From 0d347b7967a299abdfb8744d68baaeb2295cfa61 Mon Sep 17 00:00:00 2001
From: "w.pomp" <w.pomp@nki.nl>
Date: Tue, 14 Jul 2026 12:49:16 +0200
Subject: [PATCH] - suppress most java warnings

---
 pyproject.toml                 |  4 ++--
 src/readers/bioformats_java.rs | 14 ++++++++++----
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index e970754..44eadf3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "ndbioimage"
-version = "2027.0.0"
+version = "2027.0.1"
 requires-python = ">=3.10"
 classifiers = [
     "License :: OSI Approved :: MIT License",
@@ -35,7 +35,7 @@ ndbioimage_generate_stub = "ndbioimage:ndbioimage_generate_stub"
 
 [tool.maturin]
 python-source = "py"
-features = ["python", "bioformats_java", "tiffwrite"]
+features = ["python", "bioformats_java", "tiffwrite", "czi"]
 module-name = "ndbioimage.ndbioimage_rs"
 include = ["py/ndbioimage/jassets/j4rs*", "py/ndbioimage/deps/libj4rs*"]
 
diff --git a/src/readers/bioformats_java.rs b/src/readers/bioformats_java.rs
index a44ba65..c81dd7e 100644
--- a/src/readers/bioformats_java.rs
+++ b/src/readers/bioformats_java.rs
@@ -106,11 +106,19 @@ fn jvm() -> Rc<Jvm> {
                     Jvm::attach_thread().expect("Failed to attach to JVM")
                 } else {
                     *jvm_built = true;
-                    JvmBuilder::new()
+                    let j = JvmBuilder::new()
                         .skip_setting_native_lib()
                         .with_base_path(class_path.to_str().unwrap())
                         .build()
-                        .expect("Failed to build JVM")
+                        .expect("Failed to build JVM");
+                    if let Ok(e) = InvocationArg::try_from("ERROR") {
+                        let _ = j.invoke_static(
+                            "loci.common.DebugTools",
+                            "setRootLevel",
+                            &[e],
+                        );
+                    }
+                    j
                 })
             }
         })
@@ -484,7 +492,6 @@ impl Reader for BioFormatsJavaReader {
     where
         P: AsRef<Path>,
     {
-        DebugTools::set_root_level("ERROR")?;
         let mut path = path.as_ref().to_path_buf();
         if path.is_dir() {
             let orig = path.clone();
@@ -562,7 +569,6 @@ impl Reader for BioFormatsJavaReader {
     where
         P: AsRef<Path>,
     {
-        DebugTools::set_root_level("ERROR")?;
         let mut path = path.as_ref().to_path_buf();
         if path.is_dir() {
             let orig = path.clone();