- implement shape in Rust
- implement more readers - fix downloading of bioformats jar - (mostly) compatible with python version
This commit is contained in:
w.pomp
@@ -0,0 +1,612 @@
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use crate::error::Error;
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use ndarray::Array2;
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use ome_metadata::Ome;
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use serde::{Deserialize, Serialize};
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use std::fmt::Debug;
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use std::path::{Path, PathBuf};
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pub use crate::readers::{ArrayT, PixelType, Reader};
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use crate::readers::{DynReader, Frame, Shape};
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use j4rs::{Instance, InvocationArg, Jvm, JvmBuilder};
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use std::cell::OnceCell;
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use std::collections::HashSet;
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use std::hash::{Hash, Hasher};
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use std::ops::Deref;
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use std::rc::Rc;
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use std::sync::Mutex;
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use thread_local::ThreadLocal;
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include!(concat!(env!("OUT_DIR"), "/constants.rs"));
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thread_local! {
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static JVM: OnceCell<Rc<Jvm>> = const { OnceCell::new() }
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}
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static DOWNLOAD_LOCK: Mutex<()> = Mutex::new(());
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static JVM_BUILT: Mutex<bool> = Mutex::new(false);
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/// Ensure 1 jvm per thread
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fn jvm() -> Rc<Jvm> {
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JVM.with(|cell| {
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cell.get_or_init(move || {
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#[cfg(feature = "python")]
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let path = crate::py::ndbioimage_file();
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#[cfg(not(feature = "python"))]
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let path = std::env::current_exe()
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.unwrap()
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.parent()
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.unwrap()
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.to_path_buf();
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let class_path = if path.join("jassets").exists() {
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path.as_path()
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} else {
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path.parent().unwrap()
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};
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// download jars if needed, but make sure only one thread will do this
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{
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let _guard = DOWNLOAD_LOCK.lock().unwrap();
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let jassets = class_path.join("jassets");
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if !jassets.exists() {
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std::fs::create_dir_all(&jassets).unwrap();
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}
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if !jassets.join(format!("j4rs-{}-jar-with-dependencies.jar", J4RS_VERSION)).exists() {
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println!("downloading j4rs-{}-jar-with-dependencies.jar into {}", J4RS_VERSION, jassets.display());
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let download = downloader::Download::new(&format!(
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"https://github.com/astonbitecode/j4rs/raw/v{}/rust/jassets/j4rs-{}-jar-with-dependencies.jar",
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J4RS_VERSION, J4RS_VERSION
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));
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let mut downloader = downloader::Downloader::builder()
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.download_folder(&jassets)
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.build().unwrap();
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downloader
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.download(&[download]).unwrap()
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.into_iter()
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.collect::<Result<Vec<_>, _>>().unwrap();
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}
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if !jassets.join(format!("bioformats_package-{}.jar", BIOFORMATS_VERSION)).exists() {
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println!("downloading bioformats_package-{}.jar into {}", BIOFORMATS_VERSION, jassets.display());
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let download = downloader::Download::new(&format!(
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"https://artifacts.openmicroscopy.org/artifactory/ome.releases/ome/bioformats_package/{}/bioformats_package-{}.jar",
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BIOFORMATS_VERSION, BIOFORMATS_VERSION
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));
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let mut downloader = downloader::Downloader::builder()
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.download_folder(&jassets)
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.build().unwrap();
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downloader
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.download(&[download]).unwrap()
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.into_iter()
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.collect::<Result<Vec<_>, _>>().unwrap();
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}
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#[cfg(feature = "gpl-formats")]
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if !jassets.join(format!("formats-gpl-{}.jar", BIOFORMATS_VERSION)).exists() {
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println!("downloading formats-gpl-{}.jar into {}", BIOFORMATS_VERSION, jassets.display());
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let download = downloader::Download::new(&format!(
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"https://artifacts.openmicroscopy.org/artifactory/ome.releases/ome/formats-gpl/{}/formats-gpl-{}.jar",
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BIOFORMATS_VERSION, BIOFORMATS_VERSION
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));
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let mut downloader = downloader::Downloader::builder()
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.download_folder(&jassets)
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.build().unwrap();
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downloader
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.download(&[download]).unwrap()
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.into_iter()
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.collect::<Result<Vec<_>, _>>().unwrap();
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}
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}
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{
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let mut jvm_built = JVM_BUILT.lock().unwrap();
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Rc::new(if *jvm_built {
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Jvm::attach_thread().expect("Failed to attach to JVM")
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} else {
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*jvm_built = true;
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JvmBuilder::new()
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.skip_setting_native_lib()
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.with_base_path(class_path.to_str().unwrap())
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.build()
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.expect("Failed to build JVM")
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})
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}
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})
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.clone()
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})
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}
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macro_rules! method_return {
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($R:ty$(|c)?) => { Result<$R, Error> };
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() => { Result<(), Error> };
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}
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macro_rules! method_arg {
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($n:tt: $t:ty|p) => {
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InvocationArg::try_from($n)?.into_primitive()?
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};
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($n:tt: $t:ty) => {
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InvocationArg::try_from($n)?
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};
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}
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macro_rules! method {
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($name:ident, $method:expr $(,[$($n:tt: $t:ty$(|$p:tt)?),*])? $(=> $tt:ty$(|$c:tt)?)?) => {
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#[allow(dead_code)]
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pub(crate) fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) {
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let args: Vec<InvocationArg> = vec![$($( method_arg!($n:$t$(|$p)?) ),*)?];
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let _result = jvm().invoke(&self.0, $method, &args)?;
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macro_rules! method_result {
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($R:ty|c) => {
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Ok(jvm().to_rust(_result)?)
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};
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($R:ty|d) => {
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Ok(jvm().to_rust_deserialized(_result)?)
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};
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($R:ty) => {
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Ok(_result)
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};
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() => {
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Ok(())
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};
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}
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method_result!($($tt$(|$c)?)?)
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}
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};
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}
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fn transmute_vec<T, U>(vec: Vec<T>) -> Vec<U> {
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unsafe {
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// Ensure the original vector is not dropped.
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let mut v_clone = std::mem::ManuallyDrop::new(vec);
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Vec::from_raw_parts(
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v_clone.as_mut_ptr() as *mut U,
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v_clone.len(),
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v_clone.capacity(),
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)
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}
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}
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/// Wrapper around bioformats java class loci.common.DebugTools
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pub struct DebugTools;
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impl DebugTools {
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/// set debug root level: ERROR, DEBUG, TRACE, INFO, OFF
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pub fn set_root_level(level: &str) -> Result<(), Error> {
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jvm().invoke_static(
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"loci.common.DebugTools",
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"setRootLevel",
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&[InvocationArg::try_from(level)?],
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)?;
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Ok(())
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}
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}
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/// Wrapper around bioformats java class loci.formats.ChannelSeparator
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pub(crate) struct ChannelSeparator(Instance);
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impl ChannelSeparator {
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pub(crate) fn new(image_reader: &ImageReader) -> Result<Self, Error> {
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let jvm = jvm();
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let channel_separator = jvm.create_instance(
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"loci.formats.ChannelSeparator",
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&[InvocationArg::from(jvm.clone_instance(&image_reader.0)?)],
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)?;
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Ok(ChannelSeparator(channel_separator))
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}
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pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>, Error> {
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Ok(transmute_vec(self.open_bi8(index)?))
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}
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method!(open_bi8, "openBytes", [index: i32|p] => Vec<i8>|c);
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method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
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}
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/// Wrapper around bioformats java class loci.formats.ImageReader
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pub struct ImageReader(Instance);
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impl Drop for ImageReader {
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fn drop(&mut self) {
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self.close().unwrap()
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}
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}
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impl ImageReader {
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pub(crate) fn new() -> Result<Self, Error> {
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let reader = jvm().create_instance("loci.formats.ImageReader", InvocationArg::empty())?;
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Ok(ImageReader(reader))
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}
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pub(crate) fn open_bytes(&self, index: i32) -> Result<Vec<u8>, Error> {
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Ok(transmute_vec(self.open_bi8(index)?))
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}
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pub(crate) fn ome_xml(&self) -> Result<String, Error> {
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let mds = self.get_metadata_store()?;
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Ok(jvm()
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.chain(&mds)?
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.cast("loci.formats.ome.OMEPyramidStore")?
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.invoke("dumpXML", InvocationArg::empty())?
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.to_rust()?)
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}
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method!(close, "close");
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method!(is_indexed, "isIndexed" => bool|c);
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method!(is_interleaved, "isInterleaved" => bool|c);
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method!(is_little_endian, "isLittleEndian" => bool|c);
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method!(is_rgb, "isRGB" => bool|c);
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method!(get_8bit_lookup_table, "get8BitLookupTable" => Instance);
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method!(get_16bit_lookup_table, "get16BitLookupTable" => Instance);
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method!(get_dimension_order, "getDimensionOrder" => String|c);
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method!(set_id, "setId", [id: &str]);
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method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
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method!(set_metadata_store, "setMetadataStore", [ome_data: Instance]);
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method!(get_metadata_store, "getMetadataStore" => Instance);
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method!(get_pixel_type, "getPixelType" => i32|c);
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method!(get_rgb_channel_count, "getRGBChannelCount" => i32|c);
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method!(get_series, "getSeries" => i32|c);
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method!(set_series, "setSeries", [series: i32|p]);
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method!(get_series_count, "getSeriesCount" => i32|c);
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method!(get_size_x, "getSizeX" => i32|c);
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method!(get_size_y, "getSizeY" => i32|c);
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method!(get_size_c, "getSizeC" => i32|c);
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method!(get_size_t, "getSizeT" => i32|c);
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method!(get_size_z, "getSizeZ" => i32|c);
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method!(open_bi8, "openBytes", [index: i32|p] => Vec<i8>|c);
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}
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/// Wrapper around bioformats java class loci.formats.MetadataTools
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pub(crate) struct MetadataTools(Instance);
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impl MetadataTools {
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pub(crate) fn new() -> Result<Self, Error> {
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let meta_data_tools =
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jvm().create_instance("loci.formats.MetadataTools", InvocationArg::empty())?;
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Ok(MetadataTools(meta_data_tools))
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}
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method!(create_ome_xml_metadata, "createOMEXMLMetadata" => Instance);
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}
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/// Reader interface to file. Use get_frame to get data.
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#[derive(Serialize, Deserialize)]
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pub struct BioFormatsJavaReader {
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#[serde(skip)]
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reader: ThreadLocal<ImageReader>,
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/// path to file
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path: PathBuf,
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/// which (if more than 1) of the series in the file to open
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series: usize,
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shape: Shape,
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pixel_type: PixelType,
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little_endian: bool,
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}
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impl From<BioFormatsJavaReader> for DynReader {
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fn from(value: BioFormatsJavaReader) -> Self {
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DynReader::BioFormatsJava(value)
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}
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}
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impl Hash for BioFormatsJavaReader {
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fn hash<H: Hasher>(&self, state: &mut H) {
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self.path.hash(state);
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self.series.hash(state);
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}
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}
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impl PartialEq for BioFormatsJavaReader {
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fn eq(&self, other: &Self) -> bool {
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self.path == other.path
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&& self.series == other.series
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&& self.shape == other.shape
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&& self.pixel_type == other.pixel_type
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&& self.little_endian == other.little_endian
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}
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}
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impl Eq for BioFormatsJavaReader {}
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impl Deref for BioFormatsJavaReader {
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type Target = ImageReader;
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fn deref(&self) -> &Self::Target {
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self.get_reader().unwrap()
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}
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}
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impl Clone for BioFormatsJavaReader {
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fn clone(&self) -> Self {
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// BioFormatsReader::new(&self.path, self.series, 0).unwrap()
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Self {
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reader: ThreadLocal::default(),
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path: self.path.clone(),
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series: self.series,
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shape: self.shape.clone(),
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pixel_type: self.pixel_type,
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little_endian: self.little_endian,
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}
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}
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}
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impl Debug for BioFormatsJavaReader {
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fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
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f.debug_struct("BioFormatsJavaReader")
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.field("path", &self.path)
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.field("series", &self.series)
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.field("shape", &self.shape)
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.field("pixel_type", &self.pixel_type)
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.field("little_endian", &self.little_endian)
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.finish()
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}
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}
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impl BioFormatsJavaReader {
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fn get_reader(&self) -> Result<&ImageReader, Error> {
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self.reader.get_or_try(|| {
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let reader = ImageReader::new()?;
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let meta_data_tools = MetadataTools::new()?;
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let ome_meta = meta_data_tools.create_ome_xml_metadata()?;
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reader.set_metadata_store(ome_meta)?;
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reader.set_id(self.path.to_str().ok_or(Error::InvalidFileName)?)?;
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reader.set_series(self.series as i32)?;
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Ok(reader)
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})
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}
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// pub fn set_reader(&self) -> Result<(), Error> {
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// self.get_reader().map(|_| ())
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// }
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/// Get ome metadata as ome structure
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pub fn get_ome(&self) -> Result<Ome, Error> {
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let mut ome = Ome::from_xml(self.ome_xml()?)?;
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if ome.image.len() > 1 {
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ome.image = vec![ome.image[self.series].clone()];
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}
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Ok(ome)
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}
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/// Get ome metadata as xml string
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pub fn get_ome_xml(&self) -> Result<String, Error> {
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self.ome_xml()
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}
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fn deinterleave(&self, bytes: Vec<u8>, channel: usize) -> Result<Vec<u8>, Error> {
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let chunk_size = match self.pixel_type {
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PixelType::I8 => 1,
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PixelType::U8 => 1,
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PixelType::I16 => 2,
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PixelType::U16 => 2,
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PixelType::I32 => 4,
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PixelType::U32 => 4,
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PixelType::F32 => 4,
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PixelType::F64 => 8,
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PixelType::I64 => 8,
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PixelType::U64 => 8,
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PixelType::I128 => 16,
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PixelType::U128 => 16,
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PixelType::F128 => 8,
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};
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Ok(bytes
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.chunks(chunk_size)
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.skip(channel)
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.step_by(self.shape.c)
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.flat_map(|a| a.to_vec())
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.collect())
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}
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fn bytes_to_frame(&self, bytes: Vec<u8>) -> Result<Frame, Error> {
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macro_rules! get_frame {
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($t:tt, <$n:expr) => {
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Ok(ArrayT::from(Array2::from_shape_vec(
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(self.shape.y, self.shape.x),
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bytes
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.chunks($n)
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.map(|x| $t::from_le_bytes(x.try_into().unwrap()))
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.collect(),
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)?))
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};
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($t:tt, >$n:expr) => {
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Ok(ArrayT::from(Array2::from_shape_vec(
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(self.shape.y, self.shape.x),
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bytes
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.chunks($n)
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.map(|x| $t::from_be_bytes(x.try_into().unwrap()))
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.collect(),
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)?))
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};
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}
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match (&self.pixel_type, self.little_endian) {
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(PixelType::I8, true) => get_frame!(i8, <1),
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(PixelType::U8, true) => get_frame!(u8, <1),
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(PixelType::I16, true) => get_frame!(i16, <2),
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(PixelType::U16, true) => get_frame!(u16, <2),
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(PixelType::I32, true) => get_frame!(i32, <4),
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(PixelType::U32, true) => get_frame!(u32, <4),
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(PixelType::F32, true) => get_frame!(f32, <4),
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(PixelType::F64, true) => get_frame!(f64, <8),
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(PixelType::I64, true) => get_frame!(i64, <8),
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(PixelType::U64, true) => get_frame!(u64, <8),
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(PixelType::I128, true) => get_frame!(i128, <16),
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(PixelType::U128, true) => get_frame!(u128, <16),
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(PixelType::F128, true) => get_frame!(f64, <8),
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(PixelType::I8, false) => get_frame!(i8, >1),
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(PixelType::U8, false) => get_frame!(u8, >1),
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(PixelType::I16, false) => get_frame!(i16, >2),
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(PixelType::U16, false) => get_frame!(u16, >2),
|
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(PixelType::I32, false) => get_frame!(i32, >4),
|
||||
(PixelType::U32, false) => get_frame!(u32, >4),
|
||||
(PixelType::F32, false) => get_frame!(f32, >4),
|
||||
(PixelType::F64, false) => get_frame!(f64, >8),
|
||||
(PixelType::I64, false) => get_frame!(i64, >8),
|
||||
(PixelType::U64, false) => get_frame!(u64, >8),
|
||||
(PixelType::I128, false) => get_frame!(i128, >16),
|
||||
(PixelType::U128, false) => get_frame!(u128, >16),
|
||||
(PixelType::F128, false) => get_frame!(f64, >8),
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
impl Drop for BioFormatsJavaReader {
|
||||
fn drop(&mut self) {
|
||||
if let Ok(reader) = self.get_reader() {
|
||||
reader.close().unwrap();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
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>
|
||||
where
|
||||
P: AsRef<Path>,
|
||||
{
|
||||
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 mut new = BioFormatsJavaReader {
|
||||
reader: ThreadLocal::default(),
|
||||
path,
|
||||
series,
|
||||
shape: Shape::default(),
|
||||
pixel_type: PixelType::I8,
|
||||
little_endian: false,
|
||||
};
|
||||
// new.set_reader()?;
|
||||
new.shape.x = new.get_size_x()? as usize;
|
||||
new.shape.y = new.get_size_y()? as usize;
|
||||
new.shape.c = new.get_size_c()? as usize;
|
||||
new.shape.z = new.get_size_z()? as usize;
|
||||
new.shape.t = new.get_size_t()? as usize;
|
||||
new.pixel_type = PixelType::try_from(new.get_pixel_type()?)?;
|
||||
new.little_endian = new.is_little_endian()?;
|
||||
Ok(new)
|
||||
}
|
||||
|
||||
fn metadata(&self) -> Result<Ome, Error> {
|
||||
self.get_ome()
|
||||
}
|
||||
|
||||
/// Retrieve fame at channel c, slize z and time t.
|
||||
fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame, Error> {
|
||||
let bytes = if self.is_rgb()? && self.is_interleaved()? {
|
||||
let index = self.get_index(z as i32, 0, t as i32)?;
|
||||
self.deinterleave(self.open_bytes(index)?, c)?
|
||||
} else if self.get_rgb_channel_count()? > 1 {
|
||||
let channel_separator = ChannelSeparator::new(self)?;
|
||||
let index = channel_separator.get_index(z as i32, c as i32, t as i32)?;
|
||||
channel_separator.open_bytes(index)?
|
||||
} else {
|
||||
let index = self.get_index(z as i32, c as i32, t as i32)?;
|
||||
self.open_bytes(index)?
|
||||
};
|
||||
self.bytes_to_frame(bytes)
|
||||
}
|
||||
|
||||
fn path(&self) -> &Path {
|
||||
&self.path
|
||||
}
|
||||
|
||||
fn series(&self) -> usize {
|
||||
self.series
|
||||
}
|
||||
|
||||
fn position(&self) -> usize {
|
||||
0
|
||||
}
|
||||
|
||||
fn shape(&self) -> &Shape {
|
||||
&self.shape
|
||||
}
|
||||
|
||||
fn pixel_type(&self) -> &PixelType {
|
||||
&self.pixel_type
|
||||
}
|
||||
|
||||
fn get_available_positions<P>(_path: P, _series: usize) -> Result<HashSet<usize>, Error>
|
||||
where
|
||||
P: AsRef<Path>,
|
||||
{
|
||||
Ok(HashSet::from([0]))
|
||||
}
|
||||
|
||||
fn get_available_series<P>(path: P) -> Result<HashSet<usize>, Error>
|
||||
where
|
||||
P: AsRef<Path>,
|
||||
{
|
||||
DebugTools::set_root_level("ERROR")?;
|
||||
let new = BioFormatsJavaReader {
|
||||
reader: ThreadLocal::default(),
|
||||
path: path.as_ref().to_path_buf(),
|
||||
series: 0,
|
||||
shape: Shape::default(),
|
||||
pixel_type: PixelType::I8,
|
||||
little_endian: false,
|
||||
};
|
||||
Ok(HashSet::from_iter(0..(new.get_series_count()? as usize)))
|
||||
}
|
||||
}
|
||||
|
||||
#[cfg(test)]
|
||||
mod tests {
|
||||
use super::*;
|
||||
|
||||
fn open(file: &str) -> Result<BioFormatsJavaReader, Error> {
|
||||
let path = std::env::current_dir()?
|
||||
.join("tests")
|
||||
.join("files")
|
||||
.join(file);
|
||||
BioFormatsJavaReader::new(&path, 0, 0)
|
||||
}
|
||||
|
||||
macro_rules! test_metadata {
|
||||
($($name:ident: $file:expr $(,)?)*) => {
|
||||
$(
|
||||
#[test]
|
||||
fn $name() -> Result<(), Error> {
|
||||
let bf = open($file)?;
|
||||
println!("{}", bf.view().squeeze()?.summary()?);
|
||||
Ok(())
|
||||
}
|
||||
)*
|
||||
};
|
||||
}
|
||||
|
||||
test_metadata! {
|
||||
metadata_a: "czi/1xp53-01-AP1.czi",
|
||||
metadata_b: "czi/beads_2023_05_04__19_00_22.czi",
|
||||
metadata_c: "czi/Experiment-2029.czi",
|
||||
metadata_d: "czi/MK022_cE9_1-01-Airyscan Processing-01-Scene-2-P1.czi",
|
||||
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"
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn ome_xml() -> Result<(), Error> {
|
||||
let file = "czi/Experiment-2029.czi";
|
||||
let path = std::env::current_dir()?
|
||||
.join("tests")
|
||||
.join("files")
|
||||
.join(file);
|
||||
let reader = BioFormatsJavaReader::new(&path, 0, 0)?;
|
||||
let xml = reader.get_ome_xml()?;
|
||||
println!("{}", xml);
|
||||
Ok(())
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user