- inital transforms code

Cargo.toml

@@ -19,12 +19,14 @@ name = "ndbioimage"
 crate-type = ["cdylib", "rlib"]
 
 [dependencies]
+bioformats = { version = "0.1", optional = true }
 clap = { version = "4", features = ["derive"] }
 color-eyre = { version = "0.6", optional = true }
 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 }
@@ -50,7 +52,6 @@ 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 }
-bioformats = { version = "0.1", optional = true }
 
 [dev-dependencies]
 rayon = "1"
@@ -64,7 +65,7 @@ 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"]
+all = ["bioformats_java", "bioformats_rust", "czi", "gpl-formats", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]
 gpl-formats = []
 python = ["dep:pyo3", "dep:numpy", "dep:color-eyre", "dep:pyo3-stub-gen", "dep:postcard", "ome-metadata/python"]
 czi = ["dep:libczirw-sys", "dep:xmltree", "dep:thread_local"]
@@ -74,9 +75,11 @@ tiffwrite = ["dep:tiffwrite", "dep:indicatif", "dep:console", "dep:rayon"]
 tiffseq = ["dep:tiff", "dep:serde_yaml"]
 tiff = ["dep:tiff", "dep:thread_local"]
 movie = ["dep:ffmpeg-sidecar", "dep:tokio", "dep:ordered-float", "dep:indicatif", "dep:console"]
+transforms = ["dep:image-registration"]
 
 [package.metadata.docs.rs]
-features = ["bioformats_java", "czi", "tiff", "tiffseq", "movie", "tiffwrite", "movie"]
+no-default-features = true
+features = ["bioformats_java", "bioformats_rust", "czi", "movie", "tiffseq", "tiffwrite", "tiff", "transforms"]
 
 [profile.test]
 inherits = "release"

README.md

@@ -20,7 +20,7 @@ To transition to semver, versions before 0.1.0 were yanked from crates.io.
 
 ## Installation
 
-```
+```sh
 pip install ndbioimage
 ```
 
@@ -28,7 +28,7 @@ pip install ndbioimage
 
 Work in progress! Make sure ffmpeg is installed.
 
-```
+```sh
 pip install ndbioimage[write]
 ```
 
@@ -38,7 +38,7 @@ pip install ndbioimage[write]
 
 - Reading an image file and plotting the frame at channel=2, time=1
 
-```
+```python
 import matplotlib.pyplot as plt
 from ndbioimage import Imread
 with Imread('image_file.tif', axes='ctyx', dtype=int) as im:
@@ -47,7 +47,7 @@ with Imread('image_file.tif', axes='ctyx', dtype=int) as im:
 
 - Showing some image metadata
 
-```
+```python
 from ndbioimage import Imread
 from pprint import pprint
 with Imread('image_file.tif') as im:
@@ -56,7 +56,7 @@ with Imread('image_file.tif') as im:
 
 - Slicing the image without loading the image into memory
 
-```
+```python
 from ndbioimage import Imread
 with Imread('image_file.tif', axes='cztyx') as im:
     sliced_im = im[1, :, :, 100:200, 100:200]
@@ -66,7 +66,7 @@ sliced_im is an instance of Imread which will load any image data from file only
 
 - Converting (part) of the image to a numpy ndarray
 
-```
+```python
 from ndbioimage import Imread
 import numpy as np
 with Imread('image_file.tif', axes='cztyx') as im:

build.rs

@@ -159,13 +159,13 @@ mod python_bioformats {
 fn main() -> Result<(), Box<dyn std::error::Error>> {
     println!("cargo::rerun-if-changed=build.rs");
 
+    #[cfg(feature = "bioformats_java")]
+    bioformats::build()?;
+
     if std::env::var("DOCS_RS").is_err() {
         #[cfg(feature = "movie")]
         ffmpeg_sidecar::download::auto_download()?;
 
-        #[cfg(feature = "bioformats_java")]
-        bioformats::build()?;
-
         #[cfg(all(not(feature = "python"), feature = "bioformats_java"))]
         no_python_bioformats::build()?;
 

src/lib.rs

@@ -1,5 +1,5 @@
 #![cfg_attr(docsrs, feature(doc_cfg))]
-//! The ndbioimage crate exposes (bio) images a struct that can be sliced like an ndarray Array
+//! The ndbioimage crate exposes (bio) images as a struct that can be sliced like an ndarray Array
 //! (Rust), but without loading the whole image into memory, reading from the file only when needed.
 //! Some metadata is read
 //! and stored in an [ome](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47)
@@ -68,6 +68,9 @@ pub mod readers;
 #[cfg(feature = "tiffwrite")]
 /// saving views as tiff files
 pub mod tiffwrite;
+#[cfg(feature = "transforms")]
+/// image registration and warping images using affine transforms
+mod transforms;
 mod utils;
 
 /// main entry point for the application

src/readers/bioformats_rust.rs

@@ -2,6 +2,7 @@ use crate::error::Error;
 use crate::readers::ArrayT;
 use crate::readers::{DynReader, Frame, PixelType, Reader, Shape};
 use bioformats::{DimensionOrder, ImageReader};
+use itertools::Itertools;
 use ndarray::Array2;
 use ome_metadata::Ome;
 use std::cell::{RefCell, RefMut};
@@ -200,18 +201,41 @@ impl BioFormatsRustReader {
     }
 }
 
+fn find_tiff(path: &Path) -> Result<Option<PathBuf>, Error> {
+    if let Some(ext) = path.extension()
+        && path.is_file()
+        && (["tif", "tiff"].contains(&ext.to_string_lossy().to_lowercase().as_str()))
+    {
+        return Ok(Some(path.to_path_buf()));
+    } else if path.is_dir() {
+        for file in path.read_dir()?.flatten().sorted_by_key(|i| i.file_name()) {
+            if let Ok(Some(file)) = find_tiff(file.path().as_path()) {
+                return Ok(Some(file));
+            }
+        }
+    }
+    Ok(None)
+}
+
 impl Reader for BioFormatsRustReader {
     fn new<P>(path: P, series: usize, _position: usize) -> Result<Self, Error>
     where
         P: AsRef<Path>,
     {
+        let mut path = path.as_ref().to_path_buf();
+        if path.is_dir() {
+            let orig = path.clone();
+            path = find_tiff(&path)?.ok_or_else(|| {
+                Error::FileDoesNotExist(orig.join("**").join("*.tif").display().to_string())
+            })?;
+        }
         let mut new = Self {
             reader: ThreadLocal::default(),
-            path: path.as_ref().to_path_buf(),
+            path,
             series,
             shape: Shape::default(),
-            pixel_type: PixelType::U16,
+            pixel_type: PixelType::I8,
-            little_endian: true,
+            little_endian: false,
         };
         let reader = new.get_reader()?;
         let metadata = reader.metadata().clone();

src/transforms.rs

@@ -0,0 +1,30 @@
+use crate::readers::Reader;
+use crate::view::View;
+pub use image_registration::transform::Transform;
+use ndarray::{Dimension, Ix2, Ix3};
+use serde::{Deserialize, Serialize};
+
+pub enum TransformD {
+    YX(Transform<Ix2>),
+    ZYX(Transform<Ix3>),
+}
+
+impl<D: Dimension, R: Reader> View<D, R> {}
+
+#[derive(Clone, Debug, Default, Eq, PartialEq, Serialize, Deserialize)]
+pub struct Transforms {
+    channel: Vec<TransformD>,
+    drift: Vec<TransformD>,
+}
+
+#[cfg(test)]
+mod tests {
+    use crate::transforms::Transforms;
+
+    #[test]
+    fn test_transforms() -> Result<(), Box<dyn std::error::Error>> {
+        let t = Transforms::default();
+
+        Ok(())
+    }
+}

src/view.rs

@@ -4,6 +4,8 @@ use crate::error::Error;
 use crate::metadata::Metadata;
 use crate::readers::{Dimensions, DynReader, Frame, Reader};
 use crate::stats::MinMax;
+#[cfg(feature = "transforms")]
+use crate::transforms::Transforms;
 use indexmap::IndexMap;
 use itertools::{Itertools, iproduct};
 use ndarray::{
@@ -88,6 +90,8 @@ pub struct View<D: Dimension, R: Reader = DynReader> {
     axes: Vec<Axis>,
     operations: IndexMap<Axis, Operation>,
     dimensionality: PhantomData<D>,
+    #[cfg(feature = "transforms")]
+    transforms: Transforms,
 }
 
 impl<D, R> Hash for View<D, R>
@@ -114,6 +118,8 @@ impl<D: Dimension, R: Reader> View<D, R> {
             axes,
             operations: IndexMap::new(),
             dimensionality: PhantomData,
+            #[cfg(feature = "transforms")]
+            transforms: Transforms::default(),
         }
     }
 
@@ -177,6 +183,8 @@ impl<D: Dimension, R: Reader> View<D, R> {
             axes,
             operations: IndexMap::new(),
             dimensionality: PhantomData,
+            #[cfg(feature = "transforms")]
+            transforms: Transforms::default(),
         })
     }
 
@@ -227,6 +235,8 @@ impl<D: Dimension, R: Reader> View<D, R> {
             axes: self.axes,
             operations: self.operations,
             dimensionality: PhantomData,
+            #[cfg(feature = "transforms")]
+            transforms: Transforms::default(),
         }
     }
 
@@ -240,6 +250,8 @@ impl<D: Dimension, R: Reader> View<D, R> {
                     axes: self.axes,
                     operations: self.operations,
                     dimensionality: PhantomData,
+                    #[cfg(feature = "transforms")]
+                    transforms: Transforms::default(),
                 })
             } else {
                 Err(Error::DimensionalityMismatch(d, self.ndim()))
@@ -251,6 +263,8 @@ impl<D: Dimension, R: Reader> View<D, R> {
                 axes: self.axes,
                 operations: self.operations,
                 dimensionality: PhantomData,
+                #[cfg(feature = "transforms")]
+                transforms: Transforms::default(),
             })
         }
     }