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*
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package ucar.nc2.iosp.mcidas;
import com.google.common.base.MoreObjects;
import edu.wisc.ssec.mcidas.AREAnav;
import edu.wisc.ssec.mcidas.AreaDirectory;
import edu.wisc.ssec.mcidas.AreaFile;
import edu.wisc.ssec.mcidas.AreaFileException;
import edu.wisc.ssec.mcidas.Calibrator;
import edu.wisc.ssec.mcidas.CalibratorException;
import edu.wisc.ssec.mcidas.CalibratorFactory;
import edu.wisc.ssec.mcidas.McIDASException;
import edu.wisc.ssec.mcidas.McIDASUtil;
import ucar.ma2.Array;
import ucar.ma2.ArrayChar;
import ucar.ma2.ArrayInt;
import ucar.ma2.DataType;
import ucar.ma2.Index;
import ucar.ma2.InvalidRangeException;
import ucar.ma2.Range;
import ucar.ma2.Section;
import ucar.nc2.Attribute;
import ucar.nc2.Dimension;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Variable;
import ucar.nc2.constants.CDM;
import ucar.nc2.constants.CF;
import ucar.nc2.constants.FeatureType;
import ucar.nc2.units.DateFormatter;
import ucar.unidata.geoloc.ProjectionImpl;
import ucar.unidata.io.RandomAccessFile;
import ucar.unidata.util.Parameter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
/**
* Class to read an AREA file and create a netCDF data structure
* from it.
*
* @author Don Murray
*/
public class AreaReader {
/**
* The AREA file
*/
AreaFile af;
/**
* The AREA navigation
*/
private AREAnav nav;
/**
* The raw AREA directory
*/
private int[] dirBlock;
/**
* The raw nav block
*/
private int[] navBlock;
/**
* The AREA directory
*/
private AreaDirectory ad;
/**
* The calibrator
*/
Calibrator calibrator = null;
/**
* list of bands
*/
int[] bandMap = null;
/**
* calibration scale
*/
private float calScale = 1.f;
/**
* calibration scale
*/
private String calUnit;
/**
* Default ctor
*/
public AreaReader() {
}
/**
* initialize; note that the file is reopened here
*
* @param location the AREA file to open
* @param ncfile the netCDF file to fill out
* @return true if successful
* @throws AreaFileException problem opening the area file
*/
public boolean init(String location, NetcdfFile ncfile) throws AreaFileException {
af = new AreaFile(location);
//read metadata
dirBlock = af.getDir();
ad = af.getAreaDirectory();
int numElements = ad.getElements();
int numLines = ad.getLines();
int numBands = ad.getNumberOfBands();
bandMap = ad.getBands();
navBlock = af.getNav();
Date nomTime = ad.getNominalTime();
DateFormatter df = new DateFormatter();
try {
nav = AREAnav.makeAreaNav(navBlock, af.getAux());
} catch (McIDASException me) {
throw new AreaFileException(me.getMessage());
}
int sensor = dirBlock[AreaFile.AD_SENSORID];
String calName = McIDASUtil.intBitsToString(dirBlock[AreaFile.AD_CALTYPE]);
int calType = getCalType(calName);
// TODO: Need to support calibrated data.
if ((af.getCal() != null)
&& CalibratorFactory.hasCalibrator(sensor)) {
//System.out.println("can calibrate");
try {
calibrator = CalibratorFactory.getCalibrator(sensor, calType, af.getCal());
} catch (CalibratorException ce) {
// System.out.println("can't make calibrator");
calibrator = null;
}
//System.out.println("calibrator = " + calibrator);
}
calUnit = ad.getCalibrationUnitName();
calScale = (1.0f / ad.getCalibrationScaleFactor());
// make the dimensions
Dimension elements = new Dimension("elements", numElements, true);
Dimension lines = new Dimension("lines", numLines, true);
Dimension bands = new Dimension("bands", numBands, true);
Dimension time = new Dimension("time", 1, true);
Dimension dirDim = new Dimension("dirSize", AreaFile.AD_DIRSIZE,
true);
Dimension navDim = new Dimension("navSize", navBlock.length, true);
List<Dimension> image = new ArrayList<>();
image.add(time);
image.add(bands);
image.add(lines);
image.add(elements);
ncfile.addDimension(null, elements);
ncfile.addDimension(null, lines);
ncfile.addDimension(null, bands);
ncfile.addDimension(null, time);
ncfile.addDimension(null, dirDim);
ncfile.addDimension(null, navDim);
Array varArray;
// make the variables
// time
Variable timeVar = new Variable(ncfile, null, null, "time");
timeVar.setDataType(DataType.INT);
timeVar.setDimensions("time");
timeVar.addAttribute(new Attribute(CDM.UNITS,
"seconds since "
+ df.toDateTimeString(nomTime)));
timeVar.addAttribute(new Attribute("long_name", "time"));
varArray = new ArrayInt.D1(1);
((ArrayInt.D1) varArray).set(0, 0);
timeVar.setCachedData(varArray, false);
ncfile.addVariable(null, timeVar);
// lines and elements
Variable lineVar = new Variable(ncfile, null, null, "lines");
lineVar.setDataType(DataType.INT);
lineVar.setDimensions("lines");
//lineVar.addAttribute(new Attribute(CDM.UNITS, "km"));
lineVar.addAttribute(new Attribute("standard_name",
"projection_y_coordinate"));
varArray = new ArrayInt.D1(numLines);
for (int i = 0; i < numLines; i++) {
int pos = nav.isFlippedLineCoordinates()
? i
: numLines - i - 1;
((ArrayInt.D1) varArray).set(i, pos);
}
lineVar.setCachedData(varArray, false);
ncfile.addVariable(null, lineVar);
Variable elementVar = new Variable(ncfile, null, null, "elements");
elementVar.setDataType(DataType.INT);
elementVar.setDimensions("elements");
//elementVar.addAttribute(new Attribute(CDM.UNITS, "km"));
elementVar.addAttribute(new Attribute("standard_name",
"projection_x_coordinate"));
varArray = new ArrayInt.D1(numElements);
for (int i = 0; i < numElements; i++) {
((ArrayInt.D1) varArray).set(i, i);
}
elementVar.setCachedData(varArray, false);
ncfile.addVariable(null, elementVar);
// TODO: handle bands and calibrations
Variable bandVar = new Variable(ncfile, null, null, "bands");
bandVar.setDataType(DataType.INT);
bandVar.setDimensions("bands");
bandVar.addAttribute(new Attribute("long_name",
"spectral band number"));
bandVar.addAttribute(new Attribute("axis", "Z"));
Array bandArray = new ArrayInt.D1(numBands);
for (int i = 0; i < numBands; i++) {
((ArrayInt.D1) bandArray).set(i, bandMap[i]);
}
bandVar.setCachedData(bandArray, false);
ncfile.addVariable(null, bandVar);
// the image
Variable imageVar = new Variable(ncfile, null, null, "image");
imageVar.setDataType(DataType.INT);
imageVar.setDimensions(image);
setCalTypeAttributes(imageVar, getCalType(calName));
imageVar.addAttribute(new Attribute(getADDescription(AreaFile.AD_CALTYPE),
calName));
imageVar.addAttribute(new Attribute("bands", bandArray));
imageVar.addAttribute(new Attribute("grid_mapping", "AREAnav"));
ncfile.addVariable(null, imageVar);
Variable dirVar = new Variable(ncfile, null, null, "areaDirectory");
dirVar.setDataType(DataType.INT);
dirVar.setDimensions("dirSize");
setAreaDirectoryAttributes(dirVar);
ArrayInt.D1 dirArray = new ArrayInt.D1(AreaFile.AD_DIRSIZE);
for (int i = 0; i < AreaFile.AD_DIRSIZE; i++) {
dirArray.set(i, dirBlock[i]);
}
dirVar.setCachedData(dirArray, false);
ncfile.addVariable(null, dirVar);
Variable navVar = new Variable(ncfile, null, null, "navBlock");
navVar.setDataType(DataType.INT);
navVar.setDimensions("navSize");
setNavBlockAttributes(navVar);
ArrayInt.D1 navArray = new ArrayInt.D1(navBlock.length);
for (int i = 0; i < navBlock.length; i++) {
navArray.set(i, navBlock[i]);
}
navVar.setCachedData(navArray, false);
ncfile.addVariable(null, navVar);
// projection variable
ProjectionImpl projection = new McIDASAreaProjection(af);
Variable proj = new Variable(ncfile, null, null, "AREAnav");
proj.setDataType(DataType.CHAR);
proj.setDimensions("");
for (Parameter p : projection.getProjectionParameters()) {
proj.addAttribute(new Attribute(p));
}
// For now, we have to overwrite the parameter versions of thes
proj.addAttribute(new Attribute("grid_mapping_name", McIDASAreaProjection.GRID_MAPPING_NAME));
/*
proj.addAttribute(new Attribute(McIDASAreaProjection.ATTR_AREADIR,
dirArray));
proj.addAttribute(new Attribute(McIDASAreaProjection.ATTR_NAVBLOCK,
navArray));
*/
varArray = new ArrayChar.D0();
((ArrayChar.D0) varArray).set(' ');
proj.setCachedData(varArray, false);
ncfile.addVariable(null, proj);
// add global attributes
ncfile.addAttribute(null, new Attribute("Conventions", "CF-1.0"));
ncfile.addAttribute(null, new Attribute(CF.FEATURE_TYPE, FeatureType.GRID.toString()));
ncfile.addAttribute(null, new Attribute("nominal_image_time", df.toDateTimeString(nomTime)));
String encStr = "netCDF encoded on " + df.toDateTimeString(new Date());
ncfile.addAttribute(null, new Attribute("history", encStr));
//Lastly, finish the file
ncfile.finish();
return true;
}
/**
* Check to see if this is a valid AREA file.
*
* @param raf the file in question
* @return true if it is an AREA file.
*/
public static boolean isValidFile(RandomAccessFile raf) {
String fileName = raf.getLocation();
AreaFile af = null;
try {
af = new AreaFile(fileName); // LOOK opening again not ok for isValidFile
return true;
} catch (AreaFileException e) {
return false; // barfola
} finally {
if (af != null) af.close(); // LOOK need to look at this code
}
}
/**
* Read the values for a variable
*
* @param v2 the variable
* @param section the section info (time,x,y range);
* @return the data
* @throws IOException problem reading file
* @throws InvalidRangeException range doesn't match data
*/
public Array readVariable(Variable v2, Section section) throws IOException, InvalidRangeException {
// not sure why timeRange isn't used...will comment out
// for now
// TODO: use timeRange in readVariable
//Range timeRange = null;
Range bandRange = null;
Range geoXRange = null;
Range geoYRange = null;
Array dataArray;
if (section == null) {
dataArray = Array.factory(v2.getDataType().getPrimitiveClassType(), v2.getShape());
} else if (section.getRank() > 0) {
if (section.getRank() > 3) {
//timeRange = (Range) section.getRange(0);
bandRange = section.getRange(1);
geoYRange = section.getRange(2);
geoXRange = section.getRange(3);
} else if (section.getRank() > 2) {
//timeRange = (Range) section.getRange(0);
geoYRange = section.getRange(1);
geoXRange = section.getRange(2);
} else if (section.getRank() > 1) {
geoYRange = section.getRange(0);
geoXRange = section.getRange(1);
}
dataArray = Array.factory(v2.getDataType().getPrimitiveClassType(), section.getShape());
} else {
String strRank = Integer.toString(section.getRank());
String msg = "Invalid Rank: " + strRank + ". Must be > 0.";
throw new IndexOutOfBoundsException(msg);
}
String varname = v2.getFullName();
Index dataIndex = dataArray.getIndex();
if (varname.equals("latitude") || varname.equals("longitude")) {
double[][] pixel = new double[2][1];
double[][] latLon;
assert geoXRange != null;
assert geoYRange != null;
// Use Range object, which calculates requested i, j
// values and incorporates stride
for (int i = 0; i < geoXRange.length(); i++) {
for (int j = 0; j < geoYRange.length(); j++) {
pixel[0][0] = (double) geoXRange.element(i);
pixel[1][0] = (double) geoYRange.element(j);
latLon = nav.toLatLon(pixel);
if (varname.equals("lat")) {
dataArray.setFloat(dataIndex.set(j, i), (float) (latLon[0][0]));
} else {
dataArray.setFloat(dataIndex.set(j, i), (float) (latLon[1][0]));
}
}
}
}
if (varname.equals("image")) {
try {
int[][] pixelData;
if (bandRange != null) {
for (int k = 0; k < bandRange.length(); k++) {
int bandIndex = bandRange.element(k) + 1; // band numbers in McIDAS are 1 based
for (int j = 0; j < geoYRange.length(); j++) {
for (int i = 0; i < geoXRange.length(); i++) {
pixelData = af.getData(geoYRange.element(j),
geoXRange.element(i), 1, 1,
bandIndex);
dataArray.setInt(dataIndex.set(0, k, j, i),
(pixelData[0][0]));
}
}
}
} else {
assert geoXRange != null;
assert geoYRange != null;
for (int j = 0; j < geoYRange.length(); j++) {
for (int i = 0; i < geoXRange.length(); i++) {
pixelData = af.getData(geoYRange.element(j),
geoXRange.element(i), 1, 1);
dataArray.setInt(dataIndex.set(0, j, i),
(pixelData[0][0]));
}
}
}
} catch (AreaFileException afe) {
throw new IOException(afe.toString());
}
}
return dataArray;
}
/**
* Set the area directory attributes on the variable
*
* @param v the variable to set them on
*/
private void setAreaDirectoryAttributes(Variable v) {
if ((dirBlock == null) || (ad == null)) {
return;
}
for (int i = 1; i < 14; i++) {
if (i == 7) {
continue;
}
v.addAttribute(new Attribute(getADDescription(i), dirBlock[i]));
}
}
/**
* Set the navigation block attributes on the variable
*
* @param v the variable to set them on
*/
private void setNavBlockAttributes(Variable v) {
if ((navBlock == null) || (ad == null)) {
return;
}
v.addAttribute(
new Attribute(
"navigation_type", McIDASUtil.intBitsToString(navBlock[0])));
}
// TODO: Move to use edu.wisc.ssec.mcidas.AreaDirectory.getDescription
// once it's released
/**
* Get a description for a particular Area Directory entry
*
* @param index the index
* @return a description
*/
private String getADDescription(int index) {
String desc = "dir(" + index + ")";
switch (index) {
case AreaFile.AD_STATUS:
desc = "relative position of the image object in the ADDE dataset";
break;
case AreaFile.AD_VERSION:
desc = "AREA version";
break;
case AreaFile.AD_SENSORID:
desc = "SSEC sensor source number";
break;
case AreaFile.AD_IMGDATE:
desc = "nominal year and Julian day of the image (yyyddd)";
break;
case AreaFile.AD_IMGTIME:
desc = "nominal time of the image (hhmmss)";
break;
case AreaFile.AD_STLINE:
desc = "upper-left image line coordinate";
break;
case AreaFile.AD_STELEM:
desc = "upper-left image element coordinate";
break;
case AreaFile.AD_NUMLINES:
desc = "number of lines in the image";
break;
case AreaFile.AD_NUMELEMS:
desc = "number of data points per line";
break;
case AreaFile.AD_DATAWIDTH:
desc = "number of bytes per data point";
break;
case AreaFile.AD_LINERES:
desc = "line resolution";
break;
case AreaFile.AD_ELEMRES:
desc = "element resolution";
break;
case AreaFile.AD_NUMBANDS:
desc = "number of spectral bands";
break;
case AreaFile.AD_PFXSIZE:
desc = "length of the line prefix";
break;
case AreaFile.AD_PROJNUM:
desc = "SSEC project number used when creating the file";
break;
case AreaFile.AD_CRDATE:
desc = "year and Julian day the image file was created (yyyddd)";
break;
case AreaFile.AD_CRTIME:
desc = "image file creation time (hhmmss)";
break;
case AreaFile.AD_BANDMAP:
desc = "spectral band map: bands 1-32";
break;
case AreaFile.AD_DATAOFFSET:
desc = "byte offset to the start of the data block";
break;
case AreaFile.AD_NAVOFFSET:
desc = "byte offset to the start of the navigation block";
break;
case AreaFile.AD_VALCODE:
desc = "validity code";
break;
case AreaFile.AD_STARTDATE:
desc = "actual image start year and Julian day (yyyddd)";
break;
case AreaFile.AD_STARTTIME:
desc = "actual image start time (hhmmss) in milliseconds for POES data";
break;
case AreaFile.AD_STARTSCAN:
desc = "actual image start scan";
break;
case AreaFile.AD_DOCLENGTH:
desc = "length of the prefix documentation";
break;
case AreaFile.AD_CALLENGTH:
desc = "length of the prefix calibration";
break;
case AreaFile.AD_LEVLENGTH:
desc = "length of the prefix band list";
break;
case AreaFile.AD_SRCTYPE:
desc = "source type";
break;
case AreaFile.AD_CALTYPE:
desc = "calibration type";
break;
case AreaFile.AD_SRCTYPEORIG:
desc = "original source type";
break;
case AreaFile.AD_CALTYPEUNIT:
desc = "calibration unit";
break;
case AreaFile.AD_CALTYPESCALE:
desc = "calibration scaling";
break;
case AreaFile.AD_AUXOFFSET:
desc = "byte offset to the supplemental block";
break;
case AreaFile.AD_CALOFFSET:
desc = "byte offset to the calibration block";
break;
case AreaFile.AD_NUMCOMMENTS:
desc = "number of comment cards";
break;
}
desc = desc.replaceAll("\\s", "_");
return desc;
}
/**
* Get the calibration type from the name
*
* @param calName calibration name
* @return the Calibrator class type
*/
private int getCalType(String calName) {
int calTypeOut = Calibrator.CAL_NONE;
if (calName.trim().equals("ALB")) {
calTypeOut = Calibrator.CAL_ALB;
} else if (calName.trim().equals("BRIT")) {
calTypeOut = Calibrator.CAL_BRIT;
} else if (calName.trim().equals("RAD")) {
calTypeOut = Calibrator.CAL_RAD;
} else if (calName.trim().equals("RAW")) {
calTypeOut = Calibrator.CAL_RAW;
} else if (calName.trim().equals("TEMP")) {
calTypeOut = Calibrator.CAL_TEMP;
}
return calTypeOut;
}
/**
* Set the long name and units for the calibration type
*
* @param image image variable
* @param calType calibration type
*/
private void setCalTypeAttributes(Variable image, int calType) {
String longName = "image values";
//String unit = "";
switch (calType) {
case Calibrator.CAL_ALB:
longName = "albedo";
//unit = "%";
break;
case Calibrator.CAL_BRIT:
longName = "brightness values";
break;
case Calibrator.CAL_TEMP:
longName = "temperature";
//unit = "K";
break;
case Calibrator.CAL_RAD:
longName = "pixel radiance values";
//unit = "mW/m2/sr/cm-1";
break;
case Calibrator.CAL_RAW:
longName = "raw image values";
break;
default:
break;
}
image.addAttribute(new Attribute("long_name", longName));
if (calUnit != null) {
image.addAttribute(new Attribute(CDM.UNITS, calUnit));
}
if (calScale != 1.f) {
image.addAttribute(new Attribute("scale_factor", calScale));
}
}
@Override
public String toString() {
return MoreObjects.toStringHelper(this)
.add("af", af)
.add("nav", nav)
.add("ad", ad)
.add("calibrator", calibrator)
.add("calScale", calScale)
.add("calUnit", calUnit)
.toString();
}
}