supervisely 6.73.325__tar.gz → 6.73.326__tar.gz

{supervisely-6.73.325/supervisely.egg-info → supervisely-6.73.326}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.325
+Version: 6.73.326
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.325 → supervisely-6.73.326}/supervisely/convert/volume/nii/nii_planes_volume_converter.py

@@ -8,7 +8,7 @@ from supervisely.convert.volume.nii import nii_volume_helper as helper
 from supervisely.convert.volume.nii.nii_volume_converter import NiiConverter
 from supervisely.convert.volume.volume_converter import VolumeConverter
 from supervisely.geometry.mask_3d import Mask3D
-from supervisely.io.fs import get_file_name
+from supervisely.io.fs import get_file_ext, get_file_name
 from supervisely.volume.volume import is_nifti_file
 from supervisely.volume_annotation.volume_annotation import VolumeAnnotation
 from supervisely.volume_annotation.volume_object import VolumeObject
@@ -34,14 +34,46 @@ class NiiPlaneStructuredConverter(NiiConverter, VolumeConverter):
         ├── 🩻 sag_inference_1.nii class 1
         ├── 🩻 sag_inference_2.nii class 2
         └── 🩻 sag_inference_3.nii class 3
+
+    Additionally, if a TXT file with class color map is present, it will be used to
+    create the classes with names and colors corresponding to the pixel values in the NIfTI files.
+    The TXT file should be structured as follows:
+
+    ```txt
+    1 Femur 255 0 0
+    2 Femoral cartilage 0 255 0
+    3 Tibia 0 0 255
+    4 Tibia cartilage 255 255 0
+    5 Patella 0 255 255
+    6 Patellar cartilage 255 0 255
+    7 Miniscus 175 175 175
+    ```
+    where   1, 2, ... are the pixel values in the NIfTI files
+            Femur, Femoral cartilage, ... are the names of the classes
+            255, 0, 0, ... are the RGB colors of the classes
+    The class name will be used to create the corresponding ObjClass in Supervisely.
     """
 
+    class Item(VolumeConverter.BaseItem):
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, **kwargs)
+            self._is_semantic = False
+
+        @property
+        def is_semantic(self) -> bool:
+            return self._is_semantic
+
+        @is_semantic.setter
+        def is_semantic(self, value: bool):
+            self._is_semantic = value
+
     def validate_format(self) -> bool:
         # create Items
         converted_dir_name = "converted"
 
         volumes_dict = defaultdict(list)
         ann_dict = defaultdict(list)
+        cls_color_map = None
 
         for root, _, files in os.walk(self._input_data):
             if converted_dir_name in root:
@@ -56,17 +88,24 @@ class NiiPlaneStructuredConverter(NiiConverter, VolumeConverter):
                     if prefix not in helper.PlanePrefix.values():
                         continue
                     name = full_name.split("_")[1]
-                    idx = 1 if len(name.split("_")) < 3 else int(name.split("_")[2])
                     if name in helper.LABEL_NAME or name[:-1] in helper.LABEL_NAME:
                         ann_dict[prefix].append(path)
                     else:
                         volumes_dict[prefix].append(path)
+                ext = get_file_ext(path)
+                if ext == ".txt":
+                    cls_color_map = helper.read_cls_color_map(path)
+                    if cls_color_map is None:
+                        logger.warning(f"Failed to read class color map from {path}.")
 
         self._items = []
         for prefix, paths in volumes_dict.items():
             if len(paths) == 1:
                 item = self.Item(item_path=paths[0])
-                item.ann_data = ann_dict.get(prefix)
+                item.ann_data = ann_dict.get(prefix, [])
+                item.is_semantic = len(item.ann_data) == 1
+                if cls_color_map is not None:
+                    item.custom_data["cls_color_map"] = cls_color_map
                 self._items.append(item)
             elif len(paths) > 1:
                 logger.info(
@@ -79,6 +118,9 @@ class NiiPlaneStructuredConverter(NiiConverter, VolumeConverter):
                         if Path(ann_path).parent == Path(path).parent:
                             possible_ann_paths.append(ann_path)
                     item.ann_data = possible_ann_paths
+                    item.is_semantic = len(possible_ann_paths) == 1
+                    if cls_color_map is not None:
+                        item.custom_data["cls_color_map"] = cls_color_map
                     self._items.append(item)
         self._meta = ProjectMeta()
         return self.items_count > 0
@@ -96,12 +138,18 @@ class NiiPlaneStructuredConverter(NiiConverter, VolumeConverter):
             objs = []
             spatial_figures = []
             for idx, ann_path in enumerate(item.ann_data, start=1):
-                for mask, _ in helper.get_annotation_from_nii(ann_path):
-                    class_name = f"Segment_{idx}"
+                for mask, pixel_id in helper.get_annotation_from_nii(ann_path):
+                    class_id = pixel_id if item.is_semantic else idx
+                    class_name = f"Segment_{class_id}"
+                    color = None
+                    if item.custom_data.get("cls_color_map") is not None:
+                        class_info = item.custom_data["cls_color_map"].get(class_id)
+                        if class_info is not None:
+                            class_name, color = class_info
                     class_name = renamed_classes.get(class_name, class_name)
                     obj_class = meta.get_obj_class(class_name)
                     if obj_class is None:
-                        obj_class = ObjClass(class_name, Mask3D)
+                        obj_class = ObjClass(class_name, Mask3D, color)
                         meta = meta.add_obj_class(obj_class)
                         self._meta_changed = True
                         self._meta = meta

{supervisely-6.73.325 → supervisely-6.73.326}/supervisely/convert/volume/nii/nii_volume_converter.py

@@ -169,11 +169,11 @@ class NiiConverter(VolumeConverter):
             item_paths = []
 
             for item in batch:
-                if self._upload_as_links:
-                    remote_path = self.remote_files_map.get(item.path)
-                    if remote_path is not None:
-                        item.custom_data = {"remote_path": remote_path}
-                # nii_path = item.path
+                # if self._upload_as_links:
+                #     remote_path = self.remote_files_map.get(item.path)
+                #     if remote_path is not None:
+                #         item.custom_data = {"remote_path": remote_path}
+
                 item.path = helper.nifti_to_nrrd(item.path, converted_dir)
                 ext = get_file_ext(item.path)
                 if ext.lower() != ext:
@@ -195,8 +195,8 @@ class NiiConverter(VolumeConverter):
                     leave=True if progress_cb is None else False,
                     position=1,
                 )
-                if item.custom_data is not None:
-                    volume_meta.update(item.custom_data)
+                # if item.custom_data is not None:
+                #     volume_meta.update(item.custom_data)
                 api.volume.upload_np(dataset_id, item.name, volume_np, volume_meta, progress_nrrd)
                 info = api.volume.get_info_by_name(dataset_id, item.name)
                 item.volume_meta = info.meta

supervisely-6.73.326/supervisely/convert/volume/nii/nii_volume_helper.py

@@ -0,0 +1,99 @@
+import os
+from typing import Generator
+
+import nrrd
+import numpy as np
+
+from supervisely.collection.str_enum import StrEnum
+from supervisely.geometry.mask_3d import Mask3D
+from supervisely.io.fs import ensure_base_path, get_file_ext, get_file_name
+from supervisely.sly_logger import logger
+from supervisely.volume.volume import convert_3d_nifti_to_nrrd
+
+VOLUME_NAME = "anatomic"
+LABEL_NAME = ["inference", "label", "annotation", "mask", "segmentation"]
+
+
+class PlanePrefix(str, StrEnum):
+    """Prefix for plane names."""
+
+    CORONAL = "cor"
+    SAGITTAL = "sag"
+    AXIAL = "axl"
+
+
+def read_cls_color_map(path: str) -> dict:
+    """Read class color map from TXT file.
+
+    ```txt
+    1 Femur 255 0 0
+    2 Femoral cartilage 0 255 0
+    3 Tibia 0 0 255
+    4 Tibia cartilage 255 255 0
+    5 Patella 0 255 255
+    6 Patellar cartilage 255 0 255
+    7 Miniscus 175 175 175
+    ```
+    """
+
+    cls_color_map = {}
+    if not os.path.exists(path):
+        return None
+    try:
+        with open(path, "r") as file:
+            for line in file:
+                parts = line.strip().split()
+                color = None
+                try:
+                    color = list(map(int, parts[-3:]))
+                except:
+                    pass
+                cls_id = int(parts[0])
+                if not color:
+                    cls_name = " ".join(parts[1:])
+                else:
+                    cls_name = " ".join(parts[1:-3])
+                if cls_id in cls_color_map:
+                    logger.warning(f"Duplicate class ID {cls_id} found in color map.")
+                if cls_name in cls_color_map:
+                    logger.warning(f"Duplicate class name {cls_name} found in color map.")
+                if len(color) != 3:
+                    logger.warning(f"Invalid color format for class {cls_name}. Expected 3 values.")
+                if any(c < 0 or c > 255 for c in color):
+                    logger.warning(
+                        f"Invalid color value for class {cls_name}. Expected values between 0 and 255."
+                    )
+                cls_color_map[cls_id] = (cls_name, color)
+    except Exception as e:
+        logger.warning(f"Failed to read class color map from {path}: {e}")
+        return None
+    return cls_color_map
+
+
+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-6.73.325 → supervisely-6.73.326}/supervisely/volume/volume.py

@@ -816,30 +816,28 @@ def convert_3d_nifti_to_nrrd(path: str) -> Tuple[np.ndarray, dict]:
         path = "/home/admin/work/volumes/vol_01.nii"
         data, header = sly.volume.convert_nifti_to_nrrd(path)
     """
+    import SimpleITK as sitk
 
-    import nibabel as nib  # pylint: disable=import-error
+    nifti_image = sitk.ReadImage(path)
+    nifti_image = _sitk_image_orient_ras(nifti_image)
+    data = sitk.GetArrayFromImage(nifti_image)
+    data = np.transpose(data, (2, 1, 0))
+
+    direction = np.array(nifti_image.GetDirection()).reshape(3, 3)
+    spacing = np.array(nifti_image.GetSpacing())
+    origin = np.array(nifti_image.GetOrigin())
+
+    space_directions = (direction.T * spacing[:, None]).tolist()
 
-    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),
-    }
+            "dimension": 3,
+            "space": "right-anterior-superior",
+            "sizes": list(data.shape),
+            "space directions": space_directions,
+            "endian": "little",
+            "encoding": "gzip",
+            "space origin": origin
+        }
     return data, header
 
 

{supervisely-6.73.325 → supervisely-6.73.326/supervisely.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.325
+Version: 6.73.326
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

supervisely-6.73.325/supervisely/convert/volume/nii/nii_volume_helper.py

@@ -1,50 +0,0 @@
-import os
-from typing import Generator
-
-import nrrd
-import numpy as np
-
-from supervisely.collection.str_enum import StrEnum
-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
-
-VOLUME_NAME = "anatomic"
-LABEL_NAME = ["inference", "label", "annotation", "mask", "segmentation"]
-
-
-class PlanePrefix(str, StrEnum):
-    """Prefix for plane names."""
-
-    CORONAL = "cor"
-    SAGITTAL = "sag"
-    AXIAL = "axl"
-
-
-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