prtools 1.2.0__tar.gz → 1.2.1__tar.gz

prtools-1.2.1/PKG-INFO

@@ -0,0 +1,79 @@
+Metadata-Version: 2.1
+Name: prtools
+Version: 1.2.1
+Summary: Utility functions for image-based phase retrieval
+Author: Andy Kee
+License: MIT License
+        
+        Copyright (c) 2023 Andy Kee
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Project-URL: Homepage, https://github.com/andykee/prtools
+Project-URL: Documentation, https://andykee.github.io/prtools/
+Project-URL: Bug Tracker, https://github.com/andykee/prtools/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules 
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy
+Requires-Dist: scipy
+
+prtools
+=======
+|pypi version|
+
+The prtools package implements functionality and tools that may be helpful 
+when performing image-based phase retrieval including:
+
+* Image processing, reduction, and analysis
+* Creating, fitting, and removing Zernike polynomials
+* Drawing various shapes in arrays
+* Computing statistics and optical simulation parameters
+
+Installation
+------------
+Install and update prtools using `pip`_:
+
+.. code-block:: text
+
+    pip install prtools
+
+Links
+-----
+* **Docs:** https://andykee.github.io/prtools/
+* **Releases:** https://pypi.org/project/prtools/
+* **Source:** https://github.com/andykee/prtools/
+* **Issues:** https://github.com/andykee/prtools/issues/
+
+.. _pip: https://pip.pypa.io/en/stable/getting-started/
+
+.. |pypi version| image:: https://img.shields.io/pypi/v/prtools.svg
+    :target: https://pypi.python.org/pypi/prtools

{prtools-1.2.0 → prtools-1.2.1}/README.rst

@@ -20,7 +20,7 @@ Install and update prtools using `pip`_:
 
 Links
 -----
-* **Docs:** https://prtools.readthedocs.io/
+* **Docs:** https://andykee.github.io/prtools/
 * **Releases:** https://pypi.org/project/prtools/
 * **Source:** https://github.com/andykee/prtools/
 * **Issues:** https://github.com/andykee/prtools/issues/

{prtools-1.2.0 → prtools-1.2.1}/prtools/__init__.py

@@ -1,8 +1,8 @@
 
-__version__ = '1.2.0'
+__version__ = '1.2.1'
 
 from prtools.array import (
-    centroid, pad, boundary, rebin, rescale, normpow,
+    centroid, pad, subarray, boundary, rebin, rescale, normpow,
     shift, register, medfix
     )
 
@@ -10,7 +10,7 @@ from prtools.fourier import dft2, idft2
 
 from prtools.misc import (
     min_sampling, pixelscale_nyquist, radial_avg, 
-    translation_defocus, fft_shape, calcpsf
+    translation_defocus, fft_shape, calcpsf, find_wrapped
     )
 
 from prtools.segmented import hex_segments

{prtools-1.2.0 → prtools-1.2.1}/prtools/array.py

@@ -160,6 +160,71 @@ def pad(a, shape, fill=0):
     return np.squeeze(out)
 
 
+def subarray(a, shape, shift=(0,0)):
+    """Extract a contiguous subarray from a larger array.
+
+    The subarray is extracted about the center of the source array unless
+    a shift is specified.
+
+    Parameters
+    ----------
+    a : array_like
+        Source array
+    shape : array_like of ints
+        Shape of subarray array in ``(nrows, ncols)``.
+    shift : array_like of ints
+        Relative shift of the center of the subarray in ``(row, col)``.
+    
+    Returns
+    -------
+    out : ndarray
+        Subarray extracted from the source array.
+
+    Examples
+    --------
+    .. plot::
+        :include-source:
+        :context: reset
+        :scale: 50
+
+        >>> circ = prtools.circle(shape=(128,128), radius=64)
+        >>> circ_subarray = prtools.subarray(circ, shape=(110,110))
+        >>> fig, ax = plt.subplots(nrows=1, ncols=2, figsize=(5,2))
+        >>> ax[0].imshow(circ, cmap='gray')
+        >>> ax[0].set_title('Original array')
+        >>> ax[1].imshow(circ_subarray, cmap='gray')
+        >>> ax[1].set_title('Subarray')
+    
+    .. plot::
+        :include-source:
+        :context: reset
+        :scale: 50
+
+        >>> circ = prtools.circle(shape=(128,128), radius=64)
+        >>> circ_subarray = prtools.subarray(circ, shape=(64,64), shift=(32,32))
+        >>> fig, ax = plt.subplots(nrows=1, ncols=2, figsize=(5,2))
+        >>> ax[0].imshow(circ, cmap='gray')
+        >>> ax[0].set_title('Original array')
+        >>> ax[1].imshow(circ_subarray, cmap='gray')
+        >>> ax[1].set_title('Subarray')
+
+    """
+
+    a = np.asarray(a)
+    shape = np.asarray(shape)
+
+
+    rmin = a.shape[0]//2 - shape[0]//2 + shift[0]
+    cmin = a.shape[1]//2 - shape[1]//2 + shift[1]
+    rmax = rmin + shape[0]
+    cmax = cmin + shape[1]
+
+    if any((rmin<0, cmin<0, rmax>a.shape[0], cmax>a.shape[1])):
+        raise ValueError('window lies outside of array')
+
+    return a[rmin:rmax, cmin:cmax]
+
+
 def boundary(x, threshold=0):
     """Find bounding row and column indices of data within an array.
 

{prtools-1.2.0 → prtools-1.2.1}/prtools/misc.py

@@ -234,3 +234,42 @@ def pixelscale_nyquist(wave, f_number):
 
     """
     return f_number * wave / 2
+
+
+def find_wrapped(opd, grad_thresh):
+    """Attempt to find phase wrapping using gradient edge detection while
+    automatically ignoring large gradients at mask edges.
+
+    Parameters
+    ----------
+    opd : array_like
+        OPD to detect wrapping in
+    grad_thresh : float
+        Threshold on magnitude of OPD gradient for determining wrapping
+
+    Returns
+    -------
+    wrapped : ndarray
+        Map of wrapped pixels
+    grad : ndarray
+        Gradient amplitude
+
+    """
+    opd = np.asarray(opd)
+
+    # compute gradient magnitude
+    gr, gc = np.gradient(opd)
+    G = np.sqrt(gr**2 + gc**2)
+
+    # compute mask to ignore gradient boundary
+    mask = np.zeros_like(opd)
+    mask[np.where(opd != 0)] = 1
+    grm, gcm = np.gradient(mask)
+    Gm = np.zeros_like(G)
+    Gm[np.where(np.sqrt(grm**2 + gcm**2) == 0)] = 1
+
+    grad = G * Gm
+    wrapped = np.zeros_like(grad)
+    wrapped[np.where(grad > grad_thresh)] = 1
+    
+    return wrapped, grad

prtools-1.2.1/prtools.egg-info/PKG-INFO

@@ -0,0 +1,79 @@
+Metadata-Version: 2.1
+Name: prtools
+Version: 1.2.1
+Summary: Utility functions for image-based phase retrieval
+Author: Andy Kee
+License: MIT License
+        
+        Copyright (c) 2023 Andy Kee
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Project-URL: Homepage, https://github.com/andykee/prtools
+Project-URL: Documentation, https://andykee.github.io/prtools/
+Project-URL: Bug Tracker, https://github.com/andykee/prtools/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: Software Development :: Libraries :: Python Modules 
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: numpy
+Requires-Dist: scipy
+
+prtools
+=======
+|pypi version|
+
+The prtools package implements functionality and tools that may be helpful 
+when performing image-based phase retrieval including:
+
+* Image processing, reduction, and analysis
+* Creating, fitting, and removing Zernike polynomials
+* Drawing various shapes in arrays
+* Computing statistics and optical simulation parameters
+
+Installation
+------------
+Install and update prtools using `pip`_:
+
+.. code-block:: text
+
+    pip install prtools
+
+Links
+-----
+* **Docs:** https://andykee.github.io/prtools/
+* **Releases:** https://pypi.org/project/prtools/
+* **Source:** https://github.com/andykee/prtools/
+* **Issues:** https://github.com/andykee/prtools/issues/
+
+.. _pip: https://pip.pypa.io/en/stable/getting-started/
+
+.. |pypi version| image:: https://img.shields.io/pypi/v/prtools.svg
+    :target: https://pypi.python.org/pypi/prtools

{prtools-1.2.0 → prtools-1.2.1}/prtools.egg-info/SOURCES.txt

@@ -1,8 +1,7 @@
 LICENSE
 NOTICE
 README.rst
-setup.cfg
-setup.py
+pyproject.toml
 prtools/__init__.py
 prtools/array.py
 prtools/fourier.py
@@ -16,4 +15,5 @@ prtools.egg-info/PKG-INFO
 prtools.egg-info/SOURCES.txt
 prtools.egg-info/dependency_links.txt
 prtools.egg-info/requires.txt
-prtools.egg-info/top_level.txt
+prtools.egg-info/top_level.txt
+tests/test_array.py

prtools-1.2.1/pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "prtools"
+description = "Utility functions for image-based phase retrieval"
+authors = [
+    {name = "Andy Kee"},
+]
+readme = "README.rst"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+dependencies = [
+    "numpy",
+    "scipy",
+]
+dynamic = ["version"]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Topic :: Scientific/Engineering :: Image Processing",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Topic :: Scientific/Engineering :: Physics",
+    "Topic :: Software Development",
+    "Topic :: Software Development :: Libraries",
+    "Topic :: Software Development :: Libraries :: Python Modules "
+]
+
+[project.urls]
+Homepage = "https://github.com/andykee/prtools"
+Documentation = "https://andykee.github.io/prtools/"
+"Bug Tracker" = "https://github.com/andykee/prtools/issues"
+
+[tool.setuptools]
+packages = ["prtools"]
+
+[tool.setuptools.dynamic]
+version = {attr = "prtools.__version__"} 

prtools-1.2.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

prtools-1.2.1/tests/test_array.py

@@ -0,0 +1,45 @@
+import warnings
+
+import numpy as np
+
+import prtools
+
+
+def test_centroid():
+    x = np.zeros((5,5))
+    x[2,2] = 1
+    assert(np.array_equal(prtools.centroid(x), [2,2]))
+
+
+def test_centroid_where():
+    x = np.zeros((5,5))
+    x[2,2] = 1
+    x[1,1] = 1
+    mask = np.ones_like(x)
+    mask[1,1] = 0
+    assert(np.array_equal(prtools.centroid(x, where=mask), [2,2]))
+
+
+def test_centroid_nan():
+    x = np.zeros((5,5))
+    x[2,2] = 1
+    x[2,3] = np.nan
+    assert(np.array_equal(prtools.centroid(x), [2,2]))
+
+
+x, _ = np.meshgrid(range(10), range(10))
+x[2,2] = 100
+
+def test_medfix():
+    m = np.zeros_like(x)
+    m[2,2] = 1
+    y = prtools.medfix(x, mask=m, kernel=(3,3))
+    assert(y[2,2] == 2)
+
+def test_medfix_bigmask():
+    m = np.zeros_like(x)
+    m[2:6, 2:6] = 1
+    with warnings.catch_warnings():
+        warnings.simplefilter('error')
+        y = prtools.medfix(x, mask=m, kernel=(3,3))
+    assert(np.all(np.isnan(y[3:5,3:5])))

prtools-1.2.0/PKG-INFO

@@ -1,20 +0,0 @@
-Metadata-Version: 2.1
-Name: prtools
-Version: 1.2.0
-Summary: Utility functions for image-based phase retrieval
-Author: Andy Kee
-License: MIT
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Astronomy
-Classifier: Topic :: Scientific/Engineering :: Image Processing
-Classifier: Topic :: Scientific/Engineering :: Mathematics
-Classifier: Topic :: Scientific/Engineering :: Physics
-Classifier: Topic :: Software Development
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-License-File: LICENSE
-License-File: NOTICE

prtools-1.2.0/prtools.egg-info/PKG-INFO

@@ -1,20 +0,0 @@
-Metadata-Version: 2.1
-Name: prtools
-Version: 1.2.0
-Summary: Utility functions for image-based phase retrieval
-Author: Andy Kee
-License: MIT
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
-Classifier: Programming Language :: Python :: 3
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Astronomy
-Classifier: Topic :: Scientific/Engineering :: Image Processing
-Classifier: Topic :: Scientific/Engineering :: Mathematics
-Classifier: Topic :: Scientific/Engineering :: Physics
-Classifier: Topic :: Software Development
-Classifier: Topic :: Software Development :: Libraries
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-License-File: LICENSE
-License-File: NOTICE

prtools-1.2.0/setup.cfg

@@ -1,24 +0,0 @@
-[metadata]
-name = prtools
-author = Andy Kee
-version = attr:prtools.__version__
-license = MIT
-description = Utility functions for image-based phase retrieval
-classifiers = 
-	Development Status :: 4 - Beta
-	Intended Audience :: Science/Research
-	License :: OSI Approved :: BSD License
-	Programming Language :: Python :: 3
-	Topic :: Scientific/Engineering
-	Topic :: Scientific/Engineering :: Astronomy
-	Topic :: Scientific/Engineering :: Image Processing
-	Topic :: Scientific/Engineering :: Mathematics
-	Topic :: Scientific/Engineering :: Physics
-	Topic :: Software Development
-	Topic :: Software Development :: Libraries
-	Topic :: Software Development :: Libraries :: Python Modules
-
-[egg_info]
-tag_build = 
-tag_date = 0
-

prtools-1.2.0/setup.py

@@ -1,9 +0,0 @@
-from setuptools import setup
-
-setup(
-    name='prtools',
-    install_requires=[
-        'numpy',
-        'scipy'
-    ],
-)