[vtkusers] bit wise operations for vtkImageData

[David Gobbi]

I can't see anything that is obviously wrong, but my experience
with Java is limited.

 - David


On Mon, Mar 28, 2011 at 2:42 PM, Jonathan Morra <jonmorra at gmail.com> wrote:
> 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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