loaded dataset.
"""
return len(self.model_ids)
def __getitem__(self, idx) -> Dict:
"""
Read a model by the given index. Need to be implemented for every child class
of ShapeNetBase.
Args:
idx: The idx of the model to be retrieved in the dataset.
Returns:
dictionary containing information about the model.
"""
raise NotImplementedError(
"__getitem__ should be implemented in the child class of ShapeNetBase"
)
def _get_item_ids(self, idx) -> Dict:
"""
Read a model by the given index.
Args:
idx: The idx of the model to be retrieved in the dataset.
Returns:
dictionary with following keys:
- synset_id (str): synset id
- model_id (str): model id
"""
model = {}
model["synset_id"] = self.synset_ids[idx]
model["model_id"] = self.model_ids[idx]
return model
def _load_mesh(self, model_path) -> Tuple:
from pytorch3d.io import load_obj
verts, faces, aux = load_obj(
model_path,
create_texture_atlas=self.load_textures,
load_textures=self.load_textures,
texture_atlas_size=self.texture_resolution,
)
if self.load_textures:
textures = aux.texture_atlas
else:
textures = verts.new_ones(
faces.verts_idx.shape[0],
self.texture_resolution,
self.texture_resolution,
3,
)
return verts, faces.verts_idx, textures
class ShapeNetCore(ShapeNetBase):
"""
This class loads ShapeNetCore from a given directory into a Dataset object.
ShapeNetCore is a subset of the ShapeNet dataset and can be downloaded from
https://www.shapenet.org/.
"""
def __init__(
self,
data_dir,
split,
nb_points,
synsets=None,
version: int = 2,
load_textures: bool = False,
texture_resolution: int = 4,
dset_norm: str = "inf",
simplified_mesh=False
):
"""
Store each object's synset id and models id from data_dir.
Args:
data_dir: Path to ShapeNetCore data.
synsets: List of synset categories to load from ShapeNetCore in the form of
synset offsets or labels. A combination of both is also accepted.
When no category is specified, all categories in data_dir are loaded.
version: (int) version of ShapeNetCore data in data_dir, 1 or 2.
Default is set to be 1. Version 1 has 57 categories and verions 2 has 55
categories.
Note: version 1 has two categories 02858304(boat) and 02992529(cellphone)
that are hyponyms of categories 04530566(watercraft) and 04401088(telephone)
respectively. You can combine the categories manually if needed.
Version 2 doesn't have 02858304(boat) or 02834778(bicycle) compared to
version 1.
load_textures: Boolean indicating whether textures should loaded for the model.
Textures will be of type TexturesAtlas i.e. a texture map per face.
texture_resolution: Int specifying the resolution of the texture map per face
created using the textures in the obj file. A
(texture_resolution, texture_resolution, 3) map is created per face.
"""
super().__init__()
self.shapenet_dir = data_dir
self.nb_points = nb_points
self.load_textures = load_textures
self.texture_resolution = texture_resolution
self.dset_norm = dset_norm
self.split = split
self.simplified_mesh = simplified_mesh
if version not in [1, 2]:
raise ValueError("Version number must be either 1 or 2.")
self.model_dir = "model.obj" if version == 1 else "models/model_normalized.obj"
if self.simplified_mesh:
self.model_dir = "models/model_normalized_SMPLER.obj"
splits = pd.read_csv(os.path.join(
self.shapenet_dir, "shapenet_split.csv"), sep=",", dtype=str)
dict_file = "shapenet_synset_dict_v%d.json" % version
with open(path.join(self.shapenet_dir, dict_file), "r") as read_dict:
self.synset_dict = json.load(read_dict)
self.synset_inv = {label: offset for offset,
label in self.synset_dict.items()}
if synsets is not None:
synset_set = set()
for synset in synsets:
if (synset in self.synset_dict.keys()) and (
path.isdir(path.join(data_dir, synset))
):
synset_set.add(synset)
elif (synset in self.synset_inv.keys()) and (
(path.isdir(path.join(data_dir, self.synset_inv[synset])))
):
synset_set.add(self.synset_inv[synset])
else:
msg = (
"Synset category %s either not part of ShapeNetCore dataset "
"or cannot be found in %s."
) % (synset, data_dir)
warnings.warn(msg)
else:
synset_set = {
synset
for synset in os.listdir(data_dir)
if path.isdir(path.join(data_dir, synset))
and synset in self.synset_dict
}
synset_not_present = set(
self.synset_dict.keys()).difference(synset_set)
[self.synset_inv.pop(self.synset_dict[synset])
for synset in synset_not_present]
if len(synset_not_present) > 0:
msg = (
"The following categories are included in ShapeNetCore ver.%d's "
"official mapping but not found in the dataset location %s: %s"
""
) % (version, data_dir, ", ".join(synset_not_present))
warnings.warn(msg)
for synset in synset_set:
self.synset_start_idxs[synset] = len(self.synset_ids)
for model in os.listdir(path.join(data_dir, synset)):
if not path.exists(path.join(data_dir, synset, model, self.model_dir)):
msg = (
"Object file not found in the model directory %s "
"under synset directory %s."
) % (model, synset)
continue
self.synset_ids.append(synset)
self.model_ids.append(model)
model_count = len(self.synset_ids) - self.synset_start_idxs[synset]
self.synset_num_models[synset] = model_count
self.model_ids, self.synset_ids = sort_jointly(
[self.model_ids, self.synset_ids], dim=0)
self.classes = sorted(list(self.synset_inv.keys()))
self.label_by_number = {k: v for v, k in enumerate(self.classes)}
split_model_ids, split_synset_ids = [], []
for ii, model in enumerate(self.model_ids):
found = splits[splits.modelId.isin([model])]["split"]
if len(found) > 0:
if found.item() in self.split:
split_model_ids.append(model)
split_synset_ids.append(self.synset_ids[ii])
self.model_ids = split_model_ids
self.synset_ids = split_synset_ids
def __getitem__(self, idx: int) -> Dict:
"""
Read a model by the given index.
Args:
idx: The idx of the model to be retrieved in the dataset.
Returns:
dictionary with following keys:
- verts: FloatTensor of shape (V, 3).
- faces: LongTensor of shape (F, 3) which indexes into the verts tensor.
- synset_id (str): synset id
- model_id (str): model id
- label (str): synset label.
"""
model = self._get_item_ids(idx)
model_path = path.join(
self.shapenet_dir, model["synset_id"], model["model_id"], self.model_dir
)
verts, faces, textures = self._load_mesh(model_path)
label_str = self.synset_dict[model["synset_id"]]
verts = torch_center_and_normalize(
verts.to(torch.float), p=self.dset_norm)
verts_rgb = torch.ones_like(verts)[None]
textures = Textures(verts_rgb=verts_rgb)
mesh = Meshes(
verts=[verts],
faces=[faces],
textures=textures
)
points = trimesh.Trimesh(vertices=verts.numpy(
), faces=faces.numpy()).sample(self.nb_points, False)
points = torch.from_numpy(points).to(torch.float)
points = torch_center_and_normalize(points, p=self.dset_norm)
return self.label_by_number[label_str], mesh, points
class ScanObjectNN(torch.utils.data.Dataset):
"""
This class loads ScanObjectNN from a given directory into a Dataset object.
ScanObjjectNN is a point cloud dataset of realistic shapes of from the ScanNet dataset and can be downloaded from
https://github.com/hkust-vgd/scanobjectnn .
"""
def __init__(
self,
data_dir,
split,
nb_points,
normals: bool = False,
suncg: bool = False,
variant: str = "obj_only",
dset_norm: str = "inf",
):
"""
Store each object's synset id and models id from data_dir.
Args:
data_dir: Path to ShapeNetCore data.
synsets: List of synset categories to load from ShapeNetCore in the form of
synset offsets or labels. A combination of both is also accepted.
When no category is specified, all categories in data_dir are loaded.
version: (int) version of ShapeNetCore data in data_dir, 1 or 2.
Default is set to be 1. Version 1 has 57 categories and verions 2 has 55
categories.
Note: version 1 has two categories 02858304(boat) and 02992529(cellphone)
that are hyponyms of categories 04530566(watercraft) and 04401088(telephone)
respectively. You can combine the categories manually if needed.
Version 2 doesn't have 02858304(boat) or 02834778(bicycle) compared to
version 1.
load_textures: Boolean indicating whether textures should loaded for the model.
Textures will be of type TexturesAtlas i.e. a texture map per face.
texture_resolution: Int specifying the resolution of the texture map per face
created using the textures in the obj file. A
(texture_resolution, texture_resolution, 3) map is created per face.
"""
super().__init__()
self.data_dir = data_dir
self.nb_points = nb_points
self.normals = normals
self.suncg = suncg
self.variant = variant
self.dset_norm = dset_norm
self.split = split
self.classes = {0: 'bag', 10: 'bed', 1: 'bin', 2: 'box', 3: 'cabinet', 4: 'chair', 5: 'desk', 6: 'display',
7: 'door', 11: 'pillow', 8: 'shelf', 12: 'sink', 13: 'sofa', 9: 'table', 14: 'toilet'}
self.labels_dict = {"train": {}, "test": {}}
self.objects_paths = {"train": [], "test": []}
if self.variant != "hardest":
pcdataset = pd.read_csv(os.path.join(
data_dir, "split_new.txt"), sep="\t", names=['obj_id', 'label', "split"])
for ii in range(len(pcdataset)):
if pcdataset["split"][ii] != "t":
self.labels_dict["train"][pcdataset["obj_id"]
[ii]] = pcdataset["label"][ii]
else:
self.labels_dict["test"][pcdataset["obj_id"]
[ii]] = pcdataset["label"][ii]
all_obj_ids = glob.glob(os.path.join(self.data_dir, "*/*.bin"))
filtered_ids = list(filter(lambda x: "part" not in os.path.split(
x)[-1] and "indices" not in os.path.split(x)[-1], all_obj_ids))
self.objects_paths["train"] = sorted(
[x for x in filtered_ids if os.path.split(x)[-1] in self.labels_dict["train"].keys()])
self.objects_paths["test"] = sorted(
[x for x in filtered_ids if os.path.split(x)[-1] in self.labels_dict["test"].keys()])
else:
filename = os.path.join(
data_dir, "{}_objectdataset_augmentedrot_scale75.h5".format(self.split))
with h5py.File(filename, "r") as f:
self.labels_dict[self.split] = np.array(f["label"])
self.objects_paths[self.split] = np.array(f["data"])
def __getitem__(self, idx: int) -> Dict:
"""
Read a model by the given index. no mesh is availble in this dataset so retrun None and correction factor of 1.0
"""
if self.variant != "hardest":
obj_path = self.objects_paths[self.split][idx]
points = self.load_pc_file(obj_path)
points = points[np.random.randint(
points.shape[0], size=self.nb_points), :]
label = self.labels_dict[self.split][os.path.split(obj_path)[-1]]
else:
points = self.objects_paths[self.split][idx]
label = self.labels_dict[self.split][idx]
points = torch.from_numpy(points).to(torch.float)
points = torch_center_and_normalize(points, p=self.dset_norm)
return label, None, points
def __len__(self):
return len(self.objects_paths[self.split])
def load_pc_file(self, filename):
pc = np.fromfile(filename, dtype=np.float32)
if(self.suncg):
pc = pc[1:].reshape((-1, 3))
else:
pc = pc[1:].reshape((-1, 11))
if self.variant == "with_bg":
pc = np.array(pc[:, 0:3])
return pc
else:
filtered_idx = np.intersect1d(np.intersect1d(np.where(
pc[:, -1] != 0)[0], np.where(pc[:, -1] != 1)[0]), np.where(pc[:, -1] != 2)[0])
(values, counts) = np.unique(
pc[filtered_idx, -1], return_counts=True)
max_ind = np.argmax(counts)
idx = np.where(pc[:, -1] == values[max_ind])[0]
pc = np.array(pc[idx, 0:3])
return pc
def pc_normalize(pc):
centroid = np.mean(pc, axis=0)
pc = pc - centroid
m = np.max(np.sqrt(np.sum(pc ** 2, axis=1)))
pc = pc / m
return pc
class PartNormalDataset(torch.utils.data.Dataset):
def __init__(self, root='./data/shapenetcore_partanno_segmentation_benchmark_v0_normal', npoints=2500, split='train', class_choice=None, normal_channel=False):
self.npoints = npoints
self.root = root
self.catfile = os.path.join(self.root, 'synsetoffset2category.txt')
self.cat = {}
self.normal_channel = normal_channel
with open(self.catfile, 'r') as f:
for line in f:
ls = line.strip().split()
self.cat[ls[0]] = ls[1]
self.cat = {k: v for k, v in self.cat.items()}
self.classes_original = dict(zip(self.cat, range(len(self.cat))))
if not class_choice is None:
self.cat = {k: v for k, v in self.cat.items() if k in class_choice}
self.meta = {}
with open(os.path.join(self.root, 'train_test_split', 'shuffled_train_file_list.json'), 'r') as f:
train_ids = set([str(d.split('/')[2]) for d in json.load(f)])
with open(os.path.join(self.root, 'train_test_split', 'shuffled_val_file_list.json'), 'r') as f:
val_ids = set([str(d.split('/')[2]) for d in json.load(f)])
with open(os.path.join(self.root, 'train_test_split', 'shuffled_test_file_list.json'), 'r') as f:
test_ids = set([str(d.split('/')[2]) for d in json.load(f)])
for item in self.cat:
self.meta[item] = []
dir_point = os.path.join(self.root, self.cat[item])
fns = sorted(os.listdir(dir_point))
if split == 'trainval':
fns = [fn for fn in fns if (
(fn[0:-4] in train_ids) or (fn[0:-4] in val_ids))]
elif split == 'train':
fns = [fn for fn in fns if fn[0:-4] in train_ids]
elif split == 'val':
fns = [fn for fn in fns if fn[0:-4] in val_ids]
elif split == 'test':
fns = [fn for fn in fns if fn[0:-4] in test_ids]
else:
print('Unknown split: %s. Exiting..' % (split))
exit(-1)
for fn in fns:
token = (os.path.splitext(os.path.basename(fn))[0])
self.meta[item].append(os.path.join(dir_point, token + '.txt'))
self.datapath = []
for item in self.cat:
for fn in self.meta[item]:
self.datapath.append((item, fn))
self.classes = {}
for i in self.cat.keys():
self.classes[i] = self.classes_original[i]
self.seg_classes = {'Earphone': [16, 17, 18], 'Motorbike': [30, 31, 32, 33, 34, 35], 'Rocket': [41, 42, 43],
'Car': [8, 9, 10, 11], 'Laptop': [28, 29], 'Cap': [6, 7], 'Skateboard': [44, 45, 46],
'Mug': [36, 37], 'Guitar': [19, 20, 21], 'Bag': [4, 5], 'Lamp': [24, 25, 26, 27],
'Table': [47, 48, 49], 'Airplane': [0, 1, 2, 3], 'Pistol': [38, 39, 40],
'Chair': [12, 13, 14, 15], 'Knife': [22, 23]}
self.clsnb_to_label = {ii: k for ii, k in enumerate(
sorted(list(self.seg_classes.keys())))}
self.cls_to_parts = {
ii: self.seg_classes[self.clsnb_to_label[ii]] for ii in range(len(self.seg_classes))}
self.part_classes = []
for k, v in self.classes.items():
self.part_classes.extend(self.seg_classes[k])
self.part_classes = sorted(self.part_classes)
skeys = sorted(list(self.seg_classes.keys()))
self.parts_per_class = [len(self.seg_classes[x]) for x in skeys]
self.cache = {}
self.cache_size = 20000
def __getitem__(self, index):
if index in self.cache:
point_set, cls, seg = self.cache[index]
else:
fn = self.datapath[index]
cat = self.datapath[index][0]
cls = self.classes[cat]
cls = np.array([cls]).astype(np.int32)
data = np.loadtxt(fn[1]).astype(np.float32)
if not self.normal_channel:
point_set = data[:, 0:3]
else:
point_set = data[:, 0:6]
seg = data[:, -1].astype(np.int32)
if len(self.cache) < self.cache_size:
self.cache[index] = (point_set, cls, seg)
point_set[:, 0:3] = pc_normalize(point_set[:, 0:3])
true_nb_points = point_set.shape[0]
if true_nb_points >= self.npoints:
choice = np.arange(self.npoints)
real_points_mask = np.ones(self.npoints, dtype=np.int)
else:
choice = np.ones(self.npoints, dtype=np.int) * (true_nb_points-1)
choice[:true_nb_points] = np.arange(true_nb_points)
real_points_mask = np.zeros(self.npoints, dtype=np.int)
real_points_mask[:true_nb_points] = 1
point_set = point_set[choice, :]
seg = seg[choice]
return point_set, cls, seg, self.cls_to_parts[int(cls)][0], len(self.cls_to_parts[int(cls)]), real_points_mask
def __len__(self):
return len(self.datapath)