- use a fork of the tiff crate to open RGBPalette tiffs

.gitignore

@@ -72,11 +72,11 @@ docs/_build/
 # Pyenv
 .python-version
 
-/tests/files/*
+/ndbioimage/tests/files/*
 AGENTS.md
 .agentbridge
 .agent-work
 
-py/ndbioimage/jassets
+/ndbioimage/py/ndbioimage/jassets
-py/ndbioimage/deps
+/ndbioimage/py/ndbioimage/deps
 /build_wheels.sh

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "image-tiff"]
+	path = image-tiff
+	url = https://git.pomppervova.nl/wim/image-tiff.git
+[submodule "image-registration"]
+	path = image-registration
+	url = https://git.pomppervova.nl/wim/image-registration.git

Cargo.toml

@@ -1,7 +1,11 @@
-[package]
+[workspace]
-name = "ndbioimage"
+resolver = "3"
+members = ["ndbioimage", "image-tiff", "image-registration"]
+
+[workspace.package]
 version = "0.2.0"
 edition = "2024"
+# the workspace must satisfy every member, so this is the highest `rust-version` of the members
 rust-version = "1.94.0"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
 license = "MIT OR Apache-2.0"
@@ -9,77 +13,13 @@ description = "Read bio image formats using the bio-formats java package."
 homepage = "https://git.pomppervova.nl/wim/ndbioimage/src/branch/rs"
 repository = "https://git.pomppervova.nl/wim/ndbioimage/src/branch/rs"
 documentation = "https://docs.rs/ndbioimage"
-readme = "README.md"
+# inherited paths are resolved relative to the workspace root, not the member, so this has to point
+# at the member's readme
+readme = "ndbioimage/README.md"
 keywords = ["bioformats", "imread", "ndarray", "metadata"]
 categories = ["multimedia::images", "science"]
-exclude = ["/tests"]
-
-[lib]
-name = "ndbioimage"
-crate-type = ["cdylib", "rlib"]
-
-[dependencies]
-bioformats = { version = "0.1", optional = true, default-features = false, features = ["zarr", "tissuefaxs"] }
-clap = { version = "4", features = ["derive"] }
-console = { version = "0.16", optional = true }
-downloader = { version = "0.2", optional = true, default-features = false, features = ["rustls-tls"] }
-ffmpeg-sidecar = { version = "2", optional = true }
-itertools = "0.15"
-image-registration = { path = "../image-registration", optional = true }
-indexmap = { version = "2", features = ["serde"] }
-indicatif = { version = "0.18", features = ["rayon"], optional = true }
-j4rs = { version = "0.25", optional = true }
-libczirw-sys = { version = "0.5", optional = true }
-ndarray = { version = "0.17", features = ["serde"] }
-num = "0.4"
-numpy = { version = "0.29", optional = true }
-ome-metadata = "0.5"
-ordered-float = { version = "5", optional = true }
-phf = { version = "0.14", features = ["macros"] }
-postcard = { version = "1", features = ["use-std"], optional = true }
-pyo3 = { version = "0.29", features = ["abi3-py310", "anyhow", "generate-import-lib"], optional = true }
-pyo3-stub-gen = { version = "0.23", optional = true }
-rayon = { version = "1", optional = true }
-regex = "1"
-serde = { version = "1", features = ["rc", "derive"] }
-serde_with = "3"
-strum = { version = "0.28", features = ["derive"] }
-thiserror = "2"
-tiff = { version = "0.11", features = ["zstd"], optional = true }
-tiffwrite = { version = "2026.6.0", optional = true }
-tokio = { version = "1", features = ["rt", "rt-multi-thread"], optional = true }
-thread_local = { version = "1", optional = true }
-xmltree = { version = "0.12", optional = true }
-yaml_serde = { version = "0.10", optional = true }
-
-[dev-dependencies]
-rayon = "1"
-regex = "1"
-
-[build-dependencies]
-j4rs = "0.25"
-ffmpeg-sidecar = "2"
-retry = "2"
-toml = "1"
-
-[features]
-default = ["bioformats_java", "gpl-formats", "czi", "tiff", "tiffseq", "movie", "tiffwrite"]
-all = ["bioformats_java", "bioformats_rust", "czi", "gpl-formats", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]
-gpl-formats = []
-python = ["dep:pyo3", "dep:numpy", "dep:pyo3-stub-gen", "dep:postcard", "ome-metadata/python"]
-czi = ["dep:libczirw-sys", "dep:xmltree", "dep:thread_local"]
-bioformats_rust = ["dep:bioformats", "dep:thread_local"]
-bioformats_java = ["dep:j4rs", "dep:thread_local", "dep:downloader"]
-tiffwrite = ["dep:tiffwrite", "dep:indicatif", "dep:console", "dep:rayon"]
-tiffseq = ["dep:tiff", "dep:yaml_serde"]
-tiff = ["dep:tiff", "dep:thread_local"]
-movie = ["dep:ffmpeg-sidecar", "dep:tokio", "dep:ordered-float", "dep:indicatif", "dep:console"]
-transforms = ["dep:image-registration", "dep:yaml_serde"]
-
-[package.metadata.docs.rs]
-no-default-features = true
-features = ["bioformats_java", "bioformats_rust", "czi", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]
 
+# profiles are only honoured in the workspace root manifest
 [profile.test]
 inherits = "release"
 

ndbioimage/Cargo.toml

@@ -0,0 +1,82 @@
+[package]
+name = "ndbioimage"
+version.workspace = true
+edition.workspace = true
+rust-version.workspace = true
+authors.workspace = true
+license.workspace = true
+description.workspace = true
+homepage.workspace = true
+repository.workspace = true
+documentation.workspace = true
+readme.workspace = true
+keywords.workspace = true
+categories.workspace = true
+exclude = ["/tests"]
+
+[lib]
+name = "ndbioimage"
+crate-type = ["cdylib", "rlib"]
+
+[dependencies]
+bioformats = { version = "0.1", optional = true, default-features = false, features = ["zarr", "tissuefaxs"] }
+clap = { version = "4", features = ["derive"] }
+console = { version = "0.16", optional = true }
+downloader = { version = "0.2", optional = true, default-features = false, features = ["rustls-tls"] }
+ffmpeg-sidecar = { version = "2", optional = true }
+itertools = "0.15"
+image-registration = { path = "../image-registration", version = "0.1", optional = true }
+indexmap = { version = "2", features = ["serde"] }
+indicatif = { version = "0.18", features = ["rayon"], optional = true }
+j4rs = { version = "0.25", optional = true }
+libczirw-sys = { version = "0.5", optional = true }
+ndarray = { version = "0.17", features = ["serde"] }
+num = "0.4"
+numpy = { version = "0.29", optional = true }
+ome-metadata = "0.5"
+ordered-float = { version = "5", optional = true }
+phf = { version = "0.14", features = ["macros"] }
+postcard = { version = "1", features = ["use-std"], optional = true }
+pyo3 = { version = "0.29", features = ["abi3-py310", "anyhow", "generate-import-lib"], optional = true }
+pyo3-stub-gen = { version = "0.23", optional = true }
+rayon = { version = "1", optional = true }
+regex = "1"
+serde = { version = "1", features = ["rc", "derive"] }
+serde_with = "3"
+strum = { version = "0.28", features = ["derive"] }
+thiserror = "2"
+tiff = { package = "ndbioimage-tiff", path = "../image-tiff", version = "0.11", features = ["zstd"], optional = true }
+tiffwrite = { version = "2026.6.0", optional = true }
+tokio = { version = "1", features = ["rt", "rt-multi-thread"], optional = true }
+thread_local = { version = "1", optional = true }
+xmltree = { version = "0.12", optional = true }
+yaml_serde = { version = "0.10", optional = true }
+
+[dev-dependencies]
+rayon = "1"
+regex = "1"
+postcard = { version = "1", features = ["use-std"] }
+
+[build-dependencies]
+j4rs = "0.25"
+ffmpeg-sidecar = "2"
+retry = "2"
+toml = "1"
+
+[features]
+default = ["bioformats_java", "gpl-formats", "czi", "tiff", "tiffseq", "movie", "tiffwrite"]
+all = ["bioformats_java", "bioformats_rust", "czi", "gpl-formats", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]
+gpl-formats = []
+python = ["dep:pyo3", "dep:numpy", "dep:pyo3-stub-gen", "dep:postcard", "ome-metadata/python"]
+czi = ["dep:libczirw-sys", "dep:xmltree", "dep:thread_local"]
+bioformats_rust = ["dep:bioformats", "dep:thread_local"]
+bioformats_java = ["dep:j4rs", "dep:thread_local", "dep:downloader"]
+tiffwrite = ["dep:tiffwrite", "dep:indicatif", "dep:console", "dep:rayon"]
+tiffseq = ["dep:tiff", "dep:yaml_serde"]
+tiff = ["dep:tiff", "dep:thread_local"]
+movie = ["dep:ffmpeg-sidecar", "dep:tokio", "dep:ordered-float", "dep:indicatif", "dep:console"]
+transforms = ["dep:image-registration", "dep:yaml_serde"]
+
+[package.metadata.docs.rs]
+no-default-features = true
+features = ["bioformats_java", "bioformats_rust", "czi", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]

ndbioimage/build.rs

@@ -9,21 +9,41 @@ mod bioformats {
     #[derive(Clone, Debug)]
     pub(crate) enum BuildError {
         J4rsVersionNotFound,
+        LockFileNotFound,
     }
 
     impl Display for BuildError {
         fn fmt(&self, fmt: &mut Formatter) -> Result<(), std::fmt::Error> {
             match self {
                 Self::J4rsVersionNotFound => write!(fmt, "J4rsVersion not found in Cargo.lock"),
+                Self::LockFileNotFound => write!(
+                    fmt,
+                    "Cargo.lock not found in any parent of CARGO_MANIFEST_DIR ({})",
+                    std::env::var("CARGO_MANIFEST_DIR").unwrap_or_default()
+                ),
             }
         }
     }
 
     impl Error for BuildError {}
 
+    /// the `Cargo.lock` that cargo resolved for this build: next to the manifest for a standalone
+    /// package, or at the workspace root when this crate is a workspace member
+    fn lock_file() -> Result<std::path::PathBuf, BuildError> {
+        let manifest_dir = std::path::PathBuf::from(
+            std::env::var("CARGO_MANIFEST_DIR").expect("CARGO_MANIFEST_DIR not set"),
+        );
+        manifest_dir
+            .ancestors()
+            .map(|dir| dir.join("Cargo.lock"))
+            .find(|lock| lock.is_file())
+            .ok_or(BuildError::LockFileNotFound)
+    }
+
     fn get_j4rs_version() -> Result<String, Box<dyn Error>> {
-        let manifest_dir = std::env::var("CARGO_MANIFEST_DIR").expect("CARGO_MANIFEST_DIR not set");
+        let lock_path = lock_file()?;
-        let lock_path = std::path::Path::new(&manifest_dir).join("Cargo.lock");
+        // the resolved j4rs version is baked into the generated constants, so rerun when it changes
+        println!("cargo::rerun-if-changed={}", lock_path.display());
         let lock_toml = std::fs::read_to_string(&lock_path)?;
         let value: toml::Value = toml::from_str(&lock_toml)?;
         if let Some(packages) = value.get("package").and_then(|v| v.as_array()) {

ndbioimage/py/ndbioimage/__init__.py

@@ -5,7 +5,7 @@ import sys
 import warnings
 from importlib.metadata import version
 from pathlib import Path
-from typing import TypeVar
+from typing import TYPE_CHECKING
 
 import numpy as np
 from numpy.typing import ArrayLike
@@ -13,14 +13,18 @@ from numpy.typing import ArrayLike
 os.environ["RUST_BACKTRACE"] = "full"
 os.environ["COLORBT_SHOW_HIDDEN"] = "1"
 
-from .ndbioimage_rs import Imread, generate_stub
+from .ndbioimage_rs import Imread, Shape, generate_stub
 
-try:
+if TYPE_CHECKING:
-    from .ndbioimage_rs import transforms
+    from .transforms import Transform as Transform
+else:
+    try:
+        from .ndbioimage_rs import transforms
 
-    sys.modules["ndbioimage.transforms"] = transforms
+        sys.modules["ndbioimage.transforms"] = transforms
-except (ImportError, ModuleNotFoundError):
+        Transform = transforms.Transform
-    pass
+    except (ImportError, ModuleNotFoundError):
+        pass
 
 try:
     from .ndbioimage_rs import batch_to_tiff
@@ -50,7 +54,16 @@ except Exception:  # noqa
     __git_commit_hash__ = "unknown"
 
 warnings.filterwarnings("ignore", "Reference to unknown ID")
-Number = int | float | np.integer | np.floating
+
+__all__ = [
+    "Imread",
+    "JVMException",
+    "ReaderNotFoundError",
+    "Shape",
+    "Transform",
+    "get_positions",
+    "is_noise",
+]
 
 
 # backwards compatibility
@@ -90,9 +103,6 @@ def ndbioimage_generate_stub():
             (nd / "ndbioimage.pyi").rename(nd / "__init__.pyi")
 
 
-R = TypeVar("R")
-
-
 def get_positions(path: str | Path) -> set[int]:
     return Imread.get_available_series(path)
 

ndbioimage/py/ndbioimage/ndbioimage_rs/__init__.pyi

@@ -228,7 +228,26 @@ class Imread:
         reader: typing.Optional[builtins.str] = None,
     ) -> Imread:
         r"""
-        new view on a file at path, open series #, open as dtype: (u)int(8/16/32) or float(32/64)
+        new view on an image file
+        path: path to image file to open, can include /Pos\d
+        dtype: when not None; will cast image to this dtype,
+            choices: (u)int(8/16/32) or float(32/64)
+        axes: the resulting object will represent the image with the axes in this order
+        reader: use a specific reader to open the file,
+            view available choices with Imread.available_readers
+        """
+    @staticmethod
+    def warm_jvm() -> None:
+        r"""
+        creates the jvm (if it does not exist yet) so that hotspot installs its signal handlers before
+        anything else does: see `crate::readers::bioformats_java::warm_jvm`
+
+        in a python process, call this before `ray.init()`, which installs CPython's faulthandler
+        """
+    @staticmethod
+    def jvm_is_running() -> builtins.bool:
+        r"""
+        returns whether the jvm was already created on this thread
         """
     def set_flags(
         self,
@@ -773,7 +792,7 @@ def batch_to_tiff(
 
 def generate_stub(dest_path: builtins.str) -> None:
     r"""
-    generates ndbioimage/__init__.pyi
+    generates .pyi files
     """
 
 def main() -> None:

ndbioimage/py/ndbioimage/ndbioimage_rs/transforms.pyi

@@ -120,6 +120,16 @@ class Transform:
     @center.setter
     def center(self, value: typing.Sequence[builtins.float]) -> None: ...
     @property
+    def origin(self) -> builtins.list[builtins.float]:
+        r"""
+        backwards compatibility
+        """
+    @origin.setter
+    def origin(self, value: typing.Sequence[builtins.float]) -> None:
+        r"""
+        backwards compatibility
+        """
+    @property
     def shape(self) -> builtins.list[builtins.int]: ...
     @shape.setter
     def shape(self, value: typing.Sequence[builtins.int]) -> None: ...
@@ -184,6 +194,12 @@ class Transform:
     def interpolate_par(
         self, order: builtins.int, image: numpy.typing.ArrayLike
     ) -> numpy.typing.NDArray[numpy.float64]: ...
+    def frame(
+        self, image: numpy.typing.ArrayLike, default: typing.Optional[typing.Any] = None
+    ) -> numpy.ndarray:
+        r"""
+        backwards compatibility, default parameter is not implemented
+        """
     def is_unity(self) -> builtins.bool: ...
     def transform_point(
         self, point: numpy.typing.ArrayLike

ndbioimage/src/cache.rs

@@ -6,6 +6,7 @@ use std::fmt::{Debug, Formatter};
 use std::hash::{Hash, Hasher};
 use std::path::{Path, PathBuf};
 use std::sync::{Arc, Mutex, OnceLock};
+use std::time::SystemTime;
 
 use crate::readers::Frame;
 
@@ -15,6 +16,68 @@ const DEFAULT_FRAME_CACHE_SIZE: usize = 128;
 /// maximum number of materialized arrays held in the cache
 const DEFAULT_ARRAY_CACHE_SIZE: usize = 32;
 
+/// fingerprint of the file(s) a reader reads from.
+///
+/// The cache is keyed partly on this stamp, so a file that is rewritten (for
+/// example an output file that is written and then read back) gets a new cache
+/// key instead of returning stale pixels. The stamp is read from the
+/// filesystem on every lookup, so a long-lived view also notices a change.
+#[derive(Debug, Clone, Copy, Default, PartialEq, Eq, Hash)]
+pub(crate) struct FileStamp {
+    /// size of the file in bytes
+    len: u64,
+    /// last modification time
+    modified: Option<SystemTime>,
+    /// last status change time; on unix this catches same-size rewrites that
+    /// happen within the timestamp resolution of `modified`
+    #[cfg(unix)]
+    changed: Option<(i64, u32)>,
+    /// inode number; on unix this catches an atomic replace that preserves the
+    /// modification time and size
+    #[cfg(unix)]
+    inode: u64,
+    /// creation time; windows has no stable `ctime` or file index, but this
+    /// changes when a file is deleted/recreated or atomically replaced, which is
+    /// the case the unix inode covers. in-place rewrites are caught by
+    /// `modified`, which has 100 ns resolution on windows.
+    #[cfg(windows)]
+    created: Option<SystemTime>,
+}
+
+impl FileStamp {
+    /// read the current stamp for `path`, returning the default (all-zero)
+    /// stamp when the metadata cannot be read
+    pub(crate) fn from_path(path: &Path) -> Self {
+        let Ok(meta) = std::fs::metadata(path) else {
+            return Self::default();
+        };
+        let len = meta.len();
+        let modified = meta.modified().ok();
+        #[cfg(unix)]
+        {
+            use std::os::unix::fs::MetadataExt;
+            Self {
+                len,
+                modified,
+                changed: Some((meta.ctime(), meta.ctime_nsec() as u32)),
+                inode: meta.ino(),
+            }
+        }
+        #[cfg(windows)]
+        {
+            Self {
+                len,
+                modified,
+                created: meta.created().ok(),
+            }
+        }
+        #[cfg(not(any(unix, windows)))]
+        {
+            Self { len, modified }
+        }
+    }
+}
+
 /// identity of the reader a frame was read from
 #[derive(Debug, Clone, PartialEq, Eq, Hash)]
 pub(crate) struct ReaderKey {
@@ -22,6 +85,7 @@ pub(crate) struct ReaderKey {
     pub(crate) path: PathBuf,
     pub(crate) series: usize,
     pub(crate) position: usize,
+    pub(crate) stamp: FileStamp,
 }
 
 /// borrowed view of [`ReaderKey`] for cache lookups without allocation.
@@ -33,6 +97,7 @@ pub(crate) struct ReaderKeyRef<'a> {
     pub(crate) path: &'a Path,
     pub(crate) series: usize,
     pub(crate) position: usize,
+    pub(crate) stamp: FileStamp,
 }
 
 impl Hash for ReaderKeyRef<'_> {
@@ -41,6 +106,7 @@ impl Hash for ReaderKeyRef<'_> {
         self.path.hash(state);
         self.series.hash(state);
         self.position.hash(state);
+        self.stamp.hash(state);
     }
 }
 
@@ -50,6 +116,7 @@ impl Equivalent<ReaderKey> for ReaderKeyRef<'_> {
             && self.path == key.path.as_path()
             && self.series == key.series
             && self.position == key.position
+            && self.stamp == key.stamp
     }
 }
 
@@ -60,6 +127,7 @@ impl ReaderKeyRef<'_> {
             path: self.path.to_path_buf(),
             series: self.series,
             position: self.position,
+            stamp: self.stamp,
         }
     }
 }
@@ -320,3 +388,42 @@ impl Debug for ArrayCache {
         f.debug_struct("ArrayCache").finish_non_exhaustive()
     }
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    fn temp_path(name: &str) -> PathBuf {
+        let dir = std::env::temp_dir().join(format!("ndbioimage-cache-{}", std::process::id()));
+        std::fs::create_dir_all(&dir).unwrap();
+        dir.join(name)
+    }
+
+    #[test]
+    fn file_stamp_detects_rewrite() {
+        let path = temp_path("stamp.bin");
+        std::fs::write(&path, b"aaaa").unwrap();
+        let before = FileStamp::from_path(&path);
+        std::fs::write(&path, b"bbbbbb").unwrap();
+        let after = FileStamp::from_path(&path);
+        assert_ne!(before, after);
+        let _ = std::fs::remove_file(&path);
+    }
+
+    #[test]
+    fn reader_key_includes_file_stamp() {
+        let key = |stamp| ReaderKey {
+            name: "test".to_string(),
+            path: PathBuf::from("test.tif"),
+            series: 0,
+            position: 0,
+            stamp,
+        };
+        let a = key(FileStamp::from_path(Path::new("does-not-exist.tif")));
+        let b = key(FileStamp {
+            len: 1,
+            ..FileStamp::default()
+        });
+        assert_ne!(a, b);
+    }
+}

ndbioimage/src/error.rs

@@ -47,7 +47,7 @@ pub enum Error {
     #[error(transparent)]
     Tiff(#[from] tiff::TiffError),
     /// a postcard (de)serialization error
-    #[cfg(feature = "python")]
+    #[cfg(any(test, feature = "python"))]
     #[error(transparent)]
     PostCard(#[from] postcard::Error),
     /// an error from the libczi binding
@@ -172,6 +172,13 @@ pub enum Error {
     /// file mismatch
     #[error("{0} do not match in {1} and {2}")]
     FileMismatch(String, String, String),
+    /// a jvm created in another process was inherited across a fork
+    #[cfg(feature = "bioformats_java")]
+    #[error(
+        "the jvm was created in process {0} but this is process {1}: a forked child inherits a jvm \
+         it cannot use. read the file before forking, or start the child with spawn/exec instead."
+    )]
+    ForkedJvm(u32, u32),
 }
 
 impl Error {

ndbioimage/src/py.rs

@@ -40,7 +40,7 @@ pub(crate) fn ndbioimage_file() -> PathBuf {
     PathBuf::from(file)
 }
 
-/// generates ndbioimage/__init__.pyi
+/// generates .pyi files
 #[gen_stub_pyfunction]
 #[pyfunction]
 pub fn generate_stub(dest_path: String) -> PyResult<()> {

ndbioimage/src/py/imread.rs

@@ -147,7 +147,13 @@ impl PyView {
 #[gen_stub_pymethods]
 #[pymethods]
 impl PyView {
-    /// new view on a file at path, open series #, open as dtype: (u)int(8/16/32) or float(32/64)
+    /// new view on an image file
+    /// path: path to image file to open, can include /Pos\d
+    /// dtype: when not None; will cast image to this dtype,
+    ///     choices: (u)int(8/16/32) or float(32/64)
+    /// axes: the resulting object will represent the image with the axes in this order
+    /// reader: use a specific reader to open the file,
+    ///     view available choices with Imread.available_readers
     #[new]
     #[pyo3(signature = (path, dtype = None, axes = "cztyx", reader = None))]
     fn new<'py>(
@@ -206,6 +212,26 @@ impl PyView {
         }
     }
 
+    /// creates the jvm (if it does not exist yet) so that hotspot installs its signal handlers before
+    /// anything else does: see `crate::readers::bioformats_java::warm_jvm`
+    ///
+    /// in a python process, call this before `ray.init()`, which installs CPython's faulthandler
+    #[cfg(feature = "bioformats_java")]
+    #[staticmethod]
+    fn warm_jvm() -> PyResult<()> {
+        Ok(crate::readers::bioformats_java::warm_jvm()?)
+    }
+
+    /// returns whether the jvm was already created in this process
+    ///
+    /// this is false in a process that inherited a jvm across a fork, since such a jvm cannot be
+    /// used; reading a bio-formats file there raises instead
+    #[cfg(feature = "bioformats_java")]
+    #[staticmethod]
+    fn jvm_is_running() -> bool {
+        crate::readers::bioformats_java::jvm_is_running()
+    }
+
     /// https://numpy.org/doc/stable/reference/generated/numpy.ndarray.flags.html
     #[getter]
     fn flags(&self) -> PyFlags {

ndbioimage/src/py/transforms.rs

@@ -5,9 +5,11 @@ use image_registration::register::{Optimizer, RegistrationStep};
 use image_registration::transform::Transform;
 use ndarray::{Ix0, Ix1, Ix2, Ix3, Ix4, Ix5, IxDyn};
 use numpy::{
-    AllowTypeChange, IntoPyArray, PyArray, PyArray1, PyArray2, PyArrayDyn, PyArrayLike1,
+    AllowTypeChange, IntoPyArray, PyArray, PyArray1, PyArray2, PyArrayDescrMethods, PyArrayDyn,
-    PyArrayLike2, PyArrayLikeDyn,
+    PyArrayLike1, PyArrayLike2, PyArrayLikeDyn, PyArrayMethods, PyUntypedArray,
+    PyUntypedArrayMethods, dtype,
 };
+use pyo3::IntoPyObjectExt;
 use pyo3::exceptions::{PyNotImplementedError, PyValueError};
 use pyo3::prelude::*;
 use pyo3_stub_gen::derive::*;
@@ -165,6 +167,18 @@ impl PyTransform {
         self.inner.center = center;
     }
 
+    /// backwards compatibility
+    #[getter]
+    fn get_origin(&self) -> Vec<f64> {
+        self.inner.center.clone()
+    }
+
+    /// backwards compatibility
+    #[setter]
+    fn set_origin(&mut self, center: Vec<f64>) {
+        self.inner.center = center;
+    }
+
     #[getter]
     fn get_shape(&self) -> Vec<usize> {
         self.inner.shape.clone()
@@ -329,6 +343,88 @@ impl PyTransform {
             .into_pyarray(py))
     }
 
+    /// backwards compatibility, default parameter is not implemented
+    #[gen_stub(override_return_type(type_repr="numpy.ndarray", imports=("numpy")))]
+    #[pyo3(signature = (image, default = None))]
+    fn frame<'py>(
+        &self,
+        py: Python<'py>,
+        #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
+        image: Bound<'py, PyUntypedArray>,
+        default: Option<Bound<'py, PyAny>>,
+    ) -> PyResult<Bound<'py, PyAny>> {
+        if default.is_some() {
+            return Err(PyNotImplementedError::new_err(
+                "default parameter is not implemented",
+            ));
+        }
+        if image.ndim() != self.inner.ndim() {
+            return Err(PyValueError::new_err(format!(
+                "dimensionality of image ({}) and transform ({}) do not correspond",
+                image.ndim(),
+                self.inner.ndim()
+            )));
+        }
+
+        macro_rules! interp {
+            ($order:expr, $t:tt) => {
+                self.inner
+                    .interpolate_par::<$order, _, _>(
+                        unsafe { image.cast::<PyArrayDyn<$t>>()?.as_array() }
+                            .mapv(|i| i as f64)
+                            .into_dimensionality()
+                            .map_err(Error::from)?
+                            .view(),
+                    )
+                    .map_err(Error::from)?
+                    .mapv(|i| i as $t)
+                    .into_pyarray(py)
+                    .into_bound_py_any(py)
+            };
+        }
+
+        let dt = image.dtype();
+        if dt.is_equiv_to(&dtype::<bool>(py)) {
+            self.inner
+                .interpolate_par::<0, _, _>(
+                    unsafe { image.cast::<PyArrayDyn<bool>>()?.as_array() }
+                        .mapv(|i| if i { 1.0 } else { 0.0 })
+                        .into_dimensionality()
+                        .map_err(Error::from)?
+                        .view(),
+                )
+                .map_err(Error::from)?
+                .mapv(|i| i > 0.5)
+                .into_pyarray(py)
+                .into_bound_py_any(py)
+        } else if dt.is_equiv_to(&dtype::<u8>(py)) {
+            interp!(0, u8)
+        } else if dt.is_equiv_to(&dtype::<i8>(py)) {
+            interp!(0, i8)
+        } else if dt.is_equiv_to(&dtype::<u16>(py)) {
+            interp!(0, u16)
+        } else if dt.is_equiv_to(&dtype::<i16>(py)) {
+            interp!(0, i16)
+        } else if dt.is_equiv_to(&dtype::<u32>(py)) {
+            interp!(0, u32)
+        } else if dt.is_equiv_to(&dtype::<i32>(py)) {
+            interp!(0, i32)
+        } else if dt.is_equiv_to(&dtype::<u64>(py)) {
+            interp!(0, u64)
+        } else if dt.is_equiv_to(&dtype::<i64>(py)) {
+            interp!(0, i64)
+        } else if dt.is_equiv_to(&dtype::<f32>(py)) {
+            interp!(3, f32)
+        } else if dt.is_equiv_to(&dtype::<f64>(py)) {
+            interp!(3, f64)
+        } else {
+            Err(PyValueError::new_err(format!(
+                "invalid dtype: {}; must be bool, (u)int(8/16/32/64) or float(32/64)",
+                dt
+            )))
+        }
+    }
+
     fn is_unity(&self) -> bool {
         self.inner.is_unity()
     }

ndbioimage/src/readers/bioformats_java.rs

@@ -14,6 +14,7 @@ use std::hash::{Hash, Hasher};
 use std::ops::Deref;
 use std::rc::Rc;
 use std::sync::Mutex;
+use std::sync::atomic::{AtomicU32, Ordering};
 use thread_local::ThreadLocal;
 
 include!(concat!(env!("OUT_DIR"), "/constants.rs"));
@@ -24,10 +25,33 @@ thread_local! {
 
 static DOWNLOAD_LOCK: Mutex<()> = Mutex::new(());
 static JVM_BUILT: Mutex<bool> = Mutex::new(false);
+/// the process that called [JvmBuilder::build], 0 if no jvm has been built yet
+static JVM_PID: AtomicU32 = AtomicU32::new(0);
+
+/// Returns `Ok(())` if the jvm in this process can still be used, and an error if it was inherited
+/// across a fork.
+///
+/// A fork copies the address space, so the child gets the parent's jvm wholesale: its threads do
+/// not exist and any lock another thread held at the moment of the fork stays held forever. There
+/// is no way to repair that, and no way to start a replacement either, because HotSpot's
+/// "a jvm already exists" flag lives in libjvm's private data and is copied along with everything
+/// else -- verified by `JNI_GetCreatedJavaVMs`, which still reports 1 in the child, so a second
+/// `JNI_CreateJavaVM` (which is what j4rs' `Jvm::attach_thread` calls) takes the already-exists
+/// path. An `exec` replaces the address space, and that does reset the count to 0.
+fn check_not_forked() -> Result<(), Error> {
+    let built_in = JVM_PID.load(Ordering::Relaxed);
+    if built_in != 0 && built_in != std::process::id() {
+        return Err(Error::ForkedJvm(built_in, std::process::id()));
+    }
+    Ok(())
+}
 
 /// Ensure 1 jvm per thread
-fn jvm() -> Rc<Jvm> {
+fn jvm() -> Result<Rc<Jvm>, Error> {
-    JVM.with(|cell| {
+    // before touching JVM: in a forked child that thread's cell may already hold an Rc<Jvm> whose
+    // vm is gone, and the guard in check_not_forked is the only thing that can catch that.
+    check_not_forked()?;
+    Ok(JVM.with(|cell| {
         cell.get_or_init(move || {
             #[cfg(feature = "python")]
             let path = crate::py::ndbioimage_file();
@@ -113,6 +137,7 @@ fn jvm() -> Rc<Jvm> {
                         .java_opt(JavaOpt::new("--sun-misc-unsafe-memory-access=allow"))
                         .build()
                         .expect("Failed to build JVM");
+                    JVM_PID.store(std::process::id(), Ordering::Relaxed);
                     if let Ok(e) = InvocationArg::try_from("ERROR") {
                         let _ = j.invoke_static(
                             "loci.common.DebugTools",
@@ -125,9 +150,103 @@ fn jvm() -> Rc<Jvm> {
             }
         })
             .clone()
-    })
+    }))
 }
 
+/// Returns `true` if the jvm was already created on the current thread.
+///
+/// The jvm is created lazily, on the first bio-formats read, and HotSpot installs its own signal
+/// handlers while starting up. So this tells whether those handlers are in place yet.
+///
+/// This is process-wide, not thread-local: a forked child inherited the parent's jvm but cannot
+/// use it, so reporting `true` there would only invite the deadlock that [check_not_forked] turns
+/// into an error.
+pub fn jvm_is_running() -> bool {
+    JVM_PID.load(Ordering::Relaxed) == std::process::id() && JVM.with(|cell| cell.get().is_some())
+}
+
+/// Creates the jvm on the current thread if it does not exist yet (no-op if it already does),
+/// and initializes bio-formats on it.
+///
+/// This exists because of how HotSpot probes the cpu features during VM init: on an avx-512
+/// capable cpu it deliberately reads through a NULL pointer (`VM_Version::_cpuinfo_segv_addr`, set
+/// to the address of the generated cpu-feature stub) and resumes from its own SIGSEGV handler after
+/// recognizing that address in `PosixSignals::pd_hotspot_signal_handler`.
+///
+/// Any SIGSEGV handler that was installed *before* the VM started is not that handler, and
+/// HotSpot chains to it instead. Then the deliberate fault is not recognized, the chained handler
+/// re-raises SIGSEGV, and the re-entrant pass no longer has a recognizable pc and ends in
+/// `VMError::report_and_die` -> `os::die()` -> `abort()`.
+///
+/// In a python process this bites when `ray.init()` has already installed CPython's faulthandler
+/// (ray/_private/worker.py), so call this before that.
+///
+/// Note that creating the VM is *not* enough: it has to be initialized far enough that the
+/// deliberate fault has been taken before the foreign handler shows up. Measured on an AMD EPYC
+/// 9124 (avx-512, XCR0 = 0x2e7) with ray: merely creating the VM leaves the crash rate unchanged,
+/// and so does loading the reader classes without opening a file. What does work is initializing a
+/// reader on an actual (tiny) image, so that is what this does.
+pub fn warm_jvm() -> Result<(), Error> {
+    let jvm = jvm()?;
+    let no_args: &[InvocationArg] = &[];
+    // jvm() only *creates* the VM; run one static method so that this only returns Ok once the VM
+    // can actually run java bytecode.
+    let version = jvm.invoke_static(
+        "java.lang.System",
+        "getProperty",
+        &[InvocationArg::try_from("java.version")?],
+    )?;
+    let _: String = jvm.to_rust(version)?;
+
+    // loads (and runs the static initializers of) every reader class in the registry
+    let _ = jvm.invoke_static(
+        "loci.formats.ImageReader",
+        "getDefaultReaderClasses",
+        no_args,
+    )?;
+
+    // then open a 1x1 image so that the reader and its OMEXML metadata store get initialized.
+    // ImageReader.setId needs a real file, so write the tiff out and clean it up again.
+    let path = std::env::temp_dir().join(format!("ndbioimage-warm-jvm-{}.tif", std::process::id()));
+    std::fs::write(&path, WARM_TIFF)?;
+    let result = (|| -> Result<(), Error> {
+        let reader = jvm.create_instance("loci.formats.ImageReader", no_args)?;
+        jvm.invoke(
+            &reader,
+            "setId",
+            &[InvocationArg::try_from(path.to_string_lossy().as_ref())?],
+        )?;
+        let _: i32 = jvm.to_rust(jvm.invoke(&reader, "getSizeY", no_args)?)?;
+        let _ = jvm.invoke(&reader, "getMetadataStore", no_args)?;
+        Ok(())
+    })();
+    let _ = std::fs::remove_file(&path);
+    result
+}
+
+/// A 1x1 8-bit grayscale tiff (written by tifffile), used by [warm_jvm] to give bio-formats
+/// something it can open.
+const WARM_TIFF: &[u8] = &[
+    0x49, 0x49, 0x2a, 0x00, 0x08, 0x00, 0x00, 0x00, 0x0e, 0x00, 0x00, 0x01, 0x04, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x01, 0x04, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x02, 0x01, 0x03, 0x00, 0x01, 0x00, 0x00, 0x00, 0x08, 0x00, 0x00, 0x00, 0x03, 0x01,
+    0x03, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x06, 0x01, 0x03, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x0e, 0x01, 0x02, 0x00, 0x12, 0x00, 0x00, 0x00, 0xb6, 0x00,
+    0x00, 0x00, 0x11, 0x01, 0x04, 0x00, 0x01, 0x00, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x15, 0x01,
+    0x03, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x16, 0x01, 0x04, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x17, 0x01, 0x04, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x1a, 0x01, 0x05, 0x00, 0x01, 0x00, 0x00, 0x00, 0xd8, 0x00, 0x00, 0x00, 0x1b, 0x01,
+    0x05, 0x00, 0x01, 0x00, 0x00, 0x00, 0xe0, 0x00, 0x00, 0x00, 0x28, 0x01, 0x03, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x31, 0x01, 0x02, 0x00, 0x0c, 0x00, 0x00, 0x00, 0xe8, 0x00,
+    0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x7b, 0x22, 0x73, 0x68, 0x61, 0x70, 0x65, 0x22, 0x3a,
+    0x20, 0x5b, 0x31, 0x2c, 0x20, 0x31, 0x5d, 0x7d, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
+    0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x00, 0x00, 0x00, 0x01, 0x00,
+    0x00, 0x00, 0x00, 0x74, 0x69, 0x66, 0x66, 0x66, 0x69, 0x6c, 0x65, 0x2e, 0x70, 0x79, 0x00, 0x00,
+    0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00,
+    0x00, 0x00,
+];
+
 macro_rules! method_return {
     ($R:ty$(|c)?) => { Result<$R, Error> };
     () => { Result<(), Error> };
@@ -147,14 +266,14 @@ macro_rules! method {
         #[allow(dead_code)]
         pub(crate) fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) {
             let args: Vec<InvocationArg> = vec![$($( method_arg!($n:$t$(|$p)?) ),*)?];
-            let _result = jvm().invoke(&self.0, $method, &args)?;
+            let _result = jvm()?.invoke(&self.0, $method, &args)?;
 
             macro_rules! method_result {
                 ($R:ty|c) => {
-                    Ok(jvm().to_rust(_result)?)
+                    Ok(jvm()?.to_rust(_result)?)
                 };
                 ($R:ty|d) => {
-                    Ok(jvm().to_rust_deserialized(_result)?)
+                    Ok(jvm()?.to_rust_deserialized(_result)?)
                 };
                 ($R:ty) => {
                     Ok(_result)
@@ -187,7 +306,7 @@ pub struct DebugTools;
 impl DebugTools {
     /// set debug root level: ERROR, DEBUG, TRACE, INFO, OFF
     pub fn set_root_level(level: &str) -> Result<(), Error> {
-        jvm().invoke_static(
+        jvm()?.invoke_static(
             "loci.common.DebugTools",
             "setRootLevel",
             &[InvocationArg::try_from(level)?],
@@ -201,7 +320,7 @@ pub(crate) struct ChannelSeparator(Instance);
 
 impl ChannelSeparator {
     pub(crate) fn new(image_reader: &ImageReader) -> Result<Self, Error> {
-        let jvm = jvm();
+        let jvm = jvm()?;
         let channel_separator = jvm.create_instance(
             "loci.formats.ChannelSeparator",
             &[InvocationArg::from(jvm.clone_instance(&image_reader.0)?)],
@@ -228,7 +347,7 @@ impl Drop for ImageReader {
 
 impl ImageReader {
     pub(crate) fn new() -> Result<Self, Error> {
-        let reader = jvm().create_instance("loci.formats.ImageReader", InvocationArg::empty())?;
+        let reader = jvm()?.create_instance("loci.formats.ImageReader", InvocationArg::empty())?;
         Ok(ImageReader(reader))
     }
 
@@ -238,7 +357,7 @@ impl ImageReader {
 
     pub(crate) fn ome_xml(&self) -> Result<String, Error> {
         let mds = self.get_metadata_store()?;
-        Ok(jvm()
+        Ok(jvm()?
             .chain(&mds)?
             .cast("loci.formats.ome.OMEPyramidStore")?
             .invoke("dumpXML", InvocationArg::empty())?
@@ -276,7 +395,7 @@ pub(crate) struct MetadataTools(Instance);
 impl MetadataTools {
     pub(crate) fn new() -> Result<Self, Error> {
         let meta_data_tools =
-            jvm().create_instance("loci.formats.MetadataTools", InvocationArg::empty())?;
+            jvm()?.create_instance("loci.formats.MetadataTools", InvocationArg::empty())?;
         Ok(MetadataTools(meta_data_tools))
     }
 
@@ -517,6 +636,10 @@ impl Reader for BioFormatsJavaReader {
     where
         P: AsRef<Path>,
     {
+        // checked here as well as in jvm() so that this entry point fails with the error rather
+        // than reaching get_size_x() below, which goes through deref() -> get_reader().unwrap()
+        // and would turn it into a panic.
+        check_not_forked()?;
         let mut path = path.as_ref().to_path_buf();
         if path.is_dir() {
             let orig = path.clone();
@@ -648,6 +771,7 @@ mod tests {
         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_i: "tiffseq/YTL1841B2-2-1_1hr_DMSO_galinduction_1",
+        metadata_j: "tiff/R1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001_MMStack_PosR1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001.ome.tif",
     }
 
     #[test]

ndbioimage/src/readers/tiff.rs

@@ -7,10 +7,11 @@ use std::cell::{RefCell, RefMut};
 use std::collections::{HashMap, HashSet};
 use std::fs::File;
 use std::hash::{Hash, Hasher};
+use std::io::{Read, Seek};
 use std::path::{Path, PathBuf};
 use thread_local::ThreadLocal;
 use tiff::decoder::ifd::Value;
-use tiff::decoder::{Decoder, DecodingResult};
+use tiff::decoder::{Decoder, DecodingSampleBuffer};
 use tiff::tags::Tag;
 
 /// reader for single tiff image files
@@ -70,8 +71,9 @@ impl TiffReader {
     fn get_reader(&self) -> Result<RefMut<'_, Decoder<File>>, Error> {
         self.reader
             .get_or_try(|| {
-                let file = File::open(&self.path)?;
+                let mut decoder = Decoder::open(File::open(&self.path)?)?;
-                Ok(RefCell::new(Decoder::new(file)?))
+                decoder.next_image()?;
+                Ok(RefCell::new(decoder))
             })
             .map(|i| i.borrow_mut())
     }
@@ -128,10 +130,11 @@ impl Reader for TiffReader {
         };
 
         let mut reader = new.get_reader()?;
-        let width = reader.get_tag(Tag::ImageWidth)?.into_u32()? as usize;
+        let width = reader.current_ifd().get_tag(Tag::ImageWidth)?.into_u32()? as usize;
-        let height = reader.get_tag(Tag::ImageLength)?.into_u32()? as usize;
+        let height = reader.current_ifd().get_tag(Tag::ImageLength)?.into_u32()? as usize;
 
         let n_samples = reader
+            .current_ifd()
             .get_tag(Tag::SamplesPerPixel)
             .ok()
             .and_then(|t| t.into_u16().ok())
@@ -139,9 +142,14 @@ impl Reader for TiffReader {
 
         let bits = tag_first_u16(&mut reader, Tag::BitsPerSample).unwrap_or(8);
         let sfmt = tag_first_u16(&mut reader, Tag::SampleFormat).unwrap_or(1);
+
+        // indexed color pages (PhotometricInterpretation::RGBPalette) are read as plain
+        // intensities: the pixel values are indices into the ColorMap palette, which is display
+        // information that ndbioimage does not use.
         let pixtype = pixel_type_from_bits_sample(bits, sfmt)?;
 
         let planar = reader
+            .current_ifd()
             .get_tag(Tag::PlanarConfiguration)
             .ok()
             .and_then(|t| t.into_u16().ok())
@@ -149,8 +157,9 @@ impl Reader for TiffReader {
             == 2;
 
         let imagej_bytes = reader
+            .current_ifd()
             .get_tag(Tag::Unknown(50839))
-            .or_else(|_| reader.get_tag(Tag::ImageDescription))?;
+            .or_else(|_| reader.current_ifd().get_tag(Tag::ImageDescription))?;
         let imagej_bytes = match imagej_bytes {
             Value::Ascii(s) => s.into_bytes(),
             other => other.into_u8_vec()?,
@@ -180,7 +189,7 @@ impl Reader for TiffReader {
 
         let mut n_ifds = 1;
         while reader.more_images() {
-            reader.next_image()?;
+            reader.next_directory()?;
             n_ifds += 1;
         }
 
@@ -212,8 +221,9 @@ impl Reader for TiffReader {
     fn metadata(&self) -> Result<Ome, Error> {
         let mut reader = self.get_reader()?;
         let imagej_bytes = reader
+            .current_ifd()
             .get_tag(Tag::Unknown(50839))
-            .or_else(|_| reader.get_tag(Tag::ImageDescription))?;
+            .or_else(|_| reader.current_ifd().get_tag(Tag::ImageDescription))?;
         let imagej_bytes = match imagej_bytes {
             Value::Ascii(s) => s.into_bytes(),
             other => other.into_u8_vec()?,
@@ -225,11 +235,13 @@ impl Reader for TiffReader {
             .get("interval")
             .and_then(|v| v.parse::<f64>().ok());
         let ru = reader
+            .current_ifd()
             .get_tag(Tag::ResolutionUnit)
             .ok()
             .and_then(|i| i.into_u16().ok())
             .unwrap_or(2);
         let pixel_size = reader
+            .current_ifd()
             .get_tag(Tag::XResolution)
             .ok()
             .and_then(|i| i.into_u64_vec().ok())
@@ -353,8 +365,8 @@ impl Reader for TiffReader {
         let mut reader = self.get_reader()?;
         reader.seek_to_image(page_idx)?;
 
-        let data: DecodingResult = if self.planar {
+        let data: DecodingSampleBuffer = if self.planar {
-            let mut result = DecodingResult::U16(Vec::new());
+            let mut result = DecodingSampleBuffer::U16(Vec::new());
             reader.read_image_to_buffer(&mut result)?;
             result
         } else {
@@ -364,7 +376,7 @@ impl Reader for TiffReader {
         macro_rules! to_frame {
             ($var:ident, $ty:ty) => {{
                 let v: Vec<$ty> = match data {
-                    DecodingResult::$var(v) => v,
+                    DecodingSampleBuffer::$var(v) => v,
                     _ => {
                         return Err(Error::Parse(format!(
                             "type mismatch: expected {}",
@@ -448,9 +460,8 @@ impl Reader for TiffReader {
     }
 }
 
-fn tag_first_u16(reader: &mut RefMut<Decoder<File>>, tag: Tag) -> Option<u16> {
+fn tag_first_u16<R: Read + Seek>(reader: &mut RefMut<Decoder<R>>, tag: Tag) -> Option<u16> {
-    let val = reader.get_tag(tag).ok()?;
+    let val = reader.current_ifd().get_tag(tag).ok()?;
-    use tiff::decoder::ifd::Value;
     match val {
         Value::Short(v) => Some(v),
         Value::List(list) => list.first().and_then(|v| match v {
@@ -464,6 +475,7 @@ fn tag_first_u16(reader: &mut RefMut<Decoder<File>>, tag: Tag) -> Option<u16> {
 #[cfg(test)]
 mod tests {
     use super::*;
+    use ndarray::s;
 
     fn open(file: &str) -> Result<TiffReader, Error> {
         let path = std::env::current_dir()?
@@ -480,6 +492,22 @@ mod tests {
                 fn $name() -> Result<(), Error> {
                     let ts = open($file)?;
                     println!("{}", ts.view().squeeze()?.summary()?);
+
+                    let view = ts.view();
+                    let first_frame = view.slice_cztyx(s![0, 0, 0, .., ..])?;
+                    let array = first_frame.as_array::<u16>()?;
+                    println!("{:?}", array);
+                    assert_eq!(ts.shape.y, array.shape()[0]);
+                    assert_eq!(ts.shape.x, array.shape()[1]);
+
+                    if view.shape.t > 1 {
+                        let second_frame = view.slice_cztyx(s![0, 0, 1, .., ..])?;
+                        let array = second_frame.as_array::<u16>()?;
+                        println!("{:?}", array);
+                        assert_eq!(ts.shape.y, array.shape()[0]);
+                        assert_eq!(ts.shape.x, array.shape()[1]);
+                    }
+
                     Ok(())
                 }
             )*
@@ -487,11 +515,12 @@ mod tests {
     }
 
     test_metadata! {
-        // metadata_a: "tiff/20251014_20-Pos_000_000_mask.tif",
+        metadata_a: "tiff/20251014_20-Pos_000_000_mask.tif",
         metadata_b: "tiff/20251014_20-Pos_000_000_max.tif",
         metadata_c: "tiff/20251014_20-Pos_000_000_loc_results_Cy3.tif",
         metadata_e: "tiff/1xp53-01-AP1.tiff",
         metadata_f: "tiff/test.tif",
-        // metadata_g: "tiff/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.tif",
+        metadata_g: "tiff/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.tif",
+        metadata_h: "tiff/Wapl-AID_C46_13_tagRFPt_MCP_well1_video1_1_max.tif"
     }
 }

ndbioimage/src/readers/tiffseq.rs

@@ -8,7 +8,7 @@ use std::collections::{HashMap, HashSet};
 use std::hash::{Hash, Hasher};
 use std::path::{Path, PathBuf};
 use std::str::FromStr;
-use tiff::decoder::{Decoder, DecodingResult};
+use tiff::decoder::{Decoder, DecodingSampleBuffer};
 use tiff::tags::Tag;
 
 /// reader for sequences of tiff files (one file per z/time plane)
@@ -84,9 +84,13 @@ impl TiffSeqReader {
 
     fn read_tiff_dimensions(path: &Path) -> Result<(usize, usize), Error> {
         let file = std::fs::File::open(path)?;
-        let mut decoder = Decoder::new(file)?;
+        let mut decoder = Decoder::open(file)?;
-        let width = decoder.get_tag(Tag::ImageWidth)?.into_u32()? as usize;
+        decoder.next_image()?;
-        let height = decoder.get_tag(Tag::ImageLength)?.into_u32()? as usize;
+        let width = decoder.current_ifd().get_tag(Tag::ImageWidth)?.into_u32()? as usize;
+        let height = decoder
+            .current_ifd()
+            .get_tag(Tag::ImageLength)?
+            .into_u32()? as usize;
         Ok((width, height))
     }
 }
@@ -514,38 +518,39 @@ impl Reader for TiffSeqReader {
             .ok_or_else(|| Error::OutOfBounds(c.max(z).max(t) as isize, 0))?;
 
         let rdr = std::fs::File::open(file)?;
-        let mut decoder = Decoder::new(rdr)?;
+        let mut decoder = Decoder::open(rdr)?;
+        decoder.next_image()?;
 
         match decoder.read_image()? {
-            DecodingResult::U8(d) => Ok(ArrayT::U8(Array2::from_shape_vec(
+            DecodingSampleBuffer::U8(d) => Ok(ArrayT::U8(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),
-            DecodingResult::U16(d) => Ok(ArrayT::U16(Array2::from_shape_vec(
+            DecodingSampleBuffer::U16(d) => Ok(ArrayT::U16(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),
-            DecodingResult::U32(d) => Ok(ArrayT::U32(Array2::from_shape_vec(
+            DecodingSampleBuffer::U32(d) => Ok(ArrayT::U32(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),
-            DecodingResult::I8(d) => Ok(ArrayT::I8(Array2::from_shape_vec(
+            DecodingSampleBuffer::I8(d) => Ok(ArrayT::I8(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),
-            DecodingResult::I16(d) => Ok(ArrayT::I16(Array2::from_shape_vec(
+            DecodingSampleBuffer::I16(d) => Ok(ArrayT::I16(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),
-            DecodingResult::I32(d) => Ok(ArrayT::I32(Array2::from_shape_vec(
+            DecodingSampleBuffer::I32(d) => Ok(ArrayT::I32(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),
-            DecodingResult::F32(d) => Ok(ArrayT::F32(Array2::from_shape_vec(
+            DecodingSampleBuffer::F32(d) => Ok(ArrayT::F32(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),
-            DecodingResult::F64(d) => Ok(ArrayT::F64(Array2::from_shape_vec(
+            DecodingSampleBuffer::F64(d) => Ok(ArrayT::F64(Array2::from_shape_vec(
                 (self.shape.y, self.shape.x),
                 d,
             )?)),

ndbioimage/src/tiffwrite.rs

@@ -321,4 +321,44 @@ mod tests {
         batch_to_tiff(&files_in, &files_out, None, None, true, true, None)?;
         Ok(())
     }
+
+    /// a rewritten file must not be served from the process-wide cache
+    #[cfg(feature = "tiff")]
+    #[test]
+    fn cache_invalidated_after_rewrite() -> Result<(), Error> {
+        use crate::view::View;
+        use ndarray::Array2;
+        use std::time::{Duration, SystemTime};
+        use tiffwrite::IJTiffFile;
+
+        let dir = std::env::temp_dir().join(format!("ndbioimage-rewrite-{}", std::process::id()));
+        create_dir_all(&dir)?;
+        let path = dir.join("cache_rewrite.tif");
+
+        let write = |value: u16| -> Result<(), Error> {
+            let mut tiff = IJTiffFile::new(&path)?;
+            tiff.save(Array2::<u16>::from_elem((4, 4), value), 0, 0, 0)?;
+            Ok(())
+        };
+
+        write(1)?;
+        let view: View<_, DynReader> = View::from_path(&path)?;
+        let frame: Array2<u16> = view.get_frame(0, 0, 0)?;
+        assert_eq!(frame[(0, 0)], 1);
+
+        write(2)?;
+        // make the modification time unambiguous even on filesystems with a
+        // coarse timestamp resolution
+        let file = std::fs::OpenOptions::new().write(true).open(&path)?;
+        file.set_modified(SystemTime::UNIX_EPOCH + Duration::from_secs(1_000_000_000))?;
+        drop(file);
+
+        let view: View<_, DynReader> = View::from_path(&path)?;
+        let frame: Array2<u16> = view.get_frame(0, 0, 0)?;
+        assert_eq!(frame[(0, 0)], 2);
+
+        let _ = std::fs::remove_file(&path);
+        let _ = std::fs::remove_dir(&dir);
+        Ok(())
+    }
 }

ndbioimage/src/transforms.rs

@@ -46,14 +46,49 @@ impl TryFrom<HashMap<String, TransformOld>> for Transforms {
     }
 }
 
-#[derive(Clone, Debug, Default, Eq, PartialEq, Serialize, Deserialize)]
+#[derive(Clone, Debug, Default, Eq, PartialEq, Deserialize)]
 pub struct Transforms {
-    #[serde(skip_serializing_if = "HashMap::is_empty", default = "HashMap::new")]
+    #[serde(default)]
     pub channel: HashMap<String, Transform<IxDyn>>,
-    #[serde(skip_serializing_if = "Vec::is_empty", default = "Vec::new")]
+    #[serde(default)]
     pub drift: Vec<Transform<IxDyn>>,
 }
 
+impl Serialize for Transforms {
+    fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
+    where
+        S: serde::Serializer,
+    {
+        #[derive(Serialize)]
+        struct HumanReadable<'a> {
+            #[serde(skip_serializing_if = "HashMap::is_empty")]
+            channel: &'a HashMap<String, Transform<IxDyn>>,
+            #[serde(skip_serializing_if = "Vec::is_empty")]
+            drift: &'a Vec<Transform<IxDyn>>,
+        }
+
+        #[derive(Serialize)]
+        struct Binary<'a> {
+            channel: &'a HashMap<String, Transform<IxDyn>>,
+            drift: &'a Vec<Transform<IxDyn>>,
+        }
+
+        if serializer.is_human_readable() {
+            HumanReadable {
+                channel: &self.channel,
+                drift: &self.drift,
+            }
+            .serialize(serializer)
+        } else {
+            Binary {
+                channel: &self.channel,
+                drift: &self.drift,
+            }
+            .serialize(serializer)
+        }
+    }
+}
+
 impl Transforms {
     pub fn load<P: AsRef<Path>>(path: P) -> Result<Self, Error> {
         let mut file = std::fs::File::open(&path)?;

ndbioimage/src/view.rs

@@ -1,5 +1,5 @@
 use crate::axes::{Ax, Axis, Operation, Shape, Slice, SliceInfoElemDef, slice_info};
-use crate::cache::{ArrayCache, ArrayKeyRef, FrameCache, FrameKeyRef, ReaderKeyRef};
+use crate::cache::{ArrayCache, ArrayKeyRef, FileStamp, FrameCache, FrameKeyRef, ReaderKeyRef};
 use crate::error::Error;
 use crate::metadata::Metadata;
 use crate::readers::{Dimensions, DynReader, Frame, Reader};
@@ -274,7 +274,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
         &self.axes
     }
 
-    #[expect(dead_code)]
+    #[allow(dead_code)]
     pub(crate) fn get_operations(&self) -> &IndexMap<Axis, Operation> {
         &self.operations
     }
@@ -964,6 +964,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
                 path: self.reader.path(),
                 series: self.reader.series(),
                 position: self.reader.position(),
+                stamp: FileStamp::from_path(self.reader.path()),
             },
             c,
             z,
@@ -978,6 +979,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
                 path: self.reader.path(),
                 series: self.reader.series(),
                 position: self.reader.position(),
+                stamp: FileStamp::from_path(self.reader.path()),
             },
             dtype: type_name::<T>(),
             slice: &self.slice,
@@ -1226,14 +1228,17 @@ to_bytes_vec_impl!(
 #[cfg(test)]
 mod tests {
     use crate::axes::{Axis, Operation};
-    use crate::cache::{ArrayCache, ArrayKey, ArrayKeyRef, FrameCache, ReaderKey, ReaderKeyRef};
+    use crate::cache::{
+        ArrayCache, ArrayKey, ArrayKeyRef, FileStamp, FrameCache, ReaderKey, ReaderKeyRef,
+    };
     use crate::error::Error;
     use crate::readers::{DynReader, Frame, Reader};
     use crate::stats::MinMax;
-    use crate::view::Item;
+    use crate::view::{Item, View};
     use indexmap::IndexMap;
-    use ndarray::{Array, Array4, Array5, NewAxis};
+    use ndarray::{Array, Array4, Array5, Ix5, NewAxis};
     use ndarray::{Array2, ArrayD, IxDyn, SliceInfoElem, s};
+    use postcard::{from_bytes, to_stdvec};
     use std::path::{Path, PathBuf};
     use std::sync::Arc;
 
@@ -1514,6 +1519,7 @@ mod tests {
                     path: PathBuf::from("test.tif"),
                     series: 0,
                     position: 0,
+                    stamp: FileStamp::default(),
                 },
                 c,
                 z,
@@ -1549,6 +1555,7 @@ mod tests {
                 path: PathBuf::from("test.tif"),
                 series: 0,
                 position: 0,
+                stamp: FileStamp::default(),
             },
             dtype,
             slice: vec![SliceInfoElem::Index(index)],
@@ -1574,6 +1581,7 @@ mod tests {
                 path: Path::new("test.tif"),
                 series: 0,
                 position: 0,
+                stamp: FileStamp::default(),
             },
             dtype: "u16",
             slice: &[SliceInfoElem::Index(0)],
@@ -1604,4 +1612,18 @@ mod tests {
         assert_eq!(a, c2);
         Ok(())
     }
+
+    #[test]
+    fn serde() -> Result<(), Error> {
+        let file = "tiff/20251014_20-Pos_000_000_max.tif";
+        let reader = open(file)?;
+        let view = reader.view();
+        let bytes = to_stdvec(&view)?;
+        let view2: View<Ix5> = from_bytes(&bytes)?;
+
+        println!("{:?}", view);
+        println!("{:?}", view2);
+
+        Ok(())
+    }
 }

py/ndbioimage/__init__.pyi

@@ -1,3 +0,0 @@
-from .ndbioimage_rs import Imread, Shape
-
-__all__ = ["Imread", "Shape"]