- open tiff seq folders with bioformats_java by finding the first tiff recursively

- make PyView serializable by skipping the ome field
- fix python tests

src/readers/bioformats_java.rs

@@ -7,6 +7,7 @@ use std::path::{Path, PathBuf};
 
 pub use crate::readers::{ArrayT, PixelType, Reader};
 use crate::readers::{DynReader, Frame, Shape};
+use itertools::Itertools;
 use j4rs::{Instance, InvocationArg, Jvm, JvmBuilder};
 use std::cell::OnceCell;
 use std::collections::HashSet;
@@ -461,6 +462,22 @@ impl Drop for BioFormatsJavaReader {
     }
 }
 
+fn find_tiff(path: PathBuf) -> Result<Option<PathBuf>, Error> {
+    if let Some(ext) = path.extension()
+        && path.is_file()
+        && (["tif", "tiff"].contains(&ext.to_string_lossy().to_lowercase().as_str()))
+    {
+        return Ok(Some(path));
+    } else if path.is_dir() {
+        for file in path.read_dir()?.flatten().sorted_by_key(|i| i.file_name()) {
+            if let Ok(Some(file)) = find_tiff(file.path()) {
+                return Ok(Some(file));
+            }
+        }
+    }
+    Ok(None)
+}
+
 impl Reader for BioFormatsJavaReader {
     /// Create a new reader for the image file at a path, and open series #.
     fn new<P>(path: P, series: usize, _position: usize) -> Result<Self, Error>
@@ -470,13 +487,10 @@ impl Reader for BioFormatsJavaReader {
         DebugTools::set_root_level("ERROR")?;
         let mut path = path.as_ref().to_path_buf();
         if path.is_dir() {
-            for file in path.read_dir()?.flatten() {
-                let p = file.path();
-                if file.path().is_file() && (p.extension() == Some("tif".as_ref())) {
-                    path = p;
-                    break;
-                }
-            }
+            let orig = path.clone();
+            path = find_tiff(path)?.ok_or_else(|| {
+                Error::FileDoesNotExist(orig.join("**").join("*.tif").display().to_string())
+            })?;
         }
         let mut new = BioFormatsJavaReader {
             reader: ThreadLocal::default(),
@@ -549,9 +563,16 @@ impl Reader for BioFormatsJavaReader {
         P: AsRef<Path>,
     {
         DebugTools::set_root_level("ERROR")?;
+        let mut path = path.as_ref().to_path_buf();
+        if path.is_dir() {
+            let orig = path.clone();
+            path = find_tiff(path)?.ok_or_else(|| {
+                Error::FileDoesNotExist(orig.join("**").join("*.tif").display().to_string())
+            })?;
+        }
         let new = BioFormatsJavaReader {
             reader: ThreadLocal::default(),
-            path: path.as_ref().to_path_buf(),
+            path,
             series: 0,
             shape: Shape::default(),
             pixel_type: PixelType::I8,
@@ -594,7 +615,8 @@ mod tests {
         metadata_e: "czi/YTL1849A131_2023_05_04__13_36_36.czi",
         metadata_f: "czi/EU_UV_t=1-01.czi",
         metadata_g: "tiffseq/4-Pos_001_002/img_000000000_Cy3-Cy3_filter_000.tif",
-        metadata_h: "tiffseq/20-Pos_005_005/img_000000000_Cy3-Cy3_filter_000.tif"
+        metadata_h: "tiffseq/20-Pos_005_005/img_000000000_Cy3-Cy3_filter_000.tif",
+        metadata_i: "tiffseq/YTL1841B2-2-1_1hr_DMSO_galinduction_1",
     }
 
     #[test]