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Convert DICOM image to jpeg image

My code

import java.awt.image.BufferedImage; import java.io.BufferedOutputStream; import java.io.File; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; import java.util.Iterator; import javax.imageio.ImageIO; import javax.imageio.ImageReader; import javax.imageio.stream.ImageInputStream; import org.dcm4che2.imageio.plugins.dcm.DicomImageReadParam; import com.sun.image.codec.jpeg.JPEGCodec; import com.sun.image.codec.jpeg.JPEGImageEncoder; public class DicomToJpeg { public static void main(String args[]) throws IOException, Exception { dicomToJpeg("d:/F74AFBC7"); } public static void dicomToJpeg(String args) throws IOException, Exception { // TODO Auto-generated method stub try { File myDicomFile = new File(args); BufferedImage myJpegImage = null; Iterator<ImageReader> iter = ImageIO.getImageReadersByFormatName("DICOM"); ImageReader reader = (ImageReader) iter.next(); DicomImageReadParam param = null; try{ param = (DicomImageReadParam) reader.getDefaultReadParam(); } catch (Exception e) { e.printStackTrace(); } ImageInputStream iis=ImageIO.createImageInputStream(myDicomFile); reader.setInput(iis, false); myJpegImage = reader.read(0, param); iis.close(); if (myJpegImage == null) { System.out.println("\nError: couldn't read dicom image!"); return; } File myJpegFile = new File("d:/demo.jpg"); OutputStream output = new BufferedOutputStream(new FileOutputStream(myJpegFile)); JPEGImageEncoder encoder = JPEGCodec.createJPEGEncoder(output); encoder.encode(myJpegImage); System.out.println("Image Create successufully"); output.close(); } catch(IOException e){ System.out.println("\nError: couldn't read dicom image!"+ e.getMessage()); return; } } }

When I execute a java project using eclipse it works fine ... But when I execute using a web application, and in this I call it from the controller page, for example

DicomToJpeg.dicomToJpeg ("D: / F74AFBC7");

then it gives an error, for example ...

 java.util.NoSuchElementException at javax.imageio.spi.FilterIterator.next(Unknown Source) at javax.imageio.ImageIO$ImageReaderIterator.next(Unknown Source) at javax.imageio.ImageIO$ImageReaderIterator.next(Unknown Source) at com.lifecare.controller.DicomToJpeg.dicomToJpeg(DicomToJpeg.java:32)

How to solve this error, please help me ....

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4 answers

The javadoc for ImageIO.getImageREadersByFormatName says:

Returns an Iterator containing all currently registered ImageReaders that claim to be able to decode the named format.

If you access the iterator without checking if it has an element, you will get an exception.

Since it works in your IDE and not on the server, you can see if image readers for DICOM are reading in the path to the application class on the server.

However, I would also like to know what you call the above class. Is this from a servlet?

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I solved this by calling ImageIO.scanForPlugins () before ImageIO.getImageReadersByFormatName ()

 ImageIO.scanForPlugins() Iterator<ImageReader> iter = ImageIO.getImageReadersByFormatName("DICOM"); ImageReader reader = (ImageReader) iter.next();

This works great on servlets

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try it

 BufferImage bi = ImageIO.read(dcm file name with path); ImageIO.write(enter pathname with filename, format);
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 import java.io.BufferedInputStream; import java.io.BufferedOutputStream; import java.io.DataInputStream; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.io.InputStream; import java.util.Date; import java.util.Enumeration; import java.util.List; import java.util.Properties; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.OptionBuilder; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.apache.commons.cli.PosixParser; import org.dcm4che2.data.BasicDicomObject; import org.dcm4che2.data.DicomObject; import org.dcm4che2.data.Tag; import org.dcm4che2.data.UID; import org.dcm4che2.data.VR; import org.dcm4che2.io.DicomOutputStream; import org.dcm4che2.util.UIDUtils; public class Jpg2Dcm { private static final String USAGE = "jpg2dcm [Options] <jpgfile> <dcmfile>"; private static final String DESCRIPTION = "Encapsulate JPEG Image into DICOM Object.\nOptions:"; private static final String EXAMPLE = "--\nExample 1: Encapulate JPEG Image verbatim with default values " + "for mandatory DICOM attributes into DICOM Secondary Capture Image:" + "\n$ jpg2dcm image.jpg image.dcm" + "\n--\nExample 2: Encapulate JPEG Image without application segments " + "and additional DICOM attributes to mandatory defaults into DICOM " + "Image Object:" + "\n$ jpg2dcm --no-appn -c patattrs.cfg homer.jpg image.dcm" + "\n--\nExample 3: Encapulate MPEG2 Video with specified DICOM " + "attributes into DICOM Video Object:" + "\n$ jpg2dcm --mpeg -C mpg2dcm.cfg video.mpg video.dcm"; private static final String LONG_OPT_CHARSET = "charset"; private static final String OPT_CHARSET_DESC = "Specific Character Set code string, ISO_IR 100 by default"; private static final String OPT_AUGMENT_CONFIG_DESC = "Specifies DICOM attributes included additional to mandatory defaults"; private static final String OPT_REPLACE_CONFIG_DESC = "Specifies DICOM attributes included instead of mandatory defaults"; private static final String LONG_OPT_TRANSFER_SYNTAX = "transfer-syntax"; private static final String OPT_TRANSFER_SYNTAX_DESC = "Transfer Syntax; 1.2.840.10008.1.2.4.50 (JPEG Baseline) by default."; private static final String LONG_OPT_MPEG = "mpeg"; private static final String OPT_MPEG_DESC = "Same as --transfer-syntax 1.2.840.10008.1.2.4.100 (MPEG2)."; private static final String LONG_OPT_UID_PREFIX = "uid-prefix"; private static final String OPT_UID_PREFIX_DESC = "Generate UIDs with given prefix, 1.2.40.0.13.1.<host-ip> by default."; private static final String LONG_OPT_NO_APPN = "no-appn"; private static final String OPT_NO_APPN_DESC = "Exclude application segments APPn from JPEG stream; " + "encapsulate JPEG stream verbatim by default."; private static final String OPT_HELP_DESC = "Print this message"; private static final String OPT_VERSION_DESC = "Print the version information and exit"; private static int FF = 0xff; private static int SOF = 0xc0; private static int DHT = 0xc4; private static int DAC = 0xcc; private static int SOI = 0xd8; private static int SOS = 0xda; private static int APP = 0xe0; private String charset = "ISO_IR 100"; private String transferSyntax = UID.JPEGBaseline1; private byte[] buffer = new byte[8192]; private int jpgHeaderLen; private int jpgLen; private boolean noAPPn = false; private Properties cfg = new Properties(); public Jpg2Dcm() { try { cfg.load(Jpg2Dcm.class.getResourceAsStream("jpg2dcm.cfg")); } catch (Exception e) { throw new RuntimeException(e); } } public final void setCharset(String charset) { this.charset = charset; } private final void setTransferSyntax(String uid) { this.transferSyntax = uid; } private final void setNoAPPn(boolean noAPPn) { this.noAPPn = noAPPn; } private void loadConfiguration(File cfgFile, boolean augment) throws IOException { Properties tmp = augment ? new Properties(cfg) : new Properties(); InputStream in = new BufferedInputStream(new FileInputStream(cfgFile)); try { tmp.load(in); } finally { in.close(); } cfg = tmp; } public void convert(File jpgFile, File dcmFile) throws IOException { jpgHeaderLen = 0; jpgLen = (int) jpgFile.length(); DataInputStream jpgInput = new DataInputStream( new BufferedInputStream(new FileInputStream(jpgFile))); try { DicomObject attrs = new BasicDicomObject(); attrs.putString(Tag.SpecificCharacterSet, VR.CS, charset); for (Enumeration en = cfg.propertyNames(); en.hasMoreElements();) { String key = (String) en.nextElement(); int[] tagPath = Tag.toTagPath(key); int last = tagPath.length-1; VR vr = attrs.vrOf(tagPath[last]); if (vr == VR.SQ) { attrs.putSequence(tagPath); } else { attrs.putString(tagPath, vr, cfg.getProperty(key)); } } if (noAPPn || missingRowsColumnsSamplesPMI(attrs)) { readHeader(attrs, jpgInput); } ensureUS(attrs, Tag.BitsAllocated, 8); ensureUS(attrs, Tag.BitsStored, attrs.getInt(Tag.BitsAllocated)); ensureUS(attrs, Tag.HighBit, attrs.getInt(Tag.BitsStored) - 1); ensureUS(attrs, Tag.PixelRepresentation, 0); ensureUID(attrs, Tag.StudyInstanceUID); ensureUID(attrs, Tag.SeriesInstanceUID); ensureUID(attrs, Tag.SOPInstanceUID); Date now = new Date(); attrs.putDate(Tag.InstanceCreationDate, VR.DA, now); attrs.putDate(Tag.InstanceCreationTime, VR.TM, now); attrs.initFileMetaInformation(transferSyntax); FileOutputStream fos = new FileOutputStream(dcmFile); BufferedOutputStream bos = new BufferedOutputStream(fos); DicomOutputStream dos = new DicomOutputStream(bos); try { dos.writeDicomFile(attrs); dos.writeHeader(Tag.PixelData, VR.OB, -1); dos.writeHeader(Tag.Item, null, 0); dos.writeHeader(Tag.Item, null, (jpgLen+1)&~1); dos.write(buffer, 0, jpgHeaderLen); int r; while ((r = jpgInput.read(buffer)) > 0) { dos.write(buffer, 0, r); } if ((jpgLen&1) != 0) { dos.write(0); } dos.writeHeader(Tag.SequenceDelimitationItem, null, 0); } finally { dos.close(); } } finally { jpgInput.close(); } } private boolean missingRowsColumnsSamplesPMI(DicomObject attrs) { return !(attrs.containsValue(Tag.Rows) && attrs.containsValue(Tag.Columns) && attrs.containsValue(Tag.SamplesPerPixel) && attrs.containsValue(Tag.PhotometricInterpretation) ); } private void readHeader(DicomObject attrs, DataInputStream jpgInput) throws IOException { if (jpgInput.read() != FF || jpgInput.read() != SOI || jpgInput.read() != FF) { throw new IOException( "JPEG stream does not start with FF D8 FF"); } int marker = jpgInput.read(); int segmLen; boolean seenSOF = false; buffer[0] = (byte) FF; buffer[1] = (byte) SOI; buffer[2] = (byte) FF; buffer[3] = (byte) marker; jpgHeaderLen = 4; while (marker != SOS) { segmLen = jpgInput.readUnsignedShort(); if (buffer.length < jpgHeaderLen + segmLen + 2) { growBuffer(jpgHeaderLen + segmLen + 2); } buffer[jpgHeaderLen++] = (byte) (segmLen >>> 8); buffer[jpgHeaderLen++] = (byte) segmLen; jpgInput.readFully(buffer, jpgHeaderLen, segmLen - 2); if ((marker & 0xf0) == SOF && marker != DHT && marker != DAC) { seenSOF = true; int p = buffer[jpgHeaderLen] & 0xff; int y = ((buffer[jpgHeaderLen+1] & 0xff) << 8) | (buffer[jpgHeaderLen+2] & 0xff); int x = ((buffer[jpgHeaderLen+3] & 0xff) << 8) | (buffer[jpgHeaderLen+4] & 0xff); int nf = buffer[jpgHeaderLen+5] & 0xff; attrs.putInt(Tag.SamplesPerPixel, VR.US, nf); if (nf == 3) { attrs.putString(Tag.PhotometricInterpretation, VR.CS, "YBR_FULL_422"); attrs.putInt(Tag.PlanarConfiguration, VR.US, 0); } else { attrs.putString(Tag.PhotometricInterpretation, VR.CS, "MONOCHROME2"); } attrs.putInt(Tag.Rows, VR.US, y); attrs.putInt(Tag.Columns, VR.US, x); attrs.putInt(Tag.BitsAllocated, VR.US, p > 8 ? 16 : 8); attrs.putInt(Tag.BitsStored, VR.US, p); attrs.putInt(Tag.HighBit, VR.US, p-1); attrs.putInt(Tag.PixelRepresentation, VR.US, 0); } if (noAPPn & (marker & 0xf0) == APP) { jpgLen -= segmLen + 2; jpgHeaderLen -= 4; } else { jpgHeaderLen += segmLen - 2; } if (jpgInput.read() != FF) { throw new IOException("Missing SOS segment in JPEG stream"); } marker = jpgInput.read(); buffer[jpgHeaderLen++] = (byte) FF; buffer[jpgHeaderLen++] = (byte) marker; } if (!seenSOF) { throw new IOException("Missing SOF segment in JPEG stream"); } } private void growBuffer(int minSize) { int newSize = buffer.length << 1; while (newSize < minSize) { newSize <<= 1; } byte[] tmp = new byte[newSize]; System.arraycopy(buffer, 0, tmp, 0, jpgHeaderLen); buffer = tmp; } private void ensureUID(DicomObject attrs, int tag) { if (!attrs.containsValue(tag)) { attrs.putString(tag, VR.UI, UIDUtils.createUID()); } } private void ensureUS(DicomObject attrs, int tag, int val) { if (!attrs.containsValue(tag)) { attrs.putInt(tag, VR.US, val); } } public static void main(String[] args) { try { CommandLine cl = parse(args); Jpg2Dcm jpg2Dcm = new Jpg2Dcm(); if (cl.hasOption(LONG_OPT_CHARSET)) { jpg2Dcm.setCharset(cl.getOptionValue(LONG_OPT_CHARSET)); } if (cl.hasOption("c")) { jpg2Dcm.loadConfiguration(new File(cl.getOptionValue("c")), true); } if (cl.hasOption("C")) { jpg2Dcm.loadConfiguration(new File(cl.getOptionValue("C")), false); } if (cl.hasOption(LONG_OPT_UID_PREFIX)) { UIDUtils.setRoot(cl.getOptionValue(LONG_OPT_UID_PREFIX)); } if (cl.hasOption(LONG_OPT_MPEG)) { jpg2Dcm.setTransferSyntax(UID.MPEG2); } if (cl.hasOption(LONG_OPT_TRANSFER_SYNTAX)) { jpg2Dcm.setTransferSyntax( cl.getOptionValue(LONG_OPT_TRANSFER_SYNTAX)); } jpg2Dcm.setNoAPPn(cl.hasOption(LONG_OPT_NO_APPN)); List argList = cl.getArgList(); File jpgFile = new File("d:\\VIPUL.jpg"); File dcmFile = new File("d:\\aa.dcm"); long start = System.currentTimeMillis(); jpg2Dcm.convert(jpgFile, dcmFile); long fin = System.currentTimeMillis(); System.out.println("Encapsulated " + jpgFile + " to " + dcmFile + " in " + (fin - start) + "ms."); } catch (IOException e) { e.printStackTrace(); } } private static CommandLine parse(String[] args) { Options opts = new Options(); OptionBuilder.withArgName("code"); OptionBuilder.hasArg(); OptionBuilder.withDescription(OPT_CHARSET_DESC); OptionBuilder.withLongOpt(LONG_OPT_CHARSET); opts.addOption(OptionBuilder.create()); OptionBuilder.withArgName("file"); OptionBuilder.hasArg(); OptionBuilder.withDescription(OPT_AUGMENT_CONFIG_DESC); opts.addOption(OptionBuilder.create("c")); OptionBuilder.withArgName("file"); OptionBuilder.hasArg(); OptionBuilder.withDescription(OPT_REPLACE_CONFIG_DESC); opts.addOption(OptionBuilder.create("C")); OptionBuilder.withArgName("prefix"); OptionBuilder.hasArg(); OptionBuilder.withDescription(OPT_UID_PREFIX_DESC); OptionBuilder.withLongOpt(LONG_OPT_UID_PREFIX); opts.addOption(OptionBuilder.create()); OptionBuilder.withArgName("uid"); OptionBuilder.hasArg(); OptionBuilder.withDescription(OPT_TRANSFER_SYNTAX_DESC); OptionBuilder.withLongOpt(LONG_OPT_TRANSFER_SYNTAX); opts.addOption(OptionBuilder.create()); opts.addOption(null, LONG_OPT_MPEG, false, OPT_MPEG_DESC); opts.addOption(null, LONG_OPT_NO_APPN, false, OPT_NO_APPN_DESC); opts.addOption("h", "help", false, OPT_HELP_DESC); opts.addOption("V", "version", false, OPT_VERSION_DESC); CommandLine cl = null; try { cl = new PosixParser().parse(opts, args); } catch (ParseException e) { exit("jpg2dcm: " + e.getMessage()); throw new RuntimeException("unreachable"); } if (cl.hasOption('V')) { Package p = Jpg2Dcm.class.getPackage(); System.out.println("jpg2dcm v" + p.getImplementationVersion()); System.exit(0); } if (cl.hasOption('h') || cl.getArgList().size() != 2) { HelpFormatter formatter = new HelpFormatter(); formatter.printHelp(USAGE, DESCRIPTION, opts, EXAMPLE); System.exit(0); } return cl; } private static void exit(String msg) { System.err.println(msg); System.err.println("Try 'jpg2dcm -h' for more information."); System.exit(1); } } import java.io.File; import java.io.IOException; public class JPG_TO_DCM { public static void main(String[] args) { Jpg2Dcm jpg2Dcm = new Jpg2Dcm(); File jpgFileOS = new File("D:\\Demo.jpg"); File dcmFileOS = new File("D:\\Demo.dcm"); try { jpg2Dcm.convert(jpgFileOS, dcmFileOS); } catch (IOException e) { e.printStackTrace(); } } }

Please try using this code @Subhojit Das For this code you are loading some lib files

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Source: https://habr.com/ru/post/958475/

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