def exportMeshes(object_names, obj_filepaths):
n_objects = len(object_names)
progress_update = 100 / n_objects
try:
for obj, obj_path, obj_n in zip(object_names, obj_filepaths,
range(n_objects)):
object_volume = get_label_volume_from_mst(mst, obj)
unique_ids = len(numpy.unique(object_volume))
if unique_ids <= 1:
logger.info(f"No voxels found for {obj}, skipping")
continue
elif unique_ids > 2:
logger.info(
f"Supervoxel segmentation not unique for {obj}, skipping, got {unique_ids}"
)
continue
logger.info(f"Generating mesh for {obj}")
_, mesh_data = list(labeling_to_mesh(object_volume,
[1]))[0]
self.parentApplet.progressSignal(
(obj_n + 0.5) * progress_update)
logger.info(f"Mesh generation for {obj} complete.")
logger.info(f"Saving mesh for {obj} to {obj_path}")
mesh_to_obj(mesh_data, obj_path, obj)
self.parentApplet.progressSignal(
(obj_n + 1) * progress_update)
finally:
self.parentApplet.busy = False
self.parentApplet.progressSignal(100)
self.parentApplet.appletStateUpdateRequested()
def onMeshesComplete(mesh):
"""
Called when mesh extraction is complete.
Writes the extracted mesh to an .obj file
"""
logger.info( "Mesh generation complete." )
# FIXME: the old comment: Mesh count can sometimes be 0 for the '<not saved yet>' object...
# FIXME: is this still relevant???
'''
mesh_count = len( window.extractor.meshes )
if mesh_count > 0:
assert mesh_count == 1, \
"Found {} meshes processing object '{}',"\
"(only expected 1)".format( mesh_count, object_name )
mesh = list(window.extractor.meshes.values())[0]
logger.info( "Saving meshes to {}".format( obj_filepath ) )
# Use VTK to write to a temporary .vtk file
tmpdir = tempfile.mkdtemp()
vtkpoly_path = os.path.join(tmpdir, 'meshes.vtk')
w = vtkPolyDataWriter()
w.SetFileTypeToASCII()
w.SetInput(mesh)
w.SetFileName(vtkpoly_path)
w.Write()
# Now convert the file to .obj format.
convertVTPtoOBJ(vtkpoly_path, obj_filepath)
'''
logger.info("Saving meshes to {}".format(obj_filepath))
mesh_to_obj(mesh, obj_filepath, object_name)
# Cleanup: We don't need the window anymore.
window.setParent(None)
# If there are still objects left to process,
# start again with the remainder of the list.
if object_names:
self._exportMeshes(object_names, obj_filepaths)
def onMeshesComplete(mesh):
"""
Called when mesh extraction is complete.
Writes the extracted mesh to an .obj file
"""
logger.info("Mesh generation complete.")
# FIXME: the old comment: Mesh count can sometimes be 0 for the '<not saved yet>' object...
# FIXME: is this still relevant???
'''
mesh_count = len( window.extractor.meshes )
if mesh_count > 0:
assert mesh_count == 1, \
"Found {} meshes processing object '{}',"\
"(only expected 1)".format( mesh_count, object_name )
mesh = list(window.extractor.meshes.values())[0]
logger.info( "Saving meshes to {}".format( obj_filepath ) )
# Use VTK to write to a temporary .vtk file
tmpdir = tempfile.mkdtemp()
vtkpoly_path = os.path.join(tmpdir, 'meshes.vtk')
w = vtkPolyDataWriter()
w.SetFileTypeToASCII()
w.SetInput(mesh)
w.SetFileName(vtkpoly_path)
w.Write()
# Now convert the file to .obj format.
convertVTPtoOBJ(vtkpoly_path, obj_filepath)
'''
logger.info("Saving meshes to {}".format(obj_filepath))
mesh_to_obj(mesh, obj_filepath, object_name)
# Cleanup: We don't need the window anymore.
window.setParent(None)
# If there are still objects left to process,
# start again with the remainder of the list.
if object_names:
self._exportMeshes(object_names, obj_filepaths)
from h5py import File
from volumina.view3d.meshgenerator import labeling_to_mesh, mesh_to_obj
if __name__ == "__main__":
parser = ArgumentParser()
parser.add_argument("--label", type=int, required=False)
parser.add_argument("input_hdf5_file")
parsed_args = parser.parse_args()
output_file = os.path.splitext(parsed_args.input_hdf5_file)[0] + ".obj"
print("Loading volume...")
with File(parsed_args.input_hdf5_file, "r") as f_input:
dataset_names = []
f_input.visit(dataset_names.append)
if len(dataset_names) != 1:
stderr.write("Input HDF5 file should have exactly 1 dataset.\n")
sysexit(1)
volume = f_input[dataset_names[0]][:].squeeze()
if parsed_args.label:
volume[:] = volume == parsed_args.label
labels = [parsed_args.label]
else:
volume[:] = volume != 0
labels = [label for label in unique(volume) if label != 0]
for label, mesh in labeling_to_mesh(volume, labels):
mesh_to_obj(mesh, "{}_{}.obj".format(output_file, label), label)