File _service:obs_scm:thredds-4.6.2-remove-jj2000-su... of Package thredds

File _service:obs_scm:thredds-4.6.2-remove-jj2000-support.patch of Package thredds

diff -Nru thredds-4.6.2/grib/pom.xml thredds-4.6.2.jj2000/grib/pom.xml
--- thredds-4.6.2/grib/pom.xml	2015-06-10 00:05:23.000000000 +0200
+++ thredds-4.6.2.jj2000/grib/pom.xml	2015-07-18 07:30:23.047031384 +0200
@@ -76,11 +76,6 @@
 </dependency>
 
 <dependency>
-	 <groupId>${project.groupId}</groupId>
-	 <artifactId>jj2000</artifactId>
- </dependency>
-
- <dependency>
 <groupId>com.google.guava</groupId>
 <artifactId>guava</artifactId>
 </dependency>
diff -Nru thredds-4.6.2/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader2.java thredds-4.6.2.jj2000/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader2.java
--- thredds-4.6.2/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader2.java	2015-06-10 00:05:23.000000000 +0200
+++ thredds-4.6.2.jj2000/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader2.java	2015-07-18 07:36:33.564519222 +0200
@@ -718,121 +718,12 @@
 
 // Grid point data - JPEG 2000 code stream format
 public float[] getData40(RandomAccessFile raf, Grib2Drs.Type40 gdrs) throws IOException {
- // 6-xx jpeg2000 data block to decode
-
- // dataPoints are number of points encoded, it could be less than the
- // totalNPoints in the grid record if bitMap is used, otherwise equal
- //int dataPoints = drs.getDataPoints();
-
- int nb = gdrs.numberOfBits;
- int D = gdrs.decimalScaleFactor;
- float DD = (float) java.lang.Math.pow((double) 10, (double) D);
- float R = gdrs.referenceValue;
- int E = gdrs.binaryScaleFactor;
- float EE = (float) java.lang.Math.pow( 2.0, (double) E);
- float ref_val = R / DD;
-
- Grib2JpegDecoder g2j = null;
- // try {
- if (nb != 0) { // there's data to decode
- g2j = new Grib2JpegDecoder(nb, false);
- byte[] buf = new byte[dataLength - 5];
- raf.readFully(buf);
- g2j.decode(buf);
- gdrs.hasSignedProblem = g2j.hasSignedProblem();
- }
-
- float[] result = new float[totalNPoints];
-
- // no data to decode, set to reference value
- if (nb == 0) {
- for (int i = 0; i < dataNPoints; i++)
- result[i] = ref_val;
- return result;
- }
-
- int[] idata = g2j.getGdata();
- if (bitmap == null) { // must be one decoded value in idata for every expected data point
- if (idata.length != dataNPoints) {
- log.debug("Number of points in the data record {} != {} expected from GDS", idata.length, dataNPoints);
- throw new IllegalStateException("Number of points in the data record {} != expected from GDS");
- }
-
- for (int i = 0; i < dataNPoints; i++) {
- // Y * 10^D = R + (X1 + X2) * 2^E ; // regulation 92.9.4
- // Y = (R + ( 0 + X2) * EE)/DD ;
- result[i] = (R + idata[i] * EE) / DD;
- }
- return result;
-
- } else { // use bitmap to skip missing values
- for (int i = 0, j = 0; i < totalNPoints; i++) {
- if ((bitmap[i / 8] & GribNumbers.bitmask[i % 8]) != 0) {
- if (j >= idata.length) {
- System.out.printf("HEY jj2000 data count %d < bitmask count %d, i=%d, totalNPoints=%d%n", idata.length, j, i, totalNPoints);
- break;
- }
- int indata = idata[j];
- result[i] = (R + indata * EE) / DD;
- j++;
- } else {
- result[i] = staticMissingValue;
- }
- }
- }
- return result;
-
- /* } catch (NullPointerException npe) {
-
- log.error("Grib2DataReader2.jpeg2000Unpacking: bit rate too small nb =" + nb + " for file" + raf.getLocation());
- float[] data = new float[dataNPoints];
- for (int i = 0; i < dataNPoints; i++) {
- data[i] = staticMissingValue; // LOOK ??
- }
- return data;
- } */
+ return null;
 }
 
 // Grid point data - JPEG 2000 code stream format
 public int[] getData40raw(RandomAccessFile raf, Grib2Drs.Type40 gdrs) throws IOException {
- int nb = gdrs.numberOfBits;
- if (nb == 0) return null;
- int missing_value = (2 << nb - 1) - 1; // all ones - reserved for missing value
-
- Grib2JpegDecoder g2j;
- g2j = new Grib2JpegDecoder(nb, false);
- byte[] buf = new byte[dataLength - 5];
- raf.readFully(buf);
- g2j.decode(buf);
- gdrs.hasSignedProblem = g2j.hasSignedProblem();
-
- int[] idata = g2j.getGdata();
-
- if (bitmap == null) { // must be one decoded value in idata for every expected data point
- if (idata.length != totalNPoints) {
- log.debug("Number of points in the data record {} != {} expected from GDS", idata.length, totalNPoints);
- return null;
- }
- return idata;
-
- } else { // use bitmap to skip missing values
- int[] result = new int[totalNPoints];
-
- for (int i = 0, j = 0; i < totalNPoints; i++) {
- if ((bitmap[i / 8] & GribNumbers.bitmask[i % 8]) != 0) {
- if (j >= idata.length) {
- System.out.printf("HEY jj2000 data count %d < bitmask count %d, i=%d, totalNPoints=%d%n", idata.length, j, i, totalNPoints);
- break;
- }
- result[i] = idata[j];
- j++;
- } else {
- result[i] = missing_value;
- }
- }
- return result;
- }
-
+ return null;
 }
 
 // Loosely based on code by earl.barker.ctr AT us.af.mil, but moved from
diff -Nru thredds-4.6.2/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader.java thredds-4.6.2.jj2000/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader.java
--- thredds-4.6.2/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader.java	2015-06-10 00:05:23.000000000 +0200
+++ thredds-4.6.2.jj2000/grib/src/main/java/ucar/nc2/grib/grib2/Grib2DataReader.java	2015-07-18 07:34:40.077189389 +0200
@@ -644,86 +644,7 @@
 
 // Grid point data - JPEG 2000 code stream format
 public float[] getData40(RandomAccessFile raf, Grib2Drs.Type40 gdrs) throws IOException {
- // 6-xx jpeg2000 data block to decode
-
- // dataPoints are number of points encoded, it could be less than the
- // totalNPoints in the grid record if bitMap is used, otherwise equal
- //int dataPoints = drs.getDataPoints();
-
- int nb = gdrs.numberOfBits;
- int D = gdrs.decimalScaleFactor;
- float DD = (float) java.lang.Math.pow((double) 10, (double) D);
- float R = gdrs.referenceValue;
- int E = gdrs.binaryScaleFactor;
- float EE = (float) java.lang.Math.pow( 2.0, (double) E);
-
- Grib2JpegDecoder g2j = null;
- try {
- if (nb != 0) { // there's data to decode
- String[] argv = new String[6];
- argv[0] = "-rate";
- argv[1] = Integer.toString(nb);
- argv[2] = "-verbose";
- argv[3] = "off";
- argv[4] = "-debug" ;
- argv[5] = "on" ;
- //argv[ 2 ] = "-nocolorspace" ;
- //argv[ 3 ] = "-Rno_roi" ;
- //argv[ 4 ] = "-cdstr_info" ;
- //argv[ 5 ] = "-verbose" ;
- g2j = new Grib2JpegDecoder(nb, false);
- // how jpeg2000.jar use to decode, used raf
- //g2j.decode(raf, length - 5);
- // jpeg-1.0.jar added method to have the data read first
- byte[] buf = new byte[dataLength - 5];
- raf.readFully(buf);
- g2j.decode(buf);
- gdrs.hasSignedProblem = g2j.hasSignedProblem();
- }
-
- float[] data = new float[totalNPoints];
-
- if (nb == 0) { // no data to decoded, set to reference or MissingValue
- for (int i = 0; i < dataNPoints; i++)
- data[i] = R;
- } else if (bitmap == null) {
- int[] idata = g2j.getGdata();
-
- if (idata.length != dataNPoints) {
- return null;
- }
- for (int i = 0; i < dataNPoints; i++) {
- // Y * 10^D = R + (X1 + X2) * 2^E ; // regulation 92.9.4
- //Y = (R + ( 0 + X2) * EE)/DD ;
- data[i] = (R + idata[i] * EE) / DD;
- }
- } else { // use bitmap
- for (int i = 0, j = 0; i < totalNPoints; i++) {
- int[] idata = g2j.getGdata();
- if ((bitmap[i / 8] & GribNumbers.bitmask[i % 8]) != 0) {
- if (j >= idata.length) {
- System.out.printf("HEY jj2000 data count %d < bitmask count %d, i=%d, totalNPoints=%d%n", idata.length, j, i, totalNPoints);
- break;
- }
- int indata = idata[j];
- data[i] = (R + indata * EE) / DD;
- j++;
- } else {
- data[i] = staticMissingValue; // LOOK ??
- }
- }
- }
- return data;
-
- } catch (NullPointerException npe) {
-
- log.error("Grib2DataSection.jpeg2000Unpacking: bit rate too small nb =" + nb + " for file" + raf.getLocation());
- float[] data = new float[dataNPoints];
- for (int i = 0; i < dataNPoints; i++) {
- data[i] = staticMissingValue; // LOOK ??
- }
- return data;
- }
+ return null;
 }
 
 // by jkaehler@meteomatics.com
diff -Nru thredds-4.6.2/grib/src/main/java/ucar/nc2/grib/grib2/Grib2JpegDecoder.java thredds-4.6.2.jj2000/grib/src/main/java/ucar/nc2/grib/grib2/Grib2JpegDecoder.java
--- thredds-4.6.2/grib/src/main/java/ucar/nc2/grib/grib2/Grib2JpegDecoder.java	2015-06-10 00:05:23.000000000 +0200
+++ thredds-4.6.2.jj2000/grib/src/main/java/ucar/nc2/grib/grib2/Grib2JpegDecoder.java	1970-01-01 01:00:00.000000000 +0100
@@ -1,673 +0,0 @@
-/*
- * Copyright 1998-2014 University Corporation for Atmospheric Research/Unidata
- *
- * Portions of this software were developed by the Unidata Program at the
- * University Corporation for Atmospheric Research.
- *
- * Access and use of this software shall impose the following obligations
- * and understandings on the user. The user is granted the right, without
- * any fee or cost, to use, copy, modify, alter, enhance and distribute
- * this software, and any derivative works thereof, and its supporting
- * documentation for any purpose whatsoever, provided that this entire
- * notice appears in all copies of the software, derivative works and
- * supporting documentation. Further, UCAR requests that the user credit
- * UCAR/Unidata in any publications that result from the use of this
- * software or in any product that includes this software. The names UCAR
- * and/or Unidata, however, may not be used in any advertising or publicity
- * to endorse or promote any products or commercial entity unless specific
- * written permission is obtained from UCAR/Unidata. The user also
- * understands that UCAR/Unidata is not obligated to provide the user with
- * any support, consulting, training or assistance of any kind with regard
- * to the use, operation and performance of this software nor to provide
- * the user with any updates, revisions, new versions or "bug fixes."
- *
- * THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
- * DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
- * INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
- * FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
- * NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
- * WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
- */
-package ucar.nc2.grib.grib2;
-
-import ucar.jpeg.jj2000.j2k.quantization.dequantizer.*;
-import ucar.jpeg.jj2000.j2k.image.invcomptransf.*;
-import ucar.jpeg.jj2000.j2k.fileformat.reader.*;
-import ucar.jpeg.jj2000.j2k.codestream.reader.*;
-import ucar.jpeg.jj2000.j2k.wavelet.synthesis.*;
-import ucar.jpeg.jj2000.j2k.entropy.decoder.*;
-import ucar.jpeg.jj2000.j2k.decoder.*;
-import ucar.jpeg.jj2000.j2k.image.output.*;
-import ucar.jpeg.jj2000.j2k.codestream.*;
-import ucar.jpeg.jj2000.j2k.image.*;
-import ucar.jpeg.jj2000.j2k.util.*;
-import ucar.jpeg.jj2000.j2k.roi.*;
-import ucar.jpeg.jj2000.j2k.io.*;
-
-import ucar.jpeg.colorspace.*;
-import ucar.jpeg.icc.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.*;
-import java.io.IOException;
-import java.io.EOFException;
-import java.io.ByteArrayInputStream;
-
-/**
- * Adaptation of jj2000.j2k.decoder.Decoder, in order to read input from memory.
- *
- * @author robb kambic
- * @author caron rewritten Aug 2014
- */
-public class Grib2JpegDecoder {
- static private final Logger logger = LoggerFactory.getLogger(Grib2JpegDecoder.class);
-
- private boolean debug;
- private int rate;
-
- /**
- * Return the packBytes ie number bytes / number 1,2 or 4
- */
- private int packBytes;
-
- /**
- * Parses the inputstream to analyze the box structure of the JP2 file.
- */
- private ColorSpace csMap = null;
-
- /**
- * The exit code of the run method
- */
- private int exitCode;
-
- /**
- * The parameter list (arguments)
- */
- private ParameterList pl;
-
- /**
- * Instantiates a decoder object, width the 'argv' command
- * line arguments. It also initializes the default parameters. If the
- * argument list is empty an IllegalArgumentException is thrown. If an
- * error occurs while parsing the arguments error messages are written to
- * stderr and the run exit code is set to non-zero, see getExitCode()
- *
- * @throws IllegalArgumentException If 'argv' is empty
- * @see Grib2JpegDecoder#getExitCode
- */
- public Grib2JpegDecoder(int nbits, boolean debug) {
- this.rate = nbits;
- this.debug = debug;
-
- // not sure if these are needed in the bowels of jj2000
- String[] argv = new String[6];
- argv[0] = "-rate";
- argv[1] = Integer.toString(nbits);
- argv[2] = "-verbose";
- argv[3] = "off";
- argv[4] = "-debug" ;
- argv[5] = "on" ;
-
- // Initialize default parameters
- //System.err.println("calling Grib2JpegDecoder with argv argument");
- /*
- The default parameter list (with modules arguments)
- */
- ParameterList defpl = new ParameterList();
- String[][] param = Grib2JpegDecoder.getAllParameters();
-
- for (int i = param.length - 1; i >= 0; i--) {
- if (param[i][3] != null)
- defpl.put(param[i][0], param[i][3]);
- }
-
- // Create parameter list using defaults
- pl = new ParameterList(defpl);
-
- if (argv.length == 0) {
- throw new IllegalArgumentException("No arguments!");
- }
-
- // Parse arguments from argv
- try {
- pl.parseArgs(argv);
- } catch (StringFormatException e) {
- System.err.println("An error occurred while parsing the arguments:\n" + e.getMessage());
- }
- } // end Grib2JpegDecoder constructor
-
- /**
- * Returns the exit code of the class. This is only initialized after the
- * constructor and when the run method returns.
- *
- * @return The exit code of the constructor and the run() method.
- */
- public int getExitCode() {
- return exitCode;
- }
-
- private boolean hasSignedProblem = false;
- public boolean hasSignedProblem() {
- return hasSignedProblem;
- }
-
- /**
- * Runs the decoder. After completion the exit code is set, a non-zero
- * value indicates that an error occurred.
- *
- * @see #getExitCode
- */
- public void decode(byte buf[]) throws IOException {
- // int dataSize = buf.length;
- final boolean verbose = false;
- int res; // resolution level to reconstruct
- FileFormatReader ff;
- HeaderDecoder hd;
- EntropyDecoder entdec;
- ROIDeScaler roids;
- Dequantizer deq;
- InverseWT invWT;
- InvCompTransf ictransf;
- //ImgWriter imwriter[];
- ImgDataConverter converter;
- DecoderSpecs decSpec;
- BlkImgDataSrc palettized;
- BlkImgDataSrc channels;
- BlkImgDataSrc resampled;
- BlkImgDataSrc color;
- int i;
- int depth[];
-
- try {
-
- // create a ByteArrayInputStream from byte array for ISRandomAccessIO
- ByteArrayInputStream bais = new ByteArrayInputStream(buf);
- RandomAccessIO in = new ISRandomAccessIO(bais, buf.length, 1, buf.length);
-
- // **** File Format ****
- // If the codestream is wrapped in the jp2 fileformat, Read the
- // file format wrapper
- ff = new FileFormatReader(in);
- ff.readFileFormat();
- if (ff.JP2FFUsed) {
- in.seek(ff.getFirstCodeStreamPos());
- System.out.println("ff.JP2FFUsed is used"); // LOOK probably not
- }
-
- // +----------------------------+
- // | Instantiate decoding chain |
- // +----------------------------+
-
- // **** Header decoder ****
- // Instantiate header decoder and read main header
- /*
- Information contained in the codestream's headers
- */
- HeaderInfo hi = new HeaderInfo();
- try {
- hd = new HeaderDecoder(in, pl, hi);
- } catch (EOFException e) {
- error("Codestream too short or bad header, unable to decode.", 2, e);
- throw e;
- }
-
- int nCompCod = hd.getNumComps();
- decSpec = hd.getDecoderSpecs();
-
- // Get demixed bitdepths
- depth = new int[nCompCod];
- for (i = 0; i < nCompCod; i++) {
- depth[i] = hd.getOriginalBitDepth(i);
- }
-
- // **** Bit stream reader ****
- BitstreamReaderAgent breader = BitstreamReaderAgent.createInstance(in, hd, pl, decSpec, false, hi);
-
- // **** Entropy decoder ****
- try {
- entdec = hd.createEntropyDecoder(breader, pl);
- } catch (IllegalArgumentException e) {
- error("Cannot instantiate entropy decoder" + ((e.getMessage() != null) ? (":\n" + e.getMessage()) : ""), 2, e);
- return;
- }
-
- // **** ROI de-scaler ****
- try {
- roids = hd.createROIDeScaler(entdec, pl, decSpec);
- } catch (IllegalArgumentException e) {
- error("Cannot instantiate roi de-scaler." + ((e.getMessage() != null) ? (":\n" + e.getMessage()) : ""), 2, e);
- return;
- }
-
- // **** Dequantizer ****
- try {
- deq = hd.createDequantizer(roids, depth, decSpec);
- } catch (IllegalArgumentException e) {
- error("Cannot instantiate dequantizer" + ((e.getMessage() != null) ? (":\n" + e.getMessage()) : ""), 2, e);
- return;
- }
-
- // **** Inverse wavelet transform ***
- try {
- // full page inverse wavelet transform
- invWT = InverseWT.createInstance(deq, decSpec);
- } catch (IllegalArgumentException e) {
- error("Cannot instantiate inverse wavelet transform" +
- ((e.getMessage() != null) ?
- (":\n" + e.getMessage()) : ""), 2, e);
- return;
- }
-
- res = breader.getImgRes();
- invWT.setImgResLevel(res);
-
- // **** Data converter **** (after inverse transform module)
- converter = new ImgDataConverter(invWT, 0);
-
- // **** Inverse component transformation ****
- ictransf = new InvCompTransf(converter, decSpec, depth, pl);
-
- // **** Color space mapping ****
- if (ff.JP2FFUsed && pl.getParameter("nocolorspace").equals("off")) {
- try {
- csMap = new ColorSpace(in, hd, pl);
- channels = hd.createChannelDefinitionMapper(ictransf, csMap);
- resampled = hd.createResampler(channels, csMap);
- palettized = hd.createPalettizedColorSpaceMapper(resampled, csMap);
- color = hd.createColorSpaceMapper(palettized, csMap);
-
- } catch (IllegalArgumentException e) {
- error("Could not instantiate ICC profiler" + ((e.getMessage() != null) ? (":\n" + e.getMessage()) : ""), 1, e);
- return;
- } catch (ColorSpaceException e) {
- error("error processing jp2 colorspace information" + ((e.getMessage() != null) ? (": " + e.getMessage()) : " "), 1, e);
- return;
- }
- } else { // Skip colorspace mapping
- color = ictransf;
- }
-
- // This is the last image in the decoding chain and should be
- // assigned by the last transformation:
- BlkImgDataSrc decodedImage = color;
- if (color == null) {
- decodedImage = ictransf;
- }
-
- int nCompImg = decodedImage.getNumComps();
-
- // code to get data
- // **** Decode and write/display result ****
-
- ImgWriter[] imwriter = new ImgWriter[nCompImg];
-
- // Now write the image to the array (decodes as needed)
- boolean isSigned;
- for (i = 0; i < imwriter.length; i++) {
- try {
- if (csMap != null) {
- isSigned = csMap.isOutputSigned(i);
- imwriter[i] = new ImgWriterArray(decodedImage, i, csMap.isOutputSigned(i));
- //System.out.println( "csMap!=null" );
- } else {
- isSigned = hd.isOriginalSigned(i);
- imwriter[i] = new ImgWriterArray(decodedImage, i, hd.isOriginalSigned(i));
- //System.out.println( "csMap==null" );
- }
- } catch (IOException e) {
- if (debug) e.printStackTrace();
- return;
- }
-
- try {
- imwriter[i].writeAll(); // write data to array
- ImgWriterArray iwa = (ImgWriterArray) imwriter[i];
- data = iwa.getGdata();
- // unSigned data processing here
- //System.out.println("[INFO]: isSigned = " + isSigned);
- if (!isSigned) {
- //float unSignIt = (float) java.lang.Math.pow((double) 2.0, fnb - 1); // LOOK WTF ?
- int nb = depth[i];
- int levShift = 1 << (nb - 1); // check
- if (nb != rate) hasSignedProblem = true;
-
- for (int j = 0; j < data.length; j++)
- data[j] += levShift;
- }
- packBytes = iwa.getPackBytes();
- } catch (IOException e) {
- if (debug) e.printStackTrace();
- return;
- }
- } // end for(i=0; i<imwriter.length; i++)
-
- // **** Print some resulting info ****
- if (verbose) {
- // Print actually read bitrate
- // if file format used add the read file format bytes
- float bitrate = breader.getActualRate();
- int numBytes = breader.getActualNbytes();
- if (ff.JP2FFUsed) {
- int imageSize = (int) ((8.0f * numBytes) / bitrate);
- numBytes += ff.getFirstCodeStreamPos();
- bitrate = (numBytes * 8.0f) / imageSize;
- }
-
- if (pl.getIntParameter("ncb_quit") == -1) {
- System.out.println("Actual bit rate = " + bitrate + " bpp (i.e. " + numBytes + " bytes)");
- } else {
- System.out.println("Number of packet body bytes read = " + numBytes);
- }
- }
-
- } catch (IllegalArgumentException e) {
- error(e.getMessage(), 2);
- if (debug) e.printStackTrace();
-
-
- } catch (RuntimeException e) {
- if (e.getMessage() != null) {
- error("An uncaught runtime exception has occurred:\n" +
- e.getMessage(), 2);
- } else {
- error("An uncaught runtime exception has occurred.", 2);
- }
- throw new IOException(e);
-
- } catch (Throwable e) {
- throw new IOException(e);
- //error("An uncaught exception has occurred.", 2);
- //if (debug) e.printStackTrace();
- }
- } // end decode
-
- private void error(String msg, int code) {
- exitCode = code;
- logger.debug(msg);
- }
-
- private void error(String msg, int code, Throwable ex) {
- exitCode = code;
- logger.debug(msg);
- if (debug) ex.printStackTrace();
- }
-
- /**
- * Return the packBytes ie number bytes / number 1,2 or 4
- */
- public int getPackBytes() {
- return packBytes;
- }
-
- /**
- * Return the "raw" decoded data as an int array
- */
- public int[] getGdata() {
- return data;
- }
- private int[] data;
-
- /**
- * Returns all the parameters used in the decoding chain. It calls
- * parameter from each module and store them in one array (one row per
- * parameter and 4 columns).
- *
- * @return All decoding parameters
- */
- public static String[][] getAllParameters() {
- List<String[]> vec = new ArrayList<>();
- int i;
-
- String[][] str = BitstreamReaderAgent.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- str = EntropyDecoder.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- str = ROIDeScaler.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- str = Dequantizer.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- str = InvCompTransf.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- str = HeaderDecoder.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- str = ICCProfiler.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- str = ucar.jpeg.jj2000.j2k.decoder.Decoder.getParameterInfo();
- if (str != null) for (i = str.length - 1; i >= 0; i--) vec.add(str[i]);
-
- String[][] result = new String[vec.size()][];
- for (i = vec.size() - 1; i >= 0; i--) // fill it backwards
- result[i] = vec.get(i);
-
- return result;
- }
-
- /**
- * This class extends the ImgWriter abstract class for writing Array .
- * 
- * Data: The image binary values appear one after the other (in raster
- * order) immediately after the last header character ('\n') and are
- * byte-aligned (they are packed into 1,2 or 4 bytes per sample, depending
- * upon the bit-depth value).
- * 
- * 
- * If the data is unsigned, level shifting is applied adding 2^(bit depth
- * - 1)
- * 
- * NOTE: This class is not thread safe, for reasons of internal
- * buffering.
- *
- * @see ImgWriter
- * @see BlkImgDataSrc
- */
- private static class ImgWriterArray extends ImgWriter {
-
- /**
- * Whether the data must be signed when writing or not. In the latter
- * case inverse level shifting must be applied
- */
- boolean isSigned;
-
- /**
- * The bit-depth of the input file (must be between 1 and 31)
- */
- private int bitDepth;
-
- /**
- * A DataBlk, just used to avoid allocating a new one each time it is
- * needed
- */
- private DataBlkInt db = new DataBlkInt();
-
- /** The number of fractional bits in the source data */
- //private int fb;
-
- /**
- * The index of the component from where to get the data
- */
- private int c;
-
- /**
- * The pack length of one sample (in bytes, according to the output
- * bit-depth
- */
- private int packBytes;
-
- /**
- * Creates a new writer to the specified Array object, to write data from
- * the specified component.
- * 
- * The size of the image that is written to the file is the size of the
- * component from which to get the data, specified by b, not the size of
- * the source image (they differ if there is some sub-sampling).
- *
- * @param imgSrc The source from where to get the image data to write.
- * @param c The index of the component from where to get the data.
- * @param isSigned Whether the data are signed or not (needed only when
- * writing header).
- * @see DataBlk
- */
- public ImgWriterArray(BlkImgDataSrc imgSrc, int c, boolean isSigned) throws IOException {
- //Initialize
- this.c = c;
- this.isSigned = isSigned;
- //System.out.println("sign = " + isSigned );
- src = imgSrc;
- w = src.getImgWidth();
- h = src.getImgHeight();
- //System.out.println(" constructor iwa w=" + w +" h=" +h ) ;
-
- bitDepth = src.getNomRangeBits(this.c);
- if ((bitDepth <= 0) || (bitDepth > 31)) {
- throw new IOException("Array supports only bit-depth between 1 and 31");
- }
- if (bitDepth <= 8) {
- packBytes = 1;
- } else if (bitDepth <= 16) {
- packBytes = 2;
- } else { // <= 31
- packBytes = 4;
- }
-
- } // end ImgWriterArray
-
- /**
- * Closes the underlying file or network connection to where the data is
- * written. Any call to other methods of the class become illegal after a
- * call to this one.
- *
- * @throws IOException If an I/O error occurs.
- */
- public void close() throws IOException {
- }
-
- /**
- * Writes the data of the specified area to the file, coordinates are
- * relative to the current tile of the source. Before writing, the
- * coefficients are limited to the nominal range and packed into 1,2 or 4
- * bytes (according to the bit-depth).
- * 
- * If the data is unisigned, level shifting is applied adding 2^(bit depth - 1)
- * 
- * This method may not be called concurrently from different threads.
- * 
- * If the data returned from the BlkImgDataSrc source is progressive,
- * then it is requested over and over until it is not progressive
- * anymore.
- *
- * @param ulx The horizontal coordinate of the upper-left corner of the
- * area to write, relative to the current tile.
- * @param uly The vertical coordinate of the upper-left corner of the area
- * to write, relative to the current tile.
- * @param w The width of the area to write.
- * @param h The height of the area to write.
- * @throws IOException If an I/O error occurs.
- */
- public void write(int ulx, int uly, int w, int h) throws IOException {
-
- //System.out.println( " ulx=" + ulx +" uly=" + uly +" w=" + w +" h=" + h);
- // Initialize db
- db.ulx = ulx;
- db.uly = uly;
- db.w = w;
- db.h = h;
- if (db.data != null && db.data.length < w * h) {
- // A new one will be allocated by getInternCompData()
- db.data = null;
- }
- // Request the data and make sure it is not
- // progressive
- do {
- db = (DataBlkInt) src.getInternCompData(db, c);
- //System.out.println( "Progressive Comp c =" + c );
- } while (db.progressive);
-
- //System.out.println( "Comp c =" + c );
- //System.out.println( "db.data.length = " + db.data.length );
-
- } // end int ulx, int uly, int w, int h
-
- public void writeAll() throws IOException {
- // Find the list of tile to decode.
- Coord nT = src.getNumTiles(null);
- //System.out.println( "nTiles = " + nT );
-
- // Loop on vertical tiles
- for (int y = 0; y < nT.y; y++) {
- // Loop on horizontal tiles
- for (int x = 0; x < nT.x; x++) {
- //System.out.println( "setTiles(x,y) = " + x + ", " + y );
- src.setTile(x, y);
- write(0, 0, src.getImgWidth(), src.getImgHeight());
- } // End loop on horizontal tiles
- } // End loop on vertical tiles
- }
-
- /**
- * Writes the source's current tile to the output. The requests of data
- * issued to the source BlkImgDataSrc object are done by strips, in order
- * to reduce memory usage.
- * 
- * If the data returned from the BlkImgDataSrc source is progressive,
- * then it is requested over and over until it is not progressive
- * anymore.
- *
- * @throws IOException If an I/O error occurs.
- * @see DataBlk
- */
- public void write() throws IOException {
- int i;
- int tIdx = src.getTileIdx();
- int tw = src.getTileCompWidth(tIdx, c); // Tile width
- int th = src.getTileCompHeight(tIdx, c); // Tile height
- // Write in strips
- for (i = 0; i < th; i += DEF_STRIP_HEIGHT) {
- write(0, i, tw, (th - i < DEF_STRIP_HEIGHT) ? th - i : DEF_STRIP_HEIGHT);
- }
- }
-
- /**
- * The pack length of one sample (in bytes, according to the output bit-depth
- */
- public int getPackBytes() {
- return packBytes;
- }
-
- /**
- * the jpeg data decoded into an int array
- *
- * @return a int[]
- */
- public int[] getGdata() {
- //return gdata;
- return db.data;
- }
-
- public void flush() {
- }
-
- /**
- * Returns a string of information about the object, more than 1 line
- * long. The information string includes information from the underlying
- * RandomAccessFile (its toString() method is called in turn).
- *
- * @return A string of information about the object.
- */
- public String toString() {
- return "ImgWriterArray: WxH = " + w + "x" + h + ", Component = " +
- c + ", Bit-depth = " + bitDepth + ", signed = " + isSigned +
- "\n";
- }
- } // end ImgWriterArray
-
-} // end Grib2JpegDecoder
diff -Nru thredds-4.6.2/pom.xml thredds-4.6.2.jj2000/pom.xml
--- thredds-4.6.2/pom.xml	2015-06-10 00:05:23.000000000 +0200
+++ thredds-4.6.2.jj2000/pom.xml	2015-07-18 07:30:42.288070045 +0200
@@ -505,12 +505,6 @@
 <version>${com.google.guava.version}</version>
 </dependency>
 
- <dependency>
- <groupId>${project.groupId}</groupId>
- <artifactId>jj2000</artifactId>
- <version>${edu.ucar.jj2000.version}</version>
- </dependency>
-
 
 <dependency>
 <groupId>org.tukaani</groupId>