Convert BMP Image to DICOM Image

[harshitha]

Hello All,

NEED URGENT HELP!!!!

DCM4CHE only provides support to convert a JPEG image to DICOM using a JPEG Parser. Is there any way to convert a BMP image directly to a DICOM image?

[Todd Jensen]

If using the command line, may be easier to convert the BMP to JPEG first using something like ImageMagick:

https://imagemagick.org/script/command-line-processing.php

Todd Jensen, PhD

Jensen Informatics LLC

[yeddula harshitha]

I don't want to convert BMP to any intermediate type. Is there any way for direct conversion?

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[Tatsunidas]

1.

A simple and easy way is to use the 3D slicer.

It can convert general images to dicom secondary capture with some primary attributes.

2.

If you would contribute/try programming,

for example (This procedure is not strict.),

//get image pixels as byte[]

BufferedImage bmp = ImageIO.read(new File("your.bmp"));

ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageIO.write( bmp, "bmp", baos );
byte[] pixels = baos.toByteArray();

baos.flush();
baos.close();

//get dicom attr reference to copy

DicomInputStream dis = new DicomInputStream(new FIle(path2ReferenceDcm));

Attributes refDcm4AttrCopy = dis.readDataset();

dis.close();

//set pixel

refDcm4AttrCopy.setValue(Tag.PixelData, VR.OW, new BulkData(pixels)); //should check VR.OB or OW.

//set attr values related to pixel

refDcm4AttrCopy.setInt(Tag.Rows, VR.US, bmp.getHeight());
refDcm4AttrCopy.setInt(Tag.Columns, VR.US, bmp.getWidth());

refDcm4AttrCopy.setInt(Tag.BitsAllocated, ...)

refDcm4AttrCopy.setInt(Tag.BitsStored, ...)//BitsStored - 1

refDcm4AttrCopy.setInt(Tag.HighBit, ...)

refDcm4AttrCopy.setInt(Tag.PixelRepresentation, ...)

refDcm4AttrCopy.setInt(Tag.SamplesPerPixel, ...)

refDcm4AttrCopy.setInt(Tag.PhotometricInterpretation, ...) 

// set secondary capture sop class uid

refDcm4AttrCopy.setString(Tag.SOPClassUID, ...)

//set uids

refDcm4AttrCopy.setString(Tag.StudyInstanceUID...);
refDcm4AttrCopy.setString(Tag.SeriesInstanceUID...);
refDcm4AttrCopy.setString(Tag.SOPInstanceUID...);

//create file meta info

Attributes fmi = refDcm4AttrCopy.createFileMetaInfomation(Tag.SOPClassUID);

//output

DicomOutputStream dos = new DicomOutputStream(new File("path2BmpAsDicom.dcm"));
dos.writeFileMetaInformation(fmi);
attribs.writeTo(dos);
dos.close();

You can keep in mind,

- Is that bmp compressed or not ? if compressed, decompress it first, then use it as ExplicitLittleEndian for TSUID.

- Is multiframe ? (movies ?)

- gray or rgb ? if rgb, what is order ? (which rrr...ggg...bbb... or rgbrgbrgb...), if grascale, has look up tables ?

- bit-depth ?  (8 bit or 16 bit or more grayscale?,  or 24 bit , 32 bit rgb ?)

see, this link (https://stackoverflow.com/questions/21087778/how-to-convert-jpg-image-to-dicom-file-using-dcm4che-3-2-1)

I hope this helps.

(Notice, I am not dcm4che developer)

2021年5月12日(水) 14:13 harshitha <mail2h...@gmail.com>:

Hello All,

NEED URGENT HELP!!!!

DCM4CHE only provides support to convert a JPEG image to DICOM using a JPEG Parser. Is there any way to convert a BMP image directly to a DICOM image?

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Tatsuaki KOBAYASHI

e-mail:chok...@gmail.com

TEL:080-1274-6433

Good Luck

==========================================

[Tatsunidas]

Sorry, this is my typo,

//create file meta info

//wrong

Attributes fmi = refDcm4AttrCopy.createFileMetaInfomation(Tag.SOPClassUID);

//correct

Attributes fmi = refDcm4AttrCopy.createFileMetaInfomation(TransferSyntaxUIDOnYourNeed);

2021年5月13日(木) 8:45 Tatsunidas <chok...@gmail.com>:

[harshitha]

NEED URGENT HELP!!!!!

When I did this..

refDcm4AttrCopy.setValue(Tag.PixelData, VR.OW, new BulkData(pixels)); //should check VR.OB or OW.

I was not able to open the DCM image..

Then checked out this (https://stackoverflow.com/questions/21087778/how-to-convert-jpg-image-to-dicom-file-using-dcm4che-3-2-1) link and modified the code to..

FileInputStream fis = new FileInputStream(input_file);  
DataInputStream dis = new DataInputStream(new BufferedInputStream(fis));

         byte[] buffer = new byte[8162];  
         int read;
         while ((read = dis.read(buffer)) > 0) {
             dos.write(buffer, 0, read);
         }

But the final image is empty as attached....

[Tatsunidas]

Umm, sorry, BulkData needs only DicomInputStream.

try it,

//refDcm4AttrCopy.setValue(Tag.PixelData, VR.OW, new BulkData(pixels)); //should check VR.OB or OW.  

//instead

ByteBuffer byteBuffer = ByteBuffer.allocate(pixels.length);
byteBuffer.order(ByteOrder.nativeOrder()).put(pixels);
refDcm4AttrCopy.setBytes(Tag.PixelData, VR.OW, byteBuffer.array());

2021年5月13日(木) 15:05 harshitha <mail2h...@gmail.com>:

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[harshitha]

Hi ,

I tried this, there are no errors and when I tried opening the dcm message, I am not able to open it.

[Tatsunidas]

Could you attach your sample bmp ?

2021年5月13日(木) 19:47 harshitha <mail2h...@gmail.com>:

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[yeddula harshitha]

Please find the attached BMP file

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[Tatsunidas]

 simple example, how about this ?

2021年5月13日(木) 21:55 yeddula harshitha <mail2h...@gmail.com>:

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[yeddula harshitha]

Hi,

I am able to view the DICOM image and also the DICOM tags. Can you please share the code, so that I can verify my mistake?

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[harshitha]

  Hi,

I am able to view the DICOM image and also the DICOM tags. Can you please share the code, so that I can verify my mistake?

[harshitha]

Hi,

//retrieve the pixel and header information

BufferedImage bmp = ImageIO.read(new File("your.bmp"));

ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageIO.write( bmp, "bmp", baos );
byte[] pixels = baos.toByteArray();

BMP Image has a header component included. So the variable, pixels will contain header data along with the pixel data.

//following code retrieves only the pixel data

pixels = ((DataBufferByte)bmpImage.getData().getDataBuffer()).getData();

BMP image scanning is different as compared to other image scanning. Refer to https://medium.com/sysf/bits-to-bitmaps-a-simple-walkthrough-of-bmp-image-format-765dc6857393 for more information.

The pixel information retrieved is in the (B,G,R) format. It needs to be modified to (R,G,B)

//converting (B,G,R) to (R,G,B), B & R needs to be swapped

byte temp;

for(int i=0; i< pixels.length ; i=i+3) {

     tmp = pixels[i];

     pixels[i] = pixels[i+2];

     pixels[i+2] = tmp;

 }

//pixel converted to ByteBuffer

ByteBuffer byteBuffer = ByteBuffer.allocate(pixels.length);

byteBuffer = byteBuffer.order(ByteOrder.nativeOrder()).put(pixels);

//setting the pixel information to the Pixel data Tag

Attributes dataset = new Attributes();

dataset.setBytes(Tag.PixelData, VR.OB,  byteBuffer .array());

// set other tags based on the requirement

//create dicom file

try(DicomOutputStream dos = new DicomOutputStream

(new File(dicomFilePath))

{

dos.writeFileMetaInformation(

    fileMetadata.createFileMetaInformation("1.2.840.10008.1.2.1")); // Explicit VR little Endian, transfer syntax is used

dataset.writeTo(dos); //write dataset to dicomOutputStream

        dos.flush();

    

} catch (IOException e) {

log.error("Error while writing to DICOM File!!");

e.printStackTrace();

}

[Tatsunidas]

Awesome.

2021年5月29日(土) 11:57 harshitha <mail2h...@gmail.com>:

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Tatsuaki KOBAYASHI

e-mail:chok...@gmail.com

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