Convert from byte array to DICOM using ImageJ API

Question

I am developing a Hadoop application in order to process DICOM files. The files are distributed on the HDFS.

I am using a modified RecordReader that reads a whole file and emits its content as a key-value pair. The record reader is working properly.

All the file data of the files is in the ByteWritable value. I have already checked that and the data is completely equal to the original file. Thus, inputContent has the same value of the original file.

After converting the ByteWritable to a byte array, I am unable to turn that into a stream and generate a new DICOM image - using the imageJ api - with its content.

How can i do so using this API?

Follows an example of the code:

public void inputTester()
    {
        DICOM image;
        Configuration testConf = new Configuration(false);

        /* Reads the local file system */
        testConf.set("fs.default.name", "file:///");

        File testFile = new File("path/to/dicom/file");

        Path path = new Path(testFile.getAbsoluteFile().toURI());
        FileSplit split = new FileSplit(path, 0, testFile.length(), null);

        InputFormat inputFormat = ReflectionUtils.newInstance(WholeFileInputFormat.class, testConf);
        TaskAttemptContext context = new TaskAttemptContextImpl(testConf, new TaskAttemptID());

        try
        {
            RecordReader reader = inputFormat.createRecordReader(split, context);
            while (reader.nextKeyValue())
            {
                /* get the bytes array */
                BytesWritable inputBytesWritable = (BytesWritable) reader.getCurrentValue();
                byte[] inputContent = inputBytesWritable.getBytes();

                InputStream is = new ByteArrayInputStream(inputContent);
                image = new DICOM(is);
            }
        }
        catch (Exception e)
        {

        }

    }
}

Prometheus Prometheus · Accepted Answer · 2014-07-10T01:10:49

Actually I ended up solving the question.

The thing is, the constructor of the DICOM class does not actually constructs an image with the inputStream. Is just saves the inputStream has one of its attributes.

For that, you need to use the run method, giving a file name for it.

So, one just needs to add the following line:

image.run("DICOM Test");

Right after the line

image = new DICOM(is);

Convert from byte array to DICOM using ImageJ API

2 Answers