`Tremor analysis notebook.ipynb`

This notebook helps analyze tremor data via a fast fourier transform, to report the frequency and magnitude of a tremor.

Last updated 3 years, 2 months ago

This notebook expects to analyze a data file from the "Physics Toolbox Sensor Suite" phone app.

- iOS: https://apps.apple.com/us/app/physics-toolbox-sensor-suite/id1128914250
- Android: https://play.google.com/store/apps/details?id=com.chrystianvieyra.physicstoolboxsuite

**[1] Upload your data file to the Jupyter server**- Click the "Jupyter" icon in the top left to go to your home directory.
- (You might want to "open in a new tab"!)

- Click the "upload" button to upload your data file.

- Click the "Jupyter" icon in the top left to go to your home directory.

**[2] Edit the cell below with the following information:**`target_file`

: CSV data file name.

**[3] Run all cells from the top.**There are several ways to do run cells, including...- On your keyboard, "shift" and "enter" to run each cell (one at a time)
- Use the "Run" button above (one at a time)
**Cell → Run all**to run everything at once

Before doing a fourier transform, data should be a uniform sampling – there should be an equal amount of time between each data timepoint. This isn't always true in the raw data. Use an interpolation to get uniform data.

Out[5]:

Last updated 3 years, 2 months ago

This notebook expects to analyze a data file from the "Physics Toolbox Sensor Suite" phone app.

- iOS: https://apps.apple.com/us/app/physics-toolbox-sensor-suite/id1128914250
- Android: https://play.google.com/store/apps/details?id=com.chrystianvieyra.physicstoolboxsuite

**[1] Upload your data file to the Jupyter server**- Click the "Jupyter" icon in the top left to go to your home directory.
- (You might want to "open in a new tab"!)

- Click the "upload" button to upload your data file.

- Click the "Jupyter" icon in the top left to go to your home directory.

**[2] Edit the cell below with the following information:**`target_file`

: CSV data file name.

**[3] Run all cells from the top.**There are several ways to do run cells, including...- On your keyboard, "shift" and "enter" to run each cell (one at a time)
- Use the "Run" button above (one at a time)
**Cell → Run all**to run everything at once

In [1]:

```
target_file = "sensor-4.csv"
# Edit this to change the plot title. The default uses your file name.
plot_title = "FFT tremor analysis for {}".format(target_file)
```

In [2]:

```
import math
import statistics
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.fftpack import fft
from scipy.interpolate import interp1d
import seaborn
```

In [3]:

```
data_raw = pd.read_csv(target_file, parse_dates=['time'])
```

Before doing a fourier transform, data should be a uniform sampling – there should be an equal amount of time between each data timepoint. This isn't always true in the raw data. Use an interpolation to get uniform data.

In [4]:

```
# Get the median interval time for this data (i.e. typical interval)
intervals = [data_raw.index[i] - data_raw.index[i-1] for
i in range(1, len(data_raw.index))]
interval = statistics.median(intervals)
# Convert to unix epoch timestamp for easier math.
ts_raw = [t.timestamp() for t in data_raw.time]
# Set up interpolation for total gForce.
gf_raw = list(data_raw.gFTotal)
interpolate = interp1d(ts_raw, gf_raw)
# Create uniform timepoints, derive interpolated gForce values.
ts_uniform = np.linspace(ts_raw[0], ts_raw[-1], len(ts_raw))
avg_delta = (ts_raw[-1] - ts_raw[0]) / len(ts_raw)
gf_uniform = interpolate(ts_uniform)
```

In [5]:

```
gf_fft_all = np.fft.fft(gf_uniform)
freqs_all = np.fft.fftfreq(len(ts_uniform), d=avg_delta)
# discard complex conjugate
target_len = int(len(freqs_all)/2)
freqs = freqs_all[1:target_len]
gf_fft = gf_fft_all[1:target_len]
plt.figure()
plt.plot(freqs, gf_fft)
plt.title(plot_title)
plt.xlabel("Frequency (Hz)")
plt.ylabel("Magnitude")
```

Out[5]:

In [6]:

```
# Get the maximum value, report the frequency and magintude.
peak_index = np.argmax(gf_fft)
peak_freq = freqs[peak_index]
peak_magnitude = abs(gf_fft[peak_index])
print("Peak frequency: {} Hz".format(peak_freq))
print("Peak magnitude: {}".format(peak_magnitude))
```