- bump ome-metadata dependency

- add extract-ome cli subcommand

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,