Examples with FixedRecordGroup org.mitre.synthea.input.FixedRecordGroup used on opensource projects

Example 1 with FixedRecordGroup

use of org.mitre.synthea.input.FixedRecordGroup in project synthea by synthetichealth.

the class Exporter method export.

/**
 * Export a single patient, into all the formats supported. (Formats may be enabled or disabled by
 * configuration)
 *
 * @param person   Patient to export
 * @param stopTime Time at which the simulation stopped
 * @param options Runtime exporter options
 */
public static void export(Person person, long stopTime, ExporterRuntimeOptions options) {
    if (options.deferExports) {
        deferredExports.add(new ImmutablePair<Person, Long>(person, stopTime));
    } else {
        if (options.yearsOfHistory > 0) {
            person = filterForExport(person, options.yearsOfHistory, stopTime);
        }
        if (!person.alive(stopTime)) {
            filterAfterDeath(person);
        }
        if (person.hasMultipleRecords) {
            int i = 0;
            for (String key : person.records.keySet()) {
                person.record = person.records.get(key);
                // If the person fixed Records, overwrite their attributes from the fixed records.
                if (person.attributes.get(Person.RECORD_GROUP) != null) {
                    FixedRecordGroup rg = (FixedRecordGroup) person.attributes.get(Person.RECORD_GROUP);
                    int recordToPull = i;
                    if (recordToPull >= rg.count) {
                        recordToPull = rg.count - 1;
                    }
                    FixedRecord fr = rg.records.get(recordToPull);
                    fr.totalOverwrite(person);
                }
                exportRecord(person, Integer.toString(i), stopTime, options);
                i++;
            }
        } else {
            exportRecord(person, "", stopTime, options);
        }
    }
}

Example 2 with FixedRecordGroup

use of org.mitre.synthea.input.FixedRecordGroup in project synthea by synthetichealth.

the class Generator method checkCriteria.

/**
 * Determines if a patient meets the requested criteria.
 * If a patient does not meet the criteria the process will be repeated so a new one is generated
 * @param person the patient to check if we want to export them
 * @param finishTime the time simulation finished
 * @param index Target index in the whole set of people to generate
 * @param isAlive Whether the patient is alive at end of simulation.
 * @return CriteriaCheck to determine if the patient should be exported/re-simulated
 */
public CriteriaCheck checkCriteria(Person person, long finishTime, int index, boolean isAlive) {
    CriteriaCheck check = new CriteriaCheck();
    check.rejectDeadButOverflow = !isAlive && !onlyDeadPatients && this.options.overflow;
    // if patient is not alive and the criteria isn't dead patients new patient is needed
    // however in this one case we still want to export the patient
    check.isAliveButDeadRequired = isAlive && onlyDeadPatients;
    // if patient is alive and the criteria is dead patients new patient is needed
    check.isDeadButAliveRequired = !isAlive && onlyAlivePatients;
    // if patient is not alive and the criteria is alive patients new patient is needed
    int providerCount = person.providerCount();
    int providerMinimum = 1;
    if (this.recordGroups != null) {
        // If fixed records are used, there must be 1 provider for each of this person's records.
        FixedRecordGroup recordGroup = this.recordGroups.get(index);
        providerMinimum = recordGroup.count;
    }
    check.insufficientProviders = providerCount < providerMinimum;
    if (this.keepPatientsModule != null) {
        // this one might be slow to process, so only do it if the other things are true
        if (!check.isAliveButDeadRequired && !check.isDeadButAliveRequired) {
            this.keepPatientsModule.process(person, finishTime, false);
            State terminal = person.history.get(0);
            check.failedKeepModule = !terminal.name.equals("Keep");
        }
    }
    return check;
}

Example 3 with FixedRecordGroup

use of org.mitre.synthea.input.FixedRecordGroup in project synthea by synthetichealth.

the class FixedRecordTest method fixedDemographicsImportTest.

@Test
public void fixedDemographicsImportTest() {
    // List of raw RecordGroups imported directly from the input file for later comparison.
    List<FixedRecordGroup> rawRecordGroups = generator.importFixedPatientDemographicsFile();
    // Generate each patient from the fixed record input file.
    for (int i = 0; i < generator.options.population; i++) {
        generator.generatePerson(i);
    }
    // Make sure that the correct number of people were imported from the fixed records.
    assertEquals(4, generator.internalStore.size());
    assertEquals(generator.internalStore.size(), rawRecordGroups.size());
    // Check that each person has HealthRecords that match their fixed demographic records.
    for (int p = 0; p < generator.internalStore.size(); p++) {
        // Get the current person and pull their list of records.
        Person currentPerson = generator.internalStore.get(p);
        FixedRecordGroup recordGroup = (FixedRecordGroup) currentPerson.attributes.get(Person.RECORD_GROUP);
        // Make sure the person has the correct number of records.
        assertTrue(currentPerson.records.size() >= 3);
        assertTrue(recordGroup.records.size() == 3);
        // Track the number of fixed records that match the person's attributes exactly.
        int fixedRecordMatches = 0;
        // Cycle the person's FixedRecords to compare them to the raw imported FixedRecords.
        for (int r = 0; r < currentPerson.records.size(); r++) {
            int recordToPull = Math.min(r, recordGroup.count - 1);
            FixedRecord personFixedRecord = recordGroup.records.get(recordToPull);
            recordToPull = Math.min(r, rawRecordGroups.get(p).records.size() - 1);
            FixedRecord rawFixedRecord = rawRecordGroups.get(p).records.get(recordToPull);
            // Compare the person's current FixedRecord with the raw imported FixedRecords.
            assertEquals(personFixedRecord.firstName, rawFixedRecord.firstName);
            assertEquals(personFixedRecord.lastName, rawFixedRecord.lastName);
            assertEquals(personFixedRecord.getBirthDate(), rawFixedRecord.getBirthDate());
            assertEquals(personFixedRecord.gender, rawFixedRecord.gender);
            assertEquals(personFixedRecord.phoneAreaCode, rawFixedRecord.phoneAreaCode);
            assertEquals(personFixedRecord.phoneNumber, rawFixedRecord.phoneNumber);
            assertEquals(personFixedRecord.addressLineOne, rawFixedRecord.addressLineOne);
            assertEquals(personFixedRecord.addressLineTwo, rawFixedRecord.addressLineTwo);
            assertEquals(personFixedRecord.city, rawFixedRecord.city);
            assertEquals(personFixedRecord.zipcode, rawFixedRecord.zipcode);
            assertEquals(personFixedRecord.parentFirstName, rawFixedRecord.parentFirstName);
            assertEquals(personFixedRecord.parentLastName, rawFixedRecord.parentLastName);
            assertEquals(personFixedRecord.parentEmail, rawFixedRecord.parentEmail);
            // One FixedRecord should match the person's attributes exactly as the "gold standard".
            if ((currentPerson.attributes.get(Person.FIRST_NAME).equals(rawFixedRecord.firstName)) && (currentPerson.attributes.get(Person.LAST_NAME).equals(rawFixedRecord.lastName)) && (currentPerson.attributes.get(Person.ADDRESS).equals(rawFixedRecord.addressLineOne)) && (currentPerson.attributes.get(Person.BIRTHDATE).equals(rawFixedRecord.getBirthDate())) && (currentPerson.attributes.get(Person.GENDER).equals(rawFixedRecord.gender)) && (currentPerson.attributes.get(Person.TELECOM).equals(rawFixedRecord.getTelecom())) && (currentPerson.attributes.get(Person.STATE).equals(rawFixedRecord.state)) && (currentPerson.attributes.get(Person.CITY).equals(rawFixedRecord.city)) && (currentPerson.attributes.get(Person.ZIP).equals(rawFixedRecord.zipcode)) && (currentPerson.attributes.get(Person.IDENTIFIER_RECORD_ID).equals(rawFixedRecord.recordId)) && (currentPerson.attributes.get(Person.IDENTIFIER_SITE).equals(rawFixedRecord.site))) {
                fixedRecordMatches++;
            }
        }
        // One FixedRecord should match the person's attributes exactly as a "gold standard" record.
        assertTrue(fixedRecordMatches >= 1);
    }
}

Example 4 with FixedRecordGroup

use of org.mitre.synthea.input.FixedRecordGroup in project synthea by synthetichealth.

the class Generator method pickFixedDemographics.

/**
 * Pick a person's demographics based on their FixedRecords.
 * @param index The index to use.
 * @param random Random object.
 */
private Map<String, Object> pickFixedDemographics(int index, Random random) {
    // Get the first FixedRecord from the current RecordGroup
    FixedRecordGroup recordGroup = this.recordGroups.get(index);
    FixedRecord fr = recordGroup.records.get(0);
    // Get the city from the location in the fixed record.
    this.location = new Location(fr.state, recordGroup.getSafeCity());
    Demographics city = this.location.randomCity(random);
    // Pick the rest of the demographics based on the location of the fixed record.
    Map<String, Object> demoAttributes = pickDemographics(random, city);
    // Overwrite the person's attributes with the FixedRecord.
    demoAttributes.put(Person.BIRTHDATE, recordGroup.getValidBirthdate());
    demoAttributes.put(Person.BIRTH_CITY, city.city);
    String g = fr.gender;
    if (g.equalsIgnoreCase("None") || StringUtils.isBlank(g)) {
        g = "F";
    }
    demoAttributes.put(Person.GENDER, g);
    // Give the person their FixedRecordGroup of FixedRecords.
    demoAttributes.put(Person.RECORD_GROUP, recordGroup);
    demoAttributes.put(Person.LINK_ID, recordGroup.linkId);
    // Return the Demographic Attributes of the current person.
    return demoAttributes;
}

Example 5 with FixedRecordGroup

use of org.mitre.synthea.input.FixedRecordGroup in project synthea by synthetichealth.

the class LifecycleModule method birth.

/**
 * For unto us a child is born.
 * @param person The baby.
 * @param time The time of birth.
 */
public static void birth(Person person, long time) {
    Map<String, Object> attributes = person.attributes;
    attributes.put(Person.ID, person.randUUID().toString());
    attributes.put(Person.BIRTHDATE, time);
    String gender = (String) attributes.get(Person.GENDER);
    String language = (String) attributes.get(Person.FIRST_LANGUAGE);
    String firstName = Names.fakeFirstName(gender, language, person);
    String lastName = Names.fakeLastName(language, person);
    attributes.put(Person.FIRST_NAME, firstName);
    attributes.put(Person.LAST_NAME, lastName);
    attributes.put(Person.NAME, firstName + " " + lastName);
    String motherFirstName = Names.fakeFirstName("F", language, person);
    String motherLastName = Names.fakeLastName(language, person);
    attributes.put(Person.NAME_MOTHER, motherFirstName + " " + motherLastName);
    String fatherFirstName = Names.fakeFirstName("M", language, person);
    // this is anglocentric where the baby gets the father's last name
    attributes.put(Person.NAME_FATHER, fatherFirstName + " " + lastName);
    double prevalenceOfTwins = (double) BiometricsConfig.get("lifecycle.prevalence_of_twins", 0.02);
    if ((person.rand() < prevalenceOfTwins)) {
        attributes.put(Person.MULTIPLE_BIRTH_STATUS, person.randInt(3) + 1);
    }
    String phoneNumber = "555-" + ((person.randInt(999 - 100 + 1) + 100)) + "-" + ((person.randInt(9999 - 1000 + 1) + 1000));
    attributes.put(Person.TELECOM, phoneNumber);
    boolean hasStreetAddress2 = person.rand() < 0.5;
    attributes.put(Person.ADDRESS, Names.fakeAddress(hasStreetAddress2, person));
    // If using FixedRecords, overwrite the person's attributes with the FixedRecord attributes.
    if (person.attributes.get(Person.RECORD_GROUP) != null) {
        FixedRecordGroup recordGroup = (FixedRecordGroup) person.attributes.get(Person.RECORD_GROUP);
        FixedRecord fr = recordGroup.records.get(0);
        attributes.putAll(fr.getFixedRecordAttributes());
    }
    String ssn = "999-" + ((person.randInt(99 - 10 + 1) + 10)) + "-" + ((person.randInt(9999 - 1000 + 1) + 1000));
    attributes.put(Person.IDENTIFIER_SSN, ssn);
    String city = (String) attributes.get(Person.CITY);
    Location location = (Location) attributes.get(Person.LOCATION);
    if (location != null) {
        // should never happen in practice, but can happen in unit tests
        location.assignPoint(person, city);
        person.attributes.put(Person.ZIP, location.getZipCode(city, person));
        String[] birthPlace;
        if ("english".equalsIgnoreCase((String) attributes.get(Person.FIRST_LANGUAGE))) {
            birthPlace = location.randomBirthPlace(person);
        } else {
            birthPlace = location.randomBirthplaceByLanguage(person, (String) person.attributes.get(Person.FIRST_LANGUAGE));
        }
        attributes.put(Person.BIRTH_CITY, birthPlace[0]);
        attributes.put(Person.BIRTH_STATE, birthPlace[1]);
        attributes.put(Person.BIRTH_COUNTRY, birthPlace[2]);
        // For CSV exports so we don't break any existing schemas
        attributes.put(Person.BIRTHPLACE, birthPlace[3]);
    }
    attributes.put(Person.ACTIVE_WEIGHT_MANAGEMENT, false);
    // TODO: Why are the percentiles a vital sign? Sounds more like an attribute?
    double heightPercentile = person.rand();
    PediatricGrowthTrajectory pgt = new PediatricGrowthTrajectory(person.seed, time);
    double weightPercentile = pgt.reverseWeightPercentile(gender, heightPercentile);
    person.setVitalSign(VitalSign.HEIGHT_PERCENTILE, heightPercentile);
    person.setVitalSign(VitalSign.WEIGHT_PERCENTILE, weightPercentile);
    person.attributes.put(Person.GROWTH_TRAJECTORY, pgt);
    // Temporarily generate a mother
    Person mother = new Person(person.randLong());
    mother.attributes.put(Person.GENDER, "F");
    mother.attributes.put("pregnant", true);
    mother.attributes.put(Person.RACE, person.attributes.get(Person.RACE));
    mother.attributes.put(Person.ETHNICITY, person.attributes.get(Person.ETHNICITY));
    mother.attributes.put(BirthStatistics.BIRTH_SEX, person.attributes.get(Person.GENDER));
    BirthStatistics.setBirthStatistics(mother, time);
    person.setVitalSign(VitalSign.HEIGHT, // cm
    (double) mother.attributes.get(BirthStatistics.BIRTH_HEIGHT));
    person.setVitalSign(VitalSign.WEIGHT, // kg
    (double) mother.attributes.get(BirthStatistics.BIRTH_WEIGHT));
    // cm
    person.setVitalSign(VitalSign.HEAD, childHeadCircumference(person, time));
    attributes.put(AGE, 0);
    attributes.put(AGE_MONTHS, 0);
    boolean isRHNeg = person.rand() < 0.15;
    attributes.put("RH_NEG", isRHNeg);
    double adherenceBaseline = Config.getAsDouble("lifecycle.adherence.baseline", 0.05);
    person.attributes.put(ADHERENCE_PROBABILITY, adherenceBaseline);
    // set initial height and weight from percentiles
    grow(person, time);
    // Set initial values for many vital signs.
    calculateVitalSigns(person, time);
    String orientation = sexualOrientationData.next(person);
    attributes.put(Person.SEXUAL_ORIENTATION, orientation);
    // Setup vital signs which follow the generator approach
    setupVitalSignGenerators(person);
}