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Update XMLImportExport.java #76

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308 changes: 135 additions & 173 deletions src/main/java/cz/cuni/lf1/lge/ThunderSTORM/ImportExport/XMLImportExport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,247 +8,210 @@

import javax.xml.stream.*;
import javax.xml.stream.events.*;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.*;
import java.text.DecimalFormat;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map.Entry;
import java.util.*;

public class XMLImportExport implements IImportExport {

static final String ROOT = "results";
static final String ITEM = "molecule";
static final String UNITS = "units";

@Override
public void importFromFile(String fp, GenericTable table, int startingFrame) throws IOException {
assert(table != null);
assert(fp != null);
assert(!fp.isEmpty());

//
// 1. Read the XML file into the hashmap
HashMap<String,String> units = null;
assert (table != null);
assert (fp != null && !fp.isEmpty());

HashMap<String, String> units = null;
boolean filling_units = false;
ArrayList<HashMap<String,Double>> molecules = null;
HashMap<String,Double> molecule = null;
ArrayList<HashMap<String, Double>> molecules = null;
HashMap<String, Double> molecule = null;
DecimalFormat df = StringFormatting.getDecimalFormat();
boolean skipMolecule = false;
try {
// First create a new XMLInputFactory

try (InputStream in = new FileInputStream(fp)) {
XMLInputFactory inputFactory = XMLInputFactory.newInstance();
// Setup a new eventReader
InputStream in = new FileInputStream(fp);
XMLEventReader eventReader = inputFactory.createXMLEventReader(in);
while(eventReader.hasNext()) {

while (eventReader.hasNext()) {
XMLEvent event = eventReader.nextEvent();

if(event.isStartElement()) {
if (event.isStartElement()) {
StartElement startElement = event.asStartElement();
String name = startElement.getName().getLocalPart();

// the root element?
if (startElement.getName().getLocalPart().equals(ROOT)) {
molecules = new ArrayList<>();
continue;
}

// the units element?
if (startElement.getName().getLocalPart().equals(UNITS)) {
units = new HashMap<>();
filling_units = true;
continue;
}

// an item element?
if (startElement.getName().getLocalPart().equals(ITEM)) {
molecule = new HashMap<>();
continue;
}

// fill a new item
if (event.isStartElement()) {
String name = event.asStartElement().getName().getLocalPart();
String value = eventReader.nextEvent().asCharacters().getData();
if(filling_units) { // units
units.put(name, value);
} else { // molecule
try {
molecule.put(name, df.parse(value).doubleValue());
} catch (ParseException e) {
skipMolecule = true;
switch (name) {
case ROOT:
molecules = new ArrayList<>();
break;
case UNITS:
units = new HashMap<>();
filling_units = true;
break;
case ITEM:
molecule = new HashMap<>();
break;
default:
String value = eventReader.nextEvent().asCharacters().getData();
if (filling_units) {
units.put(name, value);
} else {
try {
molecule.put(name, df.parse(value).doubleValue());
} catch (ParseException e) {
skipMolecule = true;
}
}
}
continue;
}
} else if(event.isEndElement()) {
} else if (event.isEndElement()) {
EndElement endElement = event.asEndElement();

// the units element?
if (endElement.getName().getLocalPart().equals(UNITS)) {
filling_units = false;
continue;
}

// an item element?
if (endElement.getName().getLocalPart().equals(ITEM)) {
if (skipMolecule) {
IJ.log("\\Update:Invalid number format! Skipping over...");
skipMolecule = false;
} else {
molecules.add(molecule);
}
continue;
String name = endElement.getName().getLocalPart();

switch (name) {
case UNITS:
filling_units = false;
break;
case ITEM:
if (skipMolecule) {
IJ.log("\\Update:Invalid number format! Skipping over...");
skipMolecule = false;
} else {
molecules.add(molecule);
}
break;
}
}
}
} catch (XMLStreamException ex) {
throw new IOException(ex.toString());
}

//
// 2. Fill the table by values from the hashmap
if(molecules != null) {
double [] values = null;
String [] colnames = new String[1];

if (molecules != null) {
double[] values = null;
String[] colnames = new String[1];
int r = 0, nrows = molecules.size();
for(HashMap<String,Double> mol : molecules) {
if(mol.size() != colnames.length) {
if(mol.containsKey(MoleculeDescriptor.LABEL_ID)) {
colnames = new String[mol.size()-1];

for (HashMap<String, Double> mol : molecules) {
if (mol.size() != colnames.length) {
if (mol.containsKey(MoleculeDescriptor.LABEL_ID)) {
colnames = new String[mol.size() - 1];
} else {
colnames = new String[mol.size()-1];
colnames = new String[mol.size()];
}
}

int ci = 0;
for(String key : mol.keySet()) {
if(MoleculeDescriptor.LABEL_ID.equals(key)) continue;
colnames[ci] = key;
ci++;
for (String key : mol.keySet()) {
if (MoleculeDescriptor.LABEL_ID.equals(key)) continue;
colnames[ci++] = key;
}
if(!table.columnNamesEqual(colnames)) {

if (!table.columnNamesEqual(colnames)) {
throw new IOException("Labels in the file do not correspond to the header of the table (excluding '" + MoleculeDescriptor.LABEL_ID + "')!");
}
if(table.isEmpty()) {

if (table.isEmpty()) {
table.setDescriptor(new MoleculeDescriptor(colnames));
if(units != null) {
for(Entry<String,String> col : units.entrySet()) {
if (units != null) {
for (Map.Entry<String, String> col : units.entrySet()) {
table.setColumnUnits(col.getKey(), Units.fromString(col.getValue()));
}
}
}
if(values == null) {

if (values == null) {
values = new double[colnames.length];
}
//
for(int c = 0; c < colnames.length; c++) {
if(MoleculeDescriptor.LABEL_ID.equals(colnames[c])) continue;
values[c] = mol.get(colnames[c]).doubleValue();
if(MoleculeDescriptor.LABEL_FRAME.equals(colnames[c])) {
values[c] += startingFrame-1;

for (int c = 0; c < colnames.length; c++) {
if (MoleculeDescriptor.LABEL_ID.equals(colnames[c])) continue;
values[c] = mol.get(colnames[c]);
if (MoleculeDescriptor.LABEL_FRAME.equals(colnames[c])) {
values[c] += startingFrame - 1;
}
IJ.showProgress((double)(r++) / (double)nrows);
IJ.showProgress((double) (r++) / (double) nrows);
}

table.addRow(values);
}
}

table.insertIdColumn();
table.copyOriginalToActual();
table.setActualState();
}

@Override
public void exportToFile(String fp, int floatPrecision, GenericTable table, List<String> columns) throws IOException {
assert(table != null);
assert(fp != null);
assert(!fp.isEmpty());

// Create a XMLOutputFactory
XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
// Create XMLEventWriter
XMLEventWriter eventWriter;
try {
eventWriter = outputFactory.createXMLEventWriter(new FileOutputStream(fp));

// Create a EventFactory
XMLEventFactory eventFactory = XMLEventFactory.newInstance();
XMLEvent tab = eventFactory.createDTD("\t");
XMLEvent end = eventFactory.createDTD("\n");
// Create and write Start Tag
StartDocument startDocument = eventFactory.createStartDocument();
eventWriter.add(startDocument);
eventWriter.add(end);
try (FileOutputStream fileOut = new FileOutputStream(fp)) {
XMLOutputFactory outputFactory = XMLOutputFactory.newInstance();
XMLEventWriter eventWriter = outputFactory.createXMLEventWriter(fileOut);
writeToStream(eventWriter, floatPrecision, table, columns);
eventWriter.close();
} catch (XMLStreamException ex) {
throw new IOException(ex);
}
}

// Create open tag of the root element
StartElement resultsStartElement = eventFactory.createStartElement("", "", ROOT);
eventWriter.add(resultsStartElement);
eventWriter.add(end);

int ncols = columns.size(), nrows = table.getRowCount();

// Write columns headers with units
StartElement unitsStartElement = eventFactory.createStartElement("", "", UNITS);
eventWriter.add(tab);
eventWriter.add(unitsStartElement);
eventWriter.add(end);
for (String column1 : columns) {
String units = table.getColumnUnits(column1).toString();
if ((units != null) && !units.trim().isEmpty()) {
createNode(eventWriter, column1, units);
}
}
eventWriter.add(tab);
eventWriter.add(eventFactory.createEndElement("", "", UNITS));
eventWriter.add(end);
public void writeToStream(XMLEventWriter eventWriter, int floatPrecision, GenericTable table, List<String> columns) throws XMLStreamException {
XMLEventFactory eventFactory = XMLEventFactory.newInstance();
XMLEvent tab = eventFactory.createDTD("\t");
XMLEvent end = eventFactory.createDTD("\n");

DecimalFormat df = StringFormatting.getDecimalFormat(floatPrecision);
DecimalFormat df = StringFormatting.getDecimalFormat(floatPrecision);
int nrows = table.getRowCount();

// Write molecules
for(int r = 0; r < nrows; r++) {
StartElement moleculeStartElement = eventFactory.createStartElement("", "", ITEM);
eventWriter.add(tab);
eventWriter.add(moleculeStartElement);
eventWriter.add(end);
eventWriter.add(eventFactory.createStartDocument());
eventWriter.add(end);

for (String column : columns) {
createNode(eventWriter, column, df.format(table.getValue(r, column)));
}

eventWriter.add(tab);
eventWriter.add(eventFactory.createEndElement("", "", ITEM));
eventWriter.add(end);
IJ.showProgress((double)r / (double)nrows);
eventWriter.add(eventFactory.createStartElement("", "", ROOT));
eventWriter.add(end);

// Units
eventWriter.add(tab);
eventWriter.add(eventFactory.createStartElement("", "", UNITS));
eventWriter.add(end);
for (String column : columns) {
String units = table.getColumnUnits(column).toString();
if ((units != null) && !units.trim().isEmpty()) {
createNode(eventWriter, column, units);
}
}
eventWriter.add(tab);
eventWriter.add(eventFactory.createEndElement("", "", UNITS));
eventWriter.add(end);

// Close the root element
eventWriter.add(eventFactory.createEndElement("", "", ROOT));
// Molecules
for (int r = 0; r < nrows; r++) {
eventWriter.add(tab);
eventWriter.add(eventFactory.createStartElement("", "", ITEM));
eventWriter.add(end);

eventWriter.add(eventFactory.createEndDocument());
eventWriter.close();
} catch(XMLStreamException ex) {
throw new IOException(ex.toString());
}
for (String column : columns) {
createNode(eventWriter, column, df.format(table.getValue(r, column)));
}
eventWriter.add(tab);
eventWriter.add(eventFactory.createEndElement("", "", ITEM));
eventWriter.add(end);
IJ.showProgress((double) r / nrows);
}

eventWriter.add(eventFactory.createEndElement("", "", ROOT));
eventWriter.add(end);
eventWriter.add(eventFactory.createEndDocument());
}

private void createNode(XMLEventWriter eventWriter, String name, String value) throws XMLStreamException {
XMLEventFactory eventFactory = XMLEventFactory.newInstance();
XMLEvent end = eventFactory.createDTD("\n");
XMLEvent tab = eventFactory.createDTD("\t\t");
// Create Start node

StartElement sElement = eventFactory.createStartElement("", "", name);
eventWriter.add(tab);
eventWriter.add(sElement);
// Create Content
Characters characters = eventFactory.createCharacters(value);
eventWriter.add(characters);
// Create End node
EndElement eElement = eventFactory.createEndElement("", "", name);
eventWriter.add(eElement);
eventWriter.add(eventFactory.createCharacters(value));
eventWriter.add(eventFactory.createEndElement("", "", name));
eventWriter.add(end);
}

Expand All @@ -261,5 +224,4 @@ public String getName() {
public String getSuffix() {
return "xml";
}

}