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LAStools merge in split-merge 

Former-commit-id: 8a8d51a695
pull/1161/head
Piero Toffanin 2019-10-29 14:25:12 -04:00
rodzic dce9759129
commit 458eb1b1e4
5 zmienionych plików z 77 dodań i 84 usunięć
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13
SuperBuild/CMakeLists.txt
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@ -168,3 +168,16 @@ externalproject_add(dem2points
BUILD_COMMAND make
INSTALL_COMMAND ""
)
externalproject_add(lastools
GIT_REPOSITORY https://github.com/LAStools/LAStools.git
GIT_TAG 2ef44281645999ec7217facec84a5913bbbbe165
SOURCE_DIR ${SB_SOURCE_DIR}/lastools
CONFIGURE_COMMAND ""
CMAKE_COMMAND ""
CMAKE_GENERATOR ""
UPDATE_COMMAND ""
BUILD_IN_SOURCE 1
BUILD_COMMAND make -C LASlib -j$(nproc) CXXFLAGS='-std=c++11' && make -C src -j$(nproc) CXXFLAGS='-std=c++11' lasmerge
INSTALL_COMMAND mv ${SB_SOURCE_DIR}/lastools/bin/lasmerge ${SB_INSTALL_DIR}/bin
)

50
opendm/entwine.py
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@ -1,33 +1,10 @@
import os
import json
import shutil
from pipes import quote
from opendm import io
from opendm import log
from opendm import system
from opendm import concurrency
import math
def closest_power_of_4(x):
if x <= 0:
return 1
n = 1
while n < x:
n *= 4
return n
def get_num_points(scan_file):
if not os.path.exists(scan_file):
log.ODM_WARNING("%s does not exist, cannot get number of points." % scan_file)
return 0
with open(scan_file, "r") as f:
scan = json.loads(f.read())
if not 'points' in scan:
log.ODM_WARNING("Cannot find number of points in point clouds (points key missing from scan.json). Returning 0")
return 0
return scan['points']
def build(input_point_cloud_files, output_path, max_concurrency=8, rerun=False):
num_files = len(input_point_cloud_files)
@ -45,29 +22,20 @@ def build(input_point_cloud_files, output_path, max_concurrency=8, rerun=False):
'threads': max_concurrency,
'tmpdir': tmpdir,
'all_inputs': "-i " + " ".join(map(quote, input_point_cloud_files)),
'outputdir': output_path,
'scan_file': os.path.join(output_path, "scan.json")
'outputdir': output_path
}
# Run scan to compute number of points
# Run scan to compute dataset bounds
system.run('entwine scan --threads {threads} --tmp "{tmpdir}" {all_inputs} -o "{outputdir}"'.format(**kwargs))
num_points = get_num_points(kwargs['scan_file'])
scan_json = os.path.join(output_path, "scan.json")
# TODO: choose subset
entwine_cmd = "entwine build --threads {threads} --tmp {tmpdir} -i {scan_file} -o {outputdir}".format(**kwargs)
# Need to split into subsets?
if num_files > 1:
subsets = closest_power_of_4(num_files)
for s in range(1, subsets + 1):
system.run(entwine_cmd + " --subset %s %s" % (s, subsets))
# Merge
system.run("entwine merge --threads {threads} --tmp {tmpdir} -o {outputdir}".format(**kwargs))
if os.path.exists(scan_json):
kwargs['input'] = scan_json
for _ in range(num_files):
# One at a time
system.run('entwine build --threads {threads} --tmp "{tmpdir}" -i "{input}" -o "{outputdir}" --run 1'.format(**kwargs))
else:
# Single run
system.run(entwine_cmd)
log.ODM_WARNING("%s does not exist, no point cloud will be built." % scan_json)
if os.path.exists(tmpdir):

49
opendm/point_cloud.py
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@ -3,6 +3,9 @@ from opendm import system
from opendm import log
from opendm import context
from opendm.system import run
from opendm import entwine
from opendm import io
from pipes import quote
def filter(input_point_cloud, output_point_cloud, standard_deviation=2.5, meank=16, confidence=None, verbose=False):
"""
@ -92,6 +95,50 @@ def get_extent(input_point_cloud):
raise Exception("Cannot compute bounds for %s (invalid keys) %s" % (input_point_cloud, str(bounds)))
os.remove(json_file)
return bounds
return bounds
def merge(input_point_cloud_files, output_file, rerun=False):
num_files = len(input_point_cloud_files)
if num_files == 0:
log.ODM_WARNING("No input point cloud files to process")
return
if rerun and io.file_exists(output_file):
log.ODM_WARNING("Removing previous point cloud: %s" % output_file)
os.remove(output_file)
kwargs = {
'all_inputs': " ".join(map(quote, input_point_cloud_files)),
'output': output_file
}
system.run('lasmerge -i {all_inputs} -o "{output}"'.format(**kwargs))
def post_point_cloud_steps(args, tree):
# XYZ point cloud output
if args.pc_csv:
log.ODM_INFO("Creating geo-referenced CSV file (XYZ format)")
system.run("pdal translate -i \"{}\" "
"-o \"{}\" "
"--writers.text.format=csv "
"--writers.text.order=\"X,Y,Z\" "
"--writers.text.keep_unspecified=false ".format(
tree.odm_georeferencing_model_laz,
tree.odm_georeferencing_xyz_file))
# LAS point cloud output
if args.pc_las:
log.ODM_INFO("Creating geo-referenced LAS file")
system.run("pdal translate -i \"{}\" "
"-o \"{}\" ".format(
tree.odm_georeferencing_model_laz,
tree.odm_georeferencing_model_las))
# EPT point cloud output
if args.pc_ept:
log.ODM_INFO("Creating geo-referenced Entwine Point Tile output")
entwine.build([tree.odm_georeferencing_model_laz], tree.entwine_pointcloud, max_concurrency=args.max_concurrency, rerun=False)

28
stages/odm_georeferencing.py
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@ -9,7 +9,6 @@ from opendm import system
from opendm import context
from opendm.cropper import Cropper
from opendm import point_cloud
from opendm import entwine
class ODMGeoreferencingStage(types.ODM_Stage):
def process(self, args, outputs):
@ -97,32 +96,7 @@ class ODMGeoreferencingStage(types.ODM_Stage):
if doPointCloudGeo:
reconstruction.georef.extract_offsets(odm_georeferencing_model_txt_geo_file)
# XYZ point cloud output
if args.pc_csv:
log.ODM_INFO("Creating geo-referenced CSV file (XYZ format)")
system.run("pdal translate -i \"{}\" "
"-o \"{}\" "
"--writers.text.format=csv "
"--writers.text.order=\"X,Y,Z\" "
"--writers.text.keep_unspecified=false ".format(
tree.odm_georeferencing_model_laz,
tree.odm_georeferencing_xyz_file))
# LAS point cloud output
if args.pc_las:
log.ODM_INFO("Creating geo-referenced LAS file")
system.run("pdal translate -i \"{}\" "
"-o \"{}\" ".format(
tree.odm_georeferencing_model_laz,
tree.odm_georeferencing_model_las))
# EPT point cloud output
if args.pc_ept:
log.ODM_INFO("Creating geo-referenced Entwine Point Tile output")
entwine.build([tree.odm_georeferencing_model_laz], tree.entwine_pointcloud, max_concurrency=args.max_concurrency, rerun=self.rerun())
point_cloud.post_point_cloud_steps(args, tree)
if args.crop > 0:
log.ODM_INFO("Calculating cropping area and generating bounds shapefile from point cloud")

21
stages/splitmerge.py
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@ -13,7 +13,7 @@ from opensfm.large import metadataset
from opendm.cropper import Cropper
from opendm.concurrency import get_max_memory
from opendm.remote import LocalRemoteExecutor
from opendm import entwine
from opendm import point_cloud
from pipes import quote
class ODMSplitStage(types.ODM_Stage):
@ -175,26 +175,17 @@ class ODMMergeStage(types.ODM_Stage):
# Merge point clouds
if args.merge in ['all', 'pointcloud']:
if not io.dir_exists(tree.entwine_pointcloud) or self.rerun():
if not io.file_exists(tree.odm_georeferencing_model_laz) or self.rerun():
all_point_clouds = get_submodel_paths(tree.submodels_path, "odm_georeferencing", "odm_georeferenced_model.laz")
try:
entwine.build(all_point_clouds, tree.entwine_pointcloud, max_concurrency=args.max_concurrency, rerun=self.rerun())
point_cloud.merge(all_point_clouds, tree.odm_georeferencing_model_laz, rerun=self.rerun())
point_cloud.post_point_cloud_steps(args, tree)
except Exception as e:
log.ODM_WARNING("Could not merge EPT point cloud: %s (skipping)" % str(e))
else:
log.ODM_WARNING("Found merged EPT point cloud in %s" % tree.entwine_pointcloud)
if not io.file_exists(tree.odm_georeferencing_model_laz) or self.rerun():
if io.dir_exists(tree.entwine_pointcloud):
try:
system.run('pdal translate "ept://{}" "{}"'.format(tree.entwine_pointcloud, tree.odm_georeferencing_model_laz))
except Exception as e:
log.ODM_WARNING("Cannot export EPT dataset to LAZ: %s" % str(e))
else:
log.ODM_WARNING("No EPT point cloud found (%s), skipping LAZ conversion)" % tree.entwine_pointcloud)
log.ODM_WARNING("Could not merge point cloud: %s (skipping)" % str(e))
else:
log.ODM_WARNING("Found merged point cloud in %s" % tree.odm_georeferencing_model_laz)
self.update_progress(25)