Generate a Phantom and visualize the contrast at different TE values

Example for generating a phantom and visualizing the contrast at different TE values.

from snake.core.phantom import Phantom
from snake.core.simulation import SimConfig, GreConfig

This notebook has interactive widgets, run it in google colab or locally to enjoy it fully

TR = 100
TE = 25
FA = 3
field = "7T"  # "1T5"

sim_conf = SimConfig(seq=GreConfig(TR=TR, TE=TE, FA=FA))
phantom = Phantom.from_brainweb(sub_id=4, sim_conf=sim_conf, output_res=1)

phantom

contrast_at_TE = phantom.contrast(resample=True, sim_conf=sim_conf)

from snake.toolkit.plotting import axis3dcut
import matplotlib.pyplot as plt

fig, ax = plt.subplots()
axis3dcut(contrast_at_TE.T, None, None, cuts=(0.5, 0.5, 0.5), ax=ax, width_inches=5)
fig

from ipywidgets import interact

fig = plt.figure()
sim_conf = SimConfig(seq=GreConfig(TR=TR, TE=TE, FA=FA))

phantom1T5 = Phantom.from_brainweb(
    sub_id=4, sim_conf=sim_conf, tissue_file="tissue_1T5", output_res=1
)
phantom7T = Phantom.from_brainweb(
    sub_id=4, sim_conf=sim_conf, tissue_file="tissue_7T", output_res=1
)


def live_contrast(TE: float = 10, TR: float = 100, FA: float = 3, tissue_field="1T5"):
    [ax.remove() for ax in fig.get_axes()]
    ax = fig.subplots()
    sim_conf.seq.TE = TE
    sim_conf.seq.TR = TR
    sim_conf.seq.FA = FA
    if tissue_field == "1T5":
        phantom = phantom1T5
    elif tissue_field == "7T":
        phantom = phantom7T
    contrast_at_TE = phantom.contrast(sim_conf=sim_conf, resample=True)
    axis3dcut(contrast_at_TE.T, None, cuts=(0.5, 0.5, 0.5), width_inches=5, ax=ax)
    fig.canvas.draw_idle()
    # if len(fig.get_axes()) >=5:
    #     fig.get_axes()[-1].remove()


live_contrast(TE=TE, TR=TR, FA=FA, tissue_field="1T5")

# Only for notebook interactive mode
# sphx
# interact(
#     live_contrast,
#     TE=(0, 100, 1),
#     TR=(0, 1000, 1),
#     FA=(0, 90, 1),
#     tissue_field=["1T5", "7T"],
# )

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