Glossary#

This page lists the words that the M3Resp documentation uses. Each word has one meaning on all pages. Names from the code, such as BreathEvent, are shown in code style.

baseline#: The slowly changing lower level of the EMG envelope. The step emg.moving_baseline calculates it as the 33rd percentile of the envelope in a moving window. The window is 7.5 s long and moves in steps of 0.2 s.
breath#: One breath that a detection step found in one signal. M3Resp keeps each breath as a BreathEvent, with a start time, an extremum time and an end time in seconds. EIT, EMG and ventilator detection all give BreathEvent objects, so you can compare breaths across modalities. Each breath is also an interval.
channel#: One input of a measuring device. Examples are one EMG electrode pair, or the airway pressure input of a Biopac system. One file can hold more than one channel.
ECG#: Electrocardiography: the electrical activity of the heart. The ECG is also present in the EMG of the respiratory muscles. M3Resp finds the R peak of each heartbeat and removes the ECG from the EMG.
EIT#: Electrical impedance tomography. EIT measures changes in the electrical impedance of the thorax and shows them as images of the lungs. It is one of the three modalities.
EMG#: Electromyography: the electrical activity of a muscle. In M3Resp, EMG comes from the respiratory muscles, for example the diaphragm. It is one of the three modalities.
envelope#: A smooth curve that follows the amplitude of the EMG. M3Resp calculates it from the filtered EMG over a moving window. The method is the RMS (root mean square), the ARV (average rectified value) or the median of the absolute signal. Breath detection on EMG uses the envelope.
event#: Something that happens at one moment, with one time in seconds. An example is a blood-gas draw. In code, an event is an Event.
extremum#: The turning point of one breath in a signal. For EIT and for ventilator volume, it is the change from inspiration to expiration. For EMG, it is the highest point of the envelope. For an occluded breath, it is the lowest airway pressure. A breath keeps it as extremum_time in seconds and extremum_index as a sample number.
interval#: Something that lasts, with a start_time and an end_time in seconds. Examples are an occlusion and a period of noise. In code, an interval is an Interval.
linked breath#: One breath that M3Resp matched across two or more modalities. Two breaths match when their extremum times are 0.5 s or less apart (you can change this tolerance). In code, a linked breath is a LinkedBreath.
modality#: The measuring method of a recording. M3Resp has three modalities: EIT, EMG and ventilator. Their names in code are "eit", "emg" and "ventilator".
offset#: The time in seconds between the clocks of two recordings. You measure or know the offset, and you give it to M3Resp. Synchronization uses it to calculate the start time of each recording.
parameter#: A number that M3Resp calculates from the signals, with its unit. A parameter can belong to one breath, to a group of breaths, to a time period or to the full recording. An example is the respiratory rate in breaths per minute. In code, a parameter is a ParameterResult.
pixel map#: One number for each pixel of an EIT image. An example is the tidal impedance variation of each pixel (pixel_tiv). In code, a pixel map is a PixelMap.
preset#: A fixed series of processing steps that is part of M3Resp. You run a preset with session.run_preset. There are three presets: "eit", "emg" and "multimodal".
provenance#: The record of what M3Resp did to the data: the action, the modality, the settings and the time (UTC). The session keeps this record in session.provenance.
quality flag#: The outcome of one quality check on a signal, a breath or a time period. It tells if the check passed and how serious a failure is. It can also give the measured value and the limit. In code, a quality flag is a QualityFlag.
R peak#: The highest point of one heartbeat in the ECG. M3Resp uses the R peaks to find and remove the ECG from the EMG.
recording#: The data of one modality from one file, after M3Resp loads it. Examples are an EIT .bin file, or the EMG channels of a Biopac .txt file. In code, a recording is an EITRecording, an EMGRecording or a VentilatorRecording.
result#: What a step gives back. In a workflow, each step keeps its results under a name, and a later step reads them by that name. At the end, the workflow gives back all results in a WorkflowResult.
sampling rate#: The number of samples per second of a signal, in Hz. In code, the name is sample_frequency or fs.
session#: The M3Session object of one analysis. It holds the loaded recordings, the signals, the breaths, the parameters, the quality flags and the provenance.
setting#: One value that controls a step, for example low_pass_hz: 500.0. In a workflow file, the settings of a step are under with:. In code, a StepParameter describes each setting.
signal#: One series of values over time, with a sampling rate and a unit. Examples are the global impedance of an EIT recording and the envelope of one EMG channel. A signal also tells its modality, its channel and its processing state: "raw", "intermediate", "processed" or "derived". In code, a signal is a Signal.
start time#: The time in seconds at which a recording starts on the shared clock. Each recording has one start time in session.start_times. When you do not synchronize the recordings, each start time is 0 s.
step#: One operation in a workflow, for example emg.preprocess or eit.detect_breaths. In a workflow file, the step name is under uses:. To see all steps, run m3resp steps.
synchronization#: The process that puts recordings from different devices on one shared clock. M3Resp gives each recording a start time from the offset that you enter. All samples of each recording stay.
time window#: A part of a recording between a start time and an end time, in seconds. To slice a recording to a time window, use a step such as emg.slice_recording.
ventilator#: The modality for airway pressure, flow and volume. The data can come from a ventilator export, or from channels inside an EMG or EIT file.
workflow#: A YAML or JSON file that lists steps in the order they run. For each step, it gives the step name (uses:), its settings (with:) and, if necessary, new names for its results (out:). To run a workflow, use m3resp run <file>. In code, a loaded workflow is a WorkflowSpec.