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karthikvadla16
USA
1 Posts |
 Posted - Aug 15 2016 : 18:48:18
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Hi All,
I have a requirement to create a matrix for each .dcm image using pixel data. I tried below code using dcm4che in scala. I keep getting EOF exception when i specify ds.readDataset(-1,-1).
Can anyone help me with this.
Really appreciate your help.
Code:
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import java.io.{ByteArrayInputStream}
import org.dcm4che3.data.Tag
import org.dcm4che3.imageio.plugins.dcm.{DicomMetaData}
import org.dcm4che3.io.{BulkDataDescriptor, DicomInputStream}
import org.dcm4che3.io.DicomInputStream.IncludeBulkData
import org.scalatest.Matchers
class DicomTest extends TestingSparkContextWordSpec with Matchers {
"dicom folder" should {
"contain 9 files" in {
//dicomimages folder is within spark-rk/core
val dicomRdd = sparkContext.wholeTextFiles("dicomimages")
val printbytes = dicomRdd.map { case (filepath, filedata) => filedata.getBytes().length }
printbytes.foreach(println)
val disRdd = dicomRdd.map { case (filepath, filedata) => new DicomInputStream(new ByteArrayInputStream(filedata.getBytes())) }
val dm = disRdd.map {
case dis =>
dis.setIncludeBulkData(IncludeBulkData.URI);
dis.setBulkDataDescriptor(BulkDataDescriptor.PIXELDATA);
dis.setURI("java:iis"); // avoid copy of pixeldata to temporary file
val fmi = dis.readFileMetaInformation();
val ds = dis.readDataset(-1, -1);
new DicomMetaData(fmi, ds)
}
dm.map(m => m.getAttributes.getValue(Tag.PixelData)).foreach(println)
}
}
}
Error: (Please see attachment for complete error stack)
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Caused by: java.io.EOFException
at org.dcm4che3.util.StreamUtils.readFully(StreamUtils.java:63)
at org.dcm4che3.io.DicomInputStream.readFully(DicomInputStream.java:383)
at org.dcm4che3.io.DicomInputStream.readValue(DicomInputStream.java:711)
at org.dcm4che3.io.DicomInputStream.readValue(DicomInputStream.java:536)
at org.dcm4che3.io.DicomInputStream.readAttributes(DicomInputStream.java:497)
Karthik
Download Attachment: 2016815184739_eof_exception.txt |
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[IEvolution] Reading dicom data using dcm4che3
