supervisely 6.73.361__py3-none-any.whl → 6.73.362__py3-none-any.whl

supervisely/volume/volume.py

@@ -9,9 +9,11 @@ import numpy as np
 import pydicom
 import SimpleITK as sitk
 import stringcase
+from trimesh import Trimesh
 
 import supervisely.volume.nrrd_encoder as nrrd_encoder
 from supervisely import logger
+from supervisely.geometry.mask_3d import Mask3D
 from supervisely.io.fs import get_file_ext, get_file_name, list_files_recursively
 
 # Do NOT use directly for extension validation. Use is_valid_ext() /  has_valid_ext() below instead.
@@ -783,7 +785,7 @@ def convert_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
         data, header = sly.volume.convert_nifti_to_nrrd(path)
     """
 
-    import nibabel as nib # pylint: disable=import-error
+    import nibabel as nib  # pylint: disable=import-error
 
     nifti = nib.load(path)
     reordered_to_ras_nifti = nib.as_closest_canonical(nifti)
@@ -799,6 +801,7 @@ def convert_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
     }
     return data, header
 
+
 def convert_3d_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
     """Convert 3D NIFTI volume to NRRD format.
     Volume automatically reordered to RAS orientation as closest to canonical.
@@ -830,14 +833,14 @@ def convert_3d_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
     space_directions = (direction.T * spacing[:, None]).tolist()
 
     header = {
-            "dimension": 3,
-            "space": "right-anterior-superior",
-            "sizes": list(data.shape),
-            "space directions": space_directions,
-            "endian": "little",
-            "encoding": "gzip",
-            "space origin": origin
-        }
+        "dimension": 3,
+        "space": "right-anterior-superior",
+        "sizes": list(data.shape),
+        "space directions": space_directions,
+        "endian": "little",
+        "encoding": "gzip",
+        "space origin": origin,
+    }
     return data, header
 
 
@@ -861,3 +864,96 @@ def is_nifti_file(path: str) -> bool:
         return True
     except nib.filebasedimages.ImageFileError:
         return False
+
+
+def convert_3d_geometry_to_mesh(
+    geometry: Mask3D,
+    spacing: tuple = None,
+    level: float = 0.5,
+    apply_decimation: bool = False,
+    decimation_fraction: float = 0.5,
+) -> Trimesh:
+    """
+    Converts a 3D geometry (Mask3D) to a Trimesh mesh.
+
+    :param geometry: The 3D geometry to convert.
+    :type geometry: supervisely.geometry.mask_3d.Mask3D
+    :param spacing: Voxel spacing in (x, y, z). Default is taken from geometry meta.
+    :type spacing: tuple
+    :param level: Isosurface value for marching cubes. Default is 0.5.
+    :type level: float
+    :param apply_decimation: Whether to simplify the mesh. Default is False.
+    :type apply_decimation: bool
+    :param decimation_fraction: Fraction of faces to keep if decimation is applied. Default is 0.5.
+    :type decimation_fraction: float
+    :return: The resulting Trimesh mesh.
+    :rtype: trimesh.Trimesh
+
+    :Usage example:
+
+        .. code-block:: python
+
+            mask3d = Mask3D.create_from_file("path/to/mask3d")
+            mesh = convert_3d_geometry_to_mesh(mask3d, spacing=(1.0, 1.0, 1.0), level=0.7, apply_decimation=True)
+    """
+    from skimage import measure
+
+    # Flip the mask along the x-axis to correct mirroring
+    mask = np.flip(geometry.data, axis=0)
+    if spacing is None:
+        try:
+            spacing = tuple(
+                float(abs(direction[i])) for i, direction in enumerate(geometry._space_directions)
+            )
+        except Exception as e:
+            logger.warning(
+                "Failed to get spacing from geometry meta. Using (1.0, 1.0, 1.0).", exc_info=1
+            )
+            spacing = (1.0, 1.0, 1.0)
+
+    # marching_cubes expects (z, y, x) order
+    verts, faces, normals, _ = measure.marching_cubes(
+        mask.astype(np.float32), level=level, spacing=spacing
+    )
+    mesh = Trimesh(vertices=verts, faces=faces, vertex_normals=normals, process=False)
+
+    if apply_decimation and 0 < decimation_fraction < 1:
+        mesh = mesh.simplify_quadric_decimation(int(len(mesh.faces) * decimation_fraction))
+
+    return mesh
+
+
+def export_3d_as_mesh(geometry: Mask3D, output_path: str, kwargs=None):
+    """
+    Exports the 3D mesh representation of the object to a file in either STL or OBJ format.
+
+    :param geometry: The 3D geometry to be exported.
+    :type geometry: supervisely.geometry.mask_3d.Mask3D
+    :param output_path: The path to the output file. Must have a ".stl" or ".obj" extension.
+    :type output_path: str
+    :param kwargs: Additional keyword arguments for mesh generation. Supported keys:
+        - spacing (tuple): Voxel spacing in (x, y, z). By default the value will be taken from geometry meta.
+        - level (float): Isosurface value for marching cubes. Default is 0.5.
+        - apply_decimation (bool): Whether to simplify the mesh. Default is False.
+        - decimation_fraction (float): Fraction of faces to keep if decimation is applied. Default is 0.5.
+    :type kwargs: dict, optional
+    :return: None
+
+    :Usage example:
+
+        .. code-block:: python
+
+        mask3d_path = "path/to/mask3d"
+        mask3d = Mask3D.create_from_file(mask3d_path)
+
+        mask3d.export_3d_as_mesh(mask3d, "output.stl", {"spacing": (1.0, 1.0, 1.0), "level": 0.7, "apply_decimation": True})
+    """
+
+    if kwargs is None:
+        kwargs = {}
+
+    if get_file_ext(output_path).lower() not in [".stl", ".obj"]:
+        raise ValueError('File extension must be either ".stl" or ".obj"')
+
+    mesh = convert_3d_geometry_to_mesh(geometry, **kwargs)
+    mesh.export(output_path)

supervisely/volume_annotation/volume_annotation.py

@@ -11,6 +11,7 @@ from supervisely.volume_annotation.volume_figure import VolumeFigure
 
 from supervisely.project.project_meta import ProjectMeta
 from supervisely._utils import take_with_default
+from supervisely.io.fs import file_exists
 from supervisely.video_annotation.key_id_map import KeyIdMap
 from supervisely.volume_annotation.slice import Slice
 from supervisely.volume_annotation.volume_tag_collection import VolumeTagCollection
@@ -30,7 +31,7 @@ from supervisely.volume_annotation.constants import (
     PLANES,
     SPATIAL_FIGURES,
 )
-
+from supervisely.io.fs import get_file_name
 from supervisely.io.json import dump_json_file
 
 
@@ -484,7 +485,13 @@ class VolumeAnnotation:
         )
 
     @classmethod
-    def from_json(cls, data: dict, project_meta: ProjectMeta, key_id_map: KeyIdMap = None):
+    def from_json(
+        cls,
+        data: dict,
+        project_meta: ProjectMeta,
+        key_id_map: KeyIdMap = None,
+        spatial_geometry_paths: Union[list, dict] = None,
+    ):
         """
         Convert a json dict to VolumeAnnotation.
 
@@ -494,6 +501,11 @@ class VolumeAnnotation:
         :type project_meta: ProjectMeta
         :param key_id_map: KeyIdMap object.
         :type key_id_map: KeyIdMap, optional
+        :param spatial_geometry_paths: Optional. Can be either:
+            - a list of file paths to spatial geometry files, where each file name should match either the figure's id or the hex value of its key,
+            - or a dict mapping figure ids (or keys) to their corresponding geometry file paths.
+            Used to load 3D geometry for spatial figures.
+        :type spatial_geometry_paths: list or dict, optional
         :return: VolumeAnnotation object
         :rtype: :class:`VolumeAnnotation<VolumeAnnotation>`
         :Usage example:
@@ -585,6 +597,31 @@ class VolumeAnnotation:
                 slice_index=None,
                 key_id_map=key_id_map,
             )
+            if spatial_geometry_paths:
+                figure_id = figure_json["id"]
+                if isinstance(spatial_geometry_paths, list):
+                    spatial_geometry_paths = {
+                        get_file_name(path): path for path in spatial_geometry_paths
+                    }
+                    geometry_path = spatial_geometry_paths.get(
+                        figure.key().hex
+                    ) or spatial_geometry_paths.get(str(figure_id))
+                elif isinstance(spatial_geometry_paths, dict):
+                    geometry_path = spatial_geometry_paths.get(figure_id, None)
+                else:
+                    raise ValueError(
+                        f"spatial_geometry_paths should be either a list or a dict. Got: {type(spatial_geometry_paths)}"
+                    )
+
+                if geometry_path is not None:
+                    if not file_exists(geometry_path):
+                        raise RuntimeError(
+                            f"Geometry file {geometry_path} for figure {figure_id} does not exist."
+                        )
+                    mask3d = Mask3D.create_from_file(geometry_path)
+                    mask3d.sly_id = figure_id
+                    figure._set_3d_geometry(mask3d)
+
             spatial_figures.append(figure)
 
         return cls(

supervisely/volume_annotation/volume_figure.py

@@ -1,28 +1,30 @@
 # coding: utf-8
 from __future__ import annotations
+
 import uuid
-from typing import Union, Optional, Literal
-from numpy import ndarray
+from typing import Literal, Optional, Union
 from uuid import UUID
-from supervisely.video_annotation.video_figure import VideoFigure
-from supervisely.video_annotation.key_id_map import KeyIdMap
-from supervisely.geometry.closed_surface_mesh import ClosedSurfaceMesh
-from supervisely.geometry.mask_3d import Mask3D
+
+from numpy import ndarray
+
+import supervisely.volume_annotation.constants as constants
+from supervisely._utils import take_with_default
+from supervisely.annotation.json_geometries_map import GET_GEOMETRY_FROM_STR
 from supervisely.api.module_api import ApiField
 from supervisely.geometry.any_geometry import AnyGeometry
-from supervisely.annotation.json_geometries_map import GET_GEOMETRY_FROM_STR
-from supervisely._utils import take_with_default
-from supervisely.volume_annotation.volume_object import VolumeObject
-from supervisely.geometry.geometry import Geometry
-import supervisely.volume_annotation.constants as constants
-from supervisely.volume_annotation.constants import ID, KEY, OBJECT_ID, OBJECT_KEY, META
+from supervisely.geometry.closed_surface_mesh import ClosedSurfaceMesh
 from supervisely.geometry.constants import (
+    CLASS_ID,
+    CREATED_AT,
     LABELER_LOGIN,
     UPDATED_AT,
-    CREATED_AT,
-    CLASS_ID,
 )
-
+from supervisely.geometry.geometry import Geometry
+from supervisely.geometry.mask_3d import Mask3D
+from supervisely.video_annotation.key_id_map import KeyIdMap
+from supervisely.video_annotation.video_figure import VideoFigure
+from supervisely.volume_annotation.constants import ID, KEY, META, OBJECT_ID, OBJECT_KEY
+from supervisely.volume_annotation.volume_object import VolumeObject
 from supervisely.volume_annotation.volume_object_collection import (
     VolumeObjectCollection,
 )

{supervisely-6.73.361.dist-info → supervisely-6.73.362.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.361
+Version: 6.73.362
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.361.dist-info → supervisely-6.73.362.dist-info}/RECORD

@@ -1075,13 +1075,13 @@ supervisely/volume/__init__.py,sha256=EBZBY_5mzabXzMUQh5akusIGd16XnX9n8J0jIi_JmW
 supervisely/volume/nrrd_encoder.py,sha256=1lqwwyqxEvctw1ysQ70x4xPSV1uy1g5YcH5CURwL7-c,4084
 supervisely/volume/nrrd_loader.py,sha256=_yqahKcqSRxunHZ5LtnUWIRA7UvIhPKOhAUwYijSGY4,9065
 supervisely/volume/stl_converter.py,sha256=WIMQgHO_u4JT58QdcMXcb_euF1BFhM7D52IVX_0QTxE,6285
-supervisely/volume/volume.py,sha256=bUPrDQAr4ZIkSQMzpSWXjsHRqcXUq2Z2H6Fe1uLdYmw,25687
+supervisely/volume/volume.py,sha256=ekU8gYhSXrTvWISd_HJT7lwtQ9Uh5t7qgVcFwzJ2NOc,29273
 supervisely/volume_annotation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/volume_annotation/constants.py,sha256=BdFIh56fy7vzLIjt0gH8xP01EIU-qgQIwbSHVUcABCU,569
 supervisely/volume_annotation/plane.py,sha256=wyezAcc8tLp38O44CwWY0wjdQxf3VjRdFLWooCrk-Nw,16301
 supervisely/volume_annotation/slice.py,sha256=9m3jtUYz4PYKV3rgbeh2ofDebkyg4TomNbkC6BwZ0lA,4635
-supervisely/volume_annotation/volume_annotation.py,sha256=T-50ZmfhQDUtoXkSB9ur3LySCp9xZ1AmUT9KqjPy1DA,30179
-supervisely/volume_annotation/volume_figure.py,sha256=3_X2drnt_zCGBLWPanW8_O-jM-tI9-34rSacUWqTflk,25329
+supervisely/volume_annotation/volume_annotation.py,sha256=pGu6n8_5JkFpir4HTVRf302gGD2EqJ96Gh4M0_236Qg,32047
+supervisely/volume_annotation/volume_figure.py,sha256=B4rXacAMM-eVPLZHQTBpT2USBv8Zh6eTzj0_e3tmuSA,25331
 supervisely/volume_annotation/volume_object.py,sha256=rWzOnycoSJ4-CvFgDOP_rPortU4CdcYR26txe5wJHNo,3577
 supervisely/volume_annotation/volume_object_collection.py,sha256=Tc4AovntgoFj5hpTLBv7pCQ3eL0BjorOVpOh2nAE_tA,5706
 supervisely/volume_annotation/volume_tag.py,sha256=N2eOhAlbRDVVdSVQ83dzg7URDGtb1xHjxL2g9BW6ljU,9488
@@ -1097,9 +1097,9 @@ supervisely/worker_proto/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZ
 supervisely/worker_proto/worker_api_pb2.py,sha256=VQfi5JRBHs2pFCK1snec3JECgGnua3Xjqw_-b3aFxuM,59142
 supervisely/worker_proto/worker_api_pb2_grpc.py,sha256=3BwQXOaP9qpdi0Dt9EKG--Lm8KGN0C5AgmUfRv77_Jk,28940
 supervisely_lib/__init__.py,sha256=7-3QnN8Zf0wj8NCr2oJmqoQWMKKPKTECvjH9pd2S5vY,159
-supervisely-6.73.361.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-supervisely-6.73.361.dist-info/METADATA,sha256=ZGEe4t9l88XpSPZES9bz3rmND8dJK-rMzlsXosDmXBU,35151
-supervisely-6.73.361.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-supervisely-6.73.361.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
-supervisely-6.73.361.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
-supervisely-6.73.361.dist-info/RECORD,,
+supervisely-6.73.362.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+supervisely-6.73.362.dist-info/METADATA,sha256=pEJ1fz_ct_nNeRITHBz-wp16AYlUFbNvG9zwIKwbWTI,35151
+supervisely-6.73.362.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
+supervisely-6.73.362.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
+supervisely-6.73.362.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
+supervisely-6.73.362.dist-info/RECORD,,