# -*- python -*-
#
# Copyright INRIA - CIRAD - INRA
#
# Distributed under the Cecill-C License.
# See accompanying file LICENSE.txt or copy at
# http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html
#
# ==============================================================================
from __future__ import division, print_function, absolute_import
import os
import re
import json
import csv
import numpy
from .image3D import Image3D
# ==============================================================================
[docs]
class NumpyEncoder(json.JSONEncoder):
"""Special json encoder for numpy types"""
[docs]
def default(self, o):
if isinstance(o, numpy.integer):
return int(o)
if isinstance(o, numpy.floating):
return float(o)
if isinstance(o, numpy.ndarray):
return o.tolist()
return json.JSONEncoder.default(self, o)
[docs]
class VoxelGrid:
[docs]
def __init__(self, voxels_position, voxels_size):
self._voxels_position = voxels_position
self._voxels_size = voxels_size
# ==========================================================================
# GETTER & SETTER
# ==========================================================================
@property
def voxels_position(self):
return self._voxels_position
@voxels_position.setter
def voxels_position(self, voxels_position):
self._voxels_position = voxels_position
@voxels_position.deleter
def voxels_position(self):
del self._voxels_position
@property
def voxels_size(self):
return self._voxels_size
@voxels_size.setter
def voxels_size(self, voxels_size):
self._voxels_size = voxels_size
@voxels_size.deleter
def voxels_size(self):
del self._voxels_size
# ==========================================================================
# Analysis Data
# ==========================================================================
def bounding_box(self):
if len(self._voxels_position) == 0:
raise ValueError("Empty list")
x_min = float("inf")
y_min = float("inf")
z_min = float("inf")
x_max = -float("inf")
y_max = -float("inf")
z_max = -float("inf")
for x, y, z in self._voxels_position:
x_min = min(x_min, x)
y_min = min(y_min, y)
z_min = min(z_min, z)
x_max = max(x_max, x)
y_max = max(y_max, y)
z_max = max(z_max, z)
return (x_min, y_min, z_min), (x_max, y_max, z_max)
[docs]
def volume(self):
"""
Compute the volume of the voxel point cloud
"""
return len(self._voxels_position) * self._voxels_size**3
def __len__(self):
return len(self._voxels_position)
# ==========================================================================
# SHOW
# ==========================================================================
def show(self):
raise NotImplementedError
# ==========================================================================
# TRANSFORM
# ==========================================================================
def to_image_3d(self):
(x_min, y_min, z_min), (x_max, y_max, z_max) = self.bounding_box()
len_x = int((x_max - x_min) / self.voxels_size + 1)
len_y = int((y_max - y_min) / self.voxels_size + 1)
len_z = int((z_max - z_min) / self.voxels_size + 1)
image_3d = Image3D.zeros(
(len_x, len_y, len_z),
dtype=bool,
voxels_size=self.voxels_size,
world_coordinate=(x_min, y_min, z_min),
)
bound_min = numpy.array((x_min, y_min, z_min))
vs_pos = numpy.array(self.voxels_position)
r = ((vs_pos - bound_min) / self.voxels_size).astype(int)
image_3d[r[:, 0], r[:, 1], r[:, 2]] = 1
return image_3d
@staticmethod
def from_image_3d(
image_3d, voxels_value=1, voxels_size=None, world_coordinate=None
):
xx, yy, zz = numpy.where(image_3d >= voxels_value)
if voxels_size is None:
voxels_size = image_3d.voxels_size
if world_coordinate is None:
world_coordinate = image_3d.world_coordinate
xxx = world_coordinate[0] + xx * voxels_size
yyy = world_coordinate[1] + yy * voxels_size
zzz = world_coordinate[2] + zz * voxels_size
voxels_position = numpy.column_stack((xxx, yyy, zzz))
return VoxelGrid(voxels_position, voxels_size)
# ==========================================================================
# READ / WRITE
# ==========================================================================
def write(self, filename):
ext = filename.split(".")[-1]
if ext == "npz":
return self.write_to_npz(filename)
if ext == "json":
return self.write_to_json(filename)
if ext == "csv":
return self.write_to_csv(filename)
if ext == "xyz":
return self.write_to_xyz(filename)
raise ValueError("No extension")
@staticmethod
def read(filename, voxel_size=None):
ext = filename.split(".")[-1]
if ext == "npz":
return VoxelGrid.read_from_npz(filename)
if ext == "json":
return VoxelGrid.read_from_json(filename)
if ext == "csv":
return VoxelGrid.read_from_csv(filename)
if ext == "xyz":
return VoxelGrid.read_from_xyz(filename, voxel_size)
raise ValueError("No extension")
def write_to_npz(self, filename):
image_3d = self.to_image_3d()
image_3d.write_to_npz(filename)
@staticmethod
def read_from_npz(filename):
image_3d = Image3D.read_from_npz(filename)
return VoxelGrid.from_image_3d(image_3d)
def write_to_json(self, filename):
if os.path.dirname(filename) and not os.path.exists(os.path.dirname(filename)):
os.makedirs(os.path.dirname(filename))
with open(filename, "w", encoding="UTF8") as f:
data = {"voxels_size": self.voxels_size}
vp = list(map(tuple, self.voxels_position))
data["voxels_position"] = json.dumps(vp, cls=NumpyEncoder)
json.dump(data, f)
@staticmethod
def read_from_json(filename):
with open(filename, "r", encoding="UTF8") as f:
data = json.load(f)
voxels_size = data["voxels_size"]
voxels_position = json.loads(data["voxels_position"])
return VoxelGrid(voxels_position, voxels_size)
def write_to_xyz(self, filename):
if os.path.dirname(filename) and not os.path.exists(os.path.dirname(filename)):
os.makedirs(os.path.dirname(filename))
with open(filename, "w", encoding="UTF8") as f:
for x, y, z in self.voxels_position:
f.write(f"{x} {y} {z} \n")
@staticmethod
def read_from_xyz(filename, voxels_size):
voxels_position = []
with open(filename, "r", encoding="UTF8") as f:
for line in f:
values = [float(v) for v in line.split()[:3]]
voxels_position.append(tuple(values))
f.close()
return VoxelGrid(voxels_position, voxels_size)
def write_to_csv(self, filename, header=None):
if os.path.dirname(filename) and not os.path.exists(os.path.dirname(filename)):
os.makedirs(os.path.dirname(filename))
if header is None:
header = {}
header.update({"voxels_size": self.voxels_size})
with open(filename, "w", newline="", encoding="UTF8") as f:
c = csv.writer(f)
for k, v in header.items():
c.writerow(["# " + k + ": " + str(v)])
c.writerow(["x_coord", "y_coord", "z_coord"])
for x, y, z in self.voxels_position:
c.writerow([x, y, z])
@staticmethod
def read_from_csv(filename, read_header=False):
voxels_position = []
header = {}
with open(filename, "r", newline="", encoding="UTF8") as f:
reader = csv.reader(f)
for row in reader:
if row[0].split("#")[0].strip():
break
k, v = row[0].split("#")[1].strip().split(":")
header[k.strip()] = v.strip()
if "voxels_size" in header:
voxels_size = float(header["voxels_size"])
for x, y, z in reader:
voxels_position.append((float(x), float(y), float(z)))
else:
x, y, z, vs = next(reader)
voxels_size = float(vs)
voxels_position.append((float(x), float(y), float(z)))
for x, y, z, _ in reader:
voxels_position.append((float(x), float(y), float(z)))
if read_header:
return VoxelGrid(voxels_position, voxels_size), header
return VoxelGrid(voxels_position, voxels_size)
