swcgeom 0.19.4__cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

swcgeom/images/io.py

@@ -0,0 +1,578 @@
+
+# SPDX-FileCopyrightText: 2022 - 2025 Zexin Yuan <pypi@yzx9.xyz>
+#
+# SPDX-License-Identifier: Apache-2.0
+
+"""Read and write image stack."""
+
+import os
+import re
+import warnings
+from abc import ABC, abstractmethod
+from collections.abc import Callable, Iterable
+from functools import cache, lru_cache
+from typing import Any, Generic, Literal, TypeVar, cast, overload
+
+import nrrd
+import numpy as np
+import numpy.typing as npt
+import tifffile
+from typing_extensions import deprecated
+
+from swcgeom.images.loaders import PBD, Raw
+
+__all__ = ["read_imgs", "save_tiff", "read_images"]
+
+Vec3i = tuple[int, int, int]
+ScalarType = TypeVar("ScalarType", bound=np.generic, covariant=True)
+
+RE_TERAFLY_ROOT = re.compile(r"^RES\((\d+)x(\d+)x(\d+)\)$")
+RE_TERAFLY_NAME = re.compile(r"^\d+(_\d+)?(_\d+)?")
+
+UINT_MAX = {
+    np.dtype(np.uint8): (2**8) - 1,
+    np.dtype(np.uint16): (2**16) - 1,
+    np.dtype(np.uint32): (2**32) - 1,
+    np.dtype(np.uint64): (2**64) - 1,
+}
+
+AXES_ORDER = {
+    "X": 0,
+    "Y": 1,
+    "Z": 2,
+    "C": 3,
+    "I": 2,  # vaa3d compatibility
+}
+
+
+class ImageStack(ABC, Generic[ScalarType]):
+    """Image stack."""
+
+    # fmt: off
+    @overload
+    @abstractmethod
+    def __getitem__(self, key: int) -> npt.NDArray[ScalarType]: ...                     # array of shape (Y, Z, C)
+    @overload
+    @abstractmethod
+    def __getitem__(self, key: tuple[int, int]) -> npt.NDArray[ScalarType]: ...         # array of shape (Z, C)
+    @overload
+    @abstractmethod
+    def __getitem__(self, key: tuple[int, int, int]) -> npt.NDArray[ScalarType]: ...    # array of shape (C,)
+    @overload
+    @abstractmethod
+    def __getitem__(self, key: tuple[int, int, int, int]) -> ScalarType: ...            # value
+    @overload
+    @abstractmethod
+    def __getitem__(
+        self, key: slice | tuple[slice, slice] | tuple[slice, slice, slice] |  tuple[slice, slice, slice, slice],
+    ) -> npt.NDArray[ScalarType]: ... # array of shape (X, Y, Z, C)
+    @overload
+    @abstractmethod
+    def __getitem__(self, key: npt.NDArray[np.integer[Any]]) -> npt.NDArray[ScalarType]: ...
+    # fmt: on
+    @abstractmethod
+    def __getitem__(self, key):
+        """Get pixel/patch of image stack.
+
+        Returns:
+            value: NDArray which shape depends on key. If key is tuple of ints,
+        """
+        raise NotImplementedError()
+
+    def get_full(self) -> npt.NDArray[ScalarType]:
+        """Get full image stack.
+
+        NOTE: this will load the full image stack into memory.
+        """
+        return self[:, :, :, :]
+
+    @property
+    def shape(self) -> tuple[int, int, int, int]:
+        raise NotImplementedError()
+
+
+@overload
+def read_imgs(fname: str, *, dtype: ScalarType, **kwargs) -> ImageStack[ScalarType]: ...
+@overload
+def read_imgs(fname: str, *, dtype: None = ..., **kwargs) -> ImageStack[np.float32]: ...
+def read_imgs(fname: str, **kwargs):  # type: ignore
+    """Read image stack.
+
+    Args:
+        fname: The path of image stack.
+        dtype: Casting data to specified dtype.
+            If integer and float conversions occur, they will be scaled (assuming floats
+            are between 0 and 1). Default to `np.float32`.
+        **kwargs: Forwarding to the corresponding reader.
+    """
+    kwargs.setdefault("dtype", np.float32)
+    if not os.path.exists(fname):
+        raise ValueError(f"image stack not exists: {fname}")
+
+    # match file extension
+    match os.path.splitext(fname)[-1]:
+        case ".tif" | ".tiff":
+            return TiffImageStack(fname, **kwargs)
+        case ".nrrd":
+            return NrrdImageStack(fname, **kwargs)
+        case ".v3dpbd":
+            return V3dpbdImageStack(fname, **kwargs)
+        case ".v3draw":
+            return V3drawImageStack(fname, **kwargs)
+        case ".npy":
+            return NDArrayImageStack(np.load(fname), **kwargs)
+
+    # try to read as terafly
+    if TeraflyImageStack.is_root(fname):
+        return TeraflyImageStack(fname, **kwargs)
+
+    raise ValueError("unsupported image stack")
+
+
+def save_tiff(
+    data: npt.NDArray | ImageStack,
+    fname: str,
+    *,
+    dtype: np.unsignedinteger | np.floating | None = None,
+    compression: str | Literal[False] = "zlib",
+    **kwargs,
+) -> None:
+    """Save image stack as tiff.
+
+    Args:
+        data: The image stack.
+        fname: str
+        dtype: Casting data to specified dtype.
+            If integer and float conversions occur, they will be scaled (assuming
+            floats are between 0 and 1).
+        compression: Compression algorithm, forwarding to `tifffile.imwrite`.
+            If no algorithnm is specify specified, we will use the zlib algorithm with
+            compression level 6 by default.
+        **kwargs: Forwarding to `tifffile.imwrite`
+    """
+    if isinstance(data, ImageStack):
+        data = data.get_full()  # TODO: avoid load full imgs to memory
+
+    if data.ndim == 3:
+        data = np.expand_dims(data, -1)  # (_, _, _)  -> (_, _, _, C), C === 1
+
+    axes = "ZXYC"
+    assert data.ndim == 4, "should be an array of shape (X, Y, Z, C)"
+    assert data.shape[-1] in [1, 3], "support 'miniblack' or 'rgb'"
+
+    if dtype is not None:
+        if np.issubdtype(data.dtype, np.floating) and np.issubdtype(
+            dtype, np.unsignedinteger
+        ):
+            scaler_factor = UINT_MAX[np.dtype(dtype)]
+        elif np.issubdtype(data.dtype, np.unsignedinteger) and np.issubdtype(
+            dtype, np.floating
+        ):
+            scaler_factor = 1 / UINT_MAX[np.dtype(data.dtype)]
+        else:
+            scaler_factor = 1
+
+        data = (data * scaler_factor).astype(dtype)
+
+    if compression is not False:
+        kwargs.setdefault("compression", compression)
+        if compression == "zlib":
+            kwargs.setdefault("compressionargs", {"level": 6})
+
+    data = np.moveaxis(data, 2, 0)  # (_, _, Z, _) -> (Z, _, _, _)
+    kwargs.setdefault("photometric", "rgb" if data.shape[-1] == 3 else "minisblack")
+    metadata = kwargs.get("metadata", {})
+    metadata.setdefault("axes", axes)
+    kwargs.update(metadata=metadata)
+    tifffile.imwrite(fname, data, **kwargs)
+
+
+class NDArrayImageStack(ImageStack[ScalarType]):
+    """NDArray image stack."""
+
+    def __init__(
+        self, imgs: npt.NDArray[Any], *, dtype: ScalarType | None = None
+    ) -> None:
+        super().__init__()
+
+        if imgs.ndim == 3:  # (_, _, _) -> (_, _, _, C)
+            imgs = np.expand_dims(imgs, -1)
+        assert imgs.ndim == 4, "Should be shape of (X, Y, Z, C)"
+
+        if dtype is not None:
+            dtype_raw = imgs.dtype
+            if np.issubdtype(dtype, np.floating) and np.issubdtype(
+                dtype_raw, np.unsignedinteger
+            ):
+                scalar_factor = 1.0 / UINT_MAX[dtype_raw]
+                imgs = scalar_factor * imgs.astype(dtype)
+            elif np.issubdtype(dtype, np.unsignedinteger) and np.issubdtype(
+                dtype_raw, np.floating
+            ):
+                scalar_factor = UINT_MAX[dtype]
+                imgs *= (scalar_factor * imgs).astype(dtype)
+            else:
+                imgs = imgs.astype(dtype)
+
+        self.imgs = imgs
+
+    def __getitem__(self, key):
+        return self.imgs.__getitem__(key)
+
+    def get_full(self) -> npt.NDArray[ScalarType]:
+        return self.imgs
+
+    @property
+    def shape(self) -> tuple[int, int, int, int]:
+        return cast(tuple[int, int, int, int], self.imgs.shape)
+
+
+class TiffImageStack(NDArrayImageStack[ScalarType]):
+    """Tiff image stack."""
+
+    def __init__(self, fname: str, *, dtype: ScalarType, **kwargs) -> None:
+        with tifffile.TiffFile(fname, **kwargs) as f:
+            s = f.series[0]
+            imgs, axes = s.asarray(), s.axes
+
+        if len(axes) != imgs.ndim or any(c not in AXES_ORDER for c in axes):
+            axes_raw = axes
+            axes = "ZXYC" if imgs.ndim == 4 else "ZXY"
+            warnings.warn(f"reset unexcept axes `{axes_raw}` to `{axes}` in: {fname}")
+
+        orders = [AXES_ORDER[c] for c in axes]
+        imgs = imgs.transpose(np.argsort(orders))
+        super().__init__(imgs, dtype=dtype)
+
+
+class NrrdImageStack(NDArrayImageStack[ScalarType]):
+    """Nrrd image stack."""
+
+    def __init__(self, fname: str, *, dtype: ScalarType, **kwargs) -> None:
+        imgs, header = nrrd.read(fname, **kwargs)
+        super().__init__(imgs, dtype=dtype)
+        self.header = header
+
+
+class V3dImageStack(NDArrayImageStack[ScalarType]):
+    """v3d image stack."""
+
+    def __init_subclass__(cls, loader: Raw | PBD) -> None:
+        super().__init_subclass__()
+        cls._loader = loader
+
+    def __init__(self, fname: str, *, dtype: ScalarType, **kwargs) -> None:
+        r = self._loader()
+        imgs = r.load(fname)
+        super().__init__(imgs, dtype=dtype, **kwargs)
+
+
+class V3drawImageStack(V3dImageStack[ScalarType], loader=Raw):
+    """v3draw image stack."""
+
+
+class V3dpbdImageStack(V3dImageStack[ScalarType], loader=PBD):
+    """v3dpbd image stack."""
+
+
+class TeraflyImageStack(ImageStack[ScalarType]):
+    """TeraFly image stack.
+
+    TeraFly is a terabytes of multidimensional volumetric images file
+    format as described in [1]_.
+
+    NOTE: Terafly and Vaa3d use a especial right-handed coordinate system
+    (with origin point in the left-top and z-axis points front), but we
+    flip y-axis to makes it a left-handed coordinate system (with origin
+    point in the left-bottom and z-axis points front). If you need to
+    use its coordinate system, remember to FLIP Y-AXIS BACK.
+
+    References:
+    .. [1] Bria, Alessandro, Giulio Iannello, Leonardo Onofri, and Hanchuan Peng.
+       “TeraFly: Real-Time Three-Dimensional Visualization and Annotation of Terabytes
+       of Multidimensional Volumetric Images.” Nature Methods 13, no. 3 (March 2016):
+       192-94. https://doi.org/10.1038/nmeth.3767.
+    """
+
+    _listdir: Callable[[str], list[str]]
+    _read_patch: Callable[[str], npt.NDArray]
+
+    def __init__(
+        self, root: str, *, dtype: ScalarType, lru_maxsize: int | None = 128
+    ) -> None:
+        r"""
+        Args:
+            root: The root of terafly which contains directories named as `RES(YxXxZ)`.
+            dtype: np.dtype
+            lru_maxsize: Forwarding to `functools.lru_cache`.
+                A decompressed array size of (256, 256, 256, 1), which is the typical
+                size of terafly image stack, takes about 256 * 256 * 256 * 1 * 4B = 64MB.
+                A cache size of 128 requires about 8GB memory.
+        """
+
+        super().__init__()
+        self.root = root
+        self.dtype = dtype
+        self.res, self.res_dirs, self.res_patch_sizes = self.get_resolutions(root)
+
+        @cache
+        def listdir(path: str) -> list[str]:
+            return os.listdir(path)
+
+        @lru_cache(maxsize=lru_maxsize)
+        def read_patch(path: str) -> npt.NDArray[ScalarType]:
+            match os.path.splitext(path)[-1]:
+                case "raw":
+                    # Treat it as a v3draw file
+                    return V3drawImageStack(path, dtype=dtype).get_full()
+                case _:
+                    return read_imgs(path, dtype=dtype).get_full()
+
+        self._listdir, self._read_patch = listdir, read_patch
+
+    def __getitem__(self, key):
+        """Get images in max resolution.
+
+        >>> imgs[0, 0, 0, 0]  # get value # doctest: +SKIP
+        >>> imgs[0:64, 0:64, 0:64, :]  # get patch # doctest: +SKIP
+        ```
+        """
+        if not isinstance(key, tuple):
+            raise IndexError(
+                "Potential memory issue, you are loading large images "
+                "into memory, if sure, load it explicitly with "
+                "`get_full`"
+            )
+
+        if not isinstance(key[0], slice):
+            offset = [key[i] for i in range(3)]
+            return self.get_patch(offset, np.add(offset, 1)).item()
+
+        slices = [k.indices(self.res[-1][i]) for i, k in enumerate(key)]
+        starts, ends, strides = np.array(slices).transpose()
+        return self.get_patch(starts, ends, strides)
+
+    def get_patch(
+        self, starts, ends, strides: int | Vec3i = 1, res_level=-1
+    ) -> npt.NDArray[ScalarType]:
+        """Get patch of image stack.
+
+        Returns:
+            patch: array of shape (X, Y, Z, C)
+        """
+        if isinstance(strides, int):
+            strides = (strides, strides, strides)
+
+        starts, ends = np.array(starts), np.array(ends)
+        self._check_params(res_level, starts, np.subtract(ends, 1))
+        assert np.equal(strides, [1, 1, 1]).all()  #  TODO: support stride
+
+        shape_out = np.concatenate([ends - starts, [1]])
+        out = np.zeros(shape_out, dtype=self.dtype)
+        self._get_range(starts, ends, res_level, out=out)
+
+        # flip y-axis to makes it a left-handed coordinate system
+        out = np.flip(out, axis=1)
+        return out
+
+    def find_correspond_imgs(self, p, res_level=-1):
+        """Find the image which contain this point.
+
+        Returns:
+            patch: array of shape (X, Y, Z, C)
+            patch_offset: (int, int, int)
+        """
+        p = np.array(p)
+        self._check_params(res_level, p)
+        return self._find_correspond_imgs(p, res_level)
+
+    def get_correspond_coord(self, p, in_res_level: int, out_res_level: int):
+        raise NotImplementedError()  # TODO
+
+    @property
+    def shape(self) -> tuple[int, int, int, int]:
+        res_max = self.res[-1]
+        return res_max[0], res_max[1], res_max[2], 1
+
+    @classmethod
+    def get_resolutions(cls, root: str) -> tuple[list[Vec3i], list[str], list[Vec3i]]:
+        """Get all resolutions.
+
+        Returns:
+            resolutions: Sequence of sorted resolutions (from small to large).
+            roots: Sequence of root of resolutions respectively.
+            patch_sizes: Sequence of patch size of resolutions respectively.
+        """
+
+        roots = list(cls.get_resolution_dirs(root))
+        assert len(roots) > 0, "no resolution detected"
+
+        res = [RE_TERAFLY_ROOT.search(d) for d in roots]
+        res = [[int(a) for a in d.groups()] for d in res if d is not None]
+        res = np.array(res)
+        res[:, [0, 1]] = res[:, [1, 0]]  # (Y, X, _) -> (X, Y, _)
+
+        def listdir(d: str):
+            return filter(RE_TERAFLY_NAME.match, os.listdir(d))
+
+        def get_patch_size(src: str):
+            y0 = next(listdir(src))
+            x0 = next(listdir(os.path.join(src, y0)))
+            z0 = next(listdir(os.path.join(src, y0, x0)))
+            patch = read_imgs(os.path.join(src, y0, x0, z0))
+            return patch.shape
+
+        patch_sizes = [get_patch_size(os.path.join(root, d)) for d in roots]
+
+        # sort
+        indices = np.argsort(np.prod(res, axis=1, dtype=np.longlong))
+        res = res[indices]
+        roots = np.take(roots, indices)
+        patch_sizes = np.take(patch_sizes, indices)
+        return res, roots, patch_sizes  # type: ignore
+
+    @staticmethod
+    def is_root(root: str) -> bool:
+        return os.path.isdir(root) and any(
+            RE_TERAFLY_ROOT.match(d) for d in os.listdir(root)
+        )
+
+    @staticmethod
+    def get_resolution_dirs(root: str) -> Iterable[str]:
+        return filter(RE_TERAFLY_ROOT.match, os.listdir(root))
+
+    def _check_params(self, res_level, *coords):
+        assert res_level == -1  # TODO: support multi-resolutions
+
+        res_level = len(self.res) + res_level if res_level < 0 else res_level
+        assert 0 <= res_level < len(self.res), "invalid resolution level"
+
+        res = self.res[res_level]
+        for p in coords:
+            assert np.less([0, 0, 0], p).all(), (
+                f"indices ({p[0]}, {p[1]}, {p[2]}) out of range (0, 0, 0)"
+            )
+
+            assert np.greater(res, p).all(), (
+                f"indices ({p[0]}, {p[1]}, {p[2]}) out of range ({res[0]}, {res[1]}, {res[2]})"
+            )
+
+    def _get_range(self, starts, ends, res_level, out):
+        # pylint: disable=too-many-locals
+        shape = ends - starts
+        patch, offset = self._find_correspond_imgs(starts, res_level=res_level)
+        if patch is not None:
+            coords = starts - offset
+            lens = np.min([patch.shape[:3] - coords, shape], axis=0)
+            out[: lens[0], : lens[1], : lens[2]] = patch[
+                coords[0] : coords[0] + lens[0],
+                coords[1] : coords[1] + lens[1],
+                coords[2] : coords[2] + lens[2],
+            ]
+        else:
+            size = self.res_patch_sizes[res_level]
+            lens = (np.floor(starts / size).astype(np.int64) + 1) * size - starts
+
+        if shape[0] > lens[0]:
+            starts_x = starts + [lens[0], 0, 0]
+            ends_x = ends
+            self._get_range(starts_x, ends_x, res_level, out[lens[0] :, :, :])
+
+        if shape[1] > lens[1]:
+            starts_y = starts + [0, lens[1], 0]
+            ends_y = np.array([starts[0], ends[1], ends[2]])
+            ends_y += [min(shape[0], lens[0]), 0, 0]
+            self._get_range(starts_y, ends_y, res_level, out[:, lens[1] :, :])
+
+        if shape[2] > lens[2]:
+            starts_z = starts + [0, 0, lens[2]]
+            ends_z = np.array([starts[0], starts[1], ends[2]])
+            ends_z += [min(shape[0], lens[0]), min(shape[1], lens[1]), 0]
+            self._get_range(starts_z, ends_z, res_level, out[:, :, lens[2] :])
+
+    def _find_correspond_imgs(self, p, res_level):
+        # pylint: disable=too-many-locals
+        x, y, z = p
+        cur = os.path.join(self.root, self.res_dirs[res_level])
+
+        def get_v(f: str):
+            return float(os.path.splitext(f.split("_")[-1])[0])
+
+        for v in [y, x, z]:
+            # extract v from `y/`, `y_x/`, `y_x_z.tif`
+            dirs = [d for d in self._listdir(cur) if RE_TERAFLY_NAME.match(d)]
+            diff = np.array([get_v(d) for d in dirs])
+            if (invalid := diff > 10 * v).all():
+                return None, None
+
+            diff[invalid] = -np.inf  # remove values which greater than v
+
+            # find the index of the value smaller than v and closest to v
+            idx = np.argmax(diff)
+            cur = os.path.join(cur, dirs[idx])
+
+        patch = self._read_patch(cur)
+        name = os.path.splitext(os.path.basename(cur))[0]
+        offset = [int(int(i) / 10) for i in name.split("_")]
+        offset[0], offset[1] = offset[1], offset[0]  # (Y, X, _) -> (X, Y, _)
+        if np.less_equal(np.add(offset, patch.shape[:3]), p).any():
+            return None, None
+
+        return patch, offset
+
+
+# Legacy
+
+
+class GrayImageStack:
+    """Gray Image stack."""
+
+    imgs: ImageStack
+
+    def __init__(self, imgs: ImageStack) -> None:
+        self.imgs = imgs
+
+    @overload
+    def __getitem__(self, key: Vec3i) -> np.float32: ...
+    @overload
+    def __getitem__(self, key: npt.NDArray[np.integer[Any]]) -> np.float32: ...
+    @overload
+    def __getitem__(
+        self, key: slice | tuple[slice, slice] | tuple[slice, slice, slice]
+    ) -> npt.NDArray[np.float32]: ...
+    def __getitem__(self, key):
+        """Get pixel/patch of image stack."""
+        v = self[key]
+        if not isinstance(v, np.ndarray):
+            return v
+        if v.ndim == 4:
+            return v[:, :, :, 0]
+        if v.ndim == 3:
+            return v[:, :, 0]
+        if v.ndim == 2:
+            return v[:, 0]
+        if v.ndim == 1:
+            return v[0]
+        raise ValueError("unsupported key")
+
+    def get_full(self) -> npt.NDArray[np.float32]:
+        """Get full image stack.
+
+        NOTE: this will load the full image stack into memory.
+        """
+        return self.imgs.get_full()[:, :, :, 0]
+
+    @property
+    def shape(self) -> tuple[int, int, int]:
+        return self.imgs.shape[:-1]
+
+
+@deprecated("Use `read_imgs` instead")
+def read_images(*args, **kwargs) -> GrayImageStack:
+    """Read images.
+
+    .. deprecated:: 0.16.0
+        Use :meth:`read_imgs` instead.
+    """
+
+    return GrayImageStack(read_imgs(*args, **kwargs))

swcgeom/images/loaders/__init__.py

@@ -0,0 +1,8 @@
+# SPDX-FileCopyrightText: 2022 - 2025 Zexin Yuan <pypi@yzx9.xyz>
+#
+# SPDX-License-Identifier: Apache-2.0
+
+from swcgeom.images.loaders.pbd import PBD  # noqa: F401
+from swcgeom.images.loaders.raw import Raw  # noqa: F401
+
+__all__ = ["Raw", "PBD"]