- some workarounds to get jars and shared libs in the right place for python

- add most ndbioimage python code and use rs code as bfread

src/bioformats.rs

@@ -10,11 +10,51 @@ thread_local! {
 /// Ensure 1 jvm per thread
 fn jvm() -> Rc<Jvm> {
     JVM.with(|cell| {
-        cell.get_or_init(move || Rc::new(JvmBuilder::new().build().expect("Failed to build JVM")))
-            .clone()
+        cell.get_or_init(move || {
+            #[cfg(feature = "python")]
+            let path = crate::py::ndbioimage_file().unwrap();
+
+            #[cfg(not(feature = "python"))]
+            let path = std::env::current_exe()
+                .unwrap()
+                .parent()
+                .unwrap()
+                .to_path_buf();
+
+            let class_path = path.parent().unwrap();
+            Rc::new(
+                JvmBuilder::new()
+                    .with_base_path(class_path.to_str().unwrap())
+                    .build()
+                    .expect("Failed to build JVM"),
+            )
+        })
+        .clone()
     })
 }
 
+#[cfg(feature = "python")]
+pub(crate) fn download_bioformats(gpl_formats: bool) -> Result<()> {
+    let path = crate::py::ndbioimage_file().unwrap();
+    let class_path = path.parent().unwrap();
+    let jvm = JvmBuilder::new()
+        .with_base_path(class_path.to_str().unwrap())
+        .with_maven_settings(j4rs::MavenSettings::new(vec![
+            j4rs::MavenArtifactRepo::from(
+                "openmicroscopy::https://artifacts.openmicroscopy.org/artifactory/ome.releases",
+            ),
+        ]))
+        .build()?;
+
+    jvm.deploy_artifact(&j4rs::MavenArtifact::from("ome:bioformats_package:8.1.0"))?;
+
+    if gpl_formats {
+        jvm.deploy_artifact(&j4rs::MavenArtifact::from("ome:formats-gpl:8.1.0"))?;
+    }
+
+    Ok(())
+}
+
 macro_rules! method_return {
     ($R:ty$(|c)?) => { Result<$R> };
     () => { Result<()> };
@@ -113,7 +153,7 @@ impl ImageReader {
         Ok(jvm()
             .chain(&mds)?
             .cast("loci.formats.ome.OMEPyramidStore")?
-            .invoke("dumpXML", &[])?
+            .invoke("dumpXML", InvocationArg::empty())?
             .to_rust()?)
     }
 

src/lib.rs

@@ -215,7 +215,7 @@ impl Reader {
     }
 
     /// Get ome metadata as xml string
-    pub fn ome_xml(&self) -> Result<String> {
+    pub fn get_ome_xml(&self) -> Result<String> {
         self.image_reader.ome_xml()
     }
 
@@ -396,7 +396,7 @@ mod tests {
     fn ome_xml() -> Result<()> {
         let file = "Experiment-2029.czi";
         let reader = open(file)?;
-        let xml = reader.ome_xml()?;
+        let xml = reader.get_ome_xml()?;
         println!("{}", xml);
         Ok(())
     }

src/py.rs

@@ -1,7 +1,7 @@
+use crate::bioformats::download_bioformats;
 use crate::{Frame, Reader};
-use numpy::{IntoPyArray, PyArrayMethods, ToPyArray};
+use numpy::ToPyArray;
 use pyo3::prelude::*;
-use pyo3::BoundObject;
 use std::path::PathBuf;
 
 #[pyclass(subclass)]
@@ -41,11 +41,35 @@ impl PyReader {
             Frame::DOUBLE(arr) => arr.to_pyarray(py).into_any(),
         })
     }
+
+    fn get_ome_xml(&self) -> PyResult<String> {
+        let reader = Reader::new(&self.path, self.series)?; // TODO: prevent making a new Reader each time
+        Ok(reader.get_ome_xml()?)
+    }
+}
+
+pub(crate) fn ndbioimage_file() -> anyhow::Result<PathBuf> {
+    let file = Python::with_gil(|py| {
+        py.import("ndbioimage")
+            .unwrap()
+            .filename()
+            .unwrap()
+            .to_string()
+    });
+    Ok(PathBuf::from(file))
 }
 
 #[pymodule]
 #[pyo3(name = "ndbioimage_rs")]
 fn ndbioimage_rs(m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<PyReader>()?;
+
+    #[pyfn(m)]
+    #[pyo3(name = "download_bioformats")]
+    fn py_download_bioformats(gpl_formats: bool) -> PyResult<()> {
+        download_bioformats(gpl_formats)?;
+        Ok(())
+    }
+
     Ok(())
 }