/*
 * This file is part of McIDAS-V
 *
 * Copyright 2007-2015
 * Space Science and Engineering Center (SSEC)
 * University of Wisconsin - Madison
 * 1225 W. Dayton Street, Madison, WI 53706, USA
 * https://www.ssec.wisc.edu/mcidas
 * 
 * All Rights Reserved
 * 
 * McIDAS-V is built on Unidata's IDV and SSEC's VisAD libraries, and
 * some McIDAS-V source code is based on IDV and VisAD source code.  
 * 
 * McIDAS-V is free software; you can redistribute it and/or modify
 * it under the terms of the GNU Lesser Public License as published by
 * the Free Software Foundation; either version 3 of the License, or
 * (at your option) any later version.
 * 
 * McIDAS-V is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser Public License
 * along with this program.  If not, see http://www.gnu.org/licenses.
 */

package edu.wisc.ssec.mcidasv.data.hydra;

import edu.wisc.ssec.mcidasv.Constants;
import edu.wisc.ssec.mcidasv.McIDASV;
import edu.wisc.ssec.mcidasv.PersistenceManager;
import edu.wisc.ssec.mcidasv.data.HydraDataSource;
import edu.wisc.ssec.mcidasv.data.PreviewSelection;
import edu.wisc.ssec.mcidasv.data.QualityFlag;

import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FilenameFilter;
import java.rmi.RemoteException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SimpleTimeZone;
import java.util.StringTokenizer;

import javax.swing.JCheckBox;
import javax.swing.JOptionPane;

import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.Namespace;
import org.jdom2.output.XMLOutputter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import ucar.ma2.ArrayFloat;
import ucar.ma2.DataType;
import ucar.nc2.Attribute;
import ucar.nc2.Dimension;
import ucar.nc2.Group;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Variable;
import ucar.nc2.dataset.VariableDS;
import ucar.unidata.data.DataCategory;
import ucar.unidata.data.DataChoice;
import ucar.unidata.data.DataSelection;
import ucar.unidata.data.DataSelectionComponent;
import ucar.unidata.data.DataSourceDescriptor;
import ucar.unidata.data.DirectDataChoice;
import ucar.unidata.data.GeoLocationInfo;
import ucar.unidata.data.GeoSelection;
import ucar.unidata.data.grid.GridUtil;
import ucar.unidata.idv.IdvPersistenceManager;
import ucar.unidata.util.Misc;
import visad.Data;
import visad.DateTime;
import visad.DerivedUnit;
import visad.FieldImpl;
import visad.FlatField;
import visad.FunctionType;
import visad.RealType;
import visad.SampledSet;
import visad.Unit;
import visad.VisADException;
import visad.data.units.NoSuchUnitException;
import visad.data.units.ParseException;
import visad.data.units.Parser;
import visad.util.Util;

/**
 * A data source for NPOESS Preparatory Project (Suomi NPP) data
 * This will probably move, but we are placing it here for now
 * since we are leveraging some existing code used for HYDRA.
 */

public class SuomiNPPDataSource extends HydraDataSource {

        private static final Logger logger = LoggerFactory.getLogger(SuomiNPPDataSource.class);
        
        /** Sources file */
    protected String filename;
    
    // for loading bundles, store granule lists and geo lists here
    protected List<String> oldSources = new ArrayList<String>();
    protected List<String> geoSources = new ArrayList<String>();
    
    // integrity map for grouping sets/aggregations of selected products
    Map<String, List<String>> filenameMap = null;

    protected MultiDimensionReader nppAggReader;

    protected MultiDimensionAdapter[] adapters = null;
    
    private ArrayList<MultiSpectralData> msd_CrIS = new ArrayList<MultiSpectralData>();
    private ArrayList<MultiSpectralData> multiSpectralData = new ArrayList<MultiSpectralData>();
    private HashMap<String, MultiSpectralData> msdMap = new HashMap<String, MultiSpectralData>();
    private HashMap<String, QualityFlag> qfMap = new HashMap<String, QualityFlag>();

    private static final String DATA_DESCRIPTION = "Suomi NPP Data";
    
    // instrument related variables and flags
    Attribute instrumentName = null;
    private String productName = null;
    
    // product related variables and flags
    boolean isEDR = false;
    String whichEDR = "";
    
    // for now, we are only handling CrIS variables that match this filter and SCAN dimensions
    private String crisFilter = "ES_Real";
    
    // for now, we are only handling OMPS variables that match this filter and SCAN dimensions
    private String ompsFilter = "Radiance";

    private HashMap defaultSubset;
    public TrackAdapter track_adapter;

    private List categories;
    private boolean isCombinedProduct = false;
    private boolean nameHasBeenSet = false;
    
    // need our own separator char since it's always Unix-style in the Suomi NPP files
    private static final String SEPARATOR_CHAR = "/";
    
    // date formatter for converting Suomi NPP day/time to something we can use
    SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMddHHmmss.SSS");
    
    // date formatter for how we want to show granule day/time on display
    SimpleDateFormat sdfOut = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss z");
    
    // MJH keep track of date to add time dim to FieldImpl
    Date theDate;

    /**
     * Zero-argument constructor for construction via unpersistence.
     */
    
    public SuomiNPPDataSource() {
    }
    
    public SuomiNPPDataSource(String fileName) throws VisADException {
        this(null, Misc.newList(fileName), null);
        logger.debug("filename only constructor call..");
    }

    /**
     * Construct a new Suomi NPP HDF5 data source.
     * @param  descriptor  descriptor for this {@code DataSource}
     * @param  fileName  name of the hdf file to read
     * @param  properties  hashtable of properties
     *
     * @throws VisADException problem creating data
     */
    
    public SuomiNPPDataSource(DataSourceDescriptor descriptor,
                                 String fileName, Hashtable properties)
            throws VisADException {
        this(descriptor, Misc.newList(fileName), properties);
        logger.debug("SuomiNPPDataSource called, single file selected: " + fileName);
    }

    /**
     * Construct a new Suomi NPP HDF5 data source.
     *
     * @param descriptor Descriptor for this {@code DataSource}.
     * @param newSources List of filenames.
     * @param properties Hashtable of properties.
     *
     * @throws VisADException problem creating data
     */
    
    public SuomiNPPDataSource(DataSourceDescriptor descriptor,
                                 List<String> newSources, Hashtable properties)
            throws VisADException {
        super(descriptor, newSources, DATA_DESCRIPTION, properties);
        logger.debug("SuomiNPPDataSource constructor called, file count: " + sources.size());

        filename = (String) sources.get(0);
        setDescription("Suomi NPP");
        
        // build the filename map - matches each product to set of files for that product
        filenameMap = new HashMap<String, List<String>>();
        
        // Pass 1, populate the list of products selected
        for (Object o : sources) {
                String filename = (String) o;
                // first five characters of any product go together
                int lastSeparator = filename.lastIndexOf(File.separatorChar);
                int firstUnderscore = filename.indexOf("_", lastSeparator + 1);
                String prodStr = filename.substring(lastSeparator + 1, firstUnderscore);
                if (! filenameMap.containsKey(prodStr)) {
                                List<String> l = new ArrayList<String>();
                                filenameMap.put(prodStr, l);
                }
        }
        
        // pass 2, create a list of files for each product in this data source
        for (Object o : sources) {
                String filename = (String) o;
                // first five characters of any product go together
                int lastSeparator = filename.lastIndexOf(File.separatorChar);
                int firstUnderscore = filename.indexOf("_", lastSeparator + 1);
                String prodStr = filename.substring(lastSeparator + 1, firstUnderscore);
                List l = (List) filenameMap.get(prodStr);
                l.add(filename);
                filenameMap.put(prodStr, l);
        }
        
        versionCheck();
        setup();
        initQfTranslations();
    }
    
    // alert user about possible VIIRS plugin compatibility issues
    private void versionCheck() {
        boolean pluginDialog = getIdv().getStore().get(Constants.PREF_VIIRS_PLUGIN, false);
        // don't create a dialog though if we are running in background/offscreen mode
        boolean offScreen = getIdv().getArgsManager().getIsOffScreen();
        if (! offScreen) {
                if (! pluginDialog) {
                        String msg = "There has been an update to the VIIRS Formulas plugin.\n" +
                                        "If you use the plugin, you will need to uninstall the currently installed\n" +
                                        "version of the plugin, and install the plugin called \"VIIRS Formulas\".";
                        JCheckBox jcbPlugin = new JCheckBox("Do not show this message again");
                        Object[] params = { msg, jcbPlugin };
                        JOptionPane.showMessageDialog(null, params, "Plugin Compatibility Notice", JOptionPane.OK_OPTION);
                        boolean dontShow = jcbPlugin.isSelected();
                        getIdv().getStore().put(Constants.PREF_VIIRS_PLUGIN, dontShow);
                }       
        } else {
                logger.warn("Make sure your VIIRS plugin is current, there was an update with McV 1.5");
        }
        }

        public void setup() throws VisADException {

        // store filenames for possible bundle unpersistence
        for (Object o : sources) {
                oldSources.add((String) o);
        }
        
        // time zone for product labels
        SimpleTimeZone stz = new SimpleTimeZone(0, "GMT");
        sdf.setTimeZone(stz);
        sdfOut.setTimeZone(stz);
        
        // looking to populate 3 things - path to lat, path to lon, path to relevant products
        String pathToLat = null;
        String pathToLon = null;
        LinkedHashSet<String> pathToProducts = new LinkedHashSet<String>();
        
        // flag to indicate data is 3-dimensions (X, Y, channel or band)
        boolean is3D = false;
        
        // check source filenames to see if this is a combined product. everything
        // from last file separator to first underscore should be product info
        int lastSeparator = filename.lastIndexOf(File.separatorChar);
        int firstUnderscore = filename.indexOf("_", lastSeparator + 1);
        String prodStr = filename.substring(lastSeparator + 1, firstUnderscore);
        StringTokenizer st = new StringTokenizer(prodStr, "-");
        logger.debug("SNPPDS check for embedded GEO, tokenizing: " + prodStr);
        while (st.hasMoreTokens()) {
                String singleProd = st.nextToken();
                for (int i = 0; i < JPSSUtilities.geoProductIDs.length; i++) {
                        if (singleProd.equals(JPSSUtilities.geoProductIDs[i])) {
                                logger.debug("Setting isCombinedProduct true, Found embedded GEO: " + singleProd);
                                isCombinedProduct = true;
                                break;
                        }
                }
        }
        
        // various metatdata we'll need to gather on a per-product basis
        LinkedHashMap<String, String> unsignedFlags = new LinkedHashMap<String, String>();
        LinkedHashMap<String, String> unpackFlags = new LinkedHashMap<String, String>();
        
        // geo product IDs for each granule
        LinkedHashSet<String> geoProductIDs = new LinkedHashSet<String>();
        
        // aggregations will use sets of NetCDFFile readers
        ArrayList<NetCDFFile> ncdfal = new ArrayList<NetCDFFile>();
        
        // we should be able to find an XML Product Profile for each data/product type
        SuomiNPPProductProfile nppPP = null;
        // and also Profile metadata for geolocation variables
        boolean haveGeoMetaData = false;
        
        // number of source granules which make up the data source
        int granuleCount = 1;
                
        try {
                
                nppPP = new SuomiNPPProductProfile();
                
                // for each source file provided, find the appropriate geolocation,
                // get the nominal time and various other granule-level metadata
                Iterator keyIterator = filenameMap.keySet().iterator();
                while (keyIterator.hasNext()) {
                        String keyStr = (String) keyIterator.next();
                        List fileNames = (List) filenameMap.get(keyStr);
                        granuleCount = fileNames.size();
                        setProperty(Constants.PROP_GRANULE_COUNT, granuleCount + " Granule");
                        for (int fileCount = 0; fileCount < granuleCount; fileCount++) {
                                // need to open the main NetCDF file to determine the geolocation product
                                NetcdfFile ncfile = null;
                                String fileAbsPath = null;
                                try {
                                        fileAbsPath = (String) fileNames.get(fileCount);
                                        logger.debug("Trying to open file: " + fileAbsPath);
                                        ncfile = NetcdfFile.open(fileAbsPath);
                                        if (! isCombinedProduct) {
                                                Attribute a = ncfile.findGlobalAttribute("N_GEO_Ref");
                                                logger.debug("Value of GEO global attribute: "
                                                                + a.getStringValue());
                                                String tmpGeoProductID = a.getStringValue();
                                                geoProductIDs.add(tmpGeoProductID);
                                        }
                                        Group rg = ncfile.getRootGroup();

                                        List<Group> gl = rg.getGroups();
                                        if (gl != null) {
                                                for (Group g : gl) {
                                                        logger.trace("Group name: " + g.getFullName());
                                                        // when we find the Data_Products group, go down another group level and pull out 
                                                        // what we will use for nominal day and time (for now anyway).
                                                        // XXX TJJ fileCount check is so we don't count the GEO file in time array!
                                                        if (g.getFullName().contains("Data_Products") && (fileCount != fileNames.size())) {
                                                                boolean foundDateTime = false;
                                                                List<Group> dpg = g.getGroups();

                                                                // cycle through once looking for XML Product Profiles
                                                                for (Group subG : dpg) {

                                                                        String subName = subG.getFullName();
                                                                        // use actual product, not geolocation, to id XML Product Profile
                                                                        if (! subName.contains("-GEO")) {
                                                                                // determine the instrument name (VIIRS, ATMS, CrIS, OMPS)
                                                                                instrumentName = subG.findAttribute("Instrument_Short_Name");

                                                                                // note any EDR products, will need to check for and remove
                                                                                // fill scans later
                                                                                Attribute adtt = subG.findAttribute("N_Dataset_Type_Tag");
                                                                                if (adtt != null) {
                                                                                        String baseName = adtt.getStringValue();
                                                                                        if ((baseName != null) && (baseName.equals("EDR"))) {
                                                                                                isEDR = true;
                                                                                                // have to loop through sub groups variables to determine band
                                                                                                List<Variable> tmpVar = subG.getVariables();
                                                                                                for (Variable v : tmpVar) {
                                                                                                        // if Imagery EDR attribute for band is specified, save it
                                                                                                        Attribute mBand = v.findAttribute("Band_ID");
                                                                                                        if (mBand != null) {
                                                                                                                whichEDR = mBand.getStringValue();
                                                                                                        }
                                                                                                }
                                                                                        }
                                                                                }

                                                                                // This is also where we find the attribute which tells us which
                                                                                // XML Product Profile to use!
                                                                                Attribute axpp = subG.findAttribute("N_Collection_Short_Name");
                                                                                if (axpp != null) {
                                                                                        String baseName = axpp.getStringValue();
                                                                                        productName = baseName;
                                                                                        String productProfileFileName = nppPP.getProfileFileName(baseName);
                                                                                        logger.trace("Found profile: " + productProfileFileName);
                                                                                        if (productProfileFileName == null) {
                                                                                                throw new Exception("XML Product Profile not found in catalog");
                                                                                        }
                                                                                        try {
                                                                                                nppPP.addMetaDataFromFile(productProfileFileName);
                                                                                        } catch (Exception nppppe) {
                                                                                                logger.error("Error parsing XML Product Profile: " + productProfileFileName);
                                                                                                throw new Exception("XML Product Profile Error");
                                                                                        }
                                                                                }
                                                                        }
                                                                }

                                                                // 2nd pass through sub-group to extract date/time for aggregation
                                                                for (Group subG : dpg) {
                                                                        List<Variable> vl = subG.getVariables();
                                                                        for (Variable v : vl) {
                                                                                Attribute aDate = v.findAttribute("AggregateBeginningDate");
                                                                                Attribute aTime = v.findAttribute("AggregateBeginningTime");
                                                                                // did we find the attributes we are looking for?
                                                                                if ((aDate != null) && (aTime != null)) {
                                                                                        String sDate = aDate.getStringValue();
                                                                                        String sTime = aTime.getStringValue();
                                                                                        logger.trace("For day/time, using: " + sDate + sTime.substring(0, sTime.indexOf('Z') - 3));
                                                                                        Date d = sdf.parse(sDate + sTime.substring(0, sTime.indexOf('Z') - 3));
                                                                                        theDate = d;
                                                                                        foundDateTime = true;
                                                                                        // set time for display to day/time of 1st granule examined
                                                                                        if (! nameHasBeenSet) {
                                                                                                setName(instrumentName.getStringValue() + " " + sdfOut.format(d));
                                                                                                nameHasBeenSet = true;
                                                                                        }
                                                                                        break;
                                                                                }
                                                                        }
                                                                        if (foundDateTime) break;
                                                                }
                                                                if (! foundDateTime) {
                                                                        throw new VisADException("No date time found in Suomi NPP granule");
                                                                }
                                                        }                                       
                                                }
                                        }
                                } catch (Exception e) {
                                        logger.warn("Exception during processing of file: " + fileAbsPath);
                                        throw (e);
                                } finally {
                                        ncfile.close();
                                }
                        }

                }
                
                // build each union aggregation element
                Iterator<String> iterator = geoProductIDs.iterator();
                for (int elementNum = 0; elementNum < granuleCount; elementNum++) {
                        
                        String s = null;
                        
                        // build an XML (NCML actually) representation of the union aggregation of these two files
                        Namespace ns = Namespace.getNamespace("http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2");
                        Element root = new Element("netcdf", ns);
                        Document document = new Document(root);

                        Element agg = new Element("aggregation", ns);
                        agg.setAttribute("type", "union");
                        
                        // TJJ - Loop over filename map, could be several products that need to be aggregated
                Set set = filenameMap.keySet();
                Iterator mapIter = set.iterator();
                while (mapIter.hasNext()) {
                        String key = (String) mapIter.next();
                        List l = (List) filenameMap.get(key);
                                Element fData = new Element("netcdf", ns);
                                fData.setAttribute("location", (String) l.get(elementNum));
                                agg.addContent(fData);
                                s = (String) l.get(elementNum);
                }
                        
                        if (! isCombinedProduct) {
                                Element fGeo  = new Element("netcdf", ns);
        
                                String geoFilename = s.substring(0, s.lastIndexOf(File.separatorChar) + 1);
                                // check if we have the whole file name or just the prefix
                                String geoProductID = iterator.next();
                                if (geoProductID.endsWith("h5")) {
                                        geoFilename += geoProductID;
                                } else {
                                        geoFilename += geoProductID;
                                        geoFilename += s.substring(s.lastIndexOf(File.separatorChar) + 6);
                                }
                                // Be sure file as specified by N_GEO_Ref global attribute really is there.
                                File tmpGeo = new File(geoFilename);
                                if (! tmpGeo.exists()) {
                                        // Ok, the expected file defined (supposedly) exactly by a global att is not there...
                                        // We need to check for similar geo files with different creation dates
                                        String geoFileRelative = geoFilename.substring(geoFilename.lastIndexOf(File.separatorChar) + 1);
                                        // also check for Terrain Corrected version of geo
                                        String geoTerrainCorrected = geoFileRelative;
                                        geoTerrainCorrected = geoTerrainCorrected.replace("OD", "TC");
                                        geoTerrainCorrected = geoTerrainCorrected.replace("MG", "TC");
                                        
                                        // now we make a file filter, and see if a matching geo file is present
                                        File fList = new File(geoFilename.substring(0, geoFilename.lastIndexOf(File.separatorChar) + 1)); // current directory

                                        FilenameFilter geoFilter = new FilenameFilter() {
                                                public boolean accept(File dir, String name) {
                                                        if (name.matches(JPSSUtilities.SUOMI_GEO_REGEX)) {
                                                                return true;
                                                        } else {
                                                                return false;
                                                        }
                                                }
                                        };
                                        
                                        File[] files = fList.listFiles(geoFilter);
                                        for (File file : files) {
                                                if (file.isDirectory()) {
                                                        continue;
                                                }
                                                // get the file name for convenience
                                                String fName = file.getName();
                                                // is it one of the standard Ellipsoid geo types we are looking for?
                                                if (fName.substring(0, 5).equals(geoFileRelative.substring(0, 5))) {
                                                        int geoStartIdx = geoFileRelative.indexOf("_d");
                                                        int prdStartIdx = fName.indexOf("_d");
                                                        String s1 = geoFileRelative.substring(geoStartIdx, geoStartIdx + 35);
                                                        String s2 = fName.substring(prdStartIdx, prdStartIdx + 35);
                                                        if (s1.equals(s2)) {
                                                                geoFilename = s.substring(0, s.lastIndexOf(File.separatorChar) + 1) + fName;
                                                                break;
                                                        }
                                                }
                                                // same check, but for Terrain Corrected version
                                                if (fName.substring(0, 5).equals(geoTerrainCorrected.substring(0, 5))) {
                                                        int geoStartIdx = geoTerrainCorrected.indexOf("_d");
                                                        int prdStartIdx = fName.indexOf("_d");
                                                        String s1 = geoTerrainCorrected.substring(geoStartIdx, geoStartIdx + 35);
                                                        String s2 = fName.substring(prdStartIdx, prdStartIdx + 35);
                                                        if (s1.equals(s2)) {
                                                                geoFilename = s.substring(0, s.lastIndexOf(File.separatorChar) + 1) + fName;
                                                                break;
                                                        }
                                                }
                                        }
                                }
                                logger.debug("Cobbled together GEO file name: " + geoFilename);
                                fGeo.setAttribute("location", geoFilename);
                                // add this to list used if we create a zipped bundle
                                geoSources.add(geoFilename);
                                agg.addContent(fGeo);
                        }

                        root.addContent(agg);    
                    XMLOutputter xmlOut = new XMLOutputter();
                    String ncmlStr = xmlOut.outputString(document);
                    ByteArrayInputStream is = new ByteArrayInputStream(ncmlStr.getBytes());                     
                    MultiDimensionReader netCDFReader = new NetCDFFile(is);
                    
                // let's try and look through the NetCDF reader and see what we can learn...
                NetcdfFile ncdff = ((NetCDFFile) netCDFReader).getNetCDFFile();
                
                Group rg = ncdff.getRootGroup();
                // this is a list filled with unpacked qflag products, if any
                ArrayList<VariableDS> qfProds = new ArrayList<VariableDS>();

                List<Group> gl = rg.getGroups();
                if (gl != null) {
                        for (Group g : gl) {
                                logger.debug("Group name: " + g.getFullName());
                                // XXX just temporary - we are looking through All_Data, finding displayable data
                                if (g.getFullName().contains("All_Data")) {
                                        List<Group> adg = g.getGroups();
                                        int xDim = -1;
                                        int yDim = -1;

                                        // two sub-iterations, first one to find geolocation and product dimensions
                                        for (Group subG : adg) {
                                                logger.debug("Sub group name: " + subG.getFullName());
                                                String subName = subG.getFullName();
                                                if (subName.contains("-GEO")) {
                                                        // this is the geolocation data
                                                        String geoBaseName = subG.getShortName();
                                                        geoBaseName = geoBaseName.substring(0, geoBaseName.indexOf('_'));
                                                        if (! haveGeoMetaData) {
                                                                String geoProfileFileName = nppPP.getProfileFileName(geoBaseName);
                                                                        // also add meta data from geolocation profile
                                                                        nppPP.addMetaDataFromFile(geoProfileFileName);
                                                                haveGeoMetaData = true;
                                                        }
                                                        List<Variable> vl = subG.getVariables();
                                                        for (Variable v : vl) {
                                                                if (v.getFullName().endsWith(SEPARATOR_CHAR + "Latitude")) {
                                                                        pathToLat = v.getFullName();
                                                                        logger.debug("Ellipsoid Lat/Lon Variable: " + v.getFullName());
                                                                        // get the dimensions of the lat variable
                                                                        Dimension dAlongTrack = v.getDimension(0);
                                                                        yDim = dAlongTrack.getLength();
                                                                        Dimension dAcrossTrack = v.getDimension(1);
                                                                        xDim = dAcrossTrack.getLength();
                                                                        logger.debug("Lat across track dim: " + dAcrossTrack.getLength());
                                                                }
                                                                if (v.getFullName().endsWith(SEPARATOR_CHAR + "Longitude")) {
                                                                        // we got dimensions from lat, don't need 'em twice, but need path
                                                                        pathToLon = v.getFullName();
                                                                }
                                                        } 
                                                        // one more pass in case there is terrain-corrected Lat/Lon
                                                        for (Variable v : vl) {
                                                                if (v.getFullName().endsWith(SEPARATOR_CHAR + "Latitude_TC")) {
                                                                        pathToLat = v.getFullName();
                                                                        logger.debug("Switched Lat/Lon Variable to TC: " + v.getFullName());
                                                                        // get the dimensions of the lat variable
                                                                        Dimension dAlongTrack = v.getDimension(0);
                                                                        yDim = dAlongTrack.getLength();
                                                                        Dimension dAcrossTrack = v.getDimension(1);
                                                                        xDim = dAcrossTrack.getLength();
                                                                        logger.debug("Lat across track dim: " + dAcrossTrack.getLength());
                                                                }
                                                                if (v.getFullName().endsWith(SEPARATOR_CHAR + "Longitude_TC")) {
                                                                        // we got dimensions from lat, don't need 'em twice, but need path
                                                                        pathToLon = v.getFullName();
                                                                }
                                                        }
                                                }
                                        }

                                        // second to identify displayable products
                                        for (Group subG : adg) {
                                                // this is the product data
                                                List<Variable> vl = subG.getVariables();
                                                for (Variable v : vl) {
                                                        boolean useThis = false;
                                                        String vName = v.getFullName();
                                                        logger.trace("Variable: " + vName);
                                                        String varShortName = vName.substring(vName.lastIndexOf(SEPARATOR_CHAR) + 1);

                                                        // Special code to handle quality flags. We throw out anything
                                                        // that does not match bounds of the geolocation data
                                                        
                                                        if (varShortName.startsWith("QF")) {
                                                                
                                                                logger.trace("Handling Quality Flag: " + varShortName);
                                                                
                                                                // this check is done later for ALL variables, but we need
                                                                // it early here to weed out those quality flags that are 
                                                                // simply a small set of data w/no granule geo nbounds
                                                                boolean xScanOk = false;
                                                                boolean yScanOk = false;
                                                                List<Dimension> dl = v.getDimensions();
                                                                
                                                                // toss out > 2D Quality Flags 
                                                                if (dl.size() > 2) {
                                                                        logger.trace("SKIPPING QF, > 2D: " + varShortName);
                                                                        continue;
                                                                }
                                                                
                                                                for (Dimension d : dl) {
                                                                        // in order to consider this a displayable product, make sure
                                                                        // both scan direction dimensions are present and look like a granule
                                                                        if (d.getLength() == xDim) {
                                                                                xScanOk = true;
                                                                        }
                                                                        if (d.getLength() == yDim) {
                                                                                yScanOk = true;
                                                                        }
                                                                }
                                                                
                                                                if (! (xScanOk && yScanOk)) {
                                                                        logger.trace("SKIPPING QF, does not match geo bounds: " + varShortName);
                                                                        continue;
                                                                }
                                                                
                                                                ArrayList<QualityFlag> qfal = nppPP.getQualityFlags(varShortName);
                                                                if (qfal != null) {
                                                                        for (QualityFlag qf : qfal) {
                                                                                qf.setPackedName(vName);
                                                                                // make a copy of the qflag variable
                                                                                // NOTE: by using a VariableDS here, the original
                                                                                // variable is used for the I/O, this matters!
                                                                                VariableDS vqf = new VariableDS(subG, v, false);
                                                                                // prefix with QF num to help guarantee uniqueness across groups
                                                                                // this will cover most cases, but could still be dupe names
                                                                                // within a single QF.  This is handled when fetching XMLPP metadata
                                                                                vqf.setShortName(
                                                                                                varShortName.substring(0, 3) + "_" + qf.getName()
                                                                                );
                                                                                logger.debug("New QF var full name: " + vqf.getFullName());
                                                                        qfProds.add(vqf);
                                                                        qfMap.put(vqf.getFullName(), qf);
                                                                        }
                                                                }
                                                        }

                                                        // for CrIS instrument, first find dimensions of var matching
                                                        // CrIS filter, then throw out all variables which don't match 
                                                        // those dimensions
                                                        
                                                        if (instrumentName.getStringValue().equals("CrIS")) {
                                                                if (! vName.contains("GEO")) {
                                                                        if (! varShortName.startsWith(crisFilter)) {
                                                                                logger.trace("Skipping variable: " + varShortName);
                                                                                continue;
                                                                        }
                                                                } else {
                                                                        // these variables are all GEO-related
                                                                        // if they match lat/lon bounds, keep them
                                                                        List<Dimension> dl = v.getDimensions();
                                                                        if (dl.size() == 3) {
                                                                                boolean isDisplayableCrIS = true;
                                                                                for (Dimension d : dl) {
                                                                                        if ((d.getLength() != xDim) && (d.getLength() != yDim) && (d.getLength() != 9)) {
                                                                                                isDisplayableCrIS = false;
                                                                                        }
                                                                                }
                                                                                if (! isDisplayableCrIS) {
                                                                                        continue;
                                                                                }
                                                                        }
                                                                }
                                                        }

                                                        // for OMPS, only Radiance for now...
                                                        if (instrumentName.getStringValue().contains("OMPS")) {
                                                                if (! varShortName.startsWith(ompsFilter)) {
                                                                        logger.trace("Skipping OMPS variable: " + varShortName);
                                                                        continue;
                                                                }
                                                        }

                                                        DataType dt = v.getDataType();
                                                        if ((dt.getSize() != 4) && (dt.getSize() != 2) && (dt.getSize() != 1)) {
                                                                continue;
                                                        }

                                                        List<Dimension> dl = v.getDimensions();
                                                        if (dl.size() > 4) {
                                                                continue;
                                                        }

                                                        // for now, skip any 3D VIIRS data
                                                        if (instrumentName.getStringValue().equals("VIIRS")) {
                                                                if (dl.size() == 3) {
                                                                        continue;
                                                                }
                                                        }

                                                        boolean xScanOk = false;
                                                        boolean yScanOk = false;
                                                        for (Dimension d : dl) {
                                                                // in order to consider this a displayable product, make sure
                                                                // both scan direction dimensions are present and look like a granule
                                                                if (d.getLength() == xDim) {
                                                                        xScanOk = true;
                                                                }
                                                                if (d.getLength() == yDim) {
                                                                        yScanOk = true;
                                                                }
                                                        }

                                                        if (xScanOk && yScanOk) {
                                                                useThis = true;
                                                        }

                                                        // For ATMS, only 3-D variable we pass through is BrightnessTemperature
                                                        // Dimensions for BT are (lon, lat, channel)
                                                        if (instrumentName.getStringValue().equals("ATMS")) {
                                                                if (dl.size() == 3) {
                                                                        boolean isDisplayableATMS = false;
                                                                        for (Dimension d : dl) {
                                                                                if (d.getLength() == JPSSUtilities.ATMSChannelCenterFrequencies.length) {
                                                                                        isDisplayableATMS = true;
                                                                                        logger.trace("This variable has a dimension matching num ATMS channels");
                                                                                        break;
                                                                                }
                                                                        }
                                                                        if (! isDisplayableATMS) useThis = false;
                                                                }
                                                        }

                                                        // sensor data with a channel dimension
                                                        if (useThis) {
                                                                if ((instrumentName.getStringValue().equals("CrIS")) ||
                                                                                (instrumentName.getStringValue().equals("ATMS")) || 
                                                                                (instrumentName.getStringValue().contains("OMPS"))) {
                                                                        is3D = true;
                                                                        logger.debug("Handling 3-D data source...");
                                                                }
                                                        }

                                                        if (useThis) { 
                                                                // loop through the variable list again, looking for a corresponding "Factors"
                                                                float scaleVal = 1f;
                                                                float offsetVal = 0f;
                                                                boolean unpackFlag = false;

                                                                //   if the granule has an entry for this variable name
                                                                //     get the data, data1 = scale, data2 = offset
                                                                //     create and poke attributes with this data
                                                                //   endif

                                                                String factorsVarName = nppPP.getScaleFactorName(varShortName);
                                                                logger.debug("Mapping: " + varShortName + " to: " + factorsVarName);
                                                                if (factorsVarName != null) {
                                                                        for (Variable fV : vl) {
                                                                                if (fV.getShortName().equals(factorsVarName)) {
                                                                                        logger.trace("Pulling scale and offset values from variable: " + fV.getShortName());
                                                                                        ucar.ma2.Array a = fV.read();
                                                                                        float[] so = (float[]) a.copyTo1DJavaArray();
                                                                                        scaleVal = so[0];
                                                                                        offsetVal = so[1];
                                                                                        logger.trace("Scale value: " + scaleVal + ", Offset value: " + offsetVal);
                                                                                        unpackFlag = true;
                                                                                        break;
                                                                                }
                                                                        }
                                                                }

                                                                // poke in scale/offset attributes for now

                                                                Attribute a1 = new Attribute("scale_factor", scaleVal);
                                                                v.addAttribute(a1);
                                                                Attribute a2 = new Attribute("add_offset", offsetVal);
                                                                v.addAttribute(a2);  

                                                                // add valid range and fill value attributes here
                                                                // try to fill in valid range
                                                                if (nppPP.hasNameAndMetaData(varShortName)) {
                                                                        String rangeMin = nppPP.getRangeMin(varShortName);
                                                                        String rangeMax = nppPP.getRangeMax(varShortName);
                                                                        logger.trace("range min: " + rangeMin + ", range max: " + rangeMax);
                                                                        // only store range attribute if VALID range found
                                                                        if ((rangeMin != null) && (rangeMax != null)) {
                                                                                int [] shapeArr = new int [] { 2 };
                                                                                ArrayFloat af = new ArrayFloat(shapeArr);
                                                                                try {
                                                                                        af.setFloat(0, Float.parseFloat(rangeMin));
                                                                                } catch (NumberFormatException nfe) {
                                                                                        af.setFloat(0, new Float(Integer.MIN_VALUE));
                                                                                }
                                                                                try {
                                                                                        af.setFloat(1, Float.parseFloat(rangeMax));
                                                                                } catch (NumberFormatException nfe) {
                                                                                        af.setFloat(1, new Float(Integer.MAX_VALUE));
                                                                                }
                                                                                Attribute rangeAtt = new Attribute("valid_range", af);
                                                                                v.addAttribute(rangeAtt);
                                                                        }

                                                                        // check for and load fill values too...

                                                                        // we need to check two places, first, the XML product profile
                                                                        ArrayList<Float> fval = nppPP.getFillValues(varShortName);

                                                                        // 2nd, does the variable already have one defined?
                                                                        // if there was already a fill value associated with this variable, make
                                                                        // sure we bring that along for the ride too...
                                                                        Attribute aFill = v.findAttribute("_FillValue");

                                                                        // determine size of our fill value array
                                                                        int fvArraySize = 0;
                                                                        if (aFill != null) fvArraySize++;
                                                                        if (! fval.isEmpty()) fvArraySize += fval.size();
                                                                        int [] fillShape = new int [] { fvArraySize };

                                                                        // allocate the array
                                                                        ArrayFloat afFill = new ArrayFloat(fillShape);

                                                                        // and FINALLY, fill it!
                                                                        if (! fval.isEmpty()) {
                                                                                for (int fillIdx = 0; fillIdx < fval.size(); fillIdx++) {
                                                                                        afFill.setFloat(fillIdx, fval.get(fillIdx));
                                                                                        logger.trace("Adding fill value (from XML): " + fval.get(fillIdx));
                                                                                }
                                                                        }

                                                                        if (aFill != null) {
                                                                                Number n = aFill.getNumericValue();
                                                                                // is the data unsigned?
                                                                                Attribute aUnsigned = v.findAttribute("_Unsigned");
                                                                                float fillValAsFloat = Float.NaN;
                                                                                if (aUnsigned != null) {
                                                                                        if (aUnsigned.getStringValue().equals("true")) {
                                                                                                DataType fvdt = aFill.getDataType();
                                                                                                logger.trace("Data String: " + aFill.toString());
                                                                                                logger.trace("DataType primitive type: " + fvdt.getPrimitiveClassType());
                                                                                                // signed byte that needs conversion?
                                                                                                if (fvdt.getPrimitiveClassType() == byte.class) {
                                                                                                        fillValAsFloat = (float) Util.unsignedByteToInt(n.byteValue());
                                                                                                }
                                                                                                else if (fvdt.getPrimitiveClassType() == short.class) {
                                                                                                        fillValAsFloat = (float) Util.unsignedShortToInt(n.shortValue());
                                                                                                } else {
                                                                                                        fillValAsFloat = n.floatValue();
                                                                                                }
                                                                                        }
                                                                                }
                                                                                afFill.setFloat(fvArraySize - 1, fillValAsFloat);
                                                                                logger.trace("Adding fill value (from variable): " + fillValAsFloat);
                                                                        }
                                                                        Attribute fillAtt = new Attribute("_FillValue", afFill);
                                                                        v.addAttribute(fillAtt);
                                                                }

                                                                Attribute aUnsigned = v.findAttribute("_Unsigned");
                                                                if (aUnsigned != null) {
                                                                        unsignedFlags.put(v.getFullName(), aUnsigned.getStringValue());
                                                                } else {
                                                                        unsignedFlags.put(v.getFullName(), "false");
                                                                }

                                                                if (unpackFlag) {
                                                                        unpackFlags.put(v.getFullName(), "true");
                                                                } else {
                                                                        unpackFlags.put(v.getFullName(), "false");
                                                                }

                                                                logger.debug("Adding product: " + v.getFullName());
                                                                pathToProducts.add(v.getFullName());

                                                        }
                                                }
                                        }
                                }
                        }
                }
                
                // add in any unpacked qflag products
                for (VariableDS qfV: qfProds) {
                        // skip the spares - they are reserved for future use
                        if (qfV.getFullName().endsWith("Spare")) {
                                continue;
                        }
                        // String.endsWith is case sensitive so gotta check both cases
                        if (qfV.getFullName().endsWith("spare")) {
                                continue;
                        }
                        ncdff.addVariable(qfV.getGroup(), qfV);
                        logger.trace("Adding QF product: " + qfV.getFullName());
                        pathToProducts.add(qfV.getFullName());
                        unsignedFlags.put(qfV.getFullName(), "true");
                        unpackFlags.put(qfV.getFullName(), "false");
                }
                
                    ncdfal.add((NetCDFFile) netCDFReader);
                }
                
        } catch (Exception e) {
                logger.error("cannot create NetCDF reader for files selected");
                if (e.getMessage() != null && e.getMessage().equals("XML Product Profile Error")) {
                        throw new VisADException("Unable to extract metadata from required XML Product Profile");
                }
                e.printStackTrace();
        }
        
        // initialize the aggregation reader object
        try {
                nppAggReader = new GranuleAggregation(ncdfal, pathToProducts, "Track", "XTrack", isEDR);
                ((GranuleAggregation) nppAggReader).setQfMap(qfMap);
        } catch (Exception e) {
                throw new VisADException("Unable to initialize aggregation reader");
        }

        // make sure we found valid data
        if (pathToProducts.size() == 0) {
                throw new VisADException("No data found in files selected");
        }
        
        logger.debug("Number of adapters needed: " + pathToProducts.size());
        adapters = new MultiDimensionAdapter[pathToProducts.size()];
        Hashtable<String, String[]> properties = new Hashtable<String, String[]>(); 
        
        Iterator<String> iterator = pathToProducts.iterator();
        int pIdx = 0;
        boolean adapterCreated = false;
        while (iterator.hasNext()) {
                String pStr = (String) iterator.next();
                logger.debug("Working on adapter number " + (pIdx + 1) + ": " + pStr);
                HashMap<String, Object> swathTable = SwathAdapter.getEmptyMetadataTable();
                HashMap<String, Object> spectTable = SpectrumAdapter.getEmptyMetadataTable();
                swathTable.put("array_name", pStr);
                swathTable.put("lon_array_name", pathToLon);
                swathTable.put("lat_array_name", pathToLat);
                swathTable.put("XTrack", "XTrack");
                swathTable.put("Track", "Track");
                swathTable.put("geo_Track", "Track");
                swathTable.put("geo_XTrack", "XTrack");
                swathTable.put("product_name", productName);
                
                // array_name common to spectrum table
                spectTable.put("array_name", pStr);
                spectTable.put("product_name", productName);
                
                if (is3D) {

                        // 3D data is either ATMS, OMPS, or CrIS
                        if ((instrumentName.getShortName() != null) && (instrumentName.getStringValue().equals("ATMS"))) {

                                spectTable.put(SpectrumAdapter.channelIndex_name, "Channel");
                        swathTable.put(SpectrumAdapter.channelIndex_name, "Channel");
                        
                        swathTable.put("array_dimension_names", new String[] {"Track", "XTrack", "Channel"});
                        swathTable.put("lon_array_dimension_names", new String[] {"Track", "XTrack"});
                        swathTable.put("lat_array_dimension_names", new String[] {"Track", "XTrack"});
                        spectTable.put("array_dimension_names", new String[] {"Track", "XTrack", "Channel"});
                        spectTable.put("lon_array_dimension_names", new String[] {"Track", "XTrack"});
                        spectTable.put("lat_array_dimension_names", new String[] {"Track", "XTrack"});
                        
                        spectTable.put(SpectrumAdapter.channelType, "wavelength");
                        spectTable.put(SpectrumAdapter.channels_name, "Channel");
                    spectTable.put(SpectrumAdapter.x_dim_name, "XTrack");
                    spectTable.put(SpectrumAdapter.y_dim_name, "Track");
                    
                                int numChannels = JPSSUtilities.ATMSChannelCenterFrequencies.length;
                        float[] bandArray = new float[numChannels];
                        String[] bandNames = new String[numChannels];
                        for (int bIdx = 0; bIdx < numChannels; bIdx++) {
                                bandArray[bIdx] = JPSSUtilities.ATMSChannelCenterFrequencies[bIdx];
                                bandNames[bIdx] = "Channel " + (bIdx + 1);
                        }
                        spectTable.put(SpectrumAdapter.channelValues, bandArray);
                        spectTable.put(SpectrumAdapter.bandNames, bandNames);

                        } else {
                                if (instrumentName.getStringValue().equals("CrIS")) {
                                        
                                        swathTable.put("XTrack", "dim1");
                                        swathTable.put("Track", "dim0");
                                        swathTable.put("geo_XTrack", "dim1");
                                        swathTable.put("geo_Track", "dim0");
                                        swathTable.put("product_name", "CrIS_SDR");
                                        swathTable.put(SpectrumAdapter.channelIndex_name, "dim3");
                                        swathTable.put(SpectrumAdapter.FOVindex_name, "dim2"); 
                                         
                                        spectTable.put(SpectrumAdapter.channelIndex_name, "dim3");
                                        spectTable.put(SpectrumAdapter.FOVindex_name, "dim2");
                                spectTable.put(SpectrumAdapter.x_dim_name, "dim1");
                                spectTable.put(SpectrumAdapter.y_dim_name, "dim0");
                                
                                } else if (instrumentName.getStringValue().contains("OMPS")) {
                                        
                                        spectTable.put(SpectrumAdapter.channelIndex_name, "Channel");
                                swathTable.put(SpectrumAdapter.channelIndex_name, "Channel");
                                
                                swathTable.put("array_dimension_names", new String[] {"Track", "XTrack", "Channel"});
                                swathTable.put("lon_array_dimension_names", new String[] {"Track", "XTrack"});
                                swathTable.put("lat_array_dimension_names", new String[] {"Track", "XTrack"});
                                spectTable.put("array_dimension_names", new String[] {"Track", "XTrack", "Channel"});
                                spectTable.put("lon_array_dimension_names", new String[] {"Track", "XTrack"});
                                spectTable.put("lat_array_dimension_names", new String[] {"Track", "XTrack"});
                                
                                spectTable.put(SpectrumAdapter.channelType, "wavelength");
                                spectTable.put(SpectrumAdapter.channels_name, "Channel");
                        spectTable.put(SpectrumAdapter.x_dim_name, "XTrack");
                        spectTable.put(SpectrumAdapter.y_dim_name, "Track");
                        
                                int numChannels = 200;
                                if (instrumentName.getStringValue().equals("OMPS-TC")) {
                                        numChannels = 260;
                                }
                                logger.debug("Setting up OMPS adapter, num channels: " + numChannels);
                                float[] bandArray = new float[numChannels];
                                String[] bandNames = new String[numChannels];
                                for (int bIdx = 0; bIdx < numChannels; bIdx++) {
                                        bandArray[bIdx] = bIdx;
                                        bandNames[bIdx] = "Channel " + (bIdx + 1);
                                }
                                spectTable.put(SpectrumAdapter.channelValues, bandArray);
                                spectTable.put(SpectrumAdapter.bandNames, bandNames);
                                
                                } else {
                                        // sorry, if we can't id the instrument, we can't display the data!
                                        throw new VisADException("Unable to determine instrument name");
                                }
                        }

                } else {
                        swathTable.put("array_dimension_names", new String[] {"Track", "XTrack"});
                        swathTable.put("lon_array_dimension_names", new String[] {"Track", "XTrack"});
                        swathTable.put("lat_array_dimension_names", new String[] {"Track", "XTrack"});
                }
                
                swathTable.put("scale_name", "scale_factor");
                swathTable.put("offset_name", "add_offset");
                swathTable.put("fill_value_name", "_FillValue");
                swathTable.put("range_name", pStr.substring(pStr.indexOf(SEPARATOR_CHAR) + 1));
                spectTable.put("range_name", pStr.substring(pStr.indexOf(SEPARATOR_CHAR) + 1));
                
                // set the valid range hash if data is available
                if (nppPP != null) {
                        if (nppPP.getRangeMin(pStr.substring(pStr.lastIndexOf(SEPARATOR_CHAR) + 1)) != null) {
                                swathTable.put("valid_range", "valid_range");
                        }
                }
                
                String unsignedAttributeStr = unsignedFlags.get(pStr);
                if (unsignedAttributeStr.equals("true")) {
                        swathTable.put("unsigned", unsignedAttributeStr);
                }
                
                String unpackFlagStr = unpackFlags.get(pStr);
                if (unpackFlagStr.equals("true")) {
                        swathTable.put("unpack", "true");
                }
                
                // For Suomi NPP data, do valid range check AFTER applying scale/offset
                swathTable.put("range_check_after_scaling", "true");
                
                // pass in a GranuleAggregation reader...
                if (is3D) {
                if (instrumentName.getStringValue().equals("ATMS")) {
                        adapters[pIdx] = new SwathAdapter(nppAggReader, swathTable);
                        adapterCreated = true;
                        SpectrumAdapter sa = new SpectrumAdapter(nppAggReader, spectTable);
                    DataCategory.createCategory("MultiSpectral");
                    categories = DataCategory.parseCategories("MultiSpectral;MultiSpectral;IMAGE");
                        MultiSpectralData msd = new MultiSpectralData((SwathAdapter) adapters[pIdx], sa, 
                                "BrightnessTemperature", "BrightnessTemperature", "SuomiNPP", "ATMS");
                        msd.setInitialWavenumber(JPSSUtilities.ATMSChannelCenterFrequencies[0]);
                        multiSpectralData.add(msd);
                } 
                if (instrumentName.getStringValue().equals("CrIS")) {
                        if (pStr.contains(crisFilter)) {
                                adapters[pIdx] = new CrIS_SDR_SwathAdapter(nppAggReader, swathTable);
                                adapterCreated = true;
                                CrIS_SDR_Spectrum csa = new CrIS_SDR_Spectrum(nppAggReader, spectTable);
                            DataCategory.createCategory("MultiSpectral");
                            categories = DataCategory.parseCategories("MultiSpectral;MultiSpectral;IMAGE");
                                MultiSpectralData msd = new CrIS_SDR_MultiSpectralData((CrIS_SDR_SwathAdapter) adapters[pIdx], csa); 
                            msd.setInitialWavenumber(csa.getInitialWavenumber());
                            msd_CrIS.add(msd);
                        }
                }
                if (instrumentName.getStringValue().contains("OMPS")) {
                        adapters[pIdx] = new SwathAdapter(nppAggReader, swathTable);
                        adapterCreated = true;
                        SpectrumAdapter sa = new SpectrumAdapter(nppAggReader, spectTable);
                    DataCategory.createCategory("MultiSpectral");
                    categories = DataCategory.parseCategories("MultiSpectral;MultiSpectral;IMAGE");
                        MultiSpectralData msd = new MultiSpectralData((SwathAdapter) adapters[pIdx], sa, 
                                "RadianceEarth", "RadianceEarth", "SuomiNPP", "OMPS");
                        msd.setInitialWavenumber(0);
                        multiSpectralData.add(msd);
                } 
                if (pIdx == 0) {
                        // generate default subset for ATMS and OMPS
                        if (! instrumentName.getStringValue().equals("CrIS")) {
                                defaultSubset = multiSpectralData.get(pIdx).getDefaultSubset();
                        }
                }
                
                } else {
                        String varName = pStr.substring(pStr.indexOf(SEPARATOR_CHAR) + 1);
                        String varShortName = pStr.substring(pStr.lastIndexOf(SEPARATOR_CHAR) + 1);
                        String units = nppPP.getUnits(varShortName);
                        if (units == null) units = "Unknown";
                        Unit u = null;
                        try {
                                        u = Parser.parse(units);
                                } catch (NoSuchUnitException e) {
                                        u = new DerivedUnit(units);
                                        logger.debug("Unkown units: " + units);
                                } catch (ParseException e) {
                                        u = new DerivedUnit(units);
                                        logger.debug("Unparseable units: " + units);
                                }
                        // associate this variable with these units, if not done already
                        RealType.getRealType(varName, u);
                        adapters[pIdx] = new SwathAdapter(nppAggReader, swathTable);
                        adapterCreated = true;
                        if (pIdx == 0) {
                                defaultSubset = adapters[pIdx].getDefaultSubset();
                        }
                        categories = DataCategory.parseCategories("IMAGE");
                }
                // only increment count if we created an adapter, some products are skipped
                if (adapterCreated) pIdx++;
                adapterCreated = false;
        }

        if (msd_CrIS.size() > 0) {
                try {
                        MultiSpectralAggr aggr = new MultiSpectralAggr(msd_CrIS.toArray(new MultiSpectralData[msd_CrIS.size()]));
                        aggr.setInitialWavenumber(902.25f);
                        multiSpectralData.add(aggr);
                        defaultSubset = ((MultiSpectralData) msd_CrIS.get(0)).getDefaultSubset();
                } catch (Exception e) {
                        logger.error("Exception: ", e);
                }
        }

        // Merge with pre-set properties
        Hashtable tmpHt = getProperties();
        tmpHt.putAll(properties);
        setProperties(tmpHt);
    }

    public void initAfterUnpersistence() {
        try {
            String zidvPath = 
                    McIDASV.getStaticMcv().getStateManager().
                    getProperty(IdvPersistenceManager.PROP_ZIDVPATH, "");
            if (getTmpPaths() != null) {
                // New code for zipped bundles-
                // we want 'sources' to point to wherever the zipped data was unpacked.
                sources.clear();
                // following PersistenceManager.fixBulkDataSources, get temporary data location
                for (Object o : getTmpPaths()) {
                    String tempPath = (String) o;
                    // replace macro string with actual path
                    String expandedPath = tempPath.replace(PersistenceManager.MACRO_ZIDVPATH, zidvPath);
                    // we don't want to add nav files to this list!:
                    File f = new File(expandedPath);
                    if (!f.getName().matches(JPSSUtilities.SUOMI_GEO_REGEX)) {
                        sources.add(expandedPath);
                    }
                }

                // mjh fix absolute paths in filenameMap
                logger.debug("original filenameMap: {}", filenameMap);
                Iterator keyIterator = filenameMap.keySet().iterator();
                while (keyIterator.hasNext()) {
                    String keyStr = (String) keyIterator.next();
                    List<String> fileNames = (List<String>) filenameMap.get(keyStr);
                    for (int i = 0; i < fileNames.size(); i++) {
                        String name = fileNames.get(i);
                        int lastSeparator = name.lastIndexOf(File.separatorChar);
                        String sub = name.substring(0, lastSeparator);
                        name = name.replace(sub, zidvPath);
                        fileNames.set(i, name);
                    }
                }
                logger.debug("filenameMap with zidvPath: {}", filenameMap);
            } else {
                // leave in original unpersistence code - this will get run for unzipped bundles.
                // TODO: do we need to handle the "Save with relative paths" case specially?
                    if (! oldSources.isEmpty()) {
                    sources.clear();
                    for (Object o : oldSources) {
                        sources.add((String) o);
                    }
                }
            }
            oldSources.clear();
                setup();
        } catch (Exception e) {
                logger.error("Exception: ", e);
        }
    }

    /* (non-Javadoc)
         * @see edu.wisc.ssec.mcidasv.data.HydraDataSource#canSaveDataToLocalDisk()
         */
        @Override
        public boolean canSaveDataToLocalDisk() {
                // At present, Suomi data is always data granules on disk
                return true;
        }

        /* (non-Javadoc)
         * @see ucar.unidata.data.DataSourceImpl#saveDataToLocalDisk(java.lang.String, java.lang.Object, boolean)
         */
        @Override
        protected List saveDataToLocalDisk(String filePrefix, Object loadId,
                        boolean changeLinks) throws Exception {
                // need to make a list of all data granule files
                // PLUS all geolocation granule files, but only if accessed separate!
                List<String> fileList = new ArrayList<String>();
                for (Object o : sources) {
                        fileList.add((String) o);
                }
                for (String s : geoSources) {
                        fileList.add(s);
                }
                return fileList;
        }

        public List<String> getOldSources() {
                return oldSources;
        }

        public void setOldSources(List<String> oldSources) {
                this.oldSources = oldSources;
        }
    
    public Map<String, List<String>> getFilenameMap() {
        return filenameMap;
    }

    public void setFilenameMap(Map<String, List<String>> filenameMap) {
        this.filenameMap = filenameMap;
    }

        /**
     * Make and insert the {@link DataChoice DataChoices} for this
     * {@code DataSource}.
     */
    
    public void doMakeDataChoices() {
        
        // special loop for CrIS, ATMS, and OMPS data
        if (multiSpectralData.size() > 0) {
                for (int k = 0; k < multiSpectralData.size(); k++) {
                        MultiSpectralData adapter = multiSpectralData.get(k);
                        DataChoice choice = null;
                                try {
                                        choice = doMakeDataChoice(k, adapter);
                                        choice.setObjectProperty(Constants.PROP_GRANULE_COUNT, 
                                                        getProperty(Constants.PROP_GRANULE_COUNT, "1 Granule"));
                                msdMap.put(choice.getName(), adapter);
                                addDataChoice(choice);
                                } catch (Exception e) {
                                        logger.error("Exception: ", e);
                                }
                }
                return;
        }
                
        // all other data (VIIRS and 2D EDRs)
        if (adapters != null) {
                for (int idx = 0; idx < adapters.length; idx++) {
                        DataChoice choice = null;
                        try {
                                choice = doMakeDataChoice(idx, adapters[idx].getArrayName());
                                choice.setObjectProperty(Constants.PROP_GRANULE_COUNT, 
                                                        getProperty(Constants.PROP_GRANULE_COUNT, "1 Granule")); 
                        } 
                        catch (Exception e) {
                                e.printStackTrace();
                                logger.error("doMakeDataChoice failed");
                        }

                        if (choice != null) {
                                addDataChoice(choice);
                        }
                }
        }
    }

    private DataChoice doMakeDataChoice(int idx, String var) throws Exception {
        String name = var;
        DataSelection dataSel = new MultiDimensionSubset(defaultSubset);
        Hashtable subset = new Hashtable();
        subset.put(new MultiDimensionSubset(), dataSel);
        // TJJ Hack check for uber-odd case of data type varies for same variable
        // If it's M12 - M16, it's a BrightnessTemperature, otherwise Reflectance
        if (name.endsWith("BrightnessTemperatureOrReflectance")) {
                name = name.substring(0, name.length() - "BrightnessTemperatureOrReflectance".length());
                if (whichEDR.matches("M12|M13|M14|M15|M16")) {
                        name = name + "BrightnessTemperature";
                } else {
                        name = name + "Reflectance";
                }
        }
        DirectDataChoice ddc = new DirectDataChoice(this, idx, name, name, categories, subset);
        return ddc;
    }
    
    private DataChoice doMakeDataChoice(int idx, MultiSpectralData adapter) throws Exception {
        String name = adapter.getName();
        DataSelection dataSel = new MultiDimensionSubset(defaultSubset);
        Hashtable subset = new Hashtable();
        subset.put(MultiDimensionSubset.key, dataSel);
        subset.put(MultiSpectralDataSource.paramKey, adapter.getParameter());
        // TJJ Hack check for uber-odd case of data type varies for same variable
        // If it's M12 - M16, it's a BrightnessTemperature, otherwise Reflectance
        if (name.endsWith("BrightnessTemperatureOrReflectance")) {
                name = name.substring(0, name.length() - "BrightnessTemperatureOrReflectance".length());
                if (whichEDR.matches("M12|M13|M14|M15|M16")) {
                        name = name + "BrightnessTemperature";
                } else {
                        name = name + "Reflectance";
                }
        }
        DirectDataChoice ddc = new DirectDataChoice(this, new Integer(idx), name, name, categories, subset);
        ddc.setProperties(subset);
        return ddc;
    }

    /**
     * Check to see if this {@code SuomiNPPDataSource} is equal to the object
     * in question.
     * @param o  object in question
     * @return true if they are the same or equivalent objects
     */
    
    public boolean equals(Object o) {
        if ( !(o instanceof SuomiNPPDataSource)) {
            return false;
        }
        return (this == (SuomiNPPDataSource) o);
    }

    public MultiSpectralData getMultiSpectralData() {
        return multiSpectralData.get(0);
    }
    
    public MultiSpectralData getMultiSpectralData(DataChoice choice) {
        return msdMap.get(choice.getName());
    }

    public String getDatasetName() {
      return filename;
    }

        /**
         * @return the qfMap
         */
        public HashMap<String, QualityFlag> getQfMap() {
                return qfMap;
        }

        public void setDatasetName(String name) {
      filename = name;
    }

    public HashMap getSubsetFromLonLatRect(MultiDimensionSubset select, GeoSelection geoSelection) {
      GeoLocationInfo ginfo = geoSelection.getBoundingBox();
      return adapters[0].getSubsetFromLonLatRect(select.getSubset(), ginfo.getMinLat(), ginfo.getMaxLat(),
                                        ginfo.getMinLon(), ginfo.getMaxLon());
    }

    public synchronized Data getData(DataChoice dataChoice, DataCategory category,
                                DataSelection dataSelection, Hashtable requestProperties)
                                throws VisADException, RemoteException {
       return this.getDataInner(dataChoice, category, dataSelection, requestProperties);
    }


    protected Data getDataInner(DataChoice dataChoice, DataCategory category,
                                DataSelection dataSelection, Hashtable requestProperties)
                                throws VisADException, RemoteException {

        //- this hack keeps the HydraImageProbe from doing a getData()
        //- TODO: need to use categories?
        if (requestProperties != null) {
          if ((requestProperties.toString()).equals("{prop.requester=MultiSpectral}")) {
            return null;
          }
        }

        GeoLocationInfo ginfo = null;
        GeoSelection geoSelection = null;
        
        if ((dataSelection != null) && (dataSelection.getGeoSelection() != null)) {
          geoSelection = (dataSelection.getGeoSelection().getBoundingBox() != null) ? dataSelection.getGeoSelection() :
                                    dataChoice.getDataSelection().getGeoSelection();
        }

        if (geoSelection != null) {
          ginfo = geoSelection.getBoundingBox();
        }

        Data data = null;
        if (adapters == null) {
          return data;
        }

        MultiDimensionAdapter adapter = null;
        
        // pick the adapter with the same index as the current data choice
        int aIdx = 0;
        List<DataChoice> dcl = getDataChoices();
        for (DataChoice dc : dcl) {
                if (dc.getName().equals(dataChoice.getName())) {
                        aIdx = dcl.indexOf(dc);
                        break;
                }
        }

        adapter = adapters[aIdx];

        try {
            HashMap subset = null;
            if (ginfo != null) {
                subset = adapter.getSubsetFromLonLatRect(ginfo.getMinLat(), ginfo.getMaxLat(),
                                ginfo.getMinLon(), ginfo.getMaxLon(),
                                geoSelection.getXStride(),
                                geoSelection.getYStride(),
                                geoSelection.getZStride());
            }
            else {

              MultiDimensionSubset select = null;
              Hashtable table = dataChoice.getProperties();
              Enumeration keys = table.keys();
              while (keys.hasMoreElements()) {
                Object key = keys.nextElement();
                logger.debug("Key: " + key.toString());
                if (key instanceof MultiDimensionSubset) {
                  select = (MultiDimensionSubset) table.get(key);
                }
              }  
              subset = select.getSubset();
              logger.debug("Subset size: " + subset.size());

              if (dataSelection != null) {
                Hashtable props = dataSelection.getProperties();
                if (props != null) {
                  if (props.containsKey(SpectrumAdapter.channelIndex_name)) {
                          logger.debug("Props contains channel index key...");
                    double[] coords = (double[]) subset.get(SpectrumAdapter.channelIndex_name);
                    int idx = ((Integer) props.get(SpectrumAdapter.channelIndex_name)).intValue();
                    coords[0] = (double) idx;
                    coords[1] = (double) idx;
                    coords[2] = (double) 1;
                  }
                }
              }
            }

            if (subset != null) {
              data = adapter.getData(subset);
              data = applyProperties(data, requestProperties, subset, aIdx);
            }
        } catch (Exception e) {
            logger.error("getData Exception: ", e);
        }
        ////////// inq1429 return FieldImpl with time dim /////////////////
        if (data != null) {
                List dateTimes = new ArrayList();
                dateTimes.add(new DateTime(theDate));
                SampledSet timeSet = (SampledSet) ucar.visad.Util.makeTimeSet(dateTimes);
                FunctionType ftype = new FunctionType(RealType.Time, data.getType());
                FieldImpl fi = new FieldImpl(ftype, timeSet);
                fi.setSample(0, data);
                data = fi;
        }
        //////////////////////////////////////////////////////////////////
        return data;
    }

    protected Data applyProperties(Data data, Hashtable requestProperties, HashMap subset, int adapterIndex) 
          throws VisADException, RemoteException {
      Data new_data = data;

      if (requestProperties == null) {
        new_data = data;
        return new_data;
      }

      return new_data;
    }

    protected void initDataSelectionComponents(
         List<DataSelectionComponent> components,
             final DataChoice dataChoice) {
      
                  try {
                          // inq1429: need to handle FieldImpl here
                          FieldImpl thing = (FieldImpl) dataChoice.getData(null);
                          FlatField image;
                          if (GridUtil.isTimeSequence(thing)) {
                                  image = (FlatField) thing.getSample(0);
                          } else {
                                  image = (FlatField) thing;
                          }
                          if (image != null) {
                                  PreviewSelection ps = new PreviewSelection(dataChoice, image, null);
                                  // Region subsetting not yet implemented for CrIS data
                                  if (instrumentName.getStringValue().equals("CrIS")) {
                                          ps.enableSubsetting(false);
                                  }
                                  components.add(ps);
                          }
                  } catch (Exception e) {
                          logger.error("Can't make PreviewSelection: ", e);
                  }
      
    }
    
    /**
     * Add Integer->String translations to IDV's
     * "translations" resource, so they will be made available
     * to the data probe of Image Display's.
     */
    
    public void initQfTranslations() {
        
        Map<String, Map<Integer, String>> translations =
                getIdv().getResourceManager().
                getTranslationsHashtable();
        
        for (String qfKey : qfMap.keySet()) {
                // This string needs to match up with the data choice name:
                String qfKeySubstr = qfKey.replace("All_Data/", "");
                // check if we've already added map for this QF
                if (!translations.containsKey(qfKeySubstr)) {
                        Map<String, String> hm = qfMap.get(qfKey).getHm();
                        Map<Integer, String> newMap = 
                                        new HashMap<Integer, String>(hm.size());
                        for (String dataValueKey : hm.keySet()) {
                                // convert Map<String, String> to Map<Integer, String>
                                Integer intKey = Integer.parseInt(dataValueKey);
                                newMap.put(intKey, hm.get(dataValueKey));
                        }
                        translations.put(qfKeySubstr, newMap);
                }
        }
    }
    
}