package org.autoplot.pds;
import java.io.ByteArrayOutputStream;
import java.net.URL;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.xml.transform.OutputKeys;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerConfigurationException;
import javax.xml.transform.TransformerException;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.xpath.XPath;
import javax.xml.xpath.XPathConstants;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
import org.autoplot.datasource.URISplit;
import org.json.JSONException;
import org.json.JSONObject;
import org.json.XML;
import org.w3c.dom.Node;
/**
*
* @author jbf
*/
public class PDS3DataObject {
private String name;
private String uri;
/**
* number of records or bytes into the file, 1 is the first offset into the file.
*/
private FilePointer filePointer;
private int recordBytes; // number of bytes in each record.
private int rowBytes; // number of bytes taken by each row of the dataset.
private int rowPrefixBytes; // additional bytes offset for each record (often 0).
private int rowSuffixBytes; // additional bytes after the bytes of each record (often 0).
private int rows;
private String interchangeFormat;
private String dataType;
private int startByte;
private int items;
private int itemBytes;
private int bytes;
private String dims; // dimensions for rank 2 or higher data, like "[64,48]" or "[3]"
private double validMinimum;
private double validMaximum;
private double missingConstant;
private String unit;
private String description;
/**
* spreadsheet field number, 1 is the first column.
*/
private int fieldNumber;
JSONObject labelJSONObject;
JSONObject columnJSONObject;
JSONObject tableJSONObject;
/*
86365
3
4
12
-1600000.0
1600000.0
9990000.0
nT
MAG vector in J
*/
public PDS3DataObject( Node label, Node table, Node column) {
try {
labelJSONObject= toJSONObject( label );
JSONObject jtable= toJSONObject(table);
tableJSONObject= jtable;
interchangeFormat= jtable.optString("INTERCHANGE_FORMAT", "ASCII");
rowBytes= jtable.getInt("ROW_BYTES");
recordBytes= labelJSONObject.optInt("RECORD_BYTES",-1);
rowPrefixBytes= jtable.optInt("ROW_PREFIX_BYTES",0);
rowSuffixBytes= jtable.optInt("ROW_SUFFIX_BYTES",0);
rows= jtable.optInt("ROWS",-1);
JSONObject j= toJSONObject(column);
columnJSONObject= j;
j.toString(4);
if ( j.has("ITEMS") ) {
items= j.getInt("ITEMS");
} else {
items= -1;
}
startByte= j.optInt("START_BYTE",0);
if ( items>1 ) {
bytes= j.optInt("BYTES",-1);
if ( bytes>-1 ) bytes= bytes / items;
} else {
bytes= j.optInt("BYTES",-1);
}
if ( column.getNodeName().equals("CONTAINER") ) {
// all other properties come from the innermost node.
XPathFactory factory = XPathFactory.newInstance();
XPath xpath = factory.newXPath();
Node column1= (Node) xpath.evaluate("COLUMN",column,XPathConstants.NODE);
if ( column1==null ) {
column1= (Node) xpath.evaluate("CONTAINER/COLUMN",column,XPathConstants.NODE);
String dim0=(String)xpath.evaluate("REPETITIONS/text()",column,XPathConstants.STRING);
String dim1=(String)xpath.evaluate("CONTAINER/REPETITIONS/text()",column,XPathConstants.STRING);
dims= "["+dim0+","+dim1+"]";
} else {
dims= "["+(String)xpath.evaluate("REPETITIONS/text()",column,XPathConstants.STRING)+"]";
}
j= toJSONObject(column1);
}
dataType= j.optString("DATA_TYPE","");
fieldNumber= j.optInt("FIELD_NUMBER",-1);
unit= j.optString("UNIT","");
validMaximum= j.optDouble("VALID_MAXIMUM",Double.POSITIVE_INFINITY);
validMinimum= j.optDouble("VALID_MINIMUM",Double.NEGATIVE_INFINITY);
missingConstant= j.optDouble("MISSING_CONSTANT",Double.NaN);
if ( Double.isNaN(missingConstant) ) {
missingConstant= j.optDouble("INVALID_CONSTANT",Double.NaN);
}
description= j.optString("DESCRIPTION", "");
} catch (TransformerException | JSONException ex) {
throw new IllegalArgumentException("unable to run",ex);
} catch (XPathExpressionException ex) {
Logger.getLogger(PDS3DataObject.class.getName()).log(Level.SEVERE, null, ex);
}
}
/**
* convert the Document into a JSON object which is easier to work with.
* @param n
* @return
* @throws TransformerConfigurationException
* @throws TransformerException
* @throws JSONException
*/
protected static JSONObject toJSONObject(Node n) throws TransformerConfigurationException, TransformerException, JSONException {
TransformerFactory transfac = TransformerFactory.newInstance();
transfac.setAttribute("indent-number", 4);
Transformer trans = transfac.newTransformer();
// Set up desired output format
trans.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
trans.setOutputProperty(OutputKeys.INDENT, "yes");
ByteArrayOutputStream out= new ByteArrayOutputStream();
//create string from xml tree
// StringWriter sw = new StringWriter();
StreamResult streamResult = new StreamResult(out);
DOMSource source = new DOMSource(n);
trans.transform(source, streamResult);
JSONObject result= XML.toJSONObject(out.toString());
return result.getJSONObject(n.getNodeName());
}
/**
* return the Autoplot URI to load the data.
* @param resource the granule (binary or ASCII) file to load.
* @return the URI.
*/
public String resolveUri(URL resource) {
if ( interchangeFormat.equals("ASCII") && fieldNumber>-1 ) {
return getAsciiUri(resource);
} else {
return getBinaryUri(resource) ;
}
}
private String getAsciiUri(URL resource) {
Map args= new LinkedHashMap<>();
if ( filePointer!=null ) {
switch (filePointer.getOffsetUnits()) {
case LINES:
args.put("skipLines",String.valueOf(filePointer.getOffset()));
break;
case BYTES:
int offsetBytes=filePointer.getOffset();
offsetBytes= (int)(offsetBytes * 0.98); // fudge factor, because of newlines?
args.put("skipBytes",String.valueOf(offsetBytes));
break;
default:
throw new IllegalArgumentException("unsupported file pointer");
}
}
args.put("column",String.valueOf(fieldNumber-1));
return "vap+txt:" + resource.toString() + "?" + URISplit.formatParams(args) ;
}
/**
* return a several line description of the data.
* @return a several line description of the data.
*/
private String getBinaryUri(URL resource) throws IllegalArgumentException {
Map args= new LinkedHashMap<>();
if ( recordBytes>-1 ) {
args.put( "recLength", String.valueOf(recordBytes) );
} else {
args.put( "recLength", String.valueOf(rowPrefixBytes+rowBytes+rowSuffixBytes) );
}
if ( dataType.equals("DATE") || dataType.equals("TIME") || ( dataType.equals("CHARACTER") && unit.equals("UTC") ) ) {
args.put("type", "time"+bytes);
} else if ( dataType.equals("ASCII_REAL") ) {
args.put("type", "ascii"+bytes);
} else if ( dataType.equals("ASCII_INTEGER") ) {
args.put("type", "ascii"+bytes);
} else if ( dataType.equals("PC_REAL") ) {
args.put("type", "float");
args.put("byteOrder", "little");
} else if ( dataType.equals("SUN_REAL") || dataType.equals("IEEE_REAL") ) {
args.put("type", "float");
args.put("byteOrder", "big");
} else if ( dataType.equals("LSB_UNSIGNED_INTEGER" ) ) {
switch (bytes) {
case 2:
args.put("type", "ushort");
break;
case 4:
args.put("type", "uint");
break;
case 8:
args.put("type", "ulong");
break;
}
args.put("byteOrder", "little");
} else if ( dataType.equals("LSB_INTEGER" ) ) {
switch (bytes) {
case 2:
args.put("type", "short");
break;
case 4:
args.put("type", "int");
break;
case 8:
args.put("type", "long");
break;
}
args.put("byteOrder", "little");
} else if ( dataType.equals("MSB_UNSIGNED_INTEGER" ) ) {
switch (bytes) {
case 2:
args.put("type", "ushort");
break;
case 4:
args.put("type", "uint");
break;
case 8:
args.put("type", "ulong");
break;
}
args.put("byteOrder", "big");
} else if ( dataType.equals("MSB_INTEGER") ) {
switch (bytes) {
case 2:
args.put("type", "short");
break;
case 4:
args.put("type", "int");
break;
case 8:
args.put("type", "long");
break;
}
args.put("byteOrder", "big");
} else if ( dataType.equals("UNSIGNED_INTEGER") && bytes==1 ) {
args.put("type","ubyte");
} else if ( dataType.equals("LSB_BIT_STRING" ) ) {
args.put("type","ubyte");
args.put("dims","["+bytes+"]");
} else {
throw new IllegalArgumentException("unsupported type:" +dataType);
}
if ( this.filePointer!=null ) {
switch (this.filePointer.getOffsetUnits()) {
case LINES:
args.put("byteOffset", String.valueOf(this.filePointer.getOffset()*this.rowBytes) );
break;
case BYTES:
args.put("byteOffset", String.valueOf(this.filePointer.getOffset()) );
break;
default:
throw new IllegalArgumentException("Hmmm, uncoded case. Contact Jeremy Faden.");
}
}
args.put( "recOffset", String.valueOf(startByte-1+rowPrefixBytes));
if ( missingConstant!=Double.NaN ) args.put( "fillValue", String.valueOf(missingConstant));
if ( validMaximum!=Double.POSITIVE_INFINITY ) args.put( "validMax", String.valueOf(validMaximum) );
if ( validMinimum!=Double.NEGATIVE_INFINITY ) args.put( "validMin", String.valueOf(validMinimum) );
if ( unit.trim().length()!=0 && !args.get("type").startsWith("time") ) args.put( "units", unit );
if ( items>-1 ) {
args.put( "dims", "["+items+"]");
} else if ( dims!=null ) {
args.put( "dims", dims);
}
return "vap+bin:" + resource.toString() + "?" + URISplit.formatParams(args) ;
}
/**
* return a several line description of the data.
* @return a several line description of the data.
*/
public String getDescription() {
return this.description;
}
private Map getMetadata( JSONObject jo ) {
Map result= new LinkedHashMap<>();
Iterator it= jo.keys();
while( it.hasNext() ) {
String k= (String)it.next();
try {
Object v= jo.get(k);
if ( v instanceof JSONObject ) {
result.put( k, getMetadata((JSONObject)v) );
} else {
result.put( k, v );
}
} catch (JSONException ex) {
}
}
return result;
}
public Map getMetadata() {
Map result= getMetadata(columnJSONObject);
result.put("_table", getMetadata(tableJSONObject));
result.put("_label", getMetadata(labelJSONObject));
return result;
}
public FilePointer getFilePointer() {
return filePointer;
}
/**
* the offset into the file, where 1 is the beginning.
* @param fileOffset
*/
public void setFilePointer( FilePointer p ) {
this.filePointer = p;
}
}