impy-array 2.3.3__tar.gz → 2.4.1__tar.gz

{impy_array-2.3.3 → impy_array-2.4.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: impy-array
-Version: 2.3.3
+Version: 2.4.1
 Summary: Speed up coding/extending image analysis in Python.
 Project-URL: Download, https://github.com/hanjinliu/impy
 Author-email: Hanjin Liu <liuhanjin-sc@g.ecc.u-tokyo.ac.jp>
@@ -70,14 +70,17 @@ Provides-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)
+[![BSD 3-Clause License](https://img.shields.io/pypi/l/impy-array.svg?color=green)](https://github.com/hanjinliu/impy/blob/main/LICENSE)
+[![Python package index download statistics](https://img.shields.io/pypi/dm/impy-array.svg)](https://pypistats.org/packages/impy-array)
 [![PyPI version](https://badge.fury.io/py/impy-array.svg)](https://badge.fury.io/py/impy-array)
 
 # A numpy extension for efficient and powerful image analysis workflow
 
-`impy` is an all-in-one image analysis library, equipped with parallel processing, GPU support, GUI based tools and so on.
+`impy` is an all-in-one image analysis library, equipped with parallel processing, GPU
+support, GUI-based tools and so on.
 
-The core array, `ImgArray`, is a subclass of `numpy.ndarray`, tagged with information such as
+The core array, `ImgArray`, is a subclass of `numpy.ndarray`, tagged with information
+such as:
 
 - image axes
 - scale of each axis
@@ -108,7 +111,10 @@ git clone https://github.com/hanjinliu/impy
 
 ### Code as fast as you speak
 
-Almost all the functions, such as filtering, deconvolution, labeling, single molecule detection, and even those pure `numpy` functions, are aware of image metadata. They "know" which dimension corresponds to `"z"` axis, which axes they should iterate along or where to save the image. As a result, **your code will be very concise**:
+Almost all the functions, such as filtering, deconvolution, labeling, single molecule
+detection, and even those pure `numpy` functions, are aware of image metadata. They
+"know" which dimension corresponds to `"z"` axis, which axes they should iterate along
+or where to save the image. As a result, **your code will be very concise**:
 
 ```python
 import impy as ip
@@ -121,19 +127,31 @@ img_prj = np.max(img_fil, axis="z")    # Z-projection (numpy is aware of image a
 img_prj.imsave(f"Max-{img.name}")      # Save in the same place. Don't spend time on searching for the directory!
 ```
 
-### Supported file formats
+### Supports many file formats
 
-`impy` automatically chooses proper reader/writer according to the extension.
+`impy` automatically chooses the proper reader/writer according to the extension.
 
 - Tiff file (".tif", ".tiff")
 - MRC file (".mrc", ".rec", ".st", ".map", ".map.gz")
 - Zarr file (".zarr")
 - Other image file (".png", ".jpg")
 
+### Lazy loading
+
+With the `lazy` submodule, you can easily make image processing workflows for large
+images.
+
+```python
+import impy as ip
+
+img = ip.lazy.imread("path/to/very-large-image.tif")
+out = img.gaussian_filter()
+out.imsave("image_filtered.tif")
+```
+
 ### Switch between CPU and GPU
 
 `impy` can internally switches the functions between `numpy` and `cupy`.
-You can use GPU for calculation very easily.
 
 ```python
 img.gaussian_filter()  # <- CPU
@@ -170,10 +188,10 @@ img.imfilter(param=1.0)
 
 ### Command line usage
 
-`impy` also supports command line based image analysis. All method of `ImgArray` is available
-from commad line, such as
+`impy` also supports command-line-based image analysis. All methods of `ImgArray` are
+available from the command line, such as
 
-```powershell
+```shell
 impy path/to/image.tif ./output.tif --method gaussian_filter --sigma 2.0
 ```
 
@@ -186,7 +204,7 @@ out = img.gaussian_filter(sigma=2.0)
 out.imsave("./output.tif")
 ```
 
-For more complex procedure, it is possible to send image directly to `IPython`
+For more complex procedures, it is possible to send images directly to `IPython`
 
 ```
 impy path/to/image.tif -i

{impy_array-2.3.3 → impy_array-2.4.1}/README.md

@@ -1,11 +1,14 @@
-[![Downloads](https://pepy.tech/badge/impy-array/month)](https://pepy.tech/project/impy-array)
+[![BSD 3-Clause License](https://img.shields.io/pypi/l/impy-array.svg?color=green)](https://github.com/hanjinliu/impy/blob/main/LICENSE)
+[![Python package index download statistics](https://img.shields.io/pypi/dm/impy-array.svg)](https://pypistats.org/packages/impy-array)
 [![PyPI version](https://badge.fury.io/py/impy-array.svg)](https://badge.fury.io/py/impy-array)
 
 # A numpy extension for efficient and powerful image analysis workflow
 
-`impy` is an all-in-one image analysis library, equipped with parallel processing, GPU support, GUI based tools and so on.
+`impy` is an all-in-one image analysis library, equipped with parallel processing, GPU
+support, GUI-based tools and so on.
 
-The core array, `ImgArray`, is a subclass of `numpy.ndarray`, tagged with information such as
+The core array, `ImgArray`, is a subclass of `numpy.ndarray`, tagged with information
+such as:
 
 - image axes
 - scale of each axis
@@ -36,7 +39,10 @@ git clone https://github.com/hanjinliu/impy
 
 ### Code as fast as you speak
 
-Almost all the functions, such as filtering, deconvolution, labeling, single molecule detection, and even those pure `numpy` functions, are aware of image metadata. They "know" which dimension corresponds to `"z"` axis, which axes they should iterate along or where to save the image. As a result, **your code will be very concise**:
+Almost all the functions, such as filtering, deconvolution, labeling, single molecule
+detection, and even those pure `numpy` functions, are aware of image metadata. They
+"know" which dimension corresponds to `"z"` axis, which axes they should iterate along
+or where to save the image. As a result, **your code will be very concise**:
 
 ```python
 import impy as ip
@@ -49,19 +55,31 @@ img_prj = np.max(img_fil, axis="z")    # Z-projection (numpy is aware of image a
 img_prj.imsave(f"Max-{img.name}")      # Save in the same place. Don't spend time on searching for the directory!
 ```
 
-### Supported file formats
+### Supports many file formats
 
-`impy` automatically chooses proper reader/writer according to the extension.
+`impy` automatically chooses the proper reader/writer according to the extension.
 
 - Tiff file (".tif", ".tiff")
 - MRC file (".mrc", ".rec", ".st", ".map", ".map.gz")
 - Zarr file (".zarr")
 - Other image file (".png", ".jpg")
 
+### Lazy loading
+
+With the `lazy` submodule, you can easily make image processing workflows for large
+images.
+
+```python
+import impy as ip
+
+img = ip.lazy.imread("path/to/very-large-image.tif")
+out = img.gaussian_filter()
+out.imsave("image_filtered.tif")
+```
+
 ### Switch between CPU and GPU
 
 `impy` can internally switches the functions between `numpy` and `cupy`.
-You can use GPU for calculation very easily.
 
 ```python
 img.gaussian_filter()  # <- CPU
@@ -98,10 +116,10 @@ img.imfilter(param=1.0)
 
 ### Command line usage
 
-`impy` also supports command line based image analysis. All method of `ImgArray` is available
-from commad line, such as
+`impy` also supports command-line-based image analysis. All methods of `ImgArray` are
+available from the command line, such as
 
-```powershell
+```shell
 impy path/to/image.tif ./output.tif --method gaussian_filter --sigma 2.0
 ```
 
@@ -114,7 +132,7 @@ out = img.gaussian_filter(sigma=2.0)
 out.imsave("./output.tif")
 ```
 
-For more complex procedure, it is possible to send image directly to `IPython`
+For more complex procedures, it is possible to send images directly to `IPython`
 
 ```
 impy path/to/image.tif -i

{impy_array-2.3.3 → impy_array-2.4.1}/impy/__init__.py

@@ -1,19 +1,19 @@
-__version__ = "2.3.3"
+__version__ = "2.4.1"
 __author__ = "Hanjin Liu"
 __email__ = "liuhanjin-sc@g.ecc.u-tokyo.ac.jp"
 
 import logging
 
-from ._const import Const, SetConst, use
+from ._const import Const, SetConst, use  # noqa
 
-from .collections import DataList, DataDict
-from .core import *
-from .binder import bind
-from .viewer import gui
-from .correlation import *
-from .arrays import ImgArray, LazyImgArray, BigImgArray, Label  # for typing
-from . import random, io, lazy
-from .axes import slicer
+from .collections import DataList, DataDict  # noqa
+from .core import *  # noqa
+from .binder import bind  # noqa
+from .viewer import gui  # noqa
+from .correlation import *  # noqa
+from .arrays import ImgArray, LazyImgArray, BigImgArray, Label  # noqa
+from . import random, io, lazy  # noqa
+from .axes import slicer  # noqa
 
 # Inheritance
 # -----------
@@ -34,7 +34,7 @@ logging.getLogger("tifffile").setLevel(logging.ERROR)
 del logging
 
 # dtypes
-from numpy import (
+from numpy import (  # noqa
     uint8, uint16, uint32, uint64,
     int8, int16, int32, int64,
     float16, float32, float64,

{impy_array-2.3.3 → impy_array-2.4.1}/impy/arrays/_utils/_deconv.py

@@ -1,13 +1,9 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING
 from functools import partial
 import numpy as np
 from impy.array_api import xp
 
-if TYPE_CHECKING:
-    from impy.arrays import ImgArray
-    
 try:
     gradient = xp.gradient
 except AttributeError:
@@ -17,18 +13,18 @@ except AttributeError:
         out = numpy.gradient(a.get(), axis=axis)
         return xp.asarray(out)
 
-__all__ = ["wiener", "lucy", "lucy_tv", "check_psf"]
+__all__ = ["wiener", "richardson_lucy", "richardson_lucy_tv", "check_psf"]
 
 def wiener(obs, psf_ft, psf_ft_conj, lmd):
     obs = xp.asarray(obs)
     fft = xp.fft.rfftn
     ifft = partial(xp.fft.irfftn, s=obs.shape)
-    
+
     img_ft = fft(obs)
-    
+
     estimated = xp.real(ifft(img_ft*psf_ft_conj / (psf_ft*psf_ft_conj + lmd)))
     return xp.fft.fftshift(estimated)
-    
+
 def richardson_lucy(obs, psf_ft, psf_ft_conj, niter, eps):
     # Identical to the algorithm in Deconvolution.jl of Julia.
     obs = xp.asarray(obs)
@@ -36,12 +32,12 @@ def richardson_lucy(obs, psf_ft, psf_ft_conj, niter, eps):
     ifft = partial(xp.fft.irfftn, s=obs.shape)
     conv = factor = xp.empty(obs.shape, dtype=xp.float32) # placeholder
     estimated = xp.real(ifft(fft(obs) * psf_ft))   # initialization
-    
+
     for _ in range(niter):
         conv[:] = ifft(fft(estimated) * psf_ft).real
         factor[:] = ifft(fft(_safe_div(obs, conv, eps=eps)) * psf_ft_conj).real
         estimated *= factor
-        
+
     return xp.fft.fftshift(estimated)
 
 def richardson_lucy_tv(obs, psf_ft, psf_ft_conj, max_iter, lmd, tol, eps):
@@ -51,21 +47,21 @@ def richardson_lucy_tv(obs, psf_ft, psf_ft_conj, max_iter, lmd, tol, eps):
     est_old = ifft(fft(obs) * psf_ft).real
     est_new = xp.empty(obs.shape, dtype=xp.float32)
     conv = factor = norm = gg = xp.empty(obs.shape, dtype=np.float32) # placeholder
-    
+
     for _ in range(max_iter):
         conv[:] = ifft(fft(est_old) * psf_ft).real
         factor[:] = ifft(fft(_safe_div(obs, conv, eps=eps)) * psf_ft_conj).real
         est_new[:] = est_old * factor
         grad = gradient(est_old)
         norm[:] = xp.sqrt(sum(g**2 for g in grad))
-        gg[:] = sum(gradient(_safe_div(grad[i], norm, eps=1e-8), axis=i) 
+        gg[:] = sum(gradient(_safe_div(grad[i], norm, eps=1e-8), axis=i)
                     for i in range(obs.ndim))
         est_new /= (1 - lmd * gg)
         gain = xp.sum(xp.abs(est_new - est_old))/xp.sum(xp.abs(est_old))
         if gain < tol:
             break
         est_old[:] = est_new
-        
+
     return xp.fft.fftshift(est_new)
 
 
@@ -81,7 +77,7 @@ def check_psf(img_shape: tuple[int, ...], img_scale: tuple[float, ...], psf):
         psf = psf(img_shape, img_scale)
     psf = xp.asarray(psf, dtype=np.float32)
     psf /= xp.sum(psf)
-    
+
     if img_shape != psf.shape:
         raise ValueError(
             f"observation and PSF have different shape: {img_shape} and {psf.shape}"

{impy_array-2.3.3 → impy_array-2.4.1}/impy/arrays/_utils/_filters.py

@@ -6,7 +6,7 @@ from scipy import ndimage as scipy_ndi
 
 
 __all__ = ["binary_erosion",
-    "erosion"
+    "erosion",
     "binary_dilation",
     "dilation",
     "binary_opening",

{impy_array-2.3.3 → impy_array-2.4.1}/impy/arrays/_utils/_glcm.py

@@ -1,6 +1,6 @@
 import numpy as np
-from ...collections import DataDict
 import scipy
+from impy.collections import DataDict
 
 __all__ = ["glcm_props_", "check_glcm"]
 
@@ -15,7 +15,7 @@ def asm_(glcm, ref, nei):
 
 def idm_(glcm, ref, nei):
     return np.sum(glcm/(1+(ref-nei)**2), axis=(0,1))
-    
+
 def energy_(glcm, ref, nei):
     return np.sqrt(np.sum(glcm**2, axis=(0,1)))
 
@@ -29,11 +29,11 @@ def entropy_(glcm, ref, nei):
 def correlation_(glcm, ref, nei):
     diffy = ref - np.sum(glcm * ref, axis=(0,1))
     diffx = nei - np.sum(glcm * nei, axis=(0,1))
-    
+
     stdy = np.sqrt(np.sum(glcm*diffy**2, axis=(0,1)))
     stdx = np.sqrt(np.sum(glcm*diffx**2, axis=(0,1)))
     cov = np.sum(glcm*diffx*diffy, axis=(0,1))
-    
+
     out = np.empty(glcm.shape[2:], dtype=np.float32)
     mask_0 = np.logical_or(stdx<1e-15, stdy<1e-15)
     mask_1 = ~mask_0
@@ -73,7 +73,7 @@ propdict = {"contrast": contrast_,
 def glcm_props_(data, distances, angles, levels, radius, properties):
     outshape = (len(distances), len(angles)) + \
         (data.shape[0]-2*radius, data.shape[1]-2*radius)
-        
+
     propout = DataDict()
     for prop in properties:
         if isinstance(prop, str):
@@ -82,13 +82,13 @@ def glcm_props_(data, distances, angles, levels, radius, properties):
             propout[prop.__name__] = np.empty(outshape, dtype=np.float32)
     # placeholder
     glcm = np.empty((levels, levels, len(distances), len(angles)), dtype=np.float32)
-    
+
     ref, nei = np.indices((levels, levels), dtype=np.float32)
     ref = ref[:, :, np.newaxis, np.newaxis]
     nei = nei[:, :, np.newaxis, np.newaxis]
-    
+
     from ._process_numba import _calc_glcm
-    
+
     for x in range(outshape[3]):
         for y in range(outshape[2]):
             # calc glcm
@@ -101,7 +101,7 @@ def glcm_props_(data, distances, angles, levels, radius, properties):
                 else:
                     # only callable
                     propout[prop.__name__][:,:,y,x] = prop(glcm, ref, nei)
-    
+
     return propout
 
 def check_glcm(self, bins, rescale_max):
@@ -112,22 +112,22 @@ def check_glcm(self, bins, rescale_max):
             bins = 256
     elif bins > 256:
         raise ValueError("`bins` must be smaller than 256.")
-    
+
     if self.dtype == np.uint16:
         self = self.as_uint8()
     elif self.dtype == np.uint8:
         pass
     else:
         raise TypeError(f"Cannot calculate comatrix of {self.dtype} image.")
-        
+
     imax = np.iinfo(self.dtype).max
-    
+
     if rescale_max:
         scale = int(imax/self.max())
         self *= scale
-    
+
     if (imax+1) % bins != 0 or bins > imax+1:
         raise ValueError(f"`bins` must be a divisor of {imax+1} (max value of {self.dtype}).")
     self = self // ((imax+1) // bins)
-    
-    return self, bins, rescale_max
+
+    return self, bins, rescale_max

{impy_array-2.3.3 → impy_array-2.4.1}/impy/arrays/_utils/_misc.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 import numpy as np
-from ...array_api import xp
+from impy.array_api import xp
 
 def adjust_bin(
     img: np.ndarray,
@@ -44,12 +44,12 @@ def make_rotated_axis(src, dst):
 def make_pad(pad_width, dims, all_axes, **kwargs):
     """More flexible padding than `np.pad`."""
     pad_width_ = []
-        
+
     # for consistency with scipy-format
     if "cval" in kwargs.keys():
         kwargs["constant_values"] = kwargs["cval"]
         kwargs.pop("cval")
-        
+
     if hasattr(pad_width, "__iter__") and len(pad_width) == len(dims):
         pad_iter = iter(pad_width)
         for a in all_axes:
@@ -57,7 +57,7 @@ def make_pad(pad_width, dims, all_axes, **kwargs):
                 pad_width_.append(next(pad_iter))
             else:
                 pad_width_.append((0, 0))
-        
+
     elif isinstance(pad_width, int):
         for a in all_axes:
             if a in dims:
@@ -66,7 +66,7 @@ def make_pad(pad_width, dims, all_axes, **kwargs):
                 pad_width_.append((0, 0))
     else:
         raise TypeError(f"pad_width must be iterable or int, but got {type(pad_width)}")
-    
+
     return pad_width_
 
 def dft(img: xp.ndarray, exps: list[xp.ndarray] = None):

{impy_array-2.3.3 → impy_array-2.4.1}/impy/arrays/_utils/_structures.py

@@ -1,5 +1,5 @@
 import numpy as np
-from ...array_api import xp
+from impy.array_api import xp
 
 def circle(radius, shape, dtype="bool"):
     x = xp.arange(-(shape[0] - 1) / 2, (shape[0] - 1) / 2 + 1)
@@ -10,7 +10,7 @@ def circle(radius, shape, dtype="bool"):
 def ball_like(radius, ndim:int):
     half_int = int(2*radius)/2
     L = xp.arange(-half_int, half_int + 1)
-    
+
     if ndim == 1:
         return xp.ones(int(radius)*2+1, dtype=np.uint8)
     elif ndim == 2:
@@ -32,9 +32,9 @@ def ball_like_odd(radius, ndim):
      [1, 1, 1, 1],
      [0, 1, 1, 0]]
     This is not suitable for specify().
-    """    
+    """
     xc = int(radius)
     l = xc*2 + 1
     coords = xp.indices((l,)*ndim)
     s = xp.sum((a-xc)**2 for a in coords)
-    return xp.array(s <= radius*radius, dtype=bool)
+    return xp.array(s <= radius*radius, dtype=bool)