Merge remote-tracking branch 'origin/master' into further-revisions

.github/workflows/pytest.yml

@@ -1,7 +1,7 @@
 name: PyTest
 
 on:
-# [workflow_call, push, pull_request]
+  [workflow_call, push, pull_request]
 
 jobs:
   build:

STYLEGUIDE.md

@@ -6,8 +6,18 @@
 
 # General
 
-- 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. 
+- 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
 
-- Tests must *not* plot figures.
+- Tests must *not* plot figures.
+
+# Sphinx
+
+Common warnings:
+
+- All line numbers are relative to the start of the docstring.
+- 'WARNING: Block quote ends without a blank line; unexpected unindent'. This happens if a block of text is not properly
+  wrapped and one of the lines starts with a space. To fox, remove the space at the beginning of the line.
+- 'ERROR: Unexpected indentation' can be caused if a line ends with ':' and the next line is not indented or empty.

docs/source/references.bib

@@ -525,11 +525,6 @@ @article{Park2012
 }
 
 
-@misc{pydevice,
-    title = {{PyDevice} {GitHub} repository},
-    url = {https://www.github.com/IvoVellekoop/pydevice},
-}
-
 @article{Pinkard2021,
     author = {Henry Pinkard and Nico Stuurman and Ivan E Ivanov and Nicholas M Anthony and Wei Ouyang and Bin Li and Bin Yang and Mark A Tsuchida and Bryant Chhun and Grace Zhang and Ryan Mei and Michael Anderson and Douglas P Shepherd and Ian Hunt-Isaak and Raymond L Dunn and Wiebke Jahr and Saul Kato and Loïc A Royer and Jay R Thiagarajah and Kevin W Eliceiri and Emma Lundberg and Shalin B Mehta and Laura Waller},
     journal = {Nature Methods},

examples/micro_manager_microscope.py

@@ -1,5 +1,5 @@
 """ Micro-Manager simulated microscope
-=======================
+======================================================================
 This script simulates a microscope with a random noise image as a mock specimen.
 The numerical aperture, stage position, and other parameters can be modified through the Micro-Manager GUI.
 To use this script as a device in Micro-Manager, make sure you have the PyDevice adapter installed and

examples/micro_manager_scanning_microscope.py

@@ -1,17 +1,17 @@
 """ Micro-Manager simulated scanning microscope
-=======================
+======================================================================
 This script simulates a scanning microscope with a pre-set image as a mock specimen.
 The scan parameters can be modified through the Micro-Manager GUI.
 To use this script as a device in Micro-Manager, make sure you have the PyDevice adapter installed and
 select this script in the hardware configuration wizard for the PyDevice component.
 """
 
 import astropy.units as u
+import skimage
 
 # add 'openwfs' to the search path. This is only needed when developing openwfs
 # otherwise it is just installed as a package
 import set_path  # noqa
-import skimage
 from openwfs.devices import ScanningMicroscope, Axis
 from openwfs.devices.galvo_scanner import InputChannel
 

openwfs/algorithms/basic_fourier.py

@@ -9,14 +9,14 @@
 
 
 class FourierDualReference(DualReference):
-    """
-    Fourier double reference algorithm, based on Mastiani et al. [1].
+    """Fourier double reference algorithm, based on Mastiani et al. [1].
 
     Improvements over [1]:
-    * The set of plane waves is taken from a disk in k-space instead of a square.
-    * No overlap between the two halves is needed, instead the final stitching step is done using measurements already in the data set.
-    * When only a single target is optimized, the algorithm can be used in an iterative version to increase SNR during the measurument,
-       similar to [2].
+
+    - The set of plane waves is taken from a disk in k-space instead of a square.
+    - No overlap between the two halves is needed, instead the final stitching step is done using measurements already in the data set.
+    - When only a single target is optimized, the algorithm can be used in an iterative version to increase SNR during the measurument,
+      similar to [2].
 
     [1]: Bahareh Mastiani, Gerwin Osnabrugge, and Ivo M. Vellekoop,
     "Wavefront shaping for forward scattering," Opt. Express 30, 37436-37445 (2022)