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*
* The contents of this file are subject to the Mozilla Public License Version
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* the License. You may obtain a copy of the License at
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*
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* WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License
* for the specific language governing rights and limitations under the
* License.
*
* The Original Code is part of dcm4che, an implementation of DICOM(TM) in
* Java(TM), hosted at https://github.com/gunterze/dcm4che.
*
* The Initial Developer of the Original Code is
* Agfa Healthcare.
* Portions created by the Initial Developer are Copyright (C) 2011
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* See @authors listed below
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package org.dcm4che3.tool.json2dcm;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileDescriptor;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.util.List;
import java.util.ResourceBundle;
import javax.json.Json;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.OptionBuilder;
import org.apache.commons.cli.OptionGroup;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.dcm4che3.data.Attributes;
import org.dcm4che3.data.Tag;
import org.dcm4che3.data.UID;
import org.dcm4che3.io.BulkDataDescriptor;
import org.dcm4che3.io.DicomEncodingOptions;
import org.dcm4che3.io.DicomInputStream;
import org.dcm4che3.io.DicomInputStream.IncludeBulkData;
import org.dcm4che3.io.DicomOutputStream;
import org.dcm4che3.json.JSONReader;
import org.dcm4che3.tool.common.CLIUtils;
import org.dcm4che3.util.SafeClose;
/**
* @author Gunter Zeilinger <gunterze@gmail.com>
*/
public class Json2Dcm {
private static ResourceBundle rb =
ResourceBundle.getBundle("org.dcm4che3.tool.json2dcm.messages");
private IncludeBulkData includeBulkData = IncludeBulkData.URI;
private boolean catBlkFiles = false;
private String blkFilePrefix = "blk";
private String blkFileSuffix;
private File blkDirectory;
private Attributes blkAttrs;
private String tsuid;
private boolean withfmi;
private boolean nofmi;
private DicomEncodingOptions encOpts = DicomEncodingOptions.DEFAULT;
private List<File> bulkDataFiles;
private Attributes fmi;
private Attributes dataset;
public final void setIncludeBulkData(IncludeBulkData includeBulkData) {
this.includeBulkData = includeBulkData;
}
public final void setConcatenateBulkDataFiles(boolean catBlkFiles) {
this.catBlkFiles = catBlkFiles;
}
public final void setBulkDataFilePrefix(String blkFilePrefix) {
this.blkFilePrefix = blkFilePrefix;
}
public final void setBulkDataFileSuffix(String blkFileSuffix) {
this.blkFileSuffix = blkFileSuffix;
}
public final void setBulkDataDirectory(File blkDirectory) {
this.blkDirectory = blkDirectory;
}
public final void setBulkDataAttributes(Attributes blkAttrs) {
this.blkAttrs = blkAttrs;
}
public final void setTransferSyntax(String uid) {
this.tsuid = uid;
}
public final void setWithFileMetaInformation(boolean withfmi) {
this.withfmi = withfmi;
}
public final void setNoFileMetaInformation(boolean nofmi) {
this.nofmi = nofmi;
}
public final void setEncodingOptions(DicomEncodingOptions encOpts) {
this.encOpts = encOpts;
}
private static CommandLine parseComandLine(String[] args)
throws ParseException{
Options opts = new Options();
CLIUtils.addCommonOptions(opts);
addIOFileNameOptions(opts);
addBulkdataOptions(opts);
addFileEncodingOptions(opts);
CommandLine cl = CLIUtils.parseComandLine(args, opts, rb, Json2Dcm.class);
if (!(cl.hasOption("j") || cl.hasOption("i")))
throw new ParseException(rb.getString("missing-i-j"));
return cl;
}
@SuppressWarnings("static-access")
private static void addIOFileNameOptions(Options opts) {
opts.addOption(OptionBuilder
.hasArg()
.withArgName("json-file")
.withDescription(rb.getString("j-file"))
.create("j"));
opts.addOption(OptionBuilder
.hasArg()
.withArgName("dicom-file")
.withDescription(rb.getString("i-file"))
.create("i"));
opts.addOption(OptionBuilder
.hasArg()
.withArgName("dicom-file")
.withDescription(rb.getString("o-file"))
.create("o"));
}
@SuppressWarnings("static-access")
private static void addBulkdataOptions(Options opts) {
OptionGroup blkGroup = new OptionGroup();
blkGroup.addOption(OptionBuilder
.withLongOpt("no-bulkdata")
.withDescription(rb.getString("no-bulkdata"))
.create("B"));
blkGroup.addOption(OptionBuilder
.withLongOpt("alloc-bulkdata")
.withDescription(rb.getString("alloc-bulkdata"))
.create("b"));
opts.addOptionGroup(blkGroup);
opts.addOption(OptionBuilder
.withLongOpt("blk-file-dir")
.hasArg()
.withArgName("directory")
.withDescription(rb.getString("blk-file-dir"))
.create("d"));
opts.addOption(OptionBuilder
.withLongOpt("blk-file-prefix")
.hasArg()
.withArgName("prefix")
.withDescription(rb.getString("blk-file-prefix"))
.create());
opts.addOption(OptionBuilder
.withLongOpt("blk-file-suffix")
.hasArg()
.withArgName("suffix")
.withDescription(rb.getString("blk-file-suffix"))
.create());
opts.addOption("c", "cat-blk-files", false,
rb.getString("cat-blk-files"));
opts.addOption(null, "keep-blk-files", false,
rb.getString("keep-blk-files"));
opts.addOption(OptionBuilder
.withLongOpt("blk-spec")
.hasArg()
.withArgName("json-file")
.withDescription(rb.getString("blk-spec"))
.create("J"));
}
@SuppressWarnings("static-access")
private static void addFileEncodingOptions(Options opts) {
opts.addOption(OptionBuilder
.withLongOpt("transfer-syntax")
.hasArg()
.withArgName("uid")
.withDescription(rb.getString("transfer-syntax"))
.create("t"));
OptionGroup fmiGroup = new OptionGroup();
fmiGroup.addOption(OptionBuilder
.withLongOpt("no-fmi")
.withDescription(rb.getString("no-fmi"))
.create("F"));
fmiGroup.addOption(OptionBuilder
.withLongOpt("fmi")
.withDescription(rb.getString("fmi"))
.create("f"));
opts.addOptionGroup(fmiGroup);
CLIUtils.addEncodingOptions(opts);
}
public static void main(String[] args) {
try {
CommandLine cl = parseComandLine(args);
Json2Dcm main = new Json2Dcm();
configureBulkdata(main, cl);
if (cl.hasOption("t")) {
main.setTransferSyntax(cl.getOptionValue("t"));
}
main.setWithFileMetaInformation(cl.hasOption("f"));
main.setNoFileMetaInformation(cl.hasOption("F"));
main.setEncodingOptions(CLIUtils.encodingOptionsOf(cl));
try {
if (cl.hasOption("i")) {
String fname = cl.getOptionValue("i");
if (fname.equals("-")) {
main.parse(new DicomInputStream(System.in));
} else {
DicomInputStream dis =
new DicomInputStream(new File(fname));
try {
main.parse(dis);
} finally {
dis.close();
}
}
}
if (cl.hasOption("j"))
main.mergeJSON(cl.getOptionValue("j"));
OutputStream out = cl.hasOption("o")
? new FileOutputStream(cl.getOptionValue("o"))
: new FileOutputStream(FileDescriptor.out);
try {
main.writeTo(out);
} finally {
out.close();
}
} finally {
if (!cl.hasOption("keep-blk-files"))
main.delBulkDataFiles();
}
} catch (ParseException e) {
System.err.println("json2dcm: " + e.getMessage());
System.err.println(rb.getString("try"));
System.exit(2);
} catch (Exception e) {
System.err.println("json2dcm: " + e.getMessage());
e.printStackTrace();
System.exit(2);
}
}
private static void configureBulkdata(Json2Dcm json2dcm, CommandLine cl)
throws Exception {
if (cl.hasOption("b")) {
json2dcm.setIncludeBulkData(IncludeBulkData.YES);
}
if (cl.hasOption("B")) {
json2dcm.setIncludeBulkData(IncludeBulkData.NO);
}
if (cl.hasOption("blk-file-prefix")) {
json2dcm.setBulkDataFilePrefix(
cl.getOptionValue("blk-file-prefix"));
}
if (cl.hasOption("blk-file-suffix")) {
json2dcm.setBulkDataFileSuffix(
cl.getOptionValue("blk-file-suffix"));
}
if (cl.hasOption("d")) {
File tempDir = new File(cl.getOptionValue("d"));
json2dcm.setBulkDataDirectory(tempDir);
}
json2dcm.setConcatenateBulkDataFiles(cl.hasOption("c"));
if (cl.hasOption("J")) {
json2dcm.setBulkDataAttributes(
parseJSON(cl.getOptionValue("J")));
}
}
public void writeTo(OutputStream out) throws IOException {
if (nofmi)
fmi = null;
else if (fmi == null
? withfmi
: tsuid != null && !tsuid.equals(
fmi.getString(Tag.TransferSyntaxUID, null))) {
fmi = dataset.createFileMetaInformation(tsuid);
}
@SuppressWarnings("resource")
DicomOutputStream dos = new DicomOutputStream(
new BufferedOutputStream(out),
fmi != null
? UID.ExplicitVRLittleEndian
: tsuid != null
? tsuid
: UID.ImplicitVRLittleEndian);
dos.setEncodingOptions(encOpts);
dos.writeDataset(fmi, dataset);
dos.finish();
dos.flush();
}
public void delBulkDataFiles() {
if (bulkDataFiles != null)
for (File f : bulkDataFiles)
f.delete();
}
public void parse(DicomInputStream dis) throws IOException {
dis.setIncludeBulkData(includeBulkData);
if (blkAttrs != null)
dis.setBulkDataDescriptor(BulkDataDescriptor.valueOf(blkAttrs));
dis.setBulkDataDirectory(blkDirectory);
dis.setBulkDataFilePrefix(blkFilePrefix);
dis.setBulkDataFileSuffix(blkFileSuffix);
dis.setConcatenateBulkDataFiles(catBlkFiles);
dataset = dis.readDataset(-1, -1);
fmi = dis.getFileMetaInformation();
bulkDataFiles = dis.getBulkDataFiles();
}
public void mergeJSON(String fname) throws Exception {
if (dataset == null)
dataset = new Attributes();
JSONReader reader = parseJSON(fname, dataset);
Attributes fmi2 = reader.getFileMetaInformation();
if (fmi2 != null)
fmi = fmi2;
}
public static Attributes parseJSON(String fname) throws Exception {
Attributes attrs = new Attributes();
parseJSON(fname, attrs);
return attrs;
}
private static JSONReader parseJSON(String fname, Attributes attrs)
throws IOException {
@SuppressWarnings("resource")
InputStream in = fname.equals("-") ? System.in : new FileInputStream(fname);
try {
JSONReader reader = new JSONReader(
Json.createParser(new InputStreamReader(in, "UTF-8")));
reader.readDataset(attrs);
return reader;
} finally {
if (in != System.in)
SafeClose.close(in);
}
}
}