def setUp(self):
self.useLocal = False
if self.useLocal:
self.tempdir = tempdir = '.'
else:
self.tempdir = tempdir = mkdtemp(prefix='patty-analytics')
self.drivemapLas = os.path.join(tempdir, 'testDriveMap.las')
self.sourcelas = os.path.join(tempdir, 'testSource.las')
self.footprint_csv = os.path.join(tempdir, 'testFootprint.csv')
self.foutlas = os.path.join(tempdir, 'testOutput.las')
self.min = -10
self.max = 10
self.num_rows = 1000
# Create plane with a pyramid
dm_pct = 0.5
dm_rows = np.round(self.num_rows * dm_pct)
dm_min = self.min * dm_pct
dm_max = self.max * dm_pct
delta = dm_max / dm_rows
shape_side = dm_max - dm_min
dm_offset = [0, 0, 0]
self.dense_obj_offset = [3, 2, -(1 + shape_side / 2)]
# make drivemap
plane_row = np.linspace(start=self.min,
stop=self.max,
num=self.num_rows)
plane_points = cartesian((plane_row, plane_row, [0]))
shape_points, footprint = make_tri_pyramid_with_base(
shape_side, delta, dm_offset)
np.savetxt(self.footprint_csv, footprint, fmt='%.3f', delimiter=',')
dm_points = np.vstack([plane_points, shape_points])
plane_grid = np.zeros((dm_points.shape[0], 6), dtype=np.float32)
plane_grid[:, 0:3] = dm_points
self.drivemap_pc = pcl.PointCloudXYZRGB(plane_grid)
self.drivemap_pc = downsample_voxel(self.drivemap_pc,
voxel_size=delta * 20)
# utils.set_registration(self.drivemap_pc)
utils.save(self.drivemap_pc, self.drivemapLas)
# Create a simple pyramid
dense_grid = np.zeros((shape_points.shape[0], 6), dtype=np.float32)
dense_grid[:, 0:3] = shape_points + self.dense_obj_offset
self.source_pc = pcl.PointCloudXYZRGB(dense_grid)
self.source_pc = downsample_voxel(self.source_pc, voxel_size=delta * 5)
utils.save(self.source_pc, self.sourcelas)
def setUp(self):
self.useLocal = False
if self.useLocal:
self.tempdir = tempdir = '.'
else:
self.tempdir = tempdir = mkdtemp(prefix='patty-analytics')
self.drivemapLas = os.path.join(tempdir, 'testDriveMap.las')
self.sourcelas = os.path.join(tempdir, 'testSource.las')
self.footprint_csv = os.path.join(tempdir, 'testFootprint.csv')
self.foutlas = os.path.join(tempdir, 'testOutput.las')
self.min = -10
self.max = 10
self.num_rows = 1000
# Create plane with a pyramid
dm_pct = 0.5
dm_rows = np.round(self.num_rows * dm_pct)
dm_min = self.min * dm_pct
dm_max = self.max * dm_pct
delta = dm_max / dm_rows
shape_side = dm_max - dm_min
dm_offset = [0, 0, 0]
self.dense_obj_offset = [3, 2, -(1 + shape_side / 2)]
# make drivemap
plane_row = np.linspace(
start=self.min, stop=self.max, num=self.num_rows)
plane_points = cartesian((plane_row, plane_row, [0]))
shape_points, footprint = make_tri_pyramid_with_base(
shape_side, delta, dm_offset)
np.savetxt(self.footprint_csv, footprint, fmt='%.3f', delimiter=',')
dm_points = np.vstack([plane_points, shape_points])
plane_grid = np.zeros((dm_points.shape[0], 6), dtype=np.float32)
plane_grid[:, 0:3] = dm_points
self.drivemap_pc = pcl.PointCloudXYZRGB(plane_grid)
self.drivemap_pc = downsample_voxel(self.drivemap_pc,
voxel_size=delta * 20)
# utils.set_registration(self.drivemap_pc)
utils.save(self.drivemap_pc, self.drivemapLas)
# Create a simple pyramid
dense_grid = np.zeros((shape_points.shape[0], 6), dtype=np.float32)
dense_grid[:, 0:3] = shape_points + self.dense_obj_offset
self.source_pc = pcl.PointCloudXYZRGB(dense_grid)
self.source_pc = downsample_voxel(self.source_pc, voxel_size=delta * 5)
utils.save(self.source_pc, self.sourcelas)
def _fine_registration_helper(pointcloud, drivemap, voxelsize=0.05, attempt=0):
"""
Perform ICP on pointcloud with drivemap, and return convergence indicator.
Reject large translatoins.
Returns:
transf : np.array([4,4])
transform
success : Boolean
if icp was successful
fitness : float
sort of sum of square differences, ie. smaller is better
"""
####
# Downsample to speed up
# use voxel filter to keep evenly distributed spatial extent
log(" - Downsampling with voxel filter: %s" % voxelsize)
pc = downsample_voxel(pointcloud, voxelsize)
####
# Clip to drivemap to prevent outliers confusing the ICP algorithm
log(" - Clipping to drivemap")
bb = BoundingBox(drivemap)
z = bb.center[2]
extracted = extract_mask(pc, [bb.contains([point[0], point[1], z])
for point in pc])
log(" - Remaining points: %s" % len(extracted))
####
# GICP
converged, transf, estimate, fitness = gicp(extracted, drivemap)
####
# Dont accept large translations
translation = transf[0:3, 3]
if np.dot(translation, translation) > 5 ** 2:
log(" - Translation too large, considering it a failure.")
converged = False
fitness = 1e30
else:
log(" - Success, fitness: ", converged, fitness)
force_srs(estimate, same_as=pointcloud)
save(estimate, "attempt%s.las" % attempt)
return transf, converged, fitness
def test_auto_file_format():
"""Test saving and loading pointclouds via the pcl loader"""
# make and save a pointcloud
pc = pcl.PointCloud(10)
pc_arr = np.asarray(pc)
pc_arr[:] = np.random.randn(*pc_arr.shape)
with NamedTemporaryFile(suffix=".ply") as f:
utils.save(pc, f.name)
pc2 = utils.load(f.name)
_compare(pc, pc2)
with NamedTemporaryFile(suffix=".pcd") as f:
utils.save(pc, f.name)
pc2 = utils.load(f.name)
_compare(pc, pc2)
with NamedTemporaryFile(suffix=".las") as f:
utils.save(pc, f.name, format="PLY")
pc2 = utils.load(f.name, format="PLY")
_compare(pc, pc2)
with NamedTemporaryFile(suffix=".las") as f:
utils.save(pc, f.name, format="PCD")
pc2 = utils.load(f.name, format="PCD")
_compare(pc, pc2)
def test_auto_file_format():
"""Test saving and loading pointclouds via the pcl loader"""
# make and save a pointcloud
pc = pcl.PointCloud(10)
pc_arr = np.asarray(pc)
pc_arr[:] = np.random.randn(*pc_arr.shape)
with NamedTemporaryFile(suffix='.ply') as f:
utils.save(pc, f.name)
pc2 = utils.load(f.name)
_compare(pc, pc2)
with NamedTemporaryFile(suffix='.pcd') as f:
utils.save(pc, f.name)
pc2 = utils.load(f.name)
_compare(pc, pc2)
with NamedTemporaryFile(suffix='.las') as f:
utils.save(pc, f.name, format="PLY")
pc2 = utils.load(f.name, format="PLY")
_compare(pc, pc2)
with NamedTemporaryFile(suffix='.las') as f:
utils.save(pc, f.name, format="PCD")
pc2 = utils.load(f.name, format="PCD")
_compare(pc, pc2)
def test_read_write():
""" Test read and write LAS files functionality"""
filename = "./testIO.las"
# make and save a pointcloud
pc1 = pcl.PointCloud(10)
pc1_arr = np.asarray(pc1)
pc1_arr[:] = np.random.randn(*pc1_arr.shape)
utils.save(pc1, filename)
# reload it
pc2 = utils.load(filename)
_compare(pc1, pc2)
os.remove(filename)
def test_read_write():
''' Test read and write LAS files functionality'''
filename = './testIO.las'
# make and save a pointcloud
pc1 = pcl.PointCloud(10)
pc1_arr = np.asarray(pc1)
pc1_arr[:] = np.random.randn(*pc1_arr.shape)
utils.save(pc1, filename)
# reload it
pc2 = utils.load(filename)
_compare(pc1, pc2)
os.remove(filename)
force_srs(drivemap, srs="EPSG:32633")
log("Reading footprint", footprintcsv)
footprint = load(footprintcsv)
force_srs(footprint, srs="EPSG:32633")
set_srs(footprint, same_as=drivemap)
log("Reading object", sourcefile)
pointcloud = load(sourcefile)
Up = None
try:
with open(up_file) as f:
dic = json.load(f)
Up = np.array(dic['estimatedUpDirection'])
log("Reading up_file", up_file)
except:
log("Cannot parse upfile, skipping")
initial_registration(pointcloud,
Up,
drivemap,
trust_up=Trust_up,
initial_scale=Initial_scale)
save(pointcloud, "initial.las")
center = coarse_registration(pointcloud, drivemap, footprint, Downsample)
save(pointcloud, "coarse.las")
fine_registration(pointcloud, drivemap, center, voxelsize=Voxel)
save(pointcloud, foutLas)
#!/usr/bin/env python
"""Segment points by colour from a pointcloud file and saves all reddish points
target pointcloud file. Autodectects ply, pcd and las files.
Usage: redstickdetection.py [-h] <infile> <outfile>
"""
from docopt import docopt
from patty.segmentation.segRedStick import get_red_mask
from patty.utils import extract_mask, load, save
if __name__ == '__main__':
args = docopt(__doc__)
pc = load(args['<infile>'])
red_pc = extract_mask(pc, get_red_mask(pc))
save(red_pc, args['<outfile>'])
import sys
from patty.segmentation import segment_dbscan
from patty.utils import load, save
if __name__ == '__main__':
args = docopt(__doc__, sys.argv[1:])
rgb_weight = float(args['--rgb_weight'])
eps = float(args['<epsilon>'])
minpoints = int(args['<minpoints>'])
# Kludge to get a proper exception for file not found
# (PCL will report "problem parsing header!").
with open(args['<file>']) as _:
pc = load(args['<file>'])
print("%d points" % len(pc))
clusters = segment_dbscan(pc, epsilon=eps, minpoints=minpoints,
rgb_weight=rgb_weight)
n_outliers = len(pc)
for i, cluster in enumerate(clusters):
print("%d points in cluster %d" % (len(cluster), i))
filename = '%s/cluster%d.%s' % (args['--output_dir'], i,
args['--format'])
save(cluster, filename)
n_outliers -= len(cluster)
print("%d outliers" % n_outliers)
#!/usr/bin/env python
"""Convert a pointcloud file from one format to another.
This procedure looses any information about the point normals, and the
geographic projection used. It keeps color information. It recognises
PLY, PCD and LAS files.
Usage:
convert.py [-h] <infile> <outfile>
"""
from patty.utils import load, save
from docopt import docopt
if __name__ == '__main__':
args = docopt(__doc__)
pc = load(args['<infile>'])
save(pc, args['<outfile>'])
if __name__ == '__main__':
args = docopt(__doc__)
pc = load(args['<source>'])
try:
offset = csv_read(args['-o'])
except:
offset = None
try:
matrix = csv_read(args['-r'])
pc.rotate(matrix, origin=offset)
except Exception as e:
print('Problem with rotate: ', e)
try:
factor = csv_read(args['-s'])
pc.scale(factor, origin=offset)
except Exception as e:
print('Problem with scale: ', e)
try:
vector = csv_read(args['-t'])
pc.translate(vector)
except Exception as e:
print('Problem with translate: ', e)
save(pc, args['<target>'])
#!/usr/bin/env python
"""Apply a statistical outlier filter to a pointcloud.
Usage:
statfilter.py [-k <kmeans>] [-s <stddev>] <infile> <outfile>
Description:
-k <kmeans>, --kmeans <kmeans> K means value [default: 1000].
-s <stddev>, --stddev <stddev> Standard deviation cut-off
[default: 2.0].
"""
from docopt import docopt
from patty.utils import load, save
def statfilter(pc, k, s):
"""Apply the PCL statistical outlier filter to a point cloud"""
fil = pc.make_statistical_outlier_filter()
fil.set_mean_k(k)
fil.set_std_dev_mul_thresh(s)
return fil.filter()
if __name__ == "__main__":
args = docopt(__doc__)
pc = load(args['<infile>'])
filter = statfilter(pc, int(args['--kmeans']), float(args['--stddev']))
save(filter, args['<outfile>'])
def coarse_registration(pointcloud, drivemap, footprint, downsample=None):
"""
Improve the initial registration.
Find the proper scale by looking for the red meter sticks, and calculate
and align the pointcloud's footprint.
Arguments:
pointcloud: pcl.PointCloud
The high-res object to register.
drivemap: pcl.PointCloud
A small part of the low-res drivemap on which to register
footprint: pcl.PointCloud
Pointlcloud containing the objects footprint
downsample: float, default=None, no resampling
Downsample the high-res pointcloud before footprint
calculation.
"""
log("Starting coarse registration")
###
# find redstick scale, and use it if possible
log(" - Redstick scaling")
allow_scaling = True
scale, confidence = get_stick_scale(pointcloud)
log(" - Red stick scale=%s confidence=%s" % (scale, confidence))
if (confidence > 0.5):
log(" - Applying red stick scale")
pointcloud.scale(1.0 / scale) # dont care about origin of scaling
allow_scaling = False
else:
log(" - Not applying red stick scale, confidence too low")
#####
# find all the points in the drivemap along the footprint
# use bottom two meters of drivemap (not trees)
dm_boundary = boundary_of_drivemap(drivemap, footprint)
dm_bb = BoundingBox(dm_boundary)
# set footprint height from minimum value,
# as trees, or high object make the pc.center() too high
fixed_boundary = clone(footprint)
fp_array = np.asarray(fixed_boundary)
fp_array[:, 2] = dm_bb.min[2]
save(fixed_boundary, "fixed_bound.las")
#####
# find all the boundary points of the pointcloud
loose_boundary = boundary_of_center_object(pointcloud, downsample)
if loose_boundary is None:
log(" - boundary estimation failed, using lowest 30 percent of points")
loose_boundary = boundary_of_lowest_points(pointcloud,
height_fraction=0.3)
####
# match the pointcloud boundary with the footprint boundary
log(" - Aligning footprints:")
rot_matrix, rot_center, scale, translation = align_footprints(
loose_boundary, fixed_boundary,
allow_scaling=allow_scaling,
allow_rotation=True,
allow_translation=True)
save(loose_boundary, "aligned_bound.las")
####
# Apply to the main pointcloud
pointcloud.rotate(rot_matrix, origin=rot_center)
pointcloud.scale(scale, origin=rot_center)
pointcloud.translate(translation)
rot_center += translation
return rot_center
log("Reading drivemap", drivemapfile)
drivemap = load(drivemapfile)
force_srs(drivemap, srs="EPSG:32633")
log("Reading footprint", footprintcsv)
footprint = load(footprintcsv)
force_srs(footprint, srs="EPSG:32633")
set_srs(footprint, same_as=drivemap)
log("Reading object", sourcefile)
pointcloud = load(sourcefile)
Up = None
try:
with open(up_file) as f:
dic = json.load(f)
Up = np.array(dic['estimatedUpDirection'])
log("Reading up_file", up_file)
except:
log("Cannot parse upfile, skipping")
initial_registration(pointcloud, Up, drivemap,
trust_up=Trust_up, initial_scale=Initial_scale)
save(pointcloud, "initial.las")
center = coarse_registration(pointcloud, drivemap, footprint, Downsample)
save(pointcloud, "coarse.las")
fine_registration(pointcloud, drivemap, center, voxelsize=Voxel)
save(pointcloud, foutLas)
from patty.segmentation import segment_dbscan
from patty.utils import load, save
if __name__ == '__main__':
args = docopt(__doc__, sys.argv[1:])
rgb_weight = float(args['--rgb_weight'])
eps = float(args['<epsilon>'])
minpoints = int(args['<minpoints>'])
# Kludge to get a proper exception for file not found
# (PCL will report "problem parsing header!").
with open(args['<file>']) as _:
pc = load(args['<file>'])
print("%d points" % len(pc))
clusters = segment_dbscan(pc,
epsilon=eps,
minpoints=minpoints,
rgb_weight=rgb_weight)
n_outliers = len(pc)
for i, cluster in enumerate(clusters):
print("%d points in cluster %d" % (len(cluster), i))
filename = '%s/cluster%d.%s' % (args['--output_dir'], i,
args['--format'])
save(cluster, filename)
n_outliers -= len(cluster)
print("%d outliers" % n_outliers)