.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "example_gallery/plot_snr.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_example_gallery_plot_snr.py: Signal-to-Noise Ratio (SNR) for Speckle Regions =========================================================== This example demonstrates the Signal-to-Noise Ratio (SNR) metric for ultrasound speckle analysis. We explore how SNR varies in different tissue regions and validate measurements against theoretical Rayleigh distribution values. Mathematical Definition ----------------------- The Signal-to-Noise Ratio for ultrasound speckle is defined as the ratio of mean to standard deviation: .. math:: \text{SNR} = \frac{\mathbb{E}[X]}{\sqrt{\text{Var}(X)}} = \frac{\mu}{\sigma} where :math:`\mathbb{E}[X]` is the mean and :math:`\sqrt{\text{Var}(X)}` is the standard deviation of the envelope-detected signal values. Fully developed speckle follows a Rayleigh distribution [1]_, so the theoretical SNR is: .. math:: \text{SNR}_{\text{Rayleigh}} = \sqrt{\frac{\pi}{4 - \pi}} \approx 1.91 This metric provides insight into speckle quality and can be used to: - Assess fully developed speckle regions - Compare different beamforming techniques - Validate speckle statistics in phantom studies - Quality control in ultrasound systems **ROI Selection Best Practices:** Following Perdios et al. [2]_, speckle patterns should be assessed within regions of approximately 10λx10λ (where λ is the wavelength) to ensure sufficient statistical sampling while maintaining spatial homogeneity. Regions should be placed away from boundaries and avoid compounding artifacts near field edges. References ---------- .. [1] C. B. Burckhardt, "Speckle in Ultrasound B-mode Scans," in IEEE Transactions on Sonics and Ultrasonics, vol. 25, no. 1, pp. 1-6, Jan. 1978, doi: 10.1109/T-SU.1978.30978. .. [2] D. Perdios, M. Vonlanthen, F. Martinez, M. Arditi and J. -P. Thiran, "CNN-Based Image Reconstruction Method for Ultrafast Ultrasound Imaging," in IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, vol. 69, no. 4, pp. 1154-1168, April 2022, doi: 10.1109/TUFFC.2021.3131383. .. [3] H. Liebgott, A. Rodriguez-Molares, F. Cervenansky, J. A. Jensen and O. Bernard, "Plane-Wave Imaging Challenge in Medical Ultrasound," 2016 IEEE International Ultrasonics Symposium (IUS), Tours, France, 2016, pp. 1-4, doi: 10.1109/ULTSYM.2016.7728908. Example ------- .. GENERATED FROM PYTHON SOURCE LINES 63-65 Import required modules and functions ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 65-76 .. code-block:: Python import matplotlib.pyplot as plt import numpy as np import pandas as pd from matplotlib.patches import Circle from ultrasound_metrics.data import db_zero from ultrasound_metrics.data.uff import load_uff_dataset from ultrasound_metrics.metrics.snr import snr from ultrasound_metrics.roi.masks import build_mask .. GENERATED FROM PYTHON SOURCE LINES 77-79 Load PICMUS datasets [3]_ for comparison ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 79-88 .. code-block:: Python # Load contrast/speckle dataset (contains fully developed speckle regions) image_contrast, scan_contrast = load_uff_dataset("picmus_contrast_experiment") image_contrast = image_contrast.T # Load resolution dataset (contains point targets and speckle) image_resolution, scan_resolution = load_uff_dataset("picmus_resolution_experiment") image_resolution = image_resolution.T .. GENERATED FROM PYTHON SOURCE LINES 89-91 Visualize datasets side by side ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 91-120 .. code-block:: Python fig, axes = plt.subplots(1, 2, figsize=(12, 6)) # Contrast/speckle dataset extent_contrast = [ scan_contrast.x_axis.min(), scan_contrast.x_axis.max(), scan_contrast.z_axis.max(), scan_contrast.z_axis.min(), ] axes[0].imshow(db_zero(image_contrast), cmap="gray", extent=extent_contrast, vmin=-60, vmax=0) axes[0].set_title("PICMUS Contrast/Speckle Dataset\n(Fully developed speckle)") axes[0].set_xlabel("Lateral Position (m)") axes[0].set_ylabel("Axial Position (m)") # Resolution dataset extent_resolution = [ scan_resolution.x_axis.min(), scan_resolution.x_axis.max(), scan_resolution.z_axis.max(), scan_resolution.z_axis.min(), ] axes[1].imshow(db_zero(image_resolution), cmap="gray", extent=extent_resolution, vmin=-60, vmax=0) axes[1].set_title("PICMUS Resolution Dataset\n(Point targets + speckle)") axes[1].set_xlabel("Lateral Position (m)") axes[1].set_ylabel("Axial Position (m)") plt.tight_layout() .. image-sg:: /example_gallery/images/sphx_glr_plot_snr_001.png :alt: PICMUS Contrast/Speckle Dataset (Fully developed speckle), PICMUS Resolution Dataset (Point targets + speckle) :srcset: /example_gallery/images/sphx_glr_plot_snr_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 121-123 Define ROI locations for speckle analysis ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 123-164 .. code-block:: Python # Following Perdios et al., we use regions of approximately 10λx10λ # Assuming center frequency ~5 MHz and speed of sound ~1540 m/s # λ ≈ 1540/5e6 ≈ 0.3 mm, so 10λ ≈ 3 mm radius roi_radius = 0.003 # 3 mm radius # Equation S9 from Perdios et al. [2]_ and Equation 4 from Burckhardt [1]_ theoretical_rayleigh_snr = np.sqrt(np.pi / (4 - np.pi)) # Define ROI locations for different types of regions roi_specs = [ { "name": "Fully Developed Speckle (contrast dataset)", "dataset": "contrast", "center": (-0.005, 0.035), "expected_snr": theoretical_rayleigh_snr, "description": "Homogeneous speckle region", }, { "name": "Fully Developed Speckle (resolution dataset)", "dataset": "resolution", "center": (0.008, 0.030), "expected_snr": theoretical_rayleigh_snr, "description": "Homogeneous speckle region", }, { "name": "Point Target Region", "dataset": "resolution", "center": (0.000, 0.0275), # Near a point target "expected_snr": None, # Should deviate from Rayleigh "description": "Point target + speckle", }, { "name": "Lesion Boundary", "dataset": "contrast", "center": (-0.0025, 0.028), # Near lesion boundary "expected_snr": None, # Mixed statistics "description": "Lesion boundary region", }, ] .. GENERATED FROM PYTHON SOURCE LINES 165-167 Compute SNR for each ROI ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 167-220 .. code-block:: Python results_data = [] for spec in roi_specs: # Select the appropriate dataset and scan if spec["dataset"] == "contrast": image = image_contrast scan = scan_contrast extent = extent_contrast else: image = image_resolution scan = scan_resolution extent = extent_resolution # Create ROI mask mask = build_mask( position=spec["center"], dimension=roi_radius, x_axis=scan.x_axis, z_axis=scan.z_axis, shape="circle", ) # Extract values in ROI roi_values = image[mask] # Compute SNR (function handles complex data internally) snr_linear = snr(roi_values, db=False) snr_db = snr(roi_values, db=True) # Calculate deviation from theoretical Rayleigh SNR if expected if spec["expected_snr"] is not None: deviation = abs(snr_linear - spec["expected_snr"]) deviation_percent = (deviation / spec["expected_snr"]) * 100 else: deviation = None deviation_percent = None results_data.append({ "ROI": spec["name"], "Dataset": spec["dataset"], "SNR (linear)": snr_linear, "SNR (dB)": snr_db, "Expected SNR": spec["expected_snr"], "Deviation": deviation, "Deviation (%)": deviation_percent, "Description": spec["description"], "mask": mask, "center": spec["center"], "extent": extent, "image": image, }) .. GENERATED FROM PYTHON SOURCE LINES 221-223 Display results table ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 223-244 .. code-block:: Python results_df = pd.DataFrame(results_data) print("=== SNR Analysis Results ===") display_cols = ["ROI", "Dataset", "SNR (linear)", "SNR (dB)", "Expected SNR", "Deviation (%)"] print(results_df[display_cols].round(3)) print(f"\nTheoretical Rayleigh SNR: {theoretical_rayleigh_snr:.3f}") for _, row in results_df.iterrows(): if row["Expected SNR"] is not None: if row["Deviation (%)"] < 10: status = "✅ Good agreement with theory (Rayleigh distribution)" elif row["Deviation (%)"] < 20: status = "⚠️ Moderate deviation from theory" else: status = "❌ Significant deviation from theory" print(f"{row['ROI']}: SNR = {row['SNR (linear)']:.3f}, {status}") else: print(f"{row['ROI']}: SNR = {row['SNR (linear)']:.3f} (non-Rayleigh distribution)") .. rst-class:: sphx-glr-script-out .. code-block:: none === SNR Analysis Results === ROI ... Deviation (%) 0 Fully Developed Speckle (contrast dataset) ... 2.189 1 Fully Developed Speckle (resolution dataset) ... 1.115 2 Point Target Region ... NaN 3 Lesion Boundary ... NaN [4 rows x 6 columns] Theoretical Rayleigh SNR: 1.913 Fully Developed Speckle (contrast dataset): SNR = 1.955, ✅ Good agreement with theory (Rayleigh distribution) Fully Developed Speckle (resolution dataset): SNR = 1.892, ✅ Good agreement with theory (Rayleigh distribution) Point Target Region: SNR = 0.534, ❌ Significant deviation from theory Lesion Boundary: SNR = 1.520, ❌ Significant deviation from theory .. GENERATED FROM PYTHON SOURCE LINES 245-247 Visualize ROIs and SNR measurements ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 247-279 .. code-block:: Python fig, axes = plt.subplots(2, 2, figsize=(15, 12)) axes = axes.flatten() for i, (_, row) in enumerate(results_df.iterrows()): ax = axes[i] # Display the image ax.imshow(db_zero(row["image"]), cmap="gray", extent=row["extent"], vmin=-60, vmax=0) # Overlay ROI circle circle = Circle(row["center"], roi_radius, fill=False, color="red", linewidth=2, linestyle="--") ax.add_patch(circle) # Add SNR annotation ax.text( row["center"][0], row["center"][1] - 0.008, f"SNR = {row['SNR (linear)']:.2f}", ha="center", va="top", color="white", fontweight="bold", bbox={"boxstyle": "round,pad=0.3", "facecolor": "black", "alpha": 0.8}, ) ax.set_title(f"{row['ROI']}\n{row['Description']}") ax.set_xlabel("Lateral Position (m)") ax.set_ylabel("Axial Position (m)") plt.tight_layout() .. image-sg:: /example_gallery/images/sphx_glr_plot_snr_002.png :alt: Fully Developed Speckle (contrast dataset) Homogeneous speckle region, Fully Developed Speckle (resolution dataset) Homogeneous speckle region, Point Target Region Point target + speckle, Lesion Boundary Lesion boundary region :srcset: /example_gallery/images/sphx_glr_plot_snr_002.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 280-282 Statistical analysis of speckle regions ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 282-349 .. code-block:: Python # Focus on the fully developed speckle regions speckle_rows = results_df[results_df["Expected SNR"].notna()] fig, axes = plt.subplots(1, 2, figsize=(12, 5)) colors = ["skyblue", "lightcoral"] for i, (_, row) in enumerate(speckle_rows.iterrows()): # Extract ROI values and convert to envelope (magnitude) roi_values_complex = row["image"][row["mask"]] roi_values = np.abs(roi_values_complex) # Take envelope for histogram # Create histogram of envelope values axes[0].hist( roi_values, bins=50, alpha=0.7, density=True, color=colors[i], label=f"{row['ROI']} (SNR={row['SNR (linear)']:.2f})", ) # Overlay theoretical Rayleigh distribution x_theory = np.linspace(0, roi_values.max(), 1000) # For comparison, use sigma that gives the same mean as our data sigma_rayleigh = np.mean(roi_values) / np.sqrt(np.pi / 2) rayleigh_pdf = (x_theory / sigma_rayleigh**2) * np.exp(-(x_theory**2) / (2 * sigma_rayleigh**2)) axes[0].plot(x_theory, rayleigh_pdf, "k--", linewidth=2, label="Theoretical Rayleigh") axes[0].set_xlabel("Envelope Amplitude") axes[0].set_ylabel("Probability Density") axes[0].set_title("Envelope Distribution vs Rayleigh Distribution") axes[0].legend() axes[0].grid(True, alpha=0.3) # SNR comparison bar chart roi_names = [row["ROI"] for _, row in speckle_rows.iterrows()] snr_values = [row["SNR (linear)"] for _, row in speckle_rows.iterrows()] bars = axes[1].bar(roi_names, snr_values, alpha=0.7, color=colors) axes[1].axhline( y=theoretical_rayleigh_snr, color="red", linestyle="--", linewidth=2, label="Theoretical (Rayleigh distribution)", ) axes[1].set_ylabel("SNR") axes[1].set_title("Measured SNR vs Theoretical") axes[1].legend() axes[1].grid(True, alpha=0.3) # Add value labels on bars for bar, value in zip(bars, snr_values): height = bar.get_height() axes[1].text( bar.get_x() + bar.get_width() / 2.0, height + 0.01, f"{value:.2f}", ha="center", va="bottom", fontweight="bold", ) plt.xticks(rotation=45, ha="right") plt.tight_layout() .. image-sg:: /example_gallery/images/sphx_glr_plot_snr_003.png :alt: Envelope Distribution vs Rayleigh Distribution, Measured SNR vs Theoretical :srcset: /example_gallery/images/sphx_glr_plot_snr_003.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 350-352 %% Show all figures (if run as a script) .. GENERATED FROM PYTHON SOURCE LINES 352-354 .. code-block:: Python plt.show() .. GENERATED FROM PYTHON SOURCE LINES 355-389 Best Practices for SNR Measurement ----------------------------------- Based on the analysis above, here are key guidelines for SNR measurement: 1. ROI Size Guidelines: - Use regions of approximately 10λx10λ for adequate statistical sampling - For 5 MHz transducers: ≈3mm x 3mm ROI provides good sampling - Larger ROIs provide more stable statistics but may include spatial variations 2. Region Selection Criteria: - Choose homogeneous speckle areas away from boundaries - Avoid edges with incomplete plane wave coverage 3. Regions to Avoid: - Lesion edges (mixed Rayleigh/non-Rayleigh statistics) - Point targets (coherent scattering, non-Rayleigh) - Field edges (incomplete acoustic data) - Areas with obvious artifacts 4. Expected Values for Quality Assessment: - Fully developed speckle: SNR ≈ 1.91 (Rayleigh distribution) [1]_ [2]_ - Point targets: SNR significantly < 1.91 - Mixed regions: Variable SNR depending on content mixture 5. Clinical and Research Applications: - Speckle quality assessment in different tissue types - Beamforming algorithm evaluation and optimization - System validation and quality control .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 1.103 seconds) .. _sphx_glr_download_example_gallery_plot_snr.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_snr.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_snr.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_snr.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_