updating examples with modal decomposition

examples/example_modal_decomposition_data.py

@@ -12,6 +12,7 @@
     TransverseProfileFromData,
 )
 from lasy.utils.mode_decomposition import hermite_gauss_decomposition
+from scipy.constants import epsilon_0,c
 
 # Define the transverse profile of the laser pulse
 img_url = "https://user-images.githubusercontent.com/27694869/228038930-d6ab03b1-a726-4b41-a378-5f4a83dc3778.png"
@@ -67,44 +68,66 @@
         )
 
 # Plotting the results
+# Plot the original and denoised profiles
+# Create a grid for plotting
 x = np.linspace(-5 * waist, 5 * waist, 500)
 X, Y = np.meshgrid(x, x)
 
+# Determine the figure parameters
 fig, ax = plt.subplots(1, 3, figsize=(12, 4), tight_layout=True)
+fig.suptitle(
+    "Hermite-Gauss Reconstruction using m_max = %i, n_max = %i" % (m_max, n_max)
+)
 
-pltextent = (np.min(x) * 1e6, np.max(x) * 1e6, np.min(x) * 1e6, np.max(x) * 1e6)
+# Plot the original profile
+pltextent = np.array([np.min(x), np.max(x), np.min(x), np.max(x)]) * 1e6  # in microns
 prof1 = np.abs(profile.evaluate(X, Y, 0)) ** 2
+maxInten = np.max(prof1)
+prof1 /= maxInten
 divider0 = make_axes_locatable(ax[0])
 ax0_cb = divider0.append_axes("right", size="5%", pad=0.05)
 pl0 = ax[0].imshow(prof1, cmap="magma", extent=pltextent, vmin=0, vmax=np.max(prof1))
 cbar0 = fig.colorbar(pl0, cax=ax0_cb)
 cbar0.set_label("Intensity (norm.)")
-ax[0].set_xlabel("x (micron)")
-ax[0].set_ylabel("y (micron)")
+ax[0].set_xlabel("x ($ \\mu m $)")
+ax[0].set_ylabel("y ($ \\mu m $)")
 ax[0].set_title("Original Profile")
 
+# Plot the reconstructed profile
 prof2 = np.abs(reconstructedProfile.evaluate(X, Y, 0)) ** 2
+prof2 /= maxInten
 divider1 = make_axes_locatable(ax[1])
 ax1_cb = divider1.append_axes("right", size="5%", pad=0.05)
 pl1 = ax[1].imshow(prof2, cmap="magma", extent=pltextent, vmin=0, vmax=np.max(prof1))
 cbar1 = fig.colorbar(pl1, cax=ax1_cb)
 cbar1.set_label("Intensity (norm.)")
-ax[1].set_xlabel("x (micron)")
-ax[1].set_ylabel("y (micron)")
+ax[1].set_xlabel("x ($ \\mu m $)")
+ax[1].set_ylabel("y ($ \\mu m $)")
 ax[1].set_title("Reconstructed Profile")
 
-
-prof3 = (prof1 - prof2) / np.max(prof1)
+# Plot the error
+prof3 = (prof1 - prof2) / np.max(prof1)  # Normalized error
 divider2 = make_axes_locatable(ax[2])
 ax2_cb = divider2.append_axes("right", size="5%", pad=0.05)
-pl2 = ax[2].imshow(100 * np.abs(prof3), cmap="magma", extent=pltextent, vmin=0, vmax=2)
+pl2 = ax[2].imshow(100 * np.abs(prof3), cmap="magma", extent=pltextent)
 cbar2 = fig.colorbar(pl2, cax=ax2_cb)
-cbar2.set_label("|Error| (%)")
-ax[2].set_xlabel("x (micron)")
-ax[2].set_ylabel("y (micron)")
+cbar2.set_label("|Intensity Error| (%)")
+ax[2].set_xlabel("x ($ \\mu m $)")
+ax[2].set_ylabel("y ($ \\mu m $)")
 ax[2].set_title("Error")
 
-fig.suptitle(
-    "Hermite-Gauss Reconstruction using m_max = %i, n_max = %i" % (m_max, n_max)
-)
 plt.show()
+
+fig2, ax2 = plt.subplots(2, 1, figsize=(12, 8), tight_layout=True)
+ax2[0].plot(x*1e6, prof2[int(len(x)/2),:],label='Reconstructed Profile',color=(1,0.5,0.5),lw=2.5)
+ax2[0].plot(x*1e6, prof1[int(len(x)/2),:],label='Original Profile',color=(0.3,0.3,0.3),lw=1.0)
+ax2[0].legend()
+ax2[0].set_xlim(pltextent[0],pltextent[1])
+
+ax2[1].plot(x*1e6, prof2[int(len(x)/2),:],label='Reconstructed Profile',color=(1,0.5,0.5),lw=2.5)
+ax2[1].plot(x*1e6, prof1[int(len(x)/2),:],label='Original Profile',color=(0.3,0.3,0.3),lw=1.0)
+ax2[1].legend()
+ax2[1].set_xlim(pltextent[0],pltextent[1])
+ax2[1].set_yscale('log')
+
+plt.show()