<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Hui Tang,<div><br></div><div>You can definitively modify existing code to add your own term, and that was one of the reason we came up with this new design for ITKv4: to be able to add easily new terms to any kind of PDE...</div><div><br></div><div>Can't help very much here...</div><div><br></div><div>Good luck,</div><div>Arnaud</div><div><br></div><div><div><div>On Oct 5, 2011, at 4:18 PM, Hui Tang wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear Arnaud,</div> <div> </div> <div>Thanks for the very quick reply; So I am right, there is no GAC in v4 yet:)</div> <div> </div> <div>I am not meaning combining v4 with v3, but modify v3 by adding a new term on PDE. I will try and let you know if I succeed:)</div> <div> </div> <div>Thanks a lot</div> <div> </div> <div>Best,</div> <div> </div> <div>Hui<br><br></div> <div class="gmail_quote">On Wed, Oct 5, 2011 at 4:14 PM, Arnaud Gelas <span dir="ltr"><<a href="mailto:Arnaud_Gelas@hms.harvard.edu">Arnaud_Gelas@hms.harvard.edu</a>></span> wrote:<br> <blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> <div style="WORD-WRAP: break-word">Dear Hui Tang, <div><br></div> <div>The ITKv4 level-set framework is not backward compatible with the ITKv3's one!</div> <div><br></div> <div>So it is not possible to mix v3 implementation with v4 ones. Especially the notion of terms did not exist back then...</div> <div>We are in the process of reimplementing GAC in the v4 framework, but it is not yet available (even on the master branch).</div> <div>I can keep you informed whenever it gets implemented, or if you want you could get involved in the development process and help in the implementation (which should not be too complicated at this point).</div> <div><br></div> <div>Best,</div> <div>Arnaud</div> <div><br></div> <div> <div> <div class="im"> <div>On Oct 5, 2011, at 4:05 PM, Hui Tang wrote:</div><br></div> <blockquote type="cite"> <div>Dear Arnaud,</div> <div> </div> <div class="im"> <div>I managed to modify that in itkLevelSetEquationChanAndVeseInternalTerm, but in update function but in there the m_Mean is used.</div> <div> </div> <div>No I find if I should combine regional term with GAC, I will go back to ITK3 and modify that in <font color="#010001" size="2"><font color="#010001" size="2"><font color="#010001" size="2"><font color="#010001" size="2"></font></font></font></font></div><p>itkGeodesicActiveContourAndRegionLevelSetFunction::CalculateSpeedImage<font size="2">(), the regional term in PDE will be -(I-Imean)^2 </font></p> <div>Is that right to do it in itkGeodesicActiveContourAndRegionLevelSetFunction?</div> <div> </div> <div>Thanks:)</div> <div> </div> <div>Best,</div> <div> </div> <div>Hui<br><br></div></div> <div> <div></div> <div class="h5"> <div class="gmail_quote"> <blockquote style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> <div style="WORD-WRAP: break-word"> <div> <div> <div> <div> <div>On Oct 3, 2011, at 3:55 AM, Hui Tang wrote:</div><br> <blockquote type="cite">Dear Arnaud,<br><br>Thanks for the reply!!<br>I left yestoday for washing and sleeeping, I am sorry for not reply immediately.<br>I am hacking itkLevelSetEquationChanAndVeseInternalTerm.*, but so far I did not succeed yet, I will let you know and contribute my code when it works properly!<br> Thanks again.<br><br>Best,<br><br>Hui<br><br> <div class="gmail_quote">On Sun, Oct 2, 2011 at 10:20 PM, Arnaud Gelas <span dir="ltr"><<a href="mailto:arnaud_gelas@hms.harvard.edu" target="_blank">arnaud_gelas@hms.harvard.edu</a>></span> wrote:<br> <blockquote style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0pt 0pt 0pt 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><u></u> <div text="#000000" bgcolor="#ffffff">Dear Hui,<br><br>In ITK3, the "evolution" class inherits from a ProcessObject and you are right this is the typical way to add one more input to a filter, to benefit from ITK's pipeline architecture.<br> <br>Here, LevelSetEquationChanAndVeseInternalTerm inherits from LevelSetEquationTermBase, which inherits from Object. Thus a term is not a filter, there is no input, no output.<br>You can also add as many internal members. You can now decide what is going to be inside your term.<br> <br>You can definitively add another InputImagePointer m_MeanImage.<br><br>BTW, are you hacking itkLevelSetEquationChanAndVeseInternalTerm.* ? <br><font color="#888888"><br>Arnaud</font> <div> <div></div> <div><br><br>On 10/02/2011 04:03 PM, Hui Tang wrote: <blockquote type="cite"> <div><font color="#000000">Dear Arnaud,</font></div> <div> </div> <div><font color="#000000">thanks for the quick reply!!!</font></div> <div> </div> <div><font color="#000000">Yes you are very right, I need to do that by m_Mean = m_MeanImage->GetPixel( iP ).</font></div> <div> </div> <div><font color="#000000">By the way in ITK3 I used <font size="2"><font size="2">this->ProcessObject::SetNthInput(1,InputImageType* image) to add one more image as input, but in ITK 4, it seems that ProcessObject is not a member function of <font size="2"><font size="2">itkLevelSetEquationChanAndVeseInternalTerm or <font color="#010001" size="2"><font color="#010001" size="2"><p>LevelSetEquationTermBase.</p><p>I guess I can add one more class member InputImageType* m_MeanImage?</p><p>Thanks again for the reply.</p> <div> <br></div><p>Best,</p> <div> <br></div><p>Hui</p></font></font></font></font></font></font></font><font color="#000000"><br></font></div> <div><font color="#000000">Please, let us know if it works.</font></div> <div><font color="#000000"><br><br></font></div> <div class="gmail_quote"><font color="#000000">On Sun, Oct 2, 2011 at 9:21 PM, Arnaud Gelas <span dir="ltr"><<a href="mailto:Arnaud_Gelas@hms.harvard.edu" target="_blank">Arnaud_Gelas@hms.harvard.edu</a>></span> wrote:<br> </font> <blockquote style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> <div style="WORD-WRAP: break-word"><font color="#000000">Hi Hui, </font> <div><br></div> <div><font color="#000000">The principle of Chan and Vese formulation is to assume there are two parts in your image: background and foreground and each of them are represented by a constant mean value.</font></div> <div><font color="#000000">In the implementation, we did follow the same principle, e.g. the mean is a scalar if you are working with scalar images, a vector if you are working with vector images, etc.</font></div> <div><font color="#000000"><br></font></div> <div><font color="#000000">So, now you want to create a new term / formulation (there might be a specific name for that, but I am not aware of it).</font></div> <div><font color="#000000">Once you provide the mean image, you need to replace m_Mean by the pixel value for the given input location iP. In your special case, most likely you would only need to change m_Mean by m_MeanImage->GetPixel( iP )</font></div> <div><font color="#000000"><br></font></div> <div><font color="#000000">Please, let us know if it works.</font></div> <div><font color="#000000"><br></font></div> <div><font color="#000000">Best,</font></div> <div><font color="#000000">Arnaud</font></div> <div> <div> <div><font color="#000000"><br></font></div> <div><font color="#000000"> </font></div> <div> <div> <div><font color="#000000">On Oct 2, 2011, at 1:55 PM, Hui Tang wrote:</font></div><br> <blockquote type="cite"> <div><font color="#000000">Dear Arnaud,</font></div> <div><font color="#000000"> </font></div> <div><font color="#000000">That works!!Thanks!</font></div> <div><font color="#000000">Now may I ask if my mean intensity is a constant over time but varies in the image, so I will have a mean intensity image, how can I add that to interal term? I know how to get and set image to get the mean intensity image, but in update(), it seems that this->mean can only be a scalar.......</font></div> <div><font color="#000000"> </font></div> <div><font color="#000000">Do you have any idea on solve this?</font></div> <div><font color="#000000"> </font></div> <div><font color="#000000">thanks,</font></div> <div><font color="#000000"> </font></div> <div><font color="#000000">Best,</font></div> <div><font color="#000000"> </font></div> <div><font color="#000000">Hui</font></div> <div><br><br><font color="#000000"> </font></div> <div class="gmail_quote"><font color="#000000">On Fri, Sep 30, 2011 at 3:14 PM, Arnaud Gelas <span dir="ltr"><<a href="mailto:arnaud_gelas@hms.harvard.edu" target="_blank">arnaud_gelas@hms.harvard.edu</a>></span> wrote:<br> </font> <blockquote style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"> <div text="#000000" bgcolor="#ffffff"><font color="#000000">Hi Hui,<br><br>Sorry, there was a typo in my previous email :-/...<br><br>Here you go:<br><br> $ git checkout -t origin/v4.0b01<br><br>Here are the *.h you are looking for<br> <br>$ find . | grep itkBinaryImageToWhitakerSparseLevelSetAdaptor.h<br>./Modules/Segmentation/LevelSetsv4/include/itkBinaryImageToWhitakerSparseLevelSetAdaptor.hxx<br>./Modules/Segmentation/LevelSetsv4/include/itkBinaryImageToWhitakerSparseLevelSetAdaptor.h<br> <br>To be able to use the LevelSetsv4, you should either build ITK with all modules, or explicitly turn on the LevelSetsv4 one (which is part of the Segmentation group).<br><br>Please keep the conversation on the mailing list, other users may have the same problem.<br> <br>Best,<br>Arnaud </font> <div> <div><br><br><font color="#000000">On 09/30/2011 09:06 AM, Hui Tang wrote: </font> <blockquote type="cite"> <div><font color="#000000">Dear Arnaud, </font></div> <div><font color="#000000"> </font></div> <div><font color="#000000">Thanks for your help. I still can not find itkBinaryImageToWhitakerSparseLevelSetAdaptor.h in v4.0b1. </font></div> <div><font color="#000000">git shows the version number, so it should be right.....</font></div> <div><font color="#000000">Best,</font></div> <div><font color="#000000"> </font></div> <div><font color="#000000">Hui</font></div> <div class="gmail_quote"><font color="#000000">On Thu, Sep 29, 2011 at 7:05 PM, Hui Tang <span dir="ltr"><<a href="mailto:tanghui.seu@gmail.com" target="_blank">tanghui.seu@gmail.com</a>></span> wrote:<br></font> <blockquote style="BORDER-LEFT: rgb(204,204,204) 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><p><font color="#000000">Hi arnaud thanks a loooooot for this! I will try, I will let you know how it works:) best hui </font></p> <div class="gmail_quote"><font color="#000000">Op 29 sep. 2011 18:55 schreef "Gelas, Arnaud Joel Florent" <</font><a href="mailto:Arnaud_Gelas@hms.harvard.edu" target="_blank"><font color="#000000">Arnaud_Gelas@hms.harvard.edu</font></a><font color="#000000">> het volgende: </font> <div> <div><br type="attribution"><font color="#000000">> Hi Hui Tang,<br>> <br>> I am really happy to see you are interested and are testing the new level set infrastructure!<br>> <br>> If you get this error, I can only assume that you are now using the git master version of ITK, this file has been remove recently from the repository...<br> > I would strongly recommend to stick to ITK tags, since API keeps on changing all around the place in the toolkit.<br>> <br>> Here is how you'd get the last tagged version:<br>> <br>> $ git fetch --all<br> > $ git checkout -t origin/v4.0b1<br>> <br>> With this version, you should be able to find itkBinaryImageToWhitakerSparseLevelSetAdaptor.h<br>> <br>> If you are more adventurous, and want to be part of the development, you can use master, but expect API / files / class name to change.<br> > You can also create a gerrit account to review patches (instructions are on the wiki). Note that all contributions / inputs on this effort are welcome!!<br>> <br>> Now regarding your question, this is really easy to make it happened in the v4 infrastructure. You have two possibilities:<br> > <br>> 1- grab the code from iternal or external term (depending on your case); copy the code; you modify and remove the part in which the mean gets updated.<br>> and you add itkSetMacro to set the mean at the beginning.<br> > <br>> 2- you inherit, might need to change some method to virtual (if needed, let me know that'd be easy to fix).<br>> <br>> If you need more details on how to proceed for 1 or 2, just let me know, we can definitively give you some more details on how to proceed.<br> > <br>> Thanks,<br>> <br>> Best,<br>> Arnaud<br>> <br>> ________________________________________<br>> From: Hui Tang [</font><a href="mailto:tanghui.seu@gmail.com" target="_blank"><font color="#000000">tanghui.seu@gmail.com</font></a><font color="#000000">]<br> > Sent: Thursday, September 29, 2011 12:20 PM<br>> To: Gelas, Arnaud Joel Florent<br>> Subject: Questions about ITK4<br>> <br>> Dear Arnaud,<br>> <br>> How are you?<br>> I am using ITK4, but this headfile "itkBinaryImageToWhitakerSparseLevelSetAdaptor.h" can not be found in ITK4. Did I do anything wrong?<br> > And maybe you could help me with another question:) in chanvase model, if my I would like to have a fixed average intensity ("c1") for the foreground how can I implement that using ITK4?<br>> <br>> Thanks so much.<br> > <br>> Looking forward to your reply.<br>> <br>> Best,<br>> <br>> Hui Tang<br></font></div></div></div></blockquote></div><br></blockquote><br></div></div></div></blockquote></div><br></blockquote></div> <br></div></div></div></div></blockquote></div><br></blockquote><br></div></div></div></blockquote></div><br></blockquote></div><br></div></div></div></div></blockquote></div><br></div></div></blockquote></div><br></div></div> </blockquote></div><br></blockquote></div><br></div></body></html>