128 lines
3.5 KiB
Python
128 lines
3.5 KiB
Python
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from stimuli.SinusoidalStepStimulus import SinusoidalStepStimulus
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from stimuli.SinusAmplitudeModulation import SinusAmplitudeModulationStimulus
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from parser.CellData import CellData
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import numpy as np
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import matplotlib.pyplot as plt
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import Figure_constants as consts
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def main():
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# stimuli_protocol_examples()
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am_generation()
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pass
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def am_generation():
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cell = "data/final/2013-04-17-ac-invivo-1"
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cell_data = CellData(cell)
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fig, axes = plt.subplots(3, 1, sharey=True, sharex=True, figsize=consts.FIG_SIZE_MEDIUM)
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start = 0
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end = 0.05
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time_start = -0.025
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time_end = 0.075
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step_size = 0.00005
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# frequency = 55
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contrast = 0.3
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eod = cell_data.get_base_traces(cell_data.EOD)[0]
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step = cell_data.get_sampling_interval()
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values = eod[:int(round((time_end-time_start)/step))]
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# base_stim = SinusoidalStepStimulus(frequency, 0, start, end - start)
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#
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# values = base_stim.as_array(time_start, time_end - time_start, step_size)
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time = np.arange(time_start, time_end, step_size) * 1000
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axes[0].set_title("Fish EOD")
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axes[0].plot(time, values)
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am = np.zeros(len(values))
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am[int((start-time_start)/step_size):int((end-time_start)/step_size)] = contrast
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axes[1].set_title("Amplitude Modulation")
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axes[1].plot(time, values*am)
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axes[1].plot(time, am)
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axes[1].set_ylabel("Voltage [mV]")
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axes[2].set_title("Resulting stimulus")
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axes[2].plot(time, (values*am) + values)
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axes[2].set_xlabel("Time [ms]")
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axes[2].set_xlim((time[0], time[-1]))
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axes[2].set_xticks([-25, 0, 25, 50, 75])
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plt.tight_layout()
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consts.set_figure_labels(xoffset=-2.5, yoffset=1.5)
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fig.label_axes()
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plt.savefig("thesis/figures/amGeneration.pdf")
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plt.close()
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def stimuli_protocol_examples():
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fig, axes = plt.subplots(3, 1, sharey=True, sharex=True, figsize=consts.FIG_SIZE_MEDIUM)
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start = 0
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end = 1
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time_start = -0.2
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time_end = 1.2
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step_size = 0.00005
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frequency = 55
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contrast = 0.5
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base_stim = SinusoidalStepStimulus(frequency, 0, start, end - start)
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values = base_stim.as_array(time_start, time_end - time_start, step_size)
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time = np.arange(time_start, time_end, step_size)
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axes[0].set_title("Baseline Stimulus")
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axes[0].plot(time, values)
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# axes[1].set_ylabel("Voltage [mV]")
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# Sinusoidal STEP stimulus
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# frequency, contrast, start_time=0, duration=np.inf, amplitude=1
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step_stim = SinusoidalStepStimulus(frequency, contrast, start, end - start)
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values = step_stim.as_array(time_start, time_end - time_start, step_size)
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time = np.arange(time_start, time_end, step_size)
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axes[1].set_title("Step Stimulus")
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axes[1].plot(time, values)
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axes[1].set_ylabel("Voltage [mV]")
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# SAM Stimulus:
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mod_freq = 10
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step_stim = SinusAmplitudeModulationStimulus(frequency, contrast, mod_freq, start, end - start)
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values = step_stim.as_array(time_start, time_end - time_start, step_size)
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time = np.arange(time_start, time_end, step_size)
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plt.plot(time, values)
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beat_time = np.arange(start, end, step_size)
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beat_values = np.sin(beat_time * 2 * np.pi * mod_freq) * contrast + 1
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axes[2].plot(beat_time, beat_values)
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axes[2].set_title("SAM Stimulus")
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axes[2].set_xlabel("Time [s]")
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# axes[2].set_ylabel("Voltage [mV]")
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axes[2].set_xlim((time_start, time_end))
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plt.tight_layout()
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consts.set_figure_labels(xoffset=-2.5)
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fig.label_axes()
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plt.savefig("thesis/figures/stimuliExamples.pdf")
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plt.close()
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if __name__ == '__main__':
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main()
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