Public API

This page lists the classes and functions that you import from m3resp. Each name links to a page with its arguments, its return value and the units. The page of a class or function also lists the tutorials that use it.

See the Concepts for what the objects mean.

Sessions and workflows

An M3Session holds the recordings and the results of one analysis. The presets and the workflow functions run the processing steps.

m3resp.M3Session	Recordings, processing results and provenance for a multimodal study session.
m3resp.Preset	A named preset that runs a fixed sequence of M3Session methods.
m3resp.EITPreset	Preprocess loaded EIT data and store its detected breaths.
m3resp.EMGPreset	Preprocess loaded EMG, remove ECG, detect breaths and calculate features.
m3resp.MultimodalPreset	Set recording start times and align detected breaths across modalities.
m3resp.WorkflowResult	Results, timing and execution records for one workflow run.
m3resp.available_presets	Return the names of all registered presets, sorted.
m3resp.get_preset	Return the Preset class registered under name.
m3resp.register_preset	Store preset_cls under name, replacing any existing registration.
m3resp.load_spec	Load a workflow from an object, dictionary or YAML/JSON file.
m3resp.run_workflow	Run a workflow's ordered steps and return their results and records.
m3resp.run_spec	Run a workflow file, write its manifest and apply its export settings.
m3resp.available_steps	Return a mapping of registered step name -> one-line summary.
m3resp.register_step	Register a function and its workflow inputs, outputs and descriptions.
m3resp.workflows.WorkflowSpec	An ordered workflow description with inputs, settings and export options.
m3resp.workflows.StepSpec	One operation and its input, parameter and output bindings.
m3resp.workflows.ValidationReport	Structural diagnostics and optional checks for running a workflow locally.
m3resp.workflows.CompiledWorkflow	An ordered description of workflow steps with resolved settings.
m3resp.workflows.WorkflowService	Discover workflow steps, inspect specs and run workflows for an application.
m3resp.workflows.collect_diagnostics	Collect structural errors and warnings for all resolvable workflow steps.
m3resp.workflows.compile_workflow	Validate a workflow and resolve the settings needed to run its steps.
m3resp.workflows.validate_workflow	Check workflow structure and optionally its readiness on this machine.
m3resp.workflows.validate_spec	Check workflow structure and raise for its first error.

Signals, results and quality

These objects hold the processed signals, the calculated parameters, the quality checks and the record of each processing step.

m3resp.TimeSeries	A value array paired with its time axis.
m3resp.Signal	A TimeSeries tagged with modality and provenance context.
m3resp.SignalCollection	An ordered collection of Signal objects, queryable by modality.
m3resp.interpolate_to_time	Return a copy of signal with its values at the time points time.
m3resp.ParameterResult	A named, unit-tagged metric produced by a processing step.
m3resp.ParameterResultCollection	An ordered collection of ParameterResult objects.
m3resp.QualityFlag	The outcome of one quality check against a signal, breath, or run.
m3resp.QualityReport	An ordered collection of QualityFlag results.
m3resp.ProcessingStep	A record of one executed processing operation.
m3resp.ProcessingHistory	An ordered log of ProcessingStep entries for one session or run.

Events and synchronization

These objects and functions hold breaths, events and values per breath, and put the recordings on one clock.

m3resp.Event	A timestamped event from one modality.
m3resp.Interval	A stretch of time from one modality, with a start and an end.
m3resp.BreathEvent	One breath from one modality, with a signal turning point.
m3resp.EventData	One value for each event, in the same order as the events.
m3resp.IntervalData	One value for each interval, in the same order as the intervals.
m3resp.IntervalDataCollection	An ordered collection of results with values per interval or breath.
m3resp.PixelMap	One number for each pixel of an EIT image.
m3resp.PixelMask	Which pixels of an EIT image belong to a region.
m3resp.PixelMaskCollection	An ordered collection of pixel masks, such as lung-space masks.
m3resp.pixel_breath_events	Return the breaths of one pixel as BreathEvent objects.
m3resp.LinkedBreath	One physiological breath, matched across any number of modalities.
m3resp.coerce_event	Convert one timestamped event into an Event.
m3resp.coerce_events	Convert an iterable of events into a list of Event objects.
m3resp.coerce_interval	Convert one timed interval into an Interval.
m3resp.coerce_intervals	Convert an iterable of intervals into a list of Interval objects.
m3resp.coerce_breath_event	Convert one detected breath into a BreathEvent.
m3resp.coerce_breath_events	Convert an iterable of breaths into a list of BreathEvent objects.
m3resp.event_to_dict	Return the fields of an event, interval or breath as a dictionary.
m3resp.compute_offsets_from_timestamps	Convert absolute per-device start timestamps into manual offsets (plan_stage2.md Sec 20, "timestamp alignment").
m3resp.link_breaths_by_time	Group breaths across modalities by their timing in seconds.

Data model

The data model is a set of checked records of a finished analysis. See Provenance and processing history.

m3resp.Case	Opaque grouping of sessions belonging to one external study subject.
m3resp.ClinicalEvent	Time-stamped intervention or notable occurrence (doc Sec 7.9).
m3resp.DataFile	A physical file holding raw/processed/derived data (doc Sec 8.1).
m3resp.DataModelRecorder	Store a session's recordings, results and processing provenance.
m3resp.DataModelStore	A dict-of-id-to-entity table per entity type, plus relational lookups.
m3resp.DerivedFeature	A quantitative result computed from one or more source streams (doc Sec 7.11).
m3resp.Device	Physical or software system that produces data (doc Sec 7.3).
m3resp.ProcessingRun	A stored record of a workflow, processing step or session action.
m3resp.QualityAnnotation	Polymorphic quality label (doc Sec 11).
m3resp.RecordingSession	One continuous acquisition period (doc Sec 7.2).
m3resp.SignalStream	Base type for every continuous signal (doc Sec 7.4).
m3resp.export_store	Write one JSON file per table to out_dir.
m3resp.validate_store	Return a list of readable problem descriptions (empty if none found).

Export

This function writes the results of a session to CSV, JSON and array files.

m3resp.export.export_session_summary

Write session summaries, result tables and array archives.

Load a recording

These functions load one recording without a session.

m3resp.io.load_eit	Load an EIT recording through the EIT adapter.
m3resp.io.load_emg	Load an EMG recording through the EMG adapter (ReSurfEMGAdapter by default).

Plots

These functions make figures with Matplotlib.

m3resp.visualization.plot_eit_processing_summary	Plot the results of the EIT processing of a session.
m3resp.visualization.plot_session_overview	Plot the loaded EIT signal and the processed EMG signals of a session.
m3resp.visualization.plot_synchronization_comparison	Plot each signal before and after synchronization.

Synthetic data

These classes and functions make synthetic EIT, EMG and ventilator recordings for tests and examples.

m3resp.synthetic.SyntheticGeneratorConfig	Top-level configuration for a synthetic multimodal dataset.
m3resp.synthetic.SyntheticDataset	Generated multimodal dataset.
m3resp.synthetic.SyntheticRecord	Generated signal plus metadata and export paths.
m3resp.synthetic.RespiratoryPatternConfig	Shared respiratory timing and occlusion settings.
m3resp.synthetic.EITGeneratorConfig	Synthetic EIT signal and Draeger export settings.
m3resp.synthetic.EMGGeneratorConfig	Synthetic EMG settings passed to ReSurfEMG.
m3resp.synthetic.VentilatorGeneratorConfig	Synthetic ventilator settings passed to ReSurfEMG.
m3resp.synthetic.generate_synthetic_dataset	Generate synthetic EIT, EMG, and ventilator data from one configuration.
m3resp.synthetic.generate_realistic_eit_signal	Generate a realistic synthetic breathing-related impedance waveform.
m3resp.synthetic.load_synthetic_generator_config	Load a synthetic generator configuration from a YAML file.