- added ome_xml method

- some pyo3 methods

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ndbioimage"
-version = "2025.1.2"
+version = "2025.2.0"
 edition = "2021"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
 license = "GPL-3.0-or-later"
@@ -31,9 +31,9 @@ optional = true
 rayon = "1.10.0"
 
 [build-dependencies]
+anyhow = { version = "1.0.95"}
 j4rs = { version = "0.22", features = [] }
 retry = { version = "2.0.0"}
-anyhow = { version = "1.0.95"}
 
 [features]
 python = ["dep:pyo3", "dep:numpy"]

src/bioformats.rs

@@ -31,7 +31,7 @@ macro_rules! method_arg {
 
 macro_rules! method {
     ($name:ident, $method:expr $(,[$($n:tt: $t:ty$(|$p:tt)?),*])? $(=> $tt:ty$(|$c:tt)?)?) => {
-        pub fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) {
+        pub(crate) fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) {
             let args: Vec<InvocationArg> = vec![$($( method_arg!($n:$t$(|$p)?) ),*)?];
             let _result = jvm().invoke(&self.0, $method, &args)?;
 
@@ -55,10 +55,10 @@ macro_rules! method {
     };
 }
 
-pub struct DebugTools;
+pub(crate) struct DebugTools;
 
 impl DebugTools {
-    pub fn set_root_level(level: &str) -> Result<()> {
+    pub(crate) fn set_root_level(level: &str) -> Result<()> {
         jvm().invoke_static(
             "loci.common.DebugTools",
             "setRootLevel",
@@ -68,10 +68,10 @@ impl DebugTools {
     }
 }
 
-pub struct ChannelSeparator(Instance);
+pub(crate) struct ChannelSeparator(Instance);
 
 impl ChannelSeparator {
-    pub fn new(image_reader: &ImageReader) -> Result<Self> {
+    pub(crate) fn new(image_reader: &ImageReader) -> Result<Self> {
         let jvm = jvm();
         let channel_separator = jvm.create_instance(
             "loci.formats.ChannelSeparator",
@@ -80,7 +80,7 @@ impl ChannelSeparator {
         Ok(ChannelSeparator(channel_separator))
     }
 
-    pub fn open_bytes(&self, index: i32) -> Result<Vec<u8>> {
+    pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>> {
         let bi8 = self.open_bi8(index)?;
         Ok(unsafe { std::mem::transmute::<Vec<i8>, Vec<u8>>(bi8) })
     }
@@ -89,7 +89,7 @@ impl ChannelSeparator {
     method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
 }
 
-pub struct ImageReader(Instance);
+pub(crate) struct ImageReader(Instance);
 
 impl Drop for ImageReader {
     fn drop(&mut self) {
@@ -98,17 +98,27 @@ impl Drop for ImageReader {
 }
 
 impl ImageReader {
-    pub fn new() -> Result<Self> {
+    pub(crate) fn new() -> Result<Self> {
         let reader = jvm().create_instance("loci.formats.ImageReader", InvocationArg::empty())?;
         Ok(ImageReader(reader))
     }
 
-    pub fn open_bytes(&self, index: i32) -> Result<Vec<u8>> {
+    pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>> {
         let bi8 = self.open_bi8(index)?;
         Ok(unsafe { std::mem::transmute::<Vec<i8>, Vec<u8>>(bi8) })
     }
 
+    pub(crate) fn ome_xml(&self) -> Result<String> {
+        let mds = self.get_metadata_store()?;
+        Ok(jvm()
+            .chain(&mds)?
+            .cast("loci.formats.ome.OMEPyramidStore")?
+            .invoke("dumpXML", &[])?
+            .to_rust()?)
+    }
+
     method!(set_metadata_store, "setMetadataStore", [ome_data: Instance]);
+    method!(get_metadata_store, "getMetadataStore" => Instance);
     method!(set_id, "setId", [id: &str]);
     method!(set_series, "setSeries", [series: i32|p]);
     method!(open_bi8, "openBytes", [index: i32|p] => Vec<i8>|c);
@@ -129,10 +139,10 @@ impl ImageReader {
     method!(close, "close");
 }
 
-pub struct MetadataTools(Instance);
+pub(crate) struct MetadataTools(Instance);
 
 impl MetadataTools {
-    pub fn new() -> Result<Self> {
+    pub(crate) fn new() -> Result<Self> {
         let meta_data_tools =
             jvm().create_instance("loci.formats.MetadataTools", InvocationArg::empty())?;
         Ok(MetadataTools(meta_data_tools))

src/lib.rs

@@ -144,7 +144,7 @@ pub struct Reader {
     image_reader: ImageReader,
     /// path to file
     pub path: PathBuf,
-    /// which (if more) than 1 of the series in the file to open
+    /// which (if more than 1) of the series in the file to open
     pub series: i32,
     /// size x (horizontal)
     pub size_x: usize,
@@ -154,7 +154,7 @@ pub struct Reader {
     pub size_c: usize,
     /// size z (# slices)
     pub size_z: usize,
-    /// size t (time/frames)
+    /// size t (# time/frames)
     pub size_t: usize,
     /// pixel type ((u)int(8/16/32) or float(32/64))
     pub pixel_type: PixelType,
@@ -214,6 +214,11 @@ impl Reader {
         })
     }
 
+    /// Get ome metadata as xml string
+    pub fn ome_xml(&self) -> Result<String> {
+        self.image_reader.ome_xml()
+    }
+
     fn deinterleave(&self, bytes: Vec<u8>, channel: usize) -> Result<Vec<u8>> {
         let chunk_size = match self.pixel_type {
             PixelType::INT8 => 1,
@@ -311,7 +316,10 @@ mod tests {
     use rayon::prelude::*;
 
     fn open(file: &str) -> Result<Reader> {
-        let path = std::env::current_dir()?.join("tests").join("files").join(file);
+        let path = std::env::current_dir()?
+            .join("tests")
+            .join("files")
+            .join(file);
         Reader::new(&path, 0)
     }
 
@@ -363,4 +371,33 @@ mod tests {
         println!("{:?}", frames);
         Ok(())
     }
+
+    #[test]
+    fn read_sequence() -> Result<()> {
+        let file = "YTL1841B2-2-1_1hr_DMSO_galinduction_1/Pos0/img_000000000_mScarlet_GFP-mSc-filter_004.tif";
+        let reader = open(file)?;
+        println!("reader: {:?}", reader);
+        let frame = reader.get_frame(0, 4, 0)?;
+        println!("frame: {:?}", frame);
+        let frame = reader.get_frame(0, 2, 0)?;
+        println!("frame: {:?}", frame);
+        Ok(())
+    }
+
+    #[test]
+    fn read_sequence1() -> Result<()> {
+        let file = "4-Pos_001_002/img_000000000_Cy3-Cy3_filter_000.tif";
+        let reader = open(file)?;
+        println!("reader: {:?}", reader);
+        Ok(())
+    }
+
+    #[test]
+    fn ome_xml() -> Result<()> {
+        let file = "Experiment-2029.czi";
+        let reader = open(file)?;
+        let xml = reader.ome_xml()?;
+        println!("{}", xml);
+        Ok(())
+    }
 }

src/py.rs

@@ -1,14 +1,51 @@
+use crate::{Frame, Reader};
+use numpy::{IntoPyArray, PyArrayMethods, ToPyArray};
 use pyo3::prelude::*;
+use pyo3::BoundObject;
+use std::path::PathBuf;
 
-/// Formats the sum of two numbers as string.
+#[pyclass(subclass)]
-#[pyfunction]
+#[pyo3(name = "Reader")]
-fn sum_as_string(a: usize, b: usize) -> PyResult<String> {
+#[derive(Debug)]
-    Ok((a + b).to_string())
+struct PyReader {
+    path: PathBuf,
+    series: i32,
+}
+
+#[pymethods]
+impl PyReader {
+    #[new]
+    fn new(path: &str, series: usize) -> PyResult<Self> {
+        Ok(PyReader {
+            path: PathBuf::from(path),
+            series: series as i32,
+        })
+    }
+
+    fn get_frame<'py>(
+        &self,
+        py: Python<'py>,
+        c: usize,
+        z: usize,
+        t: usize,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        let reader = Reader::new(&self.path, self.series)?; // TODO: prevent making a new Reader each time
+        Ok(match reader.get_frame(c, z, t)? {
+            Frame::INT8(arr) => arr.to_pyarray(py).into_any(),
+            Frame::UINT8(arr) => arr.to_pyarray(py).into_any(),
+            Frame::INT16(arr) => arr.to_pyarray(py).into_any(),
+            Frame::UINT16(arr) => arr.to_pyarray(py).into_any(),
+            Frame::INT32(arr) => arr.to_pyarray(py).into_any(),
+            Frame::UINT32(arr) => arr.to_pyarray(py).into_any(),
+            Frame::FLOAT(arr) => arr.to_pyarray(py).into_any(),
+            Frame::DOUBLE(arr) => arr.to_pyarray(py).into_any(),
+        })
+    }
 }
 
-/// A Python module implemented in Rust.
 #[pymodule]
+#[pyo3(name = "ndbioimage_rs")]
 fn ndbioimage_rs(m: &Bound<'_, PyModule>) -> PyResult<()> {
-    m.add_function(wrap_pyfunction!(sum_as_string, m)?)?;
+    m.add_class::<PyReader>()?;
     Ok(())
 }