wip

Author: imagejan

pyproject.toml

@@ -31,6 +31,7 @@ dependencies = [
   "confuse",
   "rich",
   "scikit-image",
+  "scyjava",
   "tqdm",
   "typer"
 ]

src/faim_wako_searchfirst/segment.py

@@ -72,3 +72,25 @@ def cellpose(
         **kwargs,
     )
     return mask
+
+
+def weka_classifier(
+    img,
+    classifier_path: Path,
+    logger=logging,
+):
+    """Apply a classifier.model file.
+
+    Use Trainable Weka Segmentation (via pyimagej)
+    to apply a trained classifier to the input image.
+    """
+    # initialize imagej
+    import imagej
+
+    ij = imagej.init("sc.fiji:fiji:2.15.0")
+    assert ij is not None
+    # convert img to_java
+    # call WekaSegmentation API
+    # get result imp
+    # convert imp from_java
+    return ij.getVersion()

tests/test_weka_classifier.py

@@ -0,0 +1,11 @@
+# SPDX-FileCopyrightText: 2024 Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland)
+#
+# SPDX-License-Identifier: MIT
+"""Test segment.weka_classifier functionality."""
+from faim_wako_searchfirst.segment import weka_classifier
+
+
+def test_weka_classifier():
+    """Directly call weka_classifier."""
+    version = weka_classifier(None, None)
+    assert version == "2.15.0/1.54f"