Added env_paths option in system.run, added path to superbuild install directory for odm_dem module, fixed lidar2dems install

SuperBuild/cmake/External-Lidar2dems.cmake

@@ -8,7 +8,7 @@ ExternalProject_Add(${_proj_name}
   #--Download step--------------
   DOWNLOAD_DIR      ${SB_DOWNLOAD_DIR}/${_proj_name}
   URL               https://github.com/OpenDroneMap/lidar2dems/archive/master.zip
-  URL_MD5           ba3f7da85ae569fe2610646f540d2828
+  URL_MD5           76ae5d0182f280bec890bdfd156aa538
   #--Update/Patch step----------
   UPDATE_COMMAND    ""
   #--Configure step-------------
@@ -17,7 +17,7 @@ ExternalProject_Add(${_proj_name}
   #--Build step-----------------
   BUILD_COMMAND     ""
   #--Install step---------------
-  INSTALL_COMMAND   "${SB_SOURCE_DIR}/${_proj_name}/install.sh" 
+  INSTALL_COMMAND   "${SB_SOURCE_DIR}/${_proj_name}/install.sh" "${SB_INSTALL_DIR}"
   #--Output logging-------------
   LOG_DOWNLOAD      OFF
   LOG_CONFIGURE     OFF

opendm/context.py

@@ -8,6 +8,7 @@ scripts_path = os.path.abspath(os.path.dirname(__file__))
 root_path, _ = os.path.split(scripts_path)
 
 superbuild_path = os.path.join(root_path, 'SuperBuild')
+superbuild_bin_path = os.path.join(superbuild_path, 'install', 'bin')
 tests_path = os.path.join(root_path, 'tests')
 tests_data_path = os.path.join(root_path, 'tests/test_data')
 

opendm/system.py

@@ -17,10 +17,16 @@ def get_ccd_widths():
     return dict(zip(map(string.lower, sensor_data.keys()), sensor_data.values()))
 
 
-def run(cmd):
+def run(cmd, env_paths=[]):
     """Run a system command"""
     log.ODM_DEBUG('running %s' % cmd)
-    retcode = subprocess.call(cmd, shell=True)
+
+    env = None
+    if len(env_paths) > 0:
+        env = os.environ.copy()
+        env["PATH"] = env["PATH"] + ":" + ":".join(env_paths)
+
+    retcode = subprocess.call(cmd, shell=True, env=env)
 
     if retcode < 0:
         raise Exception("Child was terminated by signal {}".format(-retcode))

scripts/odm_dem.py

@@ -27,11 +27,12 @@ class ODMDEMCell(ecto.Cell):
         args = self.inputs.args
         tree = self.inputs.tree
         las_model_found = io.file_exists(tree.odm_georeferencing_model_las)
+        env_paths = [tree.superbuild_bin_path]
 
         # Just to make sure
         l2d_module_installed = True
         try:
-            system.run('l2d_classify --help > /dev/null')
+            system.run('l2d_classify --help > /dev/null', env_paths)
         except:
             log.ODM_WARNING('lidar2dems is not installed properly')
             l2d_module_installed = False
@@ -65,8 +66,8 @@ class ODMDEMCell(ecto.Cell):
                 summary_file_path = os.path.join(odm_dem_root, 'odm_georeferenced_model.summary.json')
                 boundary_file_path = os.path.join(odm_dem_root, 'odm_georeferenced_model.boundary.json')
 
-                system.run('pdal info --summary {0} > {1}'.format(tree.odm_georeferencing_model_las, summary_file_path))
+                system.run('pdal info --summary {0} > {1}'.format(tree.odm_georeferencing_model_las, summary_file_path), env_paths)
-                system.run('pdal info --boundary {0} > {1}'.format(tree.odm_georeferencing_model_las,  boundary_file_path))
+                system.run('pdal info --boundary {0} > {1}'.format(tree.odm_georeferencing_model_las,  boundary_file_path), env_paths)
 
                 pc_proj4 = ""
                 pc_geojson_bounds_feature = None
@@ -131,7 +132,7 @@ class ODMDEMCell(ecto.Cell):
                     system.run('l2d_classify {0} --decimation {1} '
                                '{2} {3}'.format(
                         l2d_params, args.dem_decimation,
-                        approximate, tree.odm_georeferencing))
+                        approximate, tree.odm_georeferencing), env_paths)
                 else:
                     log.ODM_INFO("Will skip classification, only DSM is needed")
                     copyfile(tree.odm_georeferencing_model_las, os.path.join(odm_dem_root, 'bounds-0_l2d_s{slope}c{cellsize}.las'.format(**kwargs)))
@@ -163,7 +164,7 @@ class ODMDEMCell(ecto.Cell):
                                '--maxsd {maxsd} --maxangle {maxangle} '
                                '--resolution {resolution} --radius {radius_steps} '
                                '{decimation} '
-                               '{gapfill} '.format(**demargs))
+                               '{gapfill} '.format(**demargs), env_paths)
 
                     # Rename final output
                     if product == 'dsm':