.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "example_gallery/visualize_picmus_dataset.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_visualize_picmus_dataset.py: Loading and Visualizing Ultrasound Images ========================================== This example demonstrates how to: 1. List available datasets 2. Download a PICMUS dataset using the public API 3. Visualize the beamformed ultrasound data This serves as a minimal example of using the ultrasound_metrics.data module. The PICMUS (Plane-wave Imaging Challenge in Medical UltraSound) dataset [1]_ provides standardized ultrasound data for algorithm comparison. References ---------- .. [1] 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 28-30 1. Import required modules and functions ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 30-42 .. code-block:: Python import matplotlib.pyplot as plt from ultrasound_metrics.data import ( create_bmode_image, db_zero, list_available_datasets, ) from ultrasound_metrics.data.uff import ( load_uff_dataset, ) .. GENERATED FROM PYTHON SOURCE LINES 43-45 2. List available datasets ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 45-51 .. code-block:: Python print("Available datasets:") datasets = list_available_datasets() for name, info in datasets.items(): print(f"- {name}: {info['description']}") print() .. rst-class:: sphx-glr-script-out .. code-block:: none Available datasets: - picmus_resolution_experiment: PICMUS challenge resolution/distortion test (experiment) - picmus_contrast_experiment: PICMUS challenge contrast/speckle test (experiment) .. GENERATED FROM PYTHON SOURCE LINES 52-54 3. Choose a dataset to visualize ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 54-58 .. code-block:: Python dataset_name = "picmus_resolution_experiment" print(f"Loading dataset: {dataset_name}") .. rst-class:: sphx-glr-script-out .. code-block:: none Loading dataset: picmus_resolution_experiment .. GENERATED FROM PYTHON SOURCE LINES 59-61 4. Load the dataset ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 61-70 .. code-block:: Python beamformed_image, scan = load_uff_dataset(dataset_name) print("Dataset loaded successfully!") print(f"Data shape: {beamformed_image.shape}") print(f"Data type: {beamformed_image.dtype}") print(f"Data range: [{beamformed_image.min():.3f}, {beamformed_image.max():.3f}]") print(f"Scan geometry: x={scan.x_axis.size}, z={scan.z_axis.size}") .. rst-class:: sphx-glr-script-out .. code-block:: none Dataset loaded successfully! Data shape: (387, 609) Data type: complex64 Data range: [-56.675+21.870j, 52.407-5.226j] Scan geometry: x=387, z=609 .. GENERATED FROM PYTHON SOURCE LINES 71-73 5. Convert to B-mode magnitude for visualization ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 73-78 .. code-block:: Python data_array = create_bmode_image(beamformed_image) print(f"After taking magnitude - Data range: [{data_array.min():.3f}, {data_array.max():.3f}]") .. rst-class:: sphx-glr-script-out .. code-block:: none After taking magnitude - Data range: [0.003, 62.383] .. GENERATED FROM PYTHON SOURCE LINES 79-81 6. Simple visualization with physical coordinates ------------------------------------------------------------------------ .. GENERATED FROM PYTHON SOURCE LINES 81-121 .. code-block:: Python fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 5)) # Get physical coordinates from scan geometry x_coords = scan.x_axis z_coords = scan.z_axis # Plot the magnitude data with physical coordinates # Use 'equal' aspect for square pixels, assuming isotropic grid spacing im1 = ax1.imshow( data_array.T, cmap="gray", aspect="equal", extent=[x_coords.min(), x_coords.max(), z_coords.max(), z_coords.min()], ) ax1.set_title(f"Magnitude of Beamformed Data\n{dataset_name}") ax1.set_xlabel("Lateral Position (m)") ax1.set_ylabel("Axial Position (m)") # Add colorbar for linear magnitude image fig.colorbar(im1, ax=ax1, orientation="vertical", label="Magnitude (linear)") # Plot in dB scale (common for ultrasound visualization) data_db = db_zero(data_array) im2 = ax2.imshow( data_db.T, cmap="gray", aspect="equal", vmin=-60, vmax=0, extent=[x_coords.min(), x_coords.max(), z_coords.max(), z_coords.min()], ) ax2.set_title("B-mode (dB scale)\nNormalized to 0dB") ax2.set_xlabel("Lateral Position (m)") ax2.set_ylabel("Axial Position (m)") # Add colorbar for dB scale image fig.colorbar(im2, ax=ax2, orientation="vertical", label="dB") .. image-sg:: /example_gallery/images/sphx_glr_visualize_picmus_dataset_001.png :alt: Magnitude of Beamformed Data picmus_resolution_experiment, B-mode (dB scale) Normalized to 0dB :srcset: /example_gallery/images/sphx_glr_visualize_picmus_dataset_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 122-128 .. code-block:: Python print("\nVisualization complete!") print("Left: Raw beamformed data") print("Right: B-mode in dB scale (typical ultrasound display)") print("\nNote: This example demonstrates the new module structure:") print("- General utilities (create_bmode_image, db_zero) from ultrasound_metrics.data") print("- UFF-specific functionality (load_uff_dataset) from ultrasound_metrics.data.uff") .. rst-class:: sphx-glr-script-out .. code-block:: none Visualization complete! Left: Raw beamformed data Right: B-mode in dB scale (typical ultrasound display) Note: This example demonstrates the new module structure: - General utilities (create_bmode_image, db_zero) from ultrasound_metrics.data - UFF-specific functionality (load_uff_dataset) from ultrasound_metrics.data.uff .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 0.192 seconds) .. _sphx_glr_download_example_gallery_visualize_picmus_dataset.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: visualize_picmus_dataset.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: visualize_picmus_dataset.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: visualize_picmus_dataset.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_