Bayer example

docs/examples/_thumbnails/bayer.py

@@ -0,0 +1,29 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import scipy.signal
+
+gaussian = scipy.signal.windows.gaussian(250, 25)
+gaussian = gaussian[25:-25]
+qe_wave = np.arange(350, 750)*1e-9
+
+qe_red = np.zeros(qe_wave.size)
+qe_green = np.zeros(qe_wave.size)
+qe_blue = np.zeros(qe_wave.size)
+
+qe_blue[10:210] = gaussian
+qe_green[90:290] = gaussian
+qe_red[170:370] = gaussian
+
+
+plt.plot(qe_wave, qe_blue, '#5E81AC')
+plt.fill_between(qe_wave, qe_blue, color='#5E81AC', alpha=0.4)
+
+plt.plot(qe_wave, qe_green, '#A3BE8C')
+plt.fill_between(qe_wave, qe_green, color='#A3BE8C', alpha=0.4)
+
+plt.plot(qe_wave, qe_red, '#BF616A')
+plt.fill_between(qe_wave, qe_red, color='#BF616A', alpha=0.4)
+
+plt.axis('off')
+
+plt.savefig('bayer.png', dpi=150, bbox_inches='tight')

docs/examples/bayer.rst

@@ -0,0 +1,111 @@
+.. _examples.bayer:
+
+*************************
+Modeling a Bayer detector
+*************************
+
+.. plot::
+    :context: reset
+    :include-source:
+    :scale: 50
+
+    import lentil
+    import numpy as np
+    import matplotlib.pyplot as plt
+    import scipy.signal
+
+    gaussian = scipy.signal.windows.gaussian(250, 25)
+    gaussian = gaussian[25:-25]
+    qe_wave = np.arange(350, 750)*1e-9
+
+    qe_red = np.zeros(qe_wave.size)
+    qe_green = np.zeros(qe_wave.size)
+    qe_blue = np.zeros(qe_wave.size)
+
+    qe_blue[10:210] = gaussian
+    qe_green[90:290] = gaussian
+    qe_red[170:370] = gaussian
+
+
+    plt.plot(qe_wave, qe_blue, 'b', label='Blue')
+    plt.plot(qe_wave, qe_green, 'g', label='Green')
+    plt.plot(qe_wave, qe_red, 'r', label='Red')
+    plt.legend()
+    plt.title('Quantum Efficiency')
+    plt.xlabel('Wavelength [nm]')
+    plt.grid()
+
+
+.. plot::
+    :context: close-figs
+    :include-source:
+    :scale: 50
+
+    amp = lentil.circle((256,256), 120)
+    amp -= lentil.circle(shape=(256,256), radius=40)
+    for angle in (0, 90, 180, 270):
+        amp *= lentil.spider((256,256), 2, angle)
+        
+    opd = lentil.zernike(amp, 4)*1e-6
+
+    psf = []
+
+    p = lentil.Pupil(amplitude=amp, opd=opd, focal_length=10, pixelscale=1/240)
+
+    for wave in np.arange(350, 750):
+        w = lentil.Wavefront(wave*1e-9)
+        w *= p
+        w = lentil.propagate_dft(w, pixelscale=5e-6, shape=(64, 64), 
+                                oversample=2)
+        psf.append(w.intensity)
+
+    psf = np.asarray(psf)
+    psf = lentil.rebin(psf, 2)
+
+    psf_flat = np.sum(psf, axis=0)
+
+    fig, ax = plt.subplots(figsize=(2.5,2.5))
+    ax.imshow(psf_flat, cmap='inferno')
+    ax.set_title('Broadband PSF')
+    plt.axis('off')
+
+
+.. plot::
+    :context: close-figs
+    :include-source:
+    :scale: 50
+
+    img = lentil.detector.collect_charge_bayer(psf, qe_wave, qe_red, qe_green,
+                                            qe_blue, 'BGGR')
+
+    red_kernel = np.array([[0,0],[0,1]])
+    green_kernel = np.array([[0,1],[1,0]])
+    blue_kernel = np.array([[1,0],[0,0]])
+
+    red_mosaic = np.tile(red_kernel, (img.shape[0]//2, img.shape[1]//2))
+    green_mosaic = np.tile(green_kernel, (img.shape[0]//2, img.shape[1]//2))
+    blue_mosaic = np.tile(blue_kernel, (img.shape[0]//2, img.shape[1]//2))
+
+    img = img/np.max(img)
+
+    r = red_mosaic * img
+    g = green_mosaic * img
+    b = blue_mosaic * img
+
+    fig, ax = plt.subplots(nrows=1, ncols=4, figsize=(7,3))
+
+    ax[0].imshow(r, cmap='gray')
+    ax[0].set_title('Red')
+    ax[0].axis('off')
+
+    ax[1].imshow(g, cmap='gray')
+    ax[1].set_title('Green')
+    ax[1].axis('off')
+
+    ax[2].imshow(b, cmap='gray')
+    ax[2].set_title('Blue')
+    ax[2].axis('off')
+
+    ax[3].imshow(img, cmap='gray')
+    ax[3].set_title('Full Bayer image')
+    ax[3].axis('off')

docs/examples/index.rst

@@ -91,10 +91,22 @@ Focal plane modeling
             Including a detector model
 
     .. grid-item-card::
-            :margin: 2 2 0 0
+        :link: bayer
+        :link-type: doc
+        :margin: 2 2 0 0
+
+        .. image:: /examples/_thumbnails/bayer.png
+            :width: 175px
+            :align: center
+
+        Modeling a Bayer detector
+
 
-            Modeling a Bayer detector
+.. toctree::
+    :caption: Focal plane modeling
+    :hidden:
 
+    bayer
 
 .. _examples.advanced: