/**
* Return Semantic Type of the concept code passed in
*
* @param conceptCode
* @return
*/
public String getSemanticType(String conceptCode) {
Vector<String> code_vec = new Vector<String>();
code_vec.add(conceptCode);
HashMap<?, ?> map =
DataUtils.getPropertyValuesForCodes(
Constants.CODING_SCHEME_NAME, null, code_vec, SEMANTIC_TYPE);
return (String) map.get(conceptCode);
}
/**
* Delete {@code books} from Realm, along with any {@link RBookListItem}s which may exist for
* them, and their cover images if they have them. Optionally delete the real files they were
* imported from as well.
*
* @param realm Instance of Realm to use.
* @param books Books to delete.
* @param deleteRealFiles If true, also delete the books' corresponding files.
*/
public static void deleteBooks(Realm realm, Collection<RBook> books, boolean deleteRealFiles) {
// Null checks.
if (books == null || books.isEmpty()) return;
// If deleteRealFiles is true, check permissions before doing anything.
if (deleteRealFiles
&& !Util.checkForStoragePermAndFireEventIfNeeded(R.id.action_execute_deferred)) {
//noinspection unchecked Defer this action while we ask for permission.
setDeferredAction(params -> deleteBooks(realm, (Collection<RBook>) params[0], true), books);
return;
}
List<String> relPaths = new ArrayList<>(books.size());
// Delete what we created.
realm.executeTransaction(
tRealm -> {
for (RBook book : books) {
// Delete any RBookListItems which may exist for these books.
tRealm
.where(RBookListItem.class)
.contains("book.relPath", book.relPath)
.findAll()
.deleteAllFromRealm();
// Get the relative path of the book, in case we wish to delete the real files too.
String relPath = book.relPath;
relPaths.add(relPath);
// Be sure to delete the cover file, if we have one.
if (book.hasCoverImage) DataUtils.deleteCoverImage(relPath);
// Delete the actual RBook from Realm.
book.deleteFromRealm();
}
});
// If the user wants us to, also try to delete the corresponding files from the device.
if (deleteRealFiles) {
for (String relPath : relPaths) {
File file = Util.getFileFromRelPath(relPath);
if (file != null) // noinspection ResultOfMethodCallIgnored
file.delete();
}
}
}
/**
* Convert the given object into a value appropriate for being defined as the value of a variable
* in an XQuery. This will extract a sequence out of all database objects, convert collections and
* arrays into sequences recursively, convert <code>null</code> into an empty sequence, and pass
* other objects through untouched. Convertible objects that are defined in the JDK will be
* automatically converted by eXist.
*
* @see org.exist.xquery.XPathUtil#javaObjectToXPath(Object, XQueryContext, boolean)
* @param o the object to convert to a database value
* @return the converted value, ready for assignment to an XQuery variable
*/
@SuppressWarnings("unchecked")
private Object convertValue(Object o) {
if (o == null) return Collections.emptyList();
if (o instanceof Resource) {
try {
return ((Resource) o).convertToSequence();
} catch (UnsupportedOperationException e) {
return o;
}
}
List<Object> list = null;
if (o instanceof Collection) list = new ArrayList<Object>((Collection) o);
else if (o instanceof Object[]) list = new ArrayList<Object>(Arrays.asList((Object[]) o));
if (list != null) {
for (ListIterator<Object> it = list.listIterator(); it.hasNext(); ) {
it.set(convertValue(it.next()));
}
return list;
}
return DataUtils.toXMLObject(o);
}
public void rtest4() {
System.out.println("SHD\tP");
// System.out.println("MB1\tMB2\tMB3\tMB4\tMB5\tMB6");
Graph mim = DataGraphUtils.randomSingleFactorModel(5, 5, 8, 0, 0, 0);
Graph mimStructure = structure(mim);
SemPm pm = new SemPm(mim);
SemImInitializationParams params = new SemImInitializationParams();
params.setCoefRange(0.5, 1.5);
NumberFormat nf = new DecimalFormat("0.0000");
int totalError = 0;
int errorCount = 0;
int maxScore = 0;
int maxNumMeasures = 0;
double maxP = 0.0;
for (int r = 0; r < 1; r++) {
SemIm im = new SemIm(pm, params);
DataSet data = im.simulateData(1000, false);
mim = GraphUtils.replaceNodes(mim, data.getVariables());
List<List<Node>> trueClusters = MimUtils.convertToClusters2(mim);
CovarianceMatrix _cov = new CovarianceMatrix(data);
ICovarianceMatrix cov = DataUtils.reorderColumns(_cov);
String algorithm = "FOFC";
Graph searchGraph;
List<List<Node>> partition;
if (algorithm.equals("FOFC")) {
FindOneFactorClusters fofc =
new FindOneFactorClusters(cov, TestType.TETRAD_WISHART, 0.001f);
searchGraph = fofc.search();
searchGraph = GraphUtils.replaceNodes(searchGraph, data.getVariables());
partition = MimUtils.convertToClusters2(searchGraph);
} else if (algorithm.equals("BPC")) {
TestType testType = TestType.TETRAD_WISHART;
TestType purifyType = TestType.TETRAD_BASED2;
BuildPureClusters bpc = new BuildPureClusters(data, 0.001, testType, purifyType);
searchGraph = bpc.search();
partition = MimUtils.convertToClusters2(searchGraph);
} else {
throw new IllegalStateException();
}
mimStructure = GraphUtils.replaceNodes(mimStructure, data.getVariables());
List<String> latentVarList = reidentifyVariables(mim, data, partition, 2);
Graph mimbuildStructure;
Mimbuild2 mimbuild = new Mimbuild2();
mimbuild.setAlpha(0.001);
mimbuild.setMinClusterSize(3);
try {
mimbuildStructure = mimbuild.search(partition, latentVarList, cov);
} catch (Exception e) {
e.printStackTrace();
continue;
}
mimbuildStructure = GraphUtils.replaceNodes(mimbuildStructure, data.getVariables());
mimbuildStructure = condense(mimStructure, mimbuildStructure);
// Graph mimSubgraph = new EdgeListGraph(mimStructure);
//
// for (Node node : mimSubgraph.getNodes()) {
// if (!mimStructure.getNodes().contains(node)) {
// mimSubgraph.removeNode(node);
// }
// }
int shd = SearchGraphUtils.structuralHammingDistance(mimStructure, mimbuildStructure);
boolean impureCluster = containsImpureCluster(partition, trueClusters);
double pValue = mimbuild.getpValue();
boolean pBelow05 = pValue < 0.05;
boolean numClustersGreaterThan5 = partition.size() != 5;
boolean error = false;
// boolean condition = impureCluster || numClustersGreaterThan5 || pBelow05;
// boolean condition = numClustersGreaterThan5 || pBelow05;
boolean condition = numClustered(partition) == 40;
if (!condition && (shd > 5)) {
error = true;
}
if (!condition) {
totalError += shd;
errorCount++;
}
// if (numClustered(partition) > maxNumMeasures) {
// maxNumMeasures = numClustered(partition);
// maxP = pValue;
// maxScore = shd;
// System.out.println("maxNumMeasures = " + maxNumMeasures);
// System.out.println("maxScore = " + maxScore);
// System.out.println("maxP = " + maxP);
// System.out.println("clusters = " + clusterSizes(partition, trueClusters));
// }
// else
if (pValue > maxP) {
maxScore = shd;
maxP = mimbuild.getpValue();
maxNumMeasures = numClustered(partition);
System.out.println("maxNumMeasures = " + maxNumMeasures);
System.out.println("maxScore = " + maxScore);
System.out.println("maxP = " + maxP);
System.out.println("clusters = " + clusterSizes(partition, trueClusters));
}
System.out.print(
shd
+ "\t"
+ nf.format(pValue)
+ " "
// + (error ? 1 : 0) + " "
// + (pBelow05 ? "P < 0.05 " : "")
// + (impureCluster ? "Impure cluster " : "")
// + (numClustersGreaterThan5 ? "# Clusters != 5 " : "")
// + clusterSizes(partition, trueClusters)
+ numClustered(partition));
System.out.println();
}
System.out.println("\nAvg SHD for not-flagged cases = " + (totalError / (double) errorCount));
System.out.println("maxNumMeasures = " + maxNumMeasures);
System.out.println("maxScore = " + maxScore);
System.out.println("maxP = " + maxP);
}
public void rtest3() {
Node x = new GraphNode("X");
Node y = new GraphNode("Y");
Node z = new GraphNode("Z");
Node w = new GraphNode("W");
List<Node> nodes = new ArrayList<Node>();
nodes.add(x);
nodes.add(y);
nodes.add(z);
nodes.add(w);
Graph g = new EdgeListGraph(nodes);
g.addDirectedEdge(x, y);
g.addDirectedEdge(x, z);
g.addDirectedEdge(y, w);
g.addDirectedEdge(z, w);
Graph maxGraph = null;
double maxPValue = -1.0;
ICovarianceMatrix maxLatentCov = null;
Graph mim = DataGraphUtils.randomMim(g, 8, 0, 0, 0, true);
// Graph mim = DataGraphUtils.randomSingleFactorModel(5, 5, 8, 0, 0, 0);
Graph mimStructure = structure(mim);
SemPm pm = new SemPm(mim);
System.out.println("\n\nTrue graph:");
System.out.println(mimStructure);
SemImInitializationParams params = new SemImInitializationParams();
params.setCoefRange(0.5, 1.5);
SemIm im = new SemIm(pm, params);
int N = 1000;
DataSet data = im.simulateData(N, false);
CovarianceMatrix cov = new CovarianceMatrix(data);
for (int i = 0; i < 1; i++) {
ICovarianceMatrix _cov = DataUtils.reorderColumns(cov);
List<List<Node>> partition;
FindOneFactorClusters fofc = new FindOneFactorClusters(_cov, TestType.TETRAD_WISHART, .001);
fofc.search();
partition = fofc.getClusters();
System.out.println(partition);
List<String> latentVarList = reidentifyVariables(mim, data, partition, 2);
Mimbuild2 mimbuild = new Mimbuild2();
mimbuild.setAlpha(0.001);
// mimbuild.setMinimumSize(5);
// To test knowledge.
// Knowledge knowledge = new Knowledge2();
// knowledge.setEdgeForbidden("L.Y", "L.W", true);
// knowledge.setEdgeRequired("L.Y", "L.Z", true);
// mimbuild.setKnowledge(knowledge);
Graph mimbuildStructure = mimbuild.search(partition, latentVarList, _cov);
double pValue = mimbuild.getpValue();
System.out.println(mimbuildStructure);
System.out.println("P = " + pValue);
System.out.println("Latent Cov = " + mimbuild.getLatentsCov());
if (pValue > maxPValue) {
maxPValue = pValue;
maxGraph = new EdgeListGraph(mimbuildStructure);
maxLatentCov = mimbuild.getLatentsCov();
}
}
System.out.println("\n\nTrue graph:");
System.out.println(mimStructure);
System.out.println("\nBest graph:");
System.out.println(maxGraph);
System.out.println("P = " + maxPValue);
System.out.println("Latent Cov = " + maxLatentCov);
System.out.println();
}