Note
Go to the end to download the full example code
GSD Iluz#
This example shows how to use the GSD Iluz algorithm and some examples on how the results compare to the original matlab implementation.
We start by defining some helpers for plotting and loading the data. You can skip them for now and jump directly to “Performance on a single lab trial”, if you just want to see how to apply the algorithm.
Plotting Helper#
We define a helper function to plot the results of the algorithm. Just ignore this function for now.
import matplotlib.pyplot as plt
def plot_gsd_outputs(data, **kwargs):
fig, ax = plt.subplots()
ax.plot(data["acc_is"].to_numpy(), label="acc_is")
color_cycle = iter(plt.rcParams["axes.prop_cycle"])
y_max = 1.1
plot_props = [
{
"data": v,
"label": k,
"alpha": 0.2,
"ymax": (y_max := y_max - 0.1),
"color": next(color_cycle)["color"],
}
for k, v in kwargs.items()
]
for props in plot_props:
for gsd in props.pop("data").itertuples(index=False):
ax.axvspan(
gsd.start, gsd.end, label=props.pop("label", None), **props
)
ax.legend()
return fig, ax
Loading some example data#
Note
More infos about data loading can be found in the data loading example.
We load example data from the lab dataset together with the INDIP reference system. We will use the INDIP “WB” output as ground truth. Note, that the “WB” (Walking Bout) output is further processed than a normal “Gait Sequence”. This means we expect Gait Sequences to contain some false positives compared to the “WB” output. However, a good gait sequence detection algorithm should have high sensitivity (i.e. contain all the “WBs” of the reference system).
import json
import pandas as pd
from mobgap import PACKAGE_ROOT
from mobgap.data import LabExampleDataset
lab_example_data = LabExampleDataset(reference_system="INDIP")
def load_matlab_output(datapoint):
p = datapoint.group_label
with (
PACKAGE_ROOT.parent
/ f"example_data/original_results/gsd_iluz/lab/{p.cohort}/{p.participant_id}/GSDA_Output.json"
).open() as f:
original_results = json.load(f)["GSDA_Output"][p.time_measure][p.test][
p.trial
]["SU"]["LowerBack"]["GSD"]
if not isinstance(original_results, list):
original_results = [original_results]
return (
pd.DataFrame.from_records(original_results).rename(
{"GaitSequence_Start": "start", "GaitSequence_End": "end"}, axis=1
)[["start", "end"]]
* datapoint.sampling_rate_hz
)
Performance on a single lab trial#
Below we apply the algorithm to a lab trail, where we only expect a single gait sequence.
Like most algorithms, the GsdIluz requires the data to be in body frame coordinates.
As we know the sensor was well aligned, we can just use to_body_frame to transform the data.
from mobgap.gait_sequences import GsdIluz
from mobgap.utils.conversions import to_body_frame
short_trial = lab_example_data.get_subset(
cohort="HA", participant_id="001", test="Test5", trial="Trial2"
)
short_trial_data = to_body_frame(short_trial.data_ss)
short_trial_matlab_output = load_matlab_output(short_trial)
short_trial_reference_parameters = short_trial.reference_parameters_.wb_list
short_trial_output = GsdIluz().detect(
short_trial_data, sampling_rate_hz=short_trial.sampling_rate_hz
)
print("Reference Parameters:\n\n", short_trial_reference_parameters)
print("\nMatlab Output:\n\n", short_trial_matlab_output)
print("\nPython Output:\n\n", short_trial_output.gs_list_)
Reference Parameters:
start end ... avg_stride_length_m termination_reason
wb_id ...
0 392 862 ... 1.211187 Pause
[1 rows x 9 columns]
Matlab Output:
start end
0 299.0 1049.0
Python Output:
start end
gs_id
0 150 1051
When we plot the output, we can see that the python version is a little more sensitive than the matlab version. It includes a section of the signal before the region classified as WB by the reference system. Both algorithm implementations produce a gait sequence that extends beyond the end of the reference system.
fig, ax = plot_gsd_outputs(
short_trial_data,
reference=short_trial_reference_parameters,
matlab=short_trial_matlab_output,
python=short_trial_output.gs_list_,
)
fig.show()
Performance on a longer lab trial#
Below we apply the algorithm to a lab trail that contains activities of daily living. This is a more challenging scenario, as we expect multiple gait sequences.
long_trial = lab_example_data.get_subset(
cohort="MS", participant_id="001", test="Test11", trial="Trial1"
)
long_trial_data = to_body_frame(long_trial.data_ss)
long_trial_matlab_output = load_matlab_output(long_trial)
long_trial_reference_parameters = long_trial.reference_parameters_.wb_list
long_trial_output = GsdIluz().detect(
long_trial_data, sampling_rate_hz=long_trial.sampling_rate_hz
)
print("Reference Parameters:\n\n", long_trial_reference_parameters)
print("\nMatlab Output:\n\n", long_trial_matlab_output)
print("\nPython Output:\n\n", long_trial_output.gs_list_)
/home/docs/checkouts/readthedocs.org/user_builds/mobgap/checkouts/v0.9.0/mobgap/data/_mobilised_matlab_loader.py:1082: UserWarning: There were multiple ICs with the same index value, but different LR labels. This is likely an issue with the reference system you should further investigate. For now, we set the `lr_label` of the stride corresponding to this IC to Nan. However, both values still remain in the IC list.
return parse_reference_parameters(
Reference Parameters:
start end ... avg_stride_length_m termination_reason
wb_id ...
0 1019 1768 ... 0.942678 Pause
1 4534 5549 ... 0.483923 Pause
2 9665 10569 ... 0.506458 Pause
3 12337 14633 ... 0.803933 Pause
4 20151 20982 ... 0.507484 Pause
5 21378 22129 ... 0.599360 Pause
[6 rows x 9 columns]
Matlab Output:
start end
0 899.0 1799.0
1 13049.0 13949.0
2 14099.0 14849.0
3 20249.0 21149.0
4 21299.0 22349.0
Python Output:
start end
gs_id
0 750 1651
1 4650 6151
2 12900 14851
3 20100 21151
4 21300 22501
When we plot the output, we can see again that the python version is more sensitive. It detects longer gait sequences and even one entire gait sequence that is not detected by the matlab version.
fig, _ = plot_gsd_outputs(
long_trial_data,
reference=long_trial_reference_parameters,
matlab=long_trial_matlab_output,
python=long_trial_output.gs_list_,
)
fig.show()
Changing the parameters#
The Python version aims to expose all relevant parameters of the algorithm.
The GsdlIluz algorithm has a lot of parameters that can be modified.
Finding a combination of parameters that works well for all scenarios is difficult.
Below we show, just how to modify them in general.
We modify one of the basic parameters, the window length. This can effect all parts of the output. In this case, we can see that all GSDs are slightly longer and that we now detect a gait sequence that was not detected before.
long_trial_output_modified = GsdIluz(
window_length_s=5, window_overlap=0.8
).detect(long_trial_data, sampling_rate_hz=long_trial.sampling_rate_hz)
print("Reference Parameters:\n\n", long_trial_reference_parameters)
print("\nPython Output:\n\n", long_trial_output.gs_list_)
print("\nPython Output Modified:\n\n", long_trial_output_modified.gs_list_)
fig, _ = plot_gsd_outputs(
long_trial_data,
reference=long_trial_reference_parameters,
python=long_trial_output.gs_list_,
python_modified=long_trial_output_modified.gs_list_,
)
fig.show()
Reference Parameters:
start end ... avg_stride_length_m termination_reason
wb_id ...
0 1019 1768 ... 0.942678 Pause
1 4534 5549 ... 0.483923 Pause
2 9665 10569 ... 0.506458 Pause
3 12337 14633 ... 0.803933 Pause
4 20151 20982 ... 0.507484 Pause
5 21378 22129 ... 0.599360 Pause
[6 rows x 9 columns]
Python Output:
start end
gs_id
0 750 1651
1 4650 6151
2 12900 14851
3 20100 21151
4 21300 22501
Python Output Modified:
start end
gs_id
0 600 1901
1 4500 6201
2 9700 10301
3 12700 14901
4 20100 22701
Evaluation of the algorithm against a reference#
To quantify how the Python output compares to the reference labels, we are providing a range of evaluation functions. See the example on GSD evaluation for more details.
Total running time of the script: (0 minutes 1.907 seconds)
Estimated memory usage: 9 MB