- improve Imread slicing

- can_open function for Reader trait

ndbioimage/py/ndbioimage/ndbioimage_rs/__init__.pyi

@@ -52,6 +52,8 @@ 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"""
@@ -211,6 +213,16 @@ class Imread:
         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
@@ -293,7 +305,9 @@ class Imread:
         r"""
         reshape the view with a new axis order
         """
-    def squeeze(self) -> numpy.ndarray | int | float: ...
+    def squeeze(
+        self, axes: str | typing.Sequence[int | str] = None
+    ) -> Imread | float | int: ...
     def close(self) -> None:
         r"""
         close the file: does nothing as this is handled automatically
@@ -306,7 +320,19 @@ 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
         """
@@ -314,7 +340,7 @@ 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
         """
@@ -322,139 +348,199 @@ 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
         """
@@ -507,13 +593,19 @@ 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
         """
@@ -529,6 +621,10 @@ 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
@@ -539,7 +635,7 @@ class 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
         """
@@ -573,10 +669,6 @@ class Imread:
         r"""
         the name of a particular channel
         """
-    def summary(self) -> builtins.str:
-        r"""
-        gives a helpful summary of the recorded experiment
-        """
     @staticmethod
     def get_available_series(
         path: str | pathlib.Path | Imread, reader: typing.Optional[builtins.str] = None
@@ -793,7 +885,7 @@ 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/pyproject.toml

@@ -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

@@ -314,16 +314,16 @@ impl Index<&Axis> for Shape {
 impl Index<usize> for Shape {
     type Output = usize;
 
-    fn index(&self, dim: usize) -> &Self::Output {
-        &self[self.order[dim % self.order.len()]]
+    fn index(&self, index: usize) -> &Self::Output {
+        &self[self.order[index]]
     }
 }
 
 impl Index<&usize> for Shape {
     type Output = usize;
 
-    fn index(&self, dim: &usize) -> &Self::Output {
-        &self[self.order[dim % self.order.len()]]
+    fn index(&self, index: &usize) -> &Self::Output {
+        &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/readers.rs

@@ -188,6 +188,12 @@ pub trait Reader: Clone + Sized + Debug + Send + Hash + Into<DynReader> {
     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>()
@@ -478,6 +484,34 @@ 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")]

ndbioimage/src/readers/bioformats_java.rs

@@ -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()
     }

ndbioimage/src/readers/bioformats_rust.rs

@@ -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();

ndbioimage/src/readers/czi.rs

@@ -215,6 +215,13 @@ impl Reader for CziReader {
         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())?;

ndbioimage/src/readers/tiff.rs

@@ -232,6 +232,24 @@ 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);
@@ -466,18 +484,36 @@ impl Reader for TiffReader {
         &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(),
+            ))
+        }
     }
 }
 

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());
@@ -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/view.rs

@@ -284,6 +284,21 @@ impl<D: Dimension, R: Reader> View<D, R> {
             .ok_or(Error::NoChannel(channel))
     }
 
+    /// names of the channels in order
+    pub fn channel_names(&self) -> Result<HashMap<usize, String>, Error> {
+        if self.channel_names.get().is_none() {
+            let names = self.metadata()?.image[0]
+                .pixels
+                .channel
+                .iter()
+                .enumerate()
+                .map(|(i, c)| (i, c.name.clone().unwrap_or_else(|| format!("{}", i))))
+                .collect::<HashMap<_, _>>();
+            let _ = self.channel_names.set(names);
+        }
+        Ok(self.channel_names.get().cloned().unwrap_or_default())
+    }
+
     /// set the maximum number of frames the process-wide cache may hold,
     /// evicting the least recently used frames
     pub fn with_cache_capacity(self, capacity: usize) -> Self {
@@ -404,6 +419,28 @@ impl<D: Dimension, R: Reader> View<D, R> {
         view.slice(slice.as_slice())
     }
 
+    /// remove axes of size 1 in axes
+    pub fn squeeze_axes(&self, axes: HashSet<Axis>) -> Result<View<IxDyn, R>, Error> {
+        let view = self.clone().into_dyn();
+        let slice: Vec<_> = self
+            .shape()
+            .into_iter()
+            .zip(self.axes().iter())
+            .map(|(s, a)| {
+                if s == 1 && axes.contains(a) {
+                    SliceInfoElem::Index(0)
+                } else {
+                    SliceInfoElem::Slice {
+                        start: 0,
+                        end: None,
+                        step: 1,
+                    }
+                }
+            })
+            .collect();
+        view.slice(slice.as_slice())
+    }
+
     pub(crate) fn op_axes(&self) -> Vec<Axis> {
         self.operations.keys().cloned().collect()
     }

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
+        )
     ),
 )
 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):