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import nixio
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import docutils
def create_example_data(nixfile):
sampling_interval = 0.001
total_duration = 3.0
time = np.arange(0., total_duration, sampling_interval)
stim = np.ones(time.shape)
stim_duration = 0.25
intervals = np.arange(0.25, total_duration, stim_duration * 3)
stim_frequencies = np.zeros_like(intervals)
stim_onsets = np.zeros_like(intervals)
stim_extents = np.zeros_like(intervals)
base_freq = 5
for i, interval in enumerate(intervals):
stim[(time >= interval) & (time < interval + stim_duration)] = i + 2
stim_frequencies[i] = (i + 2) * base_freq
stim_onsets[i] = interval
stim_extents[i] = stim_duration
stim *= base_freq
signal = np.sin(time * 2 * np.pi * stim)
block = nixfile.create_block("multiple regions", "nix.session")
data_array = block.create_data_array("signal", "nix.data.sampled", data=signal)
data_array.label = "voltage"
data_array.unit = "mV"
data_array.append_sampled_dimension(sampling_interval, label="time", unit="s")
positions = block.create_data_array("stimulus onsets", "nix.region.onsets", data=stim_onsets)
positions.append_set_dimension()
extents = block.create_data_array("stimulus extents", "nix.region.extents", data=stim_extents)
extents.append_set_dimension()
frequencies = block.create_data_array("stimulus frequency", "nix.feature", data=stim_frequencies)
frequencies.label = "frequency"
frequencies.unit = "Hz"
frequencies.append_set_dimension()
mtag = block.create_multi_tag("stimulus segments", "nix.segments.stimulus", positions=positions, extents=extents)
mtag.references.append(data_array)
mtag.create_feature(frequencies, nixio.LinkType.Indexed)
def plot(nixfile):
block = nixfile.blocks[0]
signal_da = block.data_arrays["signal"]
signal = signal_da[:]
signal_dim = signal_da.dimensions[0]
time = np.asarray(signal_dim.axis(len(signal)))
mtag = block.multi_tags[0]
fig = plt.figure()
fig.set_size_inches(5.5, 2.5)
ax = fig.add_subplot(111)
l, = ax.plot(time, signal, label=signal_da.name)
ax.set_xlim([0., 3.])
ax.set_ylim([-1.45, 1.45])
ax.set_xticks(np.arange(0., 3.01, 0.5))
ax.set_yticks(np.arange(-1.5, 1.6, 0.5))
ax.set_xlabel("%s %s" % (signal_dim.label, "[%s]" % signal_dim.unit if signal_dim.unit else ""))
ax.set_ylabel("%s %s" % (signal_da.label, "[%s]" % signal_da.unit if signal_da.unit else ""))
for i, (interval, extent) in enumerate(zip(mtag.positions[:], mtag.extents[:])):
rect = patches.Rectangle((interval, 1.05), extent, -2.1, alpha=0.5,
facecolor="silver", edgecolor='k', lw=0.75, ls='--')
ax.add_patch(rect)
stim_freq = mtag.feature_data(i, "stimulus frequency")[:] # should be scalar, we will use item() to read it
ax.text(interval + extent / 2, -1.25,
"%.1f %s" % (stim_freq.item(),
mtag.features["stimulus frequency"].data.unit), fontsize=8, ha="center")
ax.legend((l, rect), (signal_da.name, mtag.name), loc=1, frameon=False, ncol=2)
ax.spines["top"].set_visible(False)
ax.spines["right"].set_visible(False)
fig.subplots_adjust(bottom=0.175, left=0.15, right=0.95, top=0.95)
if docutils.is_running_under_pytest():
plt.close()
else:
# fig.savefig("../images/multiple_regions.png")
plt.show()
def plot_tagged_data(nixfile):
block = nixfile.blocks[0]
mtag = block.multi_tags[0]
signal_da = mtag.references["signal"]
signal_dim = signal_da.dimensions[0]
xlabel = "%s %s" % (signal_dim.label, "[%s]" % signal_dim.unit if signal_dim.unit else "")
ylabel = "%s %s" % (signal_da.label, "[%s]" % signal_da.unit if signal_da.unit else "")
fig = plt.figure(figsize=(5.5, 2.5))
num_segments = len(mtag.positions[:])
for i in range(num_segments):
data = mtag.tagged_data(i, "signal")[:]
time = signal_dim.axis(len(data), start_position=mtag.positions[i])
ax = fig.add_subplot(1, num_segments, i + 1)
ax.plot(time, data)
ax.spines["top"].set_visible(False)
ax.spines["right"].set_visible(False)
ax.set_xlabel(xlabel)
if i == 0:
ax.set_ylabel(ylabel)
else:
ax.set_yticklabels([])
fig.subplots_adjust(left=0.15, bottom=0.2, wspace=0.5, right=0.975)
if docutils.is_running_under_pytest():
plt.close()
else:
# fig.savefig("../images/reading_tagged_data.png")
plt.show()
def main():
nixfile = nixio.File.open("multiple_regions.nix", nixio.FileMode.Overwrite)
create_example_data(nixfile)
plot(nixfile)
plot_tagged_data(nixfile)
nixfile.close()
if __name__ == "__main__":
main()
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