supervisely 6.73.205__py3-none-any.whl → 6.73.206__py3-none-any.whl

supervisely/convert/__init__.py

@@ -29,7 +29,7 @@ from supervisely.convert.image.yolo.yolo_converter import YOLOConverter
 from supervisely.convert.image.multi_view.multi_view import MultiViewImageConverter
 from supervisely.convert.image.label_me.label_me_converter import LabelmeConverter
 from supervisely.convert.image.label_studio.label_studio_converter import LabelStudioConverter
-
+from supervisely.convert.image.high_color.high_color_depth import HighColorDepthImageConverter
 
 
 # Pointcloud
@@ -52,4 +52,3 @@ from supervisely.convert.video.sly.sly_video_converter import SLYVideoConverter
 # Volume
 from supervisely.convert.volume.sly.sly_volume_converter import SLYVolumeConverter
 from supervisely.convert.volume.dicom.dicom_converter import DICOMConverter
-

supervisely/convert/base_converter.py

@@ -31,6 +31,7 @@ class AvailableImageConverters:
     CITYSCAPES = "cityscapes"
     LABEL_ME = "label_me"
     LABEL_STUDIO = "label_studio"
+    HIGH_COLOR_DEPTH = "high_color_depth"
 
 
 class AvailableVideoConverters:

supervisely/convert/converter.py

@@ -3,15 +3,13 @@ from pathlib import Path
 
 from tqdm import tqdm
 
-try:
-    from typing import Literal
-except ImportError:
-    from typing_extensions import Literal
+from typing import Literal, Optional
 
 from supervisely._utils import is_production
 from supervisely.api.api import Api
 from supervisely.app import get_data_dir
 from supervisely.convert.image.csv.csv_converter import CSVConverter
+from supervisely.convert.image.high_color.high_color_depth import HighColorDepthImageConverter
 from supervisely.convert.image.image_converter import ImageConverter
 from supervisely.convert.pointcloud.pointcloud_converter import PointcloudConverter
 from supervisely.convert.pointcloud_episodes.pointcloud_episodes_converter import (
@@ -33,21 +31,17 @@ from supervisely.io.fs import (
 from supervisely.project.project_type import ProjectType
 from supervisely.sly_logger import logger
 from supervisely.task.progress import Progress
+from supervisely.project.project_settings import LabelingInterface
 
 
 class ImportManager:
+
     def __init__(
         self,
         input_data: str,
         project_type: ProjectType,
-        team_id: int = None,
-        labeling_interface: Literal[
-            "default",
-            "multi_view",
-            "multispectral",
-            "images_with_16_color",
-            "medical_imaging_single",
-        ] = "default",
+        team_id: Optional[int] = None,
+        labeling_interface: LabelingInterface = LabelingInterface.DEFAULT,
         upload_as_links: bool = False,
     ):
         self._api = Api.from_env()
@@ -69,7 +63,7 @@ class ImportManager:
 
         self._modality = project_type
         self._converter = self.get_converter()
-        if isinstance(self._converter, CSVConverter):
+        if isinstance(self._converter, (HighColorDepthImageConverter, CSVConverter)):
             self._converter.team_id = self._team_id
 
     @property

supervisely/convert/image/high_color/high_color_depth.py

@@ -0,0 +1,141 @@
+import os
+from collections import defaultdict
+from typing import Dict, Generator, Union
+
+import cv2
+import numpy as np
+import tqdm
+
+from supervisely import ProjectMeta, generate_free_name, is_development, logger
+from supervisely._utils import batched
+from supervisely.annotation.annotation import Annotation
+from supervisely.api.api import Api
+from supervisely.convert.base_converter import AvailableImageConverters
+from supervisely.convert.image.high_color import high_color_helper as helpers
+from supervisely.convert.image.image_converter import ImageConverter
+from supervisely.io.env import task_id as get_task_id
+from supervisely.io.env import team_id as get_team_id
+from supervisely.io.fs import list_files_recursively
+from supervisely.io.json import load_json_file
+from supervisely.project.project_settings import LabelingInterface
+from supervisely.team_files import RECOMMENDED_IMPORT_BACKUP_PATH
+
+
+class HighColorDepthImageConverter(ImageConverter):
+    # allowed_exts = [".png", ".tiff", ".tif", ".bmp", ".exr", ".hdr"]
+    allowed_exts = [".exr", ".hdr"]
+
+    class Item(ImageConverter.Item):
+
+        def __init__(self, *args, **kwargs):
+            super().__init__(*args, **kwargs)
+            self._original_path = None
+
+        @property
+        def original_path(self) -> Union[str, None]:
+            return self._original_path
+
+        @original_path.setter
+        def original_path(self, original_path: str) -> None:
+            self._original_path = original_path
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._team_id = None
+
+    def __str__(self):
+        return AvailableImageConverters.HIGH_COLOR_DEPTH
+
+    def validate_labeling_interface(self) -> bool:
+        """Only multi_view labeling interface can be used to group images on single screen."""
+        return self._labeling_interface in [
+            LabelingInterface.DEFAULT,
+            LabelingInterface.IMAGES_WITH_16_COLOR,
+        ]
+
+    def validate_format(self) -> bool:
+        logger.debug(f"Validating format: {self.__str__()}")
+
+        for image_path in self._find_high_color_depth_image_generator(self._input_data):
+            item = self.Item(image_path)
+            self._items.append(item)
+
+        if self.items_count == 0:
+            logger.debug(f"Not found any images with high color depth in '{self._input_data}'")
+            return False
+
+        return True
+
+    def _find_high_color_depth_image_generator(self, input_data: str) -> Generator[str, None, None]:
+        for image_path in list_files_recursively(input_data, valid_extensions=self.allowed_exts):
+            if self._is_high_color_depth_image(image_path):
+                yield image_path
+
+    def _is_high_color_depth_image(self, image_path: str) -> bool:
+        image = helpers.read_high_color_images(image_path)
+        if image is None:
+            return False
+        return image.dtype in self._supported_depths
+
+    @property
+    def _supported_depths(self):
+        return [np.uint16, np.int16, np.float16, np.float32, np.float64, np.uint32]
+
+    def to_supervisely(self, *args, **kwargs):
+        return None
+
+    def upload_dataset(
+        self,
+        api: Api,
+        dataset_id: int,
+        batch_size: int = 50,
+        log_progress=True,
+    ) -> None:
+        """Upload converted data to Supervisely"""
+        team_id = get_team_id()
+        backup_dir = os.path.join(RECOMMENDED_IMPORT_BACKUP_PATH, str(get_task_id()))
+
+        # progress, progress_cb = None, None
+        # if log_progress:
+        #     progress, progress_cb = self.get_progress(
+        #         len(self.get_items()),
+        #         "Backing up original files and converting images to nrrd...",
+        #     )
+
+        # Back up original files to avoid data loss and convert images to nrrd format
+        with tqdm.tqdm(
+            total=len(self.get_items()),
+            desc="Backing up original files and converting images to nrrd...",
+        ) as pbar:
+            for batch_items in batched(self.get_items(), batch_size=batch_size):
+
+                local_paths, remote_paths = [], []
+
+                for item in batch_items:
+                    local_paths.append(item.path)
+
+                    remote_path = os.path.join(backup_dir, item.name)
+                    remote_paths.append(remote_path)
+
+                    item.original_path = remote_path
+                    image = helpers.read_high_color_images(item.path)
+
+                    orig_item_name = item.name
+                    nrrd_path = item.path + ".nrrd"
+                    nrrd_path = helpers.save_nrrd(image, nrrd_path)
+                    item.path = nrrd_path
+
+                    item_meta = {}
+                    # Add original file path to image meta
+                    item_meta["original_file_path"] = os.path.join(backup_dir, orig_item_name)
+                    if item.meta:
+                        item_meta.update(item.meta)
+                    item.set_meta_data(item_meta)
+
+                api.file.upload_bulk(team_id, local_paths, remote_paths)
+                pbar.update(len(batch_items))
+
+        if log_progress and is_development():
+            pbar.close()
+
+        super().upload_dataset(api, dataset_id, batch_size, log_progress, self.get_items())

supervisely/convert/image/high_color/high_color_helper.py

@@ -0,0 +1,57 @@
+import os
+
+import cv2
+import nrrd
+import numpy as np
+
+from supervisely._utils import generate_free_name
+from supervisely.imaging.image import fliplr
+from supervisely.io.fs import get_file_ext
+
+
+def read_high_color_images(image_path: str) -> np.ndarray:
+    """Read high color images"""
+
+    ext = get_file_ext(image_path).lower()
+    if ext in [".exr", ".hdr"]:
+        os.environ["OPENCV_IO_ENABLE_OPENEXR"] = "1"
+
+        image = cv2.imread(image_path, cv2.IMREAD_ANYCOLOR | cv2.IMREAD_ANYDEPTH)
+        if image.ndim == 3:
+            # Convert the image to grayscale if it has 3 dimensions
+            image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
+            # Normalize the image to 0-255
+            image = cv2.normalize(image, None, 0, 255, cv2.NORM_MINMAX)
+            # Convert to uint16
+            image = image.astype(np.uint16)
+
+    elif ext in [".tiff", ".tif"]:
+        import tifffile
+
+        image = tifffile.imread(image_path)
+    else:
+        image = cv2.imread(image_path)
+
+    return image
+
+
+def save_nrrd(image: np.ndarray, save_path: str) -> str:
+    """Save numpy image as nrrd file"""
+
+    # Ensure the image is 2D
+    if image.ndim != 2:
+        raise ValueError("The image must be 2D to save as NRRD.")
+
+    image = cv2.rotate(image, cv2.ROTATE_90_CLOCKWISE)
+    image = fliplr(image)
+
+    used_names = {os.path.basename(save_path)}
+
+    name = os.path.basename(save_path)
+    while os.path.exists(save_path):
+        name = generate_free_name(used_names, name, True, True)
+        save_path = os.path.join(os.path.dirname(save_path), name)
+
+    nrrd.write(save_path, image)
+
+    return save_path

supervisely/convert/image/image_converter.py

@@ -1,5 +1,5 @@
-import os
 import mimetypes
+import os
 from typing import Dict, List, Optional, Tuple, Union
 
 import cv2
@@ -16,10 +16,10 @@ from supervisely import (
     is_development,
     logger,
 )
-from supervisely.convert.base_converter import BaseConverter
 from supervisely.api.api import ApiContext
+from supervisely.convert.base_converter import BaseConverter
 from supervisely.imaging.image import SUPPORTED_IMG_EXTS, is_valid_ext
-from supervisely.io.fs import get_file_ext, get_file_name, dirs_filter, list_files
+from supervisely.io.fs import dirs_filter, get_file_ext, get_file_name, list_files
 from supervisely.io.json import load_json_file
 from supervisely.project.project_settings import LabelingInterface
 
@@ -31,12 +31,13 @@ class ImageConverter(BaseConverter):
     modality = "images"
 
     class Item(BaseConverter.BaseItem):
+
         def __init__(
             self,
             item_path: str,
             ann_data: Union[str, dict] = None,
             meta_data: Union[str, dict] = None,
-            shape: Union[Tuple, List] = None,
+            shape: Optional[Union[Tuple, List]] = None,
             custom_data: Optional[dict] = None,
         ):
             self._path: str = item_path
@@ -51,7 +52,7 @@ class ImageConverter(BaseConverter):
         def meta(self) -> Union[str, dict]:
             return self._meta_data
 
-        def set_shape(self, shape: Tuple[int, int] = None) -> None:
+        def set_shape(self, shape: Optional[Tuple[int, int]] = None) -> None:
             try:
                 if shape is not None:
                     self._shape = shape
@@ -145,7 +146,14 @@ class ImageConverter(BaseConverter):
                 )
                 item_names.append(name)
                 item_paths.append(item.path)
-                item_metas.append(load_json_file(item.meta) if item.meta else {})
+
+                if isinstance(item.meta, str):  # path to file
+                    item_metas.append(load_json_file(item.meta))
+                elif isinstance(item.meta, dict):
+                    item_metas.append(item.meta)
+                else:
+                    item_metas.append({})
+
                 if ann is not None:
                     anns.append(ann)
 
@@ -199,7 +207,11 @@ class ImageConverter(BaseConverter):
 
         def _is_meta_dir(dirpath: str) -> bool:
             if os.path.basename(dirpath).lower() == "meta":
-                jsons = list_files(dirpath, valid_extensions=[".json"], ignore_valid_extensions_case=True)
+                jsons = list_files(
+                    dirpath,
+                    valid_extensions=[".json"],
+                    ignore_valid_extensions_case=True,
+                )
                 return len(jsons) > 0
             return False
 

supervisely/team_files/__init__.py

@@ -1 +1,5 @@
-from supervisely.team_files.team_files_path import RECOMMENDED_EXPORT_PATH
+from supervisely.team_files.team_files_path import (
+    RECOMMENDED_BACKUP_PATH,
+    RECOMMENDED_EXPORT_PATH,
+    RECOMMENDED_IMPORT_BACKUP_PATH,
+)

supervisely/team_files/team_files_path.py

@@ -1,3 +1,5 @@
 # coding: utf-8
 
 RECOMMENDED_EXPORT_PATH = "/tmp/supervisely/export/"
+RECOMMENDED_BACKUP_PATH = "/system/"
+RECOMMENDED_IMPORT_BACKUP_PATH = RECOMMENDED_BACKUP_PATH + "imports/"

{supervisely-6.73.205.dist-info → supervisely-6.73.206.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: supervisely
-Version: 6.73.205
+Version: 6.73.206
 Summary: Supervisely Python SDK.
 Home-page: https://github.com/supervisely/supervisely
 Author: Supervisely

{supervisely-6.73.205.dist-info → supervisely-6.73.206.dist-info}/RECORD

@@ -553,11 +553,11 @@ supervisely/cli/teamfiles/teamfiles_upload.py,sha256=xnsW2rvdq1e-KGjF1tMBu7Oxh3n
 supervisely/collection/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/collection/key_indexed_collection.py,sha256=x2UVlkprspWhhae9oLUzjTWBoIouiWY9UQSS_MozfH0,37643
 supervisely/collection/str_enum.py,sha256=Zp29yFGvnxC6oJRYNNlXhO2lTSdsriU1wiGHj6ahEJE,1250
-supervisely/convert/__init__.py,sha256=JZJl9I8bqiACgRi6mBdTQA6SwMxQQ82FQIGPgr3v0us,2478
-supervisely/convert/base_converter.py,sha256=dAUjG8ZPNbURZmZ1iy2O7VJlwPMN4zwlEETaL1Q1Wcg,14301
-supervisely/convert/converter.py,sha256=gOdi_2JQClrLkT303IQxKC7FKrUj3TGTyFiI0BZAIeg,8665
+supervisely/convert/__init__.py,sha256=gRTV93OYJPI3FNfy78HO2SfR59qQ3FFKFSy_jw1adJ8,2571
+supervisely/convert/base_converter.py,sha256=F5oCwQZ_w7XlIIQnW-y-2scvA9sC8vCJL2XMP3DtPZg,14343
+supervisely/convert/converter.py,sha256=0F93xZmyprua63C6KxIeh0AbaFab81LiWqlkOVrkaYU,8672
 supervisely/convert/image/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-supervisely/convert/image/image_converter.py,sha256=T53qY5A84TkspZJA4MVXqWmPi6OHt4Igtb0QQyAra5g,9135
+supervisely/convert/image/image_converter.py,sha256=Er-QX6qyVO4p72iJ3ae0YMF9gSfm_SUimoH6id0MIIs,9446
 supervisely/convert/image/image_helper.py,sha256=21cpHiSzHS7brQpP15MAkrGh1lj7pOWh9Z976cObyIw,3145
 supervisely/convert/image/cityscapes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/image/cityscapes/cityscapes_converter.py,sha256=msmsR2W-Xiod06dwn-MzmkbrEmQQqlKh7zyfTrW6YQw,7854
@@ -569,6 +569,9 @@ supervisely/convert/image/coco/coco_helper.py,sha256=ZjHlQIF7RReNROVGo5ZUANGv5iR
 supervisely/convert/image/csv/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/image/csv/csv_converter.py,sha256=iLyc2PAVtlsAq7blnGH4iS1_D7Ai6-4UsdI_RlDVB9Q,11677
 supervisely/convert/image/csv/csv_helper.py,sha256=-nR192IfMU0vTlNRoKXu5FS6tTs9fENqySyeKKyemRs,8409
+supervisely/convert/image/high_color/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+supervisely/convert/image/high_color/high_color_depth.py,sha256=t1LsOnEwhSmXUWxs2K7e_EHit5H0132_UibtFIt1P_w,5276
+supervisely/convert/image/high_color/high_color_helper.py,sha256=bD5Jl6lmKbiNG_8Bpy-WvIYjSJqwdaVmXrHGVZT6o2w,1630
 supervisely/convert/image/label_me/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/convert/image/label_me/label_me_converter.py,sha256=E8epO8METLslVLy51AW7FoZto1jrPSFUZHDwzOnHbTk,3081
 supervisely/convert/image/label_me/label_me_helper.py,sha256=_JO-IS2iiGVcWBHFoC8-LDBW4deJ_Rt4s3Sl5rFjXFg,8279
@@ -909,8 +912,8 @@ supervisely/task/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,
 supervisely/task/paths.py,sha256=Zk9zPhuJuq2eZnb8rLt1ED6sbwX6ikHYRSZQvDP0OBg,1197
 supervisely/task/progress.py,sha256=C7E9rDNnNYJezjmjCJPL1oXqH-LVm15p3OLetvapWaE,27667
 supervisely/task/task_logger.py,sha256=_uDfqEtiwetga6aDAqcTKCKqHjZJSuUXTsHSQFNxAvI,3531
-supervisely/team_files/__init__.py,sha256=3A43gNg_NL9ZHPrmHzOc1CLF6EUlDCfrT-gDcGiNj2E,74
-supervisely/team_files/team_files_path.py,sha256=AN7Ff80RwUtHt58R97MzJWDsYOeUp604yS0NakIUehI,70
+supervisely/team_files/__init__.py,sha256=mtz0Z7eFvsykOcEnSVZ-5bNHsq0_YsNBjZK3qngO-DY,149
+supervisely/team_files/team_files_path.py,sha256=dSqz-bycImQYwAs62TD1zCD1NQdysqCQIBhEVh9EDjw,177
 supervisely/user/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 supervisely/user/user.py,sha256=4GSVIupPAxWjIxZmUtH3Dtms_vGV82-49kM_aaR2gBI,319
 supervisely/video/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -953,9 +956,9 @@ 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-6.73.205.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-supervisely-6.73.205.dist-info/METADATA,sha256=Ie1M5PxEQCoDhgiXb2RL1NiA8tkVmDO5h0QRzbOJ140,33077
-supervisely-6.73.205.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-supervisely-6.73.205.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
-supervisely-6.73.205.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
-supervisely-6.73.205.dist-info/RECORD,,
+supervisely-6.73.206.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+supervisely-6.73.206.dist-info/METADATA,sha256=MQ9ZNLjLwIGBKpZiYf2S-F148rr3-bWJgg55ndrpleo,33077
+supervisely-6.73.206.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+supervisely-6.73.206.dist-info/entry_points.txt,sha256=U96-5Hxrp2ApRjnCoUiUhWMqijqh8zLR03sEhWtAcms,102
+supervisely-6.73.206.dist-info/top_level.txt,sha256=kcFVwb7SXtfqZifrZaSE3owHExX4gcNYe7Q2uoby084,28
+supervisely-6.73.206.dist-info/RECORD,,