Merge remote-tracking branch 'origin/main'

- add pytest workflow

.github/workflows/publish_crates.yml

@@ -1,4 +1,4 @@
-name: Publish
+name: Publish_rs
 
 on: [ workflow_dispatch ]
 
@@ -10,23 +10,27 @@ jobs:
     name: Publish (crates.io)
     runs-on: ubuntu-latest
     timeout-minutes: 25
+    env:
+      CARGO_HOME: ${{ github.workspace }}/.cargo
     steps:
       - uses: actions/checkout@v6
+        with:
+          submodules: recursive
       - name: Restore cache
         uses: actions/cache/restore@v4
         with:
-          path: |
+          path: ${{ env.CARGO_HOME }}
-            ~/.cargo
           key: cache-ubuntu-cargo-publish
 
       - name: Install Rust
         run: |-
-          export PATH="$HOME/.cargo/bin:$PATH"
+          export PATH="$CARGO_HOME/bin:$PATH"
           if ! command -v rustc >/dev/null 2>&1; then
             curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
           else
             rustup update
           fi
+          echo "$CARGO_HOME/bin" >> "$GITHUB_PATH"
           cargo install cargo-release
         shell: bash
 
@@ -46,9 +50,9 @@ jobs:
       # which is reasonable, since this job only runs after the Linux, Windows, and WASM builds
       # have passed.
       - name: "cargo release publish"
+        env:
+          CARGO_REGISTRY_TOKEN: ${{ secrets.CRATES_IO_API_TOKEN }}
         run: |-
-          export PATH="$HOME/.osxcross/bin:$PATH"
-          cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
           cargo release \
             publish \
             --workspace \
@@ -61,6 +65,5 @@ jobs:
       - name: Store cache
         uses: actions/cache/save@v4
         with:
-          path: |
+          path: ${{ env.CARGO_HOME }}
-            ~/.cargo
           key: cache-ubuntu-cargo-publish

.github/workflows/publish_pypi.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Publish_py
 
 on: [ workflow_dispatch ]
 
@@ -9,8 +9,14 @@ jobs:
   pypi_publish:
     name: Publish (pypi.org)
     runs-on: ubuntu-latest
+    env:
+      CARGO_HOME: ${{ github.workspace }}/.cargo
+      RUSTUP_HOME: ${{ github.workspace }}/.rustup
+      RUSTUP_TOOLCHAIN: stable
     steps:
       - uses: actions/checkout@v6
+        with:
+          submodules: recursive
       - uses: actions/setup-python@v5
         with:
           python-version: 3.x
@@ -23,33 +29,62 @@ jobs:
             ~/.cache/pip-wheel
             ~/.cache/sccache
             ~/.cache/cargo-xwin
-            ~/.cargo
+            ${{ env.CARGO_HOME }}
             ~/.osxcross
           key: cache-ubuntu-maturin-cross-compile
 
-      - name: Install llvm
+      - name: Install build dependencies
         run: |
-          if ! command -v llvm-dlltool >/dev/null 2>&1; then
+          # the stock clang on noble (18) is too old for the 2025+ MSVC STL that
+          # cargo-xwin downloads (yvals_core.h: "error STL1000: expected Clang
+          # 19.0.0 or newer"), so take a newer clang toolchain from apt.llvm.org.
+          # apt.llvm.org sometimes half-publishes a new version, in which case the
+          # unversioned meta packages become uninstallable ("clang: Depends:
+          # clang-NN ... not installable"); so pick the newest versioned set that
+          # actually resolves (a dry-run checks the whole dependency closure) -
+          # nothing is hardcoded, this tracks the newest working release.
           sudo apt update
-            sudo apt install -y llvm
+          echo "deb [trusted=yes] https://apt.llvm.org/noble/ llvm-toolchain-noble main" | sudo tee /etc/apt/sources.list.d/llvm-toolchain-noble.list >/dev/null
+          sudo apt update
+          sudo apt install -y build-essential cmake
+          NEWEST=""
+          for name in $(apt-cache search '^clang-[0-9]+$' | awk '{print $1}' | sort -rV); do
+            v=${name#clang-}
+            if sudo apt-get install --dry-run -y "clang-$v" "llvm-$v" "lld-$v" "libclang-$v-dev" >/dev/null 2>&1; then
+              NEWEST=$v
+              break
             fi
+          done
+          [ -n "$NEWEST" ] || { echo "no installable clang toolchain found in apt.llvm.org" >&2; exit 1; }
+          echo "using clang/llvm toolchain $NEWEST"
+          sudo apt install -y "clang-$NEWEST" "llvm-$NEWEST" "lld-$NEWEST" "libclang-$NEWEST-dev"
+          # expose the toolchain's own bin/lib dirs (clang, clang-cl, lld-link,
+          # llvm-lib, libclang) to the later steps
+          echo "LLVM_BIN=/usr/lib/llvm-$NEWEST/bin" >> "$GITHUB_ENV"
+          echo "LIBCLANG_PATH=/usr/lib/llvm-$NEWEST/lib" >> "$GITHUB_ENV"
+          export PATH="/usr/lib/llvm-$NEWEST/bin:$PATH"
+          clang --version | head -1
+          command -v clang clang-cl lld-link llvm-lib
         shell: bash
 
       - name: Install Rust
         run: |
-          export PATH="$HOME/.cargo/bin:$PATH"
+          export PATH="$CARGO_HOME/bin:$PATH"
-          if ! command -v rustc >/dev/null 2>&1; then
+          if ! command -v rustup >/dev/null 2>&1; then
             curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
-          else
-            rustup update
           fi
+          rustup toolchain install stable --profile minimal
+          rustup default stable
+          echo "$CARGO_HOME/bin" >> "$GITHUB_PATH"
+          cargo --version
         shell: bash
 
       - name: Install sccache and maturin
         run: |
-          export PATH="$HOME/.cargo/bin:$PATH"
+          python -m pip install --upgrade pip maturin ziglang cargo-zigbuild
-          python -m pip install --upgrade pip
+          # in case an older copy was cargo-installed into the CARGO_HOME cache,
-          pip install maturin ziglang
+          # prevent it from shadowing the pip-installed one
+          rm -f "${CARGO_HOME:?}/bin/cargo-zigbuild" || true
           if ! command -v sccache >/dev/null 2>&1; then
             cargo install sccache || pip install sccache
           fi
@@ -57,7 +92,6 @@ jobs:
 
       - name: Install xwin
         run: |
-          export PATH="$HOME/.cargo/bin:$PATH"
           if ! command -v cargo-xwin >/dev/null 2>&1; then
             cargo install cargo-xwin || pip install cargo-xwin
             cargo xwin cache xwin
@@ -67,32 +101,87 @@ jobs:
       - name: Install osxcross
         run: |
           export PATH="$HOME/.osxcross/bin:$PATH"
-          if ! command -v osxcross >/dev/null 2>&1; then
+          if [ ! -d "$HOME/.osxcross/bin" ]; then
             wget ${{ secrets.OSXCROSS_LINK }} -O osxcross.tar.gz
             tar -xzf osxcross.tar.gz -C ~/
             mv ~/osxcross ~/.osxcross
           fi
+        shell: bash
+
+      - name: Shim clang for ring's aarch64-windows build
+        run: |
+          # ring 0.17.14 forces a plain `clang` for its C build on
+          # aarch64-pc-windows-msvc (its "must use Clang on Win AArch64"
+          # workaround), while the CFLAGS injected by cargo-xwin carry
+          # clang-cl-style `/imsvc <dir>` pairs that plain clang rejects.
+          # This shim rewrites them to `-I <dir>` and execs the real clang
+          # found further down PATH; all other invocations pass through
+          # untouched, and tools with other names (clang-cl, lld-link) are not
+          # affected.
+          mkdir -p /root/ci-shims
+          cat > /root/ci-shims/clang <<'EOF'
+          #!/usr/bin/env bash
+          args=()
+          prev_imsvc=0
+          for a in "$@"; do
+            if [ "$prev_imsvc" = "1" ]; then
+              args+=("-I$a")
+              prev_imsvc=0
+              continue
+            fi
+            case "$a" in
+              /imsvc)   prev_imsvc=1 ;;
+              /imsvc:*) args+=("-I${a#/imsvc:}") ;;
+              *)        args+=("$a") ;;
+            esac
+          done
+          self_dir=$(CDPATH= cd -- "$(dirname -- "$0")" && pwd)
+          real=""
+          IFS=":" read -r -a _dirs <<< "$PATH"
+          IFS=""
+          for d in "${_dirs[@]}"; do
+            [ "$d" = "$self_dir" ] && continue
+            if [ -x "$d/clang" ]; then real="$d/clang"; break; fi
+          done
+          [ -n "$real" ] || real=/usr/bin/clang
+          exec "$real" "${args[@]}"
+          EOF
+          chmod +x /root/ci-shims/clang
+        shell: bash
 
       - name: Build wheels
+        shell: bash
         run: |
-          export PATH="$HOME/.cargo/bin:$HOME/.osxcross/bin:$PATH"
+          export PATH="$HOME/.osxcross/bin:$PATH"
-          maturin sdist --out dist
+          # LLVM_BIN and LIBCLANG_PATH were set by the "Install build
-          rustup default nightly
+          # dependencies" step; put the shim (for ring's forced plain `clang`)
+          # in front of the toolchain so clang-cl / lld-link (distinct names)
+          # still resolve to the real toolchain
+          export PATH="/root/ci-shims:$LLVM_BIN:$PATH"
+          rm -rf dist
+          maturin sdist --out dist -m ndbioimage/Cargo.toml
 
-          rustup target add x86_64-unknown-linux-gnu --toolchain nightly
+          rustup target add x86_64-apple-darwin
-          maturin build --release --out dist --target x86_64-unknown-linux-gnu
+          maturin build --release --out dist --target x86_64-apple-darwin --zig --auditwheel repair -m ndbioimage/Cargo.toml
-          rustup target add aarch64-unknown-linux-gnu --toolchain nightly
+          rustup target add aarch64-apple-darwin
-          maturin build --release --out dist --target aarch64-unknown-linux-gnu --zig
+          maturin build --release --out dist --target aarch64-apple-darwin --zig --auditwheel repair -m ndbioimage/Cargo.toml
 
-          rustup target add x86_64-pc-windows-msvc --toolchain nightly
+          rustup target add x86_64-unknown-linux-gnu
-          maturin build --release --out dist --target x86_64-pc-windows-msvc
+          # the x86_64-gnu build links the runner's host liblzma (lzma-sys),
-          rustup target add aarch64-pc-windows-msvc --toolchain nightly
+          # which needs glibc symbols up to 2.34 - higher than the
-          maturin build --release --out dist --target aarch64-pc-windows-msvc
+          # manylinux_2_17 baseline
+          maturin build --release --out dist --target x86_64-unknown-linux-gnu --zig --auditwheel repair --compatibility manylinux_2_34 -m ndbioimage/Cargo.toml
+          rustup target add aarch64-unknown-linux-gnu
+          maturin build --release --out dist --target aarch64-unknown-linux-gnu --zig --auditwheel repair --compatibility manylinux_2_34 -m ndbioimage/Cargo.toml
+          rustup target add x86_64-unknown-linux-musl
+          maturin build --release --out dist --target x86_64-unknown-linux-musl --zig --auditwheel repair -m ndbioimage/Cargo.toml
+          rustup target add aarch64-unknown-linux-musl
+          maturin build --release --out dist --target aarch64-unknown-linux-musl --zig --auditwheel repair -m ndbioimage/Cargo.toml
 
-          rustup target add x86_64-apple-darwin --toolchain nightly
+          rustup target add x86_64-pc-windows-msvc
-          maturin build --release --out dist --target x86_64-apple-darwin --zig
+          maturin build --release --out dist --target x86_64-pc-windows-msvc --auditwheel repair -m ndbioimage/Cargo.toml
-          rustup target add aarch64-apple-darwin --toolchain nightly
+          rustup target add aarch64-pc-windows-msvc
-          maturin build --release --out dist --target aarch64-apple-darwin --zig
+          maturin build --release --out dist --target aarch64-pc-windows-msvc --auditwheel repair -m ndbioimage/Cargo.toml
 
       - name: Store cache
         uses: actions/cache/save@v4
@@ -102,7 +191,7 @@ jobs:
             ~/.cache/pip-wheel
             ~/.cache/sccache
             ~/.cache/cargo-xwin
-            ~/.cargo
+            ${{ env.CARGO_HOME }}
             ~/.osxcross
           key: cache-ubuntu-maturin-cross-compile
 
@@ -110,5 +199,6 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
           password: ${{ secrets.PYPI_API_TOKEN }}
+          skip-existing: true
         env:
           GITHUB_WORKFLOW_REF: 1.10.1

.github/workflows/pytest.yml

@@ -0,0 +1,79 @@
+name: pytest
+
+on: [ workflow_dispatch, workflow_call, push, pull_request ]
+
+permissions:
+  contents: read
+
+jobs:
+  pypi_publish:
+    name: Publish (pypi.org)
+    runs-on: ubuntu-latest
+    env:
+      CARGO_HOME: ${{ github.workspace }}/.cargo
+      RUSTUP_HOME: ${{ github.workspace }}/.rustup
+      RUSTUP_TOOLCHAIN: stable
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          submodules: recursive
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Restore cache
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ${{ env.CARGO_HOME }}
+          key: cache-ubuntu-maturin-cross-compile
+
+      - name: Install build dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y llvm cmake build-essential libclang-dev clang
+        shell: bash
+
+      - name: Install Rust
+        run: |
+          export PATH="$CARGO_HOME/bin:$PATH"
+          if ! command -v rustup >/dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+          fi
+          rustup toolchain install stable --profile minimal
+          rustup default stable
+          echo "$CARGO_HOME/bin" >> "$GITHUB_PATH"
+          cargo --version
+        shell: bash
+
+      - name: Install sccache and maturin
+        run: |
+          python -m pip install --upgrade pip maturin ziglang cargo-zigbuild
+          # in case an older copy was cargo-installed into the CARGO_HOME cache,
+          # prevent it from shadowing the pip-installed one
+          rm -f "${CARGO_HOME:?}/bin/cargo-zigbuild" || true
+          if ! command -v sccache >/dev/null 2>&1; then
+            cargo install sccache || pip install sccache
+          fi
+        shell: bash
+
+      - name: PyTest
+        run: |
+          cd ndbioimage
+          python -m pip install .[test]
+          python -m pytest 
+
+      - name: Store cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ~/.cache/cargo-xwin
+            ${{ env.CARGO_HOME }}
+            ~/.osxcross
+          key: cache-ubuntu-maturin-cross-compile

.gitignore

@@ -29,6 +29,7 @@ venv/
 *.egg-info/
 .installed.cfg
 *.egg
+.cargo
 
 # Installer logs
 pip-log.txt
@@ -72,11 +73,11 @@ docs/_build/
 # Pyenv
 .python-version
 
-/ndbioimage/tests/files/*
 AGENTS.md
 .agentbridge
 .agent-work
 
+/ndbioimage/tests/files/*
 /ndbioimage/py/ndbioimage/jassets
 /ndbioimage/py/ndbioimage/deps
 /build_wheels.sh

Cargo.toml

@@ -3,28 +3,24 @@ resolver = "3"
 members = ["ndbioimage", "image-tiff", "image-registration"]
 
 [workspace.package]
-version = "0.2.0"
+version = "0.3.2"
 edition = "2024"
-# the workspace must satisfy every member, so this is the highest `rust-version` of the members
+rust-version = "1.94.1"
-rust-version = "1.94.0"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
 license = "MIT OR Apache-2.0"
 description = "Read bio image formats using the bio-formats java package."
-homepage = "https://git.pomppervova.nl/wim/ndbioimage/src/branch/rs"
+repository = "https://git.pomppervova.nl/wim/ndbioimage"
-repository = "https://git.pomppervova.nl/wim/ndbioimage/src/branch/rs"
 documentation = "https://docs.rs/ndbioimage"
-# inherited paths are resolved relative to the workspace root, not the member, so this has to point
+readme = "README.md"
-# at the member's readme
-readme = "ndbioimage/README.md"
 keywords = ["bioformats", "imread", "ndarray", "metadata"]
 categories = ["multimedia::images", "science"]
 
-# profiles are only honoured in the workspace root manifest
 [profile.test]
 inherits = "release"
+debug = true
 
 [profile.release]
-debug = true
+#debug = true
 
 [profile.dev.package.backtrace]
 opt-level = 3

README.md

@@ -1,11 +1,10 @@
-# ndbioimage
+[![pytest](https://git.pomppervova.nl/wim/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://git.pomppervova.nl/wim/ndbioimage/actions?workflow=pytest.yml)
-
-[![Pytest](https://github.com/pomppervova/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/pomppervova/ndbioimage/actions/workflows/pytest.yml)
 
+# NDBioImage
 ## Work in progress
 
-Rust rewrite of python version. Read bio image formats using the bio-formats java package.
+Rust rewrite of python version. Read bio image formats using some Rust code, the libczi api, and if needed the
-[https://www.openmicroscopy.org/bio-formats/](https://www.openmicroscopy.org/bio-formats/)
+bio-formats java package.
 
 Exposes (bio) images as a numpy ndarray-like object (Python) or 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
@@ -18,20 +17,6 @@ Currently, it supports imagej tif files, czi files, micromanager tif sequences a
 
 To transition to semver, versions before 0.1.0 were yanked from crates.io.
 
-## Installation
-
-```sh
-pip install ndbioimage
-```
-
-### Installation with option to write mp4 or mkv:
-
-Work in progress! Make sure ffmpeg is installed.
-
-```sh
-pip install ndbioimage[write]
-```
-
 ## Usage
 
 ### Python

ndbioimage/Cargo.toml

@@ -6,12 +6,11 @@ rust-version.workspace = true
 authors.workspace = true
 license.workspace = true
 description.workspace = true
-homepage.workspace = true
 repository.workspace = true
 documentation.workspace = true
-readme.workspace = true
 keywords.workspace = true
 categories.workspace = true
+readme = "../README.md"
 exclude = ["/tests"]
 
 [lib]
@@ -29,15 +28,15 @@ image-registration = { path = "../image-registration", version = "0.1", optional
 indexmap = { version = "2", features = ["serde"] }
 indicatif = { version = "0.18", features = ["rayon"], optional = true }
 j4rs = { version = "0.25", optional = true }
-libczirw-sys = { version = "0.5", optional = true }
+libczirw-sys = { version = "0.5.2", optional = true }
 ndarray = { version = "0.17", features = ["serde"] }
 num = "0.4"
 numpy = { version = "0.29", optional = true }
-ome-metadata = "0.5"
+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"
@@ -51,6 +50,9 @@ tokio = { version = "1", features = ["rt", "rt-multi-thread"], optional = true }
 thread_local = { version = "1", optional = true }
 xmltree = { version = "0.12", optional = true }
 yaml_serde = { version = "0.10", optional = true }
+# "bioformats 0.1.8" is written for "zip 2.4.x", where zip::read::ZipFile has a single lifetime parameter.
+# "zip >= 2.5" added a second "R: Read" generic (2.6.1 breaks bioformats), so the build fails.
+zip = { version = "=2.4.2", optional = true, default-features = false }
 
 [dev-dependencies]
 rayon = "1"
@@ -69,7 +71,7 @@ all = ["bioformats_java", "bioformats_rust", "czi", "gpl-formats", "movie", "tif
 gpl-formats = []
 python = ["dep:pyo3", "dep:numpy", "dep:pyo3-stub-gen", "dep:postcard", "ome-metadata/python"]
 czi = ["dep:libczirw-sys", "dep:xmltree", "dep:thread_local"]
-bioformats_rust = ["dep:bioformats", "dep:thread_local"]
+bioformats_rust = ["dep:bioformats", "dep:thread_local", "dep:zip"]
 bioformats_java = ["dep:j4rs", "dep:thread_local", "dep:downloader"]
 tiffwrite = ["dep:tiffwrite", "dep:indicatif", "dep:console", "dep:rayon"]
 tiffseq = ["dep:tiff", "dep:yaml_serde"]

ndbioimage/py/ndbioimage/ndbioimage_rs/__init__.pyi

@@ -2,6 +2,8 @@
 # ruff: noqa: E501, F401, F403, F405
 
 import builtins
+import collections
+import collections.abc
 import os
 import pathlib
 import typing
@@ -52,6 +54,8 @@ class Flags:
     def __new__(cls) -> Flags: ...
     def __getnewargs__(self) -> None: ...
     def __getitem__(self, item: builtins.str) -> builtins.bool: ...
+    def __str__(self) -> builtins.str: ...
+    def __repr__(self) -> builtins.str: ...
 
 class Imread:
     r"""
@@ -96,16 +100,6 @@ class Imread:
         the name of the reader used to open the file
         """
     @property
-    def transforms(self) -> transforms.Transforms:
-        r"""
-        get the transformation
-        """
-    @transforms.setter
-    def transforms(self, value: transforms.Transforms) -> None:
-        r"""
-        set the transformation
-        """
-    @property
     def path(self) -> pathlib.Path:
         r"""
         the file path
@@ -220,6 +214,38 @@ class Imread:
         r"""
         the name of the tube lens
         """
+    @property
+    def channel_names(self) -> builtins.dict[builtins.int, builtins.str]:
+        r"""
+        names of the channels in order
+        """
+    @property
+    def summary(self) -> builtins.str:
+        r"""
+        gives a helpful summary of the recorded experiment
+        """
+    @property
+    def interpolation_order(self) -> typing.Optional[builtins.int]:
+        r"""
+        the bspline order used for interpolation when using transforms
+        None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+        """
+    @interpolation_order.setter
+    def interpolation_order(self, value: typing.Optional[builtins.int]) -> None:
+        r"""
+        the bspline order used for interpolation when using transforms
+        None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+        """
+    @property
+    def transforms(self) -> transforms.Transforms:
+        r"""
+        get the transformation
+        """
+    @transforms.setter
+    def transforms(self, value: transforms.Transforms) -> None:
+        r"""
+        set the transformation
+        """
     def __new__(
         cls,
         path: str | pathlib.Path | Imread | bytes,
@@ -236,6 +262,10 @@ class Imread:
         reader: use a specific reader to open the file,
             view available choices with Imread.available_readers
         """
+    def debug(self) -> None:
+        r"""
+        some debug info
+        """
     @staticmethod
     def warm_jvm() -> None:
         r"""
@@ -247,7 +277,10 @@ class Imread:
     @staticmethod
     def jvm_is_running() -> builtins.bool:
         r"""
-        returns whether the jvm was already created on this thread
+        returns whether the jvm was already created in this process
+
+        this is false in a process that inherited a jvm across a fork, since such a jvm cannot be
+        used; reading a bio-formats file there raises instead
         """
     def set_flags(
         self,
@@ -270,47 +303,19 @@ class Imread:
         r"""
         only remains for backwards compatibility
         """
-    def reshape(self, order: builtins.str, copy: builtins.bool) -> typing.Any:
+    def reshape(
-        r"""
-        reshape the view with a new axis order
-        """
-    def with_transform(
         self,
-        channels: builtins.bool = True,
+        *shape: typing.Any,
-        drift: builtins.bool = False,
+        order: builtins.str = "C",
-        file: typing.Optional[typing.Any] = None,
+        copy: typing.Optional[builtins.bool] = None,
-        bead_files: typing.Optional[typing.Any] = None,
+    ) -> Imread | numpy.NDArray:
-        main_channel: typing.Optional[builtins.int] = None,
-        default_transform: typing.Optional[typing.Sequence[builtins.float]] = None,
-    ) -> Imread:
         r"""
-        return a new view with transformations applied (channel alignment, drift correction)
+        reshape the view with a new axis order, arguments order and copy cannot be used and will
-        backward compatibility
+        raise an exception if order != "C" or copy is False
         """
-    def with_transforms(
+    def squeeze(
-        self,
+        self, axes: str | collections.abc.Sequence[int | str] = None
-        channels: builtins.bool = True,
+    ) -> Imread | float | int: ...
-        drift: builtins.bool = False,
-        file: typing.Optional[typing.Any] = None,
-        bead_files: typing.Optional[typing.Any] = None,
-        main_channel: typing.Optional[builtins.int] = None,
-        default_transform: typing.Optional[typing.Sequence[builtins.float]] = None,
-    ) -> Imread:
-        r"""
-        return a new view with transformations applied (channel alignment, drift correction)
-        """
-    def load_transforms_from_yaml(
-        self, path: builtins.str | os.PathLike | pathlib.Path
-    ) -> None: ...
-    def calculate_channel_transforms_2d(
-        self, main_channel: builtins.int
-    ) -> builtins.dict[builtins.str, transforms.Transform]: ...
-    def calculate_channel_transforms_3d(
-        self, main_channel: builtins.int
-    ) -> builtins.dict[builtins.str, transforms.Transform]: ...
-    def calculate_drift_transforms_2d(self) -> builtins.list[transforms.Transform]: ...
-    def calculate_drift_transforms_3d(self) -> builtins.list[transforms.Transform]: ...
-    def squeeze(self) -> numpy.ndarray | int | float: ...
     def close(self) -> None:
         r"""
         close the file: does nothing as this is handled automatically
@@ -323,7 +328,19 @@ class Imread:
         r"""
         change the data type of the view: (u)int(8/16/32) or float(32/64)
         """
-    def __getitem__(self, n: typing.Any) -> typing.Any:
+    def __call__(
+        self,
+        c: typing.Optional[int | slice | numpy.ArrayLike] = None,
+        z: typing.Optional[int | slice | numpy.ArrayLike] = None,
+        t: typing.Optional[int | slice | numpy.ArrayLike] = None,
+        y: typing.Optional[int | slice | numpy.ArrayLike] = None,
+        x: typing.Optional[int | slice | numpy.ArrayLike] = None,
+    ) -> typing.Optional[int | Imread]:
+        r"""
+        same as im[] but allowing keyword axes, but slices need to made with slice()
+        also, no ellipsis or new axes
+        """
+    def __getitem__(self, n: typing.Any) -> typing.Optional[int | Imread]:
         r"""
         slice the view and return a new view or a single number
         """
@@ -331,7 +348,7 @@ class Imread:
         self,
         dtype: typing.Optional[numpy.typing.DTypeLike] = None,
         copy: typing.Optional[builtins.bool] = None,
-    ) -> typing.Any:
+    ) -> numpy.typing.NDArray:
         r"""
         convert to a numpy array, optionally with a different dtype
         """
@@ -339,139 +356,199 @@ class Imread:
         r"""
         check if an item is contained in the view (not implemented)
         """
-    def __lt__(self, other: typing.Any) -> typing.Any:
+    def __lt__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise less than comparison
         """
-    def __le__(self, other: typing.Any) -> typing.Any:
+    def __le__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise less than or equal comparison
         """
-    def __eq__(self, other: typing.Any) -> typing.Any:
+    def __eq__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise equality comparison
         """
-    def __ne__(self, other: typing.Any) -> typing.Any:
+    def __ne__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise not equal comparison
         """
-    def __gt__(self, other: typing.Any) -> typing.Any:
+    def __gt__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise greater than comparison
         """
-    def __ge__(self, other: typing.Any) -> typing.Any:
+    def __ge__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise greater than or equal comparison
         """
-    def __add__(self, other: typing.Any) -> typing.Any:
+    def __add__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise addition
         """
-    def __radd__(self, other: typing.Any) -> typing.Any:
+    def __radd__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise addition (reflected)
         """
-    def __sub__(self, other: typing.Any) -> typing.Any:
+    def __sub__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise subtraction
         """
-    def __rsub__(self, other: typing.Any) -> typing.Any:
+    def __rsub__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise subtraction (reflected)
         """
-    def __mul__(self, other: typing.Any) -> typing.Any:
+    def __mul__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise multiplication
         """
-    def __rmul__(self, other: typing.Any) -> typing.Any:
+    def __rmul__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise multiplication (reflected)
         """
-    def __truediv__(self, other: typing.Any) -> typing.Any:
+    def __truediv__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise true division
         """
-    def __rtruediv__(self, other: typing.Any) -> typing.Any:
+    def __rtruediv__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise true division (reflected)
         """
-    def __floordiv__(self, other: typing.Any) -> typing.Any:
+    def __floordiv__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise floor division
         """
-    def __rfloordiv__(self, other: typing.Any) -> typing.Any:
+    def __rfloordiv__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise floor division (reflected)
         """
-    def __mod__(self, other: typing.Any) -> typing.Any:
+    def __mod__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise modulo
         """
-    def __rmod__(self, other: typing.Any) -> typing.Any:
+    def __rmod__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise modulo (reflected)
         """
-    def __matmul__(self, other: typing.Any) -> typing.Any:
+    def __matmul__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise matrix multiplication
         """
-    def __rmatmul__(self, other: typing.Any) -> typing.Any:
+    def __rmatmul__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise matrix multiplication (reflected)
         """
-    def __and__(self, other: typing.Any) -> typing.Any:
+    def __and__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise bitwise AND
         """
-    def __rand__(self, other: typing.Any) -> typing.Any:
+    def __rand__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise bitwise AND (reflected)
         """
-    def __or__(self, other: typing.Any) -> typing.Any:
+    def __or__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise bitwise OR
         """
-    def __ror__(self, other: typing.Any) -> typing.Any:
+    def __ror__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise bitwise OR (reflected)
         """
-    def __xor__(self, other: typing.Any) -> typing.Any:
+    def __xor__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise bitwise XOR
         """
-    def __rxor__(self, other: typing.Any) -> typing.Any:
+    def __rxor__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | bool:
         r"""
         element-wise bitwise XOR (reflected)
         """
-    def __lshift__(self, other: typing.Any) -> typing.Any:
+    def __lshift__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise left shift
         """
-    def __rlshift__(self, other: typing.Any) -> typing.Any:
+    def __rlshift__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise left shift (reflected)
         """
-    def __rshift__(self, other: typing.Any) -> typing.Any:
+    def __rshift__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise right shift
         """
-    def __rrshift__(self, other: typing.Any) -> typing.Any:
+    def __rrshift__(
+        self, other: float | numpy.ArrayLike | Imread
+    ) -> numpy.typing.NDArray | float:
         r"""
         element-wise right shift (reflected)
         """
-    def __neg__(self) -> typing.Any:
+    def __neg__(self) -> numpy.typing.NDArray | float:
         r"""
         element-wise negation
         """
-    def __pos__(self) -> typing.Any:
+    def __pos__(self) -> numpy.typing.NDArray | float:
         r"""
         element-wise positive
         """
-    def __abs__(self) -> typing.Any:
+    def __abs__(self) -> numpy.typing.NDArray | float:
         r"""
         element-wise absolute value
         """
-    def __invert__(self) -> typing.Any:
+    def __invert__(self) -> numpy.typing.NDArray | float:
         r"""
         element-wise bitwise inversion
         """
@@ -524,13 +601,19 @@ class Imread:
         r"""
         the file path as a string
         """
+    def frame(
+        self, c: builtins.int, z: builtins.int, t: builtins.int
+    ) -> numpy.typing.NDArray | float:
+        r"""
+        retrieve a single frame at czt, sliced accordingly, alias of get_frame
+        """
     def get_frame(
         self, c: builtins.int, z: builtins.int, t: builtins.int
-    ) -> typing.Any:
+    ) -> numpy.typing.NDArray | float:
         r"""
         retrieve a single frame at czt, sliced accordingly
         """
-    def flatten(self) -> typing.Any:
+    def flatten(self) -> numpy.typing.NDArray | float:
         r"""
         flatten the view into a 1D numpy array
         """
@@ -546,17 +629,21 @@ class Imread:
         r"""
         find the position of an axis
         """
+    def swapaxes(self, ax0: int | str, ax1: int | str) -> Imread:
+        r"""
+        swap two axes
+        """
     def swap_axes(self, ax0: int | str, ax1: int | str) -> Imread:
         r"""
         swap two axes
         """
     def transpose(
-        self, axes: typing.Optional[typing.Sequence[int | str]] = None
+        self, axes: typing.Optional[collections.abc.Sequence[int | str] | str] = None
     ) -> Imread:
         r"""
         permute the order of the axes
         """
-    def as_array(self) -> typing.Any:
+    def as_array(self) -> numpy.typing.NDArray | float:
         r"""
         collect data into a numpy array
         """
@@ -586,9 +673,9 @@ class Imread:
         r"""
         the detector gain for a given channel
         """
-    def summary(self) -> builtins.str:
+    def channel_name(self, channel: builtins.int) -> builtins.str:
         r"""
-        gives a helpful summary of the recorded experiment
+        the name of a particular channel
         """
     @staticmethod
     def get_available_series(
@@ -692,6 +779,73 @@ class Imread:
         r"""
         Return the sum along a given axis. Arguments beyond axis are not implemented
         """
+    def with_interpolation_order(self, order: typing.Optional[builtins.int]) -> Imread:
+        r"""
+        the bspline order used for interpolation when using transforms
+        None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+        """
+    def get_default_interpolation_value(
+        self, channel: builtins.int
+    ) -> transforms.DefaultValue:
+        r"""
+        the value of the interpolated image outside the data
+        """
+    def set_default_interpolation_value(
+        self,
+        channel: builtins.int,
+        value: float | transforms.DefaultValue | collections.abc.Sequence[float],
+    ) -> None:
+        r"""
+        the value of the interpolated image outside the data
+        """
+    def with_default_interpolation_value(
+        self,
+        channel: builtins.int,
+        value: float | transforms.DefaultValue | collections.abc.Sequence[float],
+    ) -> Imread:
+        r"""
+        the value of the interpolated image outside the data
+        """
+    def with_transform(
+        self,
+        channels: builtins.bool = True,
+        drift: builtins.bool = False,
+        file: typing.Optional[builtins.str | os.PathLike | pathlib.Path] = None,
+        bead_files: typing.Optional[
+            typing.Sequence[builtins.str | os.PathLike | pathlib.Path]
+        ] = None,
+        main_channel: typing.Optional[builtins.int] = None,
+        default_transform: typing.Optional[typing.Sequence[builtins.float]] = None,
+    ) -> Imread:
+        r"""
+        return a new view with transformations applied (channel alignment, drift correction)
+        backward compatibility
+        """
+    def with_transforms(
+        self,
+        channels: builtins.bool = True,
+        drift: builtins.bool = False,
+        file: typing.Optional[builtins.str | os.PathLike | pathlib.Path] = None,
+        bead_files: typing.Optional[
+            typing.Sequence[builtins.str | os.PathLike | pathlib.Path]
+        ] = None,
+        main_channel: typing.Optional[builtins.int] = None,
+        default_transform: typing.Optional[typing.Sequence[builtins.float]] = None,
+    ) -> Imread:
+        r"""
+        returns a view where channels and/or frames are registered with an affine transformation
+        """
+    def load_transforms_from_yaml(
+        self, path: builtins.str | os.PathLike | pathlib.Path
+    ) -> None: ...
+    def calculate_channel_transforms_2d(
+        self, main_channel: builtins.int
+    ) -> builtins.dict[builtins.str, transforms.Transform]: ...
+    def calculate_channel_transforms_3d(
+        self, main_channel: builtins.int
+    ) -> builtins.dict[builtins.str, transforms.Transform]: ...
+    def calculate_drift_transforms_2d(self) -> builtins.list[transforms.Transform]: ...
+    def calculate_drift_transforms_3d(self) -> builtins.list[transforms.Transform]: ...
 
 class Shape:
     r"""
@@ -761,7 +915,7 @@ class Shape:
         arguments for pickling
         """
     def __getitem__(
-        self, idx: str | int | None | Ellipsis | slice | list[int] | tuple[int]
+        self, idx: str | int | None | Ellipsis | slice | typing.Sequence[int]
     ) -> typing.Optional[int | tuple[int]]:
         r"""
         get dimension size by index or axis name

ndbioimage/py/ndbioimage/ndbioimage_rs/transforms.pyi

@@ -2,6 +2,7 @@
 # ruff: noqa: E501, F401, F403, F405
 
 import builtins
+import collections.abc
 import os
 import pathlib
 import typing
@@ -10,6 +11,7 @@ import numpy
 import numpy.typing
 
 __all__ = [
+    "DefaultValue",
     "Optimizer",
     "RegistrationStep",
     "SamplingArg",
@@ -18,6 +20,21 @@ __all__ = [
     "Transforms",
 ]
 
+class DefaultValue:
+    @property
+    def values(self) -> builtins.list[builtins.float]: ...
+    @property
+    def weights(self) -> builtins.list[builtins.float]: ...
+    def __eq__(self, other: builtins.object, /) -> builtins.bool: ...
+    def __new__(
+        cls,
+        values: typing.Sequence[builtins.float],
+        weights: typing.Optional[typing.Sequence[builtins.float]] = None,
+    ) -> DefaultValue: ...
+    def __getnewargs__(
+        self,
+    ) -> tuple[builtins.list[builtins.float], builtins.list[builtins.float]]: ...
+
 class Optimizer:
     def __eq__(self, other: builtins.object, /) -> builtins.bool: ...
     def __new__(cls, optimizer: builtins.str) -> Optimizer: ...
@@ -116,24 +133,6 @@ class Transform:
     @dparameters.setter
     def dparameters(self, value: typing.Sequence[builtins.float]) -> None: ...
     @property
-    def center(self) -> builtins.list[builtins.float]: ...
-    @center.setter
-    def center(self, value: typing.Sequence[builtins.float]) -> None: ...
-    @property
-    def origin(self) -> builtins.list[builtins.float]:
-        r"""
-        backwards compatibility
-        """
-    @origin.setter
-    def origin(self, value: typing.Sequence[builtins.float]) -> None:
-        r"""
-        backwards compatibility
-        """
-    @property
-    def shape(self) -> builtins.list[builtins.int]: ...
-    @shape.setter
-    def shape(self, value: typing.Sequence[builtins.int]) -> None: ...
-    @property
     def ndim(self) -> builtins.int: ...
     @property
     def matrix(self) -> numpy.typing.NDArray[numpy.float64]: ...
@@ -149,18 +148,12 @@ class Transform:
     def __new__(
         cls,
         parameters: typing.Optional[typing.Sequence[builtins.float]] = None,
-        shape: typing.Optional[typing.Sequence[builtins.int]] = None,
+        dparameters: typing.Optional[typing.Sequence[builtins.float]] = None,
         center: typing.Optional[typing.Sequence[builtins.float]] = None,
     ) -> Transform: ...
     def __getnewargs__(
         self,
-    ) -> tuple[
+    ) -> tuple[builtins.list[builtins.float], builtins.list[builtins.float]]: ...
-        builtins.list[builtins.float],
-        builtins.list[builtins.int],
-        typing.Optional[builtins.list[builtins.float]],
-    ]: ...
-    def __getstate__(self) -> builtins.list[builtins.float]: ...
-    def __setstate__(self, state: typing.Sequence[builtins.float]) -> None: ...
     def __add__(self, other: Transform) -> Transform: ...
     def __radd__(self, other: Transform) -> Transform: ...
     def __sub__(self, other: Transform) -> Transform: ...
@@ -168,11 +161,6 @@ class Transform:
     def __mul__(self, other: Transform | float) -> Transform: ...
     def __rmul__(self, other: Transform | float) -> Transform: ...
     def __truediv__(self, other: builtins.float) -> Transform: ...
-    def adapt(
-        self,
-        center: typing.Sequence[builtins.float],
-        shape: typing.Sequence[builtins.int],
-    ) -> None: ...
     @staticmethod
     def from_scaling(scaling: typing.Sequence[builtins.float]) -> Transform: ...
     @staticmethod
@@ -189,23 +177,32 @@ class Transform:
         self, theta: builtins.float, center: typing.Sequence[builtins.float]
     ) -> Transform: ...
     def interpolate(
-        self, order: builtins.int, image: numpy.typing.ArrayLike
+        self,
+        order: builtins.int,
+        image: numpy.typing.ArrayLike,
+        default_value: typing.Optional[DefaultValue] = None,
     ) -> numpy.typing.NDArray[numpy.float64]: ...
     def interpolate_par(
-        self, order: builtins.int, image: numpy.typing.ArrayLike
+        self,
+        order: builtins.int,
+        image: numpy.typing.ArrayLike,
+        default_value: typing.Optional[DefaultValue] = None,
     ) -> numpy.typing.NDArray[numpy.float64]: ...
     def frame(
-        self, image: numpy.typing.ArrayLike, default: typing.Optional[typing.Any] = None
+        self,
+        image: numpy.typing.ArrayLike,
+        default: typing.Optional[typing.Any] = None,
+        default_value: typing.Optional[DefaultValue] = None,
     ) -> numpy.ndarray:
         r"""
         backwards compatibility, default parameter is not implemented
         """
     def is_unity(self) -> builtins.bool: ...
     def transform_point(
-        self, point: numpy.typing.ArrayLike
+        self, point: numpy.typing.ArrayLike, center: numpy.typing.ArrayLike
     ) -> numpy.typing.NDArray[numpy.float64]: ...
     def transform_points(
-        self, points: numpy.typing.ArrayLike
+        self, points: numpy.typing.ArrayLike, center: numpy.typing.ArrayLike
     ) -> numpy.typing.NDArray[numpy.float64]: ...
     @staticmethod
     def register(
@@ -222,9 +219,25 @@ class Transform:
     def register_translation(
         fixed: numpy.typing.ArrayLike, moving: numpy.typing.ArrayLike
     ) -> Transform: ...
+    @staticmethod
+    def register_translation_fft(
+        fixed: numpy.typing.ArrayLike, moving: numpy.typing.ArrayLike
+    ) -> Transform: ...
 
 class Transforms:
     @property
+    def interpolation_order(self) -> typing.Optional[builtins.int]:
+        r"""
+        the bspline order used for interpolation when using transforms,
+        None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+        """
+    @interpolation_order.setter
+    def interpolation_order(self, value: typing.Optional[builtins.int]) -> None:
+        r"""
+        the bspline order used for interpolation when using transforms
+        None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+        """
+    @property
     def channel_transforms(self) -> builtins.dict[builtins.str, Transform]: ...
     @channel_transforms.setter
     def channel_transforms(
@@ -239,10 +252,48 @@ class Transforms:
         cls,
         channel: typing.Mapping[builtins.str, Transform] = {},
         drift: typing.Sequence[Transform] = [],
+        interpolation_order: typing.Optional[builtins.int] = None,
+        default_value: typing.Optional[
+            typing.Mapping[builtins.str, DefaultValue]
+        ] = None,
     ) -> Transforms: ...
     def __getnewargs__(
         self,
-    ) -> tuple[builtins.dict[builtins.str, Transform], builtins.list[Transform]]: ...
+    ) -> tuple[
+        builtins.dict[builtins.str, Transform],
+        builtins.list[Transform],
+        typing.Optional[builtins.int],
+        builtins.dict[builtins.str, DefaultValue],
+    ]: ...
+    def with_interpolation_order(
+        self, order: typing.Optional[builtins.int]
+    ) -> Transforms:
+        r"""
+        the bspline order used for interpolation when using transforms
+        None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+        """
+    def get_default_interpolation_value(
+        self, channel_name: builtins.str
+    ) -> DefaultValue:
+        r"""
+        the value of the interpolated image outside the data
+        """
+    def set_default_interpolation_value(
+        self,
+        channel_name: builtins.str,
+        value: float | DefaultValue | collections.abc.Sequence[float],
+    ) -> None:
+        r"""
+        the value of the interpolated image outside the data
+        """
+    def with_default_interpolation_value(
+        self,
+        channel_name: builtins.str,
+        value: float | DefaultValue | collections.abc.Sequence[float],
+    ) -> Transforms:
+        r"""
+        the value of the interpolated image outside the data
+        """
     @staticmethod
     def load(path: builtins.str | os.PathLike | pathlib.Path) -> Transforms: ...
     def save(self, path: builtins.str | os.PathLike | pathlib.Path) -> None: ...

ndbioimage/py/ndbioimage/transforms.pyi

@@ -1,4 +1,5 @@
 from .ndbioimage_rs.transforms import (
+    DefaultValue,
     Optimizer,
     RegistrationStep,
     SamplingArg,
@@ -8,6 +9,7 @@ from .ndbioimage_rs.transforms import (
 )
 
 __all__ = [
+    "DefaultValue",
     "Optimizer",
     "RegistrationStep",
     "SamplingArg",

ndbioimage/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "ndbioimage"
-version = "2027.0.5"
+version = "2027.0.8"
 requires-python = ">=3.10"
 classifiers = [
     "License :: OSI Approved :: MIT License",
@@ -35,7 +35,7 @@ ndbioimage_generate_stub = "ndbioimage:ndbioimage_generate_stub"
 
 [tool.maturin]
 python-source = "py"
-features = ["python", "bioformats_java", "gpl-formats", "czi", "tiff", "tiffseq", "tiffwrite", "movie", "transforms"]
+features = ["python", "bioformats_java", "gpl-formats", "bioformats_rust", "czi", "tiff", "tiffseq", "tiffwrite", "movie", "transforms"]
 no-default-features = true
 module-name = "ndbioimage.ndbioimage_rs"
 include = ["py/ndbioimage/jassets/j4rs*", "py/ndbioimage/deps/libj4rs*"]

ndbioimage/src/axes.rs

@@ -196,11 +196,11 @@ impl<'de> DeserializeAs<'de, SliceInfoElem> for SliceInfoElemDef {
     }
 }
 
-#[derive(Clone, Debug)]
+#[derive(Clone, Debug, Copy)]
 pub(crate) struct Slice {
-    start: isize,
+    pub(crate) start: isize,
-    end: isize,
+    pub(crate) end: isize,
-    step: isize,
+    pub(crate) step: isize,
 }
 
 impl Slice {
@@ -236,7 +236,7 @@ impl IntoIterator for &Slice {
     type IntoIter = Slice;
 
     fn into_iter(self) -> Self::IntoIter {
-        self.clone()
+        *self
     }
 }
 
@@ -314,16 +314,16 @@ impl Index<&Axis> for Shape {
 impl Index<usize> for Shape {
     type Output = usize;
 
-    fn index(&self, dim: usize) -> &Self::Output {
+    fn index(&self, index: usize) -> &Self::Output {
-        &self[self.order[dim % self.order.len()]]
+        &self[self.order[index]]
     }
 }
 
 impl Index<&usize> for Shape {
     type Output = usize;
 
-    fn index(&self, dim: &usize) -> &Self::Output {
+    fn index(&self, index: &usize) -> &Self::Output {
-        &self[self.order[dim % self.order.len()]]
+        &self[self.order[*index]]
     }
 }
 
@@ -406,6 +406,10 @@ impl Shape {
         }
     }
 
+    pub fn get(&self, index: &usize) -> Option<&usize> {
+        self.order.get(*index).map(|axis| &self[axis])
+    }
+
     /// the number of axes in the shape
     pub fn len(&self) -> usize {
         self.order.len()
@@ -421,6 +425,11 @@ impl Shape {
         self.order.iter().map(|axis| self[axis]).collect()
     }
 
+    /// the sizes in cztyx order
+    pub fn cztyx(&self) -> [usize; 5] {
+        [self.c, self.z, self.t, self.y, self.x]
+    }
+
     /// the sizes along the axes as a map from axis to size
     pub fn to_hashmap(&self) -> HashMap<Axis, usize> {
         let mut map = HashMap::new();

ndbioimage/src/cache.rs

@@ -1,15 +1,23 @@
 use crate::axes::{Axis, Operation};
+use crate::readers::Frame;
+#[cfg(feature = "transforms")]
+use crate::transforms::{DefaultValues, Transforms};
+#[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;
 
-use crate::readers::Frame;
-
 /// maximum number of frames held in the cache
 const DEFAULT_FRAME_CACHE_SIZE: usize = 128;
 
@@ -132,7 +140,33 @@ impl ReaderKeyRef<'_> {
     }
 }
 
-pub(crate) type FrameKey = (ReaderKey, usize, usize, usize);
+#[derive(Debug, PartialEq, Eq)]
+pub(crate) struct FrameKey {
+    pub(crate) reader: ReaderKey,
+    pub(crate) c: usize,
+    pub(crate) z: usize,
+    pub(crate) t: usize,
+    #[cfg(feature = "transforms")]
+    pub(crate) transform: Option<(Transform<IxDyn>, usize, DefaultValues)>,
+}
+
+impl Hash for FrameKey {
+    fn hash<H: Hasher>(&self, state: &mut H) {
+        self.reader.hash(state);
+        self.c.hash(state);
+        self.z.hash(state);
+        self.t.hash(state);
+        #[cfg(feature = "transforms")]
+        if let Some(transform) = self.transform.as_ref() {
+            transform.0.hash(state);
+            transform.1.hash(state);
+            transform.2.iter().for_each(|(k, v)| {
+                k.hash(state);
+                v.hash(state);
+            })
+        }
+    }
+}
 
 /// borrowed view of [`FrameKey`] for cache lookups without allocation.
 #[derive(Debug, PartialEq, Eq)]
@@ -141,6 +175,8 @@ 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, Cow<'a, DefaultValues>)>,
 }
 
 impl Hash for FrameKeyRef<'_> {
@@ -149,19 +185,60 @@ impl Hash for FrameKeyRef<'_> {
         self.c.hash(state);
         self.z.hash(state);
         self.t.hash(state);
+        #[cfg(feature = "transforms")]
+        if let Some(transform) = self.transform.as_ref() {
+            transform.0.hash(state);
+            transform.1.hash(state);
+            transform.2.iter().for_each(|(k, v)| {
+                k.hash(state);
+                v.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: 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, d)| (t.as_ref(), i, d.as_ref()))
+                    == transform.as_ref().map(|(t, i, d)| (t, i, d))
+        }
+        #[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: self.reader.to_owned(),
+            c: self.c,
+            z: self.z,
+            t: self.t,
+            #[cfg(feature = "transforms")]
+            transform: self
+                .transform
+                .as_ref()
+                .map(|(t, i, d)| (t.clone().into_owned(), *i, d.clone().into_owned())),
+        }
     }
 }
 
@@ -173,6 +250,8 @@ 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 +262,8 @@ 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 +277,15 @@ 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 +296,21 @@ 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 +326,8 @@ impl ArrayKeyRef<'_> {
                 .iter()
                 .map(|(ax, op)| (*ax, op.clone()))
                 .collect(),
+            #[cfg(feature = "transforms")]
+            transforms: self.transforms.to_owned(),
         }
     }
 }

ndbioimage/src/error.rs

@@ -65,10 +65,6 @@ pub enum Error {
     #[cfg(feature = "czi")]
     #[error(transparent)]
     XmlTreeParse(#[from] xmltree::ParseError),
-    /// a czi-specific error
-    #[cfg(feature = "czi")]
-    #[error(transparent)]
-    Czi(#[from] crate::readers::czi::CziError),
     /// an error joining a tokio task
     #[cfg(feature = "movie")]
     #[error(transparent)]
@@ -121,6 +117,9 @@ pub enum Error {
     /// the view is empty
     #[error("empty view")]
     EmptyView,
+    /// the view cannot be parsed as a scalar
+    #[error("not a scalar")]
+    NotScalar,
     /// the color string could not be parsed
     #[error("invalid color: {0}")]
     InvalidColor(String),
@@ -173,12 +172,23 @@ pub enum Error {
     #[error("{0} do not match in {1} and {2}")]
     FileMismatch(String, String, String),
     /// a jvm created in another process was inherited across a fork
-    #[cfg(feature = "bioformats_java")]
     #[error(
         "the jvm was created in process {0} but this is process {1}: a forked child inherits a jvm \
          it cannot use. read the file before forking, or start the child with spawn/exec instead."
     )]
+    /// jvm was forked, so it cannot run in this process
     ForkedJvm(u32, u32),
+    /// only 2d and 3d transformations are implemented
+    #[error("{0}D transformation is not implemented")]
+    TransformationNotImplemented(usize),
+    /// cannot find the name for some channel because it does not exist
+    #[error("no channel {0} present")]
+    NoChannel(usize),
+    /// no valid blocks in czi file
+    #[error("czi file has no valid blocks")]
+    CziNoValidBlocks,
+    #[error("f128 is not supported")]
+    F128NotSupported,
 }
 
 impl Error {

ndbioimage/src/lib.rs

@@ -6,8 +6,8 @@
 //! structure. Additionally, it can automatically calculate an affine transform that corrects for
 //! chromatic aberrations etc. and apply it on the fly to the image.
 //!
-//! Currently, it supports imagej tif files, czi files, micromanager tif sequences and anything
+//! Currently, it supports imagej and ome tif files, czi files, micromanager tif sequences and
-//! [bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
+//! anything [bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
 //!
 //! ```rust,no_run
 //! use ndarray::Array2;
@@ -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]
@@ -100,6 +101,9 @@ mod ndbioimage_rs {
         #[pymodule_export]
         use super::super::transforms::PyTransforms;
 
+        #[pymodule_export]
+        use super::super::transforms::PyDefaultValue;
+
         #[pymodule_export]
         use super::super::transforms::PyRegistrationStep;
 

ndbioimage/src/py/transforms.rs

@@ -1,5 +1,7 @@
 use crate::error::Error;
+use crate::py::imread::PyView;
 use crate::transforms::Transforms;
+use image_registration::bspline::DefaultValue;
 use image_registration::metric::{SamplingArg, Sigma};
 use image_registration::register::{Optimizer, RegistrationStep};
 use image_registration::transform::Transform;
@@ -17,6 +19,45 @@ use serde::{Deserialize, Serialize};
 use std::collections::HashMap;
 use std::path::PathBuf;
 
+#[gen_stub_pyclass]
+#[pyclass(
+    subclass,
+    from_py_object,
+    eq,
+    name = "DefaultValue",
+    module = "ndbioimage.transforms"
+)]
+#[derive(Clone, Debug, Serialize, Deserialize, PartialEq)]
+pub(crate) struct PyDefaultValue {
+    inner: DefaultValue,
+}
+
+#[gen_stub_pymethods]
+#[pymethods]
+impl PyDefaultValue {
+    #[new]
+    #[pyo3(signature = (values, weights = None))]
+    fn new(values: Vec<f64>, weights: Option<Vec<f64>>) -> Self {
+        Self {
+            inner: DefaultValue::new(values, weights.unwrap_or_default()),
+        }
+    }
+
+    #[getter]
+    fn values(&self) -> Vec<f64> {
+        self.inner.values().to_vec()
+    }
+
+    #[getter]
+    fn weights(&self) -> Vec<f64> {
+        self.inner.weights().to_vec()
+    }
+
+    fn __getnewargs__(&self) -> (Vec<f64>, Vec<f64>) {
+        (self.inner.values().to_vec(), self.inner.weights().to_vec())
+    }
+}
+
 #[gen_stub_pyclass]
 #[pyclass(
     subclass,
@@ -34,41 +75,31 @@ pub(crate) struct PyTransform {
 #[pymethods]
 impl PyTransform {
     #[new]
-    #[pyo3(signature = (parameters = None, shape = None, center = None))]
+    #[pyo3(signature = (parameters = None, dparameters = None, center = None))]
     fn new(
         parameters: Option<Vec<f64>>,
-        shape: Option<Vec<usize>>,
+        dparameters: Option<Vec<f64>>,
         center: Option<Vec<f64>>,
     ) -> Self {
         let parameters = parameters.unwrap_or_else(|| vec![1.0, 0.0, 0.0, 1.0, 0.0, 0.0]);
-        let shape = shape.unwrap_or_else(|| vec![512, 512]);
+        let mut transform = if let Some(center) = center {
-        if let Some(center) = center {
+            Transform::new_around_center(parameters, &center)
-            Self {
-                inner: Transform::new_with_center(parameters, center, shape),
-            }
         } else {
-            Self {
+            Transform::new(parameters)
-                inner: Transform::new(parameters, shape),
+        };
-            }
+        if let Some(dparameters) = dparameters {
+            transform.dparameters = dparameters;
         }
+        Self { inner: transform }
     }
 
-    fn __getnewargs__(&self) -> (Vec<f64>, Vec<usize>, Option<Vec<f64>>) {
+    fn __getnewargs__(&self) -> (Vec<f64>, Vec<f64>) {
         (
             self.inner.parameters.clone(),
-            self.inner.shape.clone(),
+            self.inner.dparameters.clone(),
-            Some(self.inner.center.clone()),
         )
     }
 
-    fn __getstate__(&self) -> Vec<f64> {
-        self.inner.dparameters.clone()
-    }
-
-    fn __setstate__(&mut self, state: Vec<f64>) {
-        self.inner.dparameters = state;
-    }
-
     fn __add__(&self, other: &PyTransform) -> PyTransform {
         PyTransform {
             inner: &self.inner + &other.inner,
@@ -98,9 +129,9 @@ impl PyTransform {
         py: Python,
         #[gen_stub(override_type(type_repr = "Transform | float"))] other: &Bound<PyAny>,
     ) -> PyResult<PyTransform> {
-        if other.is_instance_of::<PyTransform>() {
+        if let Ok(other) = other.extract::<PyTransform>() {
             Ok(PyTransform {
-                inner: &self.inner * &other.extract::<PyTransform>()?.inner,
+                inner: &self.inner * other.inner,
             })
         } else {
             let builtins = PyModule::import(py, "builtins")?;
@@ -116,9 +147,9 @@ impl PyTransform {
         py: Python,
         #[gen_stub(override_type(type_repr = "Transform | float"))] other: &Bound<PyAny>,
     ) -> PyResult<PyTransform> {
-        if other.is_instance_of::<PyTransform>() {
+        if let Ok(other) = other.extract::<PyTransform>() {
             Ok(PyTransform {
-                inner: &other.extract::<PyTransform>()?.inner * &self.inner,
+                inner: &other.inner * &self.inner,
             })
         } else {
             let builtins = PyModule::import(py, "builtins")?;
@@ -157,38 +188,6 @@ impl PyTransform {
         self.inner.dparameters = dparameters;
     }
 
-    #[getter]
-    fn get_center(&self) -> Vec<f64> {
-        self.inner.center.clone()
-    }
-
-    #[setter]
-    fn set_center(&mut self, center: Vec<f64>) {
-        self.inner.center = center;
-    }
-
-    /// backwards compatibility
-    #[getter]
-    fn get_origin(&self) -> Vec<f64> {
-        self.inner.center.clone()
-    }
-
-    /// backwards compatibility
-    #[setter]
-    fn set_origin(&mut self, center: Vec<f64>) {
-        self.inner.center = center;
-    }
-
-    #[getter]
-    fn get_shape(&self) -> Vec<usize> {
-        self.inner.shape.clone()
-    }
-
-    #[setter]
-    fn set_shape(&mut self, shape: Vec<usize>) {
-        self.inner.shape = shape;
-    }
-
     #[getter]
     fn get_ndim(&self) -> usize {
         self.inner.ndim()
@@ -231,10 +230,6 @@ impl PyTransform {
         })
     }
 
-    fn adapt(&mut self, center: Vec<f64>, shape: Vec<usize>) {
-        self.inner.adapt(center.as_slice(), shape.as_slice());
-    }
-
     #[staticmethod]
     fn from_scaling(scaling: Vec<f64>) -> PyTransform {
         PyTransform {
@@ -275,68 +270,86 @@ impl PyTransform {
         }
     }
 
+    #[pyo3(signature = (order, image, default_value = None))]
     fn interpolate<'py>(
         &self,
         py: Python<'py>,
         order: usize,
         #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
         image: PyArrayLikeDyn<f64, AllowTypeChange>,
+        default_value: Option<PyDefaultValue>,
     ) -> PyResult<Bound<'py, PyArrayDyn<f64>>> {
         let image = image.as_array();
+        let default_value = default_value.map(|i| i.inner).unwrap_or_default();
         Ok(py
             .detach(|| match order {
-                0 => Ok(self
+                0 => Ok(self.inner.interpolate::<0, _, _>(
-                    .inner
+                    image.into_dimensionality().map_err(Error::from)?,
-                    .interpolate::<0, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    &default_value,
-                1 => Ok(self
+                )),
-                    .inner
+                1 => Ok(self.inner.interpolate::<1, _, _>(
-                    .interpolate::<1, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    image.into_dimensionality().map_err(Error::from)?,
-                2 => Ok(self
+                    &default_value,
-                    .inner
+                )),
-                    .interpolate::<2, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                2 => Ok(self.inner.interpolate::<2, _, _>(
-                3 => Ok(self
+                    image.into_dimensionality().map_err(Error::from)?,
-                    .inner
+                    &default_value,
-                    .interpolate::<3, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                )),
-                4 => Ok(self
+                3 => Ok(self.inner.interpolate::<3, _, _>(
-                    .inner
+                    image.into_dimensionality().map_err(Error::from)?,
-                    .interpolate::<4, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    &default_value,
-                5 => Ok(self
+                )),
-                    .inner
+                4 => Ok(self.inner.interpolate::<4, _, _>(
-                    .interpolate::<5, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    image.into_dimensionality().map_err(Error::from)?,
+                    &default_value,
+                )),
+                5 => Ok(self.inner.interpolate::<5, _, _>(
+                    image.into_dimensionality().map_err(Error::from)?,
+                    &default_value,
+                )),
                 _ => Err(PyValueError::new_err("order must be 0 <= order < 6")),
             })?
             .map_err(Error::from)?
             .into_pyarray(py))
     }
 
+    #[pyo3(signature = (order, image, default_value = None))]
     fn interpolate_par<'py>(
         &self,
         py: Python<'py>,
         order: usize,
         #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
         image: PyArrayLikeDyn<f64, AllowTypeChange>,
+        default_value: Option<PyDefaultValue>,
     ) -> PyResult<Bound<'py, PyArrayDyn<f64>>> {
         let image = image.as_array();
+        let default_value = default_value.map(|i| i.inner).unwrap_or_default();
         Ok(py
             .detach(|| match order {
-                0 => Ok(self
+                0 => Ok(self.inner.interpolate_par::<0, _, _>(
-                    .inner
+                    image.into_dimensionality().map_err(Error::from)?,
-                    .interpolate_par::<0, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    &default_value,
-                1 => Ok(self
+                )),
-                    .inner
+                1 => Ok(self.inner.interpolate_par::<1, _, _>(
-                    .interpolate_par::<1, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    image.into_dimensionality().map_err(Error::from)?,
-                2 => Ok(self
+                    &default_value,
-                    .inner
+                )),
-                    .interpolate_par::<2, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                2 => Ok(self.inner.interpolate_par::<2, _, _>(
-                3 => Ok(self
+                    image.into_dimensionality().map_err(Error::from)?,
-                    .inner
+                    &default_value,
-                    .interpolate_par::<3, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                )),
-                4 => Ok(self
+                3 => Ok(self.inner.interpolate_par::<3, _, _>(
-                    .inner
+                    image.into_dimensionality().map_err(Error::from)?,
-                    .interpolate_par::<4, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    &default_value,
-                5 => Ok(self
+                )),
-                    .inner
+                4 => Ok(self.inner.interpolate_par::<4, _, _>(
-                    .interpolate_par::<5, _, _>(image.into_dimensionality().map_err(Error::from)?)),
+                    image.into_dimensionality().map_err(Error::from)?,
+                    &default_value,
+                )),
+                5 => Ok(self.inner.interpolate_par::<5, _, _>(
+                    image.into_dimensionality().map_err(Error::from)?,
+                    &default_value,
+                )),
                 _ => Err(PyValueError::new_err("order must be 0 <= order < 6")),
             })?
             .map_err(Error::from)?
@@ -345,13 +358,14 @@ impl PyTransform {
 
     /// backwards compatibility, default parameter is not implemented
     #[gen_stub(override_return_type(type_repr="numpy.ndarray", imports=("numpy")))]
-    #[pyo3(signature = (image, default = None))]
+    #[pyo3(signature = (image, default = None, default_value = None))]
     fn frame<'py>(
         &self,
         py: Python<'py>,
         #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
         image: Bound<'py, PyUntypedArray>,
         default: Option<Bound<'py, PyAny>>,
+        default_value: Option<PyDefaultValue>,
     ) -> PyResult<Bound<'py, PyAny>> {
         if default.is_some() {
             return Err(PyNotImplementedError::new_err(
@@ -365,6 +379,7 @@ impl PyTransform {
                 self.inner.ndim()
             )));
         }
+        let default_value = default_value.map(|i| i.inner).unwrap_or_default();
 
         macro_rules! interp {
             ($order:expr, $t:tt) => {
@@ -375,6 +390,7 @@ impl PyTransform {
                             .into_dimensionality()
                             .map_err(Error::from)?
                             .view(),
+                        &default_value,
                     )
                     .map_err(Error::from)?
                     .mapv(|i| i as $t)
@@ -392,6 +408,7 @@ impl PyTransform {
                         .into_dimensionality()
                         .map_err(Error::from)?
                         .view(),
+                    &default_value,
                 )
                 .map_err(Error::from)?
                 .mapv(|i| i > 0.5)
@@ -434,13 +451,19 @@ impl PyTransform {
         py: Python<'py>,
         #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
         point: PyArrayLike1<f64, AllowTypeChange>,
+        #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
+        center: PyArrayLike1<f64, AllowTypeChange>,
     ) -> Bound<'py, PyArray1<f64>> {
         let point = point.as_array();
-        if let Some(slice) = point.as_slice() {
+        let center = center.as_array();
-            self.inner.transform_point(slice)
+
-        } else {
+        match (point.as_slice(), center.as_slice()) {
-            let point = point.to_vec();
+            (Some(point), Some(center)) => self.inner.transform_point(point, center),
-            self.inner.transform_point(&point)
+            (Some(point), None) => self.inner.transform_point(point, &center.to_vec()),
+            (None, Some(center)) => self.inner.transform_point(&point.to_vec(), center),
+            (None, None) => self
+                .inner
+                .transform_point(&point.to_vec(), &center.to_vec()),
         }
         .into_pyarray(py)
     }
@@ -450,10 +473,19 @@ impl PyTransform {
         py: Python<'py>,
         #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
         points: PyArrayLike2<f64, AllowTypeChange>,
+        #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
+        center: PyArrayLike1<f64, AllowTypeChange>,
     ) -> PyResult<Bound<'py, PyArray2<f64>>> {
         let points = points.as_array();
+        let center = center.as_array();
         Ok(py
-            .detach(|| self.inner.transform_points(points))
+            .detach(|| {
+                if let Some(center) = center.as_slice() {
+                    self.inner.transform_points(points, center)
+                } else {
+                    self.inner.transform_points(points, &center.to_vec())
+                }
+            })
             .map_err(Error::from)?
             .into_pyarray(py))
     }
@@ -694,6 +726,29 @@ impl PyTransform {
             ))),
         })
     }
+
+    #[staticmethod]
+    fn register_translation_fft<'py>(
+        py: Python<'py>,
+        #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
+        fixed: PyArrayLikeDyn<f64, AllowTypeChange>,
+        #[gen_stub(override_type(type_repr="numpy.typing.ArrayLike", imports=("numpy.typing")))]
+        moving: PyArrayLikeDyn<f64, AllowTypeChange>,
+    ) -> PyResult<PyTransform> {
+        let fixed = fixed.as_array();
+        let moving = moving.as_array();
+        if fixed.shape() != moving.shape() {
+            return Err(PyErr::from(Error::ShapeMismatch(
+                fixed.shape().to_vec(),
+                moving.shape().to_vec(),
+            )));
+        }
+        py.detach(|| {
+            Ok(PyTransform {
+                inner: Transform::register_translation_fft(fixed, moving).map_err(Error::from)?,
+            })
+        })
+    }
 }
 
 #[gen_stub_pyclass]
@@ -709,22 +764,375 @@ pub(crate) struct PyTransforms {
     pub(crate) inner: Transforms,
 }
 
+#[gen_stub_pymethods]
+#[pymethods]
+impl PyView {
+    /// the bspline order used for interpolation when using transforms
+    /// None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+    #[getter]
+    fn get_interpolation_order(&self) -> Option<usize> {
+        self.view.transforms.interpolation_order
+    }
+
+    /// the bspline order used for interpolation when using transforms
+    /// None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+    #[setter]
+    fn set_interpolation_order(&mut self, order: Option<usize>) {
+        self.view.transforms.interpolation_order = order;
+    }
+
+    /// the bspline order used for interpolation when using transforms
+    /// None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+    fn with_interpolation_order(&self, order: Option<usize>) -> Self {
+        let mut new = self.clone();
+        new.view.transforms.interpolation_order = order;
+        new
+    }
+
+    /// the value of the interpolated image outside the data
+    fn get_default_interpolation_value(&self, channel: usize) -> PyResult<PyDefaultValue> {
+        let channel_name = self.view.channel_name(channel)?.to_string();
+        Ok(PyDefaultValue {
+            inner: self
+                .view
+                .transforms
+                .default_value
+                .get(&channel_name)
+                .cloned()
+                .unwrap_or_default(),
+        })
+    }
+
+    /// the value of the interpolated image outside the data
+    fn set_default_interpolation_value(
+        &mut self,
+        channel: usize,
+        #[gen_stub(override_type(type_repr="float | transforms.DefaultValue | collections.abc.Sequence[float]", imports=("collections.abc")))]
+        value: Bound<PyAny>,
+    ) -> PyResult<()> {
+        let channel_name = self.view.channel_name(channel)?.to_string();
+        if let Ok(value) = value.extract::<PyDefaultValue>() {
+            self.view
+                .transforms
+                .default_value
+                .insert(channel_name, value.inner);
+        } else if let Ok(value) = value.extract::<f64>() {
+            self.view
+                .transforms
+                .default_value
+                .insert(channel_name, value.into());
+        } else if let Ok(value) = value.try_iter() {
+            self.view.transforms.default_value.insert(
+                channel_name,
+                value
+                    .map(|i| i?.extract::<f64>())
+                    .collect::<PyResult<Vec<_>>>()?
+                    .into(),
+            );
+        } else {
+            return Err(PyValueError::new_err(format!(
+                "cannot parse value: {:?} into DefaultValue",
+                value
+            )));
+        }
+        Ok(())
+    }
+
+    /// the value of the interpolated image outside the data
+    fn with_default_interpolation_value(
+        &self,
+        channel: usize,
+        #[gen_stub(override_type(type_repr="float | transforms.DefaultValue | collections.abc.Sequence[float]", imports=("collections.abc")))]
+        value: Bound<PyAny>,
+    ) -> PyResult<Self> {
+        let mut new = self.clone();
+        new.set_default_interpolation_value(channel, value)?;
+        Ok(new)
+    }
+
+    /// 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(
+        &self,
+        channels: bool,
+        drift: bool,
+        file: Option<PathBuf>,
+        bead_files: Option<Vec<PathBuf>>,
+        main_channel: Option<usize>,
+        default_transform: Option<Vec<f64>>,
+    ) -> PyResult<PyView> {
+        self.with_transforms(
+            channels,
+            drift,
+            file,
+            bead_files,
+            main_channel,
+            default_transform,
+        )
+    }
+
+    /// returns a view where channels and/or frames are registered with an affine transformation
+    //         channels: True/False register channels using bead_files
+    //         drift: True/False register frames to correct drift
+    //         file: load registration from file with name file, default: transform.yml in self.path.parent
+    //         bead_files: files used to register channels, default: files in self.path.parent,
+    //             with names starting with 'beads'
+    //         main channel: which channel to transform with default_transform
+    //         default_transform: parameters of the default transform: [a, b, c, d, e, f] where the affine transform matrix is
+    //             | a b e |
+    //             | c d f |
+    //             | 0 0 1 |
+    #[cfg(feature = "transforms")]
+    #[pyo3(signature = (channels = true, drift = false, file = None, bead_files = None, main_channel = None, default_transform = None))]
+    fn with_transforms(
+        &self,
+        channels: bool,
+        drift: bool,
+        file: Option<PathBuf>,
+        bead_files: Option<Vec<PathBuf>>,
+        main_channel: Option<usize>,
+        default_transform: Option<Vec<f64>>,
+    ) -> PyResult<PyView> {
+        let mut new = self.clone();
+        let bead_files = bead_files
+            .as_ref()
+            .map(|i| i.iter().map(|j| j.as_path()).collect::<Vec<_>>());
+        new.view.transforms = Transforms::calculate_transforms_from(
+            file.as_deref(),
+            if channels {
+                bead_files.as_deref()
+            } else {
+                None
+            },
+            if drift { Some(self.view.path()) } else { None },
+            main_channel,
+            default_transform,
+        )?;
+        Ok(new)
+    }
+
+    /// 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 {
     #[new]
-    #[pyo3(signature = (channel = HashMap::new(), drift = Vec::new()))]
+    #[pyo3(signature = (channel = HashMap::new(), drift = Vec::new(), interpolation_order = None, default_value = None))]
     fn new(
         channel: HashMap<String, PyTransform>,
         drift: Vec<PyTransform>,
+        interpolation_order: Option<usize>,
+        default_value: Option<HashMap<String, PyDefaultValue>>,
     ) -> PyResult<PyTransforms> {
         let channel = channel.into_iter().map(|(n, t)| (n, t.inner)).collect();
         let drift = drift.into_iter().map(|t| t.inner).collect();
         Ok(PyTransforms {
-            inner: Transforms { channel, drift },
+            inner: Transforms {
+                default_value: default_value
+                    .into_iter()
+                    .flatten()
+                    .map(|(k, v)| (k, v.inner))
+                    .collect::<HashMap<_, _>>(),
+                interpolation_order,
+                channel,
+                drift,
+            },
         })
     }
 
+    #[allow(clippy::type_complexity)]
+    fn __getnewargs__(
+        &self,
+    ) -> (
+        HashMap<String, PyTransform>,
+        Vec<PyTransform>,
+        Option<usize>,
+        HashMap<String, PyDefaultValue>,
+    ) {
+        (
+            self.inner
+                .channel
+                .iter()
+                .map(|(k, v)| (k.to_string(), PyTransform { inner: v.clone() }))
+                .collect(),
+            self.inner
+                .drift
+                .iter()
+                .map(|i| PyTransform { inner: i.clone() })
+                .collect(),
+            self.inner.interpolation_order,
+            self.inner
+                .default_value
+                .iter()
+                .map(|(k, v)| (k.to_string(), PyDefaultValue { inner: v.clone() }))
+                .collect(),
+        )
+    }
+
+    /// the bspline order used for interpolation when using transforms,
+    /// None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+    #[getter]
+    fn get_interpolation_order(&self) -> Option<usize> {
+        self.inner.interpolation_order
+    }
+
+    /// the bspline order used for interpolation when using transforms
+    /// None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+    #[setter]
+    fn set_interpolation_order(&mut self, order: Option<usize>) {
+        self.inner.interpolation_order = order;
+    }
+
+    /// the bspline order used for interpolation when using transforms
+    /// None -> 0 (nearest neighbor) for int dtypes, 3 (cubic) for float dtypes
+    fn with_interpolation_order(&self, order: Option<usize>) -> Self {
+        let mut new = self.clone();
+        new.inner.interpolation_order = order;
+        new
+    }
+
+    /// the value of the interpolated image outside the data
+    fn get_default_interpolation_value(&self, channel_name: &str) -> PyResult<PyDefaultValue> {
+        Ok(PyDefaultValue {
+            inner: self
+                .inner
+                .default_value
+                .get(channel_name)
+                .cloned()
+                .unwrap_or_default(),
+        })
+    }
+
+    /// the value of the interpolated image outside the data
+    fn set_default_interpolation_value(
+        &mut self,
+        channel_name: String,
+        #[gen_stub(override_type(type_repr="float | DefaultValue | collections.abc.Sequence[float]", imports=("collections.abc")))]
+        value: Bound<PyAny>,
+    ) -> PyResult<()> {
+        if let Ok(value) = value.extract::<PyDefaultValue>() {
+            self.inner.default_value.insert(channel_name, value.inner);
+        } else if let Ok(value) = value.extract::<f64>() {
+            self.inner.default_value.insert(channel_name, value.into());
+        } else if let Ok(value) = value.try_iter() {
+            self.inner.default_value.insert(
+                channel_name,
+                value
+                    .map(|i| i?.extract::<f64>())
+                    .collect::<PyResult<Vec<_>>>()?
+                    .into(),
+            );
+        } else {
+            return Err(PyValueError::new_err(format!(
+                "cannot parse value: {:?} into DefaultValue",
+                value
+            )));
+        }
+        Ok(())
+    }
+
+    /// the value of the interpolated image outside the data
+    fn with_default_interpolation_value(
+        &self,
+        channel_name: String,
+        #[gen_stub(override_type(type_repr="float | DefaultValue | collections.abc.Sequence[float]", imports=("collections.abc")))]
+        value: Bound<PyAny>,
+    ) -> PyResult<Self> {
+        let mut new = self.clone();
+        new.set_default_interpolation_value(channel_name, value)?;
+        Ok(new)
+    }
+
     #[getter]
     fn get_channel_transforms(&self) -> HashMap<String, PyTransform> {
         self.inner
@@ -755,10 +1163,6 @@ impl PyTransforms {
         Ok(())
     }
 
-    fn __getnewargs__(&self) -> (HashMap<String, PyTransform>, Vec<PyTransform>) {
-        (self.get_channel_transforms(), self.get_drift_transforms())
-    }
-
     #[staticmethod]
     pub(crate) fn load(path: PathBuf) -> PyResult<PyTransforms> {
         Ok(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};
@@ -128,7 +128,7 @@ pub enum PixelType {
     I128,
     /// unsigned 128-bit integer
     U128,
-    /// 128-bit float (emulated)
+    /// 128-bit float (not supported)
     F128,
 }
 
@@ -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
@@ -168,24 +170,28 @@ pub enum ArrayT<D: Dimension> {
     I64(Array<i64, D>),
     /// unsigned 64-bit integer array
     U64(Array<u64, D>),
-    /// signed 128-bit integer array
+    /// signed 128-bit integer array (not supported by numpy)
     I128(Array<i128, D>),
-    /// unsigned 128-bit integer array
+    /// unsigned 128-bit integer array (not supported by numpy)
     U128(Array<u128, D>),
-    /// 128-bit float array (emulated as f64)
-    F128(Array<f64, D>),
 }
 
 /// type alias for a single frame (2D image)
 pub type Frame = ArrayT<Ix2>;
 
 /// trait for reading image files
-pub trait Reader: Clone + Sized + Debug + Send + Hash + Into<DynReader> {
+pub trait Reader: Clone + Sized + Debug + Sync + Send + Hash + Into<DynReader> {
     /// create a new reader for the given path, series, and position
     fn new<P>(path: P, series: usize, position: usize) -> Result<Self, Error>
     where
         P: AsRef<Path>;
 
+    /// a simple fast test to see if the reader can open a path without parsing the whole file
+    /// not a guarantee of success, but rather an early failure
+    fn can_open<P>(path: P) -> Result<bool, Error>
+    where
+        P: AsRef<Path>;
+
     /// the name of the reader type
     fn reader_name(&self) -> &'static str {
         type_name::<Self>()
@@ -197,9 +203,9 @@ 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(
+        View::new_with_slice_and_axes(
             self.clone(),
             slice.as_ref().to_vec(),
             vec![Axis::C, Axis::Z, Axis::T, Axis::Y, Axis::X],
@@ -216,7 +222,7 @@ 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 +320,7 @@ 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.$map(|x| {
                 T::from_i8(x).unwrap_or_else(|| {
                     err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
@@ -356,7 +363,7 @@ macro_rules! try_into_array_body {
                     T::zero()
                 })
             }),
-            ArrayT::F64(v) | ArrayT::F128(v) => v.$map(|x| {
+            ArrayT::F64(v) => v.$map(|x| {
                 T::from_f64(x).unwrap_or_else(|| {
                     err = Err(Error::Cast(x.to_string(), type_name::<T>().to_string()));
                     T::zero()
@@ -397,7 +404,7 @@ 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 +416,7 @@ 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;
 
@@ -475,6 +482,34 @@ impl Reader for DynReader {
         ))
     }
 
+    fn can_open<P>(path: P) -> Result<bool, Error>
+    where
+        P: AsRef<Path>,
+    {
+        let mut can_open = false;
+        #[cfg(feature = "tiff")]
+        {
+            can_open |= tiff::TiffReader::can_open(&path)?;
+        }
+        #[cfg(feature = "tiffseq")]
+        {
+            can_open |= tiffseq::TiffSeqReader::can_open(&path)?;
+        }
+        #[cfg(feature = "czi")]
+        {
+            can_open |= czi::CziReader::can_open(&path)?;
+        }
+        #[cfg(feature = "bioformats_rust")]
+        {
+            can_open |= bioformats_rust::BioFormatsRustReader::can_open(&path)?;
+        }
+        #[cfg(feature = "bioformats_java")]
+        {
+            can_open |= bioformats_java::BioFormatsJavaReader::can_open(&path)?;
+        }
+        Ok(can_open)
+    }
+
     fn reader_name(&self) -> &'static str {
         match self {
             #[cfg(feature = "tiff")]
@@ -577,18 +612,18 @@ 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()));
@@ -521,7 +521,7 @@ impl BioFormatsJavaReader {
             PixelType::U64 => 8,
             PixelType::I128 => 16,
             PixelType::U128 => 16,
-            PixelType::F128 => 8,
+            PixelType::F128 => 16,
         };
         Ok(bytes
             .chunks(chunk_size)
@@ -587,7 +587,7 @@ impl BioFormatsJavaReader {
             (PixelType::U64, true) => get_frame!(u64, <8),
             (PixelType::I128, true) => get_frame!(i128, <16),
             (PixelType::U128, true) => get_frame!(u128, <16),
-            (PixelType::F128, true) => get_frame!(f64, <8),
+            (PixelType::F128, true) => Err(Error::F128NotSupported),
             (PixelType::Bool, false) => get_frame!(bool, >1),
             (PixelType::I8, false) => get_frame!(i8, >1),
             (PixelType::U8, false) => get_frame!(u8, >1),
@@ -601,7 +601,7 @@ impl BioFormatsJavaReader {
             (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),
+            (PixelType::F128, false) => Err(Error::F128NotSupported),
         }
     }
 }
@@ -666,6 +666,13 @@ impl Reader for BioFormatsJavaReader {
         Ok(new)
     }
 
+    fn can_open<P>(_path: P) -> Result<bool, Error>
+    where
+        P: AsRef<Path>,
+    {
+        Ok(true)
+    }
+
     fn metadata(&self) -> Result<Ome, Error> {
         self.get_ome()
     }
@@ -698,7 +705,7 @@ impl Reader for BioFormatsJavaReader {
         0
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 

ndbioimage/src/readers/bioformats_rust.rs

@@ -140,7 +140,7 @@ impl BioFormatsRustReader {
             PixelType::U64 => 8,
             PixelType::I128 => 16,
             PixelType::U128 => 16,
-            PixelType::F128 => 8,
+            PixelType::F128 => 16,
         };
         Ok(bytes
             .chunks(chunk_size)
@@ -206,7 +206,7 @@ impl BioFormatsRustReader {
             (PixelType::U64, true) => get_frame!(u64, <8),
             (PixelType::I128, true) => get_frame!(i128, <16),
             (PixelType::U128, true) => get_frame!(u128, <16),
-            (PixelType::F128, true) => get_frame!(f64, <8),
+            (PixelType::F128, true) => Err(Error::F128NotSupported),
             (PixelType::Bool, false) => get_frame!(bool, >1),
             (PixelType::I8, false) => get_frame!(i8, >1),
             (PixelType::U8, false) => get_frame!(u8, >1),
@@ -220,7 +220,7 @@ impl BioFormatsRustReader {
             (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),
+            (PixelType::F128, false) => Err(Error::F128NotSupported),
         }
     }
 }
@@ -274,6 +274,13 @@ impl Reader for BioFormatsRustReader {
         Ok(new)
     }
 
+    fn can_open<P>(path: P) -> Result<bool, Error>
+    where
+        P: AsRef<Path>,
+    {
+        Ok(path.as_ref().extension() != Some(std::ffi::OsStr::new("czi")))
+    }
+
     fn metadata(&self) -> Result<Ome, Error> {
         let reader = self.get_reader()?;
         let metadata = reader.metadata();
@@ -309,7 +316,7 @@ impl Reader for BioFormatsRustReader {
         0
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 

ndbioimage/src/readers/czi.rs

@@ -122,14 +122,6 @@ impl From<Option<String>> for Version {
     }
 }
 
-/// errors specific to czi file reading
-#[derive(Debug, thiserror::Error)]
-pub enum CziError {
-    /// czi file has no valid blocks
-    #[error("czi file has no valid blocks")]
-    NoValidBlocks,
-}
-
 impl Reader for CziReader {
     fn new<P>(path: P, series: usize, position: usize) -> Result<Self, Error>
     where
@@ -195,7 +187,7 @@ impl Reader for CziReader {
         let mut max_y = i32::MIN;
         for &i in Ok(block_map.get(&(0, 0, 0)))
             .transpose()
-            .unwrap_or_else(|| block_map.values().next().ok_or(CziError::NoValidBlocks))?
+            .unwrap_or_else(|| block_map.values().next().ok_or(Error::CziNoValidBlocks))?
         {
             if let Ok(info) = reader.try_get_sub_block_info_for_index(i) {
                 let rect = info.get_logical_rect();
@@ -219,10 +211,17 @@ impl Reader for CziReader {
         new.shape.x = (max_y - min_y) as usize;
         new.shape.y = (max_x - min_x) as usize;
         new.block_map = block_map;
-        new.pixel_type = pixel_type.ok_or(CziError::NoValidBlocks)?;
+        new.pixel_type = pixel_type.ok_or(Error::CziNoValidBlocks)?;
         Ok(new)
     }
 
+    fn can_open<P>(path: P) -> Result<bool, Error>
+    where
+        P: AsRef<Path>,
+    {
+        Ok(path.as_ref().extension() == Some(std::ffi::OsStr::new("czi")))
+    }
+
     fn metadata(&self) -> Result<Ome, Error> {
         let mut ome = Ome::default();
         let xml = xmltree::Element::parse(self.metadata_xml()?.as_bytes())?;
@@ -1133,7 +1132,7 @@ impl Reader for CziReader {
             PixelType::U64 => get_frame!(u64, 8),
             PixelType::I128 => get_frame!(i128, 16),
             PixelType::U128 => get_frame!(u128, 16),
-            PixelType::F128 => get_frame!(f64, 8),
+            PixelType::F128 => Err(Error::F128NotSupported),
         }
     }
 
@@ -1149,7 +1148,7 @@ impl Reader for CziReader {
         self.position
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 

ndbioimage/src/readers/tiff.rs

@@ -156,6 +156,18 @@ impl Reader for TiffReader {
             .unwrap_or(1)
             == 2;
 
+        let image_description = reader.current_ifd().get_tag(Tag::ImageDescription);
+        let p_ndim = if n_samples > 1 { 3u8 } else { 2u8 };
+        let (size_c, size_t, size_z) = if let Ok(Value::Ascii(xml)) = image_description
+            && xml.starts_with("<?xml")
+        {
+            let ome = Ome::from_xml(xml)?;
+            (
+                ome.image[0].pixels.size_c as usize,
+                ome.image[0].pixels.size_t as usize,
+                ome.image[0].pixels.size_z as usize,
+            )
+        } else {
             let imagej_bytes = reader
                 .current_ifd()
                 .get_tag(Tag::Unknown(50839))
@@ -166,7 +178,7 @@ impl Reader for TiffReader {
             };
             let metadata_str = String::from_utf8_lossy(&imagej_bytes);
             let metadata_map = parse_imagej_metadata(&metadata_str);
-        let p_ndim = if n_samples > 1 { 3u8 } else { 2u8 };
+
             let size_c = if p_ndim == 3 {
                 n_samples
             } else {
@@ -198,6 +210,8 @@ impl Reader for TiffReader {
             } else {
                 size_z
             };
+            (size_c, size_t, size_z)
+        };
         drop(reader);
 
         new.shape = Shape {
@@ -218,8 +232,32 @@ impl Reader for TiffReader {
         Ok(new)
     }
 
+    fn can_open<P>(path: P) -> Result<bool, Error>
+    where
+        P: AsRef<Path>,
+    {
+        let path = path.as_ref();
+        let mut file = File::open(path)?;
+        let mut sig = [0; 2];
+        file.read_exact(&mut sig)?;
+        if sig == [73, 73] {
+            file.read_exact(&mut sig)?;
+            Ok((sig[0] == 42) || (sig[0] == 43))
+        } else if sig == [77, 77] {
+            Ok((sig[1] == 42) || (sig[1] == 43))
+        } else {
+            Ok(false)
+        }
+    }
+
     fn metadata(&self) -> Result<Ome, Error> {
         let mut reader = self.get_reader()?;
+        let image_description = reader.current_ifd().get_tag(Tag::ImageDescription);
+        if let Ok(Value::Ascii(xml)) = image_description
+            && xml.starts_with("<?xml")
+        {
+            Ok(Ome::from_xml(xml)?)
+        } else {
             let imagej_bytes = reader
                 .current_ifd()
                 .get_tag(Tag::Unknown(50839))
@@ -354,6 +392,7 @@ impl Reader for TiffReader {
             });
             Ok(ome)
         }
+    }
 
     fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame, Error> {
         let (page_idx, offset, stride) = if self.p_ndim == 3 {
@@ -438,25 +477,43 @@ 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 {
         &self.pixel_type
     }
 
-    fn get_available_positions<P>(_path: P, _series: usize) -> Result<HashSet<usize>, Error>
+    fn get_available_positions<P>(path: P, _series: usize) -> Result<HashSet<usize>, Error>
     where
         P: AsRef<Path>,
     {
+        let path = path.as_ref();
+        if Self::can_open(path)? {
             Ok(HashSet::from([0]))
+        } else {
+            Err(Error::InvalidReader(
+                "TiffReader".to_string(),
+                path.to_string_lossy().to_string(),
+                "it is not a tiff".to_string(),
+            ))
+        }
     }
 
-    fn get_available_series<P>(_path: P) -> Result<HashSet<usize>, Error>
+    fn get_available_series<P>(path: P) -> Result<HashSet<usize>, Error>
     where
         P: AsRef<Path>,
     {
+        let path = path.as_ref();
+        if Self::can_open(path)? {
             Ok(HashSet::from([0]))
+        } else {
+            Err(Error::InvalidReader(
+                "TiffReader".to_string(),
+                path.to_string_lossy().to_string(),
+                "it is not a tiff".to_string(),
+            ))
+        }
     }
 }
 
@@ -521,6 +578,8 @@ mod tests {
         metadata_e: "tiff/1xp53-01-AP1.tiff",
         metadata_f: "tiff/test.tif",
         metadata_g: "tiff/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.tif",
-        metadata_h: "tiff/Wapl-AID_C46_13_tagRFPt_MCP_well1_video1_1_max.tif"
+        metadata_h: "tiff/Wapl-AID_C46_13_tagRFPt_MCP_well1_video1_1_max.tif",
+        metadata_i: "tiff/R1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001_MMStack_PosR1_NRF1_Gtf3a500nM_REAL_20260731_25pct_500ms_001.ome.tif"
+        metadata_j: "tiff/20260922_Pos0_max.tif"
     }
 }

ndbioimage/src/readers/tiffseq.rs

@@ -239,6 +239,13 @@ impl Reader for TiffSeqReader {
         })
     }
 
+    fn can_open<P>(path: P) -> Result<bool, Error>
+    where
+        P: AsRef<Path>,
+    {
+        Ok(path.as_ref().is_dir())
+    }
+
     fn metadata(&self) -> Result<Ome, Error> {
         let mut ome = Ome::default();
         let info = self.metadata_map.get("Info").and_then(|v| v.as_mapping());
@@ -572,7 +579,7 @@ impl Reader for TiffSeqReader {
         self.position
     }
 
-    fn shape(&self) -> &Shape {
+    fn raw_shape(&self) -> &Shape {
         &self.shape
     }
 
@@ -580,11 +587,20 @@ impl Reader for TiffSeqReader {
         &self.pixel_type
     }
 
-    fn get_available_positions<P>(_path: P, _series: usize) -> Result<HashSet<usize>, Error>
+    fn get_available_positions<P>(path: P, _series: usize) -> Result<HashSet<usize>, Error>
     where
         P: AsRef<Path>,
     {
+        let path = path.as_ref();
+        if Self::can_open(path)? {
             Ok(HashSet::from([0]))
+        } else {
+            Err(Error::InvalidReader(
+                "TiffSeqReader".to_string(),
+                path.to_string_lossy().to_string(),
+                "not a tiff sequence".to_string(),
+            ))
+        }
     }
 
     fn get_available_series<P>(path: P) -> Result<HashSet<usize>, Error>

ndbioimage/src/tiffwrite.rs

@@ -178,7 +178,7 @@ where
             PixelType::U64 => self.save_as_tiff_with_type::<u64, P>(path, options)?,
             PixelType::I128 => self.save_as_tiff_with_type::<i64, P>(path, options)?,
             PixelType::U128 => self.save_as_tiff_with_type::<u64, P>(path, options)?,
-            PixelType::F128 => self.save_as_tiff_with_type::<f64, P>(path, options)?,
+            PixelType::F128 => Err(Error::F128NotSupported)?,
         }
 
         Ok(())

ndbioimage/src/transforms.rs

@@ -1,13 +1,19 @@
 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 image_registration::{bspline::DefaultValue, filter, transform::Transform};
-use ndarray::{Array2, Dimension, Ix2, Ix3, IxDyn, s};
+use ndarray::{Array2, Dimension, Ix2, Ix3, IxDyn, array, concatenate, s};
+use rayon::iter::{IntoParallelIterator, ParallelIterator};
 use serde::{Deserialize, Serialize};
+use std::borrow::Cow;
 use std::collections::{HashMap, HashSet};
+use std::fmt::Debug;
+use std::hash::{Hash, Hasher};
 use std::io::Seek;
 use std::path::Path;
+use std::sync::Arc;
+use tiffwrite::IJTiffFile;
 
 #[derive(Clone, Debug, Default, PartialEq, Serialize, Deserialize)]
 struct TransformOld {
@@ -26,16 +32,20 @@ impl TryFrom<HashMap<String, TransformOld>> for Transforms {
 
     fn try_from(t: HashMap<String, TransformOld>) -> Result<Self, Error> {
         Ok(Self {
+            default_value: Default::default(),
+            interpolation_order: None,
             channel: t
                 .into_iter()
                 .map(|(n, i)| {
+                    let center = i
+                        .size
+                        .iter()
+                        .zip(i.center_of_rotation_point.iter())
+                        .map(|(s, c)| c - s / 2.0 + 0.5)
+                        .collect::<Vec<_>>();
                     Ok((
                         n,
-                        Transform::new_with_center(
+                        Transform::new_around_center(i.transform_parameters, &center)
-                            i.transform_parameters,
-                            i.center_of_rotation_point,
-                            i.size.into_iter().map(|j| j as usize).collect(),
-                        )
                             .with_dparameters(i.dtransform_parameters)
                             .inverse()?,
                     ))
@@ -46,14 +56,40 @@ impl TryFrom<HashMap<String, TransformOld>> for Transforms {
     }
 }
 
+pub type DefaultValues = HashMap<String, DefaultValue>;
+
 #[derive(Clone, Debug, Default, Eq, PartialEq, Deserialize)]
 pub struct Transforms {
+    #[serde(default)]
+    pub(crate) interpolation_order: Option<usize>,
+    #[serde(default)]
+    pub(crate) default_value: DefaultValues,
+    /// a transform for each channel by channel name
     #[serde(default)]
     pub channel: HashMap<String, Transform<IxDyn>>,
+    /// a transform for each time point
     #[serde(default)]
     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
@@ -69,6 +105,8 @@ impl Serialize for Transforms {
 
         #[derive(Serialize)]
         struct Binary<'a> {
+            interpolation_order: Option<usize>,
+            default_value: &'a DefaultValues,
             channel: &'a HashMap<String, Transform<IxDyn>>,
             drift: &'a Vec<Transform<IxDyn>>,
         }
@@ -81,6 +119,8 @@ impl Serialize for Transforms {
             .serialize(serializer)
         } else {
             Binary {
+                interpolation_order: self.interpolation_order,
+                default_value: &self.default_value,
                 channel: &self.channel,
                 drift: &self.drift,
             }
@@ -89,7 +129,31 @@ impl Serialize for Transforms {
     }
 }
 
+/// the kind of corrections the transforms are meant to correct for
+#[derive(Clone, Debug, PartialEq, Copy)]
+pub enum TransformKind {
+    /// no tranforms
+    None,
+    /// correct warp between channels, ex: camera/filter misalignment, chromatic aberrations
+    Channel,
+    /// drift in the miscrocope between time points
+    Drift,
+    /// both warp between channels and drift
+    Both,
+}
+
 impl Transforms {
+    /// the kind of corrections the transforms are meant to correct for
+    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,
+        }
+    }
+
+    /// load the transforms from a yml file
     pub fn load<P: AsRef<Path>>(path: P) -> Result<Self, Error> {
         let mut file = std::fs::File::open(&path)?;
         Ok(
@@ -104,6 +168,7 @@ impl Transforms {
         )
     }
 
+    /// save the transforms to a yml file
     pub fn save<P: AsRef<Path>>(&self, path: P) -> Result<(), Error> {
         let file = std::fs::OpenOptions::new()
             .write(true)
@@ -113,57 +178,164 @@ impl Transforms {
         Ok(yaml_serde::to_writer(file, self)?)
     }
 
-    pub fn calculate_channel_transforms_2d(
+    /// helper function to eiter load transforms from file or calculate and save them
-        bead_files: &[&Path],
+    pub fn calculate_transforms_from<P, Q, R>(
+        transform_file: Option<P>,
+        bead_files: Option<&[Q]>,
+        drift_file: Option<R>,
+        main_channel: Option<usize>,
+        default_transform: Option<Vec<f64>>,
+    ) -> Result<Self, Error>
+    where
+        P: AsRef<Path>,
+        Q: AsRef<Path>,
+        R: AsRef<Path>,
+    {
+        if let Some(transform_file) = transform_file.as_ref()
+            && let Ok(transforms) = Self::load(transform_file.as_ref().with_extension("yml"))
+        {
+            Ok(transforms)
+        } else {
+            let default_transform = default_transform.map(Transform::new);
+            let mut transforms = Self::default();
+            if let Some(bead_files) = bead_files {
+                let main_channel = main_channel.unwrap_or(0);
+                transforms.channel = Self::calculate_channel_transforms_2d(
+                    bead_files,
+                    main_channel,
+                    default_transform,
+                )?
+                .into_iter()
+                .map(|(k, t)| (k, t.into_dyn()))
+                .collect();
+            };
+            if let Some(drift_file) = drift_file {
+                transforms.drift = Self::calculate_drift_transforms_2d(drift_file)?
+                    .into_iter()
+                    .map(|t| t.into_dyn())
+                    .collect();
+            };
+            if let Some(transform_file) = transform_file {
+                let transform_file = transform_file.as_ref();
+                transforms.save(transform_file.with_extension("yml"))?;
+                if let Some(bead_files) = bead_files {
+                    transforms.save_channel_transform_tiff(
+                        transform_file.with_extension("tif"),
+                        bead_files,
+                    )?;
+                }
+            }
+            Ok(transforms)
+        }
+    }
+
+    /// save a tiff file with the uncorrected and corrected frames of the bead files side by side
+    pub fn save_channel_transform_tiff<P, Q>(&self, file: P, bead_files: &[Q]) -> Result<(), Error>
+    where
+        P: AsRef<Path>,
+        Q: AsRef<Path>,
+    {
+        let mut transforms = self.clone();
+        transforms.drift = Vec::new();
+        let mut tif = IJTiffFile::new(file)?;
+        for (t, bead_file) in bead_files.iter().enumerate() {
+            let mut view = View::<_, DynReader>::from_path(bead_file)?.into_dyn();
+            let axes = view.axes();
+            if axes.contains(&Axis::Z) {
+                view = view.max_proj(Axis::Z)?;
+            }
+            if axes.contains(&Axis::T) {
+                view = view.max_proj(Axis::T)?;
+            }
+            let view_u = view.into_dimensionality::<Ix3>()?;
+            let view_t = view_u.with_transforms(transforms.clone());
+            for c in 0..view_u.shape().c {
+                let a = view_u.slice_cztyx(s![c, 0, 0, .., ..])?.as_array::<u16>()?;
+                let b = view_t.slice_cztyx(s![c, 0, 0, .., ..])?.as_array::<u16>()?;
+                let frame = concatenate(ndarray::Axis(1), &[a.view(), b.view()])?;
+                tif.save(frame, c, 0, t)?;
+            }
+        }
+        Ok(())
+    }
+
+    /// calculate drift transforms in yx using image file
+    pub fn calculate_drift_transforms_2d<P: AsRef<Path>>(
+        file: P,
+    ) -> Result<Vec<Transform<Ix2>>, Error> {
+        View::<_, DynReader>::from_path(file)?.calculate_drift_transforms_2d()
+    }
+
+    /// calculate drift transforms in zyx using image file
+    pub fn calculate_drift_transforms_3d<P: AsRef<Path>>(
+        file: P,
+    ) -> Result<Vec<Transform<Ix3>>, Error> {
+        View::<_, DynReader>::from_path(file)?.calculate_drift_transforms_3d()
+    }
+
+    /// calculate channel transforms in yx using image file
+    pub fn calculate_channel_transforms_2d<P: AsRef<Path>>(
+        bead_files: &[P],
         main_channel: usize,
         default_transform: Option<Transform<Ix2>>,
     ) -> Result<HashMap<String, Transform<Ix2>>, Error> {
+        // TODO: autodetect main channel
         let mut transforms = Vec::new();
         let default_transform = default_transform.unwrap_or_default();
         for file in bead_files {
             let view = View::<_, DynReader>::from_path(file)?;
             transforms.push(view.calculate_channel_transforms_2d(main_channel)?)
         }
-        let channels = transforms
+        let transforms = transforms.into_iter().flat_map(|map| map.into_iter()).fold(
-            .iter()
+            HashMap::new(),
-            .flat_map(|t| t.keys())
+            |mut acc, (channel, transform)| {
-            .collect::<HashSet<_>>();
+                acc.entry(channel)
-        let mut average_transforms = HashMap::new();
+                    .or_insert_with(Vec::new)
-        for channel in channels {
+                    .push(transform * &default_transform);
-            let (s, n) = transforms
+                acc
-                .iter()
+            },
-                .filter_map(|t| {
-                    if t.contains_key(channel) {
-                        Some((&t[channel] * &default_transform).matrix())
-                    } else {
-                        None
-                    }
-                })
-                .fold((Array2::zeros((3, 3)), 0), |(s, n), t| (s + t, n + 1));
-            let matrix = s / (n as f64);
-            let (s, n) = transforms
-                .iter()
-                .filter_map(|t| {
-                    if t.contains_key(channel) {
-                        Some(((&t[channel] * &default_transform).matrix() - &matrix).powi(2))
-                    } else {
-                        None
-                    }
-                })
-                .fold((Array2::zeros((3, 3)), 0), |(s, n), t| (s + t, n + 1));
-            let dmatrix = (s / n as f64).sqrt();
-            average_transforms.insert(
-                channel.clone(),
-                Transform::default()
-                    .with_matrix(matrix.view())
-                    .with_dmatrix(dmatrix.view()),
         );
+        Ok(transforms
+            .iter()
+            .map(|(channel, ts)| {
+                let n = ts.len();
+                let parameters = ts
+                    .iter()
+                    .fold(vec![0.0; 6], |mut acc, t| {
+                        for (a, p) in acc.iter_mut().zip(&t.parameters) {
+                            *a += p;
                         }
-        Ok(average_transforms)
+                        acc
+                    })
+                    .iter()
+                    .map(|i| i / n as f64)
+                    .collect::<Vec<_>>();
+                let dparameters = if n == 1 {
+                    ts[0].dparameters.clone()
+                } else {
+                    ts.iter()
+                        .fold(vec![0.0; 6], |mut acc, t| {
+                            for ((a, p), dp) in acc.iter_mut().zip(&parameters).zip(&t.dparameters)
+                            {
+                                *a += (dp - p).powi(2);
+                            }
+                            acc
+                        })
+                        .iter()
+                        .map(|i| (i / n as f64).sqrt())
+                        .collect::<Vec<_>>()
+                };
+                (
+                    channel.to_string(),
+                    Transform::new(parameters).with_dparameters(dparameters),
+                )
+            })
+            .collect())
     }
 
-    pub fn calculate_channel_transforms_3d(
+    /// calculate channel transforms in zyx using image file
-        bead_files: &[&Path],
+    pub fn calculate_channel_transforms_3d<P: AsRef<Path>>(
+        bead_files: &[P],
         main_channel: usize,
         default_transform: Option<Transform<Ix3>>,
     ) -> Result<HashMap<String, Transform<Ix3>>, Error> {
@@ -210,29 +382,56 @@ impl Transforms {
         }
         Ok(average_transforms)
     }
+
+    /// get the combination of channel and drift transforms for a certain channel and time point
+    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) * channel))),
+                (3, 2) => Ok(Some(Cow::Owned(drift * channel.add_dimension(0)))),
+                (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;
     }
 
+    /// apply transforms to a new view
+    pub fn with_transforms(&self, transforms: Transforms) -> Self {
+        let mut new = self.clone();
+        new.transforms = transforms;
+        new
+    }
+
+    /// load the transforms from a yml file and apply to a new view
     pub fn with_transforms_from_yaml(mut self, path: &Path) -> Result<Self, Error> {
         self.set_transforms(Transforms::load(path)?);
         Ok(self)
     }
 
+    /// load the transforms from a yml file and apply to the view
     pub fn load_transforms_from_yaml(&mut self, path: &Path) -> Result<(), Error> {
         self.set_transforms(Transforms::load(path)?);
         Ok(())
     }
 
+    /// calculate channel transforms in yx using this image view
     pub fn calculate_channel_transforms_2d(
         &self,
         main_channel: usize,
@@ -242,23 +441,13 @@ impl<D: Dimension, R: Reader> View<D, R> {
             .max_proj(Axis::Z)?
             .as_array::<f64>()?;
         let mut transforms = HashMap::new();
-        let shape = vec![self.shape().y, self.shape().x];
-        let center = shape
-            .iter()
-            .map(|&i| (i as f64 - 1.0) / 2.0)
-            .collect::<Vec<_>>();
         for (channel, metadata) in self.metadata()?.image[0].pixels.channel.iter().enumerate() {
             let name = metadata
                 .name
                 .clone()
                 .unwrap_or_else(|| format!("channel{}", channel));
             if channel == main_channel {
-                transforms.insert(
+                transforms.insert(name, Transform::default());
-                    name,
-                    Transform::default()
-                        .with_shape(shape.clone())
-                        .with_center(center.clone()),
-                );
             } else {
                 let max = self
                     .slice_cztyx(s![channel, .., 0, .., ..])?
@@ -273,6 +462,7 @@ impl<D: Dimension, R: Reader> View<D, R> {
         Ok(transforms)
     }
 
+    /// calculate channel transforms in zyx using this image view
     pub fn calculate_channel_transforms_3d(
         &self,
         main_channel: usize,
@@ -281,23 +471,13 @@ impl<D: Dimension, R: Reader> View<D, R> {
             .slice_cztyx(s![main_channel, .., 0, .., ..])?
             .as_array::<f64>()?;
         let mut transforms = HashMap::new();
-        let shape = vec![self.shape().z, self.shape().y, self.shape().x];
-        let center = shape
-            .iter()
-            .map(|&i| (i as f64 - 1.0) / 2.0)
-            .collect::<Vec<_>>();
         for (channel, metadata) in self.metadata()?.image[0].pixels.channel.iter().enumerate() {
             let name = metadata
                 .name
                 .clone()
                 .unwrap_or_else(|| format!("channel{}", channel));
             if channel == main_channel {
-                transforms.insert(
+                transforms.insert(name, Transform::default());
-                    name,
-                    Transform::default()
-                        .with_shape(shape.clone())
-                        .with_center(center.clone()),
-                );
             } else {
                 let max = self
                     .slice_cztyx(s![channel, .., 0, .., ..])?
@@ -311,18 +491,295 @@ impl<D: Dimension, R: Reader> View<D, R> {
         Ok(transforms)
     }
 
+    /// calculate drift transforms in yx using this image view
     pub fn calculate_drift_transforms_2d(&self) -> Result<Vec<Transform<Ix2>>, Error> {
+        let mut view = self.clone().into_dyn();
+        let axes = view.axes();
+        if axes.contains(&Axis::Z) {
+            view = view.max_proj(Axis::Z)?;
+        }
+        if axes.contains(&Axis::C) {
+            view = view.max_proj(Axis::C)?;
+        }
+        view = view.permute_axes(&[Axis::T, Axis::Y, Axis::X])?;
+        let n = view.shape().t;
+        let m = (n as f64).sqrt().round() as usize;
+        let t_groups = (0..=m)
+            .map(|i| (((i * n) as f64) / (m as f64)).round() as usize)
+            .collect::<Vec<_>>();
+        let t_keys = t_groups
+            .array_windows()
+            .map(|[start, end]| (start + end) / 2)
+            .collect::<Vec<_>>();
+        let t_pairs = t_keys
+            .iter()
+            .zip(t_groups.array_windows())
+            .flat_map(|(t_key, [start, end])| (*start..*end).map(|i| (*t_key, i)))
+            .chain(t_keys.array_windows().map(|[start, end]| (*start, *end)))
+            .collect::<Vec<_>>();
+        let fmaxz_keys = t_keys
+            .iter()
+            .map(|t| {
+                Ok((
+                    t,
+                    filter::gaussian_smooth(
+                        &view.slice(s![*t, .., ..])?.as_array::<f64>()?,
+                        &[5.0; 2],
+                    )?,
+                ))
+            })
+            .collect::<Result<HashMap<_, _>, Error>>()?;
+        let shifts = t_pairs
+            .into_par_iter()
+            .map(|(t_key, t)| {
+                if t_key == t {
+                    Ok(Transform::<Ix2>::from_translation(&vec![0.0; view.ndim()]))
+                } else {
+                    if let Some(fmaxz) = fmaxz_keys.get(&t_key) {
+                        Ok(Transform::<Ix2>::register_translation(
+                            fmaxz_keys[&t_key].view(),
+                            fmaxz,
+                        )?)
+                    } else {
+                        let fmaxz = filter::gaussian_smooth(
+                            &view.slice(s![t, .., ..])?.as_array::<f64>()?,
+                            &[5.0; 2],
+                        )?;
+                        Ok(Transform::<Ix2>::register_translation(
+                            fmaxz_keys[&t_key].view(),
+                            fmaxz.view(),
+                        )?)
+                    }
+                }
+            })
+            .collect::<Result<Vec<_>, Error>>()?;
+        let mut t = Transform::<Ix2>::from_translation(&[0.0; 2]);
+        let mut key_shifts = vec![t.clone()];
+        key_shifts.extend(shifts.iter().skip(n).map(|i| {
+            t = i * &t;
+            t.clone()
+        }));
+        Ok(key_shifts
+            .iter()
+            .zip(t_groups.array_windows())
+            .flat_map(|(s, [start, end])| {
+                let mut t = s.clone();
+                (*start..*end)
+                    .map(|i| {
+                        t = &shifts[i] * &t;
+                        t.clone()
+                    })
+                    .collect::<Vec<_>>()
+            })
+            .collect())
+    }
+
+    /// calculate drift transforms in zyx using this image view
+    pub fn calculate_drift_transforms_3d(&self) -> Result<Vec<Transform<Ix3>>, Error> {
         todo!()
     }
 
-    pub fn calculate_drift_transforms_3d(&self) -> Result<Vec<Transform<Ix3>>, Error> {
+    /// retrieve a frame and warp it according to the transform
-        todo!()
+    pub(crate) fn get_transformed_frame(
+        &self,
+        c: usize,
+        z: usize,
+        t: usize,
+        transform: &Transform<IxDyn>,
+        order: usize,
+        default_value: &DefaultValue,
+    ) -> 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,
+                                default_value,
+                            )?
+                            .mapv(|i| i > 0.5),
+                        )))
+                    };
+                    ($array:expr ,$var:ident, f64) => {
+                        Ok(Arc::from(Frame::$var(tr.interpolate_par_order(
+                            $array,
+                            order,
+                            default_value,
+                        )?)))
+                    };
+                    ($array:expr ,$var:ident, $t:ty) => {
+                        Ok(Arc::from(Frame::$var(
+                            tr.interpolate_par_order($array, order, default_value)?
+                                .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),
+                }
+            }
+            3 => {
+                let tr = transform.clone().into_dimensionality::<Ix3>()?;
+                let shape = self.shape();
+                let center = shape.iter().map(|&i| (i as f64) / 2.0).collect::<Vec<_>>();
+                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, &center)?;
+                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::$var(a) => Ok(a.view()),
+                                        _ => unreachable!(),
+                                    })
+                                    .collect::<Result<Vec<_>, Error>>()?;
+                                let stack = ndarray::stack(ndarray::Axis(0), &views)?;
+                                let transformed = tr.interpolate_par_order(
+                                    &stack.mapv(|i| if i { 1.0 } else { 0.0 }),
+                                    order,
+                                    default_value,
+                                )?;
+                                Ok(Arc::from(Frame::$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, default_value)?;
+                                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, default_value)?;
+                                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),
+                        }
+                    }
+                    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 => Err(Error::F128NotSupported)?,
+                        }))
+                    }
+                }
+            }
+            d => Err(Error::TransformationNotImplemented(d)),
+        }
     }
 }
 
 #[cfg(test)]
 mod tests {
+    use crate::axes::Axis;
+    use crate::error::Error;
+    use crate::readers::{DynReader, Reader};
     use crate::transforms::Transforms;
+    use image_registration::transform::Transform;
+    use ndarray::s;
+    use std::collections::HashMap;
+
+    fn open(file: &str) -> Result<DynReader, Error> {
+        let path = std::env::current_dir()?
+            .join("tests")
+            .join("files")
+            .join(file);
+        DynReader::new(&path, 0, 0)
+    }
 
     #[test]
     fn test_transforms() -> Result<(), Box<dyn std::error::Error>> {
@@ -348,4 +805,73 @@ mod tests {
         assert_eq!(t.channel["TV2"].ndim(), 2);
         Ok(())
     }
+
+    #[test]
+    fn transforms_as_array() -> Result<(), Box<dyn std::error::Error>> {
+        let file = "czi/beads_2020_08_05__11_43_07.czi";
+        let reader = open(file)?;
+        let view = reader.view();
+        let mut channel = HashMap::new();
+        channel.insert(
+            "TV1".to_string(),
+            Transform::new(vec![1.0, 0.0, 0.0, 1.0, 0.0, 0.0]),
+        );
+        channel.insert(
+            "TV2".to_string(),
+            Transform::new(vec![
+                0.9995868322142533,
+                0.012140955373934502,
+                0.012592501668218145,
+                0.8571690967587099,
+                -5.270859902118885,
+                -5.81118547158953,
+            ]),
+        );
+        let view_t = view.with_transforms(Transforms {
+            default_value: Default::default(),
+            interpolation_order: None,
+            channel,
+            drift: Vec::new(),
+        });
+
+        let s_a = view.max_proj(Axis::Z)?.slice_cztyx(s![1, 0, .., .., ..])?;
+
+        println!(
+            "s_a: {:?}, {:?}, {:?}",
+            s_a.get_slice(),
+            s_a.get_axes(),
+            s_a.get_operations()
+        );
+
+        let s_b = view_t
+            .max_proj(Axis::Z)?
+            .slice_cztyx(s![1, 0, .., .., ..])?;
+
+        println!(
+            "s_b: {:?}, {:?}, {:?}",
+            s_b.get_slice(),
+            s_b.get_axes(),
+            s_b.get_operations()
+        );
+
+        let a = s_a.as_array::<u16>()?;
+        let b = s_b.as_array::<u16>()?;
+        assert_ne!(a, b);
+
+        // let a = view.slice_cztyx(s![1, 0, 0, .., ..])?.as_array::<u16>()?;
+        // let b = view_t.slice_cztyx(s![1, 0, 0, .., ..])?.as_array::<u16>()?;
+        // assert_ne!(a, b);
+        //
+        // let a = view
+        //     .max_proj(Axis::Z)?
+        //     .slice(s![1, 0, .., ..])?
+        //     .as_array::<u16>()?;
+        // let b = view_t
+        //     .max_proj(Axis::Z)?
+        //     .slice(s![1, 0, .., ..])?
+        //     .as_array::<u16>()?;
+        // assert_ne!(a, b);
+
+        Ok(())
+    }
 }

ndbioimage/tests/files/tiffseq/YTL1841B2-2-1_1hr_DMSO_galinduction_1/display_and_comments.txt

@@ -0,0 +1,12 @@
+{
+  "Channels": [{
+    "Name": "mScarlet_GFP-mSc-filter",
+    "DisplayMode": 1,
+    "HistogramMax": -1,
+    "Max": 523,
+    "Gamma": 1,
+    "Min": 352,
+    "Color": -1
+  }],
+  "Comments": {"Summary": "5-GFP-mScarlet/GFP/OD2.0/100x/1x/2x2binning/15s_interval/{-2,2,0/5zstack}/autofocus/mScarlet_GFP-mSc-filter/500ms/100% OR: GFP 20%/exp150ms"}
+}

ndbioimage/tests/test_slicing.py

@@ -26,8 +26,10 @@ def image(array):
 
 @pytest.mark.parametrize(
     "s",
+    list(
         combinations_with_replacement(
-        (0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1)), 5
+            (0, -1, 1, slice(None), slice(0, 1), slice(-1, 0), slice(1, 1), slice(1, 2)), 5
+        )
     ),
 )
 def test_slicing(s, image, array):

ndbioimage/tests/test_ufuncs.py

@@ -26,6 +26,7 @@ def image(array):
 
 @pytest.mark.parametrize(
     "fun_and_axis",
+    list(
         product(
             (
                 np.sum,
@@ -44,6 +45,7 @@ def image(array):
                 np.nanstd,
             ),
             (None, 0, 1, 2, 3, 4),
+        )
     ),
 )
 def test_ufuncs(fun_and_axis, image, array):