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    Hi David,<br>
    <br>
    is it possible to connect the vtkImageConnectivityFilter to other
    filters of VTK that do not have vtkImageData as output?<br>
    <br>
    I have a pipleline that creates vtkPolyData as output, so I cannot
    use your filter directly. Using this example:<br>
<a class="moz-txt-link-freetext" href="http://www.vtk.org/Wiki/VTK/Examples/Cxx/PolyData/PolyDataToImageData">http://www.vtk.org/Wiki/VTK/Examples/Cxx/PolyData/PolyDataToImageData</a><br>
    creates one single region. I printed the number of regions and the
    size by<br>
    <br>
    s = c->GetExtractedRegionSizes();<br>
    for (int i = 0; i < c->GetNumberOfExtractedRegions(); i++)<br>
    {<br>
        cout << "num: " <<
    c->GetNumberOfExtractedRegions() << endl;  //1<br>
        cout << "size: " << s->GetTuple1(i); 
    //1.27008e+07<br>
    }<br>
    <br>
    - Imre<br>
    <br>
    <div class="moz-cite-prefix">Am 02.01.2016 um 21:45 schrieb David
      Gobbi:<br>
    </div>
    <blockquote
cite="mid:CANwS1=Fugzi6JW6xivQq8iBbiME7ffYoEq7d3Wm51xjUV=jzLw@mail.gmail.com"
      type="cite">
      <div dir="ltr">
        <div class="gmail_extra">
          <div class="gmail_quote">On Sat, Jan 2, 2016 at 1:06 PM, Imre
            Goretzki <span dir="ltr"><<a moz-do-not-send="true"
                href="mailto:goretzki.imre@gmail.com" target="_blank">goretzki.imre@gmail.com</a>></span>
            wrote:
            <blockquote class="gmail_quote" style="margin:0 0 0
              .8ex;border-left:1px #ccc solid;padding-left:1ex">
              <div bgcolor="#FFFFFF" text="#000000"> <br>
                Yes they can be partially outside the mask because I
                neither know the sizes and locations of the regions I
                want to keep nor the sizes and locations of the regions
                I want to discard for both input image and mask image
                (the mask changes dynamically)<br>
                <br>
                Ok so in later progress I could use the mask as the
                second input (the stencil) and this removes the regions?<br>
              </div>
            </blockquote>
            <div><br>
            </div>
            <div>The vtkImageConnectivityFilter ignores any pixels that
              are outside the stencil (so that might be the reverse of
              what you want, since you want to ignore the regions that
              are inside your mask).</div>
            <div><br>
            </div>
            <div>If a region is partly outside the stencil, then only
              the part that is outside will be ignored.  The rest would
              be counted.  As far as I understand, that is not what you
              want.  You would want the entire region to be ignored,
              right?</div>
            <div><br>
            </div>
            <div>Is there any reason that you even need a "mask"?  Would
              it be just as good if you could specify the unwanted
              regions by giving just one point in each unwanted region,
              i.e. the user would use the mouse to click on the unwanted
              regions?</div>
            <div><br>
            </div>
            <div>Actually, instead of using an input mask, it seems that
              it would be best to allow vtkImageConnectivityFilter to
              assign a different label value to each region.  Then, once
              you know which labels correspond to which regions, you
              could pass this label image through a lookup table that
              colors all of the unwanted regions black.</div>
            <div><br>
            </div>
            <div> - David</div>
            <div><br>
            </div>
            <div><br>
            </div>
            <div> </div>
            <blockquote class="gmail_quote" style="margin:0 0 0
              .8ex;border-left:1px #ccc solid;padding-left:1ex">
              <div bgcolor="#FFFFFF" text="#000000"> My current code
                lets me get the regions I want to discard by storing the
                polydata output of vtkPolyDataConnectivityFilter and
                then iterate over the cells and their points<span><br>
                  <br>
                  for (int i = 0; i <
                  filter->GetNumberOfExtractedRegions(); i++)<br>
                  {<br>
                </span>     vtkSmartPointer<vtkPolyData>
                extractRegionData =
                vtkSmartPointer<vtkPolyData>::New(); //fast<br>
                    extractFilter->InitializeSpecifiedRegionList();
                //fast<br>
                    extractFilter->AddSpecifiedRegion(i); //fast<br>
                    extractFilter->Modified(); //fast<br>
                    extractFilter->Update(); //very long<br>
                   
                extractRegionData->DeepCopy(extractFilter->GetOutput());
                //fast<br>
                    regionList.push_back(extractRegionData); //fast<span><br>
                  }<br>
                  for (int i = 0; i <
                  filter->GetNumberOfExtractedRegions(); i++)<br>
                  {<br>
                </span>     // some other operations<br>
                }<br>
                <br>
                The update() process takes a very long time. As an
                example, if I have about 200 regions, this would take
                about 10 minutes. All other following operations on the
                data and/or a vtkPolyDataConnectivityFilter do not take
                so long.<span><font color="#888888"><br>
                    <br>
                    - Imre</font></span>
                <div>
                  <div><br>
                    <br>
                    <div>Am 02.01.2016 um 20:48 schrieb David Gobbi:<br>
                    </div>
                    <blockquote type="cite">
                      <div dir="ltr">Thanks, that helps.  Here is my
                        understanding so far:
                        <div><br>
                        </div>
                        <div>1) The mask is, originally, a polydata
                          contour.</div>
                        <div>2) The mask indicates the regions you do
                          not want.</div>
                        <div>3) The mask will be converted into a binary
                          image before use.</div>
                        <div><br>
                        </div>
                        <div>What I still need to know is:</div>
                        <div><br>
                        </div>
                        <div>3) Will some regions be partially within
                          and partially outside the mask?  Or will they
                          always be entirely within or entirely outside?</div>
                        <div><br>
                        </div>
                        <div>The vtkImageConnectivityFilter takes two
                          inputs: the first input is just an image (of
                          course) and the second input (which is
                          optional) is an image stencil (essentially a
                          binary image).  There is a filter called
                          vtkPolyDataToImageStencil which can be used
                          create this second input from a vtkPolyData
                          object.</div>
                        <div><br>
                        </div>
                        <div> - David</div>
                        <div><br>
                        </div>
                      </div>
                      <div class="gmail_extra"><br>
                        <div class="gmail_quote">On Sat, Jan 2, 2016 at
                          12:32 PM, Imre Goretzki <span dir="ltr"><<a
                              moz-do-not-send="true"
                              href="mailto:goretzki.imre@gmail.com"
                              target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:goretzki.imre@gmail.com">goretzki.imre@gmail.com</a></a>></span>
                          wrote:<br>
                          <blockquote class="gmail_quote"
                            style="margin:0 0 0 .8ex;border-left:1px
                            #ccc solid;padding-left:1ex">
                            <div bgcolor="#FFFFFF" text="#000000"> I've
                              drawn another image you could look at. The
                              left image is the input data from which I
                              would like to extract the regions. Here
                              every region I would like to keep is
                              painted green. The other two regions, that
                              are painted red, have points that are
                              located inside a region in the binary
                              mask.<br>
                              <br>
                              <br>
                              For all points <i>P</i> in all regions <i>R</i>
                              of image 1 with binary mask <i>B</i><br>
                              <br>
                              If B_P == 255<br>
                                  color region <i>R</i> red<br>
                              else<br>
                                  color region <i>R</i> green<span><font
                                  color="#888888"><br>
                                  <br>
                                  - Imre</font></span>
                              <div>
                                <div><br>
                                  <br>
                                  <div>Am 02.01.2016 um 20:16 schrieb
                                    David Gobbi:<br>
                                  </div>
                                  <blockquote type="cite">
                                    <div dir="ltr">Sorry, but I still
                                      don't follow your explanation.  I
                                      have some vague idea of what you
                                      are trying to do, but I don't
                                      understand well enough to give you
                                      any concrete advice.  Can you try
                                      focussing on just one specific
                                      aspect of the problem, and then
                                      once I've understood that one
                                      aspect, we can move forward from
                                      there?
                                      <div><br>
                                      </div>
                                      <div> - David</div>
                                    </div>
                                    <div class="gmail_extra"><br>
                                      <div class="gmail_quote">On Sat,
                                        Jan 2, 2016 at 11:46 AM, Imre
                                        Goretzki <span dir="ltr"><<a
                                            moz-do-not-send="true"
                                            href="mailto:goretzki.imre@gmail.com"
                                            target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:goretzki.imre@gmail.com">goretzki.imre@gmail.com</a></a>></span>
                                        wrote:<br>
                                        <blockquote class="gmail_quote"
                                          style="margin:0 0 0
                                          .8ex;border-left:1px #ccc
                                          solid;padding-left:1ex">
                                          <div bgcolor="#FFFFFF"
                                            text="#000000"> Mh ok, I
                                            guess I did not explained my
                                            problem well enough.<br>
                                            <br>
                                            The
                                            vtkPolyDataConnectivityFilter
                                            returns regions, either the
                                            largest, specified, seeded
                                            or all regions (your filter
                                            returns largest, seeded or
                                            all). I'm interessted in the
                                            following:<br>
                                            <br>
                                            - all regions<br>
                                            - specified regions.<br>
                                            <br>
                                            The problem is not the
                                            filter, the performance or
                                            possible memory leaks, I
                                            need the region's polydata
                                            representation because I
                                            have a second object
                                            (vtkImageData or
                                            vtkPolyData, binary mask)
                                            that has some additional
                                            information, that are not
                                            represented by the data (the
                                            input for the
                                            vtkImageConnectivityFilter).<br>
                                            <br>
                                            Imagine the input for the
                                            filter as image 1 and the
                                            mask as image 2. Both images
                                            have the same dimensions in
                                            all 3 directions (x, y, z)
                                            but contain different
                                            information.<br>
                                            <br>
                                            image 2 will be transformed
                                            to a binary image mask<br>
                                            <br>
                                            from image 1 i need to
                                            extract regions, but if some
                                            (unknown) regions have
                                            points that are located in
                                            the binary image mask, I do
                                            not want these regions to be
                                            contained in the extracted
                                            region list.<br>
                                            <br>
                                            So it's not about your
                                            filter or the performance,
                                            but I have some problems
                                            using this filter for my
                                            issue, because I cannot
                                            reach the region's polydata.<br>
                                            <br>
                                            I hope this helps.<span><font
                                                color="#888888"><br>
                                                <br>
                                                - Imre</font></span>
                                            <div>
                                              <div><br>
                                                <br>
                                                <div>Am 02.01.2016 um
                                                  18:54 schrieb David
                                                  Gobbi:<br>
                                                </div>
                                                <blockquote type="cite">
                                                  <div dir="ltr">Hi
                                                    Imre, Happy New
                                                    Year!
                                                    <div><br>
                                                    </div>
                                                    <div>I've read your
                                                      email few times,
                                                      and I feel that I
                                                      must be missing
                                                      some important
                                                      because there are
                                                      several things
                                                      that I don't
                                                      understand about
                                                      it.</div>
                                                    <div><br>
                                                    </div>
                                                    <div>The
                                                      vtkImageConnectivityFilter
                                                      is essentially
                                                      just a connected
                                                      component filter. 
                                                      In the output of
                                                      this filter, all
                                                      pixels outside the
                                                      mask will be
                                                      colored black
                                                      (they will have a
                                                      value of zero). 
                                                      So what I don't
                                                      understand about
                                                      your email is why
                                                      you say that
                                                      non-rectangular
                                                      regions are a
                                                      problem.  Are you
                                                      just worried about
                                                      the wasted memory?</div>
                                                    <div><br>
                                                    </div>
                                                    <div> - David</div>
                                                    <div><br>
                                                      <div
                                                        class="gmail_extra"><br>
                                                        <div
                                                          class="gmail_quote">On
                                                          Sat, Jan 2,
                                                          2016 at 9:00
                                                          AM, Imre
                                                          Goretzki <span
                                                          dir="ltr"><<a
moz-do-not-send="true" href="mailto:goretzki.imre@gmail.com"
                                                          target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:goretzki.imre@gmail.com">goretzki.imre@gmail.com</a></a>></span>
                                                          wrote:<br>
                                                          <blockquote
                                                          class="gmail_quote"
                                                          style="margin:0px
                                                          0px 0px
0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
                                                          <div
                                                          bgcolor="#FFFFFF"
                                                          text="#000000">
                                                          Hey David,<br>
                                                          <br>
                                                          first of all:
                                                          Happy new year
                                                          :)<br>
                                                          <br>
                                                          I have some
                                                          questions
                                                          about your
                                                          filter. First
                                                          of all in part
                                                          A of the
                                                          attached
                                                          image, is my
                                                          understanding
                                                          of extents, so
                                                          if you have a
                                                          region, you
                                                          will get the
                                                          x_min/x_max,
                                                          y_min/y_max
                                                          (and
                                                          z_min/z_max
                                                          for 3D). If
                                                          you do not
                                                          have
                                                          rectangular
                                                          regions than
                                                          you could have
                                                          some problems
                                                          (see part A
                                                          and B). In
                                                          part B you see
                                                          my mask. The
                                                          red rectangle
                                                          shows the case
                                                          that the 4
                                                          corners of a
                                                          2D region
                                                          cannot be
                                                          directly
                                                          checked,
                                                          because the
                                                          region that
                                                          lies within
                                                          this rectangle
                                                          has little
                                                          matches with
                                                          the mask (none
                                                          of the 4
                                                          corners are
                                                          within the
                                                          mask). The
                                                          green
                                                          rectangle has
                                                          3 out of 4
                                                          edges that lie
                                                          within the
                                                          mask.<br>
                                                          <br>
                                                          Part C shows
                                                          one of the
                                                          worst cases of
                                                          this approach
                                                          (using
                                                          extents)
                                                          because there
                                                          is so much
                                                          space that
                                                          does not
                                                          belong to the
                                                          actual region.<br>
                                                          <br>
                                                          My question:
                                                          Is it possible
                                                          to extend your
                                                          filter to
                                                          directly store
                                                          the region
                                                          data (for each
                                                          region, for
                                                          example as
                                                          vtkImageData)
                                                          if the
                                                          extraction
                                                          mode is set to
                                                          "All"?<span><font
color="#888888"><br>
                                                          <br>
                                                          - Imre</font></span>
                                                          <div>
                                                          <div><br>
                                                          <br>
                                                          <div>Am
                                                          29.12.2015 um
                                                          13:27 schrieb
                                                          Imre Goretzki:<br>
                                                          </div>
                                                          <blockquote
                                                          type="cite">
                                                          Hi David,<br>
                                                          <br>
                                                          thank you.
                                                          I'll take a
                                                          look at your
                                                          class.<br>
                                                          <br>
                                                          Regards<br>
                                                          Imre<br>
                                                          <br>
                                                          <div>Am
                                                          29.12.2015 um
                                                          13:07 schrieb
                                                          David Gobbi:<br>
                                                          </div>
                                                          <blockquote
                                                          type="cite">
                                                          <div dir="ltr">Hi

                                                          Imre,
                                                          <div><br>
                                                          </div>
                                                          <div>I have a
                                                          connectivity
                                                          filter that
                                                          works directly
                                                          on images, it
                                                          can label
                                                          connected
                                                          regions
                                                          according to
                                                          size and it
                                                          should be much
                                                          faster
                                                          (probably
                                                          1000x) than
                                                          doing voxel
                                                          checks via
                                                          polydata:</div>
                                                          <div><a
                                                          moz-do-not-send="true"
href="https://github.com/dgobbi/AIRS/blob/master/ImageSegmentation/vtkImageConnectivityFilter.h"
target="_blank"><a class="moz-txt-link-freetext" href="https://github.com/dgobbi/AIRS/blob/master/ImageSegmentation/vtkImageConnectivityFilter.h">https://github.com/dgobbi/AIRS/blob/master/ImageSegmentation/vtkImageConnectivityFilter.h</a></a></div>
                                                          <div>I'll
                                                          probably be
                                                          contributing
                                                          this filter to
                                                          VTK sometime
                                                          in the near
                                                          future.</div>
                                                          <div><br>
                                                          </div>
                                                          <div> - David</div>
                                                          <div><br>
                                                          <div
                                                          class="gmail_extra"><br>
                                                          <div
                                                          class="gmail_quote">On


                                                          Tue, Dec 29,
                                                          2015 at 4:02
                                                          AM, Imre
                                                          Goretzki <span
                                                          dir="ltr"><<a
moz-do-not-send="true" href="mailto:goretzki.imre@gmail.com"
                                                          target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:goretzki.imre@gmail.com">goretzki.imre@gmail.com</a></a>></span>
                                                          wrote:<br>
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                                                          Is there an
                                                          easier way in
                                                          ITK?<br>
                                                          <br>
                                                          Thanks<span><font
color="#888888"><br>
                                                          Imre</font></span>
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                                                          <br>
                                                          <div>Am
                                                          28.12.2015 um
                                                          23:38 schrieb
                                                          Imre Goretzki:<br>
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                                                          <blockquote
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                                                          Hey guys,<br>
                                                          <br>
                                                          I use the
                                                          vtkPolyDataConnectivityFilter
                                                          from polydata
                                                          to extract
                                                          several
                                                          different and
                                                          more or less
                                                          unknown
                                                          regions. <br>
                                                          My problem is
                                                          that I want to
                                                          extract
                                                          regions from
                                                          this filter,
                                                          but if I do
                                                          this, the
                                                          update process
                                                          for all
                                                          regions takes
                                                          up to
                                                          10minutes:<br>
                                                          <br>
filter->SetExtractionModeToAllRegions();<br>
filter->Update();<br>
                                                          ...<br>
                                                          <br>
                                                          for (int i =
                                                          0; i <
                                                          filter->GetNumberOfExtractedRegions();
                                                          i++)<br>
                                                          {<br>
                                                             
                                                          extractFilter->InitializeSpecifiedRegionList();<br>
                                                             
                                                          extractFilter->AddSpecifiedRegion(i);<br>
                                                             
                                                          extractFilter->Modified();<br>
                                                             
                                                          extractFilter->Update();<br>
                                                             
                                                          extractRegionData->DeepCopy(extractFilter->GetOutput());<br>
                                                          }<br>
extractFilter->InitializeSpecifiedRegionList();<br>
                                                          <br>
                                                          Background for
                                                          this: I want
                                                          to use the
                                                          points of each
                                                          region to
                                                          check whether
                                                          they lie
                                                          within an
                                                          object in my
                                                          binary<br>
                                                          mask image. So
                                                          the pipeline
                                                          would be like
                                                          this:<br>
                                                          <br>
                                                          1) Get all
                                                          Regions <br>
                                                              2) get
                                                          region <i>i</i><br>
                                                                   3)
                                                          get points of
                                                          region <i>i</i><br>
                                                                      
                                                          4) check if
                                                          point <i>j</i>
                                                          lies within
                                                          the binary
                                                          mask <i>B</i>    



                                                          (<i>B</i>_<i>j</i>
                                                          == 255)<br>
                                                                          


                                                          4a) if true
                                                          then add
                                                          region to the
                                                          extractFilter
                                                          and break
                                                          (-> next
                                                          region <i>i</i>)<br>
                                                                          


                                                          4b) if false
                                                          then continue
                                                          with next
                                                          point <i>j</i><br>
                                                          5) Mark all
                                                          regions red
                                                          (done easily)<br>
                                                          6) Mark some
                                                          regions green
                                                          that are above
                                                          a specific
                                                          size (can be
                                                          accessed with
                                                          filter->GetRegionSizes()



                                                          )<br>
                                                          7) Mark some
                                                          regions yellow
                                                          (the regions
                                                          that are
                                                          extracted
                                                          during step
                                                          1-4a) <br>
                                                          <br>
                                                          I do not know
                                                          if the
                                                          PolyDataConnectivityFilter
                                                          is the right
                                                          class for
                                                          this, I think
                                                          it is. <br>
                                                          If I store the
                                                          extractRegionData


                                                          in a vector,
                                                          all regions
                                                          have the same
                                                          number of
                                                          points (which
                                                          is kind of
                                                          strange) but
                                                          different
                                                          number of
                                                          cells (region
                                                          size == number
                                                          of cells is
                                                          correct).<br>
                                                          <br>
                                                          I would now
                                                          try to get the
                                                          points from
                                                          the cells and
                                                          check the
                                                          binary mask,
                                                          because the <br>
                                                          <br>
vtkPolyData->GetNumberOfPoints()<br>
                                                          <br>
                                                          and<br>
                                                          <br>
                                                          vtkPolyData->GetPoint(pointCounter,



                                                          point); <br>
                                                          <br>
                                                          are not
                                                          working
                                                          correctly in
                                                          this scenario
                                                          (all regions
                                                          are extracted
                                                          because every
                                                          single region
                                                          has every
                                                          point?<br>
                                                          i did not
                                                          verify my
                                                          guess but I
                                                          think there
                                                          would be the
                                                          problem)<br>
                                                          <br>
                                                          The binary
                                                          mask is a
                                                          vtkImageData,
                                                          that could be
                                                          transformed to
                                                          vtkPolyData.<br>
                                                          The input
                                                          image (already
                                                          filtered with
                                                          vtkMarchingCubes)


                                                          and the binary
                                                          mask have the
                                                          same
                                                          dimensions
                                                          (x,y,z).<br>
                                                          <br>
                                                          I hope you can
                                                          imagine what
                                                          I'm trying to
                                                          do and have
                                                          some tips for
                                                          me, if my
                                                          approach is
                                                          correct.<br>
                                                          <br>
                                                          Regards<br>
                                                          Imre</blockquote>
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