Getting images into vtk from Java quickly (was [vtkusers] vtkImageImport in java?)

[David Marshburn]

On Fri, 10 Feb 2006 vtkusers-request at vtk.org wrote:

> ------------------------------
> Message: 3
> Date: Thu, 9 Feb 2006 10:35:49 -0800
> From: "Stewart, Terry" <Terry.Stewart at xeroxlabs.com>
> 
> Steve,
> 
>   I'm using Java and ran into a similar situation while trying to get my
> internally-generated RGB image into vtkImageData.  I'd tried the
> vtkImageImport path too only to run into the same roadblock with the
> missing [Copy|Set]ImportVoidPointer() methods for Java.  I've gotten my
> logic to a functional state via:
> 
>    vtkImageData imageData = new vtkImageData();
>          :
>    for (x = 0; ...)
>       for (y = 0; ... )
<snip>
> 
> However this is quite slow.  Did you use some other mechanism to get
> your image data inserted into vtkImageData that is perhaps more
> efficient?  

> ------------------------------
> 
> Message: 6
> Date: Thu, 09 Feb 2006 18:08:23 -0500
> From: "Steve M. Robbins" <steven.robbins at videotron.ca>
> Subject: Re: Ghosts and Extents (was [vtkusers] vtkImageImport in
> 	java?)
> 
> > However this is quite slow. 
> 
> Yep.
> 
> > Did you use some other mechanism to get
> > your image data inserted into vtkImageData that is perhaps more
> > efficient?  
> 
> Yep.  We wrote JNI code that effectively does a memcpy() to
> vtkImage.GetVoidPointer().  I'd give you the code except that the JNI
> bit is very specific to our application so it really wouldn't help
> you.
> 
> ------------------------------
> 
> Message: 7
> Date: Thu, 9 Feb 2006 15:32:19 -0800
> From: "Stewart, Terry" <Terry.Stewart at xeroxlabs.com>
> Subject: RE: Ghosts and Extents (was [vtkusers] vtkImageImport in
> 	java?)
> 
>   OK, thanks.   Updating the JNI logic was an idea that my team had been
> contemplating.  Thanks for the confirmation.  And right, the interface
> updates we'd like to make would likely be different than yours, so no
> problem there.  

Before anyone goes to the length of writing jni code, here is a fast way 
to get image data from Java down into vtk.  As with (arguably) any vtk 
issue, the solution lies in finding just the right class and function out 
of a sea of thousands of candidates! :)  (for a year or more, our group 
thought that there was no fast way to get bulk data from java into vtk)

in Java, vtkImageData has a SetScalars method that takes as an arguement a 
vtkDataArray.  vtkDataArray has a bunch of subclasses specific to 
array-element types (e.g., vtkUnsignedCharArray, vtkUnsignedShortArray, 
vtkFloatArray, etc.).  In Java, these data-array classes have a 
SetJavaArray method that does fast copying.

some code like the following should work (this is for a 3D image stack):

  protected vtkImageData imageData_vtk = new vtkImageData( );
  protected vtkDataArray dataArray_vtk = null;
  protected Object singleArray = null;
	....

	// for 8-bit pixels
	imageData_vtk.SetScalarTypeToUnsignedChar();
	imageData_vtk.SetNumberOfScalarComponents( 1 );
	dataArray_vtk = new vtkUnsignedCharArray( );
	
	imageData_vtk.SetDimensions( imageWidth, imageHeight, numImages );
	singleArray = new byte[ imageWidth * imageHeight * numImages ];
	imageData_vtk.AllocateScalars();

	// fill in singleArray, possibly using System.arraycopy

	( (vtkUnsignedCharArray) dataArray_vtk).SetJavaArray( (byte[]) singleArray );
	imageData_vtk.GetPointData().SetScalars( dataArray_vtk );

this was written to be used for images of possibly many types; the code 
would be simpler if you will only ever care about 8-bit images.

on a not-terribly-fast computer, this code will stuff a 50 or so 512x512 
images into vtk in an amount of time that isn't notable, like a second or 
two?  i've not timed it, although it is no longer wearisome to load images 
in our java/vtk application!

cheers,
-david