Examples with Attribute smile.data.Attribute used on opensource projects

Example 21 with Attribute

use of smile.data.Attribute in project smile by haifengl.

the class TXTParserTest method testParse.

/**
     * Test of parse method, of class TXTParser.
     */
@Test
public void testParse() throws Exception {
    System.out.println("parse");
    TXTParser parser = new TXTParser();
    try {
        AttributeDataset data = parser.parse("PCL", smile.data.parser.IOUtils.getTestDataFile("microarray/Dunham2002.txt"));
        double[][] x = data.toArray(new double[data.size()][]);
        String[] id = data.toArray(new String[data.size()]);
        for (Attribute attribute : data.attributes()) {
            assertEquals(Attribute.Type.NUMERIC, attribute.getType());
            System.out.println(attribute.getName());
        }
        assertEquals(6694, data.size());
        assertEquals(16, data.attributes().length);
        assertEquals("YKR005C", id[0]);
        assertEquals(-0.43, x[0][0], 1E-7);
        assertEquals(-0.47, x[0][1], 1E-7);
        assertEquals(-0.39, x[0][2], 1E-7);
        assertEquals("YKR004C", id[6693]);
        assertEquals(0.03, x[6693][13], 1E-7);
        assertEquals(-0.53, x[6693][14], 1E-7);
        assertEquals(0.3, x[6693][15], 1E-7);
    } catch (Exception ex) {
        System.err.println(ex);
    }
}

Example 22 with Attribute

use of smile.data.Attribute in project smile by haifengl.

the class ArffParser method parseAttribute.

/**
     * Parses the attribute declaration.
     *
     * @return an attributes in this relation
     * @throws IOException 	if the information is not read
     * 				successfully
     */
private Attribute parseAttribute(StreamTokenizer tokenizer) throws IOException, ParseException {
    Attribute attribute = null;
    // Get attribute name.
    getNextToken(tokenizer);
    String attributeName = tokenizer.sval;
    getNextToken(tokenizer);
    // Check if attribute is nominal.
    if (tokenizer.ttype == StreamTokenizer.TT_WORD) {
        // Attribute is real, integer, or string.
        if (tokenizer.sval.equalsIgnoreCase(ARFF_ATTRIBUTE_REAL) || tokenizer.sval.equalsIgnoreCase(ARFF_ATTRIBUTE_INTEGER) || tokenizer.sval.equalsIgnoreCase(ARFF_ATTRIBUTE_NUMERIC)) {
            attribute = new NumericAttribute(attributeName);
            readTillEOL(tokenizer);
        } else if (tokenizer.sval.equalsIgnoreCase(ARFF_ATTRIBUTE_STRING)) {
            attribute = new StringAttribute(attributeName);
            readTillEOL(tokenizer);
        } else if (tokenizer.sval.equalsIgnoreCase(ARFF_ATTRIBUTE_DATE)) {
            String format = null;
            if (tokenizer.nextToken() != StreamTokenizer.TT_EOL) {
                if ((tokenizer.ttype != StreamTokenizer.TT_WORD) && (tokenizer.ttype != '\'') && (tokenizer.ttype != '\"')) {
                    throw new ParseException("not a valid date format", tokenizer.lineno());
                }
                format = tokenizer.sval;
                readTillEOL(tokenizer);
            } else {
                tokenizer.pushBack();
            }
            attribute = new DateAttribute(attributeName, null, format);
            readTillEOL(tokenizer);
        } else if (tokenizer.sval.equalsIgnoreCase(ARFF_ATTRIBUTE_RELATIONAL)) {
            readTillEOL(tokenizer);
        } else if (tokenizer.sval.equalsIgnoreCase(ARFF_END_SUBRELATION)) {
            getNextToken(tokenizer);
        } else {
            throw new ParseException("Invalid attribute type or invalid enumeration", tokenizer.lineno());
        }
    } else {
        // Attribute is nominal.
        List<String> attributeValues = new ArrayList<>();
        tokenizer.pushBack();
        // Get values for nominal attribute.
        if (tokenizer.nextToken() != '{') {
            throw new ParseException("{ expected at beginning of enumeration", tokenizer.lineno());
        }
        while (tokenizer.nextToken() != '}') {
            if (tokenizer.ttype == StreamTokenizer.TT_EOL) {
                throw new ParseException("} expected at end of enumeration", tokenizer.lineno());
            } else {
                attributeValues.add(tokenizer.sval.trim());
            }
        }
        String[] values = new String[attributeValues.size()];
        for (int i = 0; i < values.length; i++) {
            values[i] = attributeValues.get(i);
        }
        attribute = new NominalAttribute(attributeName, values);
    }
    getLastToken(tokenizer, false);
    getFirstToken(tokenizer);
    if (tokenizer.ttype == StreamTokenizer.TT_EOF) {
        throw new ParseException(PREMATURE_END_OF_FILE, tokenizer.lineno());
    }
    return attribute;
}

Example 23 with Attribute

use of smile.data.Attribute in project smile by haifengl.

the class NumericAttributeFeatureTest method testSTANDARDIZATION.

/**
     * Test of f method, of class NumericAttributeFeature.
     */
@Test
public void testSTANDARDIZATION() {
    System.out.println("STANDARDIZATION");
    DelimitedTextParser parser = new DelimitedTextParser();
    parser.setResponseIndex(new NominalAttribute("class"), 0);
    try {
        AttributeDataset data = parser.parse("USPS Train", smile.data.parser.IOUtils.getTestDataFile("usps/zip.train"));
        double[][] x = data.toArray(new double[data.size()][]);
        double[] mean = Math.colMean(x);
        double[] sd = Math.colSd(x);
        NumericAttributeFeature naf = new NumericAttributeFeature(data.attributes(), NumericAttributeFeature.Scaling.STANDARDIZATION, x);
        Attribute[] attributes = naf.attributes();
        assertEquals(256, attributes.length);
        for (int i = 0; i < x.length; i++) {
            double[] y = new double[attributes.length];
            for (int j = 0; j < y.length; j++) {
                y[j] = naf.f(x[i], j);
                assertEquals((x[i][j] - mean[j]) / sd[j], y[j], 1E-7);
            }
        }
    } catch (Exception ex) {
        System.err.println(ex);
    }
}

Example 24 with Attribute

use of smile.data.Attribute in project smile by haifengl.

the class NumericAttributeFeatureTest method testNONE.

/**
     * Test of f method, of class NumericAttributeFeature.
     */
@Test
public void testNONE() {
    System.out.println("NONE");
    DelimitedTextParser parser = new DelimitedTextParser();
    parser.setResponseIndex(new NominalAttribute("class"), 0);
    try {
        AttributeDataset data = parser.parse("USPS Train", smile.data.parser.IOUtils.getTestDataFile("usps/zip.train"));
        double[][] x = data.toArray(new double[data.size()][]);
        NumericAttributeFeature naf = new NumericAttributeFeature(data.attributes(), NumericAttributeFeature.Scaling.NONE);
        Attribute[] attributes = naf.attributes();
        assertEquals(256, attributes.length);
        for (int i = 0; i < x.length; i++) {
            double[] y = new double[attributes.length];
            for (int j = 0; j < y.length; j++) {
                y[j] = naf.f(x[i], j);
                assertEquals(x[i][j], y[j], 1E-7);
            }
        }
    } catch (Exception ex) {
        System.err.println(ex);
    }
}

Example 25 with Attribute

use of smile.data.Attribute in project smile by haifengl.

the class NumericAttributeFeatureTest method testAttributes.

/**
     * Test of attributes method, of class NumericAttributeFeature.
     */
@SuppressWarnings("unused")
@Test
public void testAttributes() {
    System.out.println("attributes");
    DelimitedTextParser parser = new DelimitedTextParser();
    parser.setResponseIndex(new NominalAttribute("class"), 0);
    try {
        AttributeDataset data = parser.parse("USPS Train", smile.data.parser.IOUtils.getTestDataFile("usps/zip.train"));
        double[][] x = data.toArray(new double[data.size()][]);
        NumericAttributeFeature naf = new NumericAttributeFeature(data.attributes(), NumericAttributeFeature.Scaling.LOGARITHM);
        Attribute[] attributes = naf.attributes();
        assertEquals(256, attributes.length);
        for (int i = 0; i < attributes.length; i++) {
            System.out.println(attributes[i]);
            assertEquals(Attribute.Type.NUMERIC, attributes[i].getType());
        }
    } catch (Exception ex) {
        System.err.println(ex);
    }
}