supervisely 6.73.367__py3-none-any.whl → 6.73.369__py3-none-any.whl

supervisely/api/volume/volume_figure_api.py

@@ -2,7 +2,6 @@
 import os
 import re
 import tempfile
-from collections import OrderedDict
 from typing import Dict, List
 from uuid import UUID
 
@@ -470,7 +469,7 @@ class VolumeFigureApi(FigureApi):
                 for figure in figures:
                     if figure.key() == key:
                         geometry_data = figure.geometry.data
-                        header = self._create_header_for_geometry(figure.geometry)
+                        header = figure.geometry.create_header()
                         geometry_bytes = encode(geometry_data.astype(uint8), header)
                         self.upload_sf_geometries([key], {key: geometry_bytes}, key_id_map)
 
@@ -625,19 +624,6 @@ class VolumeFigureApi(FigureApi):
             geometry = Mask3D.create_from_file(figure_path)
             spatial_figure._set_3d_geometry(geometry)
 
-    def _create_header_for_geometry(self, geometry: Mask3D) -> OrderedDict:
-        """
-        Create header for encoding Mask3D to NRRD bytes
-        """
-        header = OrderedDict()
-        if geometry._space is not None:
-            header["space"] = geometry._space
-        if geometry._space_directions is not None:
-            header["space directions"] = geometry._space_directions
-        if geometry._space_origin is not None:
-            header["space origin"] = geometry._space_origin.to_json()["space_origin"]
-        return header
-
     def download(
         self, dataset_id: int, volume_ids: List[int] = None, skip_geometry: bool = False, **kwargs
     ) -> Dict[int, List[FigureInfo]]:

supervisely/convert/volume/nii/nii_volume_helper.py

@@ -1,10 +1,10 @@
 import os
+from collections import defaultdict, namedtuple
+from pathlib import Path
 from typing import Generator
 
 import nrrd
 import numpy as np
-from pathlib import Path
-from collections import defaultdict, namedtuple
 
 from supervisely import Api
 from supervisely.collection.str_enum import StrEnum
@@ -107,13 +107,13 @@ def nifti_to_nrrd(nii_file_path: str, converted_dir: str) -> str:
 def get_annotation_from_nii(path: str) -> Generator[Mask3D, None, None]:
     """Get annotation from NIfTI 3D volume file."""
 
-    data, _ = convert_3d_nifti_to_nrrd(path)
+    data, header = convert_3d_nifti_to_nrrd(path)
     unique_classes = np.unique(data)
 
     for class_id in unique_classes:
         if class_id == 0:
             continue
-        mask = Mask3D(data == class_id)
+        mask = Mask3D(data == class_id, volume_header=header)
         yield mask, class_id
 
 

supervisely/geometry/constants.py

@@ -12,6 +12,8 @@ INTERIOR = "interior"
 MULTICHANNEL_BITMAP = "multichannelBitmap"
 ORIGIN = "origin"
 SPACE_ORIGIN = "space_origin"
+SPACE = "space"
+SPACE_DIRECTIONS = "space_directions"
 POINTS = "points"
 ROWS = "rows"
 TYPE = "type"

supervisely/geometry/mask_3d.py

@@ -6,9 +6,9 @@ from __future__ import annotations
 import base64
 import gzip
 import tempfile
+from collections import OrderedDict
 from typing import Dict, List, Literal, Optional, Tuple, Union
 
-import nrrd
 import numpy as np
 
 from supervisely import logger
@@ -22,6 +22,8 @@ from supervisely.geometry.constants import (
     ID,
     LABELER_LOGIN,
     MASK_3D,
+    SPACE,
+    SPACE_DIRECTIONS,
     SPACE_ORIGIN,
     UPDATED_AT,
 )
@@ -183,6 +185,10 @@ class Mask3D(Geometry):
     :type updated_at: str, optional
     :param created_at: Date and Time when Mask 3D was created. Date Format is the same as in "updated_at" parameter.
     :type created_at: str, optional
+    :param volume_header: NRRD header dictionary. Optional.
+    :type volume_header: dict, optional
+    :param convert_to_ras: If True, converts the mask to RAS orientation. Default is True.
+    :type convert_to_ras: bool, optional
     :raises: :class:`ValueError`, if data is not bool or no pixels set to True in data
     :Usage example:
 
@@ -219,6 +225,8 @@ class Mask3D(Geometry):
         labeler_login: Optional[str] = None,
         updated_at: Optional[str] = None,
         created_at: Optional[str] = None,
+        volume_header: Optional[Dict] = None,
+        convert_to_ras: bool = True,
     ):
         super().__init__(
             sly_id=sly_id,
@@ -253,6 +261,98 @@ class Mask3D(Geometry):
         self._space = None
         self._space_directions = None
 
+        if volume_header is not None:
+            self.set_volume_space_meta(volume_header)
+            if self.space is not None and self.space != "right-anterior-superior":
+                if convert_to_ras:
+                    self.orient_ras()
+                else:
+                    logger.debug(
+                        "Mask3D is not in RAS orientation. It is recommended to use RAS orientation for 3D masks."
+                    )
+
+    @property
+    def space_origin(self) -> Optional[List[float]]:
+        """
+        Get the space origin of the Mask3D as a list of floats.
+
+        :return: Space origin of the Mask3D.
+        :rtype: List[float] or None
+        """
+        if self._space_origin is not None:
+            return [self._space_origin.x, self._space_origin.y, self._space_origin.z]
+        return None
+
+    @space_origin.setter
+    def space_origin(self, value: Union[PointVolume, List[float], np.array]):
+        """
+        Set the space origin of the Mask3D.
+
+        :param value: Space origin of the Mask3D. If provided as a list or array, it should contain 3 floats in the order [x, y, z].
+        :type value: :class:`PointVolume<PointVolume>` or List[float]
+        """
+        if isinstance(value, PointVolume):
+            self._space_origin = value
+        elif isinstance(value, list) and len(value) == 3:
+            self._space_origin = PointVolume(x=value[0], y=value[1], z=value[2])
+        elif isinstance(value, np.ndarray) and value.shape == (3,):
+            self._space_origin = PointVolume(x=value[0], y=value[1], z=value[2])
+        else:
+            raise ValueError("Space origin must be a PointVolume or a list of 3 floats.")
+
+    @property
+    def space(self) -> Optional[str]:
+        """
+        Get the space of the Mask3D.
+
+        :return: Space of the Mask3D.
+        :rtype: :class:`str`
+        """
+        return self._space
+
+    @space.setter
+    def space(self, value: str):
+        """
+        Set the space of the Mask3D.
+
+        :param value: Space of the Mask3D.
+        :type value: str
+        """
+        if not isinstance(value, str):
+            raise ValueError("Space must be a string.")
+        self._space = value
+
+    @property
+    def space_directions(self) -> Optional[List[List[float]]]:
+        """
+        Get the space directions of the Mask3D.
+
+        :return: Space directions of the Mask3D.
+        :rtype: :class:`List[List[float]]`
+        """
+        return self._space_directions
+
+    @space_directions.setter
+    def space_directions(self, value: Union[List[List[float]], np.ndarray]):
+        """
+        Set the space directions of the Mask3D.
+
+        :param value: Space directions of the Mask3D. Should be a 3x3 array-like structure.
+        :type value: List[List[float]] or np.ndarray
+        """
+        if isinstance(value, np.ndarray):
+            if value.shape != (3, 3):
+                raise ValueError("Space directions must be a 3x3 array.")
+            self._space_directions = value.tolist()
+        elif (
+            isinstance(value, list)
+            and len(value) == 3
+            and all(isinstance(row, (list, np.ndarray)) and len(row) == 3 for row in value)
+        ):
+            self._space_directions = [list(row) for row in value]
+        else:
+            raise ValueError("Space directions must be a 3x3 array or list of lists.")
+
     @staticmethod
     def geometry_name():
         """Return geometry name"""
@@ -268,22 +368,8 @@ class Mask3D(Geometry):
         :param file_path: Path to nrrd file with data
         :type file_path: str
         """
-        mask3d_data, mask3d_header = nrrd.read(file_path)
-        figure.geometry.data = mask3d_data
-        try:
-            figure.geometry._space_origin = PointVolume(
-                x=mask3d_header["space origin"][0],
-                y=mask3d_header["space origin"][1],
-                z=mask3d_header["space origin"][2],
-            )
-            figure.geometry._space = mask3d_header["space"]
-            figure.geometry._space_directions = mask3d_header["space directions"]
-        except KeyError as e:
-            header_keys = ["'space'", "'space directions'", "'space origin'"]
-            if str(e) in header_keys:
-                logger.warning(
-                    f"The Mask3D geometry for figure ID '{get_file_name(file_path)}' doesn't contain optional space attributes that have similar names to {', '.join(header_keys)}. To set the values for these attributes, you can use information from the Volume associated with this figure object."
-                )
+        mask3d = Mask3D.create_from_file(file_path)
+        figure._set_3d_geometry(mask3d)
         path_without_filename = "/".join(file_path.split("/")[:-1])
         remove_dir(path_without_filename)
 
@@ -295,22 +381,26 @@ class Mask3D(Geometry):
         :param file_path: Path to nrrd file with data
         :type file_path: str
         """
-        mask3d_data, mask3d_header = nrrd.read(file_path)
-        geometry = cls(data=mask3d_data)
-        try:
-            geometry._space_origin = PointVolume(
-                x=mask3d_header["space origin"][0],
-                y=mask3d_header["space origin"][1],
-                z=mask3d_header["space origin"][2],
-            )
-            geometry._space = mask3d_header["space"]
-            geometry._space_directions = mask3d_header["space directions"]
-        except KeyError as e:
+        from supervisely.volume.volume import read_nrrd_serie_volume_np
+
+        mask3d_data, meta = read_nrrd_serie_volume_np(file_path)
+        direction = np.array(meta["directions"]).reshape(3, 3)
+        spacing = np.array(meta["spacing"])
+        space_directions = (direction.T * spacing[:, None]).tolist()
+        mask3d_header = {
+            "space": "right-anterior-superior",
+            "space directions": space_directions,
+            "space origin": meta.get("origin", None),
+        }
+
+        geometry = cls(data=mask3d_data, volume_header=mask3d_header)
+
+        fields_to_check = ["space", "space_directions", "space_origin"]
+        if any([getattr(geometry, value) is None for value in fields_to_check]):
             header_keys = ["'space'", "'space directions'", "'space origin'"]
-            if str(e) in header_keys:
-                logger.debug(
-                    f"The Mask3D geometry created from the file '{file_path}' doesn't contain optional space attributes that have similar names to {', '.join(header_keys)}. To set the values for these attributes, you can use information from the Volume associated with this figure object."
-                )
+            logger.debug(
+                f"The Mask3D geometry created from the file '{file_path}' doesn't contain optional space attributes that have similar names to {', '.join(header_keys)}. To set the values for these attributes, you can use information from the Volume associated with this figure object."
+            )
         return geometry
 
     @classmethod
@@ -323,7 +413,7 @@ class Mask3D(Geometry):
         :return: A Mask3D geometry object.
         :rtype: Mask3D
         """
-        with tempfile.NamedTemporaryFile(delete=True) as temp_file:
+        with tempfile.NamedTemporaryFile(delete=True, suffix=".nrrd") as temp_file:
             temp_file.write(geometry_bytes)
             return cls.create_from_file(temp_file.name)
 
@@ -368,12 +458,14 @@ class Mask3D(Geometry):
             GEOMETRY_TYPE: self.name(),
         }
 
-        if self._space_origin:
-            res[f"{self._impl_json_class_name()}"][f"{SPACE_ORIGIN}"] = [
-                self._space_origin.x,
-                self._space_origin.y,
-                self._space_origin.z,
-            ]
+        if self.space_origin:
+            res[f"{self._impl_json_class_name()}"][f"{SPACE_ORIGIN}"] = self.space_origin
+
+        if self.space:
+            res[f"{self._impl_json_class_name()}"][f"{SPACE}"] = self.space
+
+        if self.space_directions:
+            res[f"{self._impl_json_class_name()}"][f"{SPACE_DIRECTIONS}"] = self.space_directions
 
         self._add_creation_info(res)
         return res
@@ -426,18 +518,30 @@ class Mask3D(Geometry):
         created_at = json_data.get(CREATED_AT, None)
         sly_id = json_data.get(ID, None)
         class_id = json_data.get(CLASS_ID, None)
-        instance = cls(
+
+        header = {}
+
+        space_origin = json_data[json_root_key].get(SPACE_ORIGIN, None)
+        if space_origin is not None:
+            header["space origin"] = space_origin
+
+        space = json_data[json_root_key].get(SPACE, None)
+        if space is not None:
+            header["space"] = space
+
+        space_directions = json_data[json_root_key].get(SPACE_DIRECTIONS, None)
+        if space_directions is not None:
+            header["space directions"] = space_directions
+
+        return cls(
             data=data.astype(np.bool_),
             sly_id=sly_id,
             class_id=class_id,
             labeler_login=labeler_login,
             updated_at=updated_at,
             created_at=created_at,
+            volume_header=header,
         )
-        if SPACE_ORIGIN in json_data[json_root_key]:
-            x, y, z = json_data[json_root_key][SPACE_ORIGIN]
-            instance._space_origin = PointVolume(x=x, y=y, z=z)
-        return instance
 
     @classmethod
     def _impl_json_class_name(cls):
@@ -474,7 +578,7 @@ class Mask3D(Geometry):
             path_for_mesh = f"meshes/{figure_id}.nrrd"
             api.volume.figure.download_stl_meshes([figure_id], [path_for_mesh])
 
-            mask3d_data, _ = nrrd.read(path_for_mesh)
+            mask3d_data, _ = sly.volume.volume.read_nrrd_serie_volume_np(path_for_mesh)
             encoded_string = sly.Mask3D.data_2_base64(mask3d_data)
 
             print(encoded_string)
@@ -619,3 +723,73 @@ class Mask3D(Geometry):
                 continue
             geometries_dict[key] = geometry_bytes
         return geometries_dict
+
+    def set_volume_space_meta(self, header: Dict):
+        """
+        Set space, space directions, and space origin attributes from a NRRD header dictionary.
+
+        :param header: NRRD header dictionary.
+        :type header: dict
+        """
+        if "space" in header:
+            self.space = header["space"]
+        if "space directions" in header:
+            self.space_directions = header["space directions"]
+        if "space origin" in header:
+            self.space_origin = PointVolume(
+                x=header["space origin"][0],
+                y=header["space origin"][1],
+                z=header["space origin"][2],
+            )
+
+    def create_header(self) -> OrderedDict:
+        """
+        Create header for encoding Mask3D to NRRD bytes
+
+        :return: Header for NRRD file
+        :rtype: OrderedDict
+        """
+        header = OrderedDict()
+        if self.space is not None:
+            header["space"] = self.space
+        if self.space_directions is not None:
+            header["space directions"] = self.space_directions
+        if self.space_origin is not None:
+            header["space origin"] = self.space_origin
+        return header
+
+    def orient_ras(self) -> None:
+        """
+        Transforms the mask data and updates spatial metadata (origin, directions, spacing)
+        to align with the RAS coordinate system using SimpleITK.
+
+        :rtype: None
+        """
+        import SimpleITK as sitk
+
+        from supervisely.volume.volume import _sitk_image_orient_ras
+
+        sitk_volume = sitk.GetImageFromArray(self.data)
+        if self.space_origin is not None:
+            sitk_volume.SetOrigin(self.space_origin)
+        if self.space_directions is not None:
+            # Convert space directions to spacing and direction
+            space_directions = np.array(self.space_directions)
+            spacing = np.linalg.norm(space_directions, axis=1)
+            direction = space_directions / spacing[:, np.newaxis]
+            sitk_volume.SetSpacing(spacing)
+            sitk_volume.SetDirection(direction.flatten())
+
+        sitk_volume = _sitk_image_orient_ras(sitk_volume)
+
+        # Extract transformed data and update object
+        self.data = sitk.GetArrayFromImage(sitk_volume)
+        new_direction = np.array(sitk_volume.GetDirection()).reshape(3, 3)
+        new_spacing = np.array(sitk_volume.GetSpacing())
+        new_space_directions = (new_direction.T * new_spacing[:, None]).tolist()
+        new_header = {
+            "space": "right-anterior-superior",
+            "space directions": new_space_directions,
+            "space origin": sitk_volume.GetOrigin(),
+        }
+        self.set_volume_space_meta(new_header)

supervisely/nn/model/prediction_session.py

@@ -1,11 +1,13 @@
 import json
 import time
 from os import PathLike
+from pathlib import Path
 from typing import Any, Dict, Iterator, List, Literal, Tuple, Union
 
 import numpy as np
 import requests
 from requests import Timeout
+from requests_toolbelt import MultipartEncoder, MultipartEncoderMonitor
 from tqdm.auto import tqdm
 
 import supervisely.io.env as env
@@ -17,6 +19,7 @@ from supervisely.io.fs import (
     dir_exists,
     file_exists,
     get_file_ext,
+    get_file_size,
     list_files,
     list_files_recursively,
 )
@@ -374,28 +377,26 @@ class PredictionSession:
         json_body = self._get_json_body()
         return self._post(method, json=json_body).json()
 
-    def _update_progress(self, tqdm: tqdm, response: Dict[str, Any]):
+    def _update_progress(
+        self,
+        tqdm: tqdm,
+        message: str = None,
+        current: int = None,
+        total: int = None,
+        is_size: bool = False,
+    ):
         if tqdm is None:
             return
-        json_progress = response.get("progress", None)
-        if json_progress is None or json_progress.get("message") is None:
-            json_progress = response.get("preparing_progress", None)
-        if json_progress is None:
-            return
         refresh = False
-        message = json_progress.get("message", json_progress.get("status", None))
-        if message is not None and tqdm.desc not in [message, f"{message}:"]:
+        if message is not None and tqdm.desc != message:
             tqdm.set_description(message, refresh=False)
             refresh = True
-        current = json_progress.get("current", None)
         if current is not None and tqdm.n != current:
             tqdm.n = current
             refresh = True
-        total = json_progress.get("total", None)
         if total is not None and tqdm.total != total:
             tqdm.total = total
             refresh = True
-        is_size = json_progress.get("is_size", False)
         if is_size and tqdm.unit == "it":
             tqdm.unit = "iB"
             tqdm.unit_scale = True
@@ -409,6 +410,20 @@ class PredictionSession:
         if refresh:
             tqdm.refresh()
 
+    def _update_progress_from_response(self, tqdm: tqdm, response: Dict[str, Any]):
+        if tqdm is None:
+            return
+        json_progress = response.get("progress", None)
+        if json_progress is None or json_progress.get("message") is None:
+            json_progress = response.get("preparing_progress", None)
+        if json_progress is None:
+            return
+        message = json_progress.get("message", json_progress.get("status", None))
+        current = json_progress.get("current", None)
+        total = json_progress.get("total", None)
+        is_size = json_progress.get("is_size", False)
+        self._update_progress(tqdm, message, current, total, is_size)
+
     def _wait_for_inference_start(
         self, delay=1, timeout=None, tqdm: tqdm = None
     ) -> Tuple[dict, bool]:
@@ -424,7 +439,7 @@ class PredictionSession:
                 last_stage = stage
             has_started = stage not in ["preparing", "preprocess", None]
             has_started = has_started or bool(resp.get("result")) or resp["progress"]["total"] != 1
-            self._update_progress(tqdm, resp)
+            self._update_progress_from_response(tqdm, resp)
             if not has_started:
                 time.sleep(delay)
             timeout_exceeded = timeout and time.time() - t0 > timeout
@@ -440,7 +455,7 @@ class PredictionSession:
         t0 = time.monotonic()
         while not has_results and not timeout_exceeded:
             resp = self._pop_pending_results()
-            self._update_progress(tqdm, resp)
+            self._update_progress_from_response(tqdm, resp)
             pending_results = resp["pending_results"]
             exception_json = resp["exception"]
             if exception_json:
@@ -567,14 +582,30 @@ class PredictionSession:
             state["video_id"] = videos[0]
             return self._start_inference(method, json=json_body)
         elif isinstance(videos[0], (str, PathLike)):
+            video_path = videos[0]
             files = []
             try:
                 method = "inference_video_async"
-                files = [("files", open(videos[0], "rb"))]
-                uploads = files + [("state", (None, json.dumps(state), "text/plain"))]
-                return self._start_inference(method, files=uploads)
+                files.append((Path(video_path).name, open(video_path, "rb"), "video/*"))
+                fields = {
+                    "files": files[-1],
+                    "state": json.dumps(state),
+                }
+                encoder = MultipartEncoder(fields)
+                if self.tqdm is not None:
+
+                    def _callback(monitor):
+                        self.tqdm.update(monitor.bytes_read)
+
+                    video_size = get_file_size(video_path)
+                    self._update_progress(self.tqdm, "Uploading video", 0, video_size, is_size=True)
+                    encoder = MultipartEncoderMonitor(encoder, _callback)
+
+                return self._start_inference(
+                    method, data=encoder, headers={"Content-Type": encoder.content_type}
+                )
             finally:
-                for _, f in files:
+                for _, f, _ in files:
                     f.close()
         else:
             raise ValueError(

supervisely/volume/volume.py

@@ -3,7 +3,7 @@
 
 
 import os
-from typing import List, Tuple, Union
+from typing import List, Optional, Tuple, Union
 
 import numpy as np
 import pydicom
@@ -15,6 +15,7 @@ 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
+from supervisely.volume.stl_converter import matrix_from_nrrd_header
 
 # Do NOT use directly for extension validation. Use is_valid_ext() /  has_valid_ext() below instead.
 ALLOWED_VOLUME_EXTENSIONS = [".nrrd", ".dcm"]
@@ -455,7 +456,7 @@ def inspect_dicom_series(root_dir: str, logging: bool = True) -> dict:
     return found_series
 
 
-def _sitk_image_orient_ras(sitk_volume):
+def _sitk_image_orient_ras(sitk_volume: sitk.Image) -> sitk.Image:
     import SimpleITK as sitk
 
     if sitk_volume.GetDimension() == 4 and sitk_volume.GetSize()[3] == 1:
@@ -704,7 +705,7 @@ def read_nrrd_serie_volume(path: str) -> Tuple[sitk.Image, dict]:
     """
     Read NRRD volume with given path.
 
-    :param path: Paths to DICOM volume files.
+    :param path: Path to NRRD volume files.
     :type path: List[str]
     :return: Volume data in SimpleITK.Image format and dictionary with metadata.
     :rtype: Tuple[SimpleITK.Image, dict]
@@ -741,12 +742,12 @@ def read_nrrd_serie_volume(path: str) -> Tuple[sitk.Image, dict]:
     return sitk_volume, meta
 
 
-def read_nrrd_serie_volume_np(paths: List[str]) -> Tuple[np.ndarray, dict]:
+def read_nrrd_serie_volume_np(paths: str) -> Tuple[np.ndarray, dict]:
     """
     Read NRRD volume with given path.
 
-    :param path: Paths to NRRD volume file.
-    :type path: List[str]
+    :param paths: Path to NRRD volume file.
+    :type paths: str
     :return: Volume data in NumPy array format and dictionary with metadata.
     :rtype: Tuple[np.ndarray, dict]
     :Usage example:
@@ -868,17 +869,18 @@ def is_nifti_file(path: str) -> bool:
 
 def convert_3d_geometry_to_mesh(
     geometry: Mask3D,
-    spacing: tuple = None,
+    spacing: tuple = (1.0, 1.0, 1.0),
     level: float = 0.5,
     apply_decimation: bool = False,
     decimation_fraction: float = 0.5,
+    volume_meta: Optional[dict] = None,
 ) -> 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.
+    :param spacing: Voxel spacing in (x, y, z).
     :type spacing: tuple
     :param level: Isosurface value for marching cubes. Default is 0.5.
     :type level: float
@@ -886,6 +888,8 @@ def convert_3d_geometry_to_mesh(
     :type apply_decimation: bool
     :param decimation_fraction: Fraction of faces to keep if decimation is applied. Default is 0.5.
     :type decimation_fraction: float
+    :param volume_meta: Metadata of the volume. Used for mesh alignment if geometry lacks specific fields. Default is None.
+    :type volume_meta: dict, optional
     :return: The resulting Trimesh mesh.
     :rtype: trimesh.Trimesh
 
@@ -893,37 +897,40 @@ def convert_3d_geometry_to_mesh(
 
         .. code-block:: python
 
+            volume_header = nrrd.read_header("path/to/volume.nrrd")
             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)
+            mesh = convert_3d_geometry_to_mesh(mask3d, spacing=(1.0, 1.0, 1.0), level=0.7, apply_decimation=True, volume_meta=volume_header)
     """
     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
-    )
+    if volume_meta is None:
+        volume_meta = {}
+
+    space_directions = geometry.space_directions or volume_meta.get("space directions")
+    space_origin = geometry.space_origin or volume_meta.get("space origin")
+
+    verts, faces, normals, _ = measure.marching_cubes(geometry.data, 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))
 
+    if space_directions is not None and space_origin is not None:
+        header = {
+            "space directions": space_directions,
+            "space origin": space_origin,
+        }
+        align_mesh_to_volume(mesh, header)
+
+    # flip x and y axes to match initial mask orientation
+    mesh.apply_transform(np.diag([-1, -1, 1, 1]))
+
+    mesh.fix_normals()
+
     return mesh
 
 
-def export_3d_as_mesh(geometry: Mask3D, output_path: str, kwargs=None):
+def export_3d_as_mesh(geometry: Mask3D, output_path: str, **kwargs):
     """
     Exports the 3D mesh representation of the object to a file in either STL or OBJ format.
 
@@ -936,7 +943,7 @@ def export_3d_as_mesh(geometry: Mask3D, output_path: str, kwargs=None):
         - 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
+        - volume_meta (dict): Metadata of the volume. Used for mesh alignment if geometry lacks specific fields. Default is None.
     :return: None
 
     :Usage example:
@@ -946,14 +953,34 @@ def export_3d_as_mesh(geometry: Mask3D, output_path: str, kwargs=None):
         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})
+        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)
+
+
+def align_mesh_to_volume(mesh: Trimesh, volume_header: dict) -> None:
+    """
+    Transforms the given mesh in-place using spatial information from an NRRD header.
+    The mesh will be tranformed to match the coordinate system defined in the header.
+
+    :param mesh: The mesh object to be transformed. The transformation is applied in-place.
+    :type mesh: Trimesh
+    :param volume_header: The NRRD header containing spatial metadata, including "space directions",
+        "space origin", and "space". Field "space" should be in the format of
+        "right-anterior-superior", "left-anterior-superior", etc.
+    :type volume_header: dict
+    :returns: None
+    :rtype: None
+    """
+    from supervisely.geometry.constants import SPACE_ORIGIN
+    from supervisely.geometry.mask_3d import PointVolume
+
+    if isinstance(volume_header["space origin"], PointVolume):
+        volume_header["space origin"] = volume_header["space origin"].to_json()[SPACE_ORIGIN]
+    transform_mat = matrix_from_nrrd_header(volume_header)
+    mesh.apply_transform(transform_mat)

supervisely/volume_annotation/volume_figure.py

@@ -675,6 +675,6 @@ class VolumeFigure(VideoFigure):
             )
 
         self.geometry.data = new_geometry.data
-        self.geometry._space = new_geometry._space
-        self.geometry._space_origin = new_geometry._space_origin
-        self.geometry._space_directions = new_geometry._space_directions
+        self.geometry.space = new_geometry.space
+        self.geometry.space_origin = new_geometry.space_origin
+        self.geometry.space_directions = new_geometry.space_directions

{supervisely-6.73.367.dist-info → supervisely-6.73.369.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.367
+Version: 6.73.369
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.367.dist-info → supervisely-6.73.369.dist-info}/RECORD

@@ -77,7 +77,7 @@ supervisely/api/video/video_tag_api.py,sha256=wPe1HeJyg9kV1z2UJq6BEte5sKBoPJ2UGA
 supervisely/api/volume/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/api/volume/volume_annotation_api.py,sha256=NOHpLeqHLCeRs1KlXWoG91vtIXdUVTO69wh1ws0VmOQ,22246
 supervisely/api/volume/volume_api.py,sha256=rz_yaBbbTkVeAHmF449zPI8Va_YpDHfHYjXgjGAjMJg,55390
-supervisely/api/volume/volume_figure_api.py,sha256=WwmcMw7o3Nvyv52tzmz64yF-WJI0qzAU-zL2JlD7_w0,26039
+supervisely/api/volume/volume_figure_api.py,sha256=upjIdiiQgOJ6och0KUg0rQo-q-PIipL5RX2V3fOBPvI,25437
 supervisely/api/volume/volume_object_api.py,sha256=F7pLV2MTlBlyN6fEKdxBSUatIMGWSuu8bWj3Hvcageo,2139
 supervisely/api/volume/volume_tag_api.py,sha256=yNGgXz44QBSW2VGlNDOVLqLXnH8Q2fFrxDFb_girYXA,3639
 supervisely/app/__init__.py,sha256=4yW79U_xvo7vjg6-vRhjtt0bO8MxMSx2PD8dMamS9Q8,633
@@ -671,7 +671,7 @@ supervisely/convert/volume/dicom/dicom_helper.py,sha256=OrKlyt1hA5BOXKhE1LF1WxBI
 supervisely/convert/volume/nii/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/volume/nii/nii_planes_volume_converter.py,sha256=dXoBA8AYUOEjLpV2cZJ5n1HDq4_gNhnD__NVsgfc_Qc,14551
 supervisely/convert/volume/nii/nii_volume_converter.py,sha256=BAOKX96-bp6WfTFLrCQNrXk2YhKqIFSU5LJ-auKiAfc,8514
-supervisely/convert/volume/nii/nii_volume_helper.py,sha256=ME_2bgbKZg4IYDFOYqhGRdt7LbwigdF2p6oSgPgPWpw,14132
+supervisely/convert/volume/nii/nii_volume_helper.py,sha256=_FepXNu1RIFuzBOv0aAtrG-J2xN3uyyEMcq6pUD9fsk,14159
 supervisely/convert/volume/sly/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/volume/sly/sly_volume_converter.py,sha256=XmSuxnRqxchG87b244f3h0UHvOt6IkajMquL1drWlCM,5595
 supervisely/convert/volume/sly/sly_volume_helper.py,sha256=gUY0GW3zDMlO2y-zQQG36uoXMrKkKz4-ErM1CDxFCxE,5620
@@ -687,7 +687,7 @@ supervisely/geometry/any_geometry.py,sha256=BOZBsuMYgtkA7cOKp-URjzV9zQkpHuvfp2QP
 supervisely/geometry/bitmap.py,sha256=-tyIXCfgvNn3c7jHs18aq693JR5xdvhfNf6Vmf4952g,21869
 supervisely/geometry/bitmap_base.py,sha256=lNamVL3gZ355oYlIEPc0yC84k1bxuCbUVI0ouaZ_Q4k,13814
 supervisely/geometry/closed_surface_mesh.py,sha256=3ZplCm3Q2bhPcxNmtv2U1UfdezRkC3_BxjwH4yl7wrs,1558
-supervisely/geometry/constants.py,sha256=TPYWGcr2GsbgEtKiZj1L_6wpmbaWU9Qjtlwjg136iVg,788
+supervisely/geometry/constants.py,sha256=6lXpwTTFuswuH9WXMy4akHKshQ5C6fgQhdY-XCdVIMA,842
 supervisely/geometry/conversions.py,sha256=ZY6xWYFWaDA5KDJkcIBBP8LAmMfZwxMeVFfYUYEM6fw,1170
 supervisely/geometry/cuboid.py,sha256=GVHeUrVgfjUjE3PorV_vtge6_thDvvUYI5-9_HZjfWs,21077
 supervisely/geometry/cuboid_2d.py,sha256=enQ-7ZVix5SqC7ZEwxgC0Kvmz9J_wXL7NH3m02snNvc,13444
@@ -697,7 +697,7 @@ supervisely/geometry/graph.py,sha256=kSShcGU4kZgwAbvTrqGzC55qha0nI7M5luiMZSbNx_4
 supervisely/geometry/helpers.py,sha256=2gdYMFWTAr836gVXcp-lkDQs9tdaV0ou33kj3mzJBQA,5132
 supervisely/geometry/image_rotator.py,sha256=wrU8cXEUfuNcmPms2myUV4BpZqz_2oDArsEUFeiTpxs,6888
 supervisely/geometry/main_tests.py,sha256=K3Olsz9igHDW2IfIA5JOpjoE8bZ3ex2PXvVR2ZCDrHU,27199
-supervisely/geometry/mask_3d.py,sha256=MNvAIALV4vmM3VT4oOJR39mhO0rjBd7QHy1nZK8PbiE,20508
+supervisely/geometry/mask_3d.py,sha256=gaac4wUoG-qmpVcttgfAh2WhS3VUWjcdNqw5V-Aa5GA,26720
 supervisely/geometry/multichannel_bitmap.py,sha256=dL0igkOCVZiIZ9LDU7srFLA50XGo4doE-B5_E1uboXM,4968
 supervisely/geometry/point.py,sha256=7ed_Ipd-Ab8ZeqJF5ft0kP9pKVb2iWXCxPuRhMuweMc,13228
 supervisely/geometry/point_3d.py,sha256=0ico0aV4fuKNBVrysDjUy1Cx1S9CEzBlEVE3AsbVd0E,1669
@@ -965,7 +965,7 @@ supervisely/nn/legacy/training/eval_planner.py,sha256=zN9b0_CX7sWGdC8e6riTvD-NOU
 supervisely/nn/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/nn/model/model_api.py,sha256=rIne6ymvL2aVwzSTJMGxAbevE0U-f-WKhDciqaneqRc,9666
 supervisely/nn/model/prediction.py,sha256=N3oO9s3NDiC5CFvW8utfU8rz3bfpCl37Sk4VEBH94Bc,11307
-supervisely/nn/model/prediction_session.py,sha256=Dk8WmO_TKuX9CbzZyzInuoGd4LniLr0oIPGTIHlcHNE,24454
+supervisely/nn/model/prediction_session.py,sha256=sy0FSQaWSmT8i0RkR4J8oIn3Ek4IDVJNBR1Tg4mulkM,25523
 supervisely/nn/tracker/__init__.py,sha256=LiojByb5kGsTQ49lWuboEh7B4JUwM1vfz81J8kJlLYo,337
 supervisely/nn/tracker/tracker.py,sha256=Hs0c07l9IVF86jvjloNAGJsSZAHuNQZf0kVaUHfw3Fs,9694
 supervisely/nn/tracker/bot_sort/__init__.py,sha256=zEs5eT8NQMrM5dtSn7kbI2aWpgS2rvO7aNmrAB8v0VU,632
@@ -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=ekU8gYhSXrTvWISd_HJT7lwtQ9Uh5t7qgVcFwzJ2NOc,29273
+supervisely/volume/volume.py,sha256=jDu_p1zPQxCojjtdJlVVTxfuKgVCYmMSY13Xz99k7pA,30765
 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=pGu6n8_5JkFpir4HTVRf302gGD2EqJ96Gh4M0_236Qg,32047
-supervisely/volume_annotation/volume_figure.py,sha256=TbwqWml7zELQJkrYxTrlblr8SYsmTjYVz-E-3Zd4oxo,25337
+supervisely/volume_annotation/volume_figure.py,sha256=3iFyknF8TlLCMBwgg8gJ26wnNTDTRaw8uEJFVkJGh78,25331
 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=MEk1ky7X8zWe2JgV-j8jXt14e8yu2g1kScU26n9lOMk,9494
@@ -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-6.73.367.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-supervisely-6.73.367.dist-info/METADATA,sha256=-TszuRFHXnXLeiPVh_RfMQ7badBe6_oFpbEtAZCrRAc,35154
-supervisely-6.73.367.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-supervisely-6.73.367.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
-supervisely-6.73.367.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
-supervisely-6.73.367.dist-info/RECORD,,
+supervisely-6.73.369.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+supervisely-6.73.369.dist-info/METADATA,sha256=IkZVEQIZSwqfmNiQuR6FoA7bYffMBsM4Ld9bJBWaOSA,35154
+supervisely-6.73.369.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
+supervisely-6.73.369.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
+supervisely-6.73.369.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
+supervisely-6.73.369.dist-info/RECORD,,