Open an ImagePlus from a stream or bytearray

[Johannes Hermen]

Hi,

Does anybody know if it is possible to create an ImagePlus directly from an
InputStream or a ByteArray.
I need to create ImagePlus objects from DICOM files that are retrieved from
a Database, so that i can only get them as Stream or ByteArray.


Thanks in advance

       _Johannes

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Johannes Hermen  -  Ingenieur de Recherche
[hidden email]
-----------------------------------------------------------------
CRP Henri Tudor  http://www.santec.tudor.lu
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L-1855 Luxembourg
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[dscho]

Hi,

On Fri, 16 Mar 2007, Johannes Hermen wrote:

> Does anybody know if it is possible to create an ImagePlus directly from
> an InputStream or a ByteArray.

AFAICT, no. The openImage() method of ij.io.Opener wants to look at the
file type first, which means that it also wants to look at the filename.

> I need to create ImagePlus objects from DICOM files that are retrieved
> from a Database, so that i can only get them as Stream or ByteArray.

That might be easier: you already _know_ that it is a DICOM file. But you
have to hack the class DicomDecoder in ij.plugin.DICOM so that it actually
takes a preinitialised BufferedInputStream instead of opening it itself
(you might do this by wrapping lines 365-369 in an "if (f == null) {...}",
and adding a new constructor which also takes a BufferedInputStream and
initialises "f" with that.

As for the ByteArray: there is java.io.ByteArrayInputStream which wraps
the array in a stream.

AFAICT DICOM.java is self-contained, so to test all this, you can just
copy it somewhere else (but do not forget to adjust the package name! I do
that regulary, and it compiles, but throws an exception...).

Hth,
Dscho

[ctrueden]

Hi Johannes,

You can construct an ImageProcessor subclass corresponding to the type
of pixel data you need, and then pass it to the ImagePlus constructor.
For example, for an 8-bit image stored as bytes:

    byte[] pix = ...; // get your bytes somehow
    int w = ...; // width of image
    int h = ...; // height of image
    ByteProcessor proc = new ByteProcessor(w, h, pix, null);
    ImagePlus imp = new ImagePlus("My Image", proc);
    imp.show();

We do a lot of array-to-ImagePlus conversions in the Bio-Formats
Importer plugin. You can check the source for a more complex example:

https://skyking.microscopy.wisc.edu/svn/java/trunk/loci/plugins/Importer.java

Lines 718-868, which constructs ImageProcessor and ImagePlus objects,
are probably most relevant.

-Curtis

On 3/16/07, Johannes Hermen <[hidden email]> wrote:

> Hi,
>
> Does anybody know if it is possible to create an ImagePlus directly from an
> InputStream or a ByteArray.
> I need to create ImagePlus objects from DICOM files that are retrieved from
> a Database, so that i can only get them as Stream or ByteArray.
>
>
> Thanks in advance
>
>        _Johannes
>
> -----------------------------------------------------------------
> Johannes Hermen  -  Ingenieur de Recherche
> [hidden email]
> -----------------------------------------------------------------
> CRP Henri Tudor  http://www.santec.tudor.lu
> 29, Avenue John F. Kennedy
> L-1855 Luxembourg
> -----------------------------------------------------------------
>

[Wayne Rasband]

> Does anybody know if it is possible to create an ImagePlus directly
> from an
> InputStream or a ByteArray.
> I need to create ImagePlus objects from DICOM files that are retrieved
> from
> a Database, so that i can only get them as Stream or ByteArray.

Starting with ImageJ 1.38m, a plugin can open and display a DICOM with
a BufferedInputStream using

     DICOM dcm = new DICOM(bis);
     dcm.run("Title");
     dcm.show();

where 'bis' is a BufferedInputStream. Note that 'dcm' is also an
ImagePlus since the DICOM class extends ImagePlus.

-wayne

[Deepak naik]

I need to save Gray and RGB images.ImageJ says it as unsupported format.How can I pass BufferedImage to ImagePlus constructor?