/**
* Initialize this separate model using a complete list.
*
* @param documents
* @param testStartIndex
*/
public void divideDocuments(InstanceList documents, int testStartIndex) {
Alphabet dataAlpha = documents.getDataAlphabet();
Alphabet targetAlpha = documents.getTargetAlphabet();
this.training = new InstanceList(dataAlpha, targetAlpha);
this.test = new InstanceList(dataAlpha, targetAlpha);
int di = 0;
for (di = 0; di < testStartIndex; di++) {
training.add(documents.get(di));
}
for (di = testStartIndex; di < documents.size(); di++) {
test.add(documents.get(di));
}
}
public static ElementInMove_c resolveInstance(
ModelRoot modelRoot,
java.util.UUID p_m_elementid,
java.util.UUID p_m_diagramid,
float p_m_startingx,
float p_m_startingy) {
InstanceList instances = modelRoot.getInstanceList(ElementInMove_c.class);
ElementInMove_c source = null;
synchronized (instances) {
Object[] key = {p_m_elementid, p_m_diagramid};
source = (ElementInMove_c) instances.get(key);
if (source != null && !modelRoot.isCompareRoot()) {
source.convertFromProxy();
source.batchUnrelate();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_elementid = IdAssigner.preprocessUUID(p_m_elementid);
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_diagramid = IdAssigner.preprocessUUID(p_m_diagramid);
source.m_startingx = p_m_startingx;
source.m_startingy = p_m_startingy;
return source;
}
}
// there is no instance matching the id
ElementInMove_c new_inst =
new ElementInMove_c(modelRoot, p_m_elementid, p_m_diagramid, p_m_startingx, p_m_startingy);
return new_inst;
}
public static void clearInstances(ModelRoot modelRoot) {
InstanceList instances = modelRoot.getInstanceList(InformalArgument_c.class);
synchronized (instances) {
for (int i = instances.size() - 1; i >= 0; i--) {
((NonRootModelElement) instances.get(i)).delete_unchecked();
}
}
}
public static BridgeInvocation_c createProxy(
ModelRoot modelRoot,
java.util.UUID p_m_statement_id,
java.util.UUID p_m_brg_id,
int p_m_bridgenamelinenumber,
int p_m_bridgenamecolumn,
int p_m_externalentitykeyletterslinenumber,
int p_m_externalentitykeyletterscolumn,
String p_contentPath,
IPath p_localPath) {
ModelRoot resolvedModelRoot = ModelRoot.findModelRoot(modelRoot, p_contentPath, p_localPath);
// if a model root was not resolved it is most likely
// due to a missing file of the proxy, defualt back to
// the original model root
if (resolvedModelRoot != null) modelRoot = resolvedModelRoot;
InstanceList instances = modelRoot.getInstanceList(BridgeInvocation_c.class);
BridgeInvocation_c new_inst = null;
synchronized (instances) {
Object[] key = {p_m_statement_id};
new_inst = (BridgeInvocation_c) instances.get(key);
}
String contentPath = PersistenceUtil.resolveRelativePath(p_localPath, new Path(p_contentPath));
if (modelRoot.isNewCompareRoot()) {
// for comparisons we do not want to change
// the content path
contentPath = p_contentPath;
}
if (new_inst != null && !modelRoot.isCompareRoot()) {
PersistableModelComponent pmc = new_inst.getPersistableComponent();
if (pmc == null) {
// dangling reference, redo this instance
new_inst.batchUnrelate();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
new_inst.m_statement_id = IdAssigner.preprocessUUID(p_m_statement_id);
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
new_inst.m_brg_id = IdAssigner.preprocessUUID(p_m_brg_id);
new_inst.m_bridgenamelinenumber = p_m_bridgenamelinenumber;
new_inst.m_bridgenamecolumn = p_m_bridgenamecolumn;
new_inst.m_externalentitykeyletterslinenumber = p_m_externalentitykeyletterslinenumber;
new_inst.m_externalentitykeyletterscolumn = p_m_externalentitykeyletterscolumn;
}
}
if (new_inst == null) {
// there is no instance matching the id, create a proxy
// if the resource doesn't exist then this will be a dangling reference
new_inst =
new BridgeInvocation_c(
modelRoot,
p_m_statement_id,
p_m_brg_id,
p_m_bridgenamelinenumber,
p_m_bridgenamecolumn,
p_m_externalentitykeyletterslinenumber,
p_m_externalentitykeyletterscolumn);
new_inst.m_contentPath = contentPath;
}
return new_inst;
}
private static Graphnode_c findGraphnodeInstance(
ModelRoot modelRoot, ClassQueryInterface_c test, boolean loadComponent) {
InstanceList instances = modelRoot.getInstanceList(Graphnode_c.class);
synchronized (instances) {
for (int i = 0; i < instances.size(); ++i) {
Graphnode_c x = (Graphnode_c) instances.get(i);
if (test == null || test.evaluate(x)) {
return x;
}
}
}
return null;
}
private static InformalArgument_c findInformalArgumentInstance(
ModelRoot modelRoot, ClassQueryInterface_c test, boolean loadComponent) {
InstanceList instances = modelRoot.getInstanceList(InformalArgument_c.class);
synchronized (instances) {
for (int i = 0; i < instances.size(); ++i) {
InformalArgument_c x = (InformalArgument_c) instances.get(i);
if (test == null || test.evaluate(x)) {
if (x.ensureLoaded(loadComponent)) return x;
}
}
}
return null;
}
public void generateTestInference() {
if (lda == null) {
System.out.println("Should run lda estimation first.");
System.exit(1);
return;
}
if (testTopicDistribution == null) testTopicDistribution = new double[test.size()][];
TopicInferencer infer = lda.getInferencer();
int iterations = 800;
int thinning = 5;
int burnIn = 100;
for (int ti = 0; ti < test.size(); ti++) {
testTopicDistribution[ti] =
infer.getSampledDistribution(test.get(ti), iterations, thinning, burnIn);
}
}
public static ComponentInComponent_c createProxy(
ModelRoot modelRoot,
java.util.UUID p_m_id,
java.util.UUID p_m_parent_id,
String p_contentPath,
IPath p_localPath) {
ModelRoot resolvedModelRoot = ModelRoot.findModelRoot(modelRoot, p_contentPath, p_localPath);
// if a model root was not resolved it is most likely
// due to a missing file of the proxy, defualt back to
// the original model root
if (resolvedModelRoot != null) modelRoot = resolvedModelRoot;
InstanceList instances = modelRoot.getInstanceList(ComponentInComponent_c.class);
ComponentInComponent_c new_inst = null;
synchronized (instances) {
Object[] key = {p_m_id};
new_inst = (ComponentInComponent_c) instances.get(key);
}
String contentPath = PersistenceUtil.resolveRelativePath(p_localPath, new Path(p_contentPath));
if (modelRoot.isNewCompareRoot()) {
// for comparisons we do not want to change
// the content path
contentPath = p_contentPath;
}
if (new_inst != null && !modelRoot.isCompareRoot()) {
PersistableModelComponent pmc = new_inst.getPersistableComponent();
if (pmc == null) {
// dangling reference, redo this instance
new_inst.batchUnrelate();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
new_inst.m_id = IdAssigner.preprocessUUID(p_m_id);
// extract 28 bit value only
new_inst.m_idLongBased = 0xfffffff & p_m_id.getLeastSignificantBits();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
new_inst.m_parent_id = IdAssigner.preprocessUUID(p_m_parent_id);
}
}
if (new_inst == null) {
// there is no instance matching the id, create a proxy
// if the resource doesn't exist then this will be a dangling reference
new_inst = new ComponentInComponent_c(modelRoot, p_m_id, p_m_parent_id);
new_inst.m_contentPath = contentPath;
}
return new_inst;
}
public void doInference() {
try {
ParallelTopicModel model = ParallelTopicModel.read(new File(inferencerFile));
TopicInferencer inferencer = model.getInferencer();
// TopicInferencer inferencer =
// TopicInferencer.read(new File(inferencerFile));
// InstanceList testing = readFile();
readFile();
InstanceList testing = generateInstanceList(); // readFile();
for (int i = 0; i < testing.size(); i++) {
StringBuilder probabilities = new StringBuilder();
double[] testProbabilities = inferencer.getSampledDistribution(testing.get(i), 10, 1, 5);
ArrayList probabilityList = new ArrayList();
for (int j = 0; j < testProbabilities.length; j++) {
probabilityList.add(new Pair<Integer, Double>(j, testProbabilities[j]));
}
Collections.sort(probabilityList, new CustomComparator());
for (int j = 0; j < testProbabilities.length && j < topN; j++) {
if (j > 0) probabilities.append(" ");
probabilities.append(
((Pair<Integer, Double>) probabilityList.get(j)).getFirst().toString()
+ ","
+ ((Pair<Integer, Double>) probabilityList.get(j)).getSecond().toString());
}
System.out.println(docIds.get(i) + "," + probabilities.toString());
}
} catch (Exception e) {
e.printStackTrace();
System.err.println(e.getMessage());
}
}
public static InformalArgument_c resolveInstance(ModelRoot modelRoot, java.util.UUID p_m_arg_id) {
InstanceList instances = modelRoot.getInstanceList(InformalArgument_c.class);
InformalArgument_c source = null;
synchronized (instances) {
Object[] key = {p_m_arg_id};
source = (InformalArgument_c) instances.get(key);
if (source != null && !modelRoot.isCompareRoot()) {
source.convertFromProxy();
source.batchUnrelate();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_arg_id = IdAssigner.preprocessUUID(p_m_arg_id);
return source;
}
}
// there is no instance matching the id
InformalArgument_c new_inst = new InformalArgument_c(modelRoot, p_m_arg_id);
return new_inst;
}
public static Graphnode_c[] GraphnodeInstances(
ModelRoot modelRoot, ClassQueryInterface_c test, boolean loadComponent) {
InstanceList instances = modelRoot.getInstanceList(Graphnode_c.class);
Vector matches = new Vector();
synchronized (instances) {
for (int i = 0; i < instances.size(); ++i) {
Graphnode_c x = (Graphnode_c) instances.get(i);
if (test == null || test.evaluate(x)) {
matches.add(x);
}
}
if (matches.size() > 0) {
Graphnode_c[] ret_set = new Graphnode_c[matches.size()];
matches.copyInto(ret_set);
return ret_set;
} else {
return new Graphnode_c[0];
}
}
}
public void test() throws Exception {
ParallelTopicModel model = ParallelTopicModel.read(new File(inferencerFile));
TopicInferencer inferencer = model.getInferencer();
ArrayList<Pipe> pipeList = new ArrayList<Pipe>();
pipeList.add(new CharSequence2TokenSequence(Pattern.compile("\\p{L}\\p{L}+")));
pipeList.add(new TokenSequence2FeatureSequence());
InstanceList instances = new InstanceList(new SerialPipes(pipeList));
Reader fileReader = new InputStreamReader(new FileInputStream(new File(fileName)), "UTF-8");
instances.addThruPipe(
new CsvIterator(
fileReader,
Pattern.compile("^(\\S*)[\\s,]*(\\S*)[\\s,]*(.*)$"),
3,
2,
1)); // data, label, name fields
double[] testProbabilities = inferencer.getSampledDistribution(instances.get(1), 10, 1, 5);
for (int i = 0; i < 1000; i++) System.out.println(i + ": " + testProbabilities[i]);
}
public static BridgeInvocation_c resolveInstance(
ModelRoot modelRoot,
java.util.UUID p_m_statement_id,
java.util.UUID p_m_brg_id,
int p_m_bridgenamelinenumber,
int p_m_bridgenamecolumn,
int p_m_externalentitykeyletterslinenumber,
int p_m_externalentitykeyletterscolumn) {
InstanceList instances = modelRoot.getInstanceList(BridgeInvocation_c.class);
BridgeInvocation_c source = null;
synchronized (instances) {
Object[] key = {p_m_statement_id};
source = (BridgeInvocation_c) instances.get(key);
if (source != null && !modelRoot.isCompareRoot()) {
source.convertFromProxy();
source.batchUnrelate();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_statement_id = IdAssigner.preprocessUUID(p_m_statement_id);
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_brg_id = IdAssigner.preprocessUUID(p_m_brg_id);
source.m_bridgenamelinenumber = p_m_bridgenamelinenumber;
source.m_bridgenamecolumn = p_m_bridgenamecolumn;
source.m_externalentitykeyletterslinenumber = p_m_externalentitykeyletterslinenumber;
source.m_externalentitykeyletterscolumn = p_m_externalentitykeyletterscolumn;
return source;
}
}
// there is no instance matching the id
BridgeInvocation_c new_inst =
new BridgeInvocation_c(
modelRoot,
p_m_statement_id,
p_m_brg_id,
p_m_bridgenamelinenumber,
p_m_bridgenamecolumn,
p_m_externalentitykeyletterslinenumber,
p_m_externalentitykeyletterscolumn);
return new_inst;
}
public static ComponentResultSet_c resolveInstance(
ModelRoot modelRoot, java.util.UUID p_m_id, String p_m_name, int p_m_type) {
InstanceList instances = modelRoot.getInstanceList(ComponentResultSet_c.class);
ComponentResultSet_c source = null;
synchronized (instances) {
Object[] key = {p_m_name, new UUID(0, new Long(p_m_type)), p_m_id};
source = (ComponentResultSet_c) instances.get(key);
if (source != null && !modelRoot.isCompareRoot()) {
source.convertFromProxy();
source.batchUnrelate();
source.m_name = p_m_name;
source.m_type = p_m_type;
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_id = IdAssigner.preprocessUUID(p_m_id);
return source;
}
}
// there is no instance matching the id
ComponentResultSet_c new_inst = new ComponentResultSet_c(modelRoot, p_m_id, p_m_name, p_m_type);
return new_inst;
}
public static Graphnode_c resolveInstance(
ModelRoot modelRoot, float p_m_width, float p_m_height, java.util.UUID p_m_elementid) {
InstanceList instances = modelRoot.getInstanceList(Graphnode_c.class);
Graphnode_c source = null;
synchronized (instances) {
Object[] key = {p_m_elementid};
source = (Graphnode_c) instances.get(key);
if (source != null && !modelRoot.isCompareRoot()) {
source.convertFromProxy();
source.batchUnrelate();
source.m_width = p_m_width;
source.m_height = p_m_height;
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_elementid = IdAssigner.preprocessUUID(p_m_elementid);
return source;
}
}
// there is no instance matching the id
Graphnode_c new_inst = new Graphnode_c(modelRoot, p_m_width, p_m_height, p_m_elementid);
return new_inst;
}
public static AssignToMember_c resolveInstance(
ModelRoot modelRoot,
java.util.UUID p_m_statement_id,
java.util.UUID p_m_r_value_id,
java.util.UUID p_m_l_value_id,
int p_m_attributelinenumber,
int p_m_attributecolumn) {
InstanceList instances = modelRoot.getInstanceList(AssignToMember_c.class);
AssignToMember_c source = null;
synchronized (instances) {
Object[] key = {p_m_statement_id};
source = (AssignToMember_c) instances.get(key);
if (source != null && !modelRoot.isCompareRoot()) {
source.convertFromProxy();
source.batchUnrelate();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_statement_id = IdAssigner.preprocessUUID(p_m_statement_id);
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_r_value_id = IdAssigner.preprocessUUID(p_m_r_value_id);
source.m_attributelinenumber = p_m_attributelinenumber;
source.m_attributecolumn = p_m_attributecolumn;
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_l_value_id = IdAssigner.preprocessUUID(p_m_l_value_id);
return source;
}
}
// there is no instance matching the id
AssignToMember_c new_inst =
new AssignToMember_c(
modelRoot,
p_m_statement_id,
p_m_r_value_id,
p_m_l_value_id,
p_m_attributelinenumber,
p_m_attributecolumn);
return new_inst;
}
public static InformalArgument_c[] InformalArgumentInstances(
ModelRoot modelRoot, ClassQueryInterface_c test, boolean loadComponent) {
if (loadComponent) {
PersistenceManager.ensureAllInstancesLoaded(modelRoot, InformalArgument_c.class);
}
InstanceList instances = modelRoot.getInstanceList(InformalArgument_c.class);
Vector matches = new Vector();
synchronized (instances) {
for (int i = 0; i < instances.size(); ++i) {
InformalArgument_c x = (InformalArgument_c) instances.get(i);
if (test == null || test.evaluate(x)) {
if (x.ensureLoaded(loadComponent)) matches.add(x);
}
}
if (matches.size() > 0) {
InformalArgument_c[] ret_set = new InformalArgument_c[matches.size()];
matches.copyInto(ret_set);
return ret_set;
} else {
return new InformalArgument_c[0];
}
}
}
public static ComponentInComponent_c resolveInstance(
ModelRoot modelRoot, java.util.UUID p_m_id, java.util.UUID p_m_parent_id) {
InstanceList instances = modelRoot.getInstanceList(ComponentInComponent_c.class);
ComponentInComponent_c source = null;
synchronized (instances) {
Object[] key = {p_m_id};
source = (ComponentInComponent_c) instances.get(key);
if (source != null && !modelRoot.isCompareRoot()) {
source.convertFromProxy();
source.batchUnrelate();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_id = IdAssigner.preprocessUUID(p_m_id);
// extract 28 bit value only
source.m_idLongBased = 0xfffffff & p_m_id.getLeastSignificantBits();
// pre-process the uuid so that we re-use null uuid instance rather then creating a new one.
source.m_parent_id = IdAssigner.preprocessUUID(p_m_parent_id);
return source;
}
}
// there is no instance matching the id
ComponentInComponent_c new_inst = new ComponentInComponent_c(modelRoot, p_m_id, p_m_parent_id);
return new_inst;
}