Examples with ITerm com.ibm.streamsx.health.vines.model.ITerm used on opensource projects

Example 1 with ITerm

use of com.ibm.streamsx.health.vines.model.ITerm 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 ITerm

use of com.ibm.streamsx.health.vines.model.ITerm 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 ITerm

use of com.ibm.streamsx.health.vines.model.ITerm in project streamsx.health by IBMStreams.

the class Tests method testWaveformTerm.

@Test
public void testWaveformTerm() {
    Vines vines = VinesMessageParser.fromJson(waveformMessage);
    Terms terms = vines.getData().getBody().getTerms();
    Assert.assertTrue(terms.containsKey("CH01"));
    /* Test waveform */
    Channel chan = terms.getChannel("CH01");
    Assert.assertTrue(chan.containsKey("MDC_ATTR_WAV"));
    ITerm t = chan.getTerm("MDC_ATTR_WAV");
    Assert.assertTrue(t instanceof TermArray);
    TermArray ta = (TermArray) t;
    Assert.assertTrue(ta.size() > 0);
    ITermValue itv = ta.get(0);
    Assert.assertTrue(itv instanceof TermValueMap);
    TermValueMap tvm = (TermValueMap) itv;
    Assert.assertTrue(tvm.containsKey("MDC_PRESS_BLD_ART_ABP"));
    t = tvm.get("MDC_PRESS_BLD_ART_ABP");
    Assert.assertTrue(t instanceof Term);
    Term term = (Term) t;
    itv = term.getValue();
    Assert.assertTrue(itv instanceof TermValueString);
    TermValueString tvs = (TermValueString) itv;
    String waveformString = "115.3125^116.5^117.4375^118.1875^118.8125^119.25^119.625^119.9375^120.125^120.25^120.125^119.875^119.375^118.75^117.9375^117^115.875^114.5^113^11 1.3125^109.8125^108.4375^107.3125^106.375^105.5625^104.875^104.25^103.6875^103.1875^102.8125^102.875^103.5625";
    Assert.assertEquals(waveformString, tvs.getValue());
    /* Test vitals */
    t = chan.getTerm("MDC_ATTR_SCALE_RANGE");
    Assert.assertTrue(t instanceof Term);
    term = (Term) t;
    Assert.assertEquals("", term.getCode());
    Assert.assertEquals("-40", term.getLowerValue());
    Assert.assertEquals("520", term.getUpperValue());
    Assert.assertEquals("MDC_DIM_MMHG", term.getUOM());
    Assert.assertEquals("266016", term.getUOMCode());
}

Example 4 with ITerm

use of com.ibm.streamsx.health.vines.model.ITerm in project streamsx.health by IBMStreams.

the class Tests method termsTest.

@Test
public void termsTest() {
    Vines vines = VinesMessageParser.fromJson(simpleMessage);
    Terms terms = vines.getData().getBody().getTerms();
    Assert.assertTrue(terms.containsKey("CH1"));
    Assert.assertTrue(terms.containsKey("CH2"));
    Channel chan = terms.getChannel("CH1");
    Assert.assertTrue(chan.containsKey("MDCX_ATTR_EVT_COND"));
    Assert.assertTrue(chan.containsKey("MDC_DEV_PUMP_INFUS_CHAN_DELIVERY"));
    Assert.assertTrue(chan.containsKey("MDC_PUMP_STAT"));
    Assert.assertTrue(chan.containsKey("MDC_PUMP_MODE"));
    Assert.assertTrue(chan.containsKey("MDC_FLOW_FLUID_PUMP"));
    chan = terms.getChannel("CH2");
    Assert.assertTrue(chan.containsKey("MDC_DEV_PUMP_INFUS_CHAN_SOURCE"));
    Assert.assertTrue(chan.containsKey("MDC_DRUG_NAME_TYPE"));
    Assert.assertTrue(chan.containsKey("MDC_CONC_DRUG"));
    Assert.assertTrue(chan.containsKey("MDC_RATE_DOSE"));
    Assert.assertTrue(chan.containsKey("MDC_FLOW_FLUID_PUMP"));
    Assert.assertTrue(chan.containsKey("MDC_VOL_FLUID_TBI"));
    Assert.assertTrue(chan.containsKey("MDC_VOL_FLUID_TBI_REMAIN"));
    Assert.assertTrue(chan.containsKey("MDC_VOL_FLUID_DELIV"));
    Assert.assertTrue(chan.containsKey("MDC_VOL_FLUID_DELIV_TOTAL_SET"));
    /* Test Term containing a Map for the value */
    ITerm t = terms.getChannel("CH1").getTerm("MDCX_ATTR_EVT_COND");
    Assert.assertTrue(t instanceof Term);
    Term term = (Term) t;
    Assert.assertEquals("0", term.getCode());
    ITermValue itv = term.getValue();
    Assert.assertTrue(itv instanceof TermValueMap);
    TermValueMap termValue = (TermValueMap) itv;
    Assert.assertTrue(termValue.containsKey("MDCX_PUMP_DELIV_STOP"));
    t = termValue.get("MDCX_PUMP_DELIV_STOP");
    Assert.assertTrue(t instanceof Term);
    term = (Term) t;
    Assert.assertEquals("0", term.getCode());
    /* Test Term containing a String for the value */
    t = terms.getChannel("CH2").getTerm("MDC_VOL_FLUID_TBI");
    Assert.assertTrue(t instanceof Term);
    term = (Term) t;
    Assert.assertEquals("999999", term.getCode());
    Assert.assertEquals("MDC_DIM_MILLI_L", term.getUOM());
    Assert.assertEquals("263762", term.getUOMCode());
    Assert.assertEquals("2010-07-06T19:36:29-05:00", term.getDate());
    itv = term.getValue();
    Assert.assertTrue(itv instanceof TermValueString);
    TermValueString tvs = (TermValueString) itv;
    Assert.assertEquals("250", tvs.getValue());
}