Read dicom pixel data to create a matrix- using dcm4che3 in scala

[Karthik Vadla]

Hello All, 

I'm trying to get the pixel data using dcm4che3 in scala. I want to create a matrix out of pixel data to do some transformations.

Before reading pixel data, i tried to get file metadata. I have End of file exception .

Can you please help me with this.

My code snippet in scala:

-----------------------------------

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 =>

           val fmi = dis.getFileMetaInformation

           val data = dis.readDataset(-1, -1)

           data

      }

      dm.foreach(println)

Error:

--------

Job aborted due to stage failure: Task 0 in stage 1.0 failed 1 times, most recent failure: Lost task 0.0 in stage 1.0 (TID 1, localhost): 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)

Please see attachment for complete error.

Thanks 

Karthik

[Karthik Vadla]

I resolved above issue by creating dicominputstream using  file object instead of ByteArrayInputStream. 

But still i'm looking to create with ByteArrayInputStream.

Here i'm reading dicom files from hdfs. 

Thanks

Karthik