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https://github.com/nqrduck/quackseq-simulator.git
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Added sequence examples.
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jupfi
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6 changed files with 228 additions and 2 deletions
59
examples/COMPFID.py
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59
examples/COMPFID.py
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"""Composite FID example.
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This example demonstrates how to simulate a composite FID signal using the quackseq simulator.
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See the paper:
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Sauer, K.L., Klug, C.A., Miller, J.B. et al. Using quaternions to design composite pulses for spin-1 NQR. Appl. Magn. Reson. 25, 485–500 (2004). https://doi.org/10.1007/BF03166543
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This also works for Samples with spin > 1.
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"""
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import logging
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from quackseq_simulator.simulator import Simulator
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from quackseq.pulsesequence import QuackSequence
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from quackseq.functions import RectFunction
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from matplotlib import pyplot as plt
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if __name__ == "__main__":
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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seq = QuackSequence("COMPFID")
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seq.add_pulse_event("tx1", "3u", 100, 0, RectFunction())
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seq.add_pulse_event("tx2", "6u", 100, 45, RectFunction())
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# This makes the phase 45, 135, 225, 315
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seq.set_tx_n_phase_cycles("tx2", 4)
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seq.add_blank_event("blank", "5u")
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seq.add_readout_event("rx", "100u")
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# No phase shifiting of the receive data but weighting of -1 for the 45 degree pulse, +1 for the 135 degree pulse, -1 for the 225 degree pulse and +1 for the 315 degree pulse
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readout_scheme = [[1, 0], [-1, 0], [1, 0], [-1, 0]]
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sim = Simulator()
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sim.set_averages(100)
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sim.settings.noise = 1 # microvolts
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result = sim.run_sequence(seq)
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# Plot time and frequency domain next to each other
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plt.subplot(1, 2, 1)
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plt.title("Time domain Simulation of BiPh3 COMPFID")
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plt.xlabel("Time (µs)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.tdx[-1], result.tdy[-1].imag, label="imaginary")
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plt.plot(result.tdx[-1], result.tdy[-1].real, label="real")
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plt.plot(result.tdx[-1], abs(result.tdy[-1]), label="abs")
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plt.subplot(1, 2, 2)
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plt.title("Frequency domain Simulation of BiPh3 COMPFID")
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plt.xlabel("Frequency (kHz)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.fdx[-1], result.fdy[-1].imag, label="imaginary")
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plt.plot(result.fdx[-1], result.fdy[-1].real, label="real")
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plt.plot(result.fdx[-1], abs(result.fdy[-1]), label="abs")
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plt.legend()
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plt.show()
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48
examples/FID.py
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48
examples/FID.py
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"""Example Free Induction Decay (FID) simulation using the quackseq simulator.
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The sample is the default BiPh3 NQR sample.
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"""
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import logging
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from quackseq_simulator.simulator import Simulator
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from quackseq.pulsesequence import QuackSequence
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from quackseq.functions import RectFunction
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from matplotlib import pyplot as plt
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if __name__ == "__main__":
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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seq = QuackSequence("FID")
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seq.add_pulse_event("tx", "3u", 100, 0, RectFunction())
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seq.add_blank_event("blank", "5u")
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seq.add_readout_event("rx", "100u")
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seq.add_blank_event("TR", "1m")
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sim = Simulator()
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sim.set_averages(100)
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sim.settings.noise = 1 # microvolts
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result = sim.run_sequence(seq)
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# Plot time and frequency domain next to each other
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plt.subplot(1, 2, 1)
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plt.title("Time domain Simulation of BiPh3 FID")
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plt.xlabel("Time (µs)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.tdx[0], result.tdy[0].imag, label="imaginary")
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plt.plot(result.tdx[0], result.tdy[0].real, label="real")
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plt.plot(result.tdx[0], abs(result.tdy[0]), label="abs")
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plt.subplot(1, 2, 2)
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plt.title("Frequency domain Simulation of BiPh3 FID")
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plt.xlabel("Frequency (kHz)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.fdx[0], result.fdy[0].imag, label="imaginary")
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plt.plot(result.fdx[0], result.fdy[0].real, label="real")
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plt.plot(result.fdx[0], abs(result.fdy[0]), label="abs")
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plt.legend()
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plt.show()
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49
examples/SE.py
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49
examples/SE.py
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"""Example Spin Echo (SE) simulation using the quackseq simulator.
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The sample is the default BiPh3 NQR sample.
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"""
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import logging
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from quackseq_simulator.simulator import Simulator
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from quackseq.pulsesequence import QuackSequence
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from quackseq.functions import RectFunction
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from matplotlib import pyplot as plt
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if __name__ == "__main__":
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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seq = QuackSequence("SE")
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seq.add_pulse_event("pi-half", "3u", 100, 0, RectFunction())
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seq.add_blank_event("te-half", "150u")
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seq.add_pulse_event("pi", "6u", 100, 0, RectFunction())
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seq.add_blank_event("blank", "50u")
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seq.add_readout_event("rx", "200u")
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sim = Simulator()
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sim.set_averages(100)
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sim.settings.noise = 1 # microvolts
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result = sim.run_sequence(seq)
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# Plot time and frequency domain next to each other
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plt.subplot(1, 2, 1)
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plt.title("Time domain Simulation of BiPh3 SE")
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plt.xlabel("Time (µs)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.tdx[0], result.tdy[0].imag, label="imaginary")
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plt.plot(result.tdx[0], result.tdy[0].real, label="real")
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plt.plot(result.tdx[0], abs(result.tdy[0]), label="abs")
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plt.subplot(1, 2, 2)
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plt.title("Frequency domain Simulation of BiPh3 SE")
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plt.xlabel("Frequency (kHz)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.fdx[0], result.fdy[0].imag, label="imaginary")
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plt.plot(result.fdx[0], result.fdy[0].real, label="real")
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plt.plot(result.fdx[0], abs(result.fdy[0]), label="abs")
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plt.legend()
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plt.show()
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58
examples/SEPC.py
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58
examples/SEPC.py
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"""Spin Echo with Phase Cycling (SEPC) simulation using the quackseq simulator.
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The sample is the default BiPh3 NQR sample.
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"""
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import logging
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from quackseq_simulator.simulator import Simulator
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from quackseq.pulsesequence import QuackSequence
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from quackseq.functions import RectFunction
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from matplotlib import pyplot as plt
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if __name__ == "__main__":
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logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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seq = QuackSequence("SEPC")
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seq.add_pulse_event("pi-half", "3u", 100, 0, RectFunction())
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# This causes the phase to cycle through 0, 90, 180, 270
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seq.set_tx_n_phase_cycles("pi-half", 4)
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seq.add_blank_event("te-half", "150u")
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# For the second pulse we just need a phase of 180
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seq.add_pulse_event("pi", "6u", 100, 180, RectFunction())
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seq.add_blank_event("blank", "50u")
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seq.add_readout_event("rx", "200u")
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# Readout scheme for phase cycling TX pulses have the scheme 0 90 180 270 for the first pulse and 180 always for the second pulse
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readout_scheme = [[1, 0], [1, 90], [1, 180], [1, 270]]
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seq.set_rx_readout_scheme("rx", readout_scheme)
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sim = Simulator()
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sim.set_averages(100)
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sim.settings.noise = 1 # microvolts
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result = sim.run_sequence(seq)
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# Plot time and frequency domain next to each other
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plt.subplot(1, 2, 1)
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plt.title("Time domain Simulation of BiPh3 SEPC")
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plt.xlabel("Time (µs)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.tdx[-1], result.tdy[-1].imag, label="imaginary")
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plt.plot(result.tdx[-1], result.tdy[-1].real, label="real")
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plt.plot(result.tdx[-1], abs(result.tdy[-1]), label="abs")
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plt.subplot(1, 2, 2)
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plt.title("Frequency domain Simulation of BiPh3 SEPC")
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plt.xlabel("Frequency (kHz)")
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plt.ylabel("Signal (a.u.)")
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plt.plot(result.fdx[-1], result.fdy[-1].imag, label="imaginary")
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plt.plot(result.fdx[-1], result.fdy[-1].real, label="real")
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plt.plot(result.fdx[-1], abs(result.fdy[-1]), label="abs")
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plt.legend()
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plt.show()
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@ -38,7 +38,7 @@ class SimulatorModel(SpectrometerModel):
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# Sample settings, this will be done in a separate module later on
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SAMPLE_NAME = "Name"
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NUMBER_ATOMS = "Number of atoms per unit volume (1/m^3)"
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NUMBER_ATOMS = "N. atoms (1/m^3)"
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DENSITY = "Density (g/cm^3)"
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MOLAR_MASS = "Molar mass (g/mol)"
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RESONANT_FREQUENCY = "Resonant freq. (MHz)"
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@ -170,10 +170,22 @@ class TestQuackSequence(unittest.TestCase):
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# Plotting the results
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plt.title("Phase cycling")
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logger.info(f"Number of data sets {len(result.tdy)}")
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plt.plot(result.tdx[0], result.tdy[0].real, label="pc 1")
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plt.plot(result.tdx[0], result.tdy[0].real, label="pc 1 real")
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plt.plot(result.tdx[0], result.tdy[0].imag, label="pc 2 imag")
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plt.legend()
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plt.show()
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plt.plot(result.tdx[1], result.tdy[1].real, label="pc 2")
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plt.plot(result.tdx[1], result.tdy[1].imag, label="pc 2")
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plt.legend()
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plt.show()
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plt.plot(result.tdx[2], result.tdy[2].real, label="pc 3")
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plt.plot(result.tdx[2], result.tdy[2].imag, label="pc 3")
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plt.legend()
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plt.show()
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plt.plot(result.tdx[3], result.tdy[3].real, label="pc 4")
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plt.plot(result.tdx[3], result.tdy[3].imag, label="pc 4")
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plt.legend()
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plt.show()
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plt.plot(result.tdx[4], abs(result.tdy[4]), label="Phase Cycling")
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plt.legend()
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plt.show()
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