Adding more introductory tutorials

LouisDesdoigts · Sep 23, 2023 · 82968a5 · 82968a5
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diff --git a/docs/API/core/optical_systems.md b/docs/API/core/optical_systems.md
@@ -1,5 +1,8 @@
 # Optical Systems
 
+???+ info "OpticalSystem"
+    ::: dLux.optical_systems.OpticalSystem
+
 ???+ info "AngularOpticalSystem"
     ::: dLux.optical_systems.AngularOpticalSystem
 

diff --git a/docs/API/layers/aberrations.md b/docs/API/layers/aberrations.md
@@ -5,66 +5,3 @@
 
 ???+ info "ZernikeBasis"
     ::: dLux.layers.aberrations.ZernikeBasis
-
-<!-- # Aberrations: aberrations.py
-
-This module contains the classes that define the behaviour of Aberration Layers in dLux.
-
-There are two public classes:
-
-- `Zernike`
-- `ZernikeBasis`
-
-These classes are designed to generate Zernike polynomials dynamically. Typically, users should not need to interact with these classes directly, but rather through the `Aperture` classes.
-
-The Zernike class hold a single Zernike polynomial. It has one main method, `.calculate(coordinates, nsides)` that takes in a set of coordinates and calculates the Zernike polynomial on those coordinates.
-
-The ZernikeBasis class holds a set of Zernike polynomials. It has one main method, `.calculate_basis(coordinates, nsides)` that takes in a set of coordinates and calculates the Zernike polynomial basis on those coordinates.
-
-??? info "Zernike Basis API"
-    :::dLux.aberrations.ZernikeBasis
-
-??? info "Zernike API"
-    :::dLux.aberrations.Zernike
-
-Let's construct a Zernike Basis:
-
-```python
-import dLux as dl
-import jax.numpy as np
-
-zernike_basis = dl.ZernikeBasis(np.arange(1, 7))
-```
-
-```python
-> ZernikeBasis(
->   zernikes=[
->     Zernike(j=1, n=0, m=0, name='Piston', _k=f32[1], _c=f32[1]),
->     Zernike(j=2, n=1, m=1, name='Tilt X', _k=f32[1], _c=f32[1]),
->     Zernike(j=3, n=1, m=-1, name='Tilt Y', _k=f32[2], _c=f32[2]),
->     Zernike(j=4, n=2, m=0, name='Defocus', _k=f32[2], _c=f32[2]),
->     Zernike(j=5, n=2, m=-2, name='Astig X', _k=f32[3], _c=f32[3]),
->     Zernike(j=6, n=2, m=2, name='Astig Y', _k=f32[1], _c=f32[1])
->   ]
-> )
-```
-
-??? abstract "Plotting code"
-    ```python
-    import matplotlib.pyplot as plt
-
-    npix = 256
-    coords = dl.utils.pixel_coords(npix, 2/npix)
-    basis = zernike_basis.calculate_basis(coords)
-
-    plt.figure(figsize=(15, 8))
-    for i in range(len(basis)):
-        plt.subplot(2, 3, i+1)
-        plt.title(f"{zernike_basis.noll_indices[i].name}")
-        plt.imshow(basis[i])
-        plt.colorbar()
-    plt.tight_layout()
-    plt.savefig("assets/zernike.png")
-    ```
-
-![zernike](../assets/zernike.png) -->
diff --git a/docs/API/layers/detector_layers.md b/docs/API/layers/detector_layers.md
@@ -13,63 +13,4 @@
     ::: dLux.layers.detector_layers.AddConstant
 
 ???+ info "Downsample"
-    ::: dLux.layers.detector_layers.Downsample
-
-<!-- # Detector Layers: `detector_layers.py`
-
-This module contains the classes that define the behaviour of detector layers in ∂Lux.
-
-There are six public classes:
-
-- `ApplyPixelResponse`
-- `ApplyJitter`
-- `ApplySaturation`
-- `AddConstant`
-- `IntegerDownsample`
-- `RotateDetector`
-
-These classes operate on `Image` classes. They have one main method: `.__call__(image)`, which takes in a ∂Lux `Image` class and applies the detector layer to it.
-
-These classes are relatively simple, so let's quickly move through them.
-
-### `ApplyPixelResponse`
-
-Applies a pixel response array to the input image via a multiplication.
-
-??? info "ApplyPixelResponse API"
-    :::dLux.detector_layers.ApplyPixelResponse
-
-### `ApplyJitter`
-
-Convolves the image with a Gaussian kernel parameterised by the standard deviation (`sigma`).
-
-??? info "ApplyJitter API"
-    :::dLux.detector_layers.ApplyJitter
-
-### `ApplySaturation`
-
-Applies a simple saturation model to the input image, by clipping any values above `saturation`.
-
-??? info "ApplySaturation API"
-    :::dLux.detector_layers.ApplySaturation
-
-### `AddConstant`
-
-Add a constant to the output image. This is typically used to model the mean value of the detector noise.
-
-??? info "AddConstant API"
-    :::dLux.detector_layers.AddConstant
-
-### `IntegerDownsample`
-
-Downsamples an input image by an integer number of pixels via a summation. The number of pixels in the input image must be integer divisible by `kernel_size`.
-
-??? info "IntegerDownsample API"
-    :::dLux.detector_layers.IntegerDownsample
-
-### `RotateDetector`
-
-Applies a rotation to the image using interpolation methods.
-
-??? info "RotateDetector API"
-    :::dLux.detector_layers.RotateDetector -->
+    ::: dLux.layers.detector_layers.Downsample
diff --git a/docs/API/layers/optical_layers.md b/docs/API/layers/optical_layers.md
@@ -1,13 +1,16 @@
 # Optical Layers
 
-???+ info "MFT"
-    ::: dLux.layers.propagators.MFT
+???+ info "TransmissiveLayer"
+    ::: dLux.layers.optical_layers.TransmissiveLayer
 
-???+ info "FFT"
-    ::: dLux.layers.propagators.FFT
+???+ info "AberratedLayer"
+    ::: dLux.layers.optical_layers.AberratedLayer
 
-???+ info "ShiftedMFT"
-    ::: dLux.layers.propagators.ShiftedMFT
+???+ info "BasisLayer"
+    ::: dLux.layers.optical_layers.BasisLayer
 
-???+ info "FarFieldFresnel"
-    ::: dLux.layers.propagators.FarFieldFresnel
+???+ info "Tilt"
+    ::: dLux.layers.optical_layers.Tilt
+
+???+ info "Normalise"
+    ::: dLux.layers.optical_layers.Normalise
diff --git a/docs/API/layers/propagators.md b/docs/API/layers/propagators.md
@@ -1,57 +1,13 @@
 # Propagators
 
-???+ info "ApplyPixelResponse"
-    ::: dLux.layers.detector_layers.ApplyPixelResponse
+???+ info "MFT"
+    ::: dLux.layers.propagators.MFT
 
-???+ info "ApplyJitter"
-    ::: dLux.layers.detector_layers.ApplyJitter
+???+ info "FFT"
+    ::: dLux.layers.propagators.FFT
 
-???+ info "ApplySaturation"
-    ::: dLux.layers.detector_layers.ApplySaturation
+???+ info "ShiftedMFT"
+    ::: dLux.layers.propagators.ShiftedMFT
 
-???+ info "AddConstant"
-    ::: dLux.layers.detector_layers.AddConstant
-
-???+ info "Downsample"
-    ::: dLux.layers.detector_layers.Downsample
-
-<!-- # Propagators: `propagators.py`
-
-This module contains the classes that define the behaviour of propagator layers in ∂Lux.
-
-These classes do not implement the propagation functionality themselves, but instead store the parameters of the propagation and call inbuilt methods of the `Wavefront` class; thus, its API is essentially a mirror of those methods.
-
-There are four public classes:
-
-- `MFT`
-- `FFT`
-- `ShiftedMFT`
-- `FarFieldFresnel`
-
-### `MFT(npixels, pixel_scale, focal_length=None, inverse=False)`
-
-Performs a Matrix Fourier Transform (MFT) on the wavefront, propagating from Pupil to Focal plane. If `focal_length` is `None`, `pixel_scale` is assumed to be in angular units (radians), otherwise it is assumed to be in Cartesian units (metres).
-
-??? info "MFT API"
-    ::: dLux.propagators.MFT
-
-### `FFT(pad, focal_length=None, inverse=False)`
-
-Performs a Fast Fourier Transform (FFT) on the wavefront, propagating from Pupil to Focal plane. If `focal_length` is `None`, the output units will angular (radians), otherwise cartesian (metres).
-
-??? info "FFT API"
-    ::: dLux.propagators.FFT
-
-### `shiftedMFT(npixels, pixel_scale, shift, focal_length=None, pixel=True, inverse=False)`
-
-Performs a Matrix Fourier Transform (MFT) on the wavefront, propagating from Pupil to Focal plane. If `focal_length` is `None`, `pixel_scale` is assumed to be in angular units (radians), otherwise it is assumed to be in Cartesian units (metres). The `shift` parameter is used to shift the center of the output plane, which is treated in units of pixels by default, otherwise it is treated in the units of `pixel_scale`.
-
-??? info "Shifted MFT API"
-    ::: dLux.propagators.ShiftedMFT
-
-### `FarFieldFresnel(npixels, pixel_scale, focal_length, focal_shift, shift, pixel=True)`
-
-Performs a Fresnel propagation on the wavefront, propagating from Pupil to Focal plane. The `focal_shift` parameter represents the distance from the focal plane at which the PSF is modelled. The `shift` parameter is used to shift the center of the output plane, which is treated in units of pixels by default, otherwise it is treated in the units of `pixel_scale`.
-
-??? info "Far Field Fresnel API"
-    ::: dLux.propagators.FarFieldFresnel -->
+???+ info "FarFieldFresnel"
+    ::: dLux.layers.propagators.FarFieldFresnel
diff --git a/docs/tutorials/advanced/HMC.md → docs/tutorials/examples/HMC.md b/docs/tutorials/advanced/HMC.md → docs/tutorials/examples/HMC.md
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diff --git a/docs/tutorials/advanced/designing_a_mask.md → docs/tutorials/examples/designing_a_mask.md b/docs/tutorials/advanced/designing_a_mask.md → docs/tutorials/examples/designing_a_mask.md
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diff --git a/...torials/advanced/flatfield_calibration.md → ...torials/examples/flatfield_calibration.md b/...torials/advanced/flatfield_calibration.md → ...torials/examples/flatfield_calibration.md
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