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Smooth pose tracks#

Smooth pose tracks using the median and Savitzky-Golay filters.

Imports#

from matplotlib import pyplot as plt
from scipy.signal import welch

from movement import sample_data

Load a sample dataset#

Let’s load a sample dataset and print it to inspect its contents. Note that if you are running this notebook interactively, you can simply type the variable name (here ds_wasp) in a cell to get an interactive display of the dataset’s contents.

ds_wasp = sample_data.fetch_dataset("DLC_single-wasp.predictions.h5")
print(ds_wasp)

<xarray.Dataset> Size: 61kB
Dimensions:      (time: 1085, individuals: 1, keypoints: 2, space: 2)
Coordinates:
  * time         (time) float64 9kB 0.0 0.025 0.05 0.075 ... 27.05 27.07 27.1
  * individuals  (individuals) <U12 48B 'individual_0'
  * keypoints    (keypoints) <U7 56B 'head' 'stinger'
  * space        (space) <U1 8B 'x' 'y'
Data variables:
    position     (time, individuals, keypoints, space) float64 35kB 1.086e+03...
    confidence   (time, individuals, keypoints) float64 17kB 0.05305 ... 0.0
Attributes:
    fps:              40.0
    time_unit:        seconds
    source_software:  DeepLabCut
    source_file:      /home/runner/.movement/data/poses/DLC_single-wasp.predi...
    ds_type:          poses
    frame_path:       /home/runner/.movement/data/frames/single-wasp_frame-10...
    video_path:       None

We see that the dataset contains the 2D pose tracks and confidence scores for a single wasp, generated with DeepLabCut. The wasp is tracked at two keypoints: “head” and “stinger” in a video that was recorded at 40 fps and lasts for approximately 27 seconds.

Define a plotting function#

Let’s define a plotting function to help us visualise the effects smoothing both in the time and frequency domains. The function takes as inputs two datasets containing raw and smooth data respectively, and plots the position time series and power spectral density (PSD) for a given individual and keypoint. The function also allows you to specify the spatial coordinate (x or y) and a time range to focus on.

def plot_raw_and_smooth_timeseries_and_psd(
    ds_raw,
    ds_smooth,
    individual="individual_0",
    keypoint="stinger",
    space="x",
    time_range=None,
):
    # If no time range is specified, plot the entire time series
    if time_range is None:
        time_range = slice(0, ds_raw.time[-1])

    selection = {
        "time": time_range,
        "individuals": individual,
        "keypoints": keypoint,
        "space": space,
    }

    fig, ax = plt.subplots(2, 1, figsize=(10, 6))

    for ds, color, label in zip(
        [ds_raw, ds_smooth], ["k", "r"], ["raw", "smooth"], strict=False
    ):
        # plot position time series
        pos = ds.position.sel(**selection)
        ax[0].plot(
            pos.time,
            pos,
            color=color,
            lw=2,
            alpha=0.7,
            label=f"{label} {space}",
        )

        # interpolate data to remove NaNs in the PSD calculation
        pos_interp = ds.sel(**selection).move.interpolate_over_time(
            print_report=False
        )
        # compute and plot the PSD
        freq, psd = welch(pos_interp, fs=ds.fps, nperseg=256)
        ax[1].semilogy(
            freq,
            psd,
            color=color,
            lw=2,
            alpha=0.7,
            label=f"{label} {space}",
        )

    ax[0].set_ylabel(f"{space} position (px)")
    ax[0].set_xlabel("Time (s)")
    ax[0].set_title("Time Domain")
    ax[0].legend()

    ax[1].set_ylabel("PSD (px$^2$/Hz)")
    ax[1].set_xlabel("Frequency (Hz)")
    ax[1].set_title("Frequency Domain")
    ax[1].legend()

    plt.tight_layout()
    fig.show()

Smooth pose tracks#

Imports#

Load a sample dataset#

Define a plotting function#

Smoothing with a median filter#

Choosing parameters for the median filter#

Smoothing with a Savitzky-Golay filter#

Combining multiple smoothing filters#