- fix slicing bug

- add pytest workflow

.github/workflows/pytest.yml

@@ -0,0 +1,78 @@
+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
+            ${{ env.CARGO_HOME }}
+          key: cache-ubuntu-maturin-cross-compile
+
+      - name: Install build dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y build-essential cmake clang llvm lld libclang
+        shell: bash
+
+      - name: Install Rust
+        run: |
+          export PATH="$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: |
+          python -m pip install .
+          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

Cargo.toml

@@ -3,7 +3,7 @@ resolver = "3"
 members = ["ndbioimage", "image-tiff", "image-registration"]
 
 [workspace.package]
-version = "0.3.1"
+version = "0.3.2"
 edition = "2024"
 rust-version = "1.94.1"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
@@ -20,6 +20,7 @@ inherits = "release"
 debug = true
 
 [profile.release]
+#debug = true
 
 [profile.dev.package.backtrace]
 opt-level = 3

ndbioimage/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "maturin"
 
 [project]
 name = "ndbioimage"
-version = "2027.0.7"
+version = "2027.0.8"
 requires-python = ">=3.10"
 classifiers = [
     "License :: OSI Approved :: MIT License",

ndbioimage/src/view.rs

@@ -964,16 +964,19 @@ impl<D: Dimension, R: Reader> View<D, R> {
                 axes_out_idx[*ax as usize] = Some(i);
             }
         }
-
-        for (c, z, t) in iproduct!(&slice_reader[0], &slice_reader[1], &slice_reader[2]) {
+        for ((ci, c), (zi, z), (ti, t)) in iproduct!(
+            slice_reader[0].enumerate(),
+            slice_reader[1].enumerate(),
+            slice_reader[2].enumerate()
+        ) {
             if let Some(i) = axes_out_idx[0] {
-                slice_out[i] = SliceInfoElem::Index(c)
+                slice_out[i] = SliceInfoElem::Index(ci as isize)
             };
             if let Some(i) = axes_out_idx[1] {
-                slice_out[i] = SliceInfoElem::Index(z)
+                slice_out[i] = SliceInfoElem::Index(zi as isize)
             };
             if let Some(i) = axes_out_idx[2] {
-                slice_out[i] = SliceInfoElem::Index(t)
+                slice_out[i] = SliceInfoElem::Index(ti as isize)
             };
             #[cfg(feature = "transforms")]
             let transform = self
@@ -1611,7 +1614,7 @@ mod tests {
     use crate::stats::MinMax;
     use crate::view::{Item, View};
     use indexmap::IndexMap;
-    use ndarray::{Array, Array4, Array5, Ix5, NewAxis};
+    use ndarray::{Array, Array4, Array5, Ix4, Ix5, NewAxis};
     use ndarray::{Array2, ArrayD, IxDyn, SliceInfoElem, s};
     use postcard::{from_bytes, to_stdvec};
     use std::path::{Path, PathBuf};
@@ -2072,4 +2075,17 @@ mod tests {
         assert_eq!(t, t2);
         Ok(())
     }
+
+    #[cfg(feature = "tiffseq")]
+    #[test]
+    fn test_slice() -> Result<(), Error> {
+        let file = "tiff/20251014_20-Pos_000_000_max.tif";
+        let reader = open(file)?;
+        let view: View<Ix4> =
+            View::new_with_axes(reader, vec![Axis::C, Axis::Z, Axis::Y, Axis::X])?;
+        let roi = view.slice(s![0, 1..2, 633..653, 853..873])?;
+        let arr = roi.as_array::<f64>()?;
+        println!("{:?}", arr);
+        Ok(())
+    }
 }

ndbioimage/tests/test_slicing.py

@@ -28,7 +28,7 @@ def image(array):
     "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
         )
     ),
 )