[vtkusers] bit wise operations for vtkImageData

[Jonathan Morra]

After playing around a little bit, I have come up with the following that's
not currently working.  Could you please advise me why this isn't working.

Thanks

put() {
        // Organ data contains a list of char[]
        final char[] storedCharArray = organData.get(imageNumber);
        final char[] binaryCharArray = getCharArray(binaryOrgan);

        int i=0;
        for (char binaryData : binaryCharArray) {
            char storedData = storedCharArray[i];
            if (binaryData == 0)
                storedData &= ~(1 << bitNumber);
            else
                storedData |= (1 << bitNumber);
            storedCharArray[i] = storedData;
            ++i;
        }

get() {
        vtkImageData binaryImage = // Get blank image of correct dimensions,
orientation, spacing, etc.
        final char[] storedCharArray = organData.get(imageNumber);
        final char[] binaryCharArray = getCharArray(binaryImage);

        int i=0;
        for (char storedData : storedCharArray) {
            binaryCharArray[i] = (char)((storedData >> bitNumber) & 1);
            ++i;
        }
        setCharArray(binaryImage, binaryCharArray);

private void setCharArray(vtkImageData image, char[] array) {

 ((vtkCharArray)image.GetPointData().GetScalars()).SetJavaArray(array);
    }

    private char[] getCharArray(vtkImageData image) {
        vtkPointData points = image.GetPointData();
        vtkCharArray ca = (vtkCharArray)points.GetScalars();
        char[] chars = ca.GetJavaArray();
        return chars;
    }


On Fri, Mar 25, 2011 at 12:48 PM, David Gobbi <david.gobbi at gmail.com> wrote:

> In python it is possible to access the VTK data arrays directly via
> python's buffer interface, so that's what I use when I want to quickly
> move pixel data back and forth from python to VTK.  It allows me to
> use a VTK array (including the one that the image uses to store its
> pixels) as if it was a native python array.
>
> I have a feeling that the only way you will be able to rapidly do VTK
> pixel operations of any kind from Java, is if someone adds a similar
> feature to the Java wrappers.
>
>  - David
>
>
> On Fri, Mar 25, 2011 at 1:31 PM, Jonathan Morra <jonmorra at gmail.com>
> wrote:
> > Your understanding is correct, however I cannot
> > use GetScalarComponentAsDouble and SetScalarComponentAsDouble because
> they
> > are way too slow in Java.  Do you have any other suggestions for how to
> do
> > this or will I have to write it myself in C++?
> >
> > On Fri, Mar 25, 2011 at 12:29 PM, David Gobbi <david.gobbi at gmail.com>
> wrote:
> >>
> >> Hi Jonathan,
> >>
> >> If I understand correctly, you have several binary images with exactly
> >> the same dimensions.  And you want to collapse them into a single
> >> image, by storing a bitfield in the pixels of that image.  So:
> >>
> >> To set bit "i" in pixel "xyz" (C++ code):
> >> int a = int(image.GetScalarComponentAsDouble(x, y, z, 0));
> >> a |= (1 << i);
> >> image.SetScalarComponentAsDouble(x, y, z, a);
> >>
> >> To clear bit "i" in pixel "xyz":
> >> int a = int(image.GetScalarComponentAsDouble(x, y, z, 0));
> >> a &= ~(1 << i);
> >> image.SetScalarComponentAsDouble(x, y, z, a);
> >>
> >> To test bit "i" in pixel "xyz":
> >> int a = int(image.GetScalarComponentAsDouble(x, y, z, 0));
> >> return ((a >> i) & 1);
> >>
> >> But I'm not sure if this is what you are trying to do.  I didn't fully
> >> understand your pseudocode.
> >>
> >>  - David
> >>
> >>
> >>
> >> On Fri, Mar 25, 2011 at 1:08 PM, Jonathan Morra <jonmorra at gmail.com>
> >> wrote:
> >> > I'm in Java and storing a large number of binary vtkImageData's.  I
> know
> >> > this is inefficient, and am searching for a better way to store them.
> >> >  Right
> >> > now I have a hash of the vtkImageData's and a get/put function.
> >> >  Basically I
> >> > want to mimic this get/put but with better storage.  I was thinking
> one
> >> > way
> >> > to do this is to use bitwise logical operations to store the
> information
> >> > in
> >> > the binary masks.  For instance, if we have 2 binary images, then we
> >> > could
> >> > store that information in 1 vtkImageData using the following pseudo
> >> > code.
> >> > private static final int IMAGE1_BIT_CHANNEL = 0;
> >> > private static final int IMAGE2_BIT_CHANNEL = 1;
> >> > private vtkImageData storedImage;
> >> > vtkImageData get(String image)  {
> >> >     int channel = image eq "image1" ? IMAGE1_BIT_CHANNEL :
> >> > IMAGE2_BIT_CHANNEL;
> >> >     vtkImageData return = new vtkImageData();
> >> >     foreach (pixel in storedImage)
> >> >         if (pixel at bit channel)
> >> >             return[pixel] = 1;
> >> >         else
> >> >             return[pixel] = 0;
> >> >     return return;
> >> > }
> >> > void put(String image, vtkImageData binaryImage) {
> >> >     int channel = image eq "image1" ? IMAGE1_BIT_CHANNEL :
> >> > IMAGE2_BIT_CHANNEL;
> >> >     foreach (pixel in binaryImage)
> >> >         if (pixel)
> >> >             storedImage at bit in channel = 1;
> >> >         else
> >> >             storedImage at bit in channel = 0;
> >> > }
> >> > This could be extended easily for 8 channels for a char image for
> >> > instance.
> >> >  This operation would have to be very fast though cause it is done
> often
> >> > on
> >> > the UI thread.
> >> > 1.  Is there a way to do this in VTK with Java?
> >> > 2.  Is this the best scheme for accomplishing my goal?
> >> > 3.  Is there a better scheme for doing this?
> >> > Thanks.
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