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+# Reading and processing NIRS data with MNE-Python
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+
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+```python
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+import mne
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+import warnings
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+import numpy as np
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+import matplotlib.pyplot as plt
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+from itertools import compress
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+
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+from almirah import Layout
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+
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+mne.set_log_level(False)
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+warnings.filterwarnings('ignore')
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+```
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+
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+```python
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+lay = Layout(root="/path/to/data", specification_name="bids")
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+print(lay)
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+```
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+
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+ <Layout root: '/path/to/data'>
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+
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+```python
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+files = lay.query(datatype="nirs", extension=".snirf")
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+len(files)
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+```
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+
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+ 1315
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+
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+```python
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+file = lay.query(subject="D0019", task="rest", datatype="nirs", extension=".snirf")[0]
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+print(file.rel_path)
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+```
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+
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+ sub-D0019/ses-111/nirs/sub-D0019_ses-111_task-rest_run-01_nirs.snirf
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+
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+```python
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+file.download()
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+```
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+
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+```python
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+raw = mne.io.read_raw_snirf(file.path)
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+raw.load_data()
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+```
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+
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+<details open>
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+ <summary><strong>General</strong></summary>
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+ <table class="table table-hover table-striped table-sm table-responsive small">
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+ <tr>
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+ <th>Measurement date</th>
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+ <td>November 12, 1917 00:00:00 GMT</td>
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+
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+ </tr>
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+ <tr>
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+ <th>Experimenter</th>
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+ <td>Unknown</td>
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+
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+ </tr>
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+ <tr>
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+ <th>Participant</th>
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+ <td>mne_anonymize</td>
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+ </tr>
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+ </table>
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+ </details>
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+ <details open>
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+ <summary><strong>Channels</strong></summary>
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+ <table class="table table-hover table-striped table-sm table-responsive small">
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+ <tr>
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+ <th>Digitized points</th>
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+ <td>21 points</td>
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+ </tr>
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+ <tr>
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+ <th>Good channels</th>
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+ <td>36 fNIRS (CW amplitude)</td>
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+ </tr>
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+ <tr>
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+ <th>Bad channels</th>
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+ <td>None</td>
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+ </tr>
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+ <tr>
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+ <th>EOG channels</th>
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+ <td>Not available</td>
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+ </tr>
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+ <tr>
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+ <th>ECG channels</th>
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+ <td>Not available</td>
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+ </tr>
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+ </table>
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+ </details>
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+ <details open>
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+ <summary><strong>Data</strong></summary>
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+ <table class="table table-hover table-striped table-sm table-responsive small">
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+ <tr>
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+ <th>Sampling frequency</th>
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+ <td>15.62 Hz</td>
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+ </tr>
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+ <tr>
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+ <th>Highpass</th>
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+ <td>0.00 Hz</td>
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+ </tr>
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+ <tr>
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+ <th>Lowpass</th>
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+ <td>7.81 Hz</td>
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+ </tr>
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+ <tr>
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+ <th>Filenames</th>
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+ <td>sub-D0019_ses-111_task-rest_run-01_nirs.snirf</td>
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+ </tr>
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+ <tr>
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+ <th>Duration</th>
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+ <td>00:10:03 (HH:MM:SS)</td>
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+ </tr>
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+ </table>
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+ </details>
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+
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+```python
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+print(raw.info)
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+```
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+
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+ <Info | 9 non-empty values
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+ bads: []
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+ ch_names: S1_D1 760, S1_D1 850, S1_D2 760, S1_D2 850, S2_D2 760, S2_D2 ...
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+ chs: 36 fNIRS (CW amplitude)
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+ custom_ref_applied: False
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+ dig: 21 items (3 Cardinal, 18 EEG)
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+ highpass: 0.0 Hz
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+ lowpass: 7.8 Hz
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+ meas_date: 1917-11-12 00:00:00 UTC
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+ nchan: 36
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+ projs: []
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+ sfreq: 15.6 Hz
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+ subject_info: 4 items (dict)
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+ >
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+
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+```python
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+picks = mne.pick_types(raw.info, meg=False, fnirs=True)
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+dists = mne.preprocessing.nirs.source_detector_distances(raw.info, picks=picks)
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+raw.pick(picks[dists > 0.01])
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+raw.plot(n_channels=len(raw.ch_names), duration=500, show_scrollbars=False)
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+plt.show()
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+```
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+
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+![png](../images/nirs/raw-plot.png)
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+
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+```python
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+raw_od = mne.preprocessing.nirs.optical_density(raw)
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+raw_od.plot(n_channels=len(raw_od.ch_names), duration=500, show_scrollbars=False)
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+plt.show()
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+```
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+
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+![png](../images/nirs/optical-density-plot.png)
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+
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+```python
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+sci = mne.preprocessing.nirs.scalp_coupling_index(raw_od)
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+fig, ax = plt.subplots()
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+ax.hist(sci)
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+ax.set(xlabel="Scalp Coupling Index", ylabel="Count", xlim=[0, 1])
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+plt.show()
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+```
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+
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+![png](../images/nirs/scalp-coupling-index-plot.png)
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+
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+```python
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+raw_od.info["bads"] = list(compress(raw_od.ch_names, sci < 0.5))
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+```
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+
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+```python
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+raw_haemo = mne.preprocessing.nirs.beer_lambert_law(raw_od, ppf=0.1)
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+raw_haemo.plot(n_channels=len(raw_haemo.ch_names), duration=500, show_scrollbars=False)
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+plt.show()
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+```
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+
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+![png](../images/nirs/raw-haemo-plot.png)
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+
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+```python
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+fig = raw_haemo.compute_psd().plot(average=True, amplitude=False)
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+fig.suptitle("Before filtering", weight="bold", size="x-large")
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+raw_haemo = raw_haemo.filter(0.05, 0.7, h_trans_bandwidth=0.2, l_trans_bandwidth=0.02)
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+fig = raw_haemo.compute_psd().plot(average=True)
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+fig.suptitle("After filtering", weight="bold", size="x-large")
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+plt.show()
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+```
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+
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+![png](../images/nirs/raw-haemo-psd-before-filtering.png)
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+
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+![png](../images/nirs/raw-haemo-psd-after-filtering.png)
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+
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+```python
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+epochs = mne.make_fixed_length_epochs(raw_haemo, duration=30, preload=False)
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+```
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+
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+```python
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+epochs.plot_image(combine="mean", vmin=-30, vmax=30,
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+ ts_args=dict(ylim=dict(hbo=[-15, 15],
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+ hbr=[-15, 15])))
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+plt.show()
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+```
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+
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+![png](deoxyhemoglobin-plot.png)
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+
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+![png](oxyhemoglobin-plot.png)
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+
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