Merge branch 'add-vsita2d-to-cellprofiler' of https://github.com/binl…

…iunls/MONAILabel into add-vsita2d-to-cellprofiler

monailabel/tasks/infer/vista.py

@@ -1,4 +1,4 @@
-    def writer(self, data: Dict[str, Any], extension=None, dtype=None) -> Tuple[Any, Any]:
+def writer(self, data: Dict[str, Any], extension=None, dtype=None) -> Tuple[Any, Any]:
         d = dict(data)
         output_dir = d.get("output_dir", "")
         output_ext = d.get("output_ext", "")
@@ -13,4 +13,4 @@ def writer(self, data: Dict[str, Any], extension=None, dtype=None) -> Tuple[Any,
         for key in self.key_iterator(d):
             label = d[key]
             output_filename = f"{basename}{'_' + self.output_postfix if self.output_postfix else ''}{output_ext}"
-            output_filepath = os.path.join(output_dir, output_filename)
+            output_filepath = os.path.join(output_dir, output_filename)

sample-apps/vista/lib/infers/vista.py

@@ -1,8 +1,9 @@
-import os
 import logging
+import os
 from typing import Any, Dict, Tuple
 
 from monai.utils import ImageMetaKey
+
 from monailabel.tasks.infer.bundle import BundleInferTask
 
 logger = logging.getLogger(__name__)
@@ -12,6 +13,7 @@ class VISTAInfer(BundleInferTask):
     """
     This provides Inference Engine for pre-trained VISTA segmentation model.
     """
+
     def writer(self, data: Dict[str, Any], extension=None, dtype=None) -> Tuple[Any, Any]:
         d = dict(data)
         output_dir = self.bundle_config.get_parsed_content("output_dir", instantiate=True)
@@ -28,4 +30,4 @@ def writer(self, data: Dict[str, Any], extension=None, dtype=None) -> Tuple[Any,
             logger.info(f"Reusing the bundle output {output_filepath}.")
             return output_filepath, {}
         else:
-            super().writer(data=data, extension=extension, dtype=dtype)
+            super().writer(data=data, extension=extension, dtype=dtype)

sample-apps/vista/main.py

@@ -13,9 +13,9 @@
 import os
 from typing import Dict
 
+from lib.infers import VISTAInfer
 from monai.transforms import Invertd, SaveImaged
 
-from lib.infers import VISTAInfer
 import monailabel
 from monailabel.interfaces.app import MONAILabelApp
 from monailabel.interfaces.tasks.infer_v2 import InferTask