package gov.nasa.gsfc.spdf.cdfj; import java.io.*; import java.nio.*; import java.util.*; import java.util.zip.*; import java.lang.reflect.*; public class TSExtractor extends Extractor { static { try { Class variableClass = Class.forName("gov.nasa.gsfc.spdf.cdfj.Variable"); Class rdrClass = Class.forName("gov.nasa.gsfc.spdf.cdfj.MetaData"); Class cl = Class.forName("gov.nasa.gsfc.spdf.cdfj.TSExtractor"); Class timeSpecClass = Class.forName("gov.nasa.gsfc.spdf.cdfj.TimeInstantModel"); double[] da = new double[0]; int[] ia = new int[0]; Class[][] arglist; arglist = new Class[][]{ new Class[] {rdrClass, variableClass, Boolean.class, da.getClass()}, new Class[] {rdrClass, variableClass, Integer.class, Boolean.class, da.getClass()}, null, null }; addFunction("TimeSeries", cl, arglist); arglist = new Class[][]{ new Class[] {rdrClass, variableClass, Boolean.class, da.getClass(), ia.getClass()}, new Class[] {rdrClass, variableClass, Integer.class, Boolean.class, da.getClass(), ia.getClass()}, null, null }; addFunction("SampledTimeSeries", cl, arglist); arglist = new Class[][]{ new Class[] {rdrClass, variableClass, Boolean.class, da.getClass(), timeSpecClass}, new Class[] {rdrClass, variableClass, Integer.class, Boolean.class, da.getClass(), timeSpecClass}, null, null }; addFunction("TimeSeriesObject", cl, arglist); } catch (ClassNotFoundException ex) { ex.printStackTrace(); } } public static double [][] getTimeSeries0(MetaData rdr, Variable var, Boolean ignoreFill, double[] timeRange) throws Throwable { return getTimeSeries(rdr, var, null, ignoreFill, timeRange); } public static double [][] getTimeSeries1(MetaData rdr, Variable var, Integer which, Boolean ignoreFill, double[] timeRange) throws Throwable { return getTimeSeries(rdr, var, which, ignoreFill, timeRange); } public static double [][] getTimeSeries(MetaData rdr, Variable var, Integer which, Boolean ignoreFill, double[] timeRange) throws Throwable { if (var.getNumberOfValues() == 0) return null; boolean ignore = ignoreFill.booleanValue(); double [] vdata; int [] recordRange = null; TimeVariable tv = TimeVariableFactory.getTimeVariable(rdr, var.getName()); double [] times = tv.getTimes(); if (times == null) return null; boolean longType = false; int type = var.getType(); int element = (which == null)?0:which.intValue(); Number pad; if (DataTypes.typeCategory[type] == DataTypes.LONG) { longType = true; pad = new Long(((long[])getPadValue(rdr.thisCDF, var))[element]); } else { pad = new Double(((double[])getPadValue(rdr.thisCDF, var))[element]); } double[] stimes; Object o = null; Object[] oa = null; if (timeRange == null) { o = (which == null)?Extractor.getSeries0(rdr.thisCDF, var): Extractor.getElement1(rdr.thisCDF, var, which); if (var.isMissingRecords()) { long[][] locations = var.getLocator().getLocations(); oa = filterPad(o, times, pad, locations, 0); } else { oa = new Object[]{times, (double[])o}; } } else { recordRange = getRecordRange(rdr, var, timeRange); if (recordRange == null) return null; if (which == null) { o = getRange0(rdr.thisCDF, var, new Integer(recordRange[0]), new Integer(recordRange[1])); } else { o = getRangeForElement1(rdr.thisCDF, var, new Integer(recordRange[0]), new Integer(recordRange[1]), which); } stimes = new double[Array.getLength(o)]; int index = recordRange[0]; for (int i = 0; i < stimes.length; i++) { stimes[i] = times[index++]; } if (var.isMissingRecords()) { long[][] locations = var.getLocator().getLocations(); oa = filterPad(o, stimes, pad, locations, recordRange[0]); } else { oa = new Object[]{stimes, (double[])o}; } } stimes = (double[])oa[0]; if (!ignore) { vdata = castToDouble(oa[1], longType); return new double [][] {stimes, vdata}; } // fill values need to be filtered Object fill = Extractor.getFillValue(rdr.thisCDF, var); boolean fillDefined = true; Number fillValue = null; if (fill.getClass().getComponentType() == Double.TYPE) { fillDefined = (((double[])fill)[0] == 0); if (fillDefined) fillValue = new Double(((double[])fill)[1]); } else { fillDefined = (((long[])fill)[0] == 0); if (fillDefined) fillValue = new Long(((long[])fill)[1]); } if (!fillDefined) { vdata = castToDouble(oa[1], longType); return new double [][] {stimes, vdata}; } return filterFill(stimes, oa[1], fillValue); } static int[] getRecordRange(MetaData rdr,Variable var, double[] timeRange) { return getRecordRange(rdr, var, timeRange, null); } static int[] getRecordRange(MetaData rdr, Variable var, double[] timeRange, TimeInstantModel ts) { try { TimeVariableX tvx = (TimeVariableX) TimeVariableFactory.getTimeVariable(rdr, var.getName()); return tvx.getRecordRange(timeRange); } catch (Throwable t) { } return null; } public static double [][] filterFill(double[] times, double [] vdata, double fill, int first) { double [][] series; int count = 0; for (int i = 0; i < vdata.length; i++) { if (vdata[i] != fill) count++; } series = new double[2][count]; int n = 0; for (int i = 0; i < vdata.length; i++) { if (vdata[i] == fill) continue; series[0][n] = times[i + first]; series[1][n] = vdata[i]; n++; } return series; } public static double [][] filterFill(double[] times, Object o, Number fillValue) { double [][] series; int count = 0; if (o.getClass().getComponentType() == Long.TYPE) { long fill = fillValue.longValue(); long[] ldata = (long[])o; for (int i = 0; i < ldata.length; i++) { if (ldata[i] != fill) count++; } series = new double[2][count]; int n = 0; for (int i = 0; i < ldata.length; i++) { if (ldata[i] == fill) continue; series[0][n] = times[i]; series[1][n] = (double)ldata[i]; n++; } } else { if (o.getClass().getComponentType() != Double.TYPE) return null; double fill = fillValue.doubleValue(); double[] data = (double[])o; for (int i = 0; i < data.length; i++) { if (data[i] != fill) count++; } series = new double[2][count]; int n = 0; for (int i = 0; i < data.length; i++) { if (data[i] == fill) continue; series[0][n] = times[i]; series[1][n] = data[i]; n++; } } return series; } static Object[] filterPad(Object o, double[] times, Number pad, long[][] locations, int first) { RecordSensor sensor = new RecordSensor(locations); if (o.getClass().getComponentType() == Double.TYPE) { double dpad = pad.doubleValue(); double[] vdata = (double[])o; int npad = 0; for (int i = 0; i < vdata.length; i++) { if (sensor.hasRecord(first + i)) continue; if (vdata[i] == dpad) npad++; } if (npad == 0) return new Object[] {times, vdata}; double[] _data = new double[vdata.length - npad]; double[] _times = new double[vdata.length - npad]; int index = 0; for (int i = 0; i < vdata.length; i++) { if (sensor.hasRecord(first + i) || (vdata[i] != dpad)) { _data[index] = vdata[i]; _times[index] = times[i]; index++; } } return new Object[] {_times, _data}; } else { if (!(o.getClass().getComponentType() == Long.TYPE)) return null; long lpad = pad.longValue(); long[] ldata = (long[])o; int npad = 0; for (int i = 0; i < ldata.length; i++) { if (sensor.hasRecord(first + i)) continue; if (ldata[i] == lpad) npad++; } if (npad == 0) { return new Object[] {times, ldata}; } long[] _data = new long[ldata.length - npad]; double[] _times = new double[ldata.length - npad]; int index = 0; for (int i = 0; i < ldata.length; i++) { if (sensor.hasRecord(first + i) || (ldata[i] != lpad)) { _data[index] = ldata[i]; _times[index] = times[i]; index++; } } return new Object[] {_times, _data}; } } public static double [][] getSampledTimeSeries0(MetaData rdr, Variable var, Boolean ignoreFill, double[] timeRange, int[] stride) throws Throwable { return getSampledTimeSeries(rdr, var, null, ignoreFill, timeRange, stride); } public static double [][] getSampledTimeSeries1(MetaData rdr, Variable var, Integer which, Boolean ignoreFill, double[] timeRange, int[] stride) throws Throwable { return getSampledTimeSeries(rdr, var, which, ignoreFill, timeRange, stride); } public static double [][] getSampledTimeSeries(MetaData rdr, Variable var, Integer which, Boolean ignoreFill, double[] timeRange, int[] stride) throws Throwable { if (var.getNumberOfValues() == 0) return null; boolean ignore = ignoreFill.booleanValue(); double [] vdata; int [] recordRange = null; TimeVariable tv = TimeVariableFactory.getTimeVariable(rdr, var.getName()); double [] times = tv.getTimes(); if (times == null) return null; double[] stimes; Stride strideObject = new Stride(stride); if (timeRange == null) { vdata = (which == null)? (double[])getSeries0(rdr.thisCDF, var, strideObject): (double[])getElement1(rdr.thisCDF, var, which, strideObject); } else { recordRange = getRecordRange(rdr, var, timeRange); if (recordRange == null) return null; if (which == null) { vdata = (double[])getRange0(rdr.thisCDF, var, new Integer(recordRange[0]), new Integer(recordRange[1]), strideObject); } else { vdata = (double[])getRangeForElement1(rdr.thisCDF, var, new Integer(recordRange[0]), new Integer(recordRange[1]), which, strideObject); } } int _stride = strideObject.getStride(); double [] fill = (double[])getFillValue(rdr.thisCDF, var); if ((!ignore) || (fill[0] != 0)) { if (timeRange == null) { if (_stride == 1) { return new double [][] {times, vdata}; } else { stimes = new double[vdata.length]; for (int i = 0; i < vdata.length; i ++) { stimes[i] = times[i*_stride]; } return new double [][] {stimes, vdata}; } } else { stimes = new double[vdata.length]; if (_stride == 1) { System.arraycopy(times, recordRange[0], stimes, 0, vdata.length); return new double [][] {stimes, vdata}; } else { int srec = recordRange[0]; for (int i = 0; i < vdata.length; i ++) { stimes[i] = times[srec + i*_stride]; } return new double [][] {stimes, vdata}; } } } // fill values need to be filtered if (timeRange == null) { if (_stride == 1) { return filterFill(times, vdata, fill[1], 0); } else { stimes = new double[vdata.length]; for (int i = 0; i < vdata.length; i ++) { stimes[i] = times[i*_stride]; } return filterFill(stimes, vdata, fill[1], 0); } } else { stimes = new double[vdata.length]; if (_stride == 1) { System.arraycopy(times, recordRange[0], stimes, 0, vdata.length); return filterFill(stimes, vdata, fill[1], 0); } else { int srec = recordRange[0]; for (int i = 0; i < vdata.length; i ++) { stimes[i] = times[srec + i*_stride]; } return filterFill(stimes, vdata, fill[1], 0); } } } public static TimeSeries getTimeSeriesObject0(MetaData rdr, Variable var, Boolean ignoreFill, double[] timeRange, TimeInstantModel ts) throws Throwable { return new GeneralTimeSeries(rdr, var, null, ignoreFill, timeRange, ts); } public static TimeSeries getTimeSeriesObject1(MetaData rdr, Variable var, Integer which, Boolean ignoreFill, double[] timeRange, TimeInstantModel ts) throws Throwable { return new GeneralTimeSeries(rdr, var, which, ignoreFill, timeRange, ts); } /** * Loss of precision may occur if type of var is LONG * times obtained are millisecond since 1970 regardless of the * precision of time variable corresponding to variable var */ public static class GeneralTimeSeries implements TimeSeries { double [] vdata; double [] times; TimeInstantModel tspec; double[][] filtered = null; public GeneralTimeSeries(MetaData rdr, Variable var, Integer which, Boolean ignoreFill, double[] timeRange, TimeInstantModel ts) throws Throwable { boolean ignore = ignoreFill.booleanValue(); int [] recordRange = null; if (ts != null) { synchronized (ts) { tspec = (TimeInstantModel)ts.clone(); } } TimeVariable tv = TimeVariableFactory.getTimeVariable(rdr, var.getName()); times = tv.getTimes(tspec); if (times == null) throw new Throwable("times not available for " + var.getName()); double[] stimes; boolean longType = false; int type = var.getType(); if (DataTypes.typeCategory[type] == DataTypes.LONG) { longType = true; } Object o = null; if (timeRange == null) { o = (which == null)?getSeries0(rdr.thisCDF, var): getElement1(rdr.thisCDF, var, which); } else { recordRange = getRecordRange(rdr, var, timeRange, ts); if (recordRange == null) throw new Throwable("no record range"); if (which == null) { o = getRange0(rdr.thisCDF, var, new Integer(recordRange[0]), new Integer(recordRange[1])); } else { o = getRangeForElement1(rdr.thisCDF, var, new Integer(recordRange[0]), new Integer(recordRange[1]), which); } } vdata = castToDouble(o, longType); if (!ignore) { if (timeRange != null) { stimes = new double[vdata.length]; System.arraycopy(times, recordRange[0], stimes, 0, vdata.length); times = stimes; } } else { // fill values need to be filtered double [] fill = (double[])getFillValue(rdr.thisCDF, var); int first = (timeRange != null)?recordRange[0]:0; if (fill[0] != 0) { // there is no fill value stimes = new double[vdata.length]; System.arraycopy(times, first, stimes, 0, vdata.length); times = stimes; } else { filtered = filterFill(times, vdata, fill[1], first); } } } public double[] getTimes() { return (filtered != null)?filtered[0]:times; } public double[] getValues() { return (filtered != null)?filtered[1]:vdata; } public TimeInstantModel getTimeInstantModel() {return tspec;} } public static class GeneralTimeSeriesX implements TimeSeriesX { final TimeInstantModel tspec; final TimeVariableX tv; final String vname; final CDFImpl thisCDF; final double[] timeRange; final boolean oned; final boolean columnMajor; public GeneralTimeSeriesX(MetaData rdr, Variable var, Boolean ignoreFill, final double[] timeRange, TimeInstantModel ts, boolean oned, boolean columnMajor) throws Throwable { boolean ignore = ignoreFill.booleanValue(); if (ts != null) { synchronized (ts) { tspec = (TimeInstantModel)ts.clone(); } } else { tspec = null; } vname = var.getName(); tv = (TimeVariableX) TimeVariableFactory.getTimeVariable(rdr, vname); thisCDF = rdr.thisCDF; this.timeRange = timeRange; this.oned = oned; this.columnMajor = columnMajor; } public double[] getTimes() throws CDFException.ReaderError { try { if (timeRange == null) return tv.getTimes(tspec); return tv.getTimes(timeRange, tspec); } catch (Throwable th) { throw new CDFException.ReaderError(th.getMessage()); } } public Object getValues() throws CDFException.ReaderError { try { if (timeRange == null) { return (oned)?thisCDF.getOneD(vname,columnMajor): thisCDF.get(vname); } int[] recordRange = tv.getRecordRange(timeRange); if (recordRange == null) { throw new CDFException.ReaderError("no data"); } if (!oned) { return thisCDF.getRange(vname, recordRange[0], recordRange[1]); } else { return thisCDF.getRangeOneD(vname, recordRange[0], recordRange[1], columnMajor); } } catch (Throwable th) { throw new CDFException.ReaderError(th.getMessage()); } } public TimeInstantModel getTimeInstantModel() {return tspec;} public boolean isOneD() {return oned;} public boolean isColumnMajor() {return columnMajor;} } public static String identifier() {return "TSExtractor";} static class RecordSensor { long[][] locations; int last = 0; RecordSensor (long[][] locations) { this.locations = locations; } boolean hasRecord(int number) { for (int i = last; i < locations.length; i++) { if ((number >= locations[i][0]) && (number <= locations[i][1])) { last = i; return true; } } return false; } } public static Method getMethod(Variable var, String name, int rank) throws Throwable { return getMethod(var, name, rank, false); } static Method getMethod(Variable var, String name, int rank, boolean checkMissing) throws Throwable { if (var == null) throw new Throwable("Internal error. Null variable " + "encountered in call to TSExtractor.getMethod()"); int _rank = var.getEffectiveRank(); if (_rank != rank) throw new Throwable("Called method is not appropriate for variables of " + "effective rank " + _rank); if (checkMissing && (var.isMissingRecords())) { System.out.println("Variable " + var.getName() + " has gaps." + " Sampled time series code is being tested. Feature is not " + " currently available if the variable has gaps."); return null; } Method method = getMethod(var, name); if (method == null) throw new Throwable("get" + name + " not " + "implemented for " + var.getName()); return method; } static Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("GMT")); public static long getTime(int[] time) { int[] t = new int[6]; for (int i = 0; i < 3; i++) t[i] = time[i]; t[1]--; for (int i = 3; i < 6; i++) t[i] = 0; int n = time.length; if (n >= 4) { t[3] = time[3]; if (n >= 5) { t[4] = time[4]; if (n >= 6) { t[5] = time[5]; } } } cal.clear(); cal.set(t[0], t[1], t[2], t[3], t[4], t[5]); cal.set(Calendar.MILLISECOND,(n > 6)?time[6]:0); return cal.getTimeInMillis(); } public static double getTime(MetaData rdr, String vname, int[] time) throws Throwable { boolean isTT2000 = TimeVariableFactory.getTimeVariable(rdr, vname).isTT2000(); long t = getTime(time); return (isTT2000)?TimeUtil.milliSecondSince1970(t):(double)t; } public static double[] getOverlap(MetaData rdr, double[] trange, String varName, int[] startTime, int[] stopTime) throws Throwable { double[] overlap = new double[] {Double.MIN_VALUE, Double.MAX_VALUE};; if (startTime != null) { if (startTime.length < 3) throw new Throwable("incomplete start" + " time " + "definition."); double _start = getTime(rdr, varName, startTime); if (_start > trange[1]) throw new Throwable("Start time is " + "beyond end of data"); overlap[0] = (_start < trange[0])?trange[0]:_start; } else { overlap[0] = trange[0]; } if (stopTime != null) { if (stopTime.length < 3) throw new Throwable("incomplete stop" + " time " + "definition."); double _stop = getTime(rdr, varName, stopTime); if (_stop < trange[0]) throw new Throwable("Stop time is " + "before start of data"); if (_stop < overlap[0]) throw new Throwable("Stop time is " + "before start time"); overlap[1] = /*(_stop > trange[1])?trange[1]:*/_stop; } else { overlap[1] = trange[1]; } return overlap; } }