Merge branch 'main' into vector-prototype

.github/workflows/pytests.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - name: Checkout repo

CITATION.cff

@@ -4,30 +4,32 @@
 cff-version: 1.2.0
 title: waveorder
 message: >-
-  A generalist library of wave optical models and inverse
-  algorithms for label-free imaging of density &
-  orientation.
+  Wave optical models and inverse algorithms for label-agnostic imaging of density & orientation.
 type: software
 authors:
-  - given-names: Li-Hao
-    family-names: Yeh
-    affiliation: CZ Biohub
-    orcid: 'https://orcid.org/0000-0003-2803-5996'
   - given-names: Talon
     family-names: Chandler
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0002-3033-674X'
+  - given-names: Li-Hao
+    family-names: Yeh
+    affiliation: Chan Zuckerberg Biohub San Francisco
+    orcid: 'https://orcid.org/0000-0003-2803-5996'
   - given-names: Ivan
     family-names: Ivanov
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0002-4675-5287'
   - given-names: Cameron
     family-names: Foltz
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0001-8933-2172'
+  - given-names: Ziwen
+    family-names: Liu
+    affiliation: Chan Zuckerberg Biohub San Francisco
+    orcid: 'https://orcid.org/0000-0001-7482-1299'
   - given-names: Shalin
     family-names: Mehta
-    affiliation: CZ Biohub
+    affiliation: Chan Zuckerberg Biohub San Francisco
     orcid: 'https://orcid.org/0000-0002-2542-3582'
 identifiers:
   - type: doi
@@ -67,6 +69,7 @@ keywords:
   - qlipp
   - mipolscope
   - simulation
+  - reconstruction
 license: BSD-3-Clause
-version: 1.0.0rc1
-date-released: '2023-02-22'
+version: 2.1.0
+date-released: '2024-03-12'

README.md

@@ -51,7 +51,7 @@ Please cite this repository, along with the relevant preprint or paper, if you u
 (Optional but recommended) install [anaconda](https://www.anaconda.com/products/distribution) and create a virtual environment:
 
 ```sh
-conda create -y -n waveorder python=3.9
+conda create -y -n waveorder python=3.11
 conda activate waveorder
 ```
 

pyproject.toml

@@ -5,9 +5,66 @@ build-backend = "setuptools.build_meta"
 [tool.setuptools_scm]
 write_to = "waveorder/_version.py"
 
+[project]
+name = "waveorder"
+description = "Wave-optical simulations and deconvolution of optical properties"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { file = "LICENSE" }
+authors = [{ name = "CZ Biohub SF", email = "[email protected]" }]
+maintainers = [
+  { name = "Talon Chandler", email = "[email protected]" },
+  { name = "Shalin Mehta", email = "[email protected]" },
+]
+keywords = [
+  "simulation",
+  'optics',
+  'phase',
+  'scattering',
+  'polarization',
+  'label-free',
+  'permittivity',
+  "reconstruction-algorithm",
+  'qlipp',
+  'mipolscope',
+  'permittivity-tensor-imaging',
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering",
+  "Topic :: Scientific/Engineering :: Image Processing",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Operating System :: POSIX :: Linux",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: MacOS",
+]
+dependencies = [
+  "numpy>=1.21, <2",
+  "matplotlib>=3.1.1",
+  "scipy>=1.3.0",
+  "pywavelets>=1.1.1",
+  "ipywidgets>=7.5.1",
+  "torch>=2.2.1",
+]
+dynamic = ["version"]
+
+[project.optional-dependencies]
+dev = ["pytest", "pytest-cov"]
+
+[project.urls]
+Homepage = "https://github.com/mehta-lab/waveorder"
+Repository = "https://github.com/mehta-lab/waveorder"
+Issues = "https://github.com/mehta-lab/waveorder/issues"
+
 [tool.black]
 line-length = 79
 
 [tool.isort]
 profile = "black"
-line_length = 79
+line_length = 79

waveorder/optics.py

@@ -365,7 +365,7 @@ def Source_subsample(Source_cont, NAx_coord, NAy_coord, subsampled_NA=0.1):
             illu_list.append(i)
             first_idx = False
         elif (
-            np.product(
+            np.prod(
                 (NAx_list[i] - NAx_list[illu_list]) ** 2
                 + (NAy_list[i] - NAy_list[illu_list]) ** 2
                 >= subsampled_NA**2