I have a raw pixel data in a byte[] from a DICOM image.
Now I would like to convert this byte[] to an Image object.
I tried:
Image img = Image.FromStream(new MemoryStream(byteArray));
but this is not working for me. What else should I be using ?
One thing to be aware of is that a dicom "image" is not necessarily just image data. The dicom file format contains much more than raw image data. This may be where you're getting hung up. Consider checking out the dicom file standard which you should be able to find linked on the wikipedia article for dicom. This should help you figure out how to parse out the information you're actually interested in.
You have to do the following
Identify the PIXEL DATA tag from the file. You may use FileStream to read byte by byte.
Read the pixel data
Convert it to RGB
Create a BitMap object from the RGB
Use Graphics class to draw the BitMap on a panel.
The pixel data usually (if not always) ends up at the end of the DICOM data. If you can figure out width, height, stride and color depth, it should be doable to skip to the (7FE0,0010) data element value and just grab the succeeding bytes. This is the trick that most normal image viewers use when they show DICOM images.
There is a C# library called EvilDicom (http://rexcardan.com/evildicom/) that can be used to pull the image out of a DICOM file. It has a tutorial on how to do it on the website.
You should use GDCM.
Grassroots DiCoM is a C++ library for DICOM medical files. It is automatically wrapped to python/C#/Java (using swig). It supports RAW, JPEG 8/12/16bits (lossy/lossless), JPEG 2000, JPEG-LS, RLE and deflated (zlib).
It is portable and is known to run on most system (Win32, linux, MacOSX).
http://gdcm.sourceforge.net/wiki/index.php/GDCM_Release_2.4
See for example:
http://gdcm.sourceforge.net/html/DecompressImage_8cs-example.html
Are you working with a pure standard DICOM File? I've been maintainning a DICOM parser for over a two years and I came across some realy strange DICOM files that didn't completely fulfill the standard (companies implementing their "own" twisted standard DICOM files) . flush you byte array into a file and test whether your image viewer(irfanview, picassa or whatever) can show it. If your code is working with a normal JPEG stream then from my experience , 99.9999% chance that this simply because the file voilate the standard in some strange way ( and believe me , medical companies does that a lot)
Also note that DICOM standard support several variants of the JPEG standard . could be that the Bitmap class doesn't support the data you get from the DICOM file. Can you please write down the transfer syntax?
You are welcome to send me the file (if it's not big) yossi1981#gmail.com , I can check it out , There was a time I've been hex-editing DICOM file for a half a year.
DICOM is a ridiculous specification and I sincerely hope it gets overhauled in the near future. That said Offis has a software suite "DCMTK" which is fairly good at converting dicoms with the various popular encodings. Just trying to skip ahead in the file x-bytes will probably be fine for a single file but if you have a volume or several volumes a more robust strategy is in order. I used DCMTK's conversion code and just grabbed the image bits before they went into a pnm. The file you'll be looking for in DCMTK is dcm2pnm or possibly dcmj2pnm depending on the encoding scheme.
I had a problem with the scale window that I fixed with one of the runtime flags. DCMTK is open source and comes with fairly simple build instructions.
Related
I'm currently trying to figure out how JPEG's are made in depth out of interest. I found documents on the different sections (soi, sof, sos, eoi etc) which are pretty straight forward, but not how to get a single pixel out of there.
My first thought was to make a small image, 2x2 for example, but with all the headers and sections it's still to big to isolate the pixel information without knowing the exact location and method to extract it. I'm sure it's compressed, but is their a way to get it out manually? (as RGB?)
Anyone has a clue on how to do this?
Getting the value of a single pixel of a JPEG image requires parsing some (if not most) of those sections anyway.
There's a good step-by-step guide available at https://www.imperialviolet.org/binary/jpeg/ (though the code is in Haskell, so it might be moderately inscrutable to mere mortals) that explains the concepts behind turning a JPEG into a bunch of RGB values.
This is the only source I know that explains JPEG end-to-end:
https://www.amazon.com/gp/product/B01JXRY4R0/ref=dbs_a_def_rwt_bibl_vppi_i4
Parsing the structure of a JPEG stream is easy. Decoding a JPEG scan is very difficult and involves several compression steps. Plus there are two different types of scan that are commonly in use (progressive & sequential).
I'm writing a service for a project that's going to handle our image processing. One such process is supposed to strip all metadata from the byte[] provided and return the same image as a byte[].
The method I'm currently working on involves always converting the image to a Bitmap, then converting it back to the original format and returning the data from a MemoryStream.
I haven't been able to test it yet but something tells me I'm going to experience some quality loss.
How can I remove all metadata from any image with a common format?
(bmp, gif, png, jpg, icon, tiff)
Not sure how I can narrow that down any further. Would be nice if I got some feedback regarding the downvotes.
For the lossless formats (except JPEG), your idea of loading it as a bitmap and re-saving is fine. Not sure if .NET natively supports TIFFs (I doubt it does).
For JPEGs, as you suggested there may be quality loss if you're re-compressing the file after decompressing it. For that, you might try the ExifLibrary and see if that has anything. If not, there are command line tools (like ImageMagick) that can strip metadata. (If you use ImageMagick, you're all set, since it supports all of your required formats. The command you want is convert -strip.)
For TIFFs, .NET has built-in TiffBitmapDecoder and ...Encoder classes you might be able to use; see here.
In short, using an external tool like ImageMagick is definitely the easiest solution. If you can't use an external tool, you're almost certainly going to need to special-case the formats that .NET doesn't support natively (and the lossy JPEG).
EDIT: I just read that ImageMagick doesn't do lossless stripping with JPEGs, sorry. I guess using the library I linked above, or some other JPEG library, is the best I can think of.
I'm having difficulties when trying to save huge images with C# (I'm talking about over one gigabyte).
Basically I'm trying to do this in parts - I have around 200 bitmap sources and I need a way to combine them before or after encoding them to a .png file.
I know this is going to require lots of RAM unless I somehow stream the data directly from hard drive but I have no idea how to do this either.
Each bitmap source is 895x895 pixels so combining the images after encoding doesn't seem easy because C# doesn't let you create a bitmap with size of 13425 x 13425.
This PngCs library (disclaimer: I'm the author) lets you read and write huge PNG images line by line, so that you don't need to keep the full image in memory; perhaps you find it useful.
We have a around 600,000 images that were converted from JPEG to TIFF files and uploaded to our FileNet repository. These TIFF images are multi-page, made by stitching multiple JPEGs.
This was done couple of years ago. Now we started getting complaints from users the quality of the TIFF images are not the same as they were when they were JPEGs.
Is there any way we can improve the quality of TIFF files? If I have to re-migrate this data, can JPEGs be of multiple pages? Please advice.
You can't just add quality to an image, so you can either try improving the appearance of the current information or you'll need to re-create the images to get better information.
To me, it sounds like the initial creation process is the most likely cause of the quality issue. How you create the image is important.
For example, I had a large number of photos I needed to re-size, so I used irfanview's batch convert and the results were horrible. Perhaps I had the settings wrong, I don't know.
I then tried using ImageMagick, and the results were great.
The point being, the conversion process isn't trivial.
If I were you, I'd look at how the images were created, experiment with different settings to determine what gives the best appearance, then re-create your photo gallery.
For photographic material, there's no real reason to use anything other than a jpeg if the target market is the general consumer.
Both TIFF and JPEG support lossless and lossy storage of your images. You mentioned that there was a previous conversion. The conversion was probably a lossy conversion as such you probably won't be able to recover that data to the way it was previously.
That said if you have the original source images you might be able to get back to where you where. Regarding multi-image jpegs, there is such a format *.mpo but I haven't seen it used before so your millage may vary.
You probably converted gray scale or color Jpeg to Tiff. The most common is Tiff G4 which is only 1 bit per pixel. So 24 or 8 bits was converted to 1 bit and you will see a lot of images losses. There are multiple methods to improve image quality but I would have to see the images first to suggest a method.
For a whole month I've been trying to find out how to load a cmyk image (8-bit tiff) and do a UCA, UCR, GCR transformations.
I know the formulas for this transformations, but I have a problem to load an cmyk image with C++ or C#.
My plan is to manipulate the image pixel by pixel and change every value C, M, Y, K of that pixel, and finally save changed image as 8-bit tiff cmyk image. So basically I want to run through each pixel, make change to cmyk values, and save the image.
I have difficulties to find and install such a library for C# or C++, and I'm using Visual Studio Express 2010 for both.
What libraries can I use to load these images?
libtiff will let you manipulate TIFF files. See also this answer on building libtiff using Visual Studio.
You'll need to read the image row by row using TIFFReadScanline to avoid conversion to RGB by the library. The open source tifftopnm utility does this; its source is here - it uses pick_cmyk_pixel to convert the data to RGB after obtaining it, but naturally you can just substitute your own logic instead.
EMGU is a c# wrapper for opencv (c++) either of these will allow Tiff files to be easily used and manipulated. They will allow you to access pixels more readily and uses highly optimised code. Since these are a dedicated image processing libraries they will allow you to do more with your image without having to worry about RGB conversion or reading the file in etc.
Hope they help,
Cheers
Chris