def write_las_grid(self,filename, lb = -10, ub = 10, granularity = 0.1):
out_file = File(filename, mode = "w", header = Header())
out_file.header.scale = (0.001,0.001,0.001)
grid = self.get_3d_grid(lb, ub, granularity)
out_file.x = grid[:,0]* 300
out_file.y = grid[:,1] * 300
out_file.z = grid[:,2] * 300
out_file.intensity = grid[:,2] * 300
return(out_file)
def getParams(self):
"""
"""
indirs = self.configs["paths"]["input"]
indir = indirs.split(":")[0]
os.chdir(indir)
infile = glob.glob("*.las")[0]
data = File(infile, mode="r")
self.header = data.header
#print self.header
self.dtype = data.points.dtype
def _update(self):
f = FileLAS(self.filename_, mode='r')
points = f.get_points()
name = points.dtype.fields.keys()
x = f.get_x_scaled()
y = f.get_y_scaled()
z = f.get_z_scaled()
#Check is the LAS File contains red property
if 'red' in points.dtype.fields[name[0]][0].fields.keys():
red = np.int32(255.0*f.red/65536.0)
green = np.int32(255.0*f.green/65536.0)
blue = np.int32(255.0*f.blue/65536.0)
self.data_ = np.c_[x, y, z, red, green, blue]
else:
N = f.X.shape[0]
color = 128*np.ones((N,), dtype=np.int32)
self.data_ = np.c_[x, y, z, color, color, color]
def converti_las_asc(source,target):
cell = 1.0
NODATA = 0
las = File(source, mode="r")
min = las.header.min
max = las.header.max
xdist = max[0] - min[0]
ydist = max[1] - min[1]
cols = int(xdist) / cell
rows = int(ydist) / cell
cols += 1
rows += 1
count = np.zeros((rows, cols)).astype(np.float32)
zsum = np.zeros((rows, cols)).astype(np.float32)
ycell = -1 * cell
projx = (las.x - min[0]) / cell
projy = (las.y - min[1]) / cell
ix = projx.astype(np.int32)
iy = projy.astype(np.int32)
# Loop through x,y,z arrays, add to grid shape,
# and aggregate values for averaging
for x, y, z in np.nditer([ix, iy, las.z]):
count[y, x] += 1
zsum[y, x] += z
# Change 0 values to 1 to avoid numpy warnings,
# and NaN values in array
nonzero = np.where(count > 0, count, 1)
# Average our z values
zavg = zsum / nonzero
# Interpolate 0 values in array to avoid any
# holes in the grid
mean = np.ones((rows, cols)) * np.mean(zavg)
left = np.roll(zavg, -1, 1)
lavg = np.where(left > 0, left, mean)
right = np.roll(zavg, 1, 1)
ravg = np.where(right > 0, right, mean)
interpolate = (lavg + ravg) / 2
fill = np.where(zavg > 0, zavg, interpolate)
# Create our ASCII DEM header
header = "ncols %s\n" % fill.shape[1]
header += "nrows %s\n" % fill.shape[0]
header += "xllcorner %s\n" % min[0]
header += "yllcorner %s\n" % min[1]
header += "cellsize %s\n" % cell
header += "NODATA_value %s\n" % NODATA
# Open the output file, add the header, save the array
with open(target, "wb") as f:
f.write(header)
# The fmt string ensures we output floats
# that have at least one number but only
# two decimal places
np.savetxt(f, fill, fmt="%1.2f")
def loadLAS2XYZ(filepath):
'''
Function to load in console the pointcloud of a LAS file
:param filepath: filepath of the LAS file
:return: xyz array containing coordinate of the points
'''
print('Start loading...')
inFile = File(filepath, mode='r')
coords = np.vstack((inFile.x, inFile.y, inFile.z)).transpose()
print('Data loaded')
return coords
def lidar(image):
las = File(image, mode="r")
for p in las:
print(las.x, las.y, las.z)
point = las.points
print(point)
print(las.header.min)
print(las.header.max)
print(las.x)
print(las.X)
print(las.Y)
def readlas(fname):
from laspy.file import File
from subprocess import call
r = call(['laszip', fname])
if r:
sys.exit('laszip ' + fname + ' failed')
fn = '%s.las' % fname[:-4]
f = File(fn)
x = f.x
y = f.y
z = f.z
l = f.classification
f.close()
r = call(['rm', fn])
if r:
sys.exit('rm ' + fn + ' failed')
return np.transpose((x, y, z, l))
def make_las_file(data, file_name=''):
my_header = header.Header()
outFile = File(file_name, mode='w', header=my_header)
# outFile.header.offset = np.amin(data, axis=0)[0:3]
outFile.header.scale = [1, 1, 1]
outFile.x = data[:, 0]
outFile.y = data[:, 1]
outFile.z = data[:, 2]
outFile.raw_classification = data[:, 3]
outFile.close()
def read_laser(directory):
# function to read '.las' files and print their size
# input: file location and its name
# output: .las file in numpy array
laser_file = File(directory, mode='r')
print('Number of points > ', len(laser_file.points))
print('Scale of axis > ', laser_file.header.scale)
print('Offset of points > ', laser_file.header.offset)
print('Each column is > ', laser_file.points.dtype)
print('Number of columns is > ', len(laser_file.points.dtype[0]))
return laser_file
def lasReader(filename):
"""
Read xyz points from single las file
:param filename: path of single point cloud
"""
f = File(filename, mode='r')
x_max, x_min = np.max(f.x), np.min(f.x)
y_max, y_min = np.max(f.y), np.min(f.y)
z_max, z_min = np.max(f.z), np.min(f.z)
return np.transpose(np.asarray([f.x, f.y, f.z])), \
[(x_min, x_max), (y_min, y_max), (z_min, z_max)], f.header
def downsample(self, filepath, skipinterval, xbounds, ybounds):
Xvalid = np.logical_and((np.min(xbounds) <= self.file.x),
np.max(xbounds) >= self.file.x)
Yvalid = np.logical_and((np.min(ybounds) <= self.file.y),
np.max(ybounds) >= self.file.y)
keep = np.where(np.logical_and(Xvalid, Yvalid))
points = self.points[keep]
shuffleinds = np.random.shuffle(np.arange(points.shape[0]))
points = np.array(points)[shuffleinds]
points = np.squeeze(points[::skipinterval].transpose())
with File(filepath, mode='w', header=self.header) as output:
output.points = points
def __init__(self, filepath: Filepath = None, build_tree=True):
if filepath is not None:
self.filepath = filepath
self.file = File(self.filepath.filepath, mode="r")
self.header = self.file.header
self.points = np.vstack([self.file.x, self.file.y,
self.file.z]).transpose()
self.tree = sklearn.neighbors.KDTree(self.points[:, :2],
leaf_size=2**4,
metric='euclidean')
self.datetime = filepath.datetime
def writeFile(directory,name,header,coords):
"""Write a laz file using laspy and numpy arrays"""
output = File(directory + name, mode = "w", header=header)
output.x = coords[0]
output.y = coords[1]
output.z = coords[2]
output.close()
def write_las_file(self):
""" Create and write a new lidar file with the desirable points
"""
if self.surfaces:
self.out_full_path = os.path.join(
self.out_dir,
('Surfaces_' + self.templates_dict['las'].format(self.name)))
elif self.terrain:
self.out_full_path = os.path.join(
self.out_dir,
('Terrain_' + self.templates_dict['las'].format(self.name)))
out_file = File(self.out_full_path,
mode='w',
header=self.in_file.header)
if self.terrain:
class_2_points, class_2_bool = self.get_points_by_class(
self.class_flag)
out_file.points = self.in_file.points[class_2_bool]
elif self.surfaces:
out_file.points = self.in_file.points[self.in_file.return_num == 1]
out_file.close()
def read_las(infile, keys=None):
try:
from laspy.file import File
except ImportError:
print "Cannot read las files without laspy module"
raise
inFile = File(infile)
datadict = {}
datadict['coords'] = np.column_stack([
np.array(a, dtype=np.float32) for a in [inFile.x, inFile.y, inFile.z]
])
return datadict
def LasToCsv(lasFileName, shift=True):
lasFile = File(lasFileName, mode='r')
X = lasFile.X
Y = lasFile.Y
Z = lasFile.Z
if shift:
X = X - min(X)
Y = Y - min(Y)
Z = Z - min(Z)
I = lasFile.intensity
index = np.arange(X.shape[0])
data = np.stack((X, Y, Z, I, index), axis=1)
np.savetxt(lasFileName + ".csv", data, fmt="%.3f,%.3f,%.3f,%d,%d")
def loadLAS2XYZAIR(filepath):
'''
Function to load in console the pointcloud of a LAS file with points attributes
:param filepath: filepath of the LAS file
:return: xyz array containing coordinate of the points
'''
print('Start loading...')
inFile = File(filepath, mode='r')
coords = np.vstack(
(inFile.x, inFile.y, inFile.z, inFile.amplitude, inFile.Intensity,
inFile.reflectance, inFile.num_returns)).transpose()
print('Data loaded')
return coords
def LAS2txt(filepath, newfile):
'''
Function to convert a pointcloud save in LAS format into a .txt format
:param filepath: filepath of the LAS file
:param newfile: name of the new file
:return: save data into a text file
'''
inFile = File(filepath, mode='r')
coords = np.vstack((inFile.x, inFile.y, inFile.z)).transpose()
if newfile[-4] != '.txt':
newfile = newfile + '.txt'
np.savetxt(newfile, coords)
print('File saved: ' + newfile)
def main():
input1 = "Data/MantecaFiltered/MantecaRailSlice.las"
with File(input1, mode='r') as f:
input_header = f.header
to_plot = [] # list of VTK Point Clouds to plot
points = subsample_frac_from_las_data(input1, .01)
pc = create_vtkpc_from_array(points)
to_plot.append(pc)
create_point_cloud_plot_qt(to_plot,
input_header=input_header,
axes_on=True)
def get_first_returns_array(self):
# Guardo el archivo para poder leerlo
if self.partials_create:
full_path = self.dirs.out_paths['las_surfaces']
self.dirs.create_dir(self.dirs.out_dirs['las'])
else:
full_path = self.dirs.temp_full_paths['las_surfaces']
self.dirs.create_dir(self.dirs.temp_dirs['temp_dir'])
out_file = File(full_path, mode='w', header=self.in_file.header)
out_file.points = self.in_file.points[
self.in_file.return_num == 1]
out_file.close()
#leo el archivo
in_file = File(full_path, mode='r')
scale = in_file.header.scale
offset = in_file.header.offset
x = in_file.X
y = in_file.Y
z = in_file.Z
x_dimension = x * scale[0] + offset[0]
y_dimension = y * scale[1] + offset[1]
z_dimension = z * scale[-1] + offset[-1]
size = x_dimension.shape[0]
x_array = x_dimension.reshape(size, 1)
y_array = y_dimension.reshape(size, 1)
z_array = z_dimension
# Cerrar archivo para poder eliminarlo
in_file.close()
if not self.partials_create:
self.dirs.remove_temp_file(full_path)
self.dirs.remove_temp_dir(self.dirs.temp_dirs['temp_dir'])
xy_array = np.concatenate((x_array, y_array), axis=1)
self.surfaces_arrays_list = [xy_array, z_array]
def save_cloud(inFile, dir_out, filename, classif, conf):
# Problème dans les données, certaines labels sont à 0
label = inFile.classification
ind = np.argwhere(label != 0)
new_header = copy.copy(inFile.header)
#Modification du point format id pour accéder au dimensions RGB
new_header.data_format_id = 3
#Create outfile
outFile = dir_out + filename.replace('.laz', '_classify' + '.laz')
outCloud = File(outFile,
mode="w",
header=new_header,
vlrs=inFile.header.vlrs)
outCloud.define_new_dimension(name='classif',
data_type=9,
description="ntd")
outCloud.define_new_dimension(name='conf', data_type=9, description="ntd")
for dimension in inFile.point_format:
if (dimension == inFile.point_format[13]):
break
dat = inFile.reader.get_dimension(dimension.name)[ind].reshape(-1)
# dat = dat[ind]
outCloud.writer.set_dimension(dimension.name, dat)
multiscale_features_raw = pd.DataFrame()
features_raw = np.hstack([classif.reshape(-1, 1), conf.reshape(-1, 1)])
features_raw = pd.DataFrame(features_raw)
features_raw.columns = np.array(["classif", "conf"])
multiscale_features_raw = pd.concat(
[multiscale_features_raw, features_raw], axis=1)
outCloud.classif = multiscale_features_raw.as_matrix(['classif']).ravel()
outCloud.conf = multiscale_features_raw.as_matrix(['conf']).ravel()
outCloud.close()
def __init__(self, file, output_file, scale=1):
inFile = File(file, mode="r")
header_file = inFile.header
self.x, self.y, self.z = inFile.x, inFile.y, inFile.z
self.rn = inFile.return_num
try:
self.red, self.green, self.blue = inFile.red, inFile.green, inFile.blue
print('LiDar file containing RGB channels')
except:
pass
inFile.close()
coords = np.vstack((self.z, self.y, self.x)).transpose()
self.max_values = np.max(coords, axis=0).astype(int)
self.min_values = np.min(coords, axis=0).astype(int)
self.xr = np.array((1 / scale) * (coords[:, 2] - self.min_values[2]),
dtype=np.int)
self.yr = np.array((1 / scale) * (self.max_values[1] - coords[:, 1]),
dtype=np.int)
self.output_file = output_file
self.scale = scale
self.dimension = np.array(
(1 / scale) * (self.max_values - self.min_values), dtype=np.int)
self.n_points = len(self.xr)
print('Metadata: ', header_file)
print('Number of LiDar points: ', self.n_points)
print('Maximum values in axis (z,y,x) are: ', self.max_values)
print('Minimum values in axis (z,y,x) are: ', self.min_values)
print('Cubic dimensions are: ', self.dimension)
def read_cloud(point_cloud_path):
# Open point cloud and read its properties
las_file = File(point_cloud_path, mode='r')
header = (las_file.header.copy(), las_file.header.scale,
las_file.header.offset, las_file.header.evlrs,
las_file.header.vlrs)
[x_scale, y_scale, z_scale] = las_file.header.scale
[x_offset, y_offset, z_offset] = las_file.header.offset
# Calculate the real coordinates
x = las_file.X * x_scale + x_offset
y = las_file.Y * y_scale + y_offset
z = las_file.Z * z_scale + z_offset
cloud = PointCloud.with_dimensions(x, y, z, las_file.Classification,
las_file.red, las_file.green,
las_file.blue)
# Close the file
las_file.close()
# Return the result
return header, cloud
def write_las_grid(self, filename, lb=-10, ub=10, granularity=0.1):
out_file = File(filename, mode="w", header=Header())
out_file.header.scale = (0.001, 0.001, 0.001)
grid = self.get_3d_grid(lb, ub, granularity)
out_file.x = grid[:, 0] * 300
out_file.y = grid[:, 1] * 300
out_file.z = grid[:, 2] * 300
out_file.intensity = grid[:, 2] * 300
return (out_file)
def __init__(self, filepath, skipinterval=1, buildTree=True):
self.filepath = filepath.filepath
self.file = File(self.filepath, mode="r")
self.scale = self.file.header.scale[0]
self.offset = self.file.header.offset[0]
if buildTree:
self.tree = KDTree(
np.vstack([
self.file.x[::skipinterval], self.file.y[::skipinterval],
self.file.z[::skipinterval]
]).transpose())
self.treeexis = True
self.datetime = filepath.datetime
def __load_ply_file(self, filename, scale=1.0):
import plyfile
data = plyfile.PlyData.read(filename)
self.points = pd.DataFrame()
self.points['x'] = data.elements[0]['x']
self.points['y'] = data.elements[0]['y']
self.points['z'] = data.elements[0]['z']
self.points['user_data'] = np.array(data.elements[0]['confidence'] * 255.0, dtype=int)
self.points['intensity'] = np.array(data.elements[0]['intensity'] * 255.0, dtype=int)
self.points['class'] = np.zeros(len(self.points), dtype=int)
self.showing = Mask(len(self.points), True)
self.render(self.showing)
with File(self.sample_las_file) as f:
self.las_header = f.header.copy()
def load_data_memory(file):
df = pd.DataFrame(np.empty(0, dtype=[('Xx',np.float),('Yy',np.float),('Zz',np.float),('intensity',np.int), ('raw_classification',np.int), ('gps_time',np.int32), ('elevation',np.float),('return',np.int),('X',np.int), ('Y',np.int), ('Z',np.int), ('hash',np.int), ('XN',np.float), ('YN',np.float), ('ZN',np.float) ]))
las_data = File(full_path, mode='r')
df['Xx'] = (las_data.x)
df['Yy'] = (las_data.y)
df['Zz'] = (las_data.z)
df['intensity'] = (las_data.intensity)
df['raw_classification'] = (las_data.raw_classification)
df['gps_time'] = (las_data.gps_time)
df['elevation'] = (las_data.user_data) / 10
df['returns'] = (las_data.return_num)
# Density
Density = len(df.index) / ((df.Xx.max() - df.Xx.min()) * (df.Yy.max() - df.Yy.min()))
print(style.GREEN('Density :%f pts/m2'% Density))
grid_size = math.sqrt(NUM_POINT / Density)
print('grid_size :%i m' % grid_size)
# origine translation
print('translation')
df['X'] = df.Xx - df.Xx.min()
df['Y'] = df.Yy - df.Yy.min()
df['Z'] = df.Zz - df.Zz.min()
# hash
print('hash')
df['mX'] = df.X // grid_size
df.mX = df.mX.astype(int)
df['mY'] = df.Y // grid_size
df.mY = df.mY.astype(int)
df['hash'] = df[['mX', 'mY']].apply(get_hash, axis=1)
del df['mX']
del df['mY']
# normallisation
print('normallisation')
df['XN'] = (df.Xx - df.Xx.min()) / (df.Xx.max() - df.Xx.min())
df['YN'] = (df.Yy - df.Yy.min()) / (df.Yy.max() - df.Yy.min())
df['ZN'] = (df.Zz - df.Zz.min()) / (df.Zz.max() - df.Zz.min())
df['intensity'] = (df.intensity - df.intensity.min()) / (df.intensity.max() - df.intensity.min())
df['elevation'] = (df.elevation - df.elevation.min()) / (df.elevation.max() - df.elevation.min())
df['returns'] = (df.returns - df.returns.min()) / (df.returns.max() - df.returns.min())
df = df.sort_values(by=['hash'])
return df
def get_bounds(arg):
if isinstance(arg, str):
'''
json = u"""
{
"pipeline": [
\"""" + arg + """\",
{
"type":"filters.stats",
"dimensions":"X,Y,Z"
}
]
}
pipeline = pdal.Pipeline(json)
'''
f = File(arg, mode='r')
min_values = f.header.min
max_values = f.header.max
return ((min_values[0], max_values[0]), (min_values[1], max_values[1]))
else:
json = u"""
{
"pipeline": [
{
"type":"filters.stats",
"dimensions":"X,Y,Z"
}
]
}
"""
pipeline = pdal.Pipeline(json, arrays=arg)
pipeline.validate()
pipeline.loglevel = 8
pipeline.execute()
import json as j
metadata = j.loads(pipeline.metadata)
metadata['metadata']['filters.stats'][0]['bbox']['native']['bbox'][
'minx']
return ((metadata['metadata']['filters.stats'][0]['bbox']['native']
['bbox']['minx'], metadata['metadata']['filters.stats'][0]
['bbox']['native']['bbox']['maxx']),
(metadata['metadata']['filters.stats'][0]['bbox']['native']
['bbox']['miny'], metadata['metadata']['filters.stats'][0]
['bbox']['native']['bbox']['maxy']))
def __write_las_file(self, filename, points):
if self.las_header is None:
self.las_header = Header()
self.las_header.x_offset, self.las_header.y_offset, self.las_header.z_offset = 0.0, 0.0, 0.0
self.las_header.x_scale, self.las_header.y_scale, self.las_header.z_scale = 0.0001, 0.0001, 0.0001
if self.las_header.data_format_id < 2:
self.las_header.data_format_id = 2
with File(filename, self.las_header, mode='w') as f:
f.x, f.y, f.z = points[['x', 'y', 'z']].values.T
if 'r' in points:
f.red, f.green, f.blue = points[['r', 'g', 'b']].values.T
if 'class' in points:
f.classification = points['class'].values
if 'user_data' in points:
f.user_data = points['user_data'].values
if 'intensity' in points:
f.intensity = points['intensity'].values
def load_las(path):
input_las = File(path, mode='r')
point_records = input_las.points.copy()
las_scale_x = input_las.header.scale[0]
las_offset_x = input_las.header.offset[0]
las_scale_y = input_las.header.scale[1]
las_offset_y = input_las.header.offset[1]
las_scale_z = input_las.header.scale[2]
las_offset_z = input_las.header.offset[2]
# calculating coordinates
p_x = np.array((point_records['point']['X'] * las_scale_x) + las_offset_x)
p_y = np.array((point_records['point']['Y'] * las_scale_y) + las_offset_y)
p_z = np.array((point_records['point']['Z'] * las_scale_z) + las_offset_z)
points = np.vstack((p_x, p_y, p_z, input_las.red, input_las.green, input_las.blue)).T
return points
def save_points_as_las(points, file_name, input_header):
with File(file_name, mode='w', header=input_header) as f:
# pdb.set_trace()
# points = pc.getPoints()
# print(points)
allx = []
ally = []
allz = []
# for p in tqdm(points, total=points.GetNumberOfPoints(), desc="Saving"):
for i in trange(len(points), desc="Saving"):
p = points[i]
# print(p)
allx.append(p[0])
ally.append(p[1])
allz.append(p[2])
f.x = np.array(allx)
f.y = np.array(ally)
f.z = np.array(allz)
def __init__(self, filepath):
#start = time.time()
self.name = filepath
self.file = File(filepath, mode="r")
#self.filesize = getsizeof(self.file)/8
self.scale = self.file.header.scale[0]
self.offset = self.file.header.offset[0]
self.tree = KDTree(
np.vstack([self.file.x, self.file.y, self.file.z]).transpose())
#self.tree.size = getsizeof(self.tree)/8
filename = splitext(basename(filepath))[0].replace("_", "")
dateobj = [int(filename[i:i + 2]) for i in range(0, len(filename), 2)
] # year, month,day,hour,min,sec
self.time = datetime.datetime(dateobj[0], dateobj[1], dateobj[2],
dateobj[3], dateobj[4], dateobj[5], 0)
#print("File Size: {}, KDTree Size: {}\n".format(self.filesize,self.treesize))
self.file = None
def read_file(file_path: FilePath) -> ArrayTuple:
"""Read .las file."""
file_path = Path(file_path)
if file_path.suffix not in [k['format'] for k in extensions.values()]:
raise NotImplementedError
xyz = np.empty(0)
rgb = np.empty(0)
with File(str(file_path), mode='r') as f:
xyz = np.array((f.x, f.y, f.z)).T
try:
if hasattr(f, 'red') and hasattr(f, 'green') and hasattr(
f, 'blue'):
rgb = np.array((f.red, f.green, f.blue)).T
except LaspyException:
pass
return xyz, rgb
from laspy.file import File
import copy
inFile = File("autzen-dd.las", mode = "r")
header = inFile.header
points = copy.deepcopy(inFile.points)
import numpy as np
X = inFile.X
Y = inFile.Y
minx = np.min(X)
miny = np.min(Y)
maxx = np.max(X)
maxy = np.max(Y)
print minx, miny, maxx, maxy
x = ((maxx - minx)/2.0 + minx) - 1.0/header.scale[0]
y = (maxy - miny)/2.0 + miny
print x, y
points[0][0][0] = x
print points[0][0][0]
outfile = File("spurious.las", mode='w', header = header)
outfile.points = points
import pdb;pdb.set_trace()