SleepHarmonizer 0.2.2

A Plugin and stand alone tool to harmonize sleep related data

Sleep Harmonizer

Harmonize polysomnograms and their annotations. Create a new harmonized dataset of EDF+-Files. Easily extend existing sources such as public datasets and PSG software vendors.

Currently supported:

• Dataset SHHS
• Dataset MESA
• Dataset MrOS

• Vendor: Philips - Alice 6
• Vendor: SOMNOmedics - Domino

Local Setup

Local setup requires the cloned git repository and a python version >= 3.8 (tested with 3.11.9)

Run pip install -r requirements.txt.

Test local setup with phases --version (if the phases command is not available, use python -m phases instead)

Docker Setup

To download and test the docker image, run docker run registry.gitlab.com/sleep-is-all-you-need/sleep-harmonizer --version.

Usage

Some configuration is required to use the sleep harmonizer. You can add additional configuration files within the run command like this

phases run -c file1.yml,configs/file2.yml Export.

For the next part we assume you have a configuration file called config.yml in the root directory.

You can run the examples with phases run -c config.yml Export after updating your config file.

Specify Source: Public Datasets (SHHS)

You need to specify the path and tell the tool that you want to use the correct data loader.

shhs-path: ./datasets/shhs
useLoader: shhs

Specify Source: Vendor (Alice 6)

You need to define a new dataloader that uses a specific RecordLoader (e.g. loader.myLoader.dataset.loadername) that needs to be registered. See available recordloaders

loader:
  my-alice:
    dataBase: myalice
    dataIsFinal: True # there will be no more updates to the data, and the record metadata can be stored
    dataBaseVersion: 0.0.1 # needs to be raised every time new data is added

    filePath: ./datasets/custom/alice/ # path to the directory where the raw data is stored
    dataset:
      loaderName: RecordLoaderAlice # registred recordloader
      filePattern: "*" # valid files that should be considered further
      downloader:
        basePath: ./datasets/custom/alice/ # path to the directory where the raw data is stored
        canReadRemote: True # if the data needs to be copied locally or the downloader.basePath can be used
        type: allFromFolder # a valid downloader type
        listFilter: acq # filters the file-list compatible with str.find(listFilter)
        extensions: [.edf, .rml] # allowed extensions, the first one is used for the id-pattern
        force: False # force download the files
        idPattern: .*/(.*[^-T]).edf # this pattern will be used to extract the record id from the filename

    # the channels that should be extracted from the edf files
    sourceChannels:
      - name: EEG F3-A2
        type: eeg
      # generate a new channel that uses the first occurence of a valid flow channel
      - name: FlowSelect
        generated: True
        requiresOne: [Flow Aux1, Flow Aux2, Flow Aux4, Flow Aux5, Flow Patient]
        type: flow
      # ... add aditional channels here

    combineChannels:
      # generate a new channel that uses the first occurence of a valid flow channel
      - name: FlowSelect
        combineType: select
        type: flow
        channel: [Flow Aux1, Flow Aux2, Flow Aux4, Flow Aux5, Flow Patient]


useLoader: my-alice

Filter the records

You can filter the records by using the dataversion config.

If you allready have a filtered recordlist

dataversion:
  version: myStudy1 # giving a name is optional, but is easier to navigate the generated files
  recordIds:
    - record1
    - record2
    - record3
    # ...

Filtering the metadata

dataversion:
  version: myStudy2
  minimalSamplingRate:
    eeg: 200 # all eeg channels require to have at least 200 HZ sampling rate
    emg: 200
    mic: 200
  filterQuery: ahi < 15 and tst > 5 # filter by metada query (compatible with pandas.Dataframe query)

Declare available Channels and Annotations

To determine what channels and annotations you want in you edf files you can use the extract options:

• annotations: The main groups apnea, arousal, limb, sleepstage and ligt or any subgroup such as resp_obstructiveapnea A complete list can be found in SleepHarmonizer/PSGEventManager.py.
• channels: Each entry is a list of channel names, the final channel name is the first channel specified in the list. The first existing channel will be used for the EDF file

export:
  annotations:
    - apnea
    - arousal
    - limb
    - sleepStage
    - light
  channels:
    - [EEG, EEG F3-A2]
    - [EEG Ch2, EEG F4-A1]
    - [EOG(L), EOG LOC-A2, E1-M2, "E1:M2"]
    - [EOG(R), EOG ROC-A1, "E2:M1"]
    - [EMG, EMG Chin, Chin1-Chin2, Chin]
    - [POSITION, Body]
    - [THOR RES, Effort THO, CHEST, RIP Thora]
    - [ABDO RES, Effort ABD, ABD, RIP Abdom]
    - [SaO2, SpO2]
    - [FLOW, FlowSelect]
    - [Leg 1]
    - [Leg 2]

Manipulate the signals

You can apply signal processing using the preprocessing config entry. All available steps are defined in SleepHarmonizer/SignalPreprocessing.py as methods. You cann also add a new method and use the method-name in the config.

preprocessing:
  targetFrequency: 8 # final sampling rate (if some sort of resampling is aplied as step)
  stepsPerType:
    eeg: [resampleFIR] # will execute the resampleFIR method on all eeg channels (defined in SignalPreprocessing.py)
    eog: [resampleFIR]
    emg: [resampleFIR]
    body: [positionAlice, resampleSimple]
    mic: [resampleFIR]
    effort: [resample,]
    sao2: [resampleSimple]
    flow: [resample]

Complete example

# folder where to write the edf files
export-path: data/export/

shhs-path: ./datasets/shhs
useLoader: shhs

dataversion:
  groupBy: Null
  recordIds: Null

export:
  annotations:
    - apnea
    - arousal
    - limb
    - sleepStage
    - light
  channels:
    - [EEG]
    - [EEG Ch2]
    - [EOG(L), EOG LOC-A2, E1-M2, "E1:M2"]
    - [EOG(R), EOG ROC-A1, "E2:M1"]
    - [EMG, EMG Chin, Chin1-Chin2, Chin]
    - [POSITION, Body]
    - [THOR RES, Effort THO, CHEST, RIP Thora]
    - [ABDO RES, Effort ABD, ABD, RIP Abdom]
    - [SaO2, SpO2]
    - [FLOW]

Execute the Export

Depending on your phases installation execute:

phases run -c config.yml Export

Expected output:

[phases] Phases v1.0.6 with pyPhases v1.2.6 (Log level: LogLevel.INFO)
[Export] RUN phase Export: Export
[Project] Data allDBRecordIdsSHHS1-70d366c5--current was not found, try to find phase to generate it
[Project] Data metadataSHHS1--current was not found, try to find phase to generate it
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:05<00:00,  1.91it/s]
  0%|                                                                                                                                                    | 0/10 [00:00<?, ?it/s]
[RecordLoaderSHHS] Added 14 signals, ignored: []
[Signal] Unkown type of signal 'hr'
[SHHSAnnotationLoader] Load xml file ./datasets/shhs/polysomnography/annotations-events-nsrr/shhs1/shhs1-200004-nsrr.xml
...
[SignalPreprocessing] Signaltype SignalType.FLOW for signal FLOW has no preprocessing steps (defined in preprocessing.stepsPerType.[type])
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [00:58<00:00,  5.82s/it]

And new created edf files in data/export.