Beamforming with a cartesian grid and a polar grid¶

In this notebook, we will demonstrate how you can do beamforming with zea using a cartesian grid and a polar grid. We will use the ScanConvert to convert the polar data to cartesian data.

[1]:

%%capture
%pip install zea

[2]:

import os

os.environ["KERAS_BACKEND"] = "jax"
os.environ["ZEA_DISABLE_CACHE"] = "1"
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"

[3]:

import matplotlib.pyplot as plt
import numpy as np

import zea
from zea import ops
from zea.beamform.delays import compute_t0_delays_focused
from zea.beamform.phantoms import fish
from zea.probes import Probe
from zea.scan import Scan
from zea.visualize import pad_or_crop_extent, set_mpl_style

zea.init_device(verbose=False)
set_mpl_style()

zea: Using backend 'jax'

WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
E0000 00:00:1752739728.747031  674733 cuda_dnn.cc:8579] Unable to register cuDNN factory: Attempting to register factory for plugin cuDNN when one has already been registered
E0000 00:00:1752739728.752641  674733 cuda_blas.cc:1407] Unable to register cuBLAS factory: Attempting to register factory for plugin cuBLAS when one has already been registered
W0000 00:00:1752739728.767638  674733 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1752739728.767654  674733 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1752739728.767657  674733 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.
W0000 00:00:1752739728.767658  674733 computation_placer.cc:177] computation placer already registered. Please check linkage and avoid linking the same target more than once.

Define `zea.Probe` and `zea.Scan`¶

Let’s initialize a linear ultrasound probe.

[4]:

n_el = 128
aperture = 30e-3
probe_geometry = np.stack(
    [
        np.linspace(-aperture / 2, aperture / 2, n_el),
        np.zeros(n_el),
        np.zeros(n_el),
    ],
    axis=1,
)

probe = Probe(
    probe_geometry=probe_geometry,
    center_frequency=2.5e6,
    sampling_frequency=10e6,
)

We will use a focused scan for this example.

[5]:

sound_speed = 1540.0
n_tx = 8

tx_apodizations = np.ones((n_tx, probe.n_el)) * np.hanning(probe.n_el)[None]
angles = np.linspace(30, -30, n_tx) * np.pi / 180
focus_distances = np.ones(n_tx) * 15e-3
t0_delays = compute_t0_delays_focused(
    origins=np.zeros((n_tx, 3)),
    focus_distances=focus_distances,
    probe_geometry=probe.probe_geometry,
    polar_angles=angles,
    sound_speed=sound_speed,
)

scan = Scan(
    n_el=n_el,
    center_frequency=probe.center_frequency,
    sampling_frequency=probe.sampling_frequency,
    probe_geometry=probe.probe_geometry,
    t0_delays=t0_delays,
    tx_apodizations=tx_apodizations,
    focus_distances=focus_distances,
    polar_angles=angles,
    initial_times=np.ones(n_tx) * 1e-6,
    n_ax=1024,
    lens_sound_speed=1000,
    lens_thickness=1e-3,
    sound_speed=sound_speed,
    xlims=(-20e-3, 20e-3),
    zlims=(0, 35e-3),
    n_tx=n_tx,
    n_ch=1,
)

Finally we initialize a scatterer phantom.

[6]:

# Initialize the fish phantom
scat_positions = fish()
n_scat = scat_positions.shape[0]
simulation_parameters = dict(
    scatterer_positions=scat_positions.astype(np.float32),
    scatterer_magnitudes=np.ones(n_scat, dtype=np.float32),
)

Initialize the pipeline¶

We initialize the default beamforming pipeline and prepend the simulator as the first operation. Finally, we normalize the beamformed data to [0, 255] range for visualization purposes.

[7]:

pipeline = ops.Pipeline.from_default()
pipeline.prepend(ops.Simulate())
pipeline.append(ops.Normalize(input_range=ops.DEFAULT_DYNAMIC_RANGE, output_range=(0, 255)))