Actually, after setting the marching squares value to 0.5 and changing the linear extrusion filter it's working now. Thanks!!!<br><br><div class="gmail_quote">On Thu, Feb 24, 2011 at 9:02 AM, Bill Lorensen <span dir="ltr"><<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Also, the stencil algorithm and marching squares use different<br>
criteria to determine whether a "pixel" is inside or outside.<br>
<br>
For the stencil, the pixel is considered a point and checked within a<br>
tolerance for inside/outside. I'm guessing here).<br>
For marching squares, a "square" is composed of four pixels. If at<br>
least one of the four pixels is of the opposite state(inside/outside)<br>
then a contour will be generated.<br>
<div><div></div><div class="h5"><br>
On Thu, Feb 24, 2011 at 11:53 AM, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com">bill.lorensen@gmail.com</a>> wrote:<br>
> Definitely set the isovalue to .5 if you have binary 0/1 images.<br>
><br>
> On Wed, Feb 23, 2011 at 2:59 PM, David Gobbi <<a href="mailto:david.gobbi@gmail.com">david.gobbi@gmail.com</a>> wrote:<br>
>> I've never used marching squares, but I have a guess as<br>
>> to what the problem might be. If your binary image has<br>
>> values "0" and "1" then you should contour it at "0.5".<br>
>><br>
>> - David<br>
>><br>
>><br>
>> On Wed, Feb 23, 2011 at 12:27 PM, Jonathan Morra <<a href="mailto:jonmorra@gmail.com">jonmorra@gmail.com</a>> wrote:<br>
>>> If that's the case, then maybe I could have issues on the other side<br>
>>> (converting binary images to contours, I do both). For this I'm using<br>
>>> vtkMarchingSquares followed by vtkStripper<br>
>>> int[] extent = binaryOrgan.GetExtent();<br>
>>> switch (orientation) {<br>
>>> case OrthoPanel.ORIENTATION_XY:<br>
>>> extent[4] = slice;<br>
>>> extent[5] = slice;<br>
>>> break;<br>
>>> case OrthoPanel.ORIENTATION_XZ:<br>
>>> extent[2] = slice;<br>
>>> extent[3] = slice;<br>
>>> break;<br>
>>> case OrthoPanel.ORIENTATION_YZ:<br>
>>> extent[0] = slice;<br>
>>> extent[1] = slice;<br>
>>> break;<br>
>>> }<br>
>>> vtkMarchingSquares marching = new vtkMarchingSquares();<br>
>>> marching.SetInput(binaryOrgan);<br>
>>> marching.SetImageRange(extent);<br>
>>> marching.SetValue(0, 1);<br>
>>> marching.Update();<br>
>>> vtkPolyData marchingOutput = marching.GetOutput();<br>
>>> vtkStripper stripper = new vtkStripper();<br>
>>> stripper.SetInput(marchingOutput);<br>
>>> stripper.Update();<br>
>>> Does anything look like it could be causing my issues there?<br>
>>> On Wed, Feb 23, 2011 at 11:18 AM, David Gobbi <<a href="mailto:david.gobbi@gmail.com">david.gobbi@gmail.com</a>> wrote:<br>
>>>><br>
>>>> The value "1e-6" is a common tolerance because it is larger than<br>
>>>> most roundoff errors that are likely to occur in the calculations,<br>
>>>> but still small enough that it won't appreciably increase size of the<br>
>>>> region.<br>
>>>><br>
>>>> Setting the tolerance to zero does exactly what you noted. If the<br>
>>>> pixel is exactly on the edge, then it is considered to be inside if the<br>
>>>> edge is a leading edge, or outside if the edge is a trailing edge.<br>
>>>> This is done so that if you have two contours which are adjacent<br>
>>>> (i.e. share an edge), the edge voxels will be considered to be in<br>
>>>> just one of the two contours instead of in both. If the tolerance is<br>
>>>> set larger than zero, then the edge pixels would always be considered<br>
>>>> to be in both contours.<br>
>>>><br>
>>>> If you are dealing with rectangular contours, then the contour<br>
>>>> lines should be made so that they lie halfway between pixels, instead<br>
>>>> of lying directly on top of the pixels. Then there is no uncertainty<br>
>>>> about whether a pixel lies inside or outside.<br>
>>>><br>
>>>> - David<br>
>>>><br>
>>>><br>
>>>> On Wed, Feb 23, 2011 at 11:58 AM, Jonathan Morra <<a href="mailto:jonmorra@gmail.com">jonmorra@gmail.com</a>><br>
>>>> wrote:<br>
>>>> > I had the tolerance set to 0, and setting it to 1e-6 didn't fix the<br>
>>>> > problem.<br>
>>>> > How did you come up with that number? What's wrong with setting it to<br>
>>>> > 0?<br>
>>>> > In my case usually the left and top side of the vtkImageData is being<br>
>>>> > eroded, such that if I call the filter many times, the vtkImageData will<br>
>>>> > eventually be blank because it will all be eroded. However, sometimes<br>
>>>> > the<br>
>>>> > bottom and right grow in size, I haven't figured out which situations<br>
>>>> > cause<br>
>>>> > which.<br>
>>>> ><br>
>>>> > On Wed, Feb 23, 2011 at 10:54 AM, David Gobbi <<a href="mailto:david.gobbi@gmail.com">david.gobbi@gmail.com</a>><br>
>>>> > wrote:<br>
>>>> >><br>
>>>> >> Hi Jonathan,<br>
>>>> >><br>
>>>> >> Whether a pixel is set depends on whether the center of the pixel<br>
>>>> >> is inside or outside the contour, irregardless of what proportion of<br>
>>>> >> the pixel's volume is inside or outside.<br>
>>>> >><br>
>>>> >> The only adjustment is the Tolerance, which should be set to<br>
>>>> >> around 1e-6 so that pixels right on the edge of the contour<br>
>>>> >> are considered to be inside. The tolerance cannot be negative.<br>
>>>> >><br>
>>>> >> - David<br>
>>>> >><br>
>>>> >><br>
>>>> >> On Wed, Feb 23, 2011 at 11:22 AM, Jonathan Morra <<a href="mailto:jonmorra@gmail.com">jonmorra@gmail.com</a>><br>
>>>> >> wrote:<br>
>>>> >> > I am currently using vtkPolyDataToImageStencil to successfully<br>
>>>> >> > convert<br>
>>>> >> > contours represented as vtkPolyData to binary vtkImageData's.<br>
>>>> >> > However,<br>
>>>> >> > I'm<br>
>>>> >> > noticing a problem with the output sometimes. Sometimes the<br>
>>>> >> > resulting<br>
>>>> >> > binary images are slightly smaller or slightly bigger than the poly<br>
>>>> >> > data<br>
>>>> >> > they were made from. I assume this is the result of partial volume<br>
>>>> >> > effects.<br>
>>>> >> > I would like to know 2 things<br>
>>>> >> > 1. How does vtkPolyDataToImageStencil handle partial volume.<br>
>>>> >> > 2. Is there a way to tune partial volume in<br>
>>>> >> > vtkPolyDataToImageStencil?<br>
>>>> >> > For<br>
>>>> >> > instance, a parameter which says if the contour includes less than x<br>
>>>> >> > percentage of the pixel then that pixel is 0.<br>
>>>> >> > Thanks,<br>
>>>> >> > Jon<br>
>>>> >> > PS If my assumption about partial volume effects is wrong, please let<br>
>>>> >> > me<br>
>>>> >> > know.<br>
>>>> >> > _______________________________________________<br>
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>>>> >> ><br>
>>>> ><br>
>>>> ><br>
>>><br>
>>><br>
>> _______________________________________________<br>
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</div></div></blockquote></div><br>