Use log y-scale on energy deposition histograms

Both Edep and PET-spectrum distributions span several orders of magnitude
because of the huge zero-deposit / Compton-continuum populations. Linear
y compresses the structure to a single spike at zero; log y exposes the
photopeak, full-energy peak, and tail features.

Updated:
- lab3 analyze_basic.py:        single-panel hist
- lab3 analyze_advanced.py:     panels 1 & 2
- lab3 compare_particles.py:    all 4 panels (3 individual + density overlay)
- lab4 analyze_spectrum.py:     PET energy spectrum

Regenerated PNGs and committed alongside the .qmd updates.

lab3_modifyB1/lab3.qmd

@@ -406,8 +406,9 @@ plt.axvline(median_edep, color='green', linestyle='--',
 plt.title(f'Energy Deposition Distribution for 6 MeV Gammas\n({len(data)} events)',
           fontsize=14, fontweight='bold')
 plt.xlabel('Energy Deposited (MeV)', fontsize=12)
-plt.ylabel('Frequency (Number of Events)', fontsize=12)
-plt.grid(True, alpha=0.3)
+plt.ylabel('Frequency (log scale)', fontsize=12)
+plt.yscale('log')
+plt.grid(True, alpha=0.3, which='both')
 plt.legend(fontsize=10)
 
 stats_text = f'mu = {mean_edep:.3f} MeV\nsigma = {std_edep:.3f} MeV\nEvents = {len(data)}'
@@ -485,24 +486,26 @@ fig, axes = plt.subplots(2, 2, figsize=(14, 10))
 fig.suptitle('Advanced Energy Deposition Analysis',
              fontsize=16, fontweight='bold')
 
-# Panel 1: Full distribution
+# Panel 1: Full distribution (log y to see the tail past the zero spike)
 ax1 = axes[0, 0]
 ax1.hist(data['Edep'], bins=100, color='steelblue',
          alpha=0.7, edgecolor='black')
 ax1.set_xlabel('Energy Deposited (MeV)')
-ax1.set_ylabel('Frequency')
+ax1.set_ylabel('Frequency (log scale)')
+ax1.set_yscale('log')
 ax1.set_title(f'Full Distribution (n={len(data)})')
-ax1.grid(True, alpha=0.3)
+ax1.grid(True, alpha=0.3, which='both')
 
-# Panel 2: Excluding zero-energy events
+# Panel 2: Excluding zero-energy events (log y for the long tail)
 ax2 = axes[0, 1]
 non_zero = data[data['Edep'] > 0]
 ax2.hist(non_zero['Edep'], bins=80, color='coral',
          alpha=0.7, edgecolor='black')
 ax2.set_xlabel('Energy Deposited (MeV)')
-ax2.set_ylabel('Frequency')
+ax2.set_ylabel('Frequency (log scale)')
+ax2.set_yscale('log')
 ax2.set_title(f'Non-Zero Events Only (n={len(non_zero)})')
-ax2.grid(True, alpha=0.3)
+ax2.grid(True, alpha=0.3, which='both')
 
 # Panel 3: Cumulative distribution
 ax3 = axes[1, 0]
@@ -644,30 +647,33 @@ ax1 = axes[0, 0]
 ax1.hist(gamma_data['Edep'], bins=80, alpha=0.7,
          color='blue', label='6 MeV gamma', edgecolor='black')
 ax1.set_xlabel('Energy Deposited (MeV)')
-ax1.set_ylabel('Frequency')
+ax1.set_ylabel('Frequency (log scale)')
+ax1.set_yscale('log')
 ax1.set_title('Gamma Rays (6 MeV)')
 ax1.legend()
-ax1.grid(True, alpha=0.3)
+ax1.grid(True, alpha=0.3, which='both')
 
 ax2 = axes[0, 1]
 ax2.hist(proton_data['Edep'], bins=80, alpha=0.7,
          color='red', label='150 MeV p+', edgecolor='black')
 ax2.set_xlabel('Energy Deposited (MeV)')
-ax2.set_ylabel('Frequency')
+ax2.set_ylabel('Frequency (log scale)')
+ax2.set_yscale('log')
 ax2.set_title('Protons (150 MeV)')
 ax2.legend()
-ax2.grid(True, alpha=0.3)
+ax2.grid(True, alpha=0.3, which='both')
 
 ax3 = axes[1, 0]
 ax3.hist(electron_data['Edep'], bins=80, alpha=0.7,
          color='green', label='50 MeV e-', edgecolor='black')
 ax3.set_xlabel('Energy Deposited (MeV)')
-ax3.set_ylabel('Frequency')
+ax3.set_ylabel('Frequency (log scale)')
+ax3.set_yscale('log')
 ax3.set_title('Electrons (50 MeV)')
 ax3.legend()
-ax3.grid(True, alpha=0.3)
+ax3.grid(True, alpha=0.3, which='both')
 
-# Normalized overlay
+# Normalized overlay (log y so the three shapes are comparable across orders)
 ax4 = axes[1, 1]
 ax4.hist(gamma_data['Edep'], bins=60, alpha=0.5, color='blue',
          label=f'gamma (mu={gamma_data["Edep"].mean():.2f})', density=True)
@@ -676,10 +682,11 @@ ax4.hist(proton_data['Edep'], bins=60, alpha=0.5, color='red',
 ax4.hist(electron_data['Edep'], bins=60, alpha=0.5, color='green',
          label=f'e- (mu={electron_data["Edep"].mean():.2f})', density=True)
 ax4.set_xlabel('Energy Deposited (MeV)')
-ax4.set_ylabel('Probability Density')
+ax4.set_ylabel('Probability Density (log scale)')
+ax4.set_yscale('log')
 ax4.set_title('Normalized Overlay Comparison')
 ax4.legend()
-ax4.grid(True, alpha=0.3)
+ax4.grid(True, alpha=0.3, which='both')
 
 plt.tight_layout()
 plt.savefig('particle_comparison.png', dpi=300)

lab4_exampleB3/lab4.qmd

@@ -236,9 +236,10 @@ plt.axvline(511, color='red', linestyle='--', linewidth=1.5,
 
 plt.title('PET Detector Crystal Energy Spectrum')
 plt.xlabel('Energy Deposited per Hit (keV)')
-plt.ylabel('Counts')
+plt.ylabel('Counts (log scale)')
+plt.yscale('log')
 plt.legend()
-plt.grid(True, alpha=0.3)
+plt.grid(True, alpha=0.3, which='both')
 plt.tight_layout()
 plt.savefig('pet_spectrum.png', dpi=200)
 print("Spectrum saved to pet_spectrum.png")