PEEP trial segmentation (layer 2b)¶

pipeline ¶

segment_peep_trial(): split a preprocessed PEEP trial into PEEP steps (layer 2b).

Steps (notebooks/06_peep_trial_segmentation.ipynb, section 7): 1. breaths of the PEEP trial phase, with the PEEP and plateau read in layer 2 (EITRecording.breaths); 2. PEEP steps: placed by hand if given, otherwise found from the PEEP of each breath; 3. breaths analysed in each step, and the step table.

segment_peep_trial ¶

segment_peep_trial(recording: EITRecording, config: SegmentationConfig | None = None, peep_steps: Sequence[Segment] = (), phase: Segment | None = None, tidal_volumes: Sequence[float | None] | None = None) -> PeepTrial

Split a preprocessed PEEP trial into PEEP steps and choose the breaths analysed.

A recording can contain more than one protocol, e.g. a tidal baseline and then a PEEP trial: phase limits the segmentation to the PEEP trial. A part that is not analysed at all (e.g. a maneuver) is an exclusion of preprocess() instead: its breaths are never analysed and do not count when the steps are found.

Parameters:

Name	Type	Description	Default
`recording`	`EITRecording`	Output of `preprocess()`.	required
`config`	`SegmentationConfig \| None`	Parameters; defaults of `SegmentationConfig` if None.	`None`
`peep_steps`	`Sequence[Segment]`	Steps placed by hand: segments with `category="peep_step"`, the PEEP level in `parameters["peep"]` (cmH2O) and optionally the plateau (`parameters["plateau"]`) or the driving pressure (`parameters["driving_pressure"]`) read on the ventilator, and the tidal volume (`parameters["tidal_volume"]`, mL). If given, they replace the steps found from the pressure, and the breaths analysed are the valid breaths inside them.	`()`
`phase`	`Segment \| None`	The PEEP trial part of the recording: a segment with `category="phase"` and `label="peep_trial"`. If None, the whole recording.	`None`
`tidal_volumes`	`Sequence[float \| None] \| None`	Tidal volume typed for each step (mL), in time order, e.g. the mean of each step on the case report form; None for a step without it. One volume for the whole recording goes in `RecordingContext.tidal_volume_ml` instead.	`None`

Returns:

Type	Description
`PeepTrial`	The PEEP trial. Breaths outside the phase or the steps have `peep_step` -1.

Raises:

Type	Description
`ValueError`	if there are no steps placed by hand and no pressure to find them, a step placed by hand or the phase is not usable, no breath is inside the phase or the steps placed by hand, or `tidal_volumes` does not have one positive value per step.

peep_steps ¶

PEEP steps of a PEEP trial and the breaths analysed in each step.

Steps come from the PEEP of each breath (EITRecording.breaths) or are placed by hand as segments with their PEEP level; steps placed by hand win over the automatic ones (notebooks/06_peep_trial_segmentation.ipynb, sections 3, 5 and 7).

find_steps ¶

find_steps(peep: ndarray, threshold: float, min_breaths: int, agreement: float) -> np.ndarray

First breath of each PEEP step.

A new step starts when min_breaths breaths in a row are further than threshold from the level of the current step and within agreement of each other; the level of the current step is the median PEEP of its breaths so far (of the first min_breaths breaths at the start). With min_breaths of 2 or more a single odd breath (a maneuver) cannot open a step. A breath without PEEP (NaN) takes the PEEP of the next breath that has one.

Parameters:

Name	Type	Description	Default
`peep`	`ndarray`	PEEP of each breath.	required
`threshold`	`float`	Half of the step of the protocol (e.g. 1 for steps of 2).	required
`min_breaths`	`int`	Breaths in a row needed to open a step.	required
`agreement`	`float`	Largest spread of those breaths.	required

Returns:

Type	Description
`ndarray`	Index of the first breath of each step; the first is always 0.

Raises:

Type	Description
`ValueError`	if no breath has a PEEP.

step_of_each_breath ¶

step_of_each_breath(step_starts: ndarray, n_breaths: int) -> np.ndarray

Step number of each breath, from the first breath of each step.

A breath belongs to the last step that starts at or before it: searchsorted counts the steps that start at or before each breath, minus one gives the step number.

protocol_levels ¶

protocol_levels(levels: ndarray, protocol: Sequence[float] | None, tolerance: float) -> np.ndarray

PEEP level of the protocol of each step.

The measured PEEP of every step can be off the set level by about the same amount (mbar to cmH2O, PEEP valve: +0.6 cmH2O in every step of a trial of notebook 06, 1.1 cmH2O at PEEP 0, nearer to 2 than to 0). That offset, the median distance of the steps from their nearest level, is removed first; then each step gets the nearest level. A step further than tolerance from every level (a level that is not in the protocol) gets NaN. An offset of half a step or more cannot be told apart from the next level.

Parameters:

Name	Type	Description	Default
`levels`	`ndarray`	PEEP of each step, measured or typed (cmH2O).	required
`protocol`	`Sequence[float] \| None`	PEEP levels of the protocol, or None.	required
`tolerance`	`float`	Largest distance from a level of the protocol (cmH2O).	required

Returns:

Type	Description
`ndarray`	One level per step; NaN where no level of the protocol is near enough, and for
`ndarray`	every step without the levels of the protocol.

steps_from_segments ¶

steps_from_segments(breath_starts: ndarray, breath_ends: ndarray, segments: Sequence[Segment]) -> tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]

Steps placed by hand: the breaths inside each segment, its PEEP and plateau.

A breath belongs to a segment when it starts and ends inside it: a breath cut by the edge of a segment is left out. Segments are numbered in time order. The plateau, or directly the driving pressure, is optional (e.g. read on the ventilator during an inspiratory hold), for recordings without a pressure signal; so is the tidal volume of the step (e.g. its mean on the case report form).

Parameters:

Name	Type	Description	Default
`breath_starts`	`ndarray`	Start time of each breath, in seconds.	required
`breath_ends`	`ndarray`	End time of each breath, in seconds.	required
`segments`	`Sequence[Segment]`	Segments with `category="peep_step"`, the PEEP level in `parameters["peep"]` (cmH2O) and optionally `parameters["plateau"]` or `parameters["driving_pressure"]` (the plateau wins if both are given) and `parameters["tidal_volume"]` (mL).	required

Returns:

Type	Description
`ndarray`	`step`: step number of each breath (-1 outside every segment);
`ndarray`	`levels`: PEEP level of each step; `plateaus`: plateau typed for each step,
`ndarray`	or PEEP + driving pressure typed (NaN if neither is given); `volumes`: tidal
`ndarray`	volume typed for each step (NaN if not given).

Raises:

Type	Description
`ValueError`	if a segment is not a PEEP step, has no PEEP level, overlaps another one, or no breath is inside any segment.

analysed_breaths ¶

analysed_breaths(breath_starts: ndarray, step: ndarray, valid: ndarray, skip_seconds: float, max_breaths: int) -> np.ndarray

Breaths analysed in each automatic step.

The breaths in the first skip_seconds of the step (from its first breath) are left out, as EELI is still moving; then the last max_breaths valid breaths of the step are analysed (notebook 06, section 5).

Parameters:

Name	Type	Description	Default
`breath_starts`	`ndarray`	Start time of each breath, in seconds.	required
`step`	`ndarray`	Step number of each breath (-1 = no step).	required
`valid`	`ndarray`	`is_valid` of each breath.	required
`skip_seconds`	`float`	Time left out after the change of PEEP.	required
`max_breaths`	`int`	Most breaths analysed per step.	required

Returns:

Type	Description
`ndarray`	Boolean array, True for the analysed breaths.

Raises:

Type	Description
`ValueError`	if `max_breaths` is less than 1.