supervisely 6.73.397__py3-none-any.whl → 6.73.398__py3-none-any.whl

supervisely/convert/pointcloud/pointcloud_converter.py

@@ -246,6 +246,7 @@ class PointcloudConverter(BaseConverter):
                     ) or dir_name.endswith("_pcd"):
                         rimg_ann_dict[file] = full_path
                 elif imghdr.what(full_path):
+                    dir_name = os.path.basename(root)
                     if dir_name not in rimg_dict:
                         rimg_dict[dir_name] = []
                     rimg_dict[dir_name].append(full_path)

supervisely/convert/volume/nii/nii_planes_volume_converter.py

@@ -164,7 +164,7 @@ class NiiPlaneStructuredConverter(NiiConverter, VolumeConverter):
                             item.custom_data["scores"] = scores
                         except Exception as e:
                             logger.warning(f"Failed to read scores from {scores_paths[0]}: {e}")
-                    item.is_semantic = len(possible_ann_paths) == 1
+                    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)
@@ -226,6 +226,7 @@ class NiiPlaneStructuredAnnotationConverter(NiiConverter, VolumeConverter):
         def __init__(self, *args, **kwargs):
             super().__init__(*args, **kwargs)
             self._is_semantic = False
+            self._is_scores = False
             self.volume_meta = None
 
         @property
@@ -236,6 +237,14 @@ class NiiPlaneStructuredAnnotationConverter(NiiConverter, VolumeConverter):
         def is_semantic(self, value: bool):
             self._is_semantic = value
 
+        @property
+        def is_scores(self) -> bool:
+            return self._is_scores
+
+        @is_scores.setter
+        def is_scores(self, value: bool):
+            self._is_scores = value
+
         def create_empty_annotation(self):
             return VolumeAnnotation(self.volume_meta)
 
@@ -274,17 +283,22 @@ class NiiPlaneStructuredAnnotationConverter(NiiConverter, VolumeConverter):
             for file in files:
                 path = os.path.join(root, file)
                 name_parts = helper.parse_name_parts(file)
-                if is_nii(file):
-                    if name_parts is None or not name_parts.is_ann:
-                        continue
-                    try:
-                        nii = load(path)
-                    except filebasedimages.ImageFileError:
-                        logger.warning(f"Failed to load NIfTI file: {path}")
-                        continue
+                if name_parts is None:
+                    continue
+                if is_nii(file) or name_parts.type == helper.SCORE_NAME:
                     item = self.Item(item_path=None, ann_data=path)
-                    item.set_shape(nii.shape)
                     item.custom_data["name_parts"] = name_parts
+                    if name_parts.is_ann:
+                        try:
+                            nii = load(path)
+                        except filebasedimages.ImageFileError:
+                            logger.warning(f"Failed to load NIfTI file: {path}")
+                            continue
+                        item.set_shape(nii.shape)
+                    elif name_parts.type == helper.SCORE_NAME:
+                        item.is_scores = True
+                        scores = helper.get_scores_from_table(path, name_parts.plane)
+                        item.custom_data["scores"] = scores
                     if cls_color_map is not None:
                         item.custom_data["cls_color_map"] = cls_color_map
                     self._items.append(item)
@@ -293,6 +307,13 @@ class NiiPlaneStructuredAnnotationConverter(NiiConverter, VolumeConverter):
         if cls_color_map is not None:
             obj_classes = [ObjClass(name, Mask3D, color) for name, color in cls_color_map.values()]
 
+        for item in self._items:
+            name_parts = item.custom_data.get("name_parts")
+            if item.is_scores:
+                continue
+            if name_parts.ending_idx is None:
+                item.is_semantic = True
+
         self._meta = ProjectMeta(obj_classes=obj_classes)
         return len(self._items) > 0
 
@@ -369,20 +390,65 @@ class NiiPlaneStructuredAnnotationConverter(NiiConverter, VolumeConverter):
         else:
             progress_cb = None
 
-        for item, volume in matched_dict.items():
+        volumeids_to_objects = defaultdict(list)
+
+        for item, volume in sorted(matched_dict.items(), key=lambda pair: pair[0].is_scores):
             item.volume_meta = volume.meta
-            ann = self.to_supervisely(item, meta, renamed_classes, None)
-            if self._meta_changed:
-                meta, renamed_classes, _ = self.merge_metas_with_conflicts(api, dataset_id)
-                self._meta_changed = False
-            api.volume.annotation.append(volume.id, ann, volume_info=volume)
+            if not item.is_scores:
+                ann = self.to_supervisely(item, meta, renamed_classes, None)
+                if self._meta_changed:
+                    meta, renamed_classes, _ = self.merge_metas_with_conflicts(api, dataset_id)
+                    self._meta_changed = False
+                api.volume.annotation.append(volume.id, ann, volume_info=volume)
+            else:
+                class_id_to_pixel_value = helper.get_class_id_to_pixel_value_map(meta)
+                scores = item.custom_data.get("scores", {})
+                if not scores:
+                    logger.warning(f"No scores found for {item.ann_data}. Skipping.")
+                    continue
+
+                if volume.dataset_id not in volumeids_to_objects:
+                    for obj in api.volume.object.get_list(volume.dataset_id):
+                        volumeids_to_objects[obj.entity_id].append(obj)
+
+                obj_id_to_class_id = {
+                    obj.id: obj.class_id for obj in volumeids_to_objects[volume.id]
+                }
+                if not obj_id_to_class_id:
+                    logger.warning(
+                        f"No objects found for volume {volume.id}. Skipping figure updates."
+                    )
+                    continue
+
+                volume_figure_dict = api.volume.figure.download(
+                    volume.dataset_id, [volume.id], skip_geometry=True
+                )
+                figures_list = volume_figure_dict.get(volume.id, [])
+                for figure in figures_list:
+                    class_id = obj_id_to_class_id.get(figure.object_id, None)
+                    if class_id is None:
+                        logger.warning(
+                            f"Class ID for figure (id: {figure.id}) not found in volume objects. Skipping figure update.",
+                            extra={
+                                "obj_id_to_class_id": obj_id_to_class_id,
+                                "object_id": figure.object_id,
+                            },
+                        )
+                        continue
+                    pixel_value = class_id_to_pixel_value.get(class_id, None)
+                    if pixel_value is None:
+                        logger.warning(
+                            f"Pixel value for class ID {class_id} not found in meta. Skipping figure update."
+                        )
+                        continue
+                    figure_custom_data = scores.get(pixel_value, {})
+                    if figure_custom_data:
+                        api.volume.figure.update_custom_data(figure.id, figure_custom_data)
+                        logger.debug(
+                            f"Updated figure {figure.id} with custom data: {figure_custom_data}"
+                        )
             progress_cb(1) if log_progress else None
 
-        res_ds_info = api.dataset.get_info_by_id(dataset_id)
-        if res_ds_info.items_count == 0:
-            logger.info("Resulting dataset is empty. Removing it.")
-            api.dataset.remove(dataset_id)
-
         if log_progress:
             if is_development():
                 progress.close()

supervisely/convert/volume/nii/nii_volume_helper.py

@@ -10,10 +10,12 @@ from supervisely import Api
 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.project.project_meta import ProjectMeta
 from supervisely.sly_logger import logger
 from supervisely.volume.volume import convert_3d_nifti_to_nrrd
 
 VOLUME_NAME = "anatomic"
+SCORE_NAME = "score"
 LABEL_NAME = ["inference", "label", "annotation", "mask", "segmentation"]
 MASK_PIXEL_VALUE = "Mask pixel value: "
 
@@ -172,20 +174,62 @@ def get_scores_from_table(csv_file_path: str, plane: str) -> dict:
     return result
 
 
+def _find_pixel_values(descr: str) -> int:
+    """
+    Find the pixel value in the description string.
+    """
+    lines = descr.split("\n")
+    for line in lines:
+        if line.strip().startswith(MASK_PIXEL_VALUE):
+            try:
+                value_part = line.strip().split(MASK_PIXEL_VALUE)[1]
+                return int(value_part.strip())
+            except (IndexError, ValueError):
+                continue
+    return None
+
+
+def get_class_id_to_pixel_value_map(meta: ProjectMeta) -> dict:
+    class_id_to_pixel_value = {}
+    for obj_class in meta.obj_classes.items():
+        pixel_value = _find_pixel_values(obj_class.description)
+        if pixel_value is not None:
+            class_id_to_pixel_value[obj_class.sly_id] = pixel_value
+        elif "Segment_" in obj_class.name:
+            try:
+                pixel_value = int(obj_class.name.split("_")[-1])
+                class_id_to_pixel_value[obj_class.sly_id] = pixel_value
+            except (ValueError, IndexError):
+                logger.warning(
+                    f"Failed to parse pixel value from class name: {obj_class.name}. "
+                    "Please ensure the class name ends with a valid integer."
+                )
+        else:
+            logger.warning(
+                f"Class {obj_class.name} does not have a pixel value defined in its description. "
+                "Please update the class description to include 'Mask pixel value: <value>'."
+            )
+    return class_id_to_pixel_value
+
+
 class AnnotationMatcher:
     def __init__(self, items, dataset_id):
-        self._items = items
-        self._ds_id = dataset_id
         self._ann_paths = defaultdict(list)
         self._item_by_filename = {}
         self._item_by_path = {}
 
-        self.set_items(items)
+        self.items = items
+        self._ds_id = dataset_id
 
         self._project_wide = False
         self._volumes = None
 
-    def set_items(self, items):
+    @property
+    def items(self):
+        return self._items
+
+    @items.setter
+    def items(self, items):
         self._items = items
         self._ann_paths.clear()
         self._item_by_filename.clear()
@@ -202,13 +246,13 @@ class AnnotationMatcher:
 
     def get_volumes(self, api: Api):
         dataset_info = api.dataset.get_info_by_id(self._ds_id)
-        datasets = {dataset_info.name: dataset_info}
-        project_id = dataset_info.project_id
-        if dataset_info.items_count > 0 and len(self._ann_paths.keys()) == 1:
+        if dataset_info.items_count > 0:
+            datasets = {dataset_info.name: dataset_info}
             self._project_wide = False
         else:
             datasets = {
-                dsinfo.name: dsinfo for dsinfo in api.dataset.get_list(project_id, recursive=True)
+                dsinfo.name: dsinfo
+                for dsinfo in api.dataset.get_list(dataset_info.project_id, recursive=True)
             }
             self._project_wide = True
 
@@ -270,6 +314,8 @@ class AnnotationMatcher:
         # items_to_remove = []
         for item, volume in item_to_volume.items():
             volume_shape = tuple(volume.file_meta["sizes"])
+            if item.shape is None:
+                continue
             if item.shape != volume_shape:
                 logger.warning(f"Volume shape mismatch: {item.shape} != {volume_shape}")
                 # items_to_remove.append(item)
@@ -363,27 +409,26 @@ def parse_name_parts(full_name: str) -> NameParts:
     type = None
     is_ann = False
     if VOLUME_NAME in full_name:
-        type = "anatomic"
-    elif any(part in full_name for part in LABEL_NAME):
+        type = VOLUME_NAME
+    elif SCORE_NAME in full_name and full_name.endswith(".csv"):
+        type = SCORE_NAME
+    else:
         type = next((part for part in LABEL_NAME if part in full_name), None)
         is_ann = type is not None
-    elif "score" in name_no_ext or get_file_ext(full_name) == ".csv":
-        type = "score"
 
     if type is None:
         return
 
     plane = None
+    tokens = name_no_ext.lower().split("_")
     for part in PlanePrefix.values():
-        if part in name:
+        if part in tokens:
             plane = part
             break
 
     if plane is None:
         return
 
-    is_ann = any(part in name.lower() for part in LABEL_NAME)
-
     patient_uuid = None
     case_uuid = None
 

supervisely/io/exception_handlers.py

@@ -9,7 +9,7 @@ from typing import Callable, Dict, List, Optional, Union
 from requests.exceptions import HTTPError, RetryError
 from rich.console import Console
 
-from supervisely import is_development, is_community
+from supervisely import is_community, is_development
 from supervisely.app import DialogWindowError
 from supervisely.sly_logger import EventType, logger
 
@@ -250,7 +250,9 @@ class ErrorHandler:
             def __init__(self, exception: Exception, stack: List[traceback.FrameSummary] = None):
                 self.code = 2004
                 self.title = "Image files size limit exceeded"
-                self.message = "The given image file size is too large (more than 1 GB) for Community Edition."
+                self.message = (
+                    "The given image file size is too large (more than 1 GB) for Community Edition."
+                )
 
                 super().__init__(
                     exception,
@@ -290,12 +292,14 @@ class ErrorHandler:
 
         class OutOfMemory(HandleException):
             def __init__(self, exception: Exception, stack: List[traceback.FrameSummary] = None):
-                device_prefix = "GPU memory" if any([s in exception.args[0] for s in ["CUDA", "cuda", "GPU"]]) else "memory"
+                device_prefix = (
+                    "GPU memory"
+                    if any([s in exception.args[0] for s in ["CUDA", "cuda", "GPU"]])
+                    else "memory"
+                )
                 self.code = 2007
                 self.title = f"Out of {device_prefix} on the computer where the agent is deployed"
-                self.message = (
-                    "Please, check your agent's memory usage, reduce batch size or use a device with more memory capacity."
-                )
+                self.message = "Please, check your agent's memory usage, reduce batch size or use a device with more memory capacity."
 
                 super().__init__(
                     exception,
@@ -471,7 +475,9 @@ class ErrorHandler:
             def __init__(self, exception: Exception, stack: List[traceback.FrameSummary] = None):
                 self.code = 2019
                 self.title = "Upload remote images is only available for PRO teams"
-                self.message = "Please, upgrade plan to upload remote images: https://supervisely.com/pricing/"
+                self.message = (
+                    "Please, upgrade plan to upload remote images: https://supervisely.com/pricing/"
+                )
 
                 super().__init__(
                     exception,
@@ -485,7 +491,9 @@ class ErrorHandler:
             def __init__(self, exception: Exception, stack: List[traceback.FrameSummary] = None):
                 self.code = 2020
                 self.title = "Upload remote videos is only available for PRO teams"
-                self.message = "Please, upgrade plan to upload remote videos: https://supervisely.com/pricing/"
+                self.message = (
+                    "Please, upgrade plan to upload remote videos: https://supervisely.com/pricing/"
+                )
 
                 super().__init__(
                     exception,
@@ -681,6 +689,7 @@ ERROR_PATTERNS = {
         r".*images\.bulk\.upload.*FileSize.*\"sizeLimit\":1073741824.*": ErrorHandler.API.ImageFilesSizeTooLarge,
         r".*videos\.bulk\.upload.*FileSize.*sizeLimit\":314572800.*": ErrorHandler.API.VideoFilesSizeTooLarge,
         r".*images\.bulk\.upload.*FileSize.*\"sizeLimit\":157286400.*": ErrorHandler.API.VolumeFilesSizeTooLarge,
+        r".*images\.bulk\.upload.*FileSize.*\"sizeLimit\":\"25mb\".*": ErrorHandler.API.VolumeFilesSizeTooLarge,
         r".*Dataset with datasetId.*is either archived, doesn't exist or you don't have enough permissions to access.*": ErrorHandler.API.DatasetNotFound,
         r".*Project with projectId.*is either archived, doesn't exist or you don't have enough permissions to access.*": ErrorHandler.API.ProjectNotFound,
         r".*api\.task\.set_field.*": ErrorHandler.API.AppSetFieldError,

supervisely/project/volume_project.py

@@ -477,8 +477,9 @@ def download_volume_project(
                         mesh_ids.append(figure_id)
                         figure_path = dataset_fs.get_interpolation_path(volume_name, sf)
                         mesh_paths.append(figure_path)
-
-                figs = api.volume.figure.download(dataset.id, [volume_id], skip_geometry=True)[volume_id]
+                
+                figs = api.volume.figure.download(dataset.id, [volume_id], skip_geometry=True)
+                figs = figs.get(volume_id, {})
                 figs_ids_map = {fig.id: fig for fig in figs}
                 for ann_fig in ann.figures + ann.spatial_figures:
                     fig = figs_ids_map.get(ann_fig.geometry.sly_id)

{supervisely-6.73.397.dist-info → supervisely-6.73.398.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.397
+Version: 6.73.398
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.397.dist-info → supervisely-6.73.398.dist-info}/RECORD

@@ -623,7 +623,7 @@ supervisely/convert/image/yolo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5
 supervisely/convert/image/yolo/yolo_converter.py,sha256=Wn5dR05y4SEPONcaxWr9ofnbvbf-SbRZN0fkksk5Dps,11391
 supervisely/convert/image/yolo/yolo_helper.py,sha256=5b0ShsVlqikA071VT8AiRW_079_WD6pdB5Bx3OU12Bw,25989
 supervisely/convert/pointcloud/__init__.py,sha256=WPeIpPoTWDIKAa0lF6t2SMUhFNZ0l-vKujf6yD6w7SA,589
-supervisely/convert/pointcloud/pointcloud_converter.py,sha256=X00tYXdIsSwaLHYX5xqqizQy30MjuhmVjhbrhtLnBjU,12078
+supervisely/convert/pointcloud/pointcloud_converter.py,sha256=-FQ-YTXu-ywrJ0yBfg0tBV_t8SB6kKD4MlqkdAZMWEA,12132
 supervisely/convert/pointcloud/bag/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/pointcloud/bag/bag_converter.py,sha256=WWd6A2hS7H4MRgtLdJ-yYgmNU-Wk2eycl6LTTJM2GKQ,11391
 supervisely/convert/pointcloud/bag/bag_helper.py,sha256=2TFe49isZTxMhya-PApqLPxrvGnvRFMBc_--BwyCpWU,4284
@@ -674,9 +674,9 @@ supervisely/convert/volume/dicom/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRk
 supervisely/convert/volume/dicom/dicom_converter.py,sha256=Hw4RxU_qvllk6M26udZE6G-m1RWR8-VVPcEPwFlqrVg,3354
 supervisely/convert/volume/dicom/dicom_helper.py,sha256=OrKlyt1hA5BOXKhE1LF1WxBIv3b6t96xRras4OSAuNM,2891
 supervisely/convert/volume/nii/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-supervisely/convert/volume/nii/nii_planes_volume_converter.py,sha256=QTdmtqLrRBFSa0IZKhAnFkLl1J3nayzQQDwpglvEN64,16915
+supervisely/convert/volume/nii/nii_planes_volume_converter.py,sha256=XQ5o7mg3OJ9UO-wM14O718TIkVXeXDAz-lJDV--0UE8,20043
 supervisely/convert/volume/nii/nii_volume_converter.py,sha256=gR1_dfUf0L-K49B8qVHF7DiiDKDmxUQKKSPLdlqoYC4,8691
-supervisely/convert/volume/nii/nii_volume_helper.py,sha256=nkfTG2NGmnf4AfrZ0lULSHaUBx1G24NJUO_5FNejolE,16032
+supervisely/convert/volume/nii/nii_volume_helper.py,sha256=oBALqwQDBuUwN9UHQP7PM-NyoH41d2FDickMSkVtksI,17597
 supervisely/convert/volume/sly/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/volume/sly/sly_volume_converter.py,sha256=TI1i_aVYFFoqLHqVzCXnFeR6xobhGcgN_xWFZcpRqbE,6730
 supervisely/convert/volume/sly/sly_volume_helper.py,sha256=gUY0GW3zDMlO2y-zQQG36uoXMrKkKz4-ErM1CDxFCxE,5620
@@ -724,7 +724,7 @@ supervisely/imaging/image.py,sha256=1KNc4qRbP9OlI4Yta07Kc2ohAgSBJ_9alF9Jag74w30,
 supervisely/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/io/docker_utils.py,sha256=hb_HXGM8IYB0PF-nD7NxMwaHgzaxIFxofsUzQ_RCUZI,7935
 supervisely/io/env.py,sha256=l-Xkil6FVxMP8FmnjF4H4p3RJQ3AoBd0OUjZHA2QVTc,21193
-supervisely/io/exception_handlers.py,sha256=_nAgMFeE94bCxEvWakR82hMtdOJUyn7Gc7OymMxI9WI,36484
+supervisely/io/exception_handlers.py,sha256=22LPlLgyq59DnrhpaFrbGBYJE7uxO64VTZjsPJC0PLE,36757
 supervisely/io/fs.py,sha256=pzNAK5fbT3G-7PKRY5oYcOPjgXeZ9x5Dyry7fzzZsr8,63604
 supervisely/io/fs_cache.py,sha256=985gvBGzveLcDudgz10E4EWVjP9jxdU1Pa0GFfCBoCA,6520
 supervisely/io/github_utils.py,sha256=jGmvQJ5bjtACuSFABzrxL0jJdh14SezovrHp8T-9y8g,1779
@@ -1047,7 +1047,7 @@ supervisely/project/project_type.py,sha256=7mQ7zg6r7Bm2oFn5aR8n_PeLqMmOaPZd6ph7Z
 supervisely/project/readme_template.md,sha256=SFAfNF_uxSBJJ45A8qZ0MRuHnwSE4Gu_Z7UJqPMgRzg,9254
 supervisely/project/upload.py,sha256=ys95MXFh-rtq-EAsNsiRi3wgbFUCEsY2un3_bd5hJkE,3753
 supervisely/project/video_project.py,sha256=7i8__1zoU2Uryicjfa2_7p3JLnSPTv14ctLJPQGgnPY,66315
-supervisely/project/volume_project.py,sha256=BhFDE6GTxbhuJ-y4Bum-70bjRJ0FiIowkMru7PZ-0mk,23548
+supervisely/project/volume_project.py,sha256=yHJ2KTPhkqxlSHkafXQqyJqDgl8KHkx2fKkkkgw86qg,23600
 supervisely/pyscripts_utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/pyscripts_utils/utils.py,sha256=scEwHJvHRQa8NHIOn2eTwH6-Zc8CGdLoxM-WzH9jcRo,314
 supervisely/report/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -1114,9 +1114,9 @@ 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-6.73.397.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
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