/** Calculate the rectangle occupied by the data */
protected Rectangle getDataRectangle(Graphics g, Rectangle r) {
Axis a;
int waxis;
int x = r.x;
int y = r.y;
int width = r.width;
int height = r.height;
for (int i = 0; i < axis.size(); i++) {
a = ((Axis) axis.elementAt(i));
waxis = a.getAxisWidth(g);
switch (a.getAxisPos()) {
case Axis.LEFT:
x += waxis;
width -= waxis;
break;
case Axis.RIGHT:
width -= waxis;
break;
case Axis.TOP:
y += waxis;
height -= waxis;
break;
case Axis.BOTTOM:
height -= waxis;
break;
}
}
return new Rectangle(x, y, width, height);
}
/**
* Return the axis values for the given pixel location on this graph.
*
* @param x The x pixel location on the graph.
* @param y The y pixel location on the graph.
* @return the x and y values for the given pixel location.
*/
public double[] getValueAt(int x, int y) {
Insets insets = getInsets();
double v[] = new double[2];
v[0] = xAxis != null ? xAxis.getValue(x - insets.left) : 0.;
v[1] = yAxis != null ? yAxis.getValue(getHeight() - y - insets.bottom) : 0.;
return v;
}
/**
* Detach a previously attached Axis.
*
* @param the Axis to dettach.
*/
public void detachAxis(Axis a) {
if (a != null) {
a.detachAll();
a.g2d = null;
axis.removeElement(a);
}
}
/**
* Create and attach an Axis to the graph. The position of the axis is one of Axis.TOP,
* Axis.BOTTOM, Axis.LEFT or Axis.RIGHT.
*
* @param position Position of the axis in the drawing window.
*/
public Axis createAxis(int position) {
Axis a;
try {
a = new Axis(position);
a.g2d = this;
axis.addElement(a);
} catch (Exception e) {
System.out.println("Failed to create Axis");
e.printStackTrace();
return null;
}
return a;
}
public void componentResized(ComponentEvent e) {
Dimension dim = getSize();
Insets insets = getInsets();
Rectangle dataArea =
new Rectangle(
insets.left,
insets.top,
dim.width - insets.left - insets.right - 1,
dim.height - insets.top - insets.bottom - 1);
if (xAxis.getSize() != dataArea.width - 2) {
xAxis.setSize(dataArea.width);
}
if (yAxis.getSize() != dataArea.height - 2) {
yAxis.setSize(dataArea.height);
}
}
/**
* Called by the paint method to draw the graph and its graph items.
*
* @param g the graphics context.
*/
public void paintComponent(Graphics g) {
Dimension dim = getSize();
Insets insets = getInsets();
dataArea =
new Rectangle(
insets.left,
insets.top,
dim.width - insets.left - insets.right - 1,
dim.height - insets.top - insets.bottom - 1);
// background
if (isOpaque()) {
g.setColor(getBackground());
g.fillRect(0, 0, dim.width, dim.height);
}
g.setColor(getForeground());
// get axis tickmarks
double xticks[] = xAxis.getTicks();
double yticks[] = yAxis.getTicks();
int yb = dataArea.y + dataArea.height;
// draw grid
if (showGrid) {
g.setColor(gridColor != null ? gridColor : getBackground().darker());
// vertical x grid lines
for (int i = 0; i < xticks.length; i += 2) {
int x = dataArea.x + (int) Math.round(xticks[i]);
g.drawLine(x, dataArea.y, x, dataArea.y + dataArea.height);
}
// horizontal y grid lines
for (int i = 0; i < yticks.length; i += 2) {
int y = yb - (int) Math.round(yticks[i]);
g.drawLine(dataArea.x, y, dataArea.x + dataArea.width, y);
}
}
for (int i = 0; i < graphItems.size(); i++) {
((GraphItem) graphItems.elementAt(i)).draw(this, g, dataArea, xAxis, yAxis);
}
if (sPt != null && ePt != null) {
g.setColor(getForeground());
g.drawRect(
Math.min(sPt.x, ePt.x), Math.min(sPt.y, ePt.y),
Math.abs(ePt.x - sPt.x), Math.abs(ePt.y - sPt.y));
}
}
/**
* Attach a previously created Axis. Only Axes that have been attached will be drawn
*
* @param the Axis to attach.
*/
public void attachAxis(Axis a) {
if (a == null) return;
try {
axis.addElement(a);
a.g2d = this;
} catch (Exception e) {
System.out.println("Failed to attach Axis");
e.printStackTrace();
}
}
private static void addAdviceToMatchedCube(Advice advice, String regex, NCube ncube, Axis axis) {
if (axis != null) { // Controller methods
for (Column column : axis.getColumnsWithoutDefault()) {
String method = column.getValue().toString();
String classMethod = ncube.getName() + '.' + method + "()";
if (classMethod.matches(regex)) {
ncube.addAdvice(advice, method);
}
}
} else { // Expressions
String classMethod = ncube.getName() + ".run()";
if (classMethod.matches(regex)) {
ncube.addAdvice(advice, "run");
}
}
}
/**
* Draw the Axis. As each axis is drawn and aligned less of the canvas is avaliable to plot the
* data. The returned Rectangle is the canvas area that the data is plotted in.
*/
protected Rectangle drawAxis(Graphics g, Rectangle r) {
Axis a;
int waxis;
Rectangle dr;
int x;
int y;
int width;
int height;
if (square) r = ForceSquare(g, r);
dr = getDataRectangle(g, r);
x = dr.x;
y = dr.y;
width = dr.width;
height = dr.height;
if (clearAll) {
Color c = g.getColor();
g.setColor(DataBackground);
g.fillRect(x, y, width, height);
g.setColor(c);
}
// Draw a frame around the data area (If requested)
if (frame) drawFrame(g, x, y, width, height);
// Now draw the axis in the order specified aligning them with the final
// data area.
for (int i = 0; i < axis.size(); i++) {
a = ((Axis) axis.elementAt(i));
a.data_window = new Dimension(width, height);
switch (a.getAxisPos()) {
case Axis.LEFT:
r.x += a.width;
r.width -= a.width;
a.positionAxis(r.x, r.x, y, y + height);
if (r.x == x) {
a.gridcolor = gridcolor;
a.drawgrid = drawgrid;
a.zerocolor = zerocolor;
a.drawzero = drawzero;
}
a.drawAxis(g);
a.drawgrid = false;
a.drawzero = false;
break;
case Axis.RIGHT:
r.width -= a.width;
a.positionAxis(r.x + r.width, r.x + r.width, y, y + height);
if (r.x + r.width == x + width) {
a.gridcolor = gridcolor;
a.drawgrid = drawgrid;
a.zerocolor = zerocolor;
a.drawzero = drawzero;
}
a.drawAxis(g);
a.drawgrid = false;
a.drawzero = false;
break;
case Axis.TOP:
r.y += a.width;
r.height -= a.width;
a.positionAxis(x, x + width, r.y, r.y);
if (r.y == y) {
a.gridcolor = gridcolor;
a.drawgrid = drawgrid;
a.zerocolor = zerocolor;
a.drawzero = drawzero;
}
a.drawAxis(g);
a.drawgrid = false;
a.drawzero = false;
break;
case Axis.BOTTOM:
r.height -= a.width;
a.positionAxis(x, x + width, r.y + r.height, r.y + r.height);
if (r.y + r.height == y + height) {
a.gridcolor = gridcolor;
a.drawgrid = drawgrid;
a.zerocolor = zerocolor;
a.drawzero = drawzero;
}
a.drawAxis(g);
a.drawgrid = false;
a.drawzero = false;
break;
}
}
return r;
}
/**
* Force the plot to have an aspect ratio of 1 by forcing the axes to have the same range. If the
* range of the axes are very different some extremely odd things can occur. All axes are forced
* to have the same range, so more than 2 axis is pointless.
*/
protected Rectangle ForceSquare(Graphics g, Rectangle r) {
Axis a;
Rectangle dr;
int x = r.x;
int y = r.y;
int width = r.width;
int height = r.height;
double xmin;
double xmax;
double ymin;
double ymax;
double xrange = 0.0;
double yrange = 0.0;
double range;
double aspect;
if (dataset == null | dataset.isEmpty()) return r;
/*
** Force all the axis to have the same range. This of course
** means that anything other than one xaxis and one yaxis
** is a bit pointless.
*/
for (int i = 0; i < axis.size(); i++) {
a = (Axis) axis.elementAt(i);
range = a.maximum - a.minimum;
if (a.isVertical()) {
yrange = Math.max(range, yrange);
} else {
xrange = Math.max(range, xrange);
}
}
if (xrange <= 0 | yrange <= 0) return r;
if (xrange > yrange) range = xrange;
else range = yrange;
for (int i = 0; i < axis.size(); i++) {
a = (Axis) axis.elementAt(i);
a.maximum = a.minimum + range;
}
/*
** Get the new data rectangle
*/
dr = getDataRectangle(g, r);
/*
** Modify the data rectangle so that it is square.
*/
if (dr.width > dr.height) {
x += (dr.width - dr.height) / 2.0;
width -= dr.width - dr.height;
} else {
y += (dr.height - dr.width) / 2.0;
height -= dr.height - dr.width;
}
return new Rectangle(x, y, width, height);
}
/**
* Parse the section file and fill in the Dbase.
*
* @return Success code
*/
public void parse() throws Exception {
JOAParameter tempProperties[] = new JOAParameter[100];
FileInputStream in = null;
DataInputStream inData = null;
short inShort = 0;
long bytesRead = 0;
long bytesInFile = mFile.length();
short[] sarray = new short[1];
int mTotalStns = 0;
EPSProgressDialog mProgress = new EPSProgressDialog(new Frame(), mProgressStr, Color.blue);
mProgress.setVisible(true);
// Get an epic key database specific to JOA
EPIC_Key_DB mEpicKeyDB = new EPIC_Key_DB("joa_epic.key");
// Get an epic key database specific to JOA
EPIC_Key_DB mOrigEpicKeyDB = new EPIC_Key_DB("epic.key");
// create a vector for temporary storage of the dbases
Vector dBases = new Vector(100);
try {
in = new FileInputStream(mFile);
BufferedInputStream bis = new BufferedInputStream(in, 1000000);
inData = new DataInputStream(bis);
// read version
short vers = inData.readShort();
bytesRead += 2;
if (vers < 2) {
FileImportException fiex = new FileImportException();
String errStr = "Invalid version for a JOA binary file";
fiex.setErrorType(errStr);
throw fiex;
}
// read number of bytes in file description string
inShort = inData.readShort();
bytesRead += 2;
// read the file description String
byte buf[] = new byte[inShort];
inData.read(buf, 0, inShort);
String fileDescrip = new String(buf);
bytesRead += inShort;
// create a new open file object
JOADataFile of = new JOADataFile(fileDescrip);
// read the number of sections
int numSections = inData.readShort();
bytesRead += 2;
// read each section
JOASection sech;
int ord = 0;
for (int s = 0; s < numSections; s++) {
mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile));
// read the section header
inShort = inData.readShort();
bytesRead += 2;
byte buf1[] = new byte[inShort];
inData.read(buf1, 0, inShort);
String sectionDescrip = new String(buf1);
bytesRead += inShort;
// read the ship code
byte bufsc[] = new byte[2];
bufsc[0] = inData.readByte();
bufsc[1] = inData.readByte();
String shipCode = new String(bufsc);
bytesRead += 2;
// read num casts
int numCasts = inData.readShort();
bytesRead += 2;
// read num parameters
int numVars = inData.readShort();
bytesRead += 2;
// quality code
int qcStd = 1;
if (vers == 4) {
qcStd = inData.readShort();
bytesRead += 2;
}
// create a new section
of.mNumSections++;
sech = new JOASection(of.mNumSections, sectionDescrip, shipCode, numCasts, numVars);
if (vers == 2) {
// read the properties
byte bufv[] = new byte[4];
for (int p = 0; p < numVars; p++) {
// parameter name
inData.read(bufv, 0, 4);
String tempVar = new String(bufv);
bytesRead += 4;
// units
inShort = inData.readShort();
bytesRead += 2;
String units = null;
if (inShort > 0) {
byte buf11[] = new byte[inShort];
inData.read(buf11, 0, inShort);
units = new String(buf11);
bytesRead += inShort;
}
// convert varnames to UC
tempVar.toUpperCase();
// create new property
tempProperties[p] = new JOAParameter(tempVar, units);
// add this property to the section property list
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits =
EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel);
}
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits = new String("na");
}
tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS;
// read the actual scale
int actScale = inData.readShort();
bytesRead += 2;
if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale;
else tempProperties[p].mActScale = 1.0;
// read the actual origin
int actOrigin = inData.readShort();
tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale;
// read reverse y
int reverseY = inData.readShort();
bytesRead += 2;
if (reverseY == 0) tempProperties[p].mReverseY = false;
else tempProperties[p].mReverseY = true;
tempProperties[p].mWasCalculated = false;
}
} else {
// read the properties
String tempVar = null;
for (int p = 0; p < numVars; p++) {
// length of parameter name
inShort = inData.readShort();
bytesRead += 2;
// parameter name
if (inShort > 0) {
byte buf13[] = new byte[inShort];
inData.read(buf13, 0, inShort);
tempVar = new String(buf13);
bytesRead += inShort;
}
// units
inShort = inData.readShort();
bytesRead += 2;
String units = null;
if (inShort > 0) {
byte buf11[] = new byte[inShort];
inData.read(buf11, 0, inShort);
units = new String(buf11);
bytesRead += inShort;
}
// convert varnames to UC
tempVar = tempVar.toUpperCase();
// create new property
tempProperties[p] = new JOAParameter(tempVar, units);
// add this property to the section property list
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits =
EPS_Util.paramNameToJOAUnits(false, tempProperties[0].mVarLabel);
}
if (tempProperties[p].mUnits == null) {
tempProperties[p].mUnits = new String("na");
}
tempProperties[p].mCastOrObs = EPSConstants.ALL_OBS;
// read the actual scale
int actScale = inData.readShort();
bytesRead += 2;
if (actScale != 0) tempProperties[p].mActScale = 1.0 / (double) actScale;
else tempProperties[p].mActScale = 1.0;
// read the actual origin
int actOrigin = inData.readShort();
tempProperties[p].mActOrigin = (double) actOrigin * tempProperties[p].mActScale;
// read reverse y
int reverseY = inData.readShort();
bytesRead += 2;
if (reverseY == 0) tempProperties[p].mReverseY = false;
else tempProperties[p].mReverseY = true;
tempProperties[p].mWasCalculated = false;
}
}
// read the cast headers
for (int c = 0; c < numCasts; c++) {
// read station number
inShort = inData.readShort();
bytesRead += 2;
byte bufx[] = new byte[inShort];
inData.read(bufx, 0, inShort);
String stnNum = new String(bufx);
bytesRead += inShort;
// read cast number
int castNum = inData.readShort();
bytesRead += 2;
double myLat = 0.0;
double myLon = 0.0;
if (vers == 2) {
// read latitude/lon
int lat = inData.readInt();
bytesRead += 4;
int lon = inData.readInt();
bytesRead += 4;
myLat = lat * 0.001;
myLon = lon * 0.001;
} else if (vers > 2) {
// read latitude/lon
myLat = inData.readDouble();
bytesRead += 8;
myLon = inData.readDouble();
bytesRead += 4;
}
// read number of bottles
int numBottles = inData.readShort();
bytesRead += 2;
// read the date
int year = inData.readInt();
bytesRead += 4;
int month = inData.readInt();
bytesRead += 4;
int day = inData.readInt();
bytesRead += 4;
int hour = inData.readInt();
bytesRead += 4;
double min = inData.readDouble();
bytesRead += 8;
// read bottom
int bottomdbar = inData.readInt();
// read station quality
int stnQual = inData.readShort();
bytesRead += 2;
ord++;
JOAStation sh =
new JOAStation(
ord,
shipCode,
stnNum,
castNum,
myLat,
myLon,
numBottles,
year,
month,
day,
hour,
min,
bottomdbar,
stnQual);
sech.mStations.addElement(sh);
sh.setType("JOA BOTTLE");
// make a DBase object
Dbase db = new Dbase();
// add the global attributes
db.addEPSAttribute(
"CRUISE", EPCHAR, sech.mSectionDescription.length(), sech.mSectionDescription);
db.addEPSAttribute("CAST", EPCHAR, sh.mStnNum.length(), sh.mStnNum);
sarray[0] = (short) sh.mBottomDepthInDBARS;
db.addEPSAttribute("WATER_DEPTH", EPSHORT, 1, sarray);
db.addEPSAttribute("DATA_ORIGIN", EPCHAR, sech.mShipCode.length(), sech.mShipCode);
String dType = sh.getType();
if (dType == null) dType = "UNKN";
db.addEPSAttribute("DATA_TYPE", EPCHAR, dType.length(), dType);
sarray[0] = (short) stnQual;
db.addEPSAttribute("STN_QUALITY", EPSHORT, 1, sarray);
db.setDataType("JOA BOTTLE");
// add to temporary collection
dBases.addElement(db);
}
int start = mTotalStns;
int end = sech.mStations.size() + mTotalStns;
for (int sc = start; sc < end; sc++) {
mProgress.setPercentComplete(100.0 * ((double) bytesRead / (double) bytesInFile));
// get a dBase
Dbase db = (Dbase) dBases.elementAt(sc);
// get a station
JOAStation sh = (JOAStation) sech.mStations.elementAt(sc - start);
// create an array of arrays to store the data
double[][] va = new double[sech.mNumVars][sh.mNumBottles];
int[][] qc = new int[sech.mNumVars][sh.mNumBottles];
short[] bqc = new short[sh.mNumBottles];
int presPos = 0;
// read the bottles
for (int b = 0; b < sh.mNumBottles; b++) {
// read the bottle quality code
bqc[b] = inData.readShort();
bytesRead += 2;
for (int v = 0; v < sech.mNumVars; v++) {
// store the position of the PRES variable
if (tempProperties[v].mVarLabel.equals("PRES")) presPos = v;
// get the measured parameter
double dVarVal = EPSConstants.MISSINGVALUE;
try {
dVarVal = inData.readDouble();
} catch (IOException e) {
FileImportException fiex = new FileImportException();
String errStr =
"Error reading the parameter data. "
+ "\n"
+ "Bottle #"
+ b
+ " Parameter #"
+ v;
fiex.setErrorType(errStr);
throw fiex;
}
bytesRead += 8;
// store the value in the multidimensional array
va[v][b] = dVarVal;
// get the quality flag
short flag = (short) EPSConstants.MISSINGVALUE;
try {
flag = inData.readShort();
} catch (IOException e) {
FileImportException fiex = new FileImportException();
String errStr =
"Error reading the parameter quality code. "
+ "\n"
+ "Bottle #"
+ b
+ " Parameter #"
+ v;
fiex.setErrorType(errStr);
throw fiex;
}
bytesRead += 2;
qc[v][b] = flag;
} // for v
} // for b
// add the bottle quality codes as an attribute
db.addEPSAttribute("BOTTLE_QUALITY_CODES", EPSHORT, sh.mNumBottles, bqc);
// create the axes time = 0, depth = 1, lat = 2, lon = 3
Axis timeAxis = new Axis();
Axis zAxis = new Axis();
Axis latAxis = new Axis();
Axis lonAxis = new Axis();
// time axis
timeAxis.setName("time");
timeAxis.setTime(true);
timeAxis.setUnlimited(false);
timeAxis.setAxisType(EPTAXIS);
timeAxis.setLen(1);
int hour = 0;
if (sh.mHour != EPSConstants.MISSINGVALUE) hour = sh.mHour;
double mins = 0;
if (sh.mMinute != EPSConstants.MISSINGVALUE) mins = sh.mMinute;
// make the time axis units
String date = "days since ";
int min = (int) mins;
double fmin = mins - min;
int secs = (int) (fmin * 60.0);
double fsec = (fmin * 60.0) - secs;
int msec = (int) (fsec * 1000.0);
String fs = String.valueOf(fsec);
fs = fs.substring(fs.indexOf(".") + 1, fs.length()).trim();
int f = 0;
if (fs != null && fs.length() > 0) f = Integer.valueOf(fs).intValue();
// sprintf(time_string,"%04d-%02d-%02d %02d:%02d:%02d.%03d",yr,mon,day,hr,min,sec,f);
String frmt =
new String(
"{0,number,####}-{1,number,00}-{2,number,00} {3,number,00}:{4,number,00}:{5,number,00}.{6,number,000}");
MessageFormat msgf = new MessageFormat(frmt);
Object[] objs = {
new Integer(sh.mYear),
new Integer(sh.mMonth),
new Integer(sh.mDay),
new Integer(hour),
new Integer(min),
new Integer(secs),
new Integer(f)
};
StringBuffer out = new StringBuffer();
msgf.format(objs, out, null);
String time_string = new String(out);
date = date + time_string;
timeAxis.addAttribute(0, "units", EPCHAR, date.length(), date);
timeAxis.setUnits(date);
GeoDate gd = null;
try {
gd = new GeoDate(sh.mMonth, sh.mDay, sh.mYear, hour, min, secs, msec);
GeoDate[] ta = {gd};
MultiArray tma = new ArrayMultiArray(ta);
timeAxis.setData(tma);
db.setAxis(timeAxis);
} catch (Exception ex) {
GeoDate[] ta = {new GeoDate()};
MultiArray tma = new ArrayMultiArray(ta);
timeAxis.setData(tma);
db.setAxis(timeAxis);
}
// add the time axes variable
EPSVariable var = new EPSVariable();
var.setOname("time");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "units", EPCHAR, date.length(), date);
var.setUnits(date);
double[] vta = {0.0};
MultiArray vtma = new ArrayMultiArray(vta);
try {
var.setData(vtma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// z axis
zAxis.setName("depth");
zAxis.setTime(false);
zAxis.setUnlimited(false);
zAxis.setLen(sh.mNumBottles);
zAxis.setAxisType(EPZAXIS);
zAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1");
zAxis.addAttribute(1, "units", EPCHAR, 4, "dbar");
zAxis.setUnits("dbar");
zAxis.setFrmt("f10.1");
// zAxis.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 1;
zAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
double[] za = new double[sh.mNumBottles];
for (int b = 0; b < sh.mNumBottles; b++) {
za[b] = va[presPos][b];
}
MultiArray zma = new ArrayMultiArray(za);
zAxis.setData(zma);
db.setAxis(zAxis);
// add the z axes variables
var = new EPSVariable();
var.setOname("depth");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.1");
var.addAttribute(1, "units", EPCHAR, 4, "dbar");
var.setUnits("dbar");
var.setFrmt("f10.1");
// var.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 1;
var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
MultiArray zvma = new ArrayMultiArray(za);
try {
var.setData(zvma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// lat axis
latAxis.setName("latitude");
latAxis.setTime(false);
latAxis.setUnlimited(false);
latAxis.setLen(1);
latAxis.setAxisType(EPYAXIS);
latAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
latAxis.addAttribute(1, "units", EPCHAR, 7, "degrees");
latAxis.setUnits("degrees");
latAxis.setFrmt("f10.4");
// latAxis.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 500;
latAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
double lat = sh.mLat;
double[] la = {lat};
MultiArray lma = new ArrayMultiArray(la);
latAxis.setData(lma);
db.setAxis(latAxis);
// add the y axes variable
var = new EPSVariable();
var.setOname("latitude");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
var.addAttribute(1, "units", EPCHAR, 7, "degrees");
var.setUnits("degrees");
var.setFrmt("f10.4");
// var.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 500;
var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
MultiArray yvma = new ArrayMultiArray(la);
try {
var.setData(yvma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// lon axis
lonAxis.setName("longitude");
lonAxis.setTime(false);
lonAxis.setUnlimited(false);
lonAxis.setLen(1);
lonAxis.setAxisType(EPXAXIS);
lonAxis.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
lonAxis.addAttribute(1, "units", EPCHAR, 7, "degrees");
lonAxis.setUnits("degrees");
lonAxis.setFrmt("f10.4");
// lonAxis.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 502;
lonAxis.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
double lon = sh.mLon;
double[] lla = {lon};
lma = new ArrayMultiArray(lla);
lonAxis.setData(lma);
db.setAxis(lonAxis);
// add the x axes variable
var = new EPSVariable();
var.setOname("longitude");
var.setDtype(EPDOUBLE);
var.setVclass(Double.TYPE);
var.addAttribute(0, "FORTRAN_format", EPCHAR, 5, "f10.4");
var.addAttribute(1, "units", EPCHAR, 7, "degrees");
var.setUnits("degrees");
var.setFrmt("f10.4");
// var.addAttribute(2, "type", EPCHAR, 0, "");
sarray[0] = 502;
var.addAttribute(2, "epic_code", EPSHORT, 1, sarray);
MultiArray xvma = new ArrayMultiArray(lla);
try {
var.setData(xvma);
} catch (Exception ex) {
}
db.addEPSVariable(var);
// add the measured variables
for (int v = 0; v < sech.mNumVars; v++) {
// if (presPos == v)
// continue;
// create an array of measured EPSVariables for this database
EPSVariable epsVar = new EPSVariable();
// initialize the new EPSVariables
// look this variable up in JOA EPIC_Key. find matching entry in original EPIC Key
String oname = tempProperties[v].mVarLabel;
String sname = null;
String lname = null;
String gname = null;
String units = null;
String ffrmt = null;
int keyID = -99;
int type = -99;
try {
keyID = mEpicKeyDB.findKey(tempProperties[v].mVarLabel);
Key key = mOrigEpicKeyDB.findKey(keyID);
gname = key.getGname();
sname = key.getSname();
lname = key.getLname();
units = key.getUnits();
ffrmt = key.getFrmt();
type = key.getType();
} catch (Exception e) {
lname = tempProperties[v].mVarLabel;
gname = tempProperties[v].mVarLabel;
sname = tempProperties[v].mVarLabel;
units = tempProperties[v].mUnits;
}
// make a new variable
epsVar = new EPSVariable();
epsVar.setOname(oname);
epsVar.setSname(sname);
epsVar.setLname(lname);
epsVar.setGname(gname);
epsVar.setDtype(EPDOUBLE);
epsVar.setVclass(Double.TYPE);
int numAttributes = 0;
if (ffrmt != null) {
epsVar.addAttribute(numAttributes++, "FORTRAN_format", EPCHAR, ffrmt.length(), ffrmt);
epsVar.setFrmt(ffrmt);
}
if (units != null && units.length() > 0) {
epsVar.addAttribute(numAttributes++, "units", EPCHAR, units.length(), units);
epsVar.setUnits(units);
}
if (keyID >= 0) {
sarray[0] = (short) type;
// epsVar.addAttribute(numAttributes++, "type", EPSHORT, 1, sarray);
}
if (keyID >= 0) {
sarray[0] = (short) keyID;
epsVar.addAttribute(numAttributes++, "epic_code", EPSHORT, 1, sarray);
}
// add the quality code attribute
String qcVar = oname + "_QC";
epsVar.addAttribute(numAttributes++, "OBS_QC_VARIABLE", EPCHAR, qcVar.length(), qcVar);
// connect variable to axis
epsVar.setDimorder(0, 0);
epsVar.setDimorder(1, 1);
epsVar.setDimorder(2, 2);
epsVar.setDimorder(3, 3);
epsVar.setT(timeAxis);
epsVar.setZ(zAxis);
epsVar.setY(latAxis);
epsVar.setX(lonAxis);
// set the data
// create storage for the measured variables
double[][][][] vaa = new double[1][sh.mNumBottles][1][1];
for (int b = 0; b < sh.mNumBottles; b++) {
vaa[0][b][0][0] = va[v][b];
}
MultiArray mdma = new ArrayMultiArray(vaa);
try {
epsVar.setData(mdma);
} catch (Exception ex) {
System.out.println("throwing");
}
// add the variable to the database
db.addEPSVariable(epsVar);
// create the quality code variable
epsVar = new EPSVariable();
epsVar.setOname(oname + "_QC");
epsVar.setSname(sname + "_QC");
epsVar.setLname(sname + "_QC");
epsVar.setGname(sname + "_QC");
epsVar.setDtype(EPSHORT);
epsVar.setVclass(Short.TYPE);
// connect variable to axis
epsVar.setDimorder(0, 0);
epsVar.setDimorder(1, 1);
epsVar.setDimorder(2, 2);
epsVar.setDimorder(3, 3);
epsVar.setT(timeAxis);
epsVar.setZ(zAxis);
epsVar.setY(latAxis);
epsVar.setX(lonAxis);
// set the data
// create storage for the qc variables
short[][][][] qcaa = new short[1][sh.mNumBottles][1][1];
for (int b = 0; b < sh.mNumBottles; b++) {
qcaa[0][b][0][0] = (short) qc[v][b];
}
MultiArray qcma = new ArrayMultiArray(qcaa);
try {
epsVar.setData(qcma);
} catch (Exception ex) {
System.out.println("throwing");
}
// add the qc variable to the database
db.addEPSVariable(epsVar);
} // for v
}
mTotalStns += numCasts;
} // for sc
// read the file comments
StringBuffer sb = null;
while (true) {
try {
// read continuation line
inShort = inData.readShort();
bytesRead += 2;
if (inShort == 1) {
// read number of bytes in file description string
inShort = inData.readShort();
bytesRead += 2;
// read the file description String
byte buf2[] = new byte[inShort];
inData.read(buf2, 0, inShort);
String commentLine = new String(buf2);
bytesRead += inShort;
if (sb == null) sb = new StringBuffer(commentLine);
else sb.append(commentLine);
}
} catch (IOException e) {
break;
}
} // while true
if (sb != null) {
// make attributes for the comments
mOwnerDBase.setDataComment(new String(sb));
}
// make a sub database in the dbase
mOwnerDBase.createSubEntries(mTotalStns, mFile.getName());
for (int d = 0; d < mTotalStns; d++) {
Dbase db = (Dbase) dBases.elementAt(d);
mOwnerDBase.addSubEntry(db);
}
mProgress.setPercentComplete(100.0);
mProgress.setVisible(false);
mProgress.dispose();
in.close();
} catch (IOException e) {
mProgress.setVisible(false);
mProgress.dispose();
throw e;
}
}