supervisely 6.73.322__tar.gz → 6.73.323__tar.gz

{supervisely-6.73.322/supervisely.egg-info → supervisely-6.73.323}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.322
+Version: 6.73.323
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.322 → supervisely-6.73.323}/supervisely/annotation/annotation.py

@@ -404,7 +404,7 @@ class Annotation:
                 f"Failed to deserialize one of the label from JSON format annotation: \n{repr(e)}"
             )
 
-        custom_data = data.get(AnnotationJsonFields.CUSTOM_DATA, {})
+        custom_data = data.get(AnnotationJsonFields.CUSTOM_DATA, {}) or {}
         prob_labels = None
         if (
             AnnotationJsonFields.PROBABILITY_LABELS in custom_data

{supervisely-6.73.322 → supervisely-6.73.323}/supervisely/convert/base_converter.py

@@ -71,6 +71,7 @@ class AvailablePointcloudEpisodesConverters:
 class AvailableVolumeConverters:
     SLY = "supervisely"
     DICOM = "dicom"
+    NII = "nii"
 
 
 class BaseConverter:

{supervisely-6.73.322 → supervisely-6.73.323}/supervisely/convert/volume/__init__.py

@@ -1,3 +1,4 @@
 # Volume
 from supervisely.convert.volume.sly.sly_volume_converter import SLYVolumeConverter
 from supervisely.convert.volume.dicom.dicom_converter import DICOMConverter
+from supervisely.convert.volume.nii.nii_volume_converter import NiiConverter

supervisely-6.73.323/supervisely/convert/volume/nii/nii_volume_converter.py

@@ -0,0 +1,151 @@
+import os
+from pathlib import Path
+
+import magic
+
+from supervisely import ProjectMeta, generate_free_name, logger
+from supervisely._utils import batched, is_development
+from supervisely.annotation.obj_class import ObjClass
+from supervisely.annotation.obj_class_collection import ObjClassCollection
+from supervisely.api.api import Api
+from supervisely.convert.base_converter import AvailableVolumeConverters
+from supervisely.convert.volume.nii import nii_volume_helper as helper
+from supervisely.convert.volume.volume_converter import VolumeConverter
+from supervisely.geometry.mask_3d import Mask3D
+from supervisely.io.fs import (
+    get_file_ext,
+    get_file_name,
+    get_file_name_with_ext,
+    list_files,
+)
+from supervisely.volume.volume import is_nifti_file
+from supervisely.volume_annotation.volume_annotation import VolumeAnnotation
+from supervisely.volume_annotation.volume_object import VolumeObject
+
+
+class NiiConverter(VolumeConverter):
+
+    def __str__(self) -> str:
+        return AvailableVolumeConverters.NII
+
+    def validate_format(self) -> bool:
+        # create Items
+        converted_dir_name = "converted"
+        # nrrds_dict = {}
+        nifti_dict = {}
+        nifti_dirs = {}
+        for root, _, files in os.walk(self._input_data):
+            dir_name = os.path.basename(root)
+            nifti_dirs[dir_name] = root
+            if converted_dir_name in root:
+                continue
+            for file in files:
+                path = os.path.join(root, file)
+                mime = magic.from_file(path, mime=True)
+                if mime == "application/gzip" or mime == "application/octet-stream":
+                    if is_nifti_file(path):  # is nifti
+                        name = get_file_name(path)
+                        if name.endswith(".nii"):
+                            name = get_file_name(name)
+                        nifti_dict[name] = path
+
+        self._items = []
+        skip_files = []
+        for name, nrrd_path in nifti_dict.items():
+            if name in nifti_dirs:
+                item = self.Item(item_path=nrrd_path)
+                ann_dir = nifti_dirs[name]
+                item.ann_data = list_files(ann_dir, [".nii", ".nii.gz", ".gz"], None, True)
+                self._items.append(item)
+                skip_files.extend(item.ann_data)
+                skip_files.append(nrrd_path)
+
+        for name, nrrd_path in nifti_dict.items():
+            if nrrd_path in skip_files:
+                continue
+            item = self.Item(item_path=nrrd_path)
+            self._items.append(item)
+
+        self._meta = ProjectMeta()
+        return self.items_count > 0
+
+    def upload_dataset(
+        self,
+        api: Api,
+        dataset_id: int,
+        batch_size: int = 1,
+        log_progress=True,
+    ):
+        """Upload converted data to Supervisely"""
+
+        meta, renamed_classes, renamed_tags = self.merge_metas_with_conflicts(api, dataset_id)
+
+        existing_names = set([vol.name for vol in api.volume.get_list(dataset_id)])
+
+        if log_progress:
+            progress, progress_cb = self.get_progress(
+                self.items_count, "Converting and uploading volumes..."
+            )
+        else:
+            progress_cb = None
+
+        converted_dir_name = "converted"
+        converted_dir = os.path.join(self._input_data, converted_dir_name)
+        meta_changed = False
+
+        for batch in batched(self._items, batch_size=batch_size):
+            item_names = []
+            item_paths = []
+
+            for item in batch:
+                # nii_path = item.path
+                item.path = helper.nifti_to_nrrd(item.path, converted_dir)
+                ext = get_file_ext(item.path)
+                if ext.lower() != ext:
+                    new_volume_path = Path(item.path).with_suffix(ext.lower()).as_posix()
+                    os.rename(item.path, new_volume_path)
+                    item.path = new_volume_path
+                item.name = get_file_name_with_ext(item.path)
+                item.name = generate_free_name(
+                    existing_names, item.name, with_ext=True, extend_used_names=True
+                )
+                item_names.append(item.name)
+                item_paths.append(item.path)
+
+                volume_info = api.volume.upload_nrrd_serie_path(
+                    dataset_id, name=item.name, path=item.path
+                )
+
+                if isinstance(item.ann_data, list) and len(item.ann_data) > 0:
+                    objs = []
+                    spatial_figures = []
+                    for ann_path in item.ann_data:
+                        ann_name = get_file_name(ann_path)
+                        if ann_name.endswith(".nii"):
+                            ann_name = get_file_name(ann_name)
+                        for mask, _ in helper.get_annotation_from_nii(ann_path):
+                            obj_class = meta.get_obj_class(ann_name)
+                            if obj_class is None:
+                                obj_class = ObjClass(ann_name, Mask3D)
+                                meta = meta.add_obj_class(obj_class)
+                                meta_changed = True
+                            obj = VolumeObject(obj_class, mask_3d=mask)
+                            spatial_figures.append(obj.figure)
+                            objs.append(obj)
+                    ann = VolumeAnnotation(
+                        volume_info.meta, objects=objs, spatial_figures=spatial_figures
+                    )
+
+                    if meta_changed:
+                        self._meta = meta
+                        _, _, _ = self.merge_metas_with_conflicts(api, dataset_id)
+
+                    api.volume.annotation.append(volume_info.id, ann)
+
+            if log_progress:
+                progress_cb(len(batch))
+
+        if log_progress:
+            if is_development():
+                progress.close()
+        logger.info(f"Dataset ID:{dataset_id} has been successfully uploaded.")

supervisely-6.73.323/supervisely/convert/volume/nii/nii_volume_helper.py

@@ -0,0 +1,38 @@
+import os
+from typing import Generator
+
+import nrrd
+import numpy as np
+
+from supervisely.geometry.mask_3d import Mask3D
+from supervisely.io.fs import ensure_base_path, get_file_ext, get_file_name
+from supervisely.volume.volume import convert_3d_nifti_to_nrrd
+
+
+def nifti_to_nrrd(nii_file_path: str, converted_dir: str) -> str:
+    """Convert NIfTI 3D volume file to NRRD 3D volume file."""
+
+    output_name = get_file_name(nii_file_path)
+    if get_file_ext(output_name) == ".nii":
+        output_name = get_file_name(output_name)
+
+    data, header = convert_3d_nifti_to_nrrd(nii_file_path)
+
+    nrrd_file_path = os.path.join(converted_dir, f"{output_name}.nrrd")
+    ensure_base_path(nrrd_file_path)
+
+    nrrd.write(nrrd_file_path, data, header)
+    return nrrd_file_path
+
+
+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)
+    unique_classes = np.unique(data)
+
+    for class_id in unique_classes:
+        if class_id == 0:
+            continue
+        mask = Mask3D(data == class_id)
+        yield mask, class_id

{supervisely-6.73.322 → supervisely-6.73.323}/supervisely/volume/volume.py

@@ -799,6 +799,49 @@ 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.
+
+    :param path: Path to NIFTI volume file.
+    :type path: str
+    :return: Volume data in NumPy array format and dictionary with metadata (NRRD header).
+    :rtype: Tuple[np.ndarray, dict]
+    :Usage example:
+
+     .. code-block:: python
+
+        import supervisely as sly
+
+        path = "/home/admin/work/volumes/vol_01.nii"
+        data, header = sly.volume.convert_nifti_to_nrrd(path)
+    """
+
+    import nibabel as nib  # pylint: disable=import-error
+
+    orientation_map = {
+        ('R', 'A', 'S'): "right-anterior-superior",
+        ('L', 'P', 'S'): "left-posterior-superior",
+        ('R', 'P', 'I'): "right-posterior-inferior",
+        ('L', 'A', 'I'): "left-anterior-inferior"
+    }
+    nifti = nib.load(path)
+    reordered_to_ras_nifti = nib.as_closest_canonical(nifti)
+    data = reordered_to_ras_nifti.get_fdata()
+    affine = reordered_to_ras_nifti.affine
+    orientation = nib.aff2axcodes(affine)
+    space_directions = affine[:3, :3].tolist()
+    space_origin = affine[:3, 3].tolist()
+    header = {
+        "space": orientation_map.get(orientation, "unknown"),
+        "space directions": space_directions,
+        "space origin": space_origin,
+        "sizes": data.shape,
+        "type": str(data.dtype),
+        "dimension": len(data.shape),
+    }
+    return data, header
+
 
 def is_nifti_file(path: str) -> bool:
     """Check if the file is a NIFTI file.

{supervisely-6.73.322 → supervisely-6.73.323/supervisely.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.322
+Version: 6.73.323
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.322 → supervisely-6.73.323}/supervisely.egg-info/SOURCES.txt

@@ -673,6 +673,9 @@ supervisely/convert/volume/volume_converter.py
 supervisely/convert/volume/dicom/__init__.py
 supervisely/convert/volume/dicom/dicom_converter.py
 supervisely/convert/volume/dicom/dicom_helper.py
+supervisely/convert/volume/nii/__init__.py
+supervisely/convert/volume/nii/nii_volume_converter.py
+supervisely/convert/volume/nii/nii_volume_helper.py
 supervisely/convert/volume/sly/__init__.py
 supervisely/convert/volume/sly/sly_volume_converter.py
 supervisely/convert/volume/sly/sly_volume_helper.py