impy-array 2.2.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

impy/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "2.2.1"
+__version__ = "2.2.2"
 __author__ = "Hanjin Liu"
 __email__ = "liuhanjin-sc@g.ecc.u-tokyo.ac.jp"
 
@@ -15,19 +15,17 @@ from .arrays import ImgArray, LazyImgArray, BigImgArray, Label  # for typing
 from . import random, io
 from .axes import slicer
 
-r"""
-Inheritance
------------
+# Inheritance
+# -----------
+#
+# AxesMixin -----> LazyImgArray ------> BigImgArray
+#     |
+#     +-----> MetaArray --+--> LabeledArray --+--> ImgArray
+#     |                   |                   |
+# np.ndarray              +--> Label          +--> PhaseArray
+#                         |
+#                         +--> PropArray
 
-AxesMixin -----> LazyImgArray ------> BigImgArray
-    |
-    +-----> MetaArray --+--> LabeledArray --+--> ImgArray
-    |                   |                   |
-np.ndarray              +--> Label          +--> PhaseArray
-                        |
-                        +--> PropArray
-
-"""
 
 logging.getLogger("skimage").setLevel(logging.ERROR)
 logging.getLogger("tifffile").setLevel(logging.ERROR)

impy/arrays/__init__.py

@@ -16,3 +16,13 @@ try:
 
 except Exception:
     pass
+
+__all__ = [
+    "ImgArray",
+    "LabeledArray",
+    "Label",
+    "PhaseArray",
+    "PropArray",
+    "LazyImgArray",
+    "BigImgArray",
+]

impy/arrays/_utils/_deconv.py

@@ -1,7 +1,13 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
 from functools import partial
 import numpy as np
-from ...array_api import xp
+from impy.array_api import xp
 
+if TYPE_CHECKING:
+    from impy.arrays import ImgArray
+    
 try:
     gradient = xp.gradient
 except AttributeError:
@@ -11,11 +17,7 @@ except AttributeError:
         out = numpy.gradient(a.get(), axis=axis)
         return xp.asarray(out)
 
-__all__ = ["wiener", 
-           "lucy",
-           "lucy_tv",
-           "check_psf",
-           ]
+__all__ = ["wiener", "lucy", "lucy_tv", "check_psf"]
 
 def wiener(obs, psf_ft, psf_ft_conj, lmd):
     obs = xp.asarray(obs)
@@ -67,20 +69,23 @@ def richardson_lucy_tv(obs, psf_ft, psf_ft_conj, max_iter, lmd, tol, eps):
     return xp.fft.fftshift(est_new)
 
 
-def _safe_div(a, b, eps=1e-8):
+def _safe_div(a: np.ndarray, b: np.ndarray, eps: float = 1e-8):
     out = xp.zeros(a.shape, dtype=np.float32)
     mask = b > eps
-    out[mask] = a[mask]/b[mask]
+    out[mask] = a[mask] / b[mask]
     return out
 
 
-def check_psf(img, psf, dims):
+def check_psf(img_shape: tuple[int, ...], img_scale: tuple[float, ...], psf):
+    if callable(psf):
+        psf = psf(img_shape, img_scale)
     psf = xp.asarray(psf, dtype=np.float32)
     psf /= xp.sum(psf)
     
-    if img.sizesof(dims) != psf.shape:
-        raise ValueError("observation and PSF have different shape: "
-                        f"{img.sizesof(dims)} and {psf.shape}")
+    if img_shape != psf.shape:
+        raise ValueError(
+            f"observation and PSF have different shape: {img_shape} and {psf.shape}"
+        )
     psf_ft = xp.fft.rfftn(psf)
     psf_ft_conj = xp.conjugate(psf_ft)
-    return psf_ft, psf_ft_conj
+    return psf_ft, psf_ft_conj

impy/arrays/_utils/_transform.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 from typing import Iterable, NamedTuple, Sequence, TYPE_CHECKING
+import math
 import numpy as np
 
 from ._skimage import sktrans
@@ -307,8 +308,8 @@ def iradon(
     # Reconstruct image by interpolation
     reconstructed = np.zeros(output_shape, dtype=dtype)
     xpr, ypr = np.indices(output_shape)
-    xpr -= output_shape[0] // 2
-    ypr -= output_shape[1] // 2
+    xpr = xpr - output_shape[0] // 2
+    ypr = ypr - output_shape[1] // 2
     
     from scipy.interpolate import interp1d
     x = np.arange(img_shape) - img_shape // 2  # NOTE: use CPU!
@@ -322,12 +323,13 @@ def iradon(
 # This function is almost ported from `skimage.transform`.
 def get_fourier_filter(size: int, filter_name: str):
     n = xp.concatenate(
-        [xp.arange(1, size / 2 + 1, 2, dtype=int),
-         xp.arange(size / 2 - 1, 0, -2, dtype=int)]
+        [xp.arange(1, size // 2 + 1, 2, dtype=np.float32),
+         xp.arange(size // 2 - 1, 0, -2, dtype=np.float32)]
     )
     f = xp.zeros(size)
     f[0] = 0.25
     f[1::2] = -1 / (np.pi * n[:len(f[1::2])]) ** 2
+
     fourier_filter = 2 * xp.real(xp.fft.fft(f))  # ramp filter
     if filter_name == "ramp":
         pass

impy/arrays/axesmixin.py

@@ -200,6 +200,9 @@ class AxesMixin:
                 {a: s for a, s in other.scale.items() if a in self.axes}  # type: ignore
             )
         
+        elif isinstance(other, (list, tuple)):
+            for a, s in zip(self.axes, other):
+                a.scale = s
         else:
             raise TypeError(
                 f"'other' must be str or axes supported object, but got {type(other)}"

impy/arrays/bases/metaarray.py

@@ -27,7 +27,7 @@ SupportSlicing = Union[
     Mapping[str, SupportOneSlicing],
 ]
 
-class MetaArray(AxesMixin, np.ndarray):
+class MetaArray(AxesMixin, np.ndarray[Any, np.dtype[np.number]]):
     additional_props = ["_source", "_metadata", "_name"]
     NP_DISPATCH = {}
     _name: str
@@ -747,7 +747,7 @@ class MetaArray(AxesMixin, np.ndarray):
         except ImageAxesError:
             self.axes = None
         
-        return None
+        return self
     
     def _process_output(self, func, args, kwargs):
         # find the largest MetaArray. Largest because of broadcasting.

impy/arrays/bases/overload.py

@@ -229,6 +229,41 @@ def _(
     out._set_info(img, new_axes=img.axes)
     return out
 
+@MetaArray.implements(np.diff)
+def _(
+    img: MetaArray,
+    n: int = 1,
+    axis: int | AxisLike = -1,
+    prepend=None,
+    append=None,
+):
+    if isinstance(axis, (str, Axis)):
+        axis = img.axisof(axis)
+    kwargs = dict(n=n, axis=axis)
+    if prepend is not None:
+        kwargs["prepend"] = prepend
+    if append is not None:
+        kwargs["append"] = append
+    out = np.diff(img.value, **kwargs)
+    out = out.view(img.__class__)
+    out._set_info(img, new_axes=img.axes)
+    return out
+
+@MetaArray.implements(np.gradient)
+def _(img: MetaArray, *varargs, axis=None, edge_order=1):
+    if isinstance(axis, (str, Axis)):
+        axis = img.axisof(axis)
+    elif isinstance(axis, Axes):
+        axis = tuple(img.axisof(ax) for ax in axis)
+    out = np.gradient(img.value, *varargs, axis=axis, edge_order=edge_order)
+    if isinstance(out, np.ndarray):
+        out = out.view(img.__class__)._set_info(img, new_axes=img.axes)
+    else:
+        out = [arr.view(img.__class__)._set_info(img, new_axes=img.axes) for arr in out]
+        out = DataList(out)
+    return out
+
+
 # This function is ported from numpy.core.numeric.normalize_axis_tuple
 def np_normalize_axis_tuple(axis, ndim, argname=None, allow_duplicate=False):
     # Optimization to speed-up the most common cases.

impy/arrays/imgarray.py

@@ -13,25 +13,24 @@ from .specials import PropArray
 from ._utils._skimage import skexp, skfeat, skfil, skimage, skmes, skres, skseg, sktrans
 from ._utils import _filters, _linalg, _deconv, _misc, _glcm, _docs, _transform, _structures, _corr
 
-from ..utils.axesop import add_axes, switch_slice, complement_axes, find_first_appeared
-from ..utils.deco import check_input_and_output, dims_to_spatial_axes, same_dtype
-from ..utils.gauss import GaussianBackground, GaussianParticle
-from ..utils.misc import check_nd, largest_zeros
-from ..utils.slicer import solve_slicer
-
-from ..collections import DataDict
-from ..axes import AxisLike, slicer, Axes, Axis
-from .._types import nDInt, nDFloat, Dims, Coords, AxesTargetedSlicer, PaddingMode
-from .._const import Const
-from ..array_api import xp, cupy_dispatcher
+from impy.utils.axesop import add_axes, switch_slice, complement_axes, find_first_appeared
+from impy.utils.deco import check_input_and_output, dims_to_spatial_axes, same_dtype
+from impy.utils.gauss import GaussianBackground, GaussianParticle
+from impy.utils.misc import check_nd, largest_zeros
+from impy.utils.slicer import solve_slicer
+
+from impy.collections import DataDict
+from impy.axes import AxisLike, slicer, Axes, Axis
+from impy._types import nDInt, nDFloat, Dims, Coords, AxesTargetedSlicer, PaddingMode
+from impy._const import Const
+from impy.array_api import xp, cupy_dispatcher
 
 if TYPE_CHECKING:
     from ..frame import MarkerFrame
     from typing import Literal, Union
-    ThreasholdMethod = Union[
-        Literal["isodata"], Literal["li"], Literal["local"], Literal["mean"], Literal["min"],
-        Literal["minimum"], Literal["niblack"], Literal["otsu"], Literal["sauvola"], 
-        Literal["triangle"], Literal["yen"]
+    ThreasholdMethod = Literal[
+        "isodata", "li", "local", "mean", "min", "minimum", "niblack", "otsu", "sauvola",
+        "triangle", "yen"
     ]
     FftShape = Literal["same", "square"]
 
@@ -220,7 +219,7 @@ class ImgArray(LabeledArray):
     @same_dtype(asfloat=True)
     def rescale(
         self,
-        scale: float = 1/16,
+        scale: nDFloat = 1/16,
         *,
         order: int = None,
         mode: PaddingMode = "reflect",
@@ -228,31 +227,45 @@ class ImgArray(LabeledArray):
         dims: Dims = None,
     ) -> ImgArray:
         """
-        Rescale image.
+        Rescale image by applying the diagonal component of Affine matrix.
 
         Parameters
         ----------
         scale : float, optional
-            scale of the new image.
+            Relative scale of the new image. scale 1/2 means that the shape of
+            the output image will be (N/2, ...).
         {order}{mode}{cval}{dims}
         
         Returns
         -------
         ImgArray
             Rescaled image.
-        """        
-        outshape = switch_slice(
-            dims, self.axes, ifin=np.array(self.shape)*scale, ifnot=self.shape
-        )
-        gb = np.prod(outshape) * 4/1e9
+        """
+        scale_is_seq = hasattr(scale, "__iter__")
+        
+        # Check if output is too large.
+        gb = -1
+        if not scale_is_seq and scale > 1:
+            gb = np.prod(self.shape) * (scale ** len(dims)) / 1e9
+        elif scale_is_seq and np.prod(list(scale)) > 1:
+            gb = np.prod(self.shape) * np.prod(list(scale)) / 1e9
         if gb > Const["MAX_GB"]:
-            raise MemoryError(f"Too large: {gb} GB")
-        scale_ = [scale if a in dims else 1 for a in self.axes]
+            raise MemoryError(f"Output image is too large: {gb} GB")
+        
+        if scale_is_seq:
+            scale = list(scale)
+            if len(scale) != len(dims):
+                raise ValueError(
+                    "scale must have the same length as the spatial dimensions."
+                )
+            it = iter(scale)
+            scale_ = [next(it) if a in dims else 1 for a in self.axes]
+        else:
+            scale_ = [scale if a in dims else 1 for a in self.axes]
         out = sktrans.rescale(
             self.value, scale_, order=order, mode=mode, cval=cval, anti_aliasing=False
         )
-        out: ImgArray = out.view(self.__class__)
-        out._set_info(self)
+        out = out.view(self.__class__)._set_info(self)
         out.axes = self.axes.copy()
         out.set_scale({a: self.scale[a]/scale for a, scale in zip(self.axes, scale_)})
         return out
@@ -303,7 +316,7 @@ class ImgArray(LabeledArray):
         )
         
         reshaped_img = img_to_reshape.reshape(shape)
-        axes_to_reduce = tuple(i*2+1 for i in range(self.ndim))
+        axes_to_reduce = tuple(i * 2 + 1 for i in range(self.ndim))
         out: np.ndarray = binfunc(reshaped_img, axis=axes_to_reduce)
         out: ImgArray = out.view(self.__class__)
         out._set_info(self)
@@ -318,7 +331,7 @@ class ImgArray(LabeledArray):
     def radial_profile(
         self,
         nbin: int = 32,
-        center: Iterable[float] = None,
+        center: Iterable[float] | None = None,
         r_max: float = None, 
         *, 
         method: str = "mean",
@@ -3111,8 +3124,7 @@ class ImgArray(LabeledArray):
         if out.ndim == 3:
             out = np.moveaxis(out, 0, 1)
         out = out[::-1]
-        out._set_info(self, new_axes)
-        return out
+        return out._set_info(self, new_axes)
 
     @check_input_and_output
     def threshold(
@@ -4195,7 +4207,7 @@ class ImgArray(LabeledArray):
     @check_input_and_output
     def wiener(
         self,
-        psf: np.ndarray,
+        psf: np.ndarray | Callable[[tuple[int, ...]], np.ndarray],
         lmd: float = 0.1,
         *, 
         dims: Dims = None, 
@@ -4213,8 +4225,9 @@ class ImgArray(LabeledArray):
 
         Parameters
         ----------
-        psf : np.ndarray
-            Point spread function.
+        psf : ndarray or callable
+            Point spread function. If a function is given, `psf(shape)` will be
+            called to generate the PSF.
         lmd : float, default is 0.1
             Constant value used in the deconvolution. See Formulation below.
         {dims}{update}
@@ -4233,22 +4246,23 @@ class ImgArray(LabeledArray):
         if lmd <= 0:
             raise ValueError(f"lmd must be positive, but got: {lmd}")
         
-        psf_ft, psf_ft_conj = _deconv.check_psf(self, psf, dims)
+        psf_ft, psf_ft_conj = _deconv.check_psf(
+            self.sizesof(dims), tuple(self.scale[axis] for axis in dims), psf,
+        )
         
         return self._apply_dask(
             _deconv.wiener, 
             c_axes=complement_axes(dims, self.axes),
             args=(psf_ft, psf_ft_conj, lmd)
-        )
-        
-    
+        )    
+
     @_docs.write_docs
     @dims_to_spatial_axes
     @same_dtype(asfloat=True)
     @check_input_and_output
     def lucy(
         self,
-        psf: np.ndarray,
+        psf: np.ndarray | Callable[[tuple[int, ...]], np.ndarray],
         niter: int = 50,
         eps: float = 1e-5,
         *, 
@@ -4260,14 +4274,15 @@ class ImgArray(LabeledArray):
         
         Parameters
         ----------
-        psf : np.ndarray
-            Point spread function.
+        psf : ndarray or callable
+            Point spread function. If a function is given, `psf(shape)` will be
+            called to generate the PSF.
         niter : int, default is 50.
             Number of iterations.
         eps : float, default is 1e-5
-            During deconvolution, division by small values in the convolve image of estimation and 
-            PSF may cause divergence. Therefore, division by values under `eps` is substituted
-            to zero.
+            During deconvolution, division by small values in the convolve image 
+            of estimation and PSF may cause divergence. Therefore, division by 
+            values under `eps` is substituted to zero.
         {dims}{update}
         
         Returns
@@ -4281,7 +4296,9 @@ class ImgArray(LabeledArray):
         wiener
         """
         
-        psf_ft, psf_ft_conj = _deconv.check_psf(self, psf, dims)
+        psf_ft, psf_ft_conj = _deconv.check_psf(
+            self.sizesof(dims), tuple(self.scale[axis] for axis in dims), psf,
+        )
 
         return self._apply_dask(
             _deconv.richardson_lucy, 
@@ -4295,7 +4312,7 @@ class ImgArray(LabeledArray):
     @check_input_and_output
     def lucy_tv(
         self,
-        psf: np.ndarray,
+        psf: np.ndarray | Callable[[tuple[int, ...]], np.ndarray],
         max_iter: int = 50,
         lmd: float = 1e-3,
         tol: float = 1e-3,
@@ -4319,8 +4336,9 @@ class ImgArray(LabeledArray):
         
         Parameters
         ----------
-        psf : np.ndarray
-            Point spread function.
+        psf : ndarray or callable
+            Point spread function. If a function is given, `psf(shape)` will be
+            called to generate the PSF.
         max_iter : int, default is 50.
             Maximum number of iterations.
         lmd : float, default is 1e-3
@@ -4361,7 +4379,9 @@ class ImgArray(LabeledArray):
                 "In Richadson-Lucy with total-variance-regularization, "
                 "parameter `lmd` must be positive."
             )
-        psf_ft, psf_ft_conj = _deconv.check_psf(self, psf, dims)
+        psf_ft, psf_ft_conj = _deconv.check_psf(
+            self.sizesof(dims), tuple(self.scale[axis] for axis in dims), psf
+        )
 
         return self._apply_dask(
             _deconv.richardson_lucy_tv, 
@@ -4369,6 +4389,39 @@ class ImgArray(LabeledArray):
             args=(psf_ft, psf_ft_conj, max_iter, lmd, tol, eps)
         )
 
+    @_docs.write_docs
+    @dims_to_spatial_axes
+    @same_dtype(asfloat=True)
+    @check_input_and_output
+    def tiled_lucy(
+        self,
+        psf: np.ndarray | Callable[[tuple[int, ...]], np.ndarray],
+        niter: int = 50,
+        eps: float = 1e-5,
+        chunks = "auto",
+        overlap: int = 32,
+        *, 
+        dims: Dims = None, 
+        update: bool = False
+    ) -> ImgArray:
+        from dask import array as da
+
+        input = da.from_array(self.value, chunks=chunks)
+        depth = switch_slice(dims, self.axes, overlap, 0)
+        scale = tuple(self.scale[axis] for axis in dims)
+        
+        def func(arr: np.ndarray):
+            psf_ft, psf_ft_conj = _deconv.check_psf(arr.shape, scale, psf)
+            return _deconv.richardson_lucy(arr, psf_ft, psf_ft_conj, niter, eps)
+            
+        out = da.map_overlap(
+            func, 
+            input,
+            depth=depth,
+            boundary="reflect",
+            dtype=self.dtype,
+        ).compute()
+        return out
 
 def _check_coordinates(coords, img: ImgArray, dims: Dims = None):
     from impy.frame import MarkerFrame

impy/arrays/labeledarray.py

@@ -337,6 +337,7 @@ class LabeledArray(MetaArray):
     def _set_info(self, other: Self, new_axes: Any = MetaArray._INHERIT):
         super()._set_info(other, new_axes)
         self._inherit_covariates(other)
+        return self
     
     def _inherit_covariates(self, other: Self):
         if isinstance(other, LabeledArray):

impy/arrays/lazy.py

@@ -1526,7 +1526,7 @@ class LazyImgArray(AxesMixin):
         except ImageAxesError:
             self.axes = None
         
-        return None
+        return self
     
 
 def _replace_inputs(img: LazyImgArray, args, kwargs):

impy/core.py

@@ -143,10 +143,10 @@ def array(
 @_write_docs
 def asarray(
     arr: ArrayLike,
-    dtype: DTypeLike = None,
+    dtype: DTypeLike | None = None,
     *, 
-    name: str = None,
-    axes: str = None,
+    name: str | None = None,
+    axes: str | None = None,
     like: MetaArray | None = None,
 ) -> ImgArray:
     """
@@ -172,8 +172,8 @@ def aslabel(
     arr: ArrayLike,
     dtype: DTypeLike = None,
     *, 
-    name: str = None,
-    axes: str = None,
+    name: str | None = None,
+    axes: str | None = None,
     like: MetaArray | None = None,
 ) -> ImgArray:
     """
@@ -227,8 +227,8 @@ def aslazy(
     arr: ArrayLike, 
     dtype: DTypeLike = None,
     *, 
-    name: str = None,
-    axes: str = None,
+    name: str | None = None,
+    axes: str | None = None,
     chunks="auto",
     like: MetaArray | None = None,
 ) -> LazyImgArray:
@@ -284,8 +284,8 @@ def asbigarray(
     arr: ArrayLike, 
     dtype: DTypeLike = None,
     *, 
-    name: str = None,
-    axes: str = None,
+    name: str | None = None,
+    axes: str | None = None,
     like: MetaArray | None = None,
 ) -> BigImgArray:
     """
@@ -354,7 +354,9 @@ def _inject_numpy_function(func: Callable[_P, Any | None]) -> Callable[_P, ImgAr
             Image axes. Must be same length as image dimension.
         name: str, optional
             Image name.
-        
+        like: MetaArray, optional
+            Reference array from which name and axes will be copied.
+
         {npfunc.__doc__}
         """
         )
@@ -374,7 +376,11 @@ def ones(shape: ShapeLike, dtype: DTypeLike = np.uint16, *, name: str | None = N
 def full(shape: ShapeLike, fill_value: Any, dtype: DTypeLike = np.uint16, *, name: str | None = None, axes: AxesLike | None = None, like: MetaArray | None = None): ...
 
 @_inject_numpy_function
-def arange(stop: int, dtype: DTypeLike = ..., like: Any = ...): ...
+def arange(stop: int, dtype: DTypeLike = None): ...
+
+@_inject_numpy_function
+def fromiter(iterable: Iterable, dtype: DTypeLike, count: int = -1): ...
+
     
 def indices(
     dimensions: ShapeLike,

{impy_array-2.2.1.dist-info → impy_array-2.2.2.dist-info}/METADATA

@@ -1,27 +1,60 @@
 Metadata-Version: 2.1
 Name: impy-array
-Version: 2.2.1
+Version: 2.2.2
 Summary: Speed up coding/extending image analysis in Python.
-Download-URL: https://github.com/hanjinliu/impy
-Author: Hanjin Liu
-Author-email: liuhanjin-sc@g.ecc.u-tokyo.ac.jp
-License: BSD 3-Clause
-Requires-Python: >=3.8
-Description-Content-Type: text/markdown
+Project-URL: Download, https://github.com/hanjinliu/impy
+Author-email: Hanjin Liu <liuhanjin-sc@g.ecc.u-tokyo.ac.jp>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2021, hanjinliu
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 License-File: LICENSE
-Requires-Dist: numpy (>=1.22)
-Requires-Dist: scikit-image (>=0.20.0)
-Requires-Dist: pandas (>=1.3)
-Requires-Dist: dask (>=2021.6.0)
-Requires-Dist: napari (>=0.4.17)
-Requires-Dist: qtpy (>=1.10.0)
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.8
+Requires-Dist: dask>=2021.6.0
+Requires-Dist: napari>=0.4.17
+Requires-Dist: numpy>=1.22
+Requires-Dist: pandas>=1.3
+Requires-Dist: scikit-image>=0.20.0
 Provides-Extra: all
-Requires-Dist: mrcfile ; extra == 'all'
-Requires-Dist: zarr ; extra == 'all'
+Requires-Dist: mrcfile; extra == 'all'
+Requires-Dist: zarr; extra == 'all'
 Provides-Extra: mrc
-Requires-Dist: mrcfile ; extra == 'mrc'
+Requires-Dist: mrcfile; extra == 'mrc'
 Provides-Extra: zarr
-Requires-Dist: zarr ; extra == 'zarr'
+Requires-Dist: zarr; extra == 'zarr'
+Description-Content-Type: text/markdown
 
 [![Downloads](https://pepy.tech/badge/impy-array/month)](https://pepy.tech/project/impy-array)
 [![PyPI version](https://badge.fury.io/py/impy-array.svg)](https://badge.fury.io/py/impy-array)
@@ -117,7 +150,7 @@ and it's ready for batch processing!
 img.imfilter(param=1.0)
 ```
 
-### Commaind line usage
+### Command line usage
 
 `impy` also supports command line based image analysis. All method of `ImgArray` is available
 from commad line, such as
@@ -143,9 +176,3 @@ impy path/to/image.tif -i
 ```python
 thr = img.gaussian_filter().threshold()
 ```
-
-or to `napari`
-
-```
-impy path/to/image.tif -n
-```

{impy_array-2.2.1.dist-info → impy_array-2.2.2.dist-info}/RECORD

@@ -1,29 +1,30 @@
-impy/__init__.py,sha256=II-V8ywKApCUt_hmjxr475QC9to-846xsxN2I5KDbBQ,1076
+setup.py,sha256=EVgemUNpwbaqXxTcA04v_cr25SHJghq8zG_nkb0Mx4o,966
+impy/__init__.py,sha256=CRD1afMAeAfMqpQ056IFiDkYG0v3MOVoyD1nOmM1Vho,1084
 impy/__main__.py,sha256=BAQkQ4X8EFo42pbNx__EqpZ5KL4MTfTUWsVbJIQF0O0,4974
 impy/_const.py,sha256=N94lStP7Xt_9yFImieKjYeED-teV8p5o0aoW3CMFn1c,3688
 impy/_types.py,sha256=gO4l0hx9qxe6eI0PyC4ukW3k4IYxCEZ9gT-rQ3jj3zU,808
 impy/array_api.py,sha256=lVHgxubTtQ6CVaLib8uIUsI1xSEB_6tmoo1ktyDmPsw,4839
 impy/binder.py,sha256=CTMb11g6uYDVVQV5Wtef865IO0G2V3vGXc8SiGYRD5k,9651
 impy/collections.py,sha256=2e55bLjZN7W4LFUCkyxekcDfLwZodMaU4JG5NQ3RS54,10946
-impy/core.py,sha256=_qF78KUy8FamzwsCW3FTUEg60JdoxdQC4EsjQuFdo8w,29407
+impy/core.py,sha256=nMfZFVwzoDQUkx0_1Q3kYMFBZD72HQsoICpu5GByBqc,29654
 impy/correlation.py,sha256=CoNboXiZjO1VYqA0rHe4Jp6gDYt6hyJtSgI3TWepxKk,28398
 impy/io.py,sha256=O270L-hFW_nXA1QPOcgIDjEsrWnQjzX_UglXYCxUpS8,19241
 impy/random.py,sha256=SJdRFopKJu0oVsI7AoromF6qpfvV4YWBoSLiIYGYc6A,7035
 impy/roi.py,sha256=p9ttjBl5SGHHXj0xg5UjPlg_V9cY3MnNZxFfYIjTYsg,14164
-impy/arrays/__init__.py,sha256=EMPDAKhUwllcrgd4SGZ-xw66qDyIpM-EGe6UhmYcy4k,397
+impy/arrays/__init__.py,sha256=qth0jRXkS3p-x3Rb_tTGZqPHcwX90rycMx-ihWKQCn4,545
 impy/arrays/_deprecated.py,sha256=YTnQNkse-tN3xRkH9pCqJhHd_MgZg1CY2woCVTzcX5A,13111
 impy/arrays/_imshow.py,sha256=nhCEBwYC8LMjwwfLw5nUrlSWLhCTuBy569X_VpWV8H8,6517
-impy/arrays/axesmixin.py,sha256=XQmUNck1VCFKJxwMgdIUGNctpBBPTcanvgKHGbj9ji0,10445
+impy/arrays/axesmixin.py,sha256=ZNf_1tp6x6Qohtd8REP_8m5S8fk0JniiIAm0Rrlg2jo,10570
 impy/arrays/big.py,sha256=0KPG_V7yKiVYLFwzGfHRxyFD2kysIyVppsq6hh7TFPg,2809
-impy/arrays/imgarray.py,sha256=rYqtej6eB5JGvv65FwnjadDJAzi1676T8XehHP-2IVs,155198
+impy/arrays/imgarray.py,sha256=z38ATBeaU3_Gqquy3ZXR45tJYhnqLti2Cfq-a-8IBgs,157482
 impy/arrays/label.py,sha256=f8Gef1JI7nZUwFpq6YYTB4rP3XheMAJXU32PnfxRaTs,6415
-impy/arrays/labeledarray.py,sha256=rBEpo8o7rhqisS2oMkPI7zZbv4HlYmeyH-0XFPHq5uQ,56924
-impy/arrays/lazy.py,sha256=k0xTjhPfxlr4-OeajD93YK7Dk-welz_-fSrN8sB0Xow,55489
+impy/arrays/labeledarray.py,sha256=tbsqKn_OjiTg9rOt15tfogRiqnyYHktUxu4lqycSq4A,56945
+impy/arrays/lazy.py,sha256=noFbaYJrJmgEaPlG30JqIzhqG1eWKJtfNDSGfzg57ak,55489
 impy/arrays/phasearray.py,sha256=23E7ZTw8vni61rvhlgPyi-1j1kBg4Q2gxQ0wlE_CFE8,13937
 impy/arrays/specials.py,sha256=FiVap4iBA96TG3zDNeQG02TCZZDawg5KLzX7DRKQ6-4,7886
 impy/arrays/_utils/__init__.py,sha256=M5HogfyUBvV8kp-X1ZthS8vDLUP7-O2f9Gvsc1ZXdT8,271
 impy/arrays/_utils/_corr.py,sha256=8RM_OeaDsrewhiYhf6wFkDYRfl1gQ8Sg2TTK4CT22K4,10031
-impy/arrays/_utils/_deconv.py,sha256=BOegQ_muDlD-hU34eT1yIEjR2AHlkaAGvybDo-J6Iuk,2887
+impy/arrays/_utils/_deconv.py,sha256=-3kfLAHP_E8-t45JXVgY-1Y5D9ZDQaXc06Z5DcbMC4I,3101
 impy/arrays/_utils/_docs.py,sha256=AwVschAFOBFDeUJPvB1pJvBbJ6JJj3q4IpJqYbBrJ60,4548
 impy/arrays/_utils/_filters.py,sha256=FRN-YX-5KiKsuDOK1siBBMD52HLPL9twiPl6ByWhEZQ,6794
 impy/arrays/_utils/_glcm.py,sha256=8vkjgDIywVqmmWniK4vgLrssvYA8XOudePMoW44JMMY,4206
@@ -33,10 +34,10 @@ impy/arrays/_utils/_plot.py,sha256=LeUKFI9H9iYKKksc3GaPgZsxEHOmhMAkNw9HArbV5b8,5
 impy/arrays/_utils/_process_numba.py,sha256=1WjNRwqggSMYyKLeXo6W97lm93A47cAFvR6sBF086PI,3428
 impy/arrays/_utils/_skimage.py,sha256=sox3kvl9u3wbK6RwbakCl2jlTkwzp6WD9o6-d4Lbmuw,1283
 impy/arrays/_utils/_structures.py,sha256=lTwceW3sjv4DThRmBsCtB9nkfZ51NaCpCGyzkces0AM,1305
-impy/arrays/_utils/_transform.py,sha256=vhMBYh1ykmKIEWVk5U6FHAPgirJkcsDWWXOY2V3_6Kc,12721
+impy/arrays/_utils/_transform.py,sha256=6HMBOItV9zMFjvB4qOUmRPg92A0hiG6moFesRkfdtBE,12762
 impy/arrays/bases/__init__.py,sha256=aHsAYta5CQkEDlbFShEtEGYN89N2qYedg99SM6Oo7wk,99
-impy/arrays/bases/metaarray.py,sha256=NnnuAWJSuYP_sz2ADuqdLbu9ftkhKtUoEXTNl1wDfQs,27078
-impy/arrays/bases/overload.py,sha256=Hx8kySgR0rtHSpTryTnR02bMCrg8-c1mnQzWp6O7wEk,8244
+impy/arrays/bases/metaarray.py,sha256=bqZ0I-3nsEDbFlu1iwPdbaUbphOMyC5Z1W-JCMZQOLw,27104
+impy/arrays/bases/overload.py,sha256=ECLxRCumEUJb4KEu1K8k4vZWbufyPEPBj-Atzv4AosU,9359
 impy/axes/__init__.py,sha256=qzhWAJMT_mc-MXcuaMEDjVd_n0dFRmZxaphh6x_Wzb4,239
 impy/axes/_axes.py,sha256=lpTPzcs_hHslbxSUBGTjicIu4XLUs79zXPfDi5ZyGLI,12134
 impy/axes/_axes_tuple.py,sha256=hkgTr_n36gFcnnffmSp3z4oJ_52MxT1JnaszdJ3JnrY,1522
@@ -54,9 +55,9 @@ impy/utils/utilcls.py,sha256=3Td9G2ZkU4C0BiW2LH0sq7RBjdco_BtyxNr-s-seLhs,437
 impy/viewer/__init__.py,sha256=NTVonxd7HMfbRXHhjLBMG_07NjFia-O1QCv5IOKdbgw,286
 impy/viewer/utils.py,sha256=fn1gA4bD9Zlabc8EJcpSC3VCy40ljDD3pffsHl4ck2U,12187
 impy/viewer/viewer.py,sha256=KVg3BceGGT1pj17md2zHRg5iaIHdBXaWVi0vDWWVOmI,17561
-impy_array-2.2.1.dist-info/LICENSE,sha256=rpxKafH9r42sxLLYYB5VbZBHOdtYeLuYJjVU1LBwrxk,1546
-impy_array-2.2.1.dist-info/METADATA,sha256=1sDIm3dUkezMDe9N6kfw6M6Z-0UAaSmmrIgX8xMG2-E,4294
-impy_array-2.2.1.dist-info/WHEEL,sha256=G16H4A3IeoQmnOrYV4ueZGKSjhipXx8zc8nu9FGlvMA,92
-impy_array-2.2.1.dist-info/entry_points.txt,sha256=reyrgy4odXvi1CcPOIIyRYBmsNGG2tO7ZkFOdG5CBkU,44
-impy_array-2.2.1.dist-info/top_level.txt,sha256=3Sw5wiwivoN-t8aUxS8YSBWZu8_MFJhP53XSC66xxyg,5
-impy_array-2.2.1.dist-info/RECORD,,
+rst/conf.py,sha256=CBA2_0Qkkj7U5gYS2hY-DW0znc8BO42cSyZqjTp7InE,2341
+impy_array-2.2.2.dist-info/METADATA,sha256=ky4sYNVbmkZ6Y4D42x_R3V1rWij-YW7VK4w0V39pcXg,6322
+impy_array-2.2.2.dist-info/WHEEL,sha256=y1bSCq4r5i4nMmpXeUJMqs3ipKvkZObrIXSvJHm1qCI,87
+impy_array-2.2.2.dist-info/entry_points.txt,sha256=reyrgy4odXvi1CcPOIIyRYBmsNGG2tO7ZkFOdG5CBkU,44
+impy_array-2.2.2.dist-info/licenses/LICENSE,sha256=rpxKafH9r42sxLLYYB5VbZBHOdtYeLuYJjVU1LBwrxk,1546
+impy_array-2.2.2.dist-info/RECORD,,

{impy_array-2.2.1.dist-info → impy_array-2.2.2.dist-info}/WHEEL

@@ -1,5 +1,4 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.37.1)
+Generator: hatchling 1.17.0
 Root-Is-Purelib: true
 Tag: py3-none-any
-

rst/conf.py

@@ -0,0 +1,64 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../'))
+import impy
+import sphinx_rtd_theme
+
+# -- Project information -----------------------------------------------------
+
+project = 'impy'
+copyright = '2021, Hanjin Liu'
+author = 'Hanjin Liu'
+
+# The full version, including alpha/beta/rc tags
+version = impy.__version__
+release = impy.__version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc', 
+              'sphinx.ext.napoleon',
+              'sphinx.ext.viewcode',
+              'sphinx.ext.githubpages',
+              'sphinxcontrib.blockdiag',
+              ]
+
+blockdiag_html_image_format = 'SVG'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

setup.py

@@ -0,0 +1,37 @@
+import sys
+
+sys.stderr.write(
+    """
+    ===============================================================
+    impy does not support `python setup.py install`. Please use
+
+        $ python -m pip install .
+
+    instead.
+    ===============================================================
+    """
+)
+sys.exit(1)
+
+setup(
+    name="impy-array",
+    author="Hanjin Liu",
+    author_email="liuhanjin-sc@g.ecc.u-tokyo.ac.jp",
+    long_description_content_type="text/markdown",
+    license="BSD 3-Clause",
+    download_url="https://github.com/hanjinliu/impy",
+    install_requires=[
+        "numpy>=1.22",
+        "scikit-image>=0.20.0",
+        "pandas>=1.3",
+        "dask>=2021.6.0",
+        "napari>=0.4.17",
+    ],
+    python_requires=">=3.8",
+    entry_points={"console_scripts": ["impy=impy.__main__:main",],},
+    extras_require={
+        "all": ["mrcfile", "zarr"],
+        "zarr": ["zarr"],
+        "mrc": ["mrcfile"],
+    },
+)

impy_array-2.2.1.dist-info/top_level.txt

@@ -1 +0,0 @@
-impy