- bump ome-metadata dependency

- add extract-ome cli subcommand

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "ndbioimage"
-version = "2026.1.1"
+version = "2026.1.2"
 edition = "2024"
 rust-version = "1.85.1"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
@@ -36,7 +36,7 @@ serde_json = { version = "1", optional = true }
 serde_with = "3"
 tiffwrite = { version = "2025.12.0", optional = true}
 thread_local = "1"
-ome-metadata = "0.3.2"
+ome-metadata = "0.4"
 lazy_static = "1"
 thiserror = "2"
 
@@ -46,8 +46,8 @@ features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
 optional = true
 
 [dev-dependencies]
-rayon = "1"
 downloader = "0.2"
+rayon = "1"
 regex = "1"
 reqwest = { version = "0.13", features = ["blocking"] }
 

src/main.rs

@@ -4,7 +4,7 @@ use ndarray::SliceInfoElem;
 use ndbioimage::error::Error;
 #[cfg(feature = "movie")]
 use ndbioimage::movie::MovieOptions;
-use ndbioimage::reader::split_path_and_series;
+use ndbioimage::reader::{split_path_and_series, Reader};
 #[cfg(feature = "tiff")]
 use ndbioimage::tiff::TiffOptions;
 use ndbioimage::view::View;
@@ -24,6 +24,11 @@ enum Commands {
         #[arg(value_name = "FILE", num_args(1..))]
         file: Vec<PathBuf>,
     },
+    /// save ome metadata as xml
+    ExtractOME {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+    },
     /// Save the image as tiff file
     #[cfg(feature = "tiff")]
     Tiff {
@@ -113,6 +118,14 @@ pub(crate) fn main() -> Result<(), Error> {
                 println!("{}", view.summary()?);
             }
         }
+        Commands::ExtractOME { file } => {
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let reader = Reader::new(&path, series.unwrap_or(0))?;
+                let xml = reader.get_ome_xml()?;
+                std::fs::write(path.with_extension("xml"), xml)?;
+            }
+        }
         #[cfg(feature = "tiff")]
         Commands::Tiff {
             file,

src/metadata.rs

@@ -9,18 +9,13 @@ impl Metadata for Ome {
     fn get_instrument(&self) -> Option<&Instrument> {
         let instrument_id = self.get_image()?.instrument_ref.as_ref()?.id.clone();
         self.instrument
-            .as_ref()?
             .iter()
             .find(|i| i.id == instrument_id)
     }
 
     fn get_image(&self) -> Option<&Image> {
-        if let Some(image) = &self.image {
-            if !image.is_empty() {
-                Some(&image[0])
-            } else {
-                None
-            }
+        if let Some(image) = &self.image.first() {
+            Some(&image)
         } else {
             None
         }
@@ -130,24 +125,22 @@ pub trait Metadata {
     /// time interval in seconds for time-lapse images
     fn time_interval(&self) -> Result<Option<f64>, Error> {
         if let Some(pixels) = self.get_pixels() {
-            if let Some(plane) = &pixels.plane {
-                if let Some(t) = plane.iter().map(|p| p.the_t).max() {
-                    if t > 0 {
-                        let plane_a = plane
-                            .iter()
-                            .find(|p| (p.the_c == 0) && (p.the_z == 0) && (p.the_t == 0));
-                        let plane_b = plane
-                            .iter()
-                            .find(|p| (p.the_c == 0) && (p.the_z == 0) && (p.the_t == t));
-                        if let (Some(a), Some(b)) = (plane_a, plane_b) {
-                            if let (Some(a_t), Some(b_t)) = (a.delta_t, b.delta_t) {
-                                return Ok(Some(
-                                    (b.delta_t_unit.convert(&UnitsTime::s, b_t as f64)?
-                                        - a.delta_t_unit.convert(&UnitsTime::s, a_t as f64)?)
-                                    .abs()
-                                        / (t as f64),
-                                ));
-                            }
+            if let Some(t) = pixels.plane.iter().map(|p| p.the_t).max() {
+                if t > 0 {
+                    let plane_a = pixels.plane
+                        .iter()
+                        .find(|p| (p.the_c == 0) && (p.the_z == 0) && (p.the_t == 0));
+                    let plane_b = pixels.plane
+                        .iter()
+                        .find(|p| (p.the_c == 0) && (p.the_z == 0) && (p.the_t == t));
+                    if let (Some(a), Some(b)) = (plane_a, plane_b) {
+                        if let (Some(a_t), Some(b_t)) = (a.delta_t, b.delta_t) {
+                            return Ok(Some(
+                                (b.delta_t_unit.convert(&UnitsTime::s, b_t as f64)?
+                                    - a.delta_t_unit.convert(&UnitsTime::s, a_t as f64)?)
+                                .abs()
+                                    / (t as f64),
+                            ));
                         }
                     }
                 }
@@ -160,14 +153,12 @@ pub trait Metadata {
     fn exposure_time(&self, channel: usize) -> Result<Option<f64>, Error> {
         let c = channel as i32;
         if let Some(pixels) = self.get_pixels() {
-            if let Some(plane) = &pixels.plane {
-                if let Some(p) = plane
-                    .iter()
-                    .find(|p| (p.the_c == c) && (p.the_z == 0) && (p.the_t == 0))
-                {
-                    if let Some(t) = p.exposure_time {
-                        return Ok(Some(p.exposure_time_unit.convert(&UnitsTime::s, t as f64)?));
-                    }
+            if let Some(p) = pixels.plane
+                .iter()
+                .find(|p| (p.the_c == c) && (p.the_z == 0) && (p.the_t == 0))
+            {
+                if let Some(t) = p.exposure_time {
+                    return Ok(Some(p.exposure_time_unit.convert(&UnitsTime::s, t as f64)?));
                 }
             }
         }

src/reader.rs

@@ -344,10 +344,8 @@ impl Reader {
     /// Get ome metadata as ome structure
     pub fn get_ome(&self) -> Result<Ome, Error> {
         let mut ome = self.ome_xml()?.parse::<Ome>()?;
-        if let Some(image) = ome.image.as_ref() {
-            if image.len() > 1 {
-                ome.image = Some(vec![image[self.series].clone()]);
-            }
+        if ome.image.len() > 1 {
+            ome.image = vec![ome.image[self.series].clone()];
         }
         Ok(ome)
     }