- implement custom error types

- less restrictive dependency versions
- some extra features and bugfixes for movie writing
- make python tests work again

src/main.rs

@@ -1,6 +1,8 @@
-use anyhow::Result;
 use clap::{Parser, Subcommand};
 #[cfg(feature = "movie")]
+use ndarray::SliceInfoElem;
+use ndbioimage::error::Error;
+#[cfg(feature = "movie")]
 use ndbioimage::movie::MovieOptions;
 use ndbioimage::reader::split_path_and_series;
 #[cfg(feature = "tiff")]
@@ -37,16 +39,26 @@ enum Commands {
     Movie {
         #[arg(value_name = "FILE", num_args(1..))]
         file: Vec<PathBuf>,
-        #[arg(short, long, value_name = "Velocity", default_value = "3.6")]
+        #[arg(short, long, value_name = "VELOCITY", default_value = "3.6")]
         velocity: f64,
-        #[arg(short, long, value_name = "BRIGHTNESS")]
+        #[arg(short, long, value_name = "BRIGHTNESS", num_args(1..))]
         brightness: Vec<f64>,
         #[arg(short, long, value_name = "SCALE", default_value = "1.0")]
         scale: f64,
-        #[arg(short, long, value_name = "COLOR", num_args(1..))]
+        #[arg(short = 'C', long, value_name = "COLOR", num_args(1..))]
         colors: Vec<String>,
         #[arg(short, long, value_name = "OVERWRITE")]
         overwrite: bool,
+        #[arg(short, long, value_name = "REGISTER")]
+        register: bool,
+        #[arg(short, long, value_name = "CHANNEL")]
+        channel: Option<isize>,
+        #[arg(short, long, value_name = "ZSLICE")]
+        zslice: Option<String>,
+        #[arg(short, long, value_name = "TIME")]
+        time: Option<String>,
+        #[arg(short, long, value_name = "NO-SCALE-BRIGHTNESS")]
+        no_scaling: bool,
     },
     /// Download the BioFormats jar into the correct folder
     DownloadBioFormats {
@@ -55,7 +67,43 @@ enum Commands {
     },
 }
 
-pub(crate) fn main() -> Result<()> {
+#[cfg(feature = "movie")]
+fn parse_slice(s: &str) -> Result<SliceInfoElem, Error> {
+    let mut t = s
+        .trim()
+        .replace("..", ":")
+        .split(":")
+        .map(|i| i.parse().ok())
+        .collect::<Vec<Option<isize>>>();
+    if t.len() > 3 {
+        return Err(Error::Parse(s.to_string()));
+    }
+    while t.len() < 3 {
+        t.push(None);
+    }
+    match t[..] {
+        [Some(start), None, None] => Ok(SliceInfoElem::Index(start)),
+        [Some(start), end, None] => Ok(SliceInfoElem::Slice {
+            start,
+            end,
+            step: 1,
+        }),
+        [Some(start), end, Some(step)] => Ok(SliceInfoElem::Slice { start, end, step }),
+        [None, end, None] => Ok(SliceInfoElem::Slice {
+            start: 0,
+            end,
+            step: 1,
+        }),
+        [None, end, Some(step)] => Ok(SliceInfoElem::Slice {
+            start: 0,
+            end,
+            step,
+        }),
+        _ => Err(Error::Parse(s.to_string())),
+    }
+}
+
+pub(crate) fn main() -> Result<(), Error> {
     let cli = Cli::parse();
     match &cli.command {
         Commands::Info { file } => {
@@ -87,6 +135,11 @@ pub(crate) fn main() -> Result<()> {
             scale,
             colors,
             overwrite,
+            register,
+            channel,
+            zslice,
+            time,
+            no_scaling,
         } => {
             let options = MovieOptions::new(
                 *speed,
@@ -94,11 +147,29 @@ pub(crate) fn main() -> Result<()> {
                 *scale,
                 colors.to_vec(),
                 *overwrite,
+                *register,
+                *no_scaling,
             )?;
             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)?;
+                let mut s = [SliceInfoElem::Slice {
+                    start: 0,
+                    end: None,
+                    step: 1,
+                }; 5];
+                if let Some(channel) = channel {
+                    s[0] = SliceInfoElem::Index(*channel);
+                };
+                if let Some(zslice) = zslice {
+                    s[1] = parse_slice(zslice)?;
+                }
+                if let Some(time) = time {
+                    s[2] = parse_slice(time)?;
+                }
+                view.into_dyn()
+                    .slice(s.as_slice())?
+                    .save_as_movie(f.with_extension("mp4"), &options)?;
             }
         }
         Commands::DownloadBioFormats { gpl_formats } => {