Examples with ReadingSource com.ibm.streamsx.health.ingest.types.model.ReadingSource used on opensource projects

Example 1 with ReadingSource

use of com.ibm.streamsx.health.ingest.types.model.ReadingSource in project streamsx.health by IBMStreams.

the class VinesToObservationParser method mapWaveformMessage.

private void mapWaveformMessage(Vines v, VinesParserResult parserResult) {
    // generate Patient ID
    String patientId = "";
    Patient patient = v.getData().getPatient();
    if (patient != null) {
        patientId = patient.get_id();
    }
    // generate device type (same for all observations)
    Device device = new Device();
    device.setId(getDeviceId(v));
    long startTime = 0;
    long period = 0;
    try {
        startTime = toEpoch(v.getData().getBody().getStartTime());
    } catch (ParseException e) {
        String msg = "Error parsing timestamp: error=" + e.getLocalizedMessage() + ", timestamp=" + v.getData().getBody().getStartTime();
        logger.error(msg);
        e.printStackTrace();
        parserResult.addErrorMesage(msg);
    }
    Terms terms = v.getData().getBody().getTerms();
    Channel channel = terms.getChannel(terms.getChannelNames().get(0));
    ReadingSource readingSource = new ReadingSource();
    readingSource.setSourceType(SOURCE_TYPE);
    readingSource.setId(terms.getChannelNames().get(0));
    readingSource.setDeviceId(getDeviceId(v));
    // get the sample rate
    ITerm iterm = channel.getTerm("MDC_ATTR_SAMP_RATE");
    if (iterm instanceof Term) {
        Term term = (Term) iterm;
        // set the multiplier based on the UOM
        // in order to convert the sample rate
        // milliseconds
        double dividend = 1;
        if (term.getUOM().equals("MDC_DIM_SEC")) {
            dividend = 1000;
        }
        ITermValue itv = term.getValue();
        if (itv instanceof TermValueString) {
            String value = ((TermValueString) itv).getValue();
            if (NumberUtils.isNumber(value)) {
                period = Math.round((dividend / Double.valueOf(value)));
            }
        }
    }
    // get the UOM
    iterm = channel.getTerm("MDC_ATTR_SCALE_RANGE");
    String uom = "";
    if (iterm instanceof Term) {
        Term term = (Term) iterm;
        uom = term.getUOM();
    }
    // map waveform samples to observations
    iterm = channel.getTerm("MDC_ATTR_WAV");
    if (iterm instanceof TermArray) {
        TermArray term = (TermArray) iterm;
        for (ITermValue itv : term) {
            if (itv instanceof TermValueMap) {
                TermValueMap tvm = (TermValueMap) itv;
                for (String waveName : tvm.keySet()) {
                    ITerm waveITerm = tvm.get(waveName);
                    if (waveITerm instanceof Term) {
                        Term waveTerm = (Term) waveITerm;
                        ITermValue waveTermValue = waveTerm.getValue();
                        if (waveTermValue instanceof TermValueString) {
                            String waveStr = ((TermValueString) waveTermValue).getValue();
                            List<Double> waveform = WaveformHelper.parseWaveform(waveStr);
                            for (int i = 0; i < waveform.size(); ++i) {
                                Reading reading = new Reading();
                                reading.setReadingType(getReadingType(waveName));
                                reading.setValue(waveform.get(i));
                                reading.setTimestamp(startTime + period * i);
                                reading.setUom(uom);
                                parserResult.addObservation(new Observation(device, patientId, readingSource, reading));
                            }
                        }
                    }
                }
            }
        }
    }
}

Example 2 with ReadingSource

use of com.ibm.streamsx.health.ingest.types.model.ReadingSource in project streamsx.health by IBMStreams.

the class VinesToObservationParser method mapVitalMessage.

private void mapVitalMessage(Vines v, VinesParserResult parserResult) {
    // generate Patient ID
    String patientId = "";
    Patient patient = v.getData().getPatient();
    if (patient != null) {
        patientId = patient.getMRN();
    }
    // generate device type (same for all observations)
    Device device = new Device();
    device.setId(getDeviceId(v));
    Terms terms = v.getData().getBody().getTerms();
    for (String channelName : terms.getChannelNames()) {
        Channel channel = terms.getChannel(channelName);
        // generate ReadingSource
        ReadingSource readingSource = new ReadingSource();
        readingSource.setId(channelName);
        readingSource.setSourceType(SOURCE_TYPE);
        readingSource.setDeviceId(getDeviceId(v));
        // iterate over all terms and generate Readings & Observations
        for (String termName : channel.getTermNames()) {
            ITerm term = channel.getTerm(termName);
            if (term instanceof Term) {
                Reading reading = new Reading();
                Term t = (Term) term;
                ITermValue itv = t.getValue();
                if (itv instanceof TermValueString) {
                    String value = ((TermValueString) itv).getValue();
                    if (!NumberUtils.isNumber(value)) {
                        // skip term as there is no numeric value
                        continue;
                    }
                    String date = t.getDate();
                    long epochTime = 0l;
                    try {
                        epochTime = toEpoch(date);
                    } catch (ParseException e) {
                        String msg = "Error parsing timestamp: error=" + e.getLocalizedMessage() + ", timestamp=" + date;
                        logger.error(msg, e);
                        e.printStackTrace();
                        parserResult.addErrorMesage(msg);
                    }
                    reading.setValue(Double.valueOf(value));
                    reading.setUom(t.getUOM());
                    reading.setTimestamp(epochTime);
                    reading.setReadingType(getReadingType(termName));
                    parserResult.addObservation(new Observation(device, patientId, readingSource, reading));
                }
            } else {
                // Array terms not expected in normal vines messages
                String msg = "Error parsing Vines message: Array terms not expected in normal vines messages.";
                logger.error(msg);
                parserResult.addErrorMesage(msg);
            }
        }
    }
}

Example 3 with ReadingSource

use of com.ibm.streamsx.health.ingest.types.model.ReadingSource in project streamsx.health by IBMStreams.

the class HealthcareDataGenerator method loadData.

public void loadData(InputStream is, String filename) throws Exception {
    Device device = new Device();
    device.setId("HealthcareDataGenerator");
    ReadingSource readingSource = new ReadingSource();
    readingSource.setDeviceId(device.getId());
    readingSource.setSourceType("file");
    readingSource.setId(filename);
    BufferedReader reader = new BufferedReader(new InputStreamReader(is));
    // skip first 2 lines
    reader.readLine();
    String[] uom = reader.readLine().replace("'", "").split(",");
    String line = null;
    while ((line = reader.readLine()) != null) {
        String[] values = line.split(",");
        for (int i = 1; i < values.length; i++) {
            Reading reading = new Reading();
            // convert to milliseconds
            Double tsMilli = Double.valueOf(values[0]) * 1000;
            reading.setTimestamp(tsMilli.longValue());
            reading.setReadingType(new ReadingType(ReadingTypeSystem.STREAMS_CODE_SYSTEM, readingTypeCode));
            reading.setUom(uom[i]);
            reading.setValue(Double.valueOf(values[i]));
            observations.add(new Observation(device, patientId, readingSource, reading));
        }
    }
}

Example 4 with ReadingSource

use of com.ibm.streamsx.health.ingest.types.model.ReadingSource in project streamsx.health by IBMStreams.

the class AbstractVitalsGenerator method get.

@Override
public Observation get() {
    Reading reading = new Reading();
    reading.setReadingType(getReadingType());
    reading.setTimestamp(++count);
    reading.setUom(getUOM());
    reading.setValue(vitalsGen.next());
    Device device = new Device();
    device.setId(getDeviceId());
    ReadingSource readingSource = new ReadingSource();
    readingSource.setDeviceId(getDeviceId());
    readingSource.setSourceType("generated");
    return new Observation(device, patientId, readingSource, reading);
}