From 2f851888742789af972aa27297ff96cb1bebc077 Mon Sep 17 00:00:00 2001
From: J-K <jakejohnrogers@gmail.com>
Date: Tue, 24 Sep 2024 16:46:02 +1000
Subject: [PATCH 01/10] Create fresnel_diffract.py

Code for wave diffraction in the Fresnel regime was missing from the algorithms list and has been added.
---
 physics/fresnel_diffract.py | 124 ++++++++++++++++++++++++++++++++++++
 1 file changed, 124 insertions(+)
 create mode 100644 physics/fresnel_diffract.py

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
new file mode 100644
index 000000000000..76f727e3e6a6
--- /dev/null
+++ b/physics/fresnel_diffract.py
@@ -0,0 +1,124 @@
+"""
+Title: Fresnel Diffraction for Coherent and Monochromatic
+        Wave Fields
+
+Fresnel Diffraction describes the behavior of a wave field as it 
+moves through free space or interacts with an object under the 
+small angle approximation. It is particularly useful for near 
+field diffraction.
+
+The following algorithm is an adaptation of the 'transfer function'
+based approach contained in the reference. It is critically 
+sampled when:
+pixel_size = wavelength * prop_dist / side_length
+
+Or equivalently:
+pixel_size = sqrt(wavelength * prop_dist / pixel_num)
+
+Under and oversampling occur when the left-hand side is less 
+than or greater than the right-hand side, respectively.
+
+This code is adapted and modified from:
+Computational Fourier Optics: A MATLAB Tutorial by David Voelz
+"""
+import numpy as np 
+from math import pi
+from scipy.fft import fft, fftshift, ifft, ifftshift, fft2, ifft2
+
+def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
+    """
+    Fresnel Diffraction of 1D or 2D Wave Fields.
+    
+    This function calculates the Fresnel diffraction of a 
+    given wave field, suitable for near field diffraction. The 
+    wave field is assumed to be coherent and monochromatic. 
+
+    Args:
+        wavefunc0 (np.ndarray): The initial wave field at the unpropagated plane.
+        pixel_size (float): The physical size of a pixel (or data point) at the unpropagated plane.
+        wavelength (float): The wavelength of the wave field.
+        prop_dist (float): The desired propagation distance.
+
+    Raises:
+        ValueError: If the input wave field is not 1D or 2D.
+
+    Returns:
+        np.ndarray: The wave field at the propagated plane. 
+    """
+    
+    if len(wavefunc0.shape) == 1:
+        return _fresnel_diffract_1D(
+            wavefunc0, pixel_size, wavelength, prop_dist)
+    elif len(wavefunc0.shape) == 2:
+        return _fresnel_diffract_2D(
+            wavefunc0, pixel_size, wavelength, prop_dist)
+    else:
+        raise ValueError(
+            f'Expected a 1D or 2D wavefield, but got {wavefunc0.shape}')  
+
+def _fresnel_diffract_2D(wavefunc0, pixel_size, wavelength, prop_dist):
+    """
+    Fresnel Diffraction of 2D Wave Fields.
+    
+    This private function is called by 'fresnel_diffract' to handle the 
+    fresnel diffraction of 2D wave fields specifically.
+
+    Args:
+        wavefunc0 (np.ndarray): The initial 2D wave field at the unpropagated plane.
+        pixel_size (float): The physical size of a pixel (or data point) at the unpropagated plane.
+        wavelength (float): The wavelength of the wave field.
+        prop_dist (float): The desired propagation distance.
+
+    Returns:
+        np.ndarray: The 2D wave field at the propagated plane. 
+    """
+    pixel_num, _ = wavefunc0.shape    
+    side_length = pixel_num * pixel_size    
+    
+    # Coordinates in Fourier space are proportionate to 1 / pixel_size 
+    f_x = np.arange(
+        -1 / (2 * pixel_size), 1 / ( 2 * pixel_size), 1 / side_length
+    )
+
+    F_X, F_Y = np.meshgrid(f_x, f_x)
+    
+    # Transfer function which models diffraction
+    transferf = np.exp(-1j*np.pi*wavelength*prop_dist*(F_X**2 + F_Y**2))
+    transferf = fftshift(transferf)
+
+    # Fourier space wave function at the unpropagated plane
+    f_wavefunc0 = fft2(fftshift(wavefunc0))
+    # Wave function at the propagated, or 'z' plane
+    wavefuncz = ifftshift(ifft2(transferf * f_wavefunc0))
+    
+    return wavefuncz
+
+def _fresnel_diffract_1D(wavefunc_0, pixel_size, wavelength, prop_dist):
+    """
+    Fresnel Diffraction of 1D Wave Fields.
+    
+    This private function is called by 'fresnel_diffract' to handle the 
+    fresnel diffraction of 1D wave fields specifically.
+
+    Args:
+        wavefunc0 (np.ndarray): The initial 1D wave field at the unpropagated plane.
+        pixel_size (float): The physical size of a pixel (or data point) at the unpropagated plane.
+        wavelength (float): The wavelength of the wave field.
+        prop_dist (float): The desired propagation distance.
+
+    Returns:
+        np.ndarray: The 1D wave field at the propagated plane. 
+    """
+    pixel_num = len(wavefunc_0)    
+    side_length = pixel_num * pixel_size    
+    fx = np.arange(
+        -1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length
+    )
+    transferf = np.exp(-1j * pi * wavelength * prop_dist * (fx**2))
+    transferf = fftshift(transferf)
+
+    f_wavefunc_0 = fft(fftshift(wavefunc_0))
+    
+    wavefunc_z = ifftshift(ifft(transferf * f_wavefunc_0))
+    
+    return wavefunc_z
\ No newline at end of file

From 490b0e66007d42d16650a35fbb5567ada7602a00 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 07:01:44 +0000
Subject: [PATCH 02/10] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 physics/fresnel_diffract.py | 81 ++++++++++++++++++-------------------
 1 file changed, 39 insertions(+), 42 deletions(-)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 76f727e3e6a6..f4d95573cfab 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -2,36 +2,38 @@
 Title: Fresnel Diffraction for Coherent and Monochromatic
         Wave Fields
 
-Fresnel Diffraction describes the behavior of a wave field as it 
-moves through free space or interacts with an object under the 
-small angle approximation. It is particularly useful for near 
+Fresnel Diffraction describes the behavior of a wave field as it
+moves through free space or interacts with an object under the
+small angle approximation. It is particularly useful for near
 field diffraction.
 
 The following algorithm is an adaptation of the 'transfer function'
-based approach contained in the reference. It is critically 
+based approach contained in the reference. It is critically
 sampled when:
 pixel_size = wavelength * prop_dist / side_length
 
 Or equivalently:
 pixel_size = sqrt(wavelength * prop_dist / pixel_num)
 
-Under and oversampling occur when the left-hand side is less 
+Under and oversampling occur when the left-hand side is less
 than or greater than the right-hand side, respectively.
 
 This code is adapted and modified from:
 Computational Fourier Optics: A MATLAB Tutorial by David Voelz
 """
-import numpy as np 
+
+import numpy as np
 from math import pi
 from scipy.fft import fft, fftshift, ifft, ifftshift, fft2, ifft2
 
+
 def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
     """
     Fresnel Diffraction of 1D or 2D Wave Fields.
-    
-    This function calculates the Fresnel diffraction of a 
-    given wave field, suitable for near field diffraction. The 
-    wave field is assumed to be coherent and monochromatic. 
+
+    This function calculates the Fresnel diffraction of a
+    given wave field, suitable for near field diffraction. The
+    wave field is assumed to be coherent and monochromatic.
 
     Args:
         wavefunc0 (np.ndarray): The initial wave field at the unpropagated plane.
@@ -43,24 +45,22 @@ def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
         ValueError: If the input wave field is not 1D or 2D.
 
     Returns:
-        np.ndarray: The wave field at the propagated plane. 
+        np.ndarray: The wave field at the propagated plane.
     """
-    
+
     if len(wavefunc0.shape) == 1:
-        return _fresnel_diffract_1D(
-            wavefunc0, pixel_size, wavelength, prop_dist)
+        return _fresnel_diffract_1D(wavefunc0, pixel_size, wavelength, prop_dist)
     elif len(wavefunc0.shape) == 2:
-        return _fresnel_diffract_2D(
-            wavefunc0, pixel_size, wavelength, prop_dist)
+        return _fresnel_diffract_2D(wavefunc0, pixel_size, wavelength, prop_dist)
     else:
-        raise ValueError(
-            f'Expected a 1D or 2D wavefield, but got {wavefunc0.shape}')  
+        raise ValueError(f"Expected a 1D or 2D wavefield, but got {wavefunc0.shape}")
+
 
 def _fresnel_diffract_2D(wavefunc0, pixel_size, wavelength, prop_dist):
     """
     Fresnel Diffraction of 2D Wave Fields.
-    
-    This private function is called by 'fresnel_diffract' to handle the 
+
+    This private function is called by 'fresnel_diffract' to handle the
     fresnel diffraction of 2D wave fields specifically.
 
     Args:
@@ -70,34 +70,33 @@ def _fresnel_diffract_2D(wavefunc0, pixel_size, wavelength, prop_dist):
         prop_dist (float): The desired propagation distance.
 
     Returns:
-        np.ndarray: The 2D wave field at the propagated plane. 
+        np.ndarray: The 2D wave field at the propagated plane.
     """
-    pixel_num, _ = wavefunc0.shape    
-    side_length = pixel_num * pixel_size    
-    
-    # Coordinates in Fourier space are proportionate to 1 / pixel_size 
-    f_x = np.arange(
-        -1 / (2 * pixel_size), 1 / ( 2 * pixel_size), 1 / side_length
-    )
+    pixel_num, _ = wavefunc0.shape
+    side_length = pixel_num * pixel_size
+
+    # Coordinates in Fourier space are proportionate to 1 / pixel_size
+    f_x = np.arange(-1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length)
 
     F_X, F_Y = np.meshgrid(f_x, f_x)
-    
+
     # Transfer function which models diffraction
-    transferf = np.exp(-1j*np.pi*wavelength*prop_dist*(F_X**2 + F_Y**2))
+    transferf = np.exp(-1j * np.pi * wavelength * prop_dist * (F_X**2 + F_Y**2))
     transferf = fftshift(transferf)
 
     # Fourier space wave function at the unpropagated plane
     f_wavefunc0 = fft2(fftshift(wavefunc0))
     # Wave function at the propagated, or 'z' plane
     wavefuncz = ifftshift(ifft2(transferf * f_wavefunc0))
-    
+
     return wavefuncz
 
+
 def _fresnel_diffract_1D(wavefunc_0, pixel_size, wavelength, prop_dist):
     """
     Fresnel Diffraction of 1D Wave Fields.
-    
-    This private function is called by 'fresnel_diffract' to handle the 
+
+    This private function is called by 'fresnel_diffract' to handle the
     fresnel diffraction of 1D wave fields specifically.
 
     Args:
@@ -107,18 +106,16 @@ def _fresnel_diffract_1D(wavefunc_0, pixel_size, wavelength, prop_dist):
         prop_dist (float): The desired propagation distance.
 
     Returns:
-        np.ndarray: The 1D wave field at the propagated plane. 
+        np.ndarray: The 1D wave field at the propagated plane.
     """
-    pixel_num = len(wavefunc_0)    
-    side_length = pixel_num * pixel_size    
-    fx = np.arange(
-        -1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length
-    )
+    pixel_num = len(wavefunc_0)
+    side_length = pixel_num * pixel_size
+    fx = np.arange(-1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length)
     transferf = np.exp(-1j * pi * wavelength * prop_dist * (fx**2))
     transferf = fftshift(transferf)
 
     f_wavefunc_0 = fft(fftshift(wavefunc_0))
-    
+
     wavefunc_z = ifftshift(ifft(transferf * f_wavefunc_0))
-    
-    return wavefunc_z
\ No newline at end of file
+
+    return wavefunc_z

From 00b567d3afd8024668dd6a9c04d3b6caf05792c3 Mon Sep 17 00:00:00 2001
From: J-K <jakejohnrogers@gmail.com>
Date: Tue, 24 Sep 2024 17:16:14 +1000
Subject: [PATCH 03/10] Altered Styling for Ruff

---
 physics/fresnel_diffract.py | 54 ++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 24 deletions(-)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 76f727e3e6a6..1ddf37c12436 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -21,9 +21,11 @@
 This code is adapted and modified from:
 Computational Fourier Optics: A MATLAB Tutorial by David Voelz
 """
-import numpy as np 
 from math import pi
-from scipy.fft import fft, fftshift, ifft, ifftshift, fft2, ifft2
+
+import numpy as np
+from scipy.fft import fft, fft2, fftshift, ifft, ifft2, ifftshift
+
 
 def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
     """
@@ -35,7 +37,8 @@ def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
 
     Args:
         wavefunc0 (np.ndarray): The initial wave field at the unpropagated plane.
-        pixel_size (float): The physical size of a pixel (or data point) at the unpropagated plane.
+        pixel_size (float): The physical size of a pixel (or data point) at the 
+        unpropagated plane.
         wavelength (float): The wavelength of the wave field.
         prop_dist (float): The desired propagation distance.
 
@@ -45,18 +48,19 @@ def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
     Returns:
         np.ndarray: The wave field at the propagated plane. 
     """
-    
+
     if len(wavefunc0.shape) == 1:
-        return _fresnel_diffract_1D(
+        return _fresnel_diffract_1d(
             wavefunc0, pixel_size, wavelength, prop_dist)
     elif len(wavefunc0.shape) == 2:
-        return _fresnel_diffract_2D(
+        return _fresnel_diffract_2d(
             wavefunc0, pixel_size, wavelength, prop_dist)
     else:
+        err_shape = wavefunc0.shape
         raise ValueError(
-            f'Expected a 1D or 2D wavefield, but got {wavefunc0.shape}')  
+            f'Expected a 1D or 2D wavefield, but got {err_shape}')
 
-def _fresnel_diffract_2D(wavefunc0, pixel_size, wavelength, prop_dist):
+def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
     """
     Fresnel Diffraction of 2D Wave Fields.
     
@@ -65,35 +69,36 @@ def _fresnel_diffract_2D(wavefunc0, pixel_size, wavelength, prop_dist):
 
     Args:
         wavefunc0 (np.ndarray): The initial 2D wave field at the unpropagated plane.
-        pixel_size (float): The physical size of a pixel (or data point) at the unpropagated plane.
+        pixel_size (float): The physical size of a pixel (or data point) at the 
+        unpropagated plane.
         wavelength (float): The wavelength of the wave field.
         prop_dist (float): The desired propagation distance.
 
     Returns:
         np.ndarray: The 2D wave field at the propagated plane. 
     """
-    pixel_num, _ = wavefunc0.shape    
-    side_length = pixel_num * pixel_size    
-    
-    # Coordinates in Fourier space are proportionate to 1 / pixel_size 
+    pixel_num, _ = wavefunc0.shape
+    side_length = pixel_num * pixel_size
+
+    # Coordinates in Fourier space are proportionate to 1 / pixel_size
     f_x = np.arange(
         -1 / (2 * pixel_size), 1 / ( 2 * pixel_size), 1 / side_length
     )
 
-    F_X, F_Y = np.meshgrid(f_x, f_x)
-    
+    f_x2d, f_y2d = np.meshgrid(f_x, f_x)
+
     # Transfer function which models diffraction
-    transferf = np.exp(-1j*np.pi*wavelength*prop_dist*(F_X**2 + F_Y**2))
+    transferf = np.exp(-1j*np.pi*wavelength*prop_dist*(f_x2d**2 + f_y2d**2))
     transferf = fftshift(transferf)
 
     # Fourier space wave function at the unpropagated plane
     f_wavefunc0 = fft2(fftshift(wavefunc0))
     # Wave function at the propagated, or 'z' plane
     wavefuncz = ifftshift(ifft2(transferf * f_wavefunc0))
-    
+
     return wavefuncz
 
-def _fresnel_diffract_1D(wavefunc_0, pixel_size, wavelength, prop_dist):
+def _fresnel_diffract_1d(wavefunc_0, pixel_size, wavelength, prop_dist):
     """
     Fresnel Diffraction of 1D Wave Fields.
     
@@ -102,15 +107,16 @@ def _fresnel_diffract_1D(wavefunc_0, pixel_size, wavelength, prop_dist):
 
     Args:
         wavefunc0 (np.ndarray): The initial 1D wave field at the unpropagated plane.
-        pixel_size (float): The physical size of a pixel (or data point) at the unpropagated plane.
+        pixel_size (float): The physical size of a pixel (or data point) at the 
+        unpropagated plane.
         wavelength (float): The wavelength of the wave field.
         prop_dist (float): The desired propagation distance.
 
     Returns:
         np.ndarray: The 1D wave field at the propagated plane. 
     """
-    pixel_num = len(wavefunc_0)    
-    side_length = pixel_num * pixel_size    
+    pixel_num = len(wavefunc_0)
+    side_length = pixel_num * pixel_size
     fx = np.arange(
         -1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length
     )
@@ -118,7 +124,7 @@ def _fresnel_diffract_1D(wavefunc_0, pixel_size, wavelength, prop_dist):
     transferf = fftshift(transferf)
 
     f_wavefunc_0 = fft(fftshift(wavefunc_0))
-    
+
     wavefunc_z = ifftshift(ifft(transferf * f_wavefunc_0))
-    
-    return wavefunc_z
\ No newline at end of file
+
+    return wavefunc_z

From 9ea5697c635e8cd872d77c6df7503616ec13919f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 07:17:58 +0000
Subject: [PATCH 04/10] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 physics/fresnel_diffract.py | 29 ++++++++++++-----------------
 1 file changed, 12 insertions(+), 17 deletions(-)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 647b5ea69265..9e49e9c472ac 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -21,13 +21,13 @@
 This code is adapted and modified from:
 Computational Fourier Optics: A MATLAB Tutorial by David Voelz
 """
+
 from math import pi
 
 import numpy as np
 from scipy.fft import fft, fft2, fftshift, ifft, ifft2, ifftshift
 
 
-
 def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
     """
     Fresnel Diffraction of 1D or 2D Wave Fields.
@@ -38,7 +38,7 @@ def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
 
     Args:
         wavefunc0 (np.ndarray): The initial wave field at the unpropagated plane.
-        pixel_size (float): The physical size of a pixel (or data point) at the 
+        pixel_size (float): The physical size of a pixel (or data point) at the
         unpropagated plane.
         wavelength (float): The wavelength of the wave field.
         prop_dist (float): The desired propagation distance.
@@ -51,15 +51,13 @@ def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
     """
 
     if len(wavefunc0.shape) == 1:
-        return _fresnel_diffract_1d(
-            wavefunc0, pixel_size, wavelength, prop_dist)
+        return _fresnel_diffract_1d(wavefunc0, pixel_size, wavelength, prop_dist)
     elif len(wavefunc0.shape) == 2:
-        return _fresnel_diffract_2d(
-            wavefunc0, pixel_size, wavelength, prop_dist)
+        return _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist)
     else:
         err_shape = wavefunc0.shape
-        raise ValueError(
-            f'Expected a 1D or 2D wavefield, but got {err_shape}')
+        raise ValueError(f"Expected a 1D or 2D wavefield, but got {err_shape}")
+
 
 def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
     """
@@ -70,7 +68,7 @@ def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
 
     Args:
         wavefunc0 (np.ndarray): The initial 2D wave field at the unpropagated plane.
-        pixel_size (float): The physical size of a pixel (or data point) at the 
+        pixel_size (float): The physical size of a pixel (or data point) at the
         unpropagated plane.
         wavelength (float): The wavelength of the wave field.
         prop_dist (float): The desired propagation distance.
@@ -82,14 +80,12 @@ def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
     side_length = pixel_num * pixel_size
 
     # Coordinates in Fourier space are proportionate to 1 / pixel_size
-    f_x = np.arange(
-        -1 / (2 * pixel_size), 1 / ( 2 * pixel_size), 1 / side_length
-    )
+    f_x = np.arange(-1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length)
 
     f_x2d, f_y2d = np.meshgrid(f_x, f_x)
 
     # Transfer function which models diffraction
-    transferf = np.exp(-1j*np.pi*wavelength*prop_dist*(f_x2d**2 + f_y2d**2))
+    transferf = np.exp(-1j * np.pi * wavelength * prop_dist * (f_x2d**2 + f_y2d**2))
     transferf = fftshift(transferf)
 
     # Fourier space wave function at the unpropagated plane
@@ -99,6 +95,7 @@ def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
 
     return wavefuncz
 
+
 def _fresnel_diffract_1d(wavefunc_0, pixel_size, wavelength, prop_dist):
     """
     Fresnel Diffraction of 1D Wave Fields.
@@ -108,7 +105,7 @@ def _fresnel_diffract_1d(wavefunc_0, pixel_size, wavelength, prop_dist):
 
     Args:
         wavefunc0 (np.ndarray): The initial 1D wave field at the unpropagated plane.
-        pixel_size (float): The physical size of a pixel (or data point) at the 
+        pixel_size (float): The physical size of a pixel (or data point) at the
         unpropagated plane.
         wavelength (float): The wavelength of the wave field.
         prop_dist (float): The desired propagation distance.
@@ -118,9 +115,7 @@ def _fresnel_diffract_1d(wavefunc_0, pixel_size, wavelength, prop_dist):
     """
     pixel_num = len(wavefunc_0)
     side_length = pixel_num * pixel_size
-    fx = np.arange(
-        -1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length
-    )
+    fx = np.arange(-1 / (2 * pixel_size), 1 / (2 * pixel_size), 1 / side_length)
     transferf = np.exp(-1j * pi * wavelength * prop_dist * (fx**2))
     transferf = fftshift(transferf)
 

From ba577dfc3ff78d794810a044be56d024ac8d17a4 Mon Sep 17 00:00:00 2001
From: J-K <jakejohnrogers@gmail.com>
Date: Tue, 24 Sep 2024 18:56:21 +1000
Subject: [PATCH 05/10] Adjusted styling for ruff

---
 physics/fresnel_diffract.py | 48 ++++++++++++++++++++++++-------------
 1 file changed, 32 insertions(+), 16 deletions(-)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 9e49e9c472ac..76f747920a4b 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -28,7 +28,12 @@
 from scipy.fft import fft, fft2, fftshift, ifft, ifft2, ifftshift
 
 
-def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
+def fresnel_diffract(
+    wavefunc_0: np.ndarray,
+    pixel_size: float,
+    wavelength: float,
+    prop_dist: float
+    ) -> np.ndarray:
     """
     Fresnel Diffraction of 1D or 2D Wave Fields.
 
@@ -39,6 +44,7 @@ def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
     Args:
         wavefunc0 (np.ndarray): The initial wave field at the unpropagated plane.
         pixel_size (float): The physical size of a pixel (or data point) at the
+        pixel_size (float): The physical size of a pixel (or data point) at the
         unpropagated plane.
         wavelength (float): The wavelength of the wave field.
         prop_dist (float): The desired propagation distance.
@@ -50,16 +56,22 @@ def fresnel_diffract(wavefunc0, pixel_size, wavelength, prop_dist):
         np.ndarray: The wave field at the propagated plane.
     """
 
-    if len(wavefunc0.shape) == 1:
-        return _fresnel_diffract_1d(wavefunc0, pixel_size, wavelength, prop_dist)
-    elif len(wavefunc0.shape) == 2:
-        return _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist)
+    if len(wavefunc_0.shape) == 1:
+        return _fresnel_diffract_1d(
+            wavefunc_0, pixel_size, wavelength, prop_dist)
+    elif len(wavefunc_0.shape) == 2:
+        return _fresnel_diffract_2d(
+            wavefunc_0, pixel_size, wavelength, prop_dist)
     else:
-        err_shape = wavefunc0.shape
-        raise ValueError(f"Expected a 1D or 2D wavefield, but got {err_shape}")
-
-
-def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
+        error_message = f"Expected a 1D or 2D wavefield, but got {wavefunc_0.shape}"
+        raise ValueError(error_message)
+
+def _fresnel_diffract_2d(
+    wavefunc_0: np.ndarray,
+    pixel_size: float,
+    wavelength: float,
+    prop_dist: float
+    ) -> np.ndarray:
     """
     Fresnel Diffraction of 2D Wave Fields.
 
@@ -67,7 +79,7 @@ def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
     fresnel diffraction of 2D wave fields specifically.
 
     Args:
-        wavefunc0 (np.ndarray): The initial 2D wave field at the unpropagated plane.
+        wavefunc_0 (np.ndarray): The initial 2D wave field at the unpropagated plane.
         pixel_size (float): The physical size of a pixel (or data point) at the
         unpropagated plane.
         wavelength (float): The wavelength of the wave field.
@@ -76,7 +88,7 @@ def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
     Returns:
         np.ndarray: The 2D wave field at the propagated plane.
     """
-    pixel_num, _ = wavefunc0.shape
+    pixel_num, _ = wavefunc_0.shape
     side_length = pixel_num * pixel_size
 
     # Coordinates in Fourier space are proportionate to 1 / pixel_size
@@ -89,14 +101,18 @@ def _fresnel_diffract_2d(wavefunc0, pixel_size, wavelength, prop_dist):
     transferf = fftshift(transferf)
 
     # Fourier space wave function at the unpropagated plane
-    f_wavefunc0 = fft2(fftshift(wavefunc0))
+    f_wavefunc_0 = fft2(fftshift(wavefunc_0))
     # Wave function at the propagated, or 'z' plane
-    wavefuncz = ifftshift(ifft2(transferf * f_wavefunc0))
+    wavefuncz = ifftshift(ifft2(transferf * f_wavefunc_0))
 
     return wavefuncz
 
-
-def _fresnel_diffract_1d(wavefunc_0, pixel_size, wavelength, prop_dist):
+def _fresnel_diffract_1d(
+    wavefunc_0: np.ndarray,
+    pixel_size: float,
+    wavelength: float,
+    prop_dist: float
+    ) -> np.ndarray:
     """
     Fresnel Diffraction of 1D Wave Fields.
 

From 40e5f1e9b155971bf4e1b7486a83ffaf5b1e82c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 08:57:48 +0000
Subject: [PATCH 06/10] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 physics/fresnel_diffract.py | 29 ++++++++++-------------------
 1 file changed, 10 insertions(+), 19 deletions(-)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 76f747920a4b..9c53b62db742 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -29,11 +29,8 @@
 
 
 def fresnel_diffract(
-    wavefunc_0: np.ndarray,
-    pixel_size: float,
-    wavelength: float,
-    prop_dist: float
-    ) -> np.ndarray:
+    wavefunc_0: np.ndarray, pixel_size: float, wavelength: float, prop_dist: float
+) -> np.ndarray:
     """
     Fresnel Diffraction of 1D or 2D Wave Fields.
 
@@ -57,21 +54,17 @@ def fresnel_diffract(
     """
 
     if len(wavefunc_0.shape) == 1:
-        return _fresnel_diffract_1d(
-            wavefunc_0, pixel_size, wavelength, prop_dist)
+        return _fresnel_diffract_1d(wavefunc_0, pixel_size, wavelength, prop_dist)
     elif len(wavefunc_0.shape) == 2:
-        return _fresnel_diffract_2d(
-            wavefunc_0, pixel_size, wavelength, prop_dist)
+        return _fresnel_diffract_2d(wavefunc_0, pixel_size, wavelength, prop_dist)
     else:
         error_message = f"Expected a 1D or 2D wavefield, but got {wavefunc_0.shape}"
         raise ValueError(error_message)
 
+
 def _fresnel_diffract_2d(
-    wavefunc_0: np.ndarray,
-    pixel_size: float,
-    wavelength: float,
-    prop_dist: float
-    ) -> np.ndarray:
+    wavefunc_0: np.ndarray, pixel_size: float, wavelength: float, prop_dist: float
+) -> np.ndarray:
     """
     Fresnel Diffraction of 2D Wave Fields.
 
@@ -107,12 +100,10 @@ def _fresnel_diffract_2d(
 
     return wavefuncz
 
+
 def _fresnel_diffract_1d(
-    wavefunc_0: np.ndarray,
-    pixel_size: float,
-    wavelength: float,
-    prop_dist: float
-    ) -> np.ndarray:
+    wavefunc_0: np.ndarray, pixel_size: float, wavelength: float, prop_dist: float
+) -> np.ndarray:
     """
     Fresnel Diffraction of 1D Wave Fields.
 

From aa9aeaa82e6879d80423d7b30737266646a5d032 Mon Sep 17 00:00:00 2001
From: J-K <jakejohnrogers@gmail.com>
Date: Thu, 26 Sep 2024 14:39:40 +1000
Subject: [PATCH 07/10] Included Tests

Tests covering dimensionality, error checking, conservation of energy, and zero propagation distance, have all been included.
---
 physics/fresnel_diffract.py | 80 +++++++++++++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 9c53b62db742..7390f33a972d 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -51,6 +51,44 @@ def fresnel_diffract(
 
     Returns:
         np.ndarray: The wave field at the propagated plane.
+        
+    Examples：
+        >>> import numpy as np
+        >>> res = fresnel_diffract(np.ones(64), 1, 1, 1)
+        >>> res.shape
+        (64,)
+        
+        >>> import numpy as np
+        >>> res = fresnel_diffract(np.ones((64, 64)), 1, 1, 1)
+        >>> res.shape
+        (64, 64)
+        
+        >>> import numpy as np
+        >>> res = fresnel_diffract(np.ones((4, 4, 4)), 1, 1, 1)
+        Traceback (most recent call last):
+            ...
+        ValueError: Expected a 1D or 2D wavefield, but got (4, 4, 4)
+        
+        # Test that conservation of energy is obeyed
+        >>> import numpy as np
+        >>> wf0 = np.ones(64)
+        >>> wfz = fresnel_diffract(wf0, 1, 1, 1)
+        >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
+        True
+        
+        >>> import numpy as np
+        >>> wf0 = np.ones((64, 64))
+        >>> wfz = fresnel_diffract(wf0, 1, 1, 1)
+        >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
+        True
+        
+        # Test that propagation distance of 0 returns the contact image
+        >>> import numpy as np
+        >>> x = np.linspace(-32, 32, 1)
+        >>> wf0 = np.where(abs(x)<=8, 1, 0)
+        >>> wfz = fresnel_diffract(wf0, 1, 1, 0)
+        >>> np.allclose(wf0, wfz)
+        True
     """
 
     if len(wavefunc_0.shape) == 1:
@@ -80,6 +118,27 @@ def _fresnel_diffract_2d(
 
     Returns:
         np.ndarray: The 2D wave field at the propagated plane.
+        
+    Examples:
+        >>> import numpy as np
+        >>> res = _fresnel_diffract_2d(np.ones((64, 64)), 1, 1, 1)
+        >>> res.shape
+        (64, 64)
+        
+        >>> import numpy as np
+        >>> wf0 = np.ones((64, 64))
+        >>> wfz = _fresnel_diffract_2d(wf0, 1, 1, 1)
+        >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
+        True
+        
+        # Test that propagation distance of 0 returns the contact image
+        >>> import numpy as np
+        >>> x = np.linspace(-32, 32, 1)
+        >>> X1, X2 = np.meshgrid(x, x)
+        >>> wf0 = np.where(abs(X1)<=8, 1, 0) * np.where(abs(X2)<=8, 1, 0)
+        >>> wfz = _fresnel_diffract_2d(wf0, 1, 1, 0)
+        >>> np.allclose(wf0, wfz)
+        True
     """
     pixel_num, _ = wavefunc_0.shape
     side_length = pixel_num * pixel_size
@@ -119,6 +178,27 @@ def _fresnel_diffract_1d(
 
     Returns:
         np.ndarray: The 1D wave field at the propagated plane.
+    
+    Examples:
+        >>> import numpy as np
+        >>> res = _fresnel_diffract_1d(np.ones(64), 1, 1, 1)
+        >>> res.shape
+        (64,)
+        
+        # Conservation of energy
+        >>> import numpy as np
+        >>> wf0 = np.ones(64)
+        >>> wfz = _fresnel_diffract_1d(wf0, 1, 1, 1)
+        >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
+        True
+        
+        # Test that propagation distance of 0 returns the contact image
+        >>> import numpy as np
+        >>> x = np.linspace(-32, 32, 1)
+        >>> wf0 = np.where(abs(x)<=8, 1, 0)
+        >>> wfz = _fresnel_diffract_1d(wf0, 1, 1, 0)
+        >>> np.allclose(wf0, wfz)
+        True
     """
     pixel_num = len(wavefunc_0)
     side_length = pixel_num * pixel_size

From c3a2a3f729ef6664486f41fa963f8600d9ec1f1c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 26 Sep 2024 04:40:12 +0000
Subject: [PATCH 08/10] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 physics/fresnel_diffract.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 7390f33a972d..999044bf8e15 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -51,37 +51,37 @@ def fresnel_diffract(
 
     Returns:
         np.ndarray: The wave field at the propagated plane.
-        
+
     Examples：
         >>> import numpy as np
         >>> res = fresnel_diffract(np.ones(64), 1, 1, 1)
         >>> res.shape
         (64,)
-        
+
         >>> import numpy as np
         >>> res = fresnel_diffract(np.ones((64, 64)), 1, 1, 1)
         >>> res.shape
         (64, 64)
-        
+
         >>> import numpy as np
         >>> res = fresnel_diffract(np.ones((4, 4, 4)), 1, 1, 1)
         Traceback (most recent call last):
             ...
         ValueError: Expected a 1D or 2D wavefield, but got (4, 4, 4)
-        
+
         # Test that conservation of energy is obeyed
         >>> import numpy as np
         >>> wf0 = np.ones(64)
         >>> wfz = fresnel_diffract(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
+
         >>> import numpy as np
         >>> wf0 = np.ones((64, 64))
         >>> wfz = fresnel_diffract(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
+
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)
@@ -118,19 +118,19 @@ def _fresnel_diffract_2d(
 
     Returns:
         np.ndarray: The 2D wave field at the propagated plane.
-        
+
     Examples:
         >>> import numpy as np
         >>> res = _fresnel_diffract_2d(np.ones((64, 64)), 1, 1, 1)
         >>> res.shape
         (64, 64)
-        
+
         >>> import numpy as np
         >>> wf0 = np.ones((64, 64))
         >>> wfz = _fresnel_diffract_2d(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
+
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)
@@ -178,20 +178,20 @@ def _fresnel_diffract_1d(
 
     Returns:
         np.ndarray: The 1D wave field at the propagated plane.
-    
+
     Examples:
         >>> import numpy as np
         >>> res = _fresnel_diffract_1d(np.ones(64), 1, 1, 1)
         >>> res.shape
         (64,)
-        
+
         # Conservation of energy
         >>> import numpy as np
         >>> wf0 = np.ones(64)
         >>> wfz = _fresnel_diffract_1d(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
+
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)

From e2751c48c9eac321307869dc81192c061eea37d1 Mon Sep 17 00:00:00 2001
From: J-K <jakejohnrogers@gmail.com>
Date: Thu, 26 Sep 2024 14:43:54 +1000
Subject: [PATCH 09/10] Updated styling for ruff

---
 physics/fresnel_diffract.py | 21 ++++-----------------
 1 file changed, 4 insertions(+), 17 deletions(-)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 7390f33a972d..4f0e8b2da39c 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -51,37 +51,32 @@ def fresnel_diffract(
 
     Returns:
         np.ndarray: The wave field at the propagated plane.
-        
-    Examples：
+
+    Examples:
         >>> import numpy as np
         >>> res = fresnel_diffract(np.ones(64), 1, 1, 1)
         >>> res.shape
         (64,)
-        
         >>> import numpy as np
         >>> res = fresnel_diffract(np.ones((64, 64)), 1, 1, 1)
         >>> res.shape
         (64, 64)
-        
         >>> import numpy as np
         >>> res = fresnel_diffract(np.ones((4, 4, 4)), 1, 1, 1)
         Traceback (most recent call last):
             ...
         ValueError: Expected a 1D or 2D wavefield, but got (4, 4, 4)
-        
         # Test that conservation of energy is obeyed
         >>> import numpy as np
         >>> wf0 = np.ones(64)
         >>> wfz = fresnel_diffract(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
         >>> import numpy as np
         >>> wf0 = np.ones((64, 64))
         >>> wfz = fresnel_diffract(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)
@@ -105,10 +100,8 @@ def _fresnel_diffract_2d(
 ) -> np.ndarray:
     """
     Fresnel Diffraction of 2D Wave Fields.
-
     This private function is called by 'fresnel_diffract' to handle the
     fresnel diffraction of 2D wave fields specifically.
-
     Args:
         wavefunc_0 (np.ndarray): The initial 2D wave field at the unpropagated plane.
         pixel_size (float): The physical size of a pixel (or data point) at the
@@ -118,19 +111,17 @@ def _fresnel_diffract_2d(
 
     Returns:
         np.ndarray: The 2D wave field at the propagated plane.
-        
+
     Examples:
         >>> import numpy as np
         >>> res = _fresnel_diffract_2d(np.ones((64, 64)), 1, 1, 1)
         >>> res.shape
         (64, 64)
-        
         >>> import numpy as np
         >>> wf0 = np.ones((64, 64))
         >>> wfz = _fresnel_diffract_2d(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)
@@ -165,10 +156,8 @@ def _fresnel_diffract_1d(
 ) -> np.ndarray:
     """
     Fresnel Diffraction of 1D Wave Fields.
-
     This private function is called by 'fresnel_diffract' to handle the
     fresnel diffraction of 1D wave fields specifically.
-
     Args:
         wavefunc0 (np.ndarray): The initial 1D wave field at the unpropagated plane.
         pixel_size (float): The physical size of a pixel (or data point) at the
@@ -178,20 +167,18 @@ def _fresnel_diffract_1d(
 
     Returns:
         np.ndarray: The 1D wave field at the propagated plane.
-    
+
     Examples:
         >>> import numpy as np
         >>> res = _fresnel_diffract_1d(np.ones(64), 1, 1, 1)
         >>> res.shape
         (64,)
-        
         # Conservation of energy
         >>> import numpy as np
         >>> wf0 = np.ones(64)
         >>> wfz = _fresnel_diffract_1d(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
-        
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)

From 28d717fc7ba5e55dc20f4ccb77adafcdea0ae77e Mon Sep 17 00:00:00 2001
From: J-K <jakejohnrogers@gmail.com>
Date: Thu, 26 Sep 2024 14:56:21 +1000
Subject: [PATCH 10/10] Updated Tests

---
 physics/fresnel_diffract.py | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/physics/fresnel_diffract.py b/physics/fresnel_diffract.py
index 0ffb30a72916..8bcf7231a91e 100644
--- a/physics/fresnel_diffract.py
+++ b/physics/fresnel_diffract.py
@@ -66,6 +66,7 @@ def fresnel_diffract(
         Traceback (most recent call last):
             ...
         ValueError: Expected a 1D or 2D wavefield, but got (4, 4, 4)
+
         # Test that conservation of energy is obeyed
         >>> import numpy as np
         >>> wf0 = np.ones(64)
@@ -77,6 +78,7 @@ def fresnel_diffract(
         >>> wfz = fresnel_diffract(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
+
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)
@@ -123,6 +125,7 @@ def _fresnel_diffract_2d(
         >>> wfz = _fresnel_diffract_2d(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
+
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)
@@ -175,12 +178,14 @@ def _fresnel_diffract_1d(
         >>> res = _fresnel_diffract_1d(np.ones(64), 1, 1, 1)
         >>> res.shape
         (64,)
+
         # Conservation of energy
         >>> import numpy as np
         >>> wf0 = np.ones(64)
         >>> wfz = _fresnel_diffract_1d(wf0, 1, 1, 1)
         >>> np.isclose(np.sum(abs(wf0)**2), np.sum(abs(wfz)**2))
         True
+
         # Test that propagation distance of 0 returns the contact image
         >>> import numpy as np
         >>> x = np.linspace(-32, 32, 1)