- testing 2d transforms

Cargo.toml

@@ -3,9 +3,9 @@ resolver = "3"
 members = ["ndbioimage", "image-tiff", "image-registration"]
 
 [workspace.package]
-version = "0.2.0"
+version = "0.3.0"
 edition = "2024"
-rust-version = "1.94.0"
+rust-version = "1.94.1"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
 license = "MIT OR Apache-2.0"
 description = "Read bio image formats using the bio-formats java package."

ndbioimage/Cargo.toml

@@ -37,7 +37,7 @@ ome-metadata = "0.6"
 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 = { version = "0.29", features = ["abi3-py310", "anyhow", "generate-import-lib", "multiple-pymethods"], optional = true }
 pyo3-stub-gen = { version = "0.23", optional = true }
 rayon = { version = "1", optional = true }
 regex = "1"

ndbioimage/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "ndbioimage"
-version = "2027.0.5"
+version = "2027.0.6"
 requires-python = ">=3.10"
 classifiers = [
     "License :: OSI Approved :: MIT License",

ndbioimage/src/axes.rs

@@ -198,9 +198,9 @@ impl<'de> DeserializeAs<'de, SliceInfoElem> for SliceInfoElemDef {
 
 #[derive(Clone, Debug)]
 pub(crate) struct Slice {
-    start: isize,
+    pub(crate) start: isize,
-    end: isize,
+    pub(crate) end: isize,
-    step: isize,
+    pub(crate) step: isize,
 }
 
 impl Slice {

ndbioimage/src/cache.rs

@@ -1,14 +1,22 @@
 use crate::axes::{Axis, Operation};
+use crate::readers::Frame;
+#[cfg(feature = "transforms")]
+use image_registration::transform::Transform;
 use indexmap::{Equivalent, IndexMap};
+#[cfg(feature = "transforms")]
+use ndarray::IxDyn;
 use ndarray::{ArrayD, SliceInfoElem};
 use std::any::Any;
+#[cfg(feature = "transforms")]
+use std::borrow::Cow;
+use std::cmp::PartialEq;
 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;
-
+#[cfg(feature = "transforms")]
-use crate::readers::Frame;
+use crate::transforms::Transforms;
 
 /// maximum number of frames held in the cache
 const DEFAULT_FRAME_CACHE_SIZE: usize = 128;
@@ -132,7 +140,15 @@ impl ReaderKeyRef<'_> {
     }
 }
 
-pub(crate) type FrameKey = (ReaderKey, usize, usize, usize);
+#[derive(Debug, PartialEq, Eq, Hash)]
+pub(crate) struct FrameKey {
+    pub(crate) reader_key: ReaderKey,
+    pub(crate) c: usize,
+    pub(crate) z: usize,
+    pub(crate) t: usize,
+    #[cfg(feature = "transforms")]
+    pub(crate) transform: Option<(Transform<IxDyn>, usize)>,
+}
 
 /// borrowed view of [`FrameKey`] for cache lookups without allocation.
 #[derive(Debug, PartialEq, Eq)]
@@ -141,6 +157,8 @@ pub(crate) struct FrameKeyRef<'a> {
     pub(crate) c: usize,
     pub(crate) z: usize,
     pub(crate) t: usize,
+    #[cfg(feature = "transforms")]
+    pub(crate) transform: Option<(Cow<'a, Transform<IxDyn>>, usize)>,
 }
 
 impl Hash for FrameKeyRef<'_> {
@@ -149,19 +167,50 @@ impl Hash for FrameKeyRef<'_> {
         self.c.hash(state);
         self.z.hash(state);
         self.t.hash(state);
+        #[cfg(feature = "transforms")]
+        self.transform.hash(state);
     }
 }
 
 impl Equivalent<FrameKey> for FrameKeyRef<'_> {
     fn equivalent(&self, key: &FrameKey) -> bool {
-        let (rk, c, z, t) = key;
+        let FrameKey {
-        self.reader.equivalent(rk) && self.c == *c && self.z == *z && self.t == *t
+            reader_key,
+            c,
+            z,
+            t,
+            #[cfg(feature = "transforms")]
+            transform,
+        } = key;
+        #[cfg(feature = "transforms")]
+        {
+            self.reader.equivalent(reader_key)
+                && self.c == *c
+                && self.z == *z
+                && self.t == *t
+                && self.transform.as_ref().map(|(t, i)| (t.as_ref(), i))
+                    == transform.as_ref().map(|(t, i)| (t, i))
+        }
+        #[cfg(not(feature = "transforms"))]
+        {
+            self.reader.equivalent(reader_key) && self.c == *c && self.z == *z && self.t == *t
+        }
     }
 }
 
 impl FrameKeyRef<'_> {
     pub(crate) fn to_owned(&self) -> FrameKey {
-        (self.reader.to_owned(), self.c, self.z, self.t)
+        FrameKey {
+            reader_key: self.reader.to_owned(),
+            c: self.c,
+            z: self.z,
+            t: self.t,
+            #[cfg(feature = "transforms")]
+            transform: self
+                .transform
+                .as_ref()
+                .map(|(t, i)| (t.clone().into_owned(), *i)),
+        }
     }
 }
 
@@ -173,6 +222,8 @@ pub(crate) struct ArrayKey {
     pub(crate) slice: Vec<SliceInfoElem>,
     pub(crate) axes: Vec<Axis>,
     pub(crate) operations: Vec<(Axis, Operation)>,
+    #[cfg(feature = "transforms")]
+    pub(crate) transforms: Transforms,
 }
 
 /// borrowed view of [`ArrayKey`] for cache lookups without allocation.
@@ -183,6 +234,8 @@ pub(crate) struct ArrayKeyRef<'a> {
     pub(crate) slice: &'a [SliceInfoElem],
     pub(crate) axes: &'a [Axis],
     pub(crate) operations: &'a IndexMap<Axis, Operation>,
+    #[cfg(feature = "transforms")]
+    pub(crate) transforms: &'a Transforms,
 }
 
 impl Hash for ArrayKeyRef<'_> {
@@ -196,11 +249,15 @@ impl Hash for ArrayKeyRef<'_> {
             ax.hash(state);
             op.hash(state);
         }
+        #[cfg(feature = "transforms")]
+        self.transforms.hash(state);
     }
 }
 
 impl Equivalent<ArrayKey> for ArrayKeyRef<'_> {
     fn equivalent(&self, key: &ArrayKey) -> bool {
+        #[cfg(feature = "transforms")]
+        {
             self.reader.equivalent(&key.reader)
                 && self.dtype == key.dtype
                 && self.slice == key.slice
@@ -211,6 +268,21 @@ impl Equivalent<ArrayKey> for ArrayKeyRef<'_> {
                 .iter()
                 .zip(&key.operations)
                 .all(|((ax, op), (key_ax, key_op))| ax == key_ax && op == key_op)
+                && self.transforms == key.transforms
+        }
+        #[cfg(not(feature = "transforms"))]
+        {
+            self.reader.equivalent(&key.reader)
+                && self.dtype == key.dtype
+                && self.slice == key.slice
+                && self.axes == key.axes
+                && self.operations.len() == key.operations.len()
+                && self
+                .operations
+                .iter()
+                .zip(&key.operations)
+                .all(|((ax, op), (key_ax, key_op))| ax == key_ax && op == key_op)
+        }
     }
 }
 
@@ -226,6 +298,8 @@ impl ArrayKeyRef<'_> {
                 .iter()
                 .map(|(ax, op)| (*ax, op.clone()))
                 .collect(),
+            #[cfg(feature = "transforms")]
+            transforms: self.transforms.to_owned(),
         }
     }
 }

ndbioimage/src/error.rs

@@ -179,6 +179,10 @@ pub enum Error {
          it cannot use. read the file before forking, or start the child with spawn/exec instead."
     )]
     ForkedJvm(u32, u32),
+    #[error("{0}D transformation is not implemented")]
+    TransformationNotImplemented(usize),
+    #[error("no channel {0} present")]
+    NoChannel(usize),
 }
 
 impl Error {

ndbioimage/src/lib.rs

@@ -1,4 +1,4 @@
-#![cfg_attr(docsrs, feature(doc_cfg))]
+#![cfg_attr(docsrs, feature(doc_cfg, doc_auto_cfg))]
 //! 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
@@ -16,7 +16,7 @@
 //! # fn main() -> Result<(), ndbioimage::error::Error> {
 //! let path = "/path/to/file";
 //! let reader = DynReader::new(&path, 0, 0)?;
-//! println!("shape: {}", reader.shape());
+//! println!("shape: {}", reader.raw_shape());
 //! let frame = reader.get_frame(0, 0, 0)?;
 //! if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
 //!     println!("{:?}", arr);
@@ -70,7 +70,7 @@ pub mod readers;
 pub mod tiffwrite;
 #[cfg(feature = "transforms")]
 /// image registration and warping images using affine transforms
-mod transforms;
+pub mod transforms;
 mod utils;
 
 /// main entry point for the application
@@ -338,7 +338,7 @@ mod tests {
     fn read_ser() -> Result<(), Error> {
         let file = "czi/Experiment-2029.czi";
         let reader = open(file)?;
-        println!("shape: {}", reader.shape());
+        println!("shape: {}", reader.raw_shape());
         let frame = reader.get_frame(0, 0, 0)?;
         if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
             println!("{:?}", arr);

ndbioimage/src/py.rs

@@ -67,6 +67,7 @@ fn main() -> PyResult<()> {
 #[pymodule]
 #[pyo3(name = "ndbioimage_rs")]
 mod ndbioimage_rs {
+    #[cfg(feature = "transforms")]
     use pyo3::prelude::*;
 
     #[pymodule_export]

ndbioimage/src/py/imread.rs

@@ -3,8 +3,6 @@ use crate::error::Error;
 use crate::metadata::Metadata;
 use crate::movie::MovieOptions;
 
-#[cfg(feature = "transforms")]
-use crate::py::transforms::{PyTransform, PyTransforms};
 use crate::readers::{DynReader, PixelType, Reader};
 use crate::view::{Item, View};
 use itertools::Itertools;
@@ -27,7 +25,7 @@ pub(crate) use pyo3::{
 use pyo3_stub_gen::derive::*;
 use pyo3_stub_gen::inventory::submit;
 use serde::{Deserialize, Serialize};
-use std::collections::{HashMap, HashSet};
+use std::collections::HashSet;
 use std::path::PathBuf;
 
 /// class to read image files, while taking good care of important metadata,
@@ -61,7 +59,7 @@ use std::path::PathBuf;
 #[pyclass(subclass, from_py_object, name = "Imread", module = "ndbioimage")]
 #[derive(Clone, Debug, Serialize, Deserialize)]
 pub(crate) struct PyView {
-    view: View<IxDyn, DynReader>,
+    pub(crate) view: View<IxDyn, DynReader>,
     dtype: PixelType,
     #[serde(skip)]
     ome: Ome,
@@ -296,141 +294,6 @@ impl PyView {
         todo!()
     }
 
-    /// return a new view with transformations applied (channel alignment, drift correction)
-    /// backward compatibility
-    #[cfg(feature = "transforms")]
-    #[pyo3(signature = (channels = true, drift = false, file = None, bead_files = None, main_channel = None, default_transform = None))]
-    fn with_transform<'py>(
-        &self,
-        channels: bool,
-        drift: bool,
-        file: Option<Bound<'py, PyAny>>,
-        bead_files: Option<Bound<'py, PyAny>>,
-        main_channel: Option<usize>,
-        default_transform: Option<Vec<f64>>,
-    ) -> PyResult<PyView> {
-        self.with_transforms(
-            channels,
-            drift,
-            file,
-            bead_files,
-            main_channel,
-            default_transform,
-        )
-    }
-
-    /// return a new view with transformations applied (channel alignment, drift correction)
-    #[cfg(feature = "transforms")]
-    #[expect(unused_variables)]
-    #[pyo3(signature = (channels = true, drift = false, file = None, bead_files = None, main_channel = None, default_transform = None))]
-    fn with_transforms<'py>(
-        &self,
-        channels: bool,
-        drift: bool,
-        file: Option<Bound<'py, PyAny>>,
-        bead_files: Option<Bound<'py, PyAny>>,
-        main_channel: Option<usize>,
-        default_transform: Option<Vec<f64>>,
-    ) -> PyResult<PyView> {
-        todo!()
-    }
-
-    /// get the transformation
-    #[cfg(feature = "transforms")]
-    #[getter]
-    fn get_transforms(&self) -> PyResult<PyTransforms> {
-        Ok(PyTransforms {
-            inner: self.view.get_transforms().clone(),
-        })
-    }
-
-    /// set the transformation
-    #[cfg(feature = "transforms")]
-    #[setter]
-    fn set_transforms(&mut self, transform: PyTransforms) {
-        self.view.set_transforms(transform.inner);
-    }
-
-    #[cfg(feature = "transforms")]
-    fn load_transforms_from_yaml(&mut self, path: PathBuf) -> PyResult<()> {
-        self.view.load_transforms_from_yaml(path.as_path())?;
-        Ok(())
-    }
-
-    #[cfg(feature = "transforms")]
-    fn calculate_channel_transforms_2d(
-        &self,
-        py: Python,
-        main_channel: usize,
-    ) -> PyResult<HashMap<String, PyTransform>> {
-        py.detach(|| {
-            Ok(self
-                .view
-                .calculate_channel_transforms_2d(main_channel)?
-                .into_iter()
-                .map(|(n, t)| {
-                    (
-                        n,
-                        PyTransform {
-                            inner: t.into_dyn(),
-                        },
-                    )
-                })
-                .collect())
-        })
-    }
-
-    #[cfg(feature = "transforms")]
-    fn calculate_channel_transforms_3d(
-        &self,
-        py: Python,
-        main_channel: usize,
-    ) -> PyResult<HashMap<String, PyTransform>> {
-        py.detach(|| {
-            Ok(self
-                .view
-                .calculate_channel_transforms_3d(main_channel)?
-                .into_iter()
-                .map(|(n, t)| {
-                    (
-                        n,
-                        PyTransform {
-                            inner: t.into_dyn(),
-                        },
-                    )
-                })
-                .collect())
-        })
-    }
-
-    #[cfg(feature = "transforms")]
-    fn calculate_drift_transforms_2d(&self, py: Python) -> PyResult<Vec<PyTransform>> {
-        py.detach(|| {
-            Ok(self
-                .view
-                .calculate_drift_transforms_2d()?
-                .into_iter()
-                .map(|t| PyTransform {
-                    inner: t.into_dyn(),
-                })
-                .collect())
-        })
-    }
-
-    #[cfg(feature = "transforms")]
-    fn calculate_drift_transforms_3d(&self, py: Python) -> PyResult<Vec<PyTransform>> {
-        py.detach(|| {
-            Ok(self
-                .view
-                .calculate_drift_transforms_3d()?
-                .into_iter()
-                .map(|t| PyTransform {
-                    inner: t.into_dyn(),
-                })
-                .collect())
-        })
-    }
-
     #[gen_stub(override_return_type(type_repr="numpy.ndarray | int | float", imports=("numpy")))]
     fn squeeze<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
         let view = self.view.squeeze()?;
@@ -1481,6 +1344,7 @@ impl PyView {
         ))]
         axes: Option<Vec<Bound<PyAny>>>,
     ) -> PyResult<Self> {
+        // TODO: transpose("xyz"), transpose(*axes)
         let view = if let Some(axes) = axes {
             let ax = axes
                 .into_iter()

ndbioimage/src/py/transforms.rs

@@ -1,4 +1,5 @@
 use crate::error::Error;
+use crate::py::imread::PyView;
 use crate::transforms::Transforms;
 use image_registration::metric::{SamplingArg, Sigma};
 use image_registration::register::{Optimizer, RegistrationStep};
@@ -709,6 +710,138 @@ pub(crate) struct PyTransforms {
     pub(crate) inner: Transforms,
 }
 
+#[gen_stub_pymethods]
+#[pymethods]
+impl PyView {
+    /// return a new view with transformations applied (channel alignment, drift correction)
+    /// backward compatibility
+    #[cfg(feature = "transforms")]
+    #[pyo3(signature = (channels = true, drift = false, file = None, bead_files = None, main_channel = None, default_transform = None))]
+    fn with_transform<'py>(
+        &self,
+        channels: bool,
+        drift: bool,
+        file: Option<Bound<'py, PyAny>>,
+        bead_files: Option<Bound<'py, PyAny>>,
+        main_channel: Option<usize>,
+        default_transform: Option<Vec<f64>>,
+    ) -> PyResult<PyView> {
+        self.with_transforms(
+            channels,
+            drift,
+            file,
+            bead_files,
+            main_channel,
+            default_transform,
+        )
+    }
+
+    /// return a new view with transformations applied (channel alignment, drift correction)
+    #[cfg(feature = "transforms")]
+    #[expect(unused_variables)]
+    #[pyo3(signature = (channels = true, drift = false, file = None, bead_files = None, main_channel = None, default_transform = None))]
+    fn with_transforms<'py>(
+        &self,
+        channels: bool,
+        drift: bool,
+        file: Option<Bound<'py, PyAny>>,
+        bead_files: Option<Bound<'py, PyAny>>,
+        main_channel: Option<usize>,
+        default_transform: Option<Vec<f64>>,
+    ) -> PyResult<PyView> {
+        todo!()
+    }
+
+    /// get the transformation
+    #[getter]
+    fn get_transforms(&self) -> PyResult<PyTransforms> {
+        Ok(PyTransforms {
+            inner: self.view.get_transforms().clone(),
+        })
+    }
+
+    /// set the transformation
+    #[setter]
+    fn set_transforms(&mut self, transform: PyTransforms) {
+        self.view.set_transforms(transform.inner);
+    }
+
+    fn load_transforms_from_yaml(&mut self, path: PathBuf) -> PyResult<()> {
+        self.view.load_transforms_from_yaml(path.as_path())?;
+        Ok(())
+    }
+
+    fn calculate_channel_transforms_2d(
+        &self,
+        py: Python,
+        main_channel: usize,
+    ) -> PyResult<HashMap<String, PyTransform>> {
+        py.detach(|| {
+            Ok(self
+                .view
+                .calculate_channel_transforms_2d(main_channel)?
+                .into_iter()
+                .map(|(n, t)| {
+                    (
+                        n,
+                        PyTransform {
+                            inner: t.into_dyn(),
+                        },
+                    )
+                })
+                .collect())
+        })
+    }
+
+    fn calculate_channel_transforms_3d(
+        &self,
+        py: Python,
+        main_channel: usize,
+    ) -> PyResult<HashMap<String, PyTransform>> {
+        py.detach(|| {
+            Ok(self
+                .view
+                .calculate_channel_transforms_3d(main_channel)?
+                .into_iter()
+                .map(|(n, t)| {
+                    (
+                        n,
+                        PyTransform {
+                            inner: t.into_dyn(),
+                        },
+                    )
+                })
+                .collect())
+        })
+    }
+
+    fn calculate_drift_transforms_2d(&self, py: Python) -> PyResult<Vec<PyTransform>> {
+        py.detach(|| {
+            Ok(self
+                .view
+                .calculate_drift_transforms_2d()?
+                .into_iter()
+                .map(|t| PyTransform {
+                    inner: t.into_dyn(),
+                })
+                .collect())
+        })
+    }
+
+    fn calculate_drift_transforms_3d(&self, py: Python) -> PyResult<Vec<PyTransform>> {
+        py.detach(|| {
+            Ok(self
+                .view
+                .calculate_drift_transforms_3d()?
+                .into_iter()
+                .map(|t| PyTransform {
+                    inner: t.into_dyn(),
+                })
+                .collect())
+        })
+    }
+}
+
 #[gen_stub_pymethods]
 #[pymethods]
 impl PyTransforms {

ndbioimage/src/readers.rs

@@ -2,7 +2,7 @@ use crate::axes::{Axis, Shape};
 use crate::error::Error;
 use crate::view::View;
 use ndarray::{Array, Dimension, Ix2, Ix5, s};
-use num::{FromPrimitive, Zero};
+use num::{FromPrimitive, One, Zero};
 use ome_metadata::Ome;
 use regex::Regex;
 use serde::{Deserialize, Serialize};
@@ -148,6 +148,8 @@ impl PixelType {
 /// array data with a specific pixel type
 #[derive(Clone, Debug)]
 pub enum ArrayT<D: Dimension> {
+    /// boolean array
+    Bool(Array<bool, D>),
     /// signed 8-bit integer array
     I8(Array<i8, D>),
     /// unsigned 8-bit integer array
@@ -197,7 +199,7 @@ pub trait Reader: Clone + Sized + Debug + Send + Hash + Into<DynReader> {
 
     /// get a sliceable view on the image file
     fn view(&self) -> View<Ix5, Self> {
-        let shape = self.shape();
+        let shape = self.raw_shape();
         let slice = s![0..shape.c, 0..shape.z, 0..shape.t, 0..shape.y, 0..shape.x,];
         View::new(
             self.clone(),
@@ -216,7 +218,7 @@ pub trait Reader: Clone + Sized + Debug + Send + Hash + Into<DynReader> {
     /// the position index
     fn position(&self) -> usize;
     /// the shape of the image data
-    fn shape(&self) -> &Shape;
+    fn raw_shape(&self) -> &Shape;
     /// the pixel type of the image data
     fn pixel_type(&self) -> &PixelType;
     /// get all available positions for a given series
@@ -314,6 +316,7 @@ macro_rules! try_into_array_body {
     ($self:expr, $map:ident) => {{
         let mut err = Ok(());
         let arr = match $self {
+            ArrayT::Bool(v) => v.$map(|x| if x { T::one() } else { T::zero() }),
             ArrayT::I8(v) => v.$map(|x| {
                 T::from_i8(x).unwrap_or_else(|| {
                     err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
@@ -397,7 +400,7 @@ macro_rules! try_into_array_body {
 impl<D, T> TryInto<Array<T, D>> for ArrayT<D>
 where
     D: Dimension,
-    T: FromPrimitive + Zero + 'static,
+    T: FromPrimitive + Zero + One + 'static,
 {
     type Error = Error;
 
@@ -409,7 +412,7 @@ where
 impl<D, T> TryInto<Array<T, D>> for &ArrayT<D>
 where
     D: Dimension,
-    T: Clone + FromPrimitive + Zero + 'static,
+    T: Clone + FromPrimitive + Zero + One + 'static,
 {
     type Error = Error;
 
@@ -577,18 +580,18 @@ impl Reader for DynReader {
         }
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         match self {
             #[cfg(feature = "tiff")]
-            DynReader::Tiff(r) => r.shape(),
+            DynReader::Tiff(r) => r.raw_shape(),
             #[cfg(feature = "tiffseq")]
-            DynReader::TiffSeq(r) => r.shape(),
+            DynReader::TiffSeq(r) => r.raw_shape(),
             #[cfg(feature = "czi")]
-            DynReader::Czi(r) => r.shape(),
+            DynReader::Czi(r) => r.raw_shape(),
             #[cfg(feature = "bioformats_rust")]
-            DynReader::BioFormatsRust(r) => r.shape(),
+            DynReader::BioFormatsRust(r) => r.raw_shape(),
             #[cfg(feature = "bioformats_java")]
-            DynReader::BioFormatsJava(r) => r.shape(),
+            DynReader::BioFormatsJava(r) => r.raw_shape(),
             #[expect(unreachable_patterns)]
             _ => unreachable!(),
         }

ndbioimage/src/readers/bioformats_java.rs

@@ -38,7 +38,7 @@ static JVM_PID: AtomicU32 = AtomicU32::new(0);
 /// 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> {
+pub 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()));
@@ -698,7 +698,7 @@ impl Reader for BioFormatsJavaReader {
         0
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 

ndbioimage/src/readers/bioformats_rust.rs

@@ -309,7 +309,7 @@ impl Reader for BioFormatsRustReader {
         0
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 

ndbioimage/src/readers/czi.rs

@@ -1149,7 +1149,7 @@ impl Reader for CziReader {
         self.position
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 

ndbioimage/src/readers/tiff.rs

@@ -459,7 +459,7 @@ impl Reader for TiffReader {
     fn position(&self) -> usize {
         self.position
     }
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
     fn pixel_type(&self) -> &PixelType {

ndbioimage/src/readers/tiffseq.rs

@@ -572,7 +572,7 @@ impl Reader for TiffSeqReader {
         self.position
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 

ndbioimage/src/transforms.rs

@@ -1,13 +1,16 @@
 use crate::axes::Axis;
 use crate::error::Error;
-use crate::readers::{DynReader, Reader};
+use crate::readers::{DynReader, Frame, PixelType, Reader};
 use crate::view::View;
 pub use image_registration::transform::Transform;
-use ndarray::{Array2, Dimension, Ix2, Ix3, IxDyn, s};
+use ndarray::{Array2, Dimension, Ix2, Ix3, IxDyn, array, s};
 use serde::{Deserialize, Serialize};
+use std::borrow::Cow;
 use std::collections::{HashMap, HashSet};
+use std::hash::{Hash, Hasher};
 use std::io::Seek;
 use std::path::Path;
+use std::sync::Arc;
 
 #[derive(Clone, Debug, Default, PartialEq, Serialize, Deserialize)]
 struct TransformOld {
@@ -54,6 +57,24 @@ pub struct Transforms {
     pub drift: Vec<Transform<IxDyn>>,
 }
 
+impl Hash for Transforms {
+    fn hash<H: Hasher>(&self, state: &mut H) {
+        let mut keys: Vec<_> = self.channel.keys().collect();
+        keys.sort();
+        for key in keys {
+            key.hash(state);
+            self.channel[key].hash(state);
+        }
+        self.drift.hash(state);
+    }
+}
+
+impl PartialEq<Transforms> for &Transforms {
+    fn eq(&self, other: &Transforms) -> bool {
+        **self == *other
+    }
+}
+
 impl Serialize for Transforms {
     fn serialize<S>(&self, serializer: S) -> Result<S::Ok, S::Error>
     where
@@ -89,7 +110,23 @@ impl Serialize for Transforms {
     }
 }
 
+pub enum TransformKind {
+    None,
+    Channel,
+    Drift,
+    Both,
+}
+
 impl Transforms {
+    pub fn kind(&self) -> TransformKind {
+        match (self.channel.is_empty(), self.drift.is_empty()) {
+            (true, true) => TransformKind::None,
+            (false, true) => TransformKind::Channel,
+            (true, false) => TransformKind::Drift,
+            (false, false) => TransformKind::Both,
+        }
+    }
+
     pub fn load<P: AsRef<Path>>(path: P) -> Result<Self, Error> {
         let mut file = std::fs::File::open(&path)?;
         Ok(
@@ -210,16 +247,32 @@ impl Transforms {
         }
         Ok(average_transforms)
     }
+
+    pub fn get_transform(
+        &self,
+        channel: &str,
+        t: usize,
+    ) -> Result<Option<Cow<'_, Transform<IxDyn>>>, Error> {
+        match (self.channel.get(channel), self.drift.get(t)) {
+            (Some(channel), Some(drift)) => match (channel.ndim(), drift.ndim()) {
+                (2, 2) | (3, 3) => Ok(Some(Cow::Owned(drift * channel))),
+                (2, 3) => Ok(Some(Cow::Owned(drift.add_dimension(0, 1) * channel))),
+                (3, 2) => Ok(Some(Cow::Owned(drift * channel.add_dimension(0, 1)))),
+                (2 | 3, n) | (n, _) => Err(Error::TransformationNotImplemented(n)),
+            },
+            (Some(channel), None) => Ok(Some(Cow::Borrowed(channel))),
+            (None, Some(drift)) => Ok(Some(Cow::Borrowed(drift))),
+            (None, None) => Ok(None),
+        }
+    }
 }
 
 impl<D: Dimension, R: Reader> View<D, R> {
-    #[cfg(feature = "transforms")]
+    pub fn get_transforms(&self) -> &Transforms {
-    pub(crate) fn get_transforms(&self) -> &Transforms {
         &self.transforms
     }
 
-    #[cfg(feature = "transforms")]
+    pub fn set_transforms(&mut self, transforms: Transforms) {
-    pub(crate) fn set_transforms(&mut self, transforms: Transforms) {
         self.transforms = transforms;
     }
 
@@ -318,6 +371,181 @@ impl<D: Dimension, R: Reader> View<D, R> {
     pub fn calculate_drift_transforms_3d(&self) -> Result<Vec<Transform<Ix3>>, Error> {
         todo!()
     }
+
+    pub(crate) fn get_transformed_frame(
+        &self,
+        c: usize,
+        z: usize,
+        t: usize,
+        transform: &Transform<IxDyn>,
+        order: usize,
+    ) -> Result<Arc<Frame>, Error> {
+        match transform.ndim() {
+            2 => {
+                let tr = transform.clone().into_dimensionality::<Ix2>()?;
+
+                macro_rules! interpolate {
+                    ($array:expr ,$var:ident, bool) => {
+                        Ok(Arc::from(Frame::$var(
+                            tr.interpolate_par_order(
+                                &$array.mapv(|i| if i { 1.0 } else { 0.0 }),
+                                order,
+                            )?
+                            .mapv(|i| i > 0.5),
+                        )))
+                    };
+                    ($array:expr ,$var:ident, f64) => {
+                        Ok(Arc::from(Frame::$var(
+                            tr.interpolate_par_order($array, order)?,
+                        )))
+                    };
+                    ($array:expr ,$var:ident, $t:ty) => {
+                        Ok(Arc::from(Frame::$var(
+                            tr.interpolate_par_order($array, order)?.mapv(|i| i as $t),
+                        )))
+                    };
+                }
+
+                match self.get_cached_frame(c, z, t, None)?.as_ref() {
+                    Frame::Bool(frame) => interpolate!(frame, Bool, bool),
+                    Frame::I8(frame) => interpolate!(frame, I8, i8),
+                    Frame::U8(frame) => interpolate!(frame, U8, u8),
+                    Frame::I16(frame) => interpolate!(frame, I16, i16),
+                    Frame::U16(frame) => interpolate!(frame, U16, u16),
+                    Frame::I32(frame) => interpolate!(frame, I32, i32),
+                    Frame::U32(frame) => interpolate!(frame, U32, u32),
+                    Frame::U64(frame) => interpolate!(frame, U64, u64),
+                    Frame::I64(frame) => interpolate!(frame, I64, i64),
+                    Frame::I128(frame) => interpolate!(frame, I128, i128),
+                    Frame::U128(frame) => interpolate!(frame, U128, u128),
+                    Frame::F32(frame) => interpolate!(frame, F32, f32),
+                    Frame::F64(frame) => interpolate!(frame, F64, f64),
+                    Frame::F128(frame) => interpolate!(frame, F128, f64),
+                }
+            }
+            3 => {
+                let tr = transform.clone().into_dimensionality::<Ix3>()?;
+                let shape = self.shape();
+                let zf = z as f64;
+                let yf = shape.y as f64 - 1.0;
+                let xf = shape.x as f64 - 1.0;
+                let corners = array![[zf, 0.0, 0.0], [zf, 0.0, xf], [zf, yf, 0.0], [zf, yf, xf]];
+                let extent = tr.transform_points(&corners)?;
+                let z_extent = extent.slice(s![.., 2]);
+                let z_min = (z_extent
+                    .iter()
+                    .min_by(|a, b| a.total_cmp(b))
+                    .unwrap()
+                    .floor() as isize
+                    - 2)
+                .max(0) as usize;
+                let z_max = (z_extent
+                    .iter()
+                    .max_by(|a, b| a.total_cmp(b))
+                    .unwrap()
+                    .ceil() as isize
+                    + 2)
+                .min(shape.z as isize - 1)
+                .max(0) as usize;
+                let frames = (z_min..=z_max)
+                    .map(|zi| self.get_cached_frame(c, zi, t, None))
+                    .collect::<Result<Vec<_>, Error>>()?;
+
+                // TODO; check these translations
+                let u0 = tr.as_translation(&[(z_min as f64), 0.0, 0.0]);
+                let u1 = tr.as_translation(&[-(z_min as f64), 0.0, 0.0]);
+                let tr = u0 * tr * u1;
+
+                match frames.first().map(|f| f.as_ref()) {
+                    Some(first) => {
+                        macro_rules! interpolate {
+                            ($var:ident, bool) => {{
+                                let views = frames
+                                    .iter()
+                                    .map(|f| match f.as_ref() {
+                                        Frame::$var(a) => Ok(a.view()),
+                                        _ => unreachable!(),
+                                    })
+                                    .collect::<Result<Vec<_>, Error>>()?;
+                                let stack = ndarray::stack(ndarray::Axis(0), &views)?;
+                                let transformed = tr.interpolate_par_order(
+                                    &stack.mapv(|i| if i { 1.0 } else { 0.0 }),
+                                    order,
+                                )?;
+                                Ok(Arc::from(Frame::$var(
+                                    transformed.slice(s![0, .., ..]).mapv(|i| i > 0.5),
+                                )))
+                            }};
+                            ($var:ident, f64) => {{
+                                let views = frames
+                                    .iter()
+                                    .map(|f| match f.as_ref() {
+                                        Frame::$var(a) => Ok(a.view()),
+                                        _ => unreachable!(),
+                                    })
+                                    .collect::<Result<Vec<_>, Error>>()?;
+                                let stack = ndarray::stack(ndarray::Axis(0), &views)?;
+                                let transformed = tr.interpolate_par_order(&stack, order)?;
+                                Ok(Arc::from(Frame::$var(
+                                    transformed.slice(s![0, .., ..]).to_owned(),
+                                )))
+                            }};
+                            ($var:ident, $t:ty) => {{
+                                let views = frames
+                                    .iter()
+                                    .map(|f| match f.as_ref() {
+                                        Frame::$var(a) => Ok(a.view()),
+                                        _ => unreachable!(),
+                                    })
+                                    .collect::<Result<Vec<_>, Error>>()?;
+                                let stack = ndarray::stack(ndarray::Axis(0), &views)?;
+                                let transformed = tr.interpolate_par_order(&stack, order)?;
+                                Ok(Arc::from(Frame::$var(
+                                    transformed.slice(s![0, .., ..]).mapv(|i| i as $t),
+                                )))
+                            }};
+                        }
+                        match first {
+                            Frame::Bool(_) => interpolate!(Bool, bool),
+                            Frame::I8(_) => interpolate!(I8, i8),
+                            Frame::U8(_) => interpolate!(U8, u8),
+                            Frame::I16(_) => interpolate!(I16, i16),
+                            Frame::U16(_) => interpolate!(U16, u16),
+                            Frame::I32(_) => interpolate!(I32, i32),
+                            Frame::U32(_) => interpolate!(U32, u32),
+                            Frame::F32(_) => interpolate!(F32, f32),
+                            Frame::F64(_) => interpolate!(F64, f64),
+                            Frame::I64(_) => interpolate!(I64, i64),
+                            Frame::U64(_) => interpolate!(U64, u64),
+                            Frame::I128(_) => interpolate!(I128, i128),
+                            Frame::U128(_) => interpolate!(U128, u128),
+                            Frame::F128(_) => interpolate!(F128, f64),
+                        }
+                    }
+                    None => {
+                        let shape = self.shape();
+                        Ok(Arc::new(match self.pixel_type() {
+                            PixelType::Bool => Frame::Bool(Array2::default((shape.y, shape.x))),
+                            PixelType::I8 => Frame::I8(Array2::zeros((shape.y, shape.x))),
+                            PixelType::U8 => Frame::U8(Array2::zeros((shape.y, shape.x))),
+                            PixelType::I16 => Frame::I16(Array2::zeros((shape.y, shape.x))),
+                            PixelType::U16 => Frame::U16(Array2::zeros((shape.y, shape.x))),
+                            PixelType::I32 => Frame::I32(Array2::zeros((shape.y, shape.x))),
+                            PixelType::U32 => Frame::U32(Array2::zeros((shape.y, shape.x))),
+                            PixelType::F32 => Frame::F32(Array2::zeros((shape.y, shape.x))),
+                            PixelType::F64 => Frame::F64(Array2::zeros((shape.y, shape.x))),
+                            PixelType::I64 => Frame::I64(Array2::zeros((shape.y, shape.x))),
+                            PixelType::U64 => Frame::U64(Array2::zeros((shape.y, shape.x))),
+                            PixelType::I128 => Frame::I128(Array2::zeros((shape.y, shape.x))),
+                            PixelType::U128 => Frame::U128(Array2::zeros((shape.y, shape.x))),
+                            PixelType::F128 => Frame::F128(Array2::zeros((shape.y, shape.x))),
+                        }))
+                    }
+                }
+            }
+            d => Err(Error::TransformationNotImplemented(d)),
+        }
+    }
 }
 
 #[cfg(test)]

ndbioimage/src/view.rs

@@ -5,18 +5,23 @@ use crate::metadata::Metadata;
 use crate::readers::{Dimensions, DynReader, Frame, Reader};
 use crate::stats::MinMax;
 #[cfg(feature = "transforms")]
-use crate::transforms::Transforms;
+use crate::transforms::{TransformKind, Transforms};
+#[cfg(feature = "transforms")]
+use image_registration::transform::Transform;
 use indexmap::IndexMap;
 use itertools::{Itertools, iproduct};
 use ndarray::{
     Array, Array0, Array1, Array2, ArrayD, Dimension, IntoDimension, Ix0, Ix1, Ix2, Ix5, IxDyn,
     SliceArg, SliceInfoElem, s,
 };
-use num::traits::ToBytes;
+use num::traits::{AsPrimitive, ToBytes};
-use num::{Bounded, FromPrimitive, ToPrimitive, Zero};
+use num::{Bounded, FromPrimitive, One, ToPrimitive, Zero};
 use serde::{Deserialize, Serialize};
 use serde_with::serde_as;
 use std::any::type_name;
+#[cfg(feature = "transforms")]
+use std::borrow::Cow;
+use std::cell::OnceCell;
 use std::collections::{HashMap, HashSet};
 use std::fmt::{Debug, Display, Formatter};
 use std::hash::{Hash, Hasher};
@@ -57,26 +62,42 @@ pub trait Number:
     + Sync
     + AddAssign
     + Bounded
-    + Clone
+    + Copy
     + Div<Self, Output = Self>
     + FromPrimitive
     + PartialOrd
     + Zero
+    + One
+    + AsPrimitive<f64>
 {
+    const ISFLOAT: bool;
 }
-impl<T> Number for T where
+
-    T: 'static
+macro_rules! impl_int {
-        + Send
+    ($($t:tt),+ $(,)?) => {
-        + Sync
+        $(
-        + AddAssign
+        impl Number for $t {
-        + Bounded
+            const ISFLOAT: bool = false;
-        + Clone
-        + Div<Self, Output = Self>
-        + FromPrimitive
-        + PartialOrd
-        + Zero
-{
         }
+        )*
+    };
+}
+
+impl_int!(
+    i8, i16, i32, i64, i128, isize, u8, u16, u32, u64, u128, usize
+);
+
+macro_rules! impl_float {
+    ($($t:tt),+ $(,)?) => {
+        $(
+        impl Number for $t {
+            const ISFLOAT: bool = true;
+        }
+        )*
+    };
+}
+
+impl_float!(f32, f64);
 
 /// sliceable view on an image file
 #[serde_as]
@@ -89,6 +110,8 @@ pub struct View<D: Dimension, R: Reader = DynReader> {
     /// always has all of cztyx with possibly some new axes added
     axes: Vec<Axis>,
     operations: IndexMap<Axis, Operation>,
+    #[serde(skip)]
+    channel_names: OnceCell<HashMap<usize, String>>,
     dimensionality: PhantomData<D>,
     #[cfg(feature = "transforms")]
     pub(crate) transforms: Transforms,
@@ -117,6 +140,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
             slice,
             axes,
             operations: IndexMap::new(),
+            channel_names: OnceCell::new(),
             dimensionality: PhantomData,
             #[cfg(feature = "transforms")]
             transforms: Transforms::default(),
@@ -126,7 +150,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
     #[expect(dead_code)]
     pub(crate) fn new_with_axes(reader: R, axes: Vec<Axis>) -> Result<Self, Error> {
         let mut slice = Vec::new();
-        let shape = reader.shape();
+        let shape = reader.raw_shape();
         for axis in axes.iter() {
             match axis {
                 Axis::C => slice.push(SliceInfoElem::Slice {
@@ -183,6 +207,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
             axes,
             operations: IndexMap::new(),
             dimensionality: PhantomData,
+            channel_names: OnceCell::new(),
             #[cfg(feature = "transforms")]
             transforms: Transforms::default(),
         })
@@ -198,6 +223,26 @@ impl<D: Dimension, R: Reader> View<D, R> {
         self.reader.series()
     }
 
+    /// the name of a particular channel
+    pub fn channel_name(&self, channel: usize) -> Result<&str, Error> {
+        if self.channel_names.get().is_none() {
+            let names = self.metadata()?.image[0]
+                .pixels
+                .channel
+                .iter()
+                .enumerate()
+                .map(|(i, c)| (i, c.name.clone().unwrap_or_else(|| format!("{}", i))))
+                .collect::<HashMap<_, _>>();
+            let _ = self.channel_names.set(names);
+        }
+
+        self.channel_names
+            .get()
+            .and_then(|names| names.get(&channel))
+            .map(String::as_str)
+            .ok_or(Error::NoChannel(channel))
+    }
+
     /// set the maximum number of frames the process-wide cache may hold,
     /// evicting the least recently used frames
     pub fn with_cache_capacity(self, capacity: usize) -> Self {
@@ -234,6 +279,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
             slice: self.slice,
             axes: self.axes,
             operations: self.operations,
+            channel_names: self.channel_names,
             dimensionality: PhantomData,
             #[cfg(feature = "transforms")]
             transforms: Transforms::default(),
@@ -249,6 +295,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
                     slice: self.slice,
                     axes: self.axes,
                     operations: self.operations,
+                    channel_names: self.channel_names,
                     dimensionality: PhantomData,
                     #[cfg(feature = "transforms")]
                     transforms: self.transforms,
@@ -262,6 +309,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
                 slice: self.slice,
                 axes: self.axes,
                 operations: self.operations,
+                channel_names: self.channel_names,
                 dimensionality: PhantomData,
                 #[cfg(feature = "transforms")]
                 transforms: self.transforms,
@@ -671,7 +719,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
         let slice: Vec<_> = index.iter().map(|s| SliceInfoElem::Index(*s)).collect();
         let view = self.clone().into_dyn().slice(slice.as_slice())?;
         let arr = view.as_array()?;
-        Ok(arr.first().unwrap().clone())
+        Ok(*arr.first().unwrap())
     }
 
     /// collect the view into an ndarray
@@ -714,7 +762,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
             IndexMap::new()
         };
         let mut shape_out = Vec::new();
-        let mut slice = Vec::new();
+        let mut slice_out = Vec::new();
         let mut ax_out = Vec::new();
         for (s, a) in self.slice.iter().zip(&self.axes) {
             match s {
@@ -722,7 +770,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
                     let end = end.expect("slice has no end");
                     if !op_xy.contains_key(a) && !op_czt.contains_key(a) {
                         shape_out.push(((end - start).max(0) / step) as usize);
-                        slice.push(SliceInfoElem::Slice {
+                        slice_out.push(SliceInfoElem::Slice {
                             start: 0,
                             end: None,
                             step: 1,
@@ -733,19 +781,18 @@ impl<D: Dimension, R: Reader> View<D, R> {
                 SliceInfoElem::Index(_) => {}
                 SliceInfoElem::NewAxis => {
                     shape_out.push(1);
-                    slice.push(SliceInfoElem::Index(0));
+                    slice_out.push(SliceInfoElem::Index(0));
                     ax_out.push(*a);
                 }
             }
         }
         let mut slice_reader = vec![Slice::empty(); 5];
         let mut xy_dim = 0usize;
-        let shape_reader = self.reader.shape();
+        let shape_reader = self.reader.raw_shape();
         for (s, &axis) in self.slice.iter().zip(&self.axes) {
-            match axis {
+            match (axis, s) {
-                Axis::New => {}
+                (Axis::New, _) => {}
-                _ => match s {
+                (_, SliceInfoElem::Slice { start, end, step }) => {
-                    SliceInfoElem::Slice { start, end, step } => {
                     if let Axis::X | Axis::Y = axis
                         && !op_xy.contains_key(&axis)
                     {
@@ -757,35 +804,31 @@ impl<D: Dimension, R: Reader> View<D, R> {
                         *step,
                     );
                 }
-                    SliceInfoElem::Index(j) => {
+                (_, SliceInfoElem::Index(j)) => {
                     slice_reader[axis as usize] = Slice::new(
                         idx_bnd(*j, shape_reader[axis] as isize)?,
                         slc_bnd(*j + 1, shape_reader[axis] as isize)?,
                         1,
                     );
                 }
-                    SliceInfoElem::NewAxis => panic!("axis cannot be a new axis"),
+                (_, SliceInfoElem::NewAxis) => panic!("axis cannot be a new axis"),
-                },
             }
         }
         let xy = [
             self.slice[Axis::Y.pos(&self.axes, &self.slice)?],
             self.slice[Axis::X.pos(&self.axes, &self.slice)?],
         ];
-        let mut array = if let Some((_, op)) = op_czt.first() {
+        let mut array = match op_czt.first() {
-            match op {
+            Some((_, Operation::Max)) => {
-                Operation::Max => {
                 ArrayD::<T>::from_elem(shape_out.into_dimension(), T::min_value())
             }
-                Operation::Min => {
+            Some((_, Operation::Min)) => {
                 ArrayD::<T>::from_elem(shape_out.into_dimension(), T::max_value())
             }
             _ => ArrayD::<T>::zeros(shape_out.into_dimension()),
-            }
-        } else {
-            ArrayD::<T>::zeros(shape_out.into_dimension())
         };
-        let shape = self.reader.shape();
+
+        let shape = self.reader.raw_shape();
         let mut axes_out_idx = [None; 5];
         for (i, ax) in ax_out.iter().enumerate() {
             if *ax < Axis::New {
@@ -793,22 +836,56 @@ impl<D: Dimension, R: Reader> View<D, R> {
             }
         }
 
+        #[cfg(feature = "transforms")]
+        let kind = self.transforms.kind();
+        #[cfg(feature = "transforms")]
+        let order = if T::ISFLOAT { 3 } else { 0 };
+        #[cfg(feature = "transforms")]
+        let mut transform_done = HashSet::new();
+
         for (c, z, t) in iproduct!(&slice_reader[0], &slice_reader[1], &slice_reader[2]) {
             if let Some(i) = axes_out_idx[0] {
-                slice[i] = SliceInfoElem::Index(c)
+                slice_out[i] = SliceInfoElem::Index(c)
             };
             if let Some(i) = axes_out_idx[1] {
-                slice[i] = SliceInfoElem::Index(z)
+                slice_out[i] = SliceInfoElem::Index(z)
             };
             if let Some(i) = axes_out_idx[2] {
-                slice[i] = SliceInfoElem::Index(t)
+                slice_out[i] = SliceInfoElem::Index(t)
             };
+            #[cfg(feature = "transforms")]
+            let transform = self
+                .transforms
+                .get_transform(self.channel_name(c as usize)?, t as usize)?;
+            #[cfg(feature = "transforms")]
+            let transform_now = if let (TransformKind::Channel, Some((&Axis::C, _)), _)
+            | (TransformKind::Drift, Some((&Axis::T, _)), _)
+            | (TransformKind::Both, Some((&Axis::C | &Axis::T, _)), _)
+            | (
+                TransformKind::Channel | TransformKind::Drift | TransformKind::Both,
+                _,
+                false,
+            ) = (&kind, op_czt.first(), xy_dim == 2)
+            {
+                transform_done.insert((c, z, t));
+                transform.map(|transform| (transform, order))
+            } else {
+                None
+            };
+            #[cfg(feature = "transforms")]
+            let frame = self.get_cached_frame(
+                (c % shape.c as isize) as usize,
+                (z % shape.z as isize) as usize,
+                (t % shape.t as isize) as usize,
+                transform_now,
+            )?;
+            #[cfg(not(feature = "transforms"))]
             let frame = self.get_cached_frame(
                 (c % shape.c as isize) as usize,
                 (z % shape.z as isize) as usize,
                 (t % shape.t as isize) as usize,
             )?;
-
+            // 0, 1 or 2d frame depending on x or y operations
             let arr_frame: Array2<T> = frame.as_ref().try_into()?;
             let arr_frame = match xy_dim {
                 0 => {
@@ -855,35 +932,28 @@ impl<D: Dimension, R: Reader> View<D, R> {
                     unreachable!("xy cannot be 3d or more");
                 }
             };
-            if let Some((_, op)) = op_czt.first() {
+            // assign arr_frame to output array, apply first of c, z or t operation
-                match op {
+            match op_czt.first() {
-                    Operation::Max => {
+                Some((_, Operation::Max)) => {
                     array
-                            .slice_mut(slice.as_slice())
+                        .slice_mut(slice_out.as_slice())
                         .zip_mut_with(&arr_frame, |x, y| {
-                                *x = if *x >= *y { x.clone() } else { y.clone() }
+                            *x = if *x >= *y { *x } else { *y }
                         });
                 }
-                    Operation::Min => {
+                Some((_, Operation::Min)) => {
                     array
-                            .slice_mut(slice.as_slice())
+                        .slice_mut(slice_out.as_slice())
                         .zip_mut_with(&arr_frame, |x, y| {
-                                *x = if *x < *y { x.clone() } else { y.clone() }
+                            *x = if *x < *y { *x } else { *y }
                         });
                 }
-                    Operation::Sum => {
+                Some((_, Operation::Mean | Operation::Sum)) => {
                     array
-                            .slice_mut(slice.as_slice())
+                        .slice_mut(slice_out.as_slice())
-                            .zip_mut_with(&arr_frame, |x, y| *x += y.clone());
+                        .zip_mut_with(&arr_frame, |x, y| *x += *y);
                 }
-                    Operation::Mean => {
+                _ => array.slice_mut(slice_out.as_slice()).assign(&arr_frame),
-                        array
-                            .slice_mut(slice.as_slice())
-                            .zip_mut_with(&arr_frame, |x, y| *x += y.clone());
-                    }
-                }
-            } else {
-                array.slice_mut(slice.as_slice()).assign(&arr_frame)
             }
         }
         let mut out = Some(array);
@@ -894,23 +964,61 @@ impl<D: Dimension, R: Reader> View<D, R> {
             .collect();
         for (ax, op) in self.operations.iter().skip(op_xy.len() + op_czt.len()) {
             if let Some(idx) = ax_out.remove(ax) {
+                #[cfg(feature = "transforms")]
+                let mut arr = out.take().unwrap();
+                #[cfg(not(feature = "transforms"))]
+                let arr = out.take().unwrap();
+
+                #[cfg(feature = "transforms")]
+                if let (Axis::C, TransformKind::Channel | TransformKind::Both)
+                | (Axis::T, TransformKind::Drift | TransformKind::Both) = (ax, &kind)
+                {
+                    let mut slice_transform = vec![
+                        SliceInfoElem::Slice {
+                            start: 0,
+                            end: None,
+                            step: 1
+                        };
+                        ax_out.len()
+                    ];
+                    for (c, z, t) in iproduct!(&slice_reader[0], &slice_reader[1], &slice_reader[2])
+                    {
+                        if let Some(transform) = self
+                            .transforms
+                            .get_transform(self.channel_name(c as usize)?, t as usize)?
+                            && !transform_done.contains(&(c, z, t))
+                        {
+                            for (axis, i) in [&Axis::C, &Axis::Z, &Axis::T].iter().zip([c, z, t]) {
+                                if let Some(axis_pos) = ax_out.get(axis) {
+                                    slice_transform[*axis_pos] = SliceInfoElem::Index(i);
+                                }
+                            }
+                            let untransformed = arr.slice(slice_transform.as_slice());
+                            let transformed = transform
+                                .interpolate_par_order(untransformed, order)?
+                                .mapv(|i| T::from_f64(i).unwrap());
+                            arr.slice_mut(slice_transform.as_slice())
+                                .assign(&transformed);
+                        }
+                        transform_done.insert((c, z, t));
+                    }
+                }
+
+                let a = op.operate(arr, idx)?;
+                let _ = out.insert(a);
+
                 for i in ax_out.values_mut() {
                     if *i > idx {
                         *i -= 1;
                     }
                 }
-                let arr = out.take().unwrap();
-                let a = op.operate(arr, idx)?;
-                let _ = out.insert(a);
             }
         }
-        let n = if let Some((&ax, op)) = op_czt.first()
+        let n = if let Some((ax, Operation::Mean)) = op_czt.first() {
-            && *op == Operation::Mean
-        {
             self.axes
                 .iter()
                 .zip(self.slice.iter())
-                .find(|(a, _)| **a == ax)
+                .find(|(a, _)| *a == ax)
                 .and_then(|(_, s)| match s {
                     SliceInfoElem::Slice { start, end, step } => {
                         end.map(|e| (((e - start).max(0) / step) as usize).max(1))
@@ -921,12 +1029,29 @@ impl<D: Dimension, R: Reader> View<D, R> {
         } else {
             1
         };
+        #[cfg(not(feature = "transforms"))]
         let array = if n == 1 {
             out.take().unwrap()
         } else {
             let m = T::from_usize(n).unwrap_or_else(|| T::zero());
-            out.take().unwrap().mapv(|x| x / m.clone())
+            out.take().unwrap().mapv(|x| x / m)
         };
+        #[cfg(feature = "transforms")]
+        let mut array = if n == 1 {
+            out.take().unwrap()
+        } else {
+            let m = T::from_usize(n).unwrap_or_else(|| T::zero());
+            out.take().unwrap().mapv(|x| x / m)
+        };
+        #[cfg(feature = "transforms")]
+        if transform_done.is_empty() {
+            let c = slice_reader[0].start;
+            let t = slice_reader[2].start;
+            if let Some(transform) = self.transforms.get_transform(self.channel_name(c as usize)?, t as usize)? {
+                array = transform.interpolate_par_order(&array, order)?.mapv(|i| T::from_f64(i).unwrap());
+            }
+        }
+
         ArrayCache::global().insert(key.to_owned(), array.clone());
         Ok(array)
     }
@@ -957,7 +1082,13 @@ impl<D: Dimension, R: Reader> View<D, R> {
             .collect())
     }
 
-    fn frame_key(&self, c: usize, z: usize, t: usize) -> FrameKeyRef<'_> {
+    fn frame_key<'a>(
+        &'a self,
+        c: usize,
+        z: usize,
+        t: usize,
+        #[cfg(feature = "transforms")] transform: Option<(Cow<'a, Transform<IxDyn>>, usize)>,
+    ) -> FrameKeyRef<'a> {
         FrameKeyRef {
             reader: ReaderKeyRef {
                 name: self.reader.reader_name(),
@@ -969,6 +1100,8 @@ impl<D: Dimension, R: Reader> View<D, R> {
             c,
             z,
             t,
+            #[cfg(feature = "transforms")]
+            transform,
         }
     }
 
@@ -985,14 +1118,37 @@ impl<D: Dimension, R: Reader> View<D, R> {
             slice: &self.slice,
             axes: &self.axes,
             operations: &self.operations,
+            #[cfg(feature = "transforms")]
+            transforms: &self.transforms,
         }
     }
 
-    fn get_cached_frame(&self, c: usize, z: usize, t: usize) -> Result<Arc<Frame>, Error> {
+    pub(crate) fn get_cached_frame(
-        let key = self.frame_key(c, z, t);
+        &self,
+        c: usize,
+        z: usize,
+        t: usize,
+        #[cfg(feature = "transforms")] transform: Option<(Cow<Transform<IxDyn>>, usize)>,
+    ) -> Result<Arc<Frame>, Error> {
+        let key = self.frame_key(
+            c,
+            z,
+            t,
+            #[cfg(feature = "transforms")]
+            transform
+                .as_ref()
+                .map(|(transform, order)| (Cow::Borrowed(&**transform), *order)),
+        );
         if let Some(frame) = FrameCache::global().get(&key) {
             return Ok(frame);
         }
+        #[cfg(feature = "transforms")]
+        let frame = if let Some((transform, order)) = transform.as_ref() {
+            self.get_transformed_frame(c, z, t, transform, *order)?
+        } else {
+            Arc::new(self.reader.get_frame(c, z, t)?)
+        };
+        #[cfg(not(feature = "transforms"))]
         let frame = Arc::new(self.reader.get_frame(c, z, t)?);
         FrameCache::global().insert(key.to_owned(), frame.clone());
         Ok(frame)
@@ -1187,7 +1343,7 @@ impl<R: Reader> Item for View<Ix0, R> {
         Array1<T>: MinMax<Output = Array0<T>>,
         Array2<T>: MinMax<Output = Array1<T>>,
     {
-        Ok(self.as_array()?.first().ok_or(Error::EmptyView)?.clone())
+        Ok(*self.as_array()?.first().ok_or(Error::EmptyView)?)
     }
 }
 
@@ -1229,7 +1385,7 @@ to_bytes_vec_impl!(
 mod tests {
     use crate::axes::{Axis, Operation};
     use crate::cache::{
-        ArrayCache, ArrayKey, ArrayKeyRef, FileStamp, FrameCache, ReaderKey, ReaderKeyRef,
+        ArrayCache, ArrayKey, ArrayKeyRef, FileStamp, FrameCache, FrameKey, ReaderKey, ReaderKeyRef,
     };
     use crate::error::Error;
     use crate::readers::{DynReader, Frame, Reader};
@@ -1241,6 +1397,8 @@ mod tests {
     use postcard::{from_bytes, to_stdvec};
     use std::path::{Path, PathBuf};
     use std::sync::Arc;
+    #[cfg(feature = "transforms")]
+    use crate::transforms::Transforms;
 
     fn open(file: &str) -> Result<DynReader, Error> {
         let path = std::env::current_dir()?
@@ -1512,9 +1670,8 @@ mod tests {
     #[test]
     fn frame_cache() -> Result<(), Error> {
         let cache = FrameCache::new(2);
-        let key = |c: usize, z: usize, t: usize| {
+        let key = |c: usize, z: usize, t: usize| FrameKey {
-            (
+            reader_key: ReaderKey {
-                ReaderKey {
                 name: "test".to_string(),
                 path: PathBuf::from("test.tif"),
                 series: 0,
@@ -1524,7 +1681,8 @@ mod tests {
             c,
             z,
             t,
-            )
+            #[cfg(feature = "transforms")]
+            transform: None,
         };
         cache.insert(
             key(0, 0, 0),
@@ -1561,6 +1719,8 @@ mod tests {
             slice: vec![SliceInfoElem::Index(index)],
             axes: axes.to_vec(),
             operations: vec![],
+            #[cfg(feature = "transforms")]
+            transforms: Transforms::default(),
         };
         let k0 = key("u16", 0, &[Axis::T]);
         let k1 = key("u16", 1, &[Axis::T]);
@@ -1587,6 +1747,8 @@ mod tests {
             slice: &[SliceInfoElem::Index(0)],
             axes: &[Axis::T],
             operations: &ops,
+            #[cfg(feature = "transforms")]
+            transforms: &Transforms::default(),
         };
         assert!(cache.get::<f64, _>(&borrowed).is_none());
         assert!(cache.get::<u16, _>(&borrowed).is_some());
@@ -1602,12 +1764,37 @@ mod tests {
         let (c, z, t) = (shape[0] - 1, shape[1] - 1, shape[2] - 1);
         let cache = FrameCache::global();
         let a: Array5<usize> = view.clone().try_into()?;
-        assert!(cache.get(&view.frame_key(c, z, t)).is_some());
+        assert!(
+            cache
+                .get(&view.frame_key(
+                    c,
+                    z,
+                    t,
+                    #[cfg(feature = "transforms")]
+                    None
+                ))
+                .is_some()
+        );
         let b: Array5<usize> = view.clone().try_into()?;
         assert_eq!(a, b);
         // a fresh reader on the same file shares the same cache key
         let view2 = open(file)?.view();
-        assert_eq!(view.frame_key(c, z, t), view2.frame_key(c, z, t));
+        assert_eq!(
+            view.frame_key(
+                c,
+                z,
+                t,
+                #[cfg(feature = "transforms")]
+                None
+            ),
+            view2.frame_key(
+                c,
+                z,
+                t,
+                #[cfg(feature = "transforms")]
+                None
+            )
+        );
         let c2: Array5<usize> = view2.clone().try_into()?;
         assert_eq!(a, c2);
         Ok(())