Fix demo to use new predict location. Also tweak imports.

reginabarzilaygroup · May 28, 2024 · 30b9ff3 · 30b9ff3
1 parent 3526498
commit 30b9ff3
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Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/scripts/run_inference_demo.sh b/scripts/run_inference_demo.sh
@@ -13,7 +13,8 @@ if [ ! -d "$demo_scan_dir" ]; then
   unzip -q sybil_example.zip
 fi
 
-python3 scripts/inference.py \
+# Either python3 sybil/predict.py or sybil-predict (if installed via pip)
+python3 sybil/predict.py \
 --loglevel DEBUG \
 --output-dir demo_prediction \
 --return-attentions \

diff --git a/sybil/__init__.py b/sybil/__init__.py
@@ -22,4 +22,4 @@
 from sybil.utils.visualization import visualize_attentions
 import sybil.utils.logging_utils
 
-__all__ = ["Sybil", "Serie", "visualize_attentions"]
+__all__ = ["Sybil", "Serie", "visualize_attentions", "__version__"]
diff --git a/sybil/predict.py b/sybil/predict.py
@@ -13,11 +13,11 @@
 
 import sybil.utils.logging_utils
 import sybil.datasets.utils
-from sybil import Serie, Sybil, visualize_attentions
+from sybil import Serie, Sybil, visualize_attentions, __version__
 
 
 def _get_parser():
-    description = __doc__ + f"\nVersion: {sybil.__version__}\n"
+    description = __doc__ + f"\nVersion: {__version__}\n"
     parser = argparse.ArgumentParser(description=description)
 
     parser.add_argument(
@@ -69,7 +69,7 @@ def _get_parser():
     parser.add_argument("-l", "--log", "--loglevel", "--log-level",
                         default="INFO", dest="loglevel")
 
-    parser.add_argument("-v", "--version", action="version", version=sybil.__version__)
+    parser.add_argument("-v", "--version", action="version", version=__version__)
 
     return parser
 
@@ -101,6 +101,7 @@ def predict(
         if extension.lower() in {".png", "png"}:
             file_type = "png"
             voxel_spacing = sybil.datasets.utils.VOXEL_SPACING
+            logger.debug(f"Using default voxel spacing: {voxel_spacing}")
     assert file_type in {"dicom", "png"}
     file_type = typing.cast(Literal["dicom", "png"], file_type)