diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..887a2c1 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore index dd6c0f4..9342405 100644 --- a/.gitignore +++ b/.gitignore @@ -24,3 +24,7 @@ lsf-config-* lsf-config_* local-config-* local-config_* + +# pixi environments +.pixi +*.egg-info diff --git a/local-config/dask-config.yaml b/local-config/dask-config.yaml index 46e9d03..a50c3e8 100644 --- a/local-config/dask-config.yaml +++ b/local-config/dask-config.yaml @@ -21,10 +21,10 @@ distributed: worker: memory: - target: 0.0 - spill: 0.0 - pause: 0.0 - terminate: 0.0 + target: 0.6 + spill: 0.7 + pause: 0.8 + terminate: 0.95 admin: log-format: '[%(asctime)s] %(levelname)s %(message)s' diff --git a/multiresolution_mesh_creator/src/create_multiresolution_meshes.py b/multiresolution_mesh_creator/src/create_multiresolution_meshes.py index ee8b879..e83fd24 100644 --- a/multiresolution_mesh_creator/src/create_multiresolution_meshes.py +++ b/multiresolution_mesh_creator/src/create_multiresolution_meshes.py @@ -2,7 +2,6 @@ import trimesh from trimesh.intersections import slice_faces_plane import numpy as np -from dvidutils import encode_faces_to_custom_drc_bytes import time import os from os import listdir @@ -10,8 +9,9 @@ import dask from dask.distributed import worker_client import pyfqmr -from ..util import mesh_util, io_util, dask_util +from multiresolution_mesh_creator.util import mesh_util, io_util, dask_util import logging +import DracoPy logger = logging.getLogger(__name__) @@ -32,7 +32,7 @@ def my_slice_faces_plane(vertices, faces, plane_normal, plane_origin): if len(vertices) > 0 and len(faces) > 0: try: - vertices, faces = slice_faces_plane( + vertices, faces, _ = slice_faces_plane( vertices, faces, plane_normal, plane_origin ) except ValueError as e: @@ -192,16 +192,24 @@ def generate_mesh_decomposition( # Return combined_fragments_dictionary for fragment_pos, fragment in combined_fragments_dictionary.items(): current_box_size = lod_0_box_size * 2**current_lod - draco_bytes = encode_faces_to_custom_drc_bytes( - fragment.vertices, - np.zeros(np.shape(fragment.vertices)), - fragment.faces, - np.asarray(3 * [current_box_size]), - np.asarray(fragment_pos) * current_box_size, - position_quantization_bits=10, - ) - if len(draco_bytes) > 12: + if len(fragment.vertices) > 0: + quantization_origin = np.asarray(fragment_pos) * current_box_size + draco_bytes = DracoPy.encode( + points=fragment.vertices, + faces=fragment.faces, + quantization_bits=10, + quantization_range=current_box_size, + quantization_origin=quantization_origin, + ) + # TODO: check if len(draco_bytes) > 12 and len(fragment.vertices) > 0 are + # equivalent; if not the user may incur in this warning for small meshes + if not len(draco_bytes) > 12: + print( + 'Warning: Draco bytes are less than 12 bytes. This may be due to a ' + 'small mesh. Skipping this mesh.' + ) + continue # Then the mesh is not empty fragment = mesh_util.CompressedFragment( draco_bytes, @@ -346,7 +354,7 @@ def generate_neuroglancer_multires_mesh( grid_origin = np.minimum( grid_origin, np.floor(vertices.min(axis=0) - 1) ) # subtract 1 in case of rounding issues - + if not lod_0_box_size and current_lod == 0: max_distance_between_vertices = np.ceil( np.max(vertices.max(axis=0) - vertices.min(axis=0)) @@ -354,12 +362,12 @@ def generate_neuroglancer_multires_mesh( # arbitrarily say around 100 faces per chunk heuristic_num_chunks = np.ceil(num_faces/100) if heuristic_num_chunks==1: - lod_0_box_size = np.ceil(max_distance_between_vertices)+1 + lod_0_box_size = np.ceil(max_distance_between_vertices)+1 else: lod_0_box_size = np.ceil(max_distance_between_vertices/np.ceil(heuristic_num_chunks**(1/2)))+1 # use square root rather than cube root since assuming surface area to volume ratio - + previous_num_faces = num_faces - + # only need as many lods until mesh stops decimating lods = lods[:idx] @@ -407,7 +415,7 @@ def generate_neuroglancer_multires_mesh( stride = np.ceil( 1.0 * (end_fragment - start_fragment) / num_chunks - ).astype(np.int) + ).astype(int) # Scattering here, unless broadcast=True, causes this issue: # https://github.com/dask/distributed/issues/4612. But that is @@ -502,7 +510,7 @@ def get_number_of_subtask_workers(output_path, ids, original_ext, num_workers): # lots of small objects are present total_file_size = 0 - file_sizes = np.zeros((len(ids),), dtype=np.int) + file_sizes = np.zeros((len(ids),), dtype=int) for idx, id in enumerate(ids): current_size = os.stat( f"{output_path}/mesh_lods/s0/{id}{original_ext}" @@ -511,7 +519,7 @@ def get_number_of_subtask_workers(output_path, ids, original_ext, num_workers): file_sizes[idx] = current_size num_workers_per_byte = num_workers / total_file_size - num_subtask_workers = np.ceil(file_sizes * num_workers_per_byte).astype(np.int) + num_subtask_workers = np.ceil(file_sizes * num_workers_per_byte).astype(int) return num_subtask_workers num_subtask_workers = get_number_of_subtask_workers( diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..bfa00b2 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,2447 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - 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