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<body class='hmmessage'><div dir='ltr'><br><br><div><hr id="stopSpelling">From: matthias.b@hotmail.com<br>To: dzenanz@gmail.com<br>Subject: RE: [ITK] Determine surface area of certain region in image<br>Date: Wed, 10 Aug 2016 18:15:39 +0200<br><br>
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<div dir="ltr">I'm sorry, I really don't get it Dženan,<div><br></div><div>Maybe another approach, I'm working with a 3D camera with a resolution of 5 by 5. Every pixel contains a X, Y and Z component, let's say in centimeters.</div><div>I put an object int front of the camera right in the center of the image, the object covers 3x3 pixels..</div><div><br></div><div>Now I want to have the surface area of this object, I now the object is located on the image like this <span style="font-size:12pt;">{</span><span style="font-size:12pt;">{0,0,0,0,0},</span><span style="font-size:12pt;">{0,1,<wbr>1,1,0},</span><span style="font-size:12pt;">{0,1,1,1,0},</span><span style="font-size:12pt;">{0,1,1,1,0}<wbr>,</span><span style="font-size:12pt;">{0,0,0,0,0}}</span></div><div><br><div>Xdata={{-4,-2,0,2,4},<span style="font-size:12pt;">{-4,-2,0,<wbr>2,4},</span><span style="font-size:12pt;">{-4,-2,0,2,4},</span><span style="font-size:12pt;">{-4,-2,0,2,<wbr>4},</span><span style="font-size:12pt;">{-4,-2,0,2,4}</span><span style="font-size:12pt;">}</span></div><div><span style="font-size:12pt;">Ydata=</span>{{3,2.5,2.1,2.5,2.2},{1.<wbr>4,1.2,1.3,1.1,1.1}<span style="font-size:12pt;">,{0,0,0,0,0},</span>{-3,-2.5,-2.1,-2.5,-2.2},{-1.<wbr>4,-1.2,-1.3,-1.1,-1.1}<span style="font-size:12pt;">}</span></div><div><span style="font-size:12pt;">Zdata={{0,0,0,0,0},</span><span style="font-size:12pt;">{0,0,0,0,0}<wbr>,</span><span style="font-size:12pt;">{0,0,0,0,0},</span><span style="font-size:12pt;">{0,0,0,0,0},</span><span style="font-size:12pt;">{0,0,<wbr>0,0,0}}</span></div><div><span style="font-size:12pt;"><br></span></div><div><span style="font-size:12pt;">So, is it possible to get the object surface area in real world, so in cm2 with the ITK library?</span></div><div><span style="font-size:12pt;"><br></span></div><div>Thank you for your effort</div><div><br></div><div><hr id="ecxstopSpelling">From: dzenanz@gmail.com<br>Date: Wed, 10 Aug 2016 11:19:28 -0400<br>Subject: Re: [ITK] Determine surface area of certain region in image<br>To: matthias.b@hotmail.com<br>CC: dan.muel@gmail.com; community@itk.org; blowekamp@mail.nih.gov<br><br><div dir="ltr"><div class="ecxgmail_default" style="font-family:verdana,sans-serif;font-size:small;">There are nine 1s in the LabelImage, which means that your object with label 1 is 9 pixels big. Content of the 3DImage is irrelevant. If the example LabelImage content you provided does not reflect what you want, you need to come up with a better LabelImage (a different, better segmentation), derived from 3DImage.</div></div><div class="ecxgmail_extra"><br><div class="ecxgmail_quote">On Wed, Aug 10, 2016 at 11:11 AM, Matthias B <span dir="ltr"><<a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a>></span> wrote:<br><blockquote class="ecxgmail_quote" style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr"><div>Thank you for the code</div><div><br></div>sp[0] and sp[1] is both 1 in my code. I don't get how I would get 12 in your example.<div>The 3DImage is also never used.</div><div><br></div><div>The spacing is also never absolute in my situation.<br><div>Ydata could also be like this<span style="font-size:12pt;">={{3,2.5,2.1,2.5,2.2},{1.<wbr>4,1.2,1.3,1.1,1.1},...}</span></div><div><br></div><div><div><hr>From: <a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@gmail.com</a><br>Date: Wed, 10 Aug 2016 09:58:32 -0400<span><br>Subject: Re: [ITK] Determine surface area of certain region in image<br>To: <a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a><br></span>CC: <a href="mailto:dan.muel@gmail.com" target="_blank">dan.muel@gmail.com</a>; <a href="mailto:community@itk.org" target="_blank">community@itk.org</a>; <a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a><div><div class="h5"><br><br><div dir="ltr"><div style="font-family:verdana,sans-serif;font-size:small;">3DImage of size 5x5x3, and LabelImage 5x5.</div><div style="font-family:verdana,sans-serif;font-size:small;"><br></div>Dim labelShapeStatistics = New simple.<wbr>LabelShapeStatisticsImageFilte<wbr>r()<br>labelShapeStatistics.Execute(<wbr>labelImage)<br>Dim perimeterValue= labelShapeStatistics.<wbr>GetPerimeter(1)<br>Dim pixelCount = labelShapeStatistics.<wbr>GetNumberOfPixels(1) //=9 in your example<br>Dim sp = labelImage.GetSpacing()<br>Dim surfaceArea=pixelCount*sp[0]*<wbr>sp[1] //sp[0]*sp[1] should be =1.25 to yield a total of 12 which you want<div><br></div><div>HTH,</div><div>Dženan</div></div><div><br><div>On Wed, Aug 10, 2016 at 9:48 AM, Matthias B <span dir="ltr"><<a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a>></span> wrote:<br><blockquote style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">I think an example is the best way to solve my problem.<br><br>Let us take following 3D Data with name 3DImage as itk.simple.image<div>Xdata={{-4,-2,0,2,4},<span style="font-size:12pt;">{-4,-2,0,<wbr>2,4},</span><span style="font-size:12pt;">{-4,-2,0,2,4},</span><span style="font-size:12pt;">{-4,-2,0,2,<wbr>4},</span><span style="font-size:12pt;">{-4,-2,0,2,4}</span><span style="font-size:12pt;">}</span></div><div><span style="font-size:12pt;">Ydata={{2,2,2,2,2},{1,1,1,1,1}<wbr>,{0,0,0,0,0},</span><span style="font-size:12pt;">{-1,-1,-1,-1,-1},<wbr>{-2,-2,-2,-2,-2}}</span></div><div><span style="font-size:12pt;">Zdata={{0,0,0,0,0},</span><span style="font-size:12pt;">{0,0,0,0,0}<wbr>,</span><span style="font-size:12pt;">{0,0,0,0,0},</span><span style="font-size:12pt;">{0,0,0,0,0},</span><span style="font-size:12pt;">{0,0,<wbr>0,0,0}}</span></div><div><span style="font-size:12pt;"><br></span></div><div><span style="font-size:12pt;">and LabelImage as </span><span style="font-size:12pt;">itk.simple.image</span></div><div><span style="font-size:12pt;">LabelImage={{</span><span style="font-size:12pt;">{0,0,0,0,0},</span><span style="font-size:12pt;">{0,1,<wbr>1,1,0},</span><span style="font-size:12pt;">{0,1,1,1,0},</span><span style="font-size:12pt;">{0,1,1,1,0}<wbr>,</span><span style="font-size:12pt;">{0,0,0,0,0}}</span></div><div><span style="font-size:12pt;"><br></span></div><div><span style="font-size:12pt;">The surface area with label 1 should be 12.</span></div><div>Which steps (<span style="font-size:12pt;">C# or C++) </span><span style="font-size:12pt;">do I need to take to solve this? </span></div><div><br></div><div>Thank you guys</div><div><div><br></div><div><div><hr>From: <a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@gmail.com</a><br>Date: Wed, 10 Aug 2016 09:27:05 -0400<span><br>Subject: Re: [ITK] Determine surface area of certain region in image<br>To: <a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a><br></span>CC: <a href="mailto:community@itk.org" target="_blank">community@itk.org</a>; <a href="mailto:dan.muel@gmail.com" target="_blank">dan.muel@gmail.com</a>; <a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a><div><div><br><br><div dir="ltr"><div style="font-family:verdana,sans-serif;font-size:small;">Sorry, I have confused <a href="https://itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1LabelShapeStatisticsImageFilter.html" target="_blank">LabelShapeStatistics</a> with <a href="https://itk.org/Doxygen/html/classitk_1_1LabelStatisticsImageFilter.html" target="_blank">LabelStatistics</a> filter.</div><div style="font-family:verdana,sans-serif;font-size:small;"><br></div><div style="font-family:verdana,sans-serif;font-size:small;">With label shape statistics, there is no intensity image, only the label image which you are already using as input.</div><div style="font-family:verdana,sans-serif;font-size:small;"><br></div><div style="font-family:verdana,sans-serif;font-size:small;">You generally don't mix (add) label and intensity images, you just keep them separate and know which two are a pair. For label statistics, you simply set two inputs like in this <a href="https://itk.org/Wiki/ITK/Examples/ImageProcessing/LabelStatisticsImageFilter" target="_blank">example</a>.</div><div style="font-family:verdana,sans-serif;font-size:small;"><br></div><div style="font-family:verdana,sans-serif;font-size:small;">Regards</div></div><div><br><div>On Wed, Aug 10, 2016 at 9:19 AM, Matthias B <span dir="ltr"><<a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a>></span> wrote:<br><blockquote style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">I understand, but how do I add the label on the 3D image programmatically?<div>preferable in C#, but C++ is also ok.</div><div><br></div><div><span>Thank you for your help<br></span><div><hr>From: <a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@gmail.com</a><br>Date: Wed, 10 Aug 2016 09:14:35 -0400<span><br>Subject: Re: [ITK] Determine surface area of certain region in image<br>To: <a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a><br></span>CC: <a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>; <a href="mailto:dan.muel@gmail.com" target="_blank">dan.muel@gmail.com</a>; <a href="mailto:community@itk.org" target="_blank">community@itk.org</a><div><div><br><br><div dir="ltr"><div style="font-family:verdana,sans-serif;font-size:small;">The 3D image where the label will be applied is need for statistics such as mean, min and max values. If you don't care about those, you can supply the same image as both label and original (intensity) image. Or you can supply an empty (all black) image there.</div><div style="font-family:verdana,sans-serif;font-size:small;"><br></div><div style="font-family:verdana,sans-serif;font-size:small;">HTH,</div><div style="font-family:verdana,sans-serif;font-size:small;">Dženan</div></div><div><br><div>On Wed, Aug 10, 2016 at 8:47 AM, Matthias B <span dir="ltr"><<a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a>></span> wrote:<br><blockquote style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">Thank you for answering <span style="font-family:verdana,sans-serif;font-size:10pt;">Dženan</span>,<div><br></div><div>ok<span style="font-size:12pt;">, the perimeter attribute is what I need.</span></div><div><span style="font-size:12pt;"><br></span></div><div>Problem is that I don't see a way where I can</div><div>1. Choose a label image to define the region</div><div>2. Choose the 3D Image where the label will be aplied</div><div><br></div><div>At this moment it looks for me that the label image already contains the 3D data, which confuses me.<br><div><br><div><hr>From: <a href="mailto:dzenanz@gmail.com" target="_blank">dzenanz@gmail.com</a><br>Date: Wed, 10 Aug 2016 08:32:53 -0400<span><br>Subject: Re: [ITK] Determine surface area of certain region in image<br></span>To: <a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a><br>CC: <a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>; <a href="mailto:community@itk.org" target="_blank">community@itk.org</a><div><div><br><br><div dir="ltr"><div style="font-family:verdana,sans-serif;font-size:small;">Hi Matthias,</div><div style="font-family:verdana,sans-serif;font-size:small;"><br></div><div style="font-family:verdana,sans-serif;font-size:small;">perimeter should be surface area in 3D (which you can divide by 2 to eliminate back side if you have a very flat object). In 2D image, it is the circumference. In 2D image, you can get object's surface area by counting how many pixels it has and then multiplying that by the size of each pixel (spacing[0]*spacing[1]).</div><div style="font-family:verdana,sans-serif;font-size:small;"><br></div><div style="font-family:verdana,sans-serif;font-size:small;">Regards,</div><div style="font-family:verdana,sans-serif;font-size:small;">Dženan</div></div><div><br><div>On Wed, Aug 10, 2016 at 2:40 AM, Matthias B <span dir="ltr"><<a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a>></span> wrote:<br><blockquote style="border-left:1px #ccc solid;padding-left:1ex;">
<div><div dir="ltr">Thank you for answering!<div><br></div><div>At this moment I get the perimeter in pixel units (not the surface area of my X,Y-data) of my labeled image.</div><div>I have also really no idea how to use my 3D data with a labeled image. <span style="font-size:12pt;">I see no way how to add 3D data to a LabelMap for example.</span></div><div><br></div><div>This is what I have at the moment.</div><div><div>Dim labelShapeStatistics = New simple.LabelShapeStatisticsIma<wbr>geFilter()</div><div>labelShapeStatistics.Execute(l<wbr>abelImage)</div><div>Dim perimeterValue= labelShapeStatistics.GetPerime<wbr>ter(1)</div><div><br></div><div>Thanks for any help, Matthias</div><div><br></div><div><div><br></div><br></div><div><div><hr>From: <a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a><br>To: <a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a><br>CC: <a href="mailto:community@itk.org" target="_blank">community@itk.org</a><br>Subject: Re: [ITK] Determine surface area of certain region in image<br>Date: Tue, 9 Aug 2016 15:58:56 +0000</div><div><div><br><br>
Hello,
<div><br>
</div>
<div>You should look into the label map framework [1]. In particular the LabelImageToShapeLabelMapFilte<wbr>r[2] and the Perimeter attribute [3] [4].</div>
<div><br>
</div>
<div>HTH,</div>
<div>Brad</div>
<div><br>
</div>
<div>[1] <a href="http://hdl.handle.net/1926/584" target="_blank">http://hdl.handle.net/1926<wbr>/584</a></div>
<div>[2] <a href="https://itk.org/Doxygen/html/classitk_1_1LabelImageToShapeLabelMapFilter.html" target="_blank">https://itk.org/Doxygen/ht<wbr>ml/classitk_1_1LabelImageToSha<wbr>peLabelMapFilter.html</a></div>
<div>[3] <a href="https://itk.org/Doxygen/html/classitk_1_1ShapeLabelObject.html#aff1209e925293c15775520ef89e97afb" target="_blank">https://itk.org/Doxygen/ht<wbr>ml/classitk_1_1ShapeLabelObjec<wbr>t.html#aff1209e925293c15775520<wbr>ef89e97afb</a></div>
<div>[4] <a href="http://hdl.handle.net/10380/3342" target="_blank">http://hdl.handle.net/1038<wbr>0/3342</a></div>
<div><br>
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<div>On Aug 9, 2016, at 11:50 AM, Matthias B <<a href="mailto:matthias.b@hotmail.com" target="_blank">matthias.b@hotmail.com</a>> wrote:</div>
<br>
<div>
<div dir="ltr" style="font-family:Calibri;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;">
Hello ITK-community,
<div><br>
</div>
<div>At the moment I'm working with 3D Images with following structure: 100x80x3. Every pixel contains a X,Y,Z value.<br>
I want to calculate the surface area of a certain region that I have defined with a boolean 2D-Image (100x80).</div>
<div>The surface area should only be calculated with the X,Y-data.</div>
<div><br>
</div>
<div>In Matlab I have experience with this by using the function bwboundaries on the boolean image. This function determines the indices of the the boundaries in clockwise direction. Next I take the corresponding X,Y values of the indices so I can
calculate the surface area with the function polyarea. <br>
</div>
<div><br>
</div>
<div>Is this possbile with the ITK-library?</div>
<div><br>
</div>
<div>Thank you for your help guys.</div>
<div><br>
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