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End-to-end pipeline runs

pull/1283/head
Piero Toffanin 2021-05-04 14:46:55 -04:00
rodzic 5ef0e7c129
commit e46ff4ee78
11 zmienionych plików z 54 dodań i 37 usunięć
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16
opendm/cropper.py
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@ -37,7 +37,7 @@ class Cropper:
# ext = .tif
original_geotiff = os.path.join(path, "{}.original{}".format(basename, ext))
os.rename(geotiff_path, original_geotiff)
os.replace(geotiff_path, original_geotiff)
try:
kwargs = {
@ -64,7 +64,7 @@ class Cropper:
log.ODM_WARNING('Something went wrong while cropping: {}'.format(e))
# Revert rename
os.rename(original_geotiff, geotiff_path)
os.replace(original_geotiff, geotiff_path)
return geotiff_path
@ -159,8 +159,8 @@ class Cropper:
if pc_geojson_boundary_feature is None: raise RuntimeError("Could not determine point cloud boundaries")
# Write bounds to GeoJSON
bounds_geojson_path = self.path('bounds.geojson')
with open(bounds_geojson_path, "w") as f:
tmp_bounds_geojson_path = self.path('tmp-bounds.geojson')
with open(tmp_bounds_geojson_path, "w") as f:
f.write(json.dumps({
"type": "FeatureCollection",
"features": [{
@ -172,7 +172,7 @@ class Cropper:
# Create a convex hull around the boundary
# as to encompass the entire area (no holes)
driver = ogr.GetDriverByName('GeoJSON')
ds = driver.Open(bounds_geojson_path, 0) # ready-only
ds = driver.Open(tmp_bounds_geojson_path, 0) # ready-only
layer = ds.GetLayer()
# Collect all Geometry
@ -202,7 +202,7 @@ class Cropper:
# Save to a new file
bounds_geojson_path = self.path('bounds.geojson')
if os.path.exists(bounds_geojson_path):
driver.DeleteDataSource(bounds_geojson_path)
os.remove(bounds_geojson_path)
out_ds = driver.CreateDataSource(bounds_geojson_path)
layer = out_ds.CreateLayer("convexhull", geom_type=ogr.wkbPolygon)
@ -219,6 +219,10 @@ class Cropper:
# Remove decimated point cloud
if os.path.exists(decimated_pointcloud_path):
os.remove(decimated_pointcloud_path)
# Remove tmp bounds
if os.path.exists(tmp_bounds_geojson_path):
os.remove(tmp_bounds_geojson_path)
return bounds_geojson_path

4
opendm/dem/commands.py
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@ -258,13 +258,13 @@ def create_dem(input_point_cloud, dem_type, output_type='max', radiuses=['0.56']
median_smoothing(geotiff_path, output_path)
os.remove(geotiff_path)
else:
os.rename(geotiff_path, output_path)
os.replace(geotiff_path, output_path)
if os.path.exists(geotiff_tmp_path):
if not keep_unfilled_copy:
os.remove(geotiff_tmp_path)
else:
os.rename(geotiff_tmp_path, io.related_file_path(output_path, postfix=".unfilled"))
os.replace(geotiff_tmp_path, io.related_file_path(output_path, postfix=".unfilled"))
for cleanup_file in [tiles_vrt_path, merged_vrt_path, geotiff_small_path, geotiff_small_filled_path]:
if os.path.exists(cleanup_file): os.remove(cleanup_file)

4
opendm/dem/pdal.py
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@ -36,9 +36,9 @@ import json as jsonlib
import tempfile
from opendm import system
from opendm import log
from opendm.utils import double_quote
from datetime import datetime
from pipes import quote
""" JSON Functions """
@ -191,7 +191,7 @@ def merge_point_clouds(input_files, output_file, verbose=False):
cmd = [
'pdal',
'merge',
' '.join(map(quote, input_files + [output_file])),
' '.join(map(double_quote, input_files + [output_file])),
]
if verbose:

2
opendm/osfm.py
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@ -349,7 +349,7 @@ class OSFMContext:
# (containing only the primary band)
if os.path.exists(self.recon_file()):
os.remove(self.recon_file())
os.rename(self.recon_backup_file(), self.recon_file())
os.replace(self.recon_backup_file(), self.recon_file())
log.ODM_INFO("Restored reconstruction.json")
def backup_reconstruction(self):

6
opendm/point_cloud.py
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@ -6,7 +6,7 @@ from opendm.system import run
from opendm import entwine
from opendm import io
from opendm.concurrency import parallel_map
from pipes import quote
from opendm.utils import double_quote
def ply_info(input_ply):
if not os.path.exists(input_ply):
@ -240,7 +240,7 @@ def merge(input_point_cloud_files, output_file, rerun=False):
os.remove(output_file)
kwargs = {
'all_inputs': " ".join(map(quote, input_point_cloud_files)),
'all_inputs': " ".join(map(double_quote, input_point_cloud_files)),
'output': output_file
}
@ -312,7 +312,7 @@ def merge_ply(input_point_cloud_files, output_file, dims=None):
'--writers.ply.sized_types=false',
'--writers.ply.storage_mode="little endian"',
('--writers.ply.dims="%s"' % dims) if dims is not None else '',
' '.join(map(quote, input_point_cloud_files + [output_file])),
' '.join(map(double_quote, input_point_cloud_files + [output_file])),
]
system.run(' '.join(cmd))

5
opendm/tiles/tiler.py
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@ -1,11 +1,12 @@
import os
import sys
from opendm import log
from opendm import system
from opendm import io
def generate_tiles(geotiff, output_dir, max_concurrency):
gdal2tiles = os.path.join(os.path.dirname(__file__), "gdal2tiles.py")
system.run('python3 "%s" --processes %s -z 5-21 -n -w none "%s" "%s"' % (gdal2tiles, max_concurrency, geotiff, output_dir))
system.run('%s "%s" --processes %s -z 5-21 -n -w none "%s" "%s"' % (sys.executable, gdal2tiles, max_concurrency, geotiff, output_dir))
def generate_orthophoto_tiles(geotiff, output_dir, max_concurrency):
try:
@ -29,7 +30,7 @@ def generate_colored_hillshade(geotiff):
system.run('gdaldem color-relief "%s" "%s" "%s" -alpha -co ALPHA=YES' % (geotiff, relief_file, colored_dem))
system.run('gdaldem hillshade "%s" "%s" -z 1.0 -s 1.0 -az 315.0 -alt 45.0' % (geotiff, hillshade_dem))
system.run('python3 "%s" "%s" "%s" "%s"' % (hsv_merge_script, colored_dem, hillshade_dem, colored_hillshade_dem))
system.run('%s "%s" "%s" "%s" "%s"' % (sys.executable, hsv_merge_script, colored_dem, hillshade_dem, colored_hillshade_dem))
return outputs
except Exception as e:

14
opendm/utils.py
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@ -1,6 +1,7 @@
from opendm import log
from opendm.photo import find_largest_photo_dim
from osgeo import gdal
from shlex import _find_unsafe
def get_depthmap_resolution(args, photos):
if 'depthmap_resolution_is_set' in args:
@ -39,4 +40,15 @@ def get_raster_stats(geotiff):
'stddev': s[3]
})
return stats
return stats
def double_quote(s):
"""Return a shell-escaped version of the string *s*."""
if not s:
return '""'
if _find_unsafe(s) is None:
return s
# use double quotes, and prefix double quotes with a \
# the string $"b is then quoted as "$\"b"
return '"' + s.replace('"', '\\\"') + '"'

26
run.py
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@ -11,9 +11,9 @@ from opendm import config
from opendm import system
from opendm import io
from opendm.progress import progressbc
from opendm.utils import double_quote
import os
from pipes import quote
from stages.odm_app import ODMApp
@ -50,18 +50,18 @@ if __name__ == '__main__':
log.ODM_INFO("Rerun all -- Removing old data")
os.system("rm -rf " +
" ".join([
quote(os.path.join(args.project_path, "odm_georeferencing")),
quote(os.path.join(args.project_path, "odm_meshing")),
quote(os.path.join(args.project_path, "odm_orthophoto")),
quote(os.path.join(args.project_path, "odm_dem")),
quote(os.path.join(args.project_path, "odm_report")),
quote(os.path.join(args.project_path, "odm_texturing")),
quote(os.path.join(args.project_path, "opensfm")),
quote(os.path.join(args.project_path, "odm_filterpoints")),
quote(os.path.join(args.project_path, "odm_texturing_25d")),
quote(os.path.join(args.project_path, "openmvs")),
quote(os.path.join(args.project_path, "entwine_pointcloud")),
quote(os.path.join(args.project_path, "submodels")),
double_quote(os.path.join(args.project_path, "odm_georeferencing")),
double_quote(os.path.join(args.project_path, "odm_meshing")),
double_quote(os.path.join(args.project_path, "odm_orthophoto")),
double_quote(os.path.join(args.project_path, "odm_dem")),
double_quote(os.path.join(args.project_path, "odm_report")),
double_quote(os.path.join(args.project_path, "odm_texturing")),
double_quote(os.path.join(args.project_path, "opensfm")),
double_quote(os.path.join(args.project_path, "odm_filterpoints")),
double_quote(os.path.join(args.project_path, "odm_texturing_25d")),
double_quote(os.path.join(args.project_path, "openmvs")),
double_quote(os.path.join(args.project_path, "entwine_pointcloud")),
double_quote(os.path.join(args.project_path, "submodels")),
]))
app = ODMApp(args)

8
stages/odm_orthophoto.py
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@ -9,7 +9,7 @@ from opendm import gsd
from opendm import orthophoto
from opendm.concurrency import get_max_memory
from opendm.cutline import compute_cutline
from pipes import quote
from opendm.utils import double_quote
from opendm import pseudogeo
from opendm.multispectral import get_primary_band_name
@ -63,11 +63,11 @@ class ODMOrthoPhotoStage(types.ODM_Stage):
if not primary:
subdir = band['name'].lower()
models.append(os.path.join(base_dir, subdir, model_file))
kwargs['bands'] = '-bands %s' % (','.join([quote(b['name']) for b in reconstruction.multi_camera]))
kwargs['bands'] = '-bands %s' % (','.join([double_quote(b['name']) for b in reconstruction.multi_camera]))
else:
models.append(os.path.join(base_dir, model_file))
kwargs['models'] = ','.join(map(quote, models))
kwargs['models'] = ','.join(map(double_quote, models))
# run odm_orthophoto
system.run('{odm_ortho_bin} -inputFiles {models} '
@ -148,7 +148,7 @@ class ODMOrthoPhotoStage(types.ODM_Stage):
if io.file_exists(tree.odm_orthophoto_render):
pseudogeo.add_pseudo_georeferencing(tree.odm_orthophoto_render)
log.ODM_INFO("Renaming %s --> %s" % (tree.odm_orthophoto_render, tree.odm_orthophoto_tif))
os.rename(tree.odm_orthophoto_render, tree.odm_orthophoto_tif)
os.replace(tree.odm_orthophoto_render, tree.odm_orthophoto_tif)
else:
log.ODM_WARNING("Could not generate an orthophoto (it did not render)")
else:

2
stages/openmvs.py
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@ -144,7 +144,7 @@ class ODMOpenMVSStage(types.ODM_Stage):
log.ODM_ERROR("Could not compute dense point cloud (no PLY files available).")
if len(scene_ply_files) == 1:
# Simply rename
os.rename(scene_ply_files[0], tree.openmvs_model)
os.replace(scene_ply_files[0], tree.openmvs_model)
log.ODM_INFO("%s --> %s"% (scene_ply_files[0], tree.openmvs_model))
else:
# Merge

4
stages/splitmerge.py
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@ -17,7 +17,7 @@ from opendm.concurrency import get_max_memory
from opendm.remote import LocalRemoteExecutor
from opendm.shots import merge_geojson_shots
from opendm import point_cloud
from pipes import quote
from opendm.utils import double_quote
from opendm.tiles.tiler import generate_dem_tiles
class ODMSplitStage(types.ODM_Stage):
@ -219,7 +219,7 @@ class ODMSplitStage(types.ODM_Stage):
argv = get_submodel_argv(args, tree.submodels_path, sp_octx.name())
# Re-run the ODM toolchain on the submodel
system.run(" ".join(map(quote, map(str, argv))), env_vars=os.environ.copy())
system.run(" ".join(map(double_quote, map(str, argv))), env_vars=os.environ.copy())
else:
lre.set_projects([os.path.abspath(os.path.join(p, "..")) for p in submodel_paths])
lre.run_toolchain()