Merge remote-tracking branch 'origin/master'

# Conflicts:
#	openwfs/algorithms/dual_reference.py
#	tests/test_wfs.py

.github/workflows/black.yml

@@ -0,0 +1,10 @@
+name: Black
+
+on: [workflow_call, push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: psf/black@stable

.github/workflows/pytest.yml

@@ -0,0 +1,24 @@
+name: PyTest
+
+on: [workflow_call, push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Test with pytest
+        run: |
+          pytest

README.md

@@ -4,6 +4,11 @@
 
 <!-- NOTE: README.MD IS AUTO-GENERATED FROM DOCS/SOURCE/README.RST. DO NOT EDIT README.MD DIRECTLY. -->
 
+[![PyTest]([https://github.com/IvoVellekoop/openwfs/actions/workflows/pytest.yml/badge.svg)](https://github.com/IvoVellekoop/openwfs/actions/workflows/pytest.yml](https://github.com/IvoVellekoop/openwfs/actions/workflows/pytest.yml/badge.svg)](https://github.com/IvoVellekoop/openwfs/actions/workflows/pytest.yml))
+[![Black]([https://github.com/IvoVellekoop/openwfs/actions/workflows/black.yml/badge.svg)](https://github.com/IvoVellekoop/openwfs/actions/workflows/black.yml](https://github.com/IvoVellekoop/openwfs/actions/workflows/black.yml/badge.svg)](https://github.com/IvoVellekoop/openwfs/actions/workflows/black.yml))
+
+What is wavefront shaping?
+
 ## What is wavefront shaping?
 
 Wavefront shaping (WFS) is a technique for controlling the propagation of light in arbitrarily complex structures, including strongly scattering materials [[1](#id62)]. In WFS, a spatial light modulator (SLM) is used to shape the phase and/or amplitude of the incident light. With a properly constructed wavefront, light can be made to focus through [[2](#id48)], or inside [[3](#id37)] scattering materials; or light can be shaped to have other desired properties, such as optimal sensitivity for specific measurements [[4](#id38)], specialized point-spread functions [[5](#id25)] or for functions like optical trapping [[6](#id28)].

STYLEGUIDE.md

@@ -6,9 +6,7 @@
 
 # General
 
-- all .py files MUST be formatted with the 'black' autoformatter. This can be done by installing the 'black' package,
-  and running `black .` in the root directory. black is automatically installed when the development dependencies are
-  included.
+- The package `black` is used to ensure correct formatting. Install with `pip install black` and run in the terminal using `black .` when located at the root of the repository. 
 
 # Tests
 

docs/source/development.rst

@@ -14,7 +14,9 @@ To download the source code, including tests and examples, clone the repository
     poetry install --with dev --with docs
     poetry run pytest
 
-The examples are located in the ``examples`` directory. Note that a lot of functionality is also demonstrated in the automatic tests located in the ``tests`` directory. As an alternative to downloading the source code, the samples can also be copied directly from the example gallery on the documentation website :cite:`readthedocsOpenWFS`.
+The examples are located in the ``examples`` directory. Note that a lot of functionality is also demonstrated in the automatic tests located in the ``tests`` directory. As an alternative to downloading the source code, the samples can also be copied directly from the example gallery on the documentation website :cite:`readthedocsOpenWFS`. 
+
+Important to note for adding hardware devices, is that many of the components rely on third-party, in some case proprietary drivers. For using NI DAQ components, the nidaqmx package needs to be installed, and for openCV and Genicam their respective drivers need to be installed. The specific requirements are always listed in the documentation of the functions and classes that require packages like these.
 
 Building the documentation
 --------------------------------------------------

docs/source/readme.rst

@@ -12,15 +12,19 @@ OpenWFS
        :target: https://openwfs.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status
 
+.. only:: markdown
+
+   [![PyTest](https://github.com/IvoVellekoop/openwfs/actions/workflows/pytest.yml/badge.svg)](https://github.com/IvoVellekoop/openwfs/actions/workflows/pytest.yml)
+   [![Black](https://github.com/IvoVellekoop/openwfs/actions/workflows/black.yml/badge.svg)](https://github.com/IvoVellekoop/openwfs/actions/workflows/black.yml)
 
 What is wavefront shaping?
 --------------------------------
 
-Wavefront shaping (WFS) is a technique for controlling the propagation of light in arbitrarily complex structures, including strongly scattering materials :cite:`kubby2019`. In WFS, a spatial light modulator (SLM) is used to shape the phase and/or amplitude of the incident light. With a properly constructed wavefront, light can be made to focus through :cite:`Vellekoop2007`, or inside :cite:`vellekoop2008demixing` scattering materials; or light can be shaped to have other desired properties, such as optimal sensitivity for specific measurements :cite:`bouchet2021maximum`, specialized point-spread functions :cite:`boniface2017transmission` or for functions like optical trapping :cite:`vcivzmar2010situ`.
+Wavefront shaping (WFS) is a technique for controlling the propagation of light in arbitrarily complex structures, including strongly scattering materials :cite:`kubby2019`. In WFS, a spatial light modulator (SLM) is used to shape the phase and/or amplitude of the incident light. With a properly constructed wavefront, light can be made to focus through :cite:`Vellekoop2007`, or inside :cite:`vellekoop2008demixing` scattering materials; or light can be shaped to have other desired properties, such as optimal sensitivity for specific measurements :cite:`bouchet2021maximum`, specialized point-spread functions :cite:`boniface2017transmission`, spectral filtering :cite:`Park2012`,, or for functions like optical trapping :cite:`vcivzmar2010situ`.
 
-It stands out that an important driving force in WFS is the development of new algorithms, for example to account for sample movement :cite:`valzania2023online`, to be optimally resilient to noise :cite:`mastiani2021noise`, or to use digital twin models to compute the required correction patterns :cite:`salter2014exploring,ploschner2015seeing,Thendiyammal2020,cox2023model`. Much progress has been made towards developing fast and noise-resilient algorithms, or algorithms designed for specific towards the methodology of wavefront shaping, such as using algorithms based on Hadamard patterns, or Fourier-based approaches :cite:`Mastiani2022`. Fast techniques that enable wavefront shaping in dynamic samples :cite:`Liu2017,Tzang2019`, and many potential applications have been developed and prototyped, including endoscopy :cite:`ploschner2015seeing`, optical trapping :cite:`Cizmar2010` and deep-tissue imaging :cite:`Streich2021`.
+It stands out that an important driving force in WFS is the development of new algorithms, for example to account for sample movement :cite:`valzania2023online`, experimental conditions :cite:`Anderson2016`, to be optimally resilient to noise :cite:`mastiani2021noise`, or to use digital twin models to compute the required correction patterns :cite:`salter2014exploring,ploschner2015seeing,Thendiyammal2020,cox2023model`. Much progress has been made towards developing fast and noise-resilient algorithms, or algorithms designed for specific towards the methodology of wavefront shaping, such as using algorithms based on Hadamard patterns, or Fourier-based approaches :cite:`Mastiani2022`. Fast techniques that enable wavefront shaping in dynamic samples :cite:`Liu2017,Tzang2019`, and many potential applications have been developed and prototyped, including endoscopy :cite:`ploschner2015seeing`, optical trapping :cite:`Cizmar2010`, Raman scattering, :cite:`Thompson2016`, and deep-tissue imaging :cite:`Streich2021`. Applications extend beyond that of microscope imaging such as optimizing photoelectrochemical absorption :cite:`Liew2016` and tuning random lasers :cite:`Bachelard2014`.
 
-With the development of these advanced algorithms, however, the  complexity of WFS software is gradually becoming a bottleneck for further advancements in the field, as well as for end-user adoption. Code for controlling wavefront shaping tends to be complex and setup-specific, and developing this code typically requires detailed technical knowledge and low-level programming. Moreover, since many labs use their own in-house programs to control the experiments, sharing and re-using code between different research groups is troublesome.
+With the development of these advanced algorithms, however, the complexity of WFS software is steadily increasing as the field matures, which hinders cooperation as well as end-user adoption. Code for controlling wavefront shaping tends to be complex and setup-specific, and developing this code typically requires detailed technical knowledge and low-level programming. A recent c++ based contribution :cite:`Anderson2024`, highlights the growing need for software based tools that enable use and development. Moreover, since many labs use their own in-house programs to control the experiments, sharing and re-using code between different research groups is troublesome.
 
 What is OpenWFS?
 ----------------------
@@ -34,11 +38,13 @@ OpenWFS is a Python package for performing and for simulating wavefront shaping
     * **GenICam cameras**. The :class:`~.devices.Camera` object uses the `harvesters` backend :cite:`harvesters` to access any camera supporting the GenICam standard :cite:`genicam`.
     * **Automatic synchronization**. OpenWFS provides tools for automatic synchronization of actuators (e. g. an SLM) and detectors (e. g. a camera). The automatic synchronization makes it trivial to perform pipelined measurements that avoid the delay normally caused by the latency of the video card and SLM.
 
-* **Wavefront shaping algorithms**. A (growing) collection of wavefront shaping algorithms. OpenWFS abstracts the hardware control, synchronization, and signal processing so that the user can focus on the algorithm itself. As a result, most algorithms can be implemented in just a few lines of code without the need for low-level or hardware-specific programming.
+* **Wavefront shaping algorithms**. A (growing) collection of wavefront shaping algorithms. OpenWFS abstracts the hardware control, synchronization, and signal processing so that the user can focus on the algorithm itself. As a result, most algorithms can be implemented cleanly without hardware-specific programming.
 
 * **Simulation**. OpenWFS provides an extensive framework for testing and simulating wavefront shaping algorithms, including the effect of measurement noise, stage drift, and user-defined aberrations. This allows for rapid prototyping and testing of new algorithms, without the need for physical hardware.
 
-* **Platform for exchange and joint collaboration**. OpenWFS can be used as a platform for sharing and exchanging wavefront shaping algorithms. The package is designed to be modular and easy to expand, and it is our hope that the community will contribute to the package by adding new algorithms, hardware control modules, and simulation tools.
+* **Platform for exchange and joint collaboration**. OpenWFS can be used as a platform for sharing and exchanging wavefront shaping algorithms. The package is designed to be modular and easy to expand, and it is our hope that the community will contribute to the package by adding new algorithms, hardware control modules, and simulation tools. Python was specifically chosen for this purpose for its active community, high level of abstraction and the ease of sharing tools. Further expansion of the supported hardware is of high priority, especially wrapping c-based software support with tools like ctypes and the Micro-Manager based device adapters. 
+
+* **Platform for simplifying use of wavefront shaping**. OpenWFS is compatible with the recently developed PyDevice :cite:`PyDevice`, and can therefore be controlled from Micro-Manager :cite:`MMoverview`, a commonly used microscopy control platform. 
 
 * **Automated troubleshooting**. OpenWFS provides tools for automated troubleshooting of wavefront shaping experiments. This includes tools for measuring the performance of wavefront shaping algorithms, and for identifying common problems such as incorrect SLM calibration, drift, measurement noise, and other experimental imperfections.