- bump bioformats to 8.3.0

- rust: command line binary, save as mp4, save as tiff, ome metadata, more methods for View, bugfixes, less unsafe code
- python: ome as dict

src/main.rs

@@ -0,0 +1,110 @@
+use anyhow::Result;
+use clap::{Parser, Subcommand};
+#[cfg(feature = "movie")]
+use ndbioimage::movie::MovieOptions;
+use ndbioimage::reader::split_path_and_series;
+#[cfg(feature = "tiff")]
+use ndbioimage::tiff::TiffOptions;
+use ndbioimage::view::View;
+use std::path::PathBuf;
+
+#[derive(Parser)]
+#[command(arg_required_else_help = true, version, about, long_about = None, propagate_version = true)]
+struct Cli {
+    #[command(subcommand)]
+    command: Commands,
+}
+
+#[derive(Subcommand)]
+enum Commands {
+    /// Print some metadata
+    Info {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+    },
+    /// Save the image as tiff file
+    #[cfg(feature = "tiff")]
+    Tiff {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+        #[arg(short, long, value_name = "COLOR", num_args(1..))]
+        colors: Vec<String>,
+        #[arg(short, long, value_name = "OVERWRITE")]
+        overwrite: bool,
+    },
+    /// Save the image as mp4 file
+    #[cfg(feature = "movie")]
+    Movie {
+        #[arg(value_name = "FILE", num_args(1..))]
+        file: Vec<PathBuf>,
+        #[arg(short, long, value_name = "Velocity", default_value = "3.6")]
+        velocity: f64,
+        #[arg(short, long, value_name = "BRIGHTNESS")]
+        brightness: Vec<f64>,
+        #[arg(short, long, value_name = "SCALE", default_value = "1.0")]
+        scale: f64,
+        #[arg(short, long, value_name = "COLOR", num_args(1..))]
+        colors: Vec<String>,
+        #[arg(short, long, value_name = "OVERWRITE")]
+        overwrite: bool,
+    },
+    /// Download the BioFormats jar into the correct folder
+    DownloadBioFormats {
+        #[arg(short, long, value_name = "GPL_FORMATS")]
+        gpl_formats: bool,
+    },
+}
+
+pub(crate) fn main() -> Result<()> {
+    let cli = Cli::parse();
+    match &cli.command {
+        Commands::Info { file } => {
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let view = View::from_path(path, series.unwrap_or(0))?.squeeze()?;
+                println!("{}", view.summary()?);
+            }
+        }
+        #[cfg(feature = "tiff")]
+        Commands::Tiff {
+            file,
+            colors,
+            overwrite,
+        } => {
+            let mut options = TiffOptions::new(true, None, colors.clone(), *overwrite)?;
+            options.enable_bar()?;
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let view = View::from_path(path, series.unwrap_or(0))?;
+                view.save_as_tiff(f.with_extension("tiff"), &options)?;
+            }
+        }
+        #[cfg(feature = "movie")]
+        Commands::Movie {
+            file,
+            velocity: speed,
+            brightness,
+            scale,
+            colors,
+            overwrite,
+        } => {
+            let options = MovieOptions::new(
+                *speed,
+                brightness.to_vec(),
+                *scale,
+                colors.to_vec(),
+                *overwrite,
+            )?;
+            for f in file {
+                let (path, series) = split_path_and_series(f)?;
+                let view = View::from_path(path, series.unwrap_or(0))?;
+                view.save_as_movie(f.with_extension("mp4"), &options)?;
+            }
+        }
+        Commands::DownloadBioFormats { gpl_formats } => {
+            ndbioimage::download_bioformats(*gpl_formats)?
+        }
+    }
+
+    Ok(())
+}