Message

From gee@rad.upenn.edu Fri Mar 1 16:35:49 2002 From: gee@rad.upenn.edu (James Gee) Date: Fri, 1 Mar 2002 11:35:49 -0500 Subject: [Insight-users] Evolution of itk::fem:: namespace In-Reply-To: <5.0.2.1.0.20020225064338.023cf6f0@pop.nycap.rr.com> Message-ID: <00d501c1c13f$27424740$bc1cd4aa@dorado2> This is a multi-part message in MIME format. ------=_NextPart_000_00D6_01C1C115.3E6C3F40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable In addition to linear analysis, ITK does plan to support FEM programming of non-linear/dynamical problems. This will hopefully facilitate development of biomedical modeling applications, ranging from image reconstruction to biomechanics. =20 =20 -----Original Message----- From: insight-users-admin@public.kitware.com [mailto:insight-users-admin@public.kitware.com] On Behalf Of Will Schroeder Sent: Monday, February 25, 2002 6:46 AM To: Nils Hanssen; insight-users@public.kitware.com Subject: Re: [Insight-users] Evolution of itk::fem:: namespace The FEM classes are fairly complete in that they do what's required for linear analysis. They need a fair amount of work to integrate into the rest of the system; and to improve the solver. Is there something in particular that you have in mind? Will At 10:37 AM 2/25/2002 +0100, Nils Hanssen wrote: Hi all, =20 I was wondering myself what will be the future of the itk::fem:: namespace in itk. Are there plans to incorporate a full-fledged fem-package within itk or is this just a small project? =20 Thank you for any information about that! =20 Regards, Nils ----------------------------------=20 Nils Han=DFen=20 Surgical Systems Laboratory=20 research center c a e s a r=20 Friedensplatz 16=20 53111 Bonn, Germany=20 fon: +49-228-9656-247=20 fax: +49-228-9656-111=20 http://www.caesar.de/ssl =20 ------=_NextPart_000_00D6_01C1C115.3E6C3F40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Message

In=20 addition to linear analysis, ITK does plan to support FEM programming of = non-linear/dynamical problems. This will hopefully facilitate = development=20 of biomedical modeling applications, ranging from image reconstruction = to=20 biomechanics.

-----Original Message-----
From:=20 insight-users-admin@public.kitware.com=20 [mailto:insight-users-admin@public.kitware.com] On Behalf Of = Will=20 Schroeder
Sent: Monday, February 25, 2002 6:46 = AM
To: Nils=20 Hanssen; insight-users@public.kitware.com
Subject: Re:=20 [Insight-users] Evolution of itk::fem:: = namespace

The FEM=20 classes are fairly complete in that they do what's required for linear = analysis. They need a fair amount of work to integrate into the rest = of the=20 system; and to improve the solver. Is there something in particular = that you=20 have in mind?
Will

At 10:37 AM 2/25/2002 +0100, Nils = Hanssen=20 wrote:

Hi=20 all,

I was wondering = myself what=20 will be the future of the itk::fem:: namespace in itk. Are there = plans to=20 incorporate a full-fledged fem-package within itk or is this just a = small=20 project?

Thank you = for any=20 information about that!

Regards,
Nils

----------------------------------=20
Nils = Han=DFen
Surgical Systems = Laboratory=20
research center c a = e s a=20 r
Friedensplatz=20 16
53111 = Bonn,=20 Germany
fon: = +49-228-9656-247
fax:=20 +49-228-9656-111
http://www.caesar.de/ssl
=

------=_NextPart_000_00D6_01C1C115.3E6C3F40-- From tsing22199@mails.tsinghua.edu.cn Mon Mar 4 07:10:59 2002 From: tsing22199@mails.tsinghua.edu.cn (fj) Date: Mon, 4 Mar 2002 15:10:59 +0800 Subject: [Insight-users] problem with FLTK Message-ID: <002e01c1c34b$bcbd9870$c73d6fa6@medsoft.eea.tsinghua.edu.cn> This is a multi-part message in MIME format. ------=_NextPart_000_002B_01C1C38E.CA745B00 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: base64 RGVhciBJVEsgdXNlcnM6DQogIEkgaGF2ZSBjb21waWxlZCBkZW1vIHByb2plY3QgZnJvbSBGTFRL IDEuMC4xMS5hbmQgdGhlbiBJIHVzZSBjbWFrZSB0byBpbnN0YWxsIElUSyxidXQgd2hlbiBJIGNv bXBpbGUgLlZDIHRvbGQgbWUgdGhhdCB0aGVyZSBpcyBzb210aGluZyBjaGFuZ2VkIGZyb20gc29t ZSAqLmRzcCxhc2sgbWUgdG8gcmVsb2FkIHRoZSAqLmRzcCAsSSBzZWxlY3QgIm5vIi5UTyB0aGUg ZW5kICx0aGVyZSBhbHNvIHNvbWUgZXJyb3IuDQpUaGUgZGV0YWlsIGlzIDoNCkNvbmZpZ3VyYXRp b246IElWaWV3IC0gV2luMzIgRGVidWctLS0tLS0tLS0tLS0tLS0tLS0tLQ0KUGVyZm9ybWluZyBD dXN0b20gQnVpbGQgU3RlcCBvbiBFOi9URU1QL2l0ay9pdGsvSVRLU291cmNlV2luMzIvSW5zaWdo dC9VbnN1cHBvcnRlZC9NZXRhSW1hZ2UvSVZpZXcvQ01ha2VMaXN0cy50eHQNCkNvbXBpbGluZy4u Lg0KSVZpZXcuY3h4DQpFOlxURU1QXGl0a1xpdGtcSVRLU291cmNlV2luMzJcSW5zaWdodFxVbnN1 cHBvcnRlZFxNZXRhSW1hZ2VcSVZpZXdcSVZpZXcuY3h4KDExKSA6IGZhdGFsIGVycm9yIEMxMDgz OiBDYW5ub3Qgb3BlbiBpbmNsdWRlIGZpbGU6ICdGTC9GbC5IJzogTm8gc3VjaCBmaWxlIG9yIGRp cmVjdG9yeQ0KSVZpZXdHVUkuY3h4DQpFOlxURU1QXGl0a1xpdGtcSVRLU291cmNlV2luMzJcSW5z aWdodFxVbnN1cHBvcnRlZFxNZXRhSW1hZ2VcSVZpZXdcSVZpZXdHVUkuaCg1KSA6IGZhdGFsIGVy cm9yIEMxMDgzOiBDYW5ub3Qgb3BlbiBpbmNsdWRlIGZpbGU6ICdGTC9GbC5IJzogTm8gc3VjaCBm aWxlIG9yIGRpcmVjdG9yeQ0KSVZpZXdHVUlCYXNlLmN4eA0KRTpcVEVNUFxpdGtcaXRrXElUS1Nv dXJjZVdpbjMyXEluc2lnaHRcVW5zdXBwb3J0ZWRcTWV0YUltYWdlXElWaWV3XElWaWV3R1VJQmFz ZS5oKDUpIDogZmF0YWwgZXJyb3IgQzEwODM6IENhbm5vdCBvcGVuIGluY2x1ZGUgZmlsZTogJ0ZM L0ZsLkgnOiBObyBzdWNoIGZpbGUgb3IgZGlyZWN0b3J5DQpHZW5lcmF0aW5nIENvZGUuLi4NCkVy cm9yIGV4ZWN1dGluZyBjbC5leGUuDQoNCkFMTF9CVUlMRCAtIDMgZXJyb3IocyksIDQ5IHdhcm5p bmcocykNCndoYXQgaXMgbWF0dGVyPw0KDQpBbmQgaWYgSSBkbyBub3QgSVRLIGV4YW1wbGVzLCBT byBJIGRvIG5vdCBuZWVkIEZMVEsuU28gd2hhdCBJIHdpbGwgbm90IHNlbGVjdCBpbiBDbWFrZT8/ Pz8/Pw0KdGhhbmtzIA0KDQp5b3VycyAgIEZhbmcgSmluZw0KDQo= ------=_NextPart_000_002B_01C1C38E.CA745B00 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgY29udGVudD0idGV4dC9odG1sOyBjaGFyc2V0PWdi MjMxMiIgaHR0cC1lcXVpdj1Db250ZW50LVR5cGU+DQo8TUVUQSBjb250ZW50PSJNU0hUTUwgNS4w MC4zMzE1LjI4NzAiIG5hbWU9R0VORVJBVE9SPg0KPFNUWUxFPjwvU1RZTEU+DQo8L0hFQUQ+DQo8 Qk9EWSBiZ0NvbG9yPSNmZmZmZmY+DQo8RElWPjxGT05UIHNpemU9Mj5EZWFyIElUSyB1c2Vyczo8 QlI+Jm5ic3A7IEkgaGF2ZSBjb21waWxlZCBkZW1vIHByb2plY3QgZnJvbSANCkZMVEsgMS4wLjEx LmFuZCB0aGVuIEkgdXNlIGNtYWtlIHRvIGluc3RhbGwgSVRLLGJ1dCB3aGVuIEkgY29tcGlsZSAu VkMgdG9sZCBtZSANCnRoYXQgdGhlcmUgaXMgc29tdGhpbmcgY2hhbmdlZCBmcm9tIHNvbWUgKi5k c3AsYXNrIG1lIHRvIHJlbG9hZCB0aGUgKi5kc3AgLEkgDQpzZWxlY3QgIm5vIi5UTyB0aGUgZW5k ICx0aGVyZSBhbHNvIHNvbWUgZXJyb3IuPEJSPlRoZSBkZXRhaWwgaXMgDQo6PEJSPkNvbmZpZ3Vy YXRpb246IElWaWV3IC0gV2luMzIgRGVidWctLS0tLS0tLS0tLS0tLS0tLS0tLTxCUj5QZXJmb3Jt aW5nIEN1c3RvbSANCkJ1aWxkIFN0ZXAgb24gDQpFOi9URU1QL2l0ay9pdGsvSVRLU291cmNlV2lu MzIvSW5zaWdodC9VbnN1cHBvcnRlZC9NZXRhSW1hZ2UvSVZpZXcvQ01ha2VMaXN0cy50eHQ8QlI+ Q29tcGlsaW5nLi4uPEJSPklWaWV3LmN4eDxCUj5FOlxURU1QXGl0a1xpdGtcSVRLU291cmNlV2lu MzJcSW5zaWdodFxVbnN1cHBvcnRlZFxNZXRhSW1hZ2VcSVZpZXdcSVZpZXcuY3h4KDExKSANCjog ZmF0YWwgZXJyb3IgQzEwODM6IENhbm5vdCBvcGVuIGluY2x1ZGUgZmlsZTogJ0ZML0ZsLkgnOiBO byBzdWNoIGZpbGUgb3IgDQpkaXJlY3Rvcnk8QlI+SVZpZXdHVUkuY3h4PEJSPkU6XFRFTVBcaXRr XGl0a1xJVEtTb3VyY2VXaW4zMlxJbnNpZ2h0XFVuc3VwcG9ydGVkXE1ldGFJbWFnZVxJVmlld1xJ Vmlld0dVSS5oKDUpIA0KOiBmYXRhbCBlcnJvciBDMTA4MzogQ2Fubm90IG9wZW4gaW5jbHVkZSBm aWxlOiAnRkwvRmwuSCc6IE5vIHN1Y2ggZmlsZSBvciANCmRpcmVjdG9yeTxCUj5JVmlld0dVSUJh c2UuY3h4PEJSPkU6XFRFTVBcaXRrXGl0a1xJVEtTb3VyY2VXaW4zMlxJbnNpZ2h0XFVuc3VwcG9y dGVkXE1ldGFJbWFnZVxJVmlld1xJVmlld0dVSUJhc2UuaCg1KSANCjogZmF0YWwgZXJyb3IgQzEw ODM6IENhbm5vdCBvcGVuIGluY2x1ZGUgZmlsZTogJ0ZML0ZsLkgnOiBObyBzdWNoIGZpbGUgb3Ig DQpkaXJlY3Rvcnk8QlI+R2VuZXJhdGluZyBDb2RlLi4uPEJSPkVycm9yIGV4ZWN1dGluZyBjbC5l eGUuPEJSPjxCUj5BTExfQlVJTEQgLSAzIA0KZXJyb3IocyksIDQ5IHdhcm5pbmcocyk8QlI+d2hh dCBpcyBtYXR0ZXI/PEJSPjxCUj5BbmQgaWYgSSBkbyBub3QgSVRLIGV4YW1wbGVzLCANClNvIEkg ZG8gbm90IG5lZWQgRkxUSy5TbyB3aGF0IEkgd2lsbCBub3Qgc2VsZWN0IGluIENtYWtlPz8/Pz8/ PEJSPnRoYW5rcyANCjxCUj48QlI+eW91cnMmbmJzcDsmbmJzcDsgRmFuZyBKaW5nPEJSPjwvRk9O VD48L0RJVj48L0JPRFk+PC9IVE1MPg0K ------=_NextPart_000_002B_01C1C38E.CA745B00-- From 赵晨光" Hi everyone, I am a new user to ITL. I got two questions to ask. (1) I have downloaded the ITL source code, configed it with CMake, and compiled it with MSVC++6.0 sucessfully. But I can not run ShapeDetection example correctlly. Here is my operation steps: a. run ShapeDetection.exe (It's a DOS executable program) b. Input file name: bt.001.pgm c. Input big image endian? [y|n]: Y (What's the meaning of "image endian"? something like edge?) d. Input image size: 512 512 1 (I want to input a 2-d image) e. PGM output directory: c:\ f. Writing PGM files of the output volume but I can find nothing under the directory of C:\. What's the problem? Thanks for your feedback. (2) I want to understand related sourcecode of ITK, including some basic functions or classes, such as image reading and writing functions. I think ITK has a wonderful programming style. To learn from it will greatly facilitate my research and communication with other domain experts. Where shall I start from? Waiting for your help. thanks. My research interest is in Content-based image retrieval in medicine. --http://www.eyou.com --稳定可靠的免费电子信箱语音邮件移动书签日历服务网络存储...亿邮未尽 From Matthias.Guenther@advancedmri.com Mon Mar 4 18:30:06 2002 From: Matthias.Guenther@advancedmri.com (Matthias Guenther) Date: Mon, 04 Mar 2002 10:30:06 -0800 Subject: [Insight-users] a question about ShapeDetection. Message-ID: <3C83BD2E.73916CA8@AdvancedMRI.com> Hi, I guess, ShapeDetection needs a raw data file, AFAIK in unsigned short. "" wrote: > > Hi everyone, > > I am a new user to ITL. I got two questions to ask. > (1) I have downloaded the ITL source code, configed it with CMake, and > compiled it with MSVC++6.0 sucessfully. But I can not run ShapeDetection > example correctlly. Here is my operation steps: > a. run ShapeDetection.exe (It's a DOS executable program) > b. Input file name: bt.001.pgm > c. Input big image endian? [y|n]: Y (What's the meaning of "image endian"? > something like edge?) It means the order of the bytes. Does the high value byte comes first or not? > d. Input image size: 512 512 1 (I want to input a 2-d image) > e. PGM output directory: c:\ > f. Writing PGM files of the output volume > but I can find nothing under the directory of C:\. What's the problem? Thanks > for your feedback. > Bye, Matthias From Matthias.Guenther@advancedmri.com Mon Mar 4 18:30:56 2002 From: Matthias.Guenther@advancedmri.com (Matthias Guenther) Date: Mon, 04 Mar 2002 10:30:56 -0800 Subject: [Insight-users] problem with FLTK Message-ID: <3C83BD60.7A65772C@AdvancedMRI.com> Hi Fang, I had the same problem. The FLTK directory seems to be missing in this particular project. You can include this directory in VC6 by just adding it under Tools->Options Subcard Directories, Show Directories for "Include Files". Then it should work. Bye, Matthias > fj wrote: > > Dear ITK users: > I have compiled demo project from FLTK 1.0.11.and then I use cmake > to install ITK,but when I compile .VC told me that there is somthing > changed from some *.dsp,ask me to reload the *.dsp ,I select "no".TO > the end ,there also some error. > The detail is : > Configuration: IView - Win32 Debug-------------------- > Performing Custom Build Step on > E:/TEMP/itk/itk/ITKSourceWin32/Insight/Unsupported/MetaImage/IView/CMakeLists.txt > Compiling... > IView.cxx > E:\TEMP\itk\itk\ITKSourceWin32\Insight\Unsupported\MetaImage\IView\IView.cxx(11) > : fatal error C1083: Cannot open include file: 'FL/Fl.H': No such file > or directory > IViewGUI.cxx > E:\TEMP\itk\itk\ITKSourceWin32\Insight\Unsupported\MetaImage\IView\IViewGUI.h(5) > : fatal error C1083: Cannot open include file: 'FL/Fl.H': No such file > or directory > IViewGUIBase.cxx > E:\TEMP\itk\itk\ITKSourceWin32\Insight\Unsupported\MetaImage\IView\IViewGUIBase.h(5) > : fatal error C1083: Cannot open include file: 'FL/Fl.H': No such file > or directory > Generating Code... > Error executing cl.exe. > > ALL_BUILD - 3 error(s), 49 warning(s) > what is matter? > > And if I do not ITK examples, So I do not need FLTK.So what I will not > select in Cmake?????? > thanks > > yours Fang Jing From lng@insightful.com Mon Mar 4 18:43:28 2002 From: lng@insightful.com (Lydia Ng) Date: Mon, 4 Mar 2002 10:43:28 -0800 Subject: [Insight-users] a question about ShapeDetection. Message-ID: Hi, The ShapeDetection app was originally intended to serve as an example to how to use the fast marching algorithm in ITK - as such the user interface is very rudimentary. Although the underlying code works for 2 or 3D, the ShapeDetection app has been hard-wired to require the input to be a single raw volume and in signed short (16 bits). The other constraint is that it can only handle 3D data (with at least 4 slices). > c. Input image big endian? [y|n]: Y (What's the meaning of "image endian"? > something like edge?) Endian-ness refers to how multi-byte numbers are stored. There should be numerous article on the web. e.g. http://www.cs.umass.edu/~verts/cs32/endian.html - Lydia > -----Original Message----- > From: =D5=D4=B3=BF=B9=E2 [mailto:zhaocg@eyou.com] > Sent: Sunday, March 03, 2002 11:36 PM > To: insight-users@public.kitware.com > Subject: [Insight-users] a question about ShapeDetection. >=20 >=20 > Hi everyone, >=20 > I am a new user to ITL. I got two questions to ask. > (1) I have downloaded the ITL source code, configed it with CMake, and > compiled it with MSVC++6.0 sucessfully. But I can not run=20 > ShapeDetection > example correctlly. Here is my operation steps: > a. run ShapeDetection.exe (It's a DOS executable program) =20 > b. Input file name: bt.001.pgm > c. Input big image endian? [y|n]: Y (What's the meaning=20 > of "image endian"? > something like edge?) > d. Input image size: 512 512 1 (I want to input a 2-d image) > e. PGM output directory: c:\ > f. Writing PGM files of the output volume=20 > but I can find nothing under the directory of C:\. What's the=20 > problem? Thanks > for your feedback. >=20 > (2) I want to understand related sourcecode of ITK, including=20 > some basic > functions or classes, such as image reading and writing=20 > functions. I think ITK > has a wonderful programming style. To learn from it will=20 > greatly facilitate my > research and communication with other domain experts. Where=20 > shall I start > from? Waiting for your help. thanks. > My research interest is in Content-based image retrieval=20 > in medicine. >=20 >=20 >=20 >=20 >=20 > --http://www.eyou.com > --=CE=C8=B6=A8=BF=C9=BF=BF=B5=C4=C3=E2=B7=D1=B5=E7=D7=D3=D0=C5=CF=E4 = =D3=EF=D2=F4=D3=CA=BC=FE =D2=C6=B6=AF=CA=E9=C7=A9 = =C8=D5=C0=FA=B7=FE=CE=F1 =20 > =CD=F8=C2=E7=B4=E6=B4=A2...=D2=DA=D3=CA=CE=B4=BE=A1 >=20 >=20 > _______________________________________________ > Insight-users mailing list > Insight-users@public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users >=20 From luis.ibanez@kitware.com Tue Mar 5 22:26:29 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Tue, 05 Mar 2002 17:26:29 -0500 Subject: [Insight-users] problem with FLTK References: <002e01c1c34b$bcbd9870$c73d6fa6@medsoft.eea.tsinghua.edu.cn> Message-ID: <3C854615.4050402@kitware.com> Hi, When you ran CMake, did you click in the check box that says "Advanced" ? That should present to you additional options for FLTK including the path for the includes, the path for the library and the path to "Fluid". The current errors reported by VC++ are due to the lack of a correct path to the FLTK includes. Hope that helps. Luis ================================================ fj wrote: > Dear ITK users: > I have compiled demo project from FLTK 1.0.11.and then I use cmake to > install ITK,but when I compile .VC told me that there is somthing > changed from some *.dsp,ask me to reload the *.dsp ,I select "no".TO > the end ,there also some error. > The detail is : > Configuration: IView - Win32 Debug-------------------- > Performing Custom Build Step on > E:/TEMP/itk/itk/ITKSourceWin32/Insight/Unsupported/MetaImage/IView/CMakeLists.txt > Compiling... > IView.cxx > E:\TEMP\itk\itk\ITKSourceWin32\Insight\Unsupported\MetaImage\IView\IView.cxx(11) > : fatal error C1083: Cannot open include file: 'FL/Fl.H': No such file > or directory > IViewGUI.cxx > E:\TEMP\itk\itk\ITKSourceWin32\Insight\Unsupported\MetaImage\IView\IViewGUI.h(5) > : fatal error C1083: Cannot open include file: 'FL/Fl.H': No such file > or directory > IViewGUIBase.cxx > E:\TEMP\itk\itk\ITKSourceWin32\Insight\Unsupported\MetaImage\IView\IViewGUIBase.h(5) > : fatal error C1083: Cannot open include file: 'FL/Fl.H': No such file > or directory > Generating Code... > Error executing cl.exe. > > ALL_BUILD - 3 error(s), 49 warning(s) > what is matter? > > And if I do not ITK examples, So I do not need FLTK.So what I will not > select in Cmake?????? > thanks > > yours Fang Jing > From dkulkarni@uh.edu Fri Mar 15 15:11:48 2002 From: dkulkarni@uh.edu (Dhananjay Kulkarni) Date: Fri, 15 Mar 2002 09:11:48 -0600 Subject: [Insight-users] Question about thresholding Message-ID: Is there any method available with ITK to Threshold an image ? All the examples I looked at had some Filter which in turn would use the Threshold function. I am looking at one single method. Any comments and Suggestions would be greatly appreciated. Thanks, -danny From luis.ibanez@kitware.com Fri Mar 15 16:07:27 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Fri, 15 Mar 2002 11:07:27 -0500 Subject: [Insight-users] Question about thresholding References: Message-ID: <3C921C3F.6000300@kitware.com> Hi Dhananjay, You can use the "itkThresholdImageFilter". http://www.itk.org/Insight/Doxygen/html/classitk_1_1ThresholdImageFilter.html#a3 you connect your image as imput, select the threshold in the filter and got a thresholded image as output. a 3D example will look like: typedef itk::Image myImageType; myImageType::Point inputImage = GotTheInputImageSomeHow(); typedef itk::ThresholdImageFilter < myImageType > myFilterType; myFilterType::Pointer filter = myFilterType::New(); filter->SetInput( inputImage ); // connect the input image filter->ThresholdAbove( 100 ); filter->SetOusideValue( 255 ); // set to 255 al the pixels above 100 filter->Update(); // run the filter. myImageType::Pointer outputImage = filter->GetOutput(); It may look like a lot of lines just for thresholding :-) but keep in mind that ITK has a data pipeline desing so in principle the rest of your processing is following and you will write the whole set of code only once. Note that the filter is leaving unchanged the pixels with values below 100. There is a test program that can also help you to play with the filter without writing a new project. Enable "TEST" in CMake and go to: Insight/Testitng/BasicFilters the test is called : itkThresholdImageFilterTest.cxx Keep in mind that tests are not exactly intended to be used as examples or as tutorials. They are designed to excersice all the functinalities of the particular class being tested.....so you will see a lot of code around that is there only to test that everything is working. Let us know if you run into any problem. Thanks Luis ====================================== Dhananjay Kulkarni wrote: >Is there any method available with ITK to Threshold an image ? >All the examples I looked at had some Filter which in turn would use the >Threshold function. >I am looking at one single method. > >Any comments and Suggestions would be greatly appreciated. > >Thanks, >-danny > >_______________________________________________ >Insight-users mailing list >Insight-users@public.kitware.com >http://public.kitware.com/mailman/listinfo/insight-users > From dkulkarni@uh.edu Fri Mar 15 16:12:04 2002 From: dkulkarni@uh.edu (Dhananjay Kulkarni) Date: Fri, 15 Mar 2002 10:12:04 -0600 Subject: [Insight-users] Linking Errors Message-ID: Thanks to Peiter Vos for the suggestions. I am trying to write a simple thresholding example. I have used the ThresholdImageFilter but while writing the file, I get the following linking errors . My Code to Write is : ....... itk::RawImageWriter::Pointer writer = itk::RawImageWriter::New(); writer->SetFileName("output.pgm"); writer->SetInput(threshold->GetOutput()); writer->Write(); ... Linking errors are ::: Compiling... main.cpp Linking... main.obj : error LNK2001: unresolved external symbol "public: virtual void __thiscall itk::Writer::Write(void)" (?Write@Writer@itk@@UAEXXZ) main.obj : error LNK2001: unresolved external symbol "protected: virtual __thiscall itk::Writer::~Writer(void)" (??1Writer@itk@@MAE@XZ) main.obj : error LNK2001: unresolved external symbol "protected: virtual void __thiscall itk::Writer::PrintSelf(class std::basic_ostream > &,class itk::Indent)const " (?PrintSelf@Writer@itk@@MBEXAAV?$basic_ostream@ DU?$char_traits@D@std@@@std@@VIndent@2@@Z) main.obj : error LNK2001: unresolved external symbol "protected: __thiscall itk::Writer::Writer(void)" (??0Writer@itk@@IAE@XZ) Debug/ITKImageTest.exe : fatal error LNK1120: 4 unresolved externals Error executing link.exe. ITKImageTest.exe - 5 error(s), 0 warning(s) I have used the settings specified in the VC_Custom_project.doc and they are working except for this linking error. Please help. From luis.ibanez@kitware.com Fri Mar 15 16:17:40 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Fri, 15 Mar 2002 11:17:40 -0500 Subject: [Insight-users] Linking Errors References: Message-ID: <3C921EA4.9070006@kitware.com> Hi Dhananjay The IO functionality in ITK is in an independent library: ITKIO.lib You may want to verify that you are linking with this library too. Luis =========================== Dhananjay Kulkarni wrote: >Thanks to Peiter Vos for the suggestions. >I am trying to write a simple thresholding example. > >I have used the ThresholdImageFilter but while writing the file, I get the >following linking errors . > >My Code to Write is : > > >....... >itk::RawImageWriter::Pointer writer = > itk::RawImageWriter::New(); > writer->SetFileName("output.pgm"); > writer->SetInput(threshold->GetOutput()); > > writer->Write(); > >... > > > >Linking errors are ::: > > >Compiling... >main.cpp >Linking... >main.obj : error LNK2001: unresolved external symbol "public: virtual void >__thiscall itk::Writer::Write(void)" (?Write@Writer@itk@@UAEXXZ) >main.obj : error LNK2001: unresolved external symbol "protected: virtual >__thiscall itk::Writer::~Writer(void)" (??1Writer@itk@@MAE@XZ) >main.obj : error LNK2001: unresolved external symbol "protected: virtual >void __thiscall itk::Writer::PrintSelf(class std::basic_ostreamstd::char_traits > &,class itk::Indent)const " >(?PrintSelf@Writer@itk@@MBEXAAV?$basic_ostream@ >DU?$char_traits@D@std@@@std@@VIndent@2@@Z) >main.obj : error LNK2001: unresolved external symbol "protected: __thiscall >itk::Writer::Writer(void)" (??0Writer@itk@@IAE@XZ) >Debug/ITKImageTest.exe : fatal error LNK1120: 4 unresolved externals >Error executing link.exe. > >ITKImageTest.exe - 5 error(s), 0 warning(s) > > > >I have used the settings specified in the VC_Custom_project.doc and they are >working except for this linking error. > > >Please help. > >_______________________________________________ >Insight-users mailing list >Insight-users@public.kitware.com >http://public.kitware.com/mailman/listinfo/insight-users > From eduardo@dsc.ulpgc.es Fri Mar 15 20:23:40 2002 From: eduardo@dsc.ulpgc.es (Eduardo =?iso-8859-15?Q?Su=E1rez?=) Date: Fri, 15 Mar 2002 20:23:40 +0000 Subject: [Insight-users] ITK compilation error Message-ID: <3C92584C.93F2142E@dsc.ulpgc.es> Hello all I'm a newbie to ITK and i am trying to compile it. I could jump over the first error by patching /home/eduardo/Insight/Utilities/png/Makefile, but i don't know how to fix the second. What am i doing wrong? Thanks, -Eduardo Second error: c++ -g -O2 -ftemplate-depth-50 -DFEM_EXPORTS -fPIC -I/home/eduardo/Insight/Code/Numerics/FEM -I/home/eduardo/Insight -I/home/eduardo/Insight/Code/Numerics -I/home/eduardo/Insight/Code/Common -I/home/eduardo/Insight/Code/Numerics/vxl -I/home/eduardo/Insight/Code/Numerics/vxl -I/home/eduardo/Insight/Code/Numerics/vxl/vcl -I/home/eduardo/Insight/Code/Numerics/vxl/vcl -I/home/eduardo/Insight/Utilities/png -I/home/eduardo/Insight/Utilities/zlib -D_PTHREADS -DFEM_USE_SMART_POINTERS -c /home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx -o itkFEMNodeXY.o In file included from /home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx:23: /home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.h: In member function `virtual itk::SmartPointer itk::fem::NodeXY::Clone() const': /home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.h:39: conversion from `itk::SmartPointer' to non-scalar type `itk::SmartPointer' requested /home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx: In function `itk::SmartPointer itk::fem::::NewNodeXY()': /home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx:134: conversion from `itk::SmartPointer' to non-scalar type `itk::SmartPointer' requested make[7]: *** [itkFEMNodeXY.o] Error 1 make[6]: *** [default_target] Error 2 make[5]: *** [default_target_FEM] Error 2 make[4]: *** [default_target] Error 2 make[3]: *** [default_target_Numerics] Error 2 make[2]: *** [default_target] Error 2 make[1]: *** [default_target_Code] Error 2 make: *** [default_target] Error 2 ********************************************************** First error, just in case: c++ -rdynamic -shared -g -O2 -ftemplate-depth-50 -o libitkpng.so pngget.o pngrio.o pngwrite.o png.o pngmem.o pngrtran.o pngtrans.o pngwtran.o pngerror.o pngpread.o pngrutil.o pngvcrd.o pngwutil.o pnggccrd.o pngread.o pngset.o pngwio.o -L/home/eduardo/Insight/Code/Common -L/home/eduardo/Insight/Code/Numerics/vxl -litkzlib -lpthread -ldl -Wl,-rpath,/home/eduardo/Insight/Code/Common:/home/eduardo/Insight/Code/Numerics/vxl /usr/bin/ld: cannot find -litkzlib collect2: ld returned 1 exit status make[5]: *** [libitkpng.so] Error 1 make[4]: *** [default_target] Error 2 make[3]: *** [default_target_png] Error 2 make[2]: *** [default_target] Error 2 make[1]: *** [default_target_Utilities] Error 2 make: *** [default_target] Error 2 Patch to /home/eduardo/Insight/Utilities/png/Makefile: 107c107 < $(itkpng_SRC_OBJS) -L/home/eduardo/Insight/Code/Common -L/home/eduardo/Insight/Code/Numerics/vxl -L/home/eduardo/Insight/Utilities/zlib -litkzlib -lpthread -ldl -Wl,-rpath,/home/eduardo/Insight/Code/Common:/home/eduardo/Insight/Code/Numerics/vxl --- > $(itkpng_SRC_OBJS) -L/home/eduardo/Insight/Code/Common -L/home/eduardo/Insight/Code/Numerics/vxl -litkzlib -lpthread -ldl -Wl,-rpath,/home/eduardo/Insight/Code/Common:/home/eduardo/Insight/Code/Numerics/vxl ************************************************** From luis.ibanez@kitware.com Fri Mar 15 20:47:15 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Fri, 15 Mar 2002 15:47:15 -0500 Subject: [Insight-users] ITK compilation error References: <3C92584C.93F2142E@dsc.ulpgc.es> Message-ID: <3C925DD3.80605@kitware.com> Hi Eduardo, ITK has a framework for computing Finite Elements with the aim of performing deformable registration. This framework can use SmartPointers as an option. Please turn this option "OFF". You can do that when by CMake at the top level of the Insight directory and looking for the option: FEM_USE_SMART_POINTERS Just put an OFF in front of it. You can do this by using the Curses interface to cmake, or you can do it by editing the CMakeCache.txt file. Then run cmake as you did for the installation. The makefiles should be fixed after that. BTW all the Makefiles are generated by CMake, patching Makefiles is always a shortcut but it is better to fix the source of the configuration problem at the CMake level. Otherwise you may have to fix *a lot* of makefiles :-) Please let us know if you encounter any further problems. Thanks Luis PS. What was the first problem that you encounter and solved by modifying /home/eduardo/Insight/Utilities/png/Makefile ?? =========================================== Eduardo Su醨ez wrote: >Hello all > >I'm a newbie to ITK and i am trying to compile it. I could jump over the >first error by patching /home/eduardo/Insight/Utilities/png/Makefile, >but i don't know how to fix the second. What am i doing wrong? > >Thanks, >-Eduardo > >Second error: > >c++ -g -O2 -ftemplate-depth-50 -DFEM_EXPORTS -fPIC >-I/home/eduardo/Insight/Code/Numerics/FEM -I/home/eduardo/Insight >-I/home/eduardo/Insight/Code/Numerics >-I/home/eduardo/Insight/Code/Common >-I/home/eduardo/Insight/Code/Numerics/vxl >-I/home/eduardo/Insight/Code/Numerics/vxl >-I/home/eduardo/Insight/Code/Numerics/vxl/vcl >-I/home/eduardo/Insight/Code/Numerics/vxl/vcl >-I/home/eduardo/Insight/Utilities/png >-I/home/eduardo/Insight/Utilities/zlib -D_PTHREADS >-DFEM_USE_SMART_POINTERS -c >/home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx -o >itkFEMNodeXY.o >In file included from >/home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx:23: >/home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.h: In member > function `virtual itk::SmartPointer > itk::fem::NodeXY::Clone() const': >/home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.h:39: conversion > from `itk::SmartPointer' to non-scalar type > `itk::SmartPointer' requested >/home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx: In > function `itk::SmartPointer > itk::fem::::NewNodeXY()': >/home/eduardo/Insight/Code/Numerics/FEM/itkFEMNodeXY.cxx:134: conversion > from `itk::SmartPointer' to non-scalar type > `itk::SmartPointer' requested >make[7]: *** [itkFEMNodeXY.o] Error 1 >make[6]: *** [default_target] Error 2 >make[5]: *** [default_target_FEM] Error 2 >make[4]: *** [default_target] Error 2 >make[3]: *** [default_target_Numerics] Error 2 >make[2]: *** [default_target] Error 2 >make[1]: *** [default_target_Code] Error 2 >make: *** [default_target] Error 2 > >********************************************************** >First error, just in case: > >c++ -rdynamic -shared -g -O2 -ftemplate-depth-50 -o libitkpng.so >pngget.o pngrio.o pngwrite.o png.o pngmem.o pngrtran.o pngtrans.o >pngwtran.o pngerror.o pngpread.o pngrutil.o pngvcrd.o pngwutil.o >pnggccrd.o pngread.o pngset.o pngwio.o >-L/home/eduardo/Insight/Code/Common >-L/home/eduardo/Insight/Code/Numerics/vxl -litkzlib -lpthread -ldl >-Wl,-rpath,/home/eduardo/Insight/Code/Common:/home/eduardo/Insight/Code/Numerics/vxl >/usr/bin/ld: cannot find -litkzlib >collect2: ld returned 1 exit status >make[5]: *** [libitkpng.so] Error 1 >make[4]: *** [default_target] Error 2 >make[3]: *** [default_target_png] Error 2 >make[2]: *** [default_target] Error 2 >make[1]: *** [default_target_Utilities] Error 2 >make: *** [default_target] Error 2 > >Patch to /home/eduardo/Insight/Utilities/png/Makefile: > >107c107 >< $(itkpng_SRC_OBJS) -L/home/eduardo/Insight/Code/Common >-L/home/eduardo/Insight/Code/Numerics/vxl >-L/home/eduardo/Insight/Utilities/zlib -litkzlib -lpthread -ldl >-Wl,-rpath,/home/eduardo/Insight/Code/Common:/home/eduardo/Insight/Code/Numerics/vxl >--- > >> $(itkpng_SRC_OBJS) -L/home/eduardo/Insight/Code/Common -L/home/eduardo/Insight/Code/Numerics/vxl -litkzlib -lpthread -ldl -Wl,-rpath,/home/eduardo/Insight/Code/Common:/home/eduardo/Insight/Code/Numerics/vxl >> > >************************************************** >_______________________________________________ >Insight-users mailing list >Insight-users@public.kitware.com >http://public.kitware.com/mailman/listinfo/insight-users > From zjzhang@ee.cuhk.edu.hk Sun Mar 17 06:53:28 2002 From: zjzhang@ee.cuhk.edu.hk (zhangzhijun) Date: Sun, 17 Mar 2002 14:53:28 +0800 Subject: [Insight-users] about TPS and EBS Message-ID: <001701c1cd80$71be7620$1223bd89@ee.cuhk.edu.hk> This is a multi-part message in MIME format. ------=_NextPart_000_0014_01C1CDC3.7FA633C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all:=20 I want to use the thin plate spline and elastic body spline = implementation in itk but I found that the speed of the thin plate spline is very slow, much = slower than that in VTK and the ebs is even slower, also, the result is different = with VTK. I use totally 80 point for a 181*217*181 data warp, I dont' know whether = the number=20 of points for the warp is ok. regards, zhang zhijun ------=_NextPart_000_0014_01C1CDC3.7FA633C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear all:

I want=20 to use the thin plate spline and elastic body spline implementation in=20 itk

but I found that the speed of the thin = plate spline=20 is very slow, much slower than

that in VTK and the ebs is even = slower, also,=20 the result is different with VTK.

I use totally 80 point for a = 181*217*181 data warp,=20 I dont' know whether the number

of points for the warp is = ok.

regards,

zhang zhijun

------=_NextPart_000_0014_01C1CDC3.7FA633C0-- From hanssen@caesar.de Mon Mar 18 10:29:36 2002 From: hanssen@caesar.de (Nils Hanssen) Date: Mon, 18 Mar 2002 11:29:36 +0100 Subject: [Insight-users] Inconsistent .dll linkage in memory.h on Win2K with Visual 6.0 Message-ID: <000d01c1ce67$cd9d5c80$0607010a@ssn4006> Hi all, I get the following error in memory.h when compiling a project with some other libraries like vtk and qt. All libraries where built with "Multithreaded DLL DEBUG": memory.h(68) : warning C4273: '_memccpy' : inconsistent DLL linkage. dllexport assumed Does itk replace functions from the run-time libraries? How can I avoid this error? Thanks in advance for any suggestions! Regards, Nils From luis.ibanez@kitware.com Mon Mar 18 16:07:08 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Mon, 18 Mar 2002 11:07:08 -0500 Subject: [Insight-users] Inconsistent .dll linkage in memory.h on Win2K with Visual 6.0 References: <000d01c1ce67$cd9d5c80$0607010a@ssn4006> Message-ID: <3C9610AC.2060402@kitware.com> Hi Nils, That looks strange,... ITK is not replacing functions from the run-time libraries. The error should be related to a mix of dlls at link time. Could you please post the full list of libraries that you are linking with. (maybe cut pasting that from the Visual Built window... or from the Project/Settings/Link/Input window) Does the original error message has more lines ? Do you receive this message for other functions too or only for "_memccpy()" ? Thanks Luis ==================================== Nils Hanssen wrote: >Hi all, > >I get the following error in memory.h when compiling a project with some >other libraries like vtk and qt. All libraries where built with >"Multithreaded DLL DEBUG": > >memory.h(68) : warning C4273: '_memccpy' : inconsistent DLL linkage. >dllexport assumed > >Does itk replace functions from the run-time libraries? >How can I avoid this error? > >Thanks in advance for any suggestions! > > >Regards, >Nils > >_______________________________________________ >Insight-users mailing list >Insight-users@public.kitware.com >http://public.kitware.com/mailman/listinfo/insight-users > From luis.ibanez@kitware.com Mon Mar 18 16:21:06 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Mon, 18 Mar 2002 11:21:06 -0500 Subject: [Insight-users] about TPS and EBS References: <001701c1cd80$71be7620$1223bd89@ee.cuhk.edu.hk> Message-ID: <3C9613F2.80506@kitware.com> Hi Zhangzhijun, ITK ThinPlateSpline and ElasticBody splines are implemented using a common framework under the class itk::KernelTransform. This classes have not been optimized for speed yet. So, it expected that VTK's version could be running faster. We are interested in pushing performance to the same level anyways :-) However, 1) The numerical results should be the same between itk and vtk 2) The time of execution for itk::TPS and itk::EBS should be the same because the Point transformation is done by a common code in KernelTransform. If you found EBS to be slower than the TPS... there should be a problem with the code or with the use of the class. Did you made this comparison in a compact application that you could send to us ? Otherwise we can make some tests in our side in order to identify time consumption. One of the suspect things done in KernelTransfom is the common extraction of submatrices from the WMatrix, which can be a costly operation. I'll look in to that. Thanks Luis ======================================================== zhangzhijun wrote: > > > Dear all: > > I want to use the thin plate spline and elastic body spline > implementation in itk > > but I found that the speed of the thin plate spline is very slow, much > slower than > > that in VTK and the ebs is even slower, also, the result is different > with VTK. > > I use totally 80 point for a 181*217*181 data warp, I dont' know > whether the number > > of points for the warp is ok. > > > > > > regards, > > zhang zhijun > From hanssen@caesar.de Mon Mar 18 17:09:53 2002 From: hanssen@caesar.de (Nils Hanssen) Date: Mon, 18 Mar 2002 18:09:53 +0100 Subject: AW: [Insight-users] Inconsistent .dll linkage in memory.h on Win2K with Visual 6.0 In-Reply-To: <3C9610AC.2060402@kitware.com> Message-ID: <001901c1ce9f$b96bdba0$0607010a@ssn4006> Hi Luis, the problem is "solved"! When i was starting with itk, i had the following error: error C2039: 'seekdir' : is no element of 'ios'. You told me, that I should include to get the proper version of the streams library. When I know put a #include _before_ each #include , there get no warning regarding memory.h any more. Thank you very much for your help Luis! Regards, Nils -----Ursprungliche Nachricht----- Von: insight-users-admin@public.kitware.com [mailto:insight-users-admin@public.kitware.com]Im Auftrag von Luis Ibanez Gesendet: Montag, 18. Marz 2002 17:07 An: Nils Hanssen Cc: insight-users@public.kitware.com Betreff: Re: [Insight-users] Inconsistent .dll linkage in memory.h on Win2K with Visual 6.0 Hi Nils, That looks strange,... ITK is not replacing functions from the run-time libraries. The error should be related to a mix of dlls at link time. Could you please post the full list of libraries that you are linking with. (maybe cut pasting that from the Visual Built window... or from the Project/Settings/Link/Input window) Does the original error message has more lines ? Do you receive this message for other functions too or only for "_memccpy()" ? Thanks Luis ==================================== Nils Hanssen wrote: >Hi all, > >I get the following error in memory.h when compiling a project with some >other libraries like vtk and qt. All libraries where built with >"Multithreaded DLL DEBUG": > >memory.h(68) : warning C4273: '_memccpy' : inconsistent DLL linkage. >dllexport assumed > >Does itk replace functions from the run-time libraries? >How can I avoid this error? > >Thanks in advance for any suggestions! > > >Regards, >Nils > >_______________________________________________ >Insight-users mailing list >Insight-users@public.kitware.com >http://public.kitware.com/mailman/listinfo/insight-users > _______________________________________________ Insight-users mailing list Insight-users@public.kitware.com http://public.kitware.com/mailman/listinfo/insight-users From dgobbi@irus.rri.ca Mon Mar 18 17:21:57 2002 From: dgobbi@irus.rri.ca (David Gobbi) Date: Mon, 18 Mar 2002 12:21:57 -0500 Subject: [Insight-users] about TPS and EBS In-Reply-To: <3C9613F2.80506@kitware.com> Message-ID: Hi Zhang, I'm interested in this too, since I'm partially responsible for the VTK TPS implementation. Note that when you use the VTK TPS you should specify which basis function to use, either R() or R2LogR(). I'm not sure which one ITK uses by default, it is possible that ITK automatically selects the correct basis function depending on the dimensionality of the transformation. - David -- David Gobbi, MSc dgobbi@irus.rri.ca Advanced Imaging Research Group Robarts Research Institute, University of Western Ontario On Mon, 18 Mar 2002, Luis Ibanez wrote: > > Hi Zhangzhijun, > > ITK ThinPlateSpline and ElasticBody splines are implemented > using a common framework under the class itk::KernelTransform. > > This classes have not been optimized for speed yet. So, it expected > that VTK's version could be running faster. We are interested in > pushing performance to the same level anyways :-) > > > However, > 1) The numerical results should be the same between itk and vtk > 2) The time of execution for itk::TPS and itk::EBS should be the > same because the Point transformation is done by a common > code in KernelTransform. If you found EBS to be slower than > the TPS... there should be a problem with the code or with the > use of the class. > > Did you made this comparison in a compact application that you > could send to us ? > > Otherwise we can make some tests in our side in order to identify > time consumption. One of the suspect things done in KernelTransfom > is the common extraction of submatrices from the WMatrix, which > can be a costly operation. > > > I'll look in to that. > > > Thanks > > Luis > > ======================================================== > > zhangzhijun wrote: > > > > > > > Dear all: > > > > I want to use the thin plate spline and elastic body spline > > implementation in itk > > > > but I found that the speed of the thin plate spline is very slow, much > > slower than > > > > that in VTK and the ebs is even slower, also, the result is different > > with VTK. > > > > I use totally 80 point for a 181*217*181 data warp, I dont' know > > whether the number > > > > of points for the warp is ok. > > > > > > > > > > > > regards, > > > > zhang zhijun > > > > > > > _______________________________________________ > Insight-users mailing list > Insight-users@public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users > From luis.ibanez@kitware.com Mon Mar 18 18:27:28 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Mon, 18 Mar 2002 13:27:28 -0500 Subject: [Insight-users] [Fwd: Building examples with ITK] Message-ID: <3C963190.4040500@kitware.com> This is a multi-part message in MIME format. --------------040604000709090003000207 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit --------------040604000709090003000207 Content-Type: message/rfc822; name="Building examples with ITK" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="Building examples with ITK" >From - Fri Mar 08 08:29:24 2002 X-Mozilla-Status2: 00000000 Return-Path: Received: from wren.cs.unc.edu ([152.2.128.86]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with ESMTP id com for ; Thu, 7 Mar 2002 12:27:21 -0500 Received: from smtp3.ev1.net (smtpout.ev1.net [207.218.192.47]) by wren.cs.unc.edu (8.9.3/8.9.3) with ESMTP id MAA02534 for ; Thu, 7 Mar 2002 12:27:20 -0500 (EST) Received: from huggies [207.218.202.15] by smtp3.ev1.net with ESMTP (SMTPD32-6.06) id A2E270C10074; Thu, 07 Mar 2002 11:26:58 -0600 From: "Buu Tien Phan" To: Subject: Building examples with ITK Date: Thu, 7 Mar 2002 09:26:49 -0800 Message-ID: <000001c1c5fd$45052f50$0fcadacf@huggies> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C1C5BA.36E1EF50" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C1C5BA.36E1EF50 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit To Whom It May Concern, I am very interested in your examples with ITK. However, I have been unable to build any of these examples (I am using ITK beta version). >From CMake, I have the following errors: "FLTK_WRAP_UI called with FLTK_WRAP_UI undefined C:/Insight/Examples/ImageRegistration" . I am writing this email in hopes that you might help me how to build the examples. Is there any way we can build the examples without using CMake. Thank you very much for your time and your help is deeply appreciated. Buu Phan ------=_NextPart_000_0001_01C1C5BA.36E1EF50 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

To Whom It May Concern,

I am very interested in your examples with ITK. = However, I have been unable to build any of these examples (I am using ITK beta = version). >From CMake, I have the following = errors:

“FLTK_WRAP_UI called with FLTK_WRAP_UI = undefined C:/Insight/Examples/ImageRegistration” .

I am writing this email in hopes that you might help = me how to build the examples. Is there any way we can build the examples without using CMake.

Thank you very much for your time and your help is = deeply appreciated.

Buu Phan

------=_NextPart_000_0001_01C1C5BA.36E1EF50-- --------------040604000709090003000207-- From luis.ibanez@kitware.com Mon Mar 18 18:27:53 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Mon, 18 Mar 2002 13:27:53 -0500 Subject: [Insight-users] [Fwd: Loading Meta Image] Message-ID: <3C9631A9.6060203@kitware.com> This is a multi-part message in MIME format. --------------050304030900080101020209 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit --------------050304030900080101020209 Content-Type: message/rfc822; name="Loading Meta Image" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="Loading Meta Image" >From - Mon Mar 18 09:20:44 2002 X-Mozilla-Status2: 00000000 Return-Path: Received: from smtp3.ev1.net ([207.218.192.47]) by mail4.nycap.rr.com (Post.Office MTA v3.5.3 release 223 ID# 0-59787U250000L250000S0V35) with ESMTP id com for ; Mon, 18 Mar 2002 00:59:16 -0500 Received: from huggies [216.12.217.109] by smtp3.ev1.net with ESMTP (SMTPD32-6.06) id A2525F040056; Sun, 17 Mar 2002 23:59:46 -0600 From: "Buu Tien Phan" To: "'Luis Ibanez'" Subject: Loading Meta Image Date: Sun, 17 Mar 2002 21:59:42 -0800 Message-ID: <000601c1ce42$19936ce0$6dd90cd8@huggies> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: <3C9248D7.10303@kitware.com> Dear Luis, The program (Gaussian Filter) did not crash. It means that I can compile and run it. However, when I load Meta image T2.mhd, the "Input Image" window pops up in black. I press some control buttons, but nothing is changed. I unzip image from brainweb site (using winzip) and I get the error message "Problems reading file format" when I tried to load this image. Could you please send me a Meta image so I can load to this program? Do you have any examples showing how to load .PNG images? Thank you very much for your help. Buu Phan -----Original Message----- From: Luis Ibanez [mailto:luis.ibanez@kitware.com] Sent: Friday, March 15, 2002 11:18 AM To: Buu Tien Phan Subject: Re: Load Jpeg file Hi Buu, I'm glad to know that things are going better. Could you be more specific about what is not working with the image when you load it. Is it not compiling ? Is it crashing at run time ? Is it showing you a distorted or noised image ? I'm familiar with the MetaImage code so we should be able to track down the problem. Please give more details about what is happening. Other format that you can read are PNG is that could be of any help... Thanks Luis =============================== Buu Tien Phan wrote: >Dear Luis, > >>From your email, I finally get one example to work (the Gaussian Filter >application), thank you very much for your help. I still have one >problem left, the Metaimage. I downloaded a MetaImage named T2.mhd, but >I couldn't see anything when I click the "INPUT" button. I also followed >the instruction from ITK website to download a image from brain web >project. However, this image does not work, and I don't know why. > >I plan to write a simple code about image segmentation. How do I load a >image (like bitmap, jpeg format) and put them on the screen? Could you >please give me some help about this. > >Again, thank you very much for your help. > > >Buu Phan > > > > --------------050304030900080101020209-- From c.p.botha@its.tudelft.nl Mon Mar 18 21:25:01 2002 From: c.p.botha@its.tudelft.nl (Charl P. Botha) Date: Mon, 18 Mar 2002 22:25:01 +0100 Subject: [Insight-users] new VTK 4.0 compatible version of vtkFlRenderWindowInteractor Message-ID: <20020318212501.GE11008@dutidad.twi.tudelft.nl> Dear ITKers, I attempted building the ITK examples today and experienced some vtkFlRenderWindowInteractor + VTK 4.0 related errors in Examples/FEMMesh/ code. Fortunately, the vtkFlRWI code is mine. This is to announce that version 0.5 of this class is available from http://cpbotha.net/vtkFlRenderWindowInteractor.html with the major change that it now builds and works with VTK 3.2 and VTK 4.0. Feel free to update the version you have in the FEMMesh example. The code is under the LGPL license. Regards, Charl PS. I'm not subscribed to this list. -- charl p. botha http://cpbotha.net/ http://visualisation.tudelft.nl/ From luis.ibanez@kitware.com Mon Mar 18 22:24:27 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Mon, 18 Mar 2002 17:24:27 -0500 Subject: [Insight-users] new VTK 4.0 compatible version of vtkFlRenderWindowInteractor References: <20020318212501.GE11008@dutidad.twi.tudelft.nl> Message-ID: <3C96691B.3000400@kitware.com> Hi Charl, That's great news, thank you for letting us know. We have found this class very useful. BTW we were wondering about the conditions under we could keep your vtkFlRenderWindowInteractor class in the ITK distribution. So far we have copied it in every Example that requires to use VTK and FLTK keeping the header copyright intact. We could ask users to directly download it from your page in the same way we ask to dowload FLTK or VTK for those examples that need it. The advantage of the direct download is that they will always get the latest version. What would you think it is the right way to proceed in this case ? Thanks Luis ===================================== Charl P. Botha wrote: >Dear ITKers, > >I attempted building the ITK examples today and experienced some >vtkFlRenderWindowInteractor + VTK 4.0 related errors in Examples/FEMMesh/ >code. Fortunately, the vtkFlRWI code is mine. > >This is to announce that version 0.5 of this class is available from >http://cpbotha.net/vtkFlRenderWindowInteractor.html with the major change >that it now builds and works with VTK 3.2 and VTK 4.0. Feel free to update >the version you have in the FEMMesh example. The code is under the LGPL >license. > >Regards, >Charl > >PS. I'm not subscribed to this list. > From c.p.botha@its.tudelft.nl Tue Mar 19 09:09:10 2002 From: c.p.botha@its.tudelft.nl (Charl P. Botha) Date: Tue, 19 Mar 2002 10:09:10 +0100 Subject: [Insight-users] new VTK 4.0 compatible version of vtkFlRenderWindowInteractor In-Reply-To: <3C96691B.3000400@kitware.com> References: <20020318212501.GE11008@dutidad.twi.tudelft.nl> <3C96691B.3000400@kitware.com> Message-ID: <20020319090910.GA14661@dutidad.twi.tudelft.nl> Dear ITKers and Luis, I am quoting most of the previous mail so that David Pont, on whom's code and concept vtkFlRenderWindowInteractor is based, also knows what's being discussed. On Mon, Mar 18, 2002 at 05:24:27PM -0500, Luis Ibanez wrote: > That's great news, thank you for letting us know. > We have found this class very useful. > > BTW we were wondering about the conditions under > we could keep your vtkFlRenderWindowInteractor > class in the ITK distribution. So far we have copied it > in every Example that requires to use VTK and FLTK > keeping the header copyright intact. > > We could ask users to directly download it from your > page in the same way we ask to dowload FLTK or > VTK for those examples that need it. The advantage of > the direct download is that they will always get the latest > version. > > What would you think it is the right way to proceed in > this case ? vtkFlRenderWindowInteractor, being as simple and single-minded as it is, is just about done and there probably won't be all that many releases in the future, unless VTK changes drastically. I would think it more convenient to include the latest version in ITK. However, and I'm no expert on this, the fact that it's under the LGPL might pose problems. In short, one is allowed to link binary applications with it, but if one distributes these, vtkFlRenderWindowInteractor itself must be made available in source form. Also, modifications _directly_ to LGPL'd source must also be LGPL. There might be experts on the ITK list who can comment on this. If the LGPL is going to pose problems, maybe we could dual-license the code. I'm hoping that it can be integrated without problems. Best regards, Charl > > Thanks > > Luis > > ===================================== > Charl P. Botha wrote: > > >Dear ITKers, > > > >I attempted building the ITK examples today and experienced some > >vtkFlRenderWindowInteractor + VTK 4.0 related errors in Examples/FEMMesh/ > >code. Fortunately, the vtkFlRWI code is mine. > > > >This is to announce that version 0.5 of this class is available from > >http://cpbotha.net/vtkFlRenderWindowInteractor.html with the major change > >that it now builds and works with VTK 3.2 and VTK 4.0. Feel free to update > >the version you have in the FEMMesh example. The code is under the LGPL > >license. > > > >Regards, > >Charl > > > >PS. I'm not subscribed to this list. > > > > > -- charl p. botha http://cpbotha.net/ http://visualisation.tudelft.nl/ From luis.ibanez@kitware.com Tue Mar 19 14:28:00 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Tue, 19 Mar 2002 09:28:00 -0500 Subject: [Insight-users] Re: question about itk install References: <000e01c1bf3b$dbf53360$c73d6fa6@medsoft.eea.tsinghua.edu.cn> <3C7C6007.70103@kitware.com> <007001c1cf0e$c5a98ec0$c73d6fa6@fj> Message-ID: <3C974AF0.7080907@kitware.com> Hi fj, It seems that you have enable most of the advanced features in ITK :-) but you may not need all of them. Let's go in order: ITK is full C++ code but we found interesting to be able to use it from interpreted languages like Tcl, Python and Java. In order to achieve this goal, ITK code needs to be wrapped in such a way to present an interface that each one of these interpreted languages could understand. The difficulty in wrapping ITK is that most of the code is templated. So the actual types of the classes is defined at the last moment by the users. In order to wrap ITK, some combination of the templated types has to be selected and according to these types, wrappers can be generated on a class-by-class basis. The program that performs this wrapping is called CABLE. It is Open Source as all of the tools that we use with ITK. Its home page is : http://public.kitware.com/Cable/ The reason why CMake is asking you about CABLE is that the option : ITK_WRAP_TCL is "ON" in your configuration. Just turning this option "OFF" will prevent CMake from asking about CABLE paths. Along the same lines, the input for CABLE is a description of the types for the ITK classes that you are using. Given that C++ is very rich in the expressions that are valid types, it turned out that the most efficient way to parse C++ code was to use the "gcc" parser itself. GCC_XML us a tool that using gcc's parser export a descritption of your types in an XML format. CABLE uses this XML description in order to generate wrappers. GCC_XML uses are not limited to wrapping and is such a powerful tool that was isolated in a repository of its own. The home page for GCC_XML is: http://public.kitware.com/GCC_XML/ Because in ITK GCC_XML is used as a first stage for wrapping, just turning ITK_WRAP_TCL "OFF" will also prevent CMake form asking for GCC_XML paths and components. == There seems to be still an error with FLTK_WRAP_UI anyways.... Please disable the Tcl wrapping and post to us the remaining errors just to make sure that at least one problem was isolated. Thanks Luis ================================================ fj wrote: >Dear Luis Ibanez: > Like you have said , >I have use fltk.dsw to compile demod.exe.and then I use Cmake to compile ITK and do the following things. >The FLTK_WRAP_UI is an advanced command. >Please run CMake and select the check box >that says "Advanced" . > >I have seen new items appear in the browser. > >Select "ON" for FLTK_WRAP_UI > >Also double check that > >FLTK_INCLUDE_PATH >FLTK_LIBRARY >FLTK_FLUID_EXE > >point to : >- the directory where FLTK is installed >- the librarly ....../lib/fltkd.lib >- the fluid program ......./fluid/fluidd.exe > >But I still meet some problem when I compile ITK by CMake, the detail is : > >CMaker Error: FLTK_WRAP_UI:error: >fltk_wrap_ui bad source list passed to: >FLTKWARPUICommand E:/TEMP/itk/itk/itksourcewin32beta/insight/auxiliary/fltkimageviewer > > >Wrapping is enabled, but GCCXML is not found!error > >wrapping is enabled, but CABLE is not found!Error > >CMakerError in generation process, project files may be invalid > >what is GCCXML? what is CABLE??? Always can not find them .I think I have give the right path of fltk to CMAKE. > > > > > From luis.ibanez@kitware.com Tue Mar 19 15:45:21 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Tue, 19 Mar 2002 10:45:21 -0500 Subject: [Insight-users] Brain Images in MetaImage format available Message-ID: <3C975D11.4020904@kitware.com> Hi Buu, We put a set of three Brain images in MetaImage format on the ftp server. These images were created from originals downloaded from the BrainWeb project: http://www.bic.mni.mcgill.ca/brainweb/ You can read these images directly with the GaussianFilter example program. In order to get the images, please go to the ITK home page and follow the link to "Data". That will bring you to: http://www.itk.org/HTML/Data.htm You will find some discussion about file formats and around the middle of the page a link to the ftp server : ftp://public.kitware.com/pub/itk/Data/ if you follow the "BrainWeb" subdirectory you will find three .tgz files. Each one containing a MRI image. They are T1, T2 and PD MRIs. Each .tgz file contains a .txt file with the original description of the image from the BrainWeb project. a .mha file which is the MetaImage text header describing the image and a .raw file which is the binaray data of the image. Please let us know if this images work (or not :-) ) for you. Thanks Luis BTW you may find interesting also the data of the Head from the VisibleHuman which is available in the same ftp site. From David.Rich@trw.com Tue Mar 19 15:46:14 2002 From: David.Rich@trw.com (David Rich) Date: Tue, 19 Mar 2002 10:46:14 -0500 Subject: [Insight-users] ITK Message-ID: This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --=_207D86BE.7E1FD99B Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable ITK users, We are currently looking at using this toolkit and are interested in the = experience of others. Have you found this open source code to be easy to = use? Was the package easy to install and learn about? Is it necessary = (or helpful) us use VTK in conjunction with it, or does ITK stand on its = own? What about FLTK, is that helpful or necessary? Any input you could = provide would be helpful. Thanks. Dave Rich David.Rich@trw.com --=_207D86BE.7E1FD99B Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Description: HTML

ITK users,

We are currently looking at using this toolkit and = are=20 interested in the experience of others. Have you found this open = source=20 code to be easy to use? Was the package easy to install and learn=20 about? Is it necessary (or helpful) us use VTK in conjunction with = it, or=20 does ITK stand on its own? What about FLTK, is that helpful or=20 necessary? Any input you could provide would be helpful. =20 Thanks.

Dave Rich

David.Rich@trw.com

--=_207D86BE.7E1FD99B-- From pieterv@radiology.azn.nl Tue Mar 19 16:02:06 2002 From: pieterv@radiology.azn.nl (Pieter Vos) Date: Tue, 19 Mar 2002 17:02:06 +0100 (CET) Subject: [Insight-users] Creating an 3D image fails with an exeptional error Message-ID: As one can see in the example below, I'm trying to create a 3D image. It is a short version of the example itkImageLinearIteratorTest.cxx Compiling goes well, but when I execute the program I get the following error: "error while loading shared libraries: unexpected reloc type 0x84" sometimes other hexa-numbers or after some changes in the code: "segmentation fault" An error what seems to occur more when one surfs on the internet. The strange part is when I compile and run itkImageLinearIteratorTest.cxx no errors occur. While stripping the code the problem lies near the declaration of the image with it's pointer. So maybe something is wrong in the CMakeList.txt or Cache, but I can't find what. I included the .txt file as well. Many thanks in advance! Pieter Vos ------------------------------------------------------- # Deformable model test program PROJECT(ITK_TEST) SET(ITK_SOURCE_DIR /data/cemri/Insight) SET(ITK_BINARY_DIR /data/cemri/Insight) # Include the ITK include and link libraries INCLUDE (${ITK_SOURCE_DIR}/itkCMakeOptions.cmake) LINK_LIBRARIES ( VXLNumerics ITKIO ITKCommon -lm ) LINK_DIRECTORIES( ${ITK_BINARY_DIR}/Code/IO ${ITK_BINARY_DIR}/Code/Numerics ${ITK_BINARY_DIR}/Code/Common ) INCLUDE_DIRECTORIES( ${ITK_SOURCE_DIR}/Code/IO ${ITK_SOURCE_DIR}/Code/BasicFilters ${ITK_SOURCE_DIR}/Code/Algorithms ) #grouping files SOURCE_FILES( ITK_SRCS test) ADD_EXECUTABLE(VTKImage ITK_SRCS) -----------------------------example---------------- #include #include "itkImage.h" #include "itkImageLinearIteratorWithIndex.h" int main() { std::cout << "Creating an image of indices" << std::endl; const unsigned int ImageDimension = 3; typedef itk::Index< ImageDimension > PixelType; typedef itk::Image< PixelType, ImageDimension > ImageType; ImageType::Pointer myImage = ImageType::New(); ImageType::SizeType size; size[0] = 100; size[1] = 100; size[2] = 100; ImageType::IndexType start; start = ImageType::IndexType::ZeroIndex; ImageType::RegionType region; region.SetIndex( start ); region.SetSize( size ); myImage->SetLargestPossibleRegion( region ); myImage->SetBufferedRegion( region ); myImage->SetRequestedRegion( region ); myImage->Allocate(); return 1; } -- Pieter Vos Doddendaal 190 Nijmegen Tel.: 06-18876433 mailto:pieterv@radiology.azn.nl From luis.ibanez@kitware.com Tue Mar 19 16:22:39 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Tue, 19 Mar 2002 11:22:39 -0500 Subject: [Insight-users] Creating an 3D image fails with an exeptional error References: Message-ID: <3C9765CF.6010708@kitware.com> Hi Pieter, Your C++ code looks fine and the CMakeList.txt seems to be Ok too. The problem could be originated by a mix of old and new versions of the libraries at link time... Are you running on Windows or Unix ? Please correct me if I'm wrong: When you said that the problem lies near the declaration of the image with it's pointer, you mean the line: ImageType::Pointer myImage = ImageType::New(); Is that right ? At this level the only library involved is ITKCommon.lib which manages the Factories for creation of new objects through the New() operator. I would suspect that for some reason your program is being linked with an old version of the ITKCommon.lib library. Are you creating dll's for ITK libraries ? Do you have by any chance, both an ITKCommon.dll and ITKCommon.lib in the same ITK binary directory ? Thanks Luis =========================================== Pieter Vos wrote: >As one can see in the example below, I'm trying to create a 3D image. >It is a short version of the example itkImageLinearIteratorTest.cxx >Compiling goes well, but when I execute the program I get the following >error: >"error while loading shared libraries: unexpected reloc type 0x84" >sometimes other hexa-numbers or after some changes in the code: >"segmentation fault" >An error what seems to occur more when one surfs on the internet. >The strange part is when I compile and run itkImageLinearIteratorTest.cxx >no errors occur. >While stripping the code the problem lies near the declaration of the >image with it's pointer. >So maybe something is wrong in the CMakeList.txt or Cache, but I >can't find what. I included the .txt file as well. > >Many thanks in advance! > >Pieter Vos > >------------------------------------------------------- > ># Deformable model test program >PROJECT(ITK_TEST) > >SET(ITK_SOURCE_DIR /data/cemri/Insight) >SET(ITK_BINARY_DIR /data/cemri/Insight) > ># Include the ITK include and link libraries >INCLUDE (${ITK_SOURCE_DIR}/itkCMakeOptions.cmake) > > >LINK_LIBRARIES ( >VXLNumerics >ITKIO >ITKCommon >-lm >) > > >LINK_DIRECTORIES( >${ITK_BINARY_DIR}/Code/IO >${ITK_BINARY_DIR}/Code/Numerics >${ITK_BINARY_DIR}/Code/Common >) > > > >INCLUDE_DIRECTORIES( >${ITK_SOURCE_DIR}/Code/IO >${ITK_SOURCE_DIR}/Code/BasicFilters >${ITK_SOURCE_DIR}/Code/Algorithms >) > >#grouping files >SOURCE_FILES( ITK_SRCS test) > >ADD_EXECUTABLE(VTKImage ITK_SRCS) > > > > >-----------------------------example---------------- >#include > >#include "itkImage.h" >#include "itkImageLinearIteratorWithIndex.h" > > >int main() >{ > std::cout << "Creating an image of indices" << std::endl; > const unsigned int ImageDimension = 3; > typedef itk::Index< ImageDimension > PixelType; > typedef itk::Image< PixelType, ImageDimension > ImageType; > ImageType::Pointer myImage = ImageType::New(); > ImageType::SizeType size; > > size[0] = 100; > size[1] = 100; > size[2] = 100; > > ImageType::IndexType start; > start = ImageType::IndexType::ZeroIndex; > > ImageType::RegionType region; > region.SetIndex( start ); > region.SetSize( size ); > > myImage->SetLargestPossibleRegion( region ); > myImage->SetBufferedRegion( region ); > myImage->SetRequestedRegion( region ); > myImage->Allocate(); > > return 1; >} > From pieterv@radiology.azn.nl Wed Mar 20 08:49:43 2002 From: pieterv@radiology.azn.nl (Pieter Vos) Date: Wed, 20 Mar 2002 09:49:43 +0100 (CET) Subject: [Insight-users] Creating an 3D image fails with an exeptional error In-Reply-To: <3C9765CF.6010708@kitware.com> Message-ID: Hi, I have installed ITK on a Linux systems and indeed I mend the line > ImageType::Pointer myImage = ImageType::New(); So the problem should be a linking problem. Maybe it's because of an addition I did in CMakeCache.txt: //Use the system's version of the standard C++ library (STL and // streams). If 'OFF', ITK will build against a supplied version // of the standard library from SGI. On SGI systems, this should // be set to 'OFF'. ITK_USE_SYSTEM_STDLIB:BOOL=ON But when I remove the line I get a lot of errors which begins with: In file included from /usr/include/g++-3/iostream.h:31, error, error etc. So iostream.h is not found??? Can I see that in some cache file, which ITKCommon is used? I included this time the compile messages, maybe does that help? Many thanks for the time being used, Pieter Vos ----------------------------------------- c++ -g -O2 -ftemplate-depth-50 -I/data/cemri/TestITK/DM/imageReader -I/data/cemri/Insight -I/data/cemri/Insight/Code/Numerics -I/data/cemri/Insight/Code/Common -I/data/cemri/Insight/Code/Numerics/vxl -I/data/cemri/Insight/Code/Numerics/vxl -I/data/cemri/Insight/Code/Numerics/vxl/vcl -I/data/cemri/Insight/Code/Numerics/vxl/vcl -I/data/cemri/Insight/Utilities/png -I/data/cemri/Insight/Utilities/zlib -I/data/cemri/Insight/Code/IO -I/data/cemri/Insight/Code/BasicFilters -I/data/cemri/Insight/Code/Algorithms -D_PTHREADS -c /data/cemri/TestITK/DM/imageReader/test.cxx -o test.o c++ -rdynamic -g -O2 -ftemplate-depth-50 test.o -L/data/cemri/Insight/Code/Common -L/data/cemri/Insight/Code/Numerics/vxl -L/data/cemri/Insight/Code/IO -L/data/cemri/Insight/Code/Numerics -lpthread -ldl -lVXLNumerics -lITKIO -lITKCommon -lm -lpthread -ldl -lVXLNumerics -lITKIO -lITKCommon -lm -Wl,-rpath,/data/cemri/Insight/Code/Common:/data/cemri/Insight/Code/Numerics/vxl:/data/cemri/Insight/Code/IO:/data/cemri/Insight/Code/Numerics -o VTKImage ------------------------------------------ On Tue, 19 Mar 2002, Luis Ibanez wrote: > > Hi Pieter, > > Your C++ code looks fine and the CMakeList.txt seems to be Ok too. > > The problem could be originated by a mix of old and new versions of the > libraries at link time... > > Are you running on Windows or Unix ? > > Please correct me if I'm wrong: > When you said that the problem lies near the declaration of the image > with it's pointer, you mean the line: > > ImageType::Pointer myImage = ImageType::New(); > > Is that right ? > > At this level the only library involved is ITKCommon.lib which manages > the Factories for creation of new objects through the New() operator. > I would suspect that for some reason your program is being linked with > an old version of the ITKCommon.lib library. Are you creating dll's for > ITK libraries ? > > Do you have by any chance, both an ITKCommon.dll and > ITKCommon.lib in the same ITK binary directory ? > > > > Thanks > > Luis > > =========================================== > > > Pieter Vos wrote: > > >As one can see in the example below, I'm trying to create a 3D image. > >It is a short version of the example itkImageLinearIteratorTest.cxx > >Compiling goes well, but when I execute the program I get the following > >error: > >"error while loading shared libraries: unexpected reloc type 0x84" > >sometimes other hexa-numbers or after some changes in the code: > >"segmentation fault" > >An error what seems to occur more when one surfs on the internet. > >The strange part is when I compile and run itkImageLinearIteratorTest.cxx > >no errors occur. > >While stripping the code the problem lies near the declaration of the > >image with it's pointer. > >So maybe something is wrong in the CMakeList.txt or Cache, but I > >can't find what. I included the .txt file as well. > > > >Many thanks in advance! > > > >Pieter Vos > > > >------------------------------------------------------- > > > ># Deformable model test program > >PROJECT(ITK_TEST) > > > >SET(ITK_SOURCE_DIR /data/cemri/Insight) > >SET(ITK_BINARY_DIR /data/cemri/Insight) > > > ># Include the ITK include and link libraries > >INCLUDE (${ITK_SOURCE_DIR}/itkCMakeOptions.cmake) > > > > > >LINK_LIBRARIES ( > >VXLNumerics > >ITKIO > >ITKCommon > >-lm > >) > > > > > >LINK_DIRECTORIES( > >${ITK_BINARY_DIR}/Code/IO > >${ITK_BINARY_DIR}/Code/Numerics > >${ITK_BINARY_DIR}/Code/Common > >) > > > > > > > >INCLUDE_DIRECTORIES( > >${ITK_SOURCE_DIR}/Code/IO > >${ITK_SOURCE_DIR}/Code/BasicFilters > >${ITK_SOURCE_DIR}/Code/Algorithms > >) > > > >#grouping files > >SOURCE_FILES( ITK_SRCS test) > > > >ADD_EXECUTABLE(VTKImage ITK_SRCS) > > > > > > > > > >-----------------------------example---------------- > >#include > > > >#include "itkImage.h" > >#include "itkImageLinearIteratorWithIndex.h" > > > > > >int main() > >{ > > std::cout << "Creating an image of indices" << std::endl; > > const unsigned int ImageDimension = 3; > > typedef itk::Index< ImageDimension > PixelType; > > typedef itk::Image< PixelType, ImageDimension > ImageType; > > ImageType::Pointer myImage = ImageType::New(); > > ImageType::SizeType size; > > > > size[0] = 100; > > size[1] = 100; > > size[2] = 100; > > > > ImageType::IndexType start; > > start = ImageType::IndexType::ZeroIndex; > > > > ImageType::RegionType region; > > region.SetIndex( start ); > > region.SetSize( size ); > > > > myImage->SetLargestPossibleRegion( region ); > > myImage->SetBufferedRegion( region ); > > myImage->SetRequestedRegion( region ); > > myImage->Allocate(); > > > > return 1; > >} > > > > > > > -- Pieter Vos Doddendaal 190 Nijmegen Tel.: 06-18876433 mailto:pieterv@radiology.azn.nl From pieterv@radiology.azn.nl Wed Mar 20 12:02:09 2002 From: pieterv@radiology.azn.nl (Pieter Vos) Date: Wed, 20 Mar 2002 13:02:09 +0100 (CET) Subject: [Insight-users] itkVTKImageIO NAN FEVER In-Reply-To: <3C963190.4040500@kitware.com> Message-ID: Hi, For a moment I thought my problems where solved, because I needed to read a VTK structured point dataset in ITK and found the example itkVTKImageIOTest.cxx as my salvation. However when I strip the code as below I receive the error: *** NAN FEVER ** inf 0 0 inf Abort The junk.vtk file was generated by the original example. Could it be that the pointer to the object itk::VTKImageIO::New() stores information about the image, when writing and uses when reading a VTK image? Are there settings necessary before reading a VTK image? If so, which? Many thanks, Pieter Vos ------------------------------------------- #include #include "itkRandomImageSource.h" #include "itkImageFileWriter.h" #include "itkImageFileReader.h" #include "itkVTKImageIO.h" /* Taken from itkImageIOTest.cxx */ int main() { typedef itk::Image FloatImageType; // Create a mapper (in this case a writer). A mapper // is templated on the input type. // itk::VTKImageIO::Pointer vtkIO; vtkIO = itk::VTKImageIO::New(); if ( !vtkIO->CanReadFile("junk.vtk") ) { cout <<"Can't read file"<::Pointer reader; reader = itk::ImageFileReader::New(); reader->SetImageIO(vtkIO); reader->SetFileName("junk.vtk"); reader->Update(); itk::ImageFileWriter::Pointer writer; writer = itk::ImageFileWriter::New(); if ( !vtkIO->CanWriteFile("junk2.vtk") ) { cout <<"Can't write file"<SetInput(reader->GetOutput()); writer->SetFileName("junk2.vtk"); writer->SetImageIO(vtkIO); writer->Write(); return EXIT_SUCCESS; } ------------------------------------------- Pieter Vos Doddendaal 190 Nijmegen Tel.: 06-18876433 mailto:pieterv@radiology.azn.nl From luis.ibanez@kitware.com Wed Mar 20 14:05:31 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Wed, 20 Mar 2002 09:05:31 -0500 Subject: [Insight-users] Re: question about itk install References: <000e01c1bf3b$dbf53360$c73d6fa6@medsoft.eea.tsinghua.edu.cn> <3C7C6007.70103@kitware.com> <007001c1cf0e$c5a98ec0$c73d6fa6@fj> <3C974AF0.7080907@kitware.com> <001001c1cfb5$a1d510d0$c73d6fa6@fj> Message-ID: <3C98972B.6020405@kitware.com> Hi fj, It is Ok if you installed CABLE and GCCXML but you don't need them unless you want to use Tcl wrapping. The remaining error message about FLTK_WRAP_UI looks like a problem in the CMakeLists.txt file. Have you edited this file ? The one at: Insight/Auxiliary/FltkImageViewer/CMakeLists.txt It should look like: SOURCE_FILES(FltkImageViewer_GUI_SRCS fltkClippingPlanes3DDrawerGUI.fl fltkDisplayGlWindowGUI.fl ..... etc fltkSphereFunctionControlGUI.fl ) and toward the end it should have a line like: FLTK_WRAP_UI( FltkImageViewer FltkImageViewer_GUI_SRCS ) The error message that you are getting suggests that the section "SOURCE_FILES" may be incorrect in your CMakeLists.txt file. If you want, just post your CMakeLists.txt file to the list, that could help us to figure out what could be wrong with the installation. Thanks Luis. ---------------------------------------- fj wrote: >Hi Luis: > I have download cable and gccxml and install them.There are not error about cable and gccxml when I compile ITK by cmake. >But still have the same error , >the detail: >CMaker Error: FLTK_WRAP_UI:error: >fltk_wrap_ui bad source list passed to: >FLTKWARPUICommand E:/TEMP/itk/itk/itksourcewin32beta/insight/auxiliary/fltkimageviewer > >CMakerError in generation process, project files may be invalid > > From luis.ibanez@kitware.com Wed Mar 20 14:35:40 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Wed, 20 Mar 2002 09:35:40 -0500 Subject: [Insight-users] Creating an 3D image fails with an exeptional error References: Message-ID: <3C989E3C.4070304@kitware.com> Hi Pieter, The option: ITK_USE_SYSTEM_STDLIB should be "ON" for a Linux system. The only reason for turning this OFF is if you are using SGI's and need to do multithreading. In that case a particular implementation of the STL library should be installed too. So,... you should be Ok on Linux with: "ITK_USE_SYSTEM_STDLIB:BOOL=ON" Now, the error you get from iostream.h looks like the compiler actually found iostream.h but have trouble interpreting it in the current context. Could you please post these errrors ? the ones you get from iostream.h (the iostream.h file *is* being found, the problem should be somewhere else) Could you give us also more details about your Linux installation. What versions are you using...etc. Is this an installation that you have used for a while and that you can be confident with ? or is it a brand new installation. have you done something fancy like updating your gcc or keeping two gcc versions on the same machine ? Thanks Luis ======================================= Pieter Vos wrote: >Hi, > >I have installed ITK on a Linux systems and indeed I mend the line > >> ImageType::Pointer myImage = ImageType::New(); >> >So the problem should be a linking problem. Maybe it's because of an >addition I did in CMakeCache.txt: > >//Use the system's version of the standard C++ library (STL and >// streams). If 'OFF', ITK will build against a supplied version >// of the standard library from SGI. On SGI systems, this should >// be set to 'OFF'. >ITK_USE_SYSTEM_STDLIB:BOOL=ON > >But when I remove the line I get a lot of errors which begins with: > >In file included from /usr/include/g++-3/iostream.h:31, >error, error etc. > >So iostream.h is not found??? >Can I see that in some cache file, which ITKCommon is used? >I included this time the compile messages, maybe does that help? > >Many thanks for the time being used, > >Pieter Vos >----------------------------------------- >c++ -g -O2 -ftemplate-depth-50 >-I/data/cemri/TestITK/DM/imageReader >-I/data/cemri/Insight >-I/data/cemri/Insight/Code/Numerics >-I/data/cemri/Insight/Code/Common >-I/data/cemri/Insight/Code/Numerics/vxl >-I/data/cemri/Insight/Code/Numerics/vxl >-I/data/cemri/Insight/Code/Numerics/vxl/vcl >-I/data/cemri/Insight/Code/Numerics/vxl/vcl >-I/data/cemri/Insight/Utilities/png >-I/data/cemri/Insight/Utilities/zlib >-I/data/cemri/Insight/Code/IO >-I/data/cemri/Insight/Code/BasicFilters >-I/data/cemri/Insight/Code/Algorithms >-D_PTHREADS -c /data/cemri/TestITK/DM/imageReader/test.cxx -o test.o > >c++ -rdynamic -g -O2 -ftemplate-depth-50 test.o >-L/data/cemri/Insight/Code/Common >-L/data/cemri/Insight/Code/Numerics/vxl >-L/data/cemri/Insight/Code/IO >-L/data/cemri/Insight/Code/Numerics >-lpthread -ldl -lVXLNumerics -lITKIO -lITKCommon -lm >-lpthread -ldl -lVXLNumerics -lITKIO -lITKCommon -lm >-Wl,-rpath,/data/cemri/Insight/Code/Common:/data/cemri/Insight/Code/Numerics/vxl:/data/cemri/Insight/Code/IO:/data/cemri/Insight/Code/Numerics >-o VTKImage > > >------------------------------------------ > > > > > >On Tue, 19 Mar 2002, Luis Ibanez wrote: > >>Hi Pieter, >> >>Your C++ code looks fine and the CMakeList.txt seems to be Ok too. >> >>The problem could be originated by a mix of old and new versions of the >>libraries at link time... >> >>Are you running on Windows or Unix ? >> >>Please correct me if I'm wrong: >>When you said that the problem lies near the declaration of the image >>with it's pointer, you mean the line: >> >> ImageType::Pointer myImage = ImageType::New(); >> >>Is that right ? >> >>At this level the only library involved is ITKCommon.lib which manages >>the Factories for creation of new objects through the New() operator. >>I would suspect that for some reason your program is being linked with >>an old version of the ITKCommon.lib library. Are you creating dll's for >>ITK libraries ? >> >>Do you have by any chance, both an ITKCommon.dll and >>ITKCommon.lib in the same ITK binary directory ? >> >> >> >> Thanks >> >> Luis >> >>=========================================== >> >> >>Pieter Vos wrote: >> >>>As one can see in the example below, I'm trying to create a 3D image. >>>It is a short version of the example itkImageLinearIteratorTest.cxx >>>Compiling goes well, but when I execute the program I get the following >>>error: >>>"error while loading shared libraries: unexpected reloc type 0x84" >>>sometimes other hexa-numbers or after some changes in the code: >>>"segmentation fault" >>>An error what seems to occur more when one surfs on the internet. >>>The strange part is when I compile and run itkImageLinearIteratorTest.cxx >>>no errors occur. >>>While stripping the code the problem lies near the declaration of the >>>image with it's pointer. >>>So maybe something is wrong in the CMakeList.txt or Cache, but I >>>can't find what. I included the .txt file as well. >>> >>>Many thanks in advance! >>> >>>Pieter Vos >>> >>>------------------------------------------------------- >>> >>># Deformable model test program >>>PROJECT(ITK_TEST) >>> >>>SET(ITK_SOURCE_DIR /data/cemri/Insight) >>>SET(ITK_BINARY_DIR /data/cemri/Insight) >>> >>># Include the ITK include and link libraries >>>INCLUDE (${ITK_SOURCE_DIR}/itkCMakeOptions.cmake) >>> >>> >>>LINK_LIBRARIES ( >>>VXLNumerics >>>ITKIO >>>ITKCommon >>>-lm >>>) >>> >>> >>>LINK_DIRECTORIES( >>>${ITK_BINARY_DIR}/Code/IO >>>${ITK_BINARY_DIR}/Code/Numerics >>>${ITK_BINARY_DIR}/Code/Common >>>) >>> >>> >>> >>>INCLUDE_DIRECTORIES( >>>${ITK_SOURCE_DIR}/Code/IO >>>${ITK_SOURCE_DIR}/Code/BasicFilters >>>${ITK_SOURCE_DIR}/Code/Algorithms >>>) >>> >>>#grouping files >>>SOURCE_FILES( ITK_SRCS test) >>> >>>ADD_EXECUTABLE(VTKImage ITK_SRCS) >>> >>> >>> >>> >>>-----------------------------example---------------- >>>#include >>> >>>#include "itkImage.h" >>>#include "itkImageLinearIteratorWithIndex.h" >>> >>> >>>int main() >>>{ >>> std::cout << "Creating an image of indices" << std::endl; >>> const unsigned int ImageDimension = 3; >>> typedef itk::Index< ImageDimension > PixelType; >>> typedef itk::Image< PixelType, ImageDimension > ImageType; >>> ImageType::Pointer myImage = ImageType::New(); >>> ImageType::SizeType size; >>> >>> size[0] = 100; >>> size[1] = 100; >>> size[2] = 100; >>> >>> ImageType::IndexType start; >>> start = ImageType::IndexType::ZeroIndex; >>> >>> ImageType::RegionType region; >>> region.SetIndex( start ); >>> region.SetSize( size ); >>> >>> myImage->SetLargestPossibleRegion( region ); >>> myImage->SetBufferedRegion( region ); >>> myImage->SetRequestedRegion( region ); >>> myImage->Allocate(); >>> >>> return 1; >>>} >>> >> >> >> >> > From David.Pont@ForestResearch.co.nz Thu Mar 21 00:26:55 2002 From: David.Pont@ForestResearch.co.nz (David.Pont@ForestResearch.co.nz) Date: Thu, 21 Mar 2002 12:26:55 +1200 Subject: [Insight-users] new VTK 4.0 compatible version of vtkFlRenderWindowInteractor Message-ID: Hi everyone, Charl, thanks for the update, I had heard of ITK but am not on its mailing lists. I am no expert on licensing..., and I am happy to see the class being used for ITK. Here are a few thoughts: Changes to vtkFlRenderWindowInteractor - For one application I extended vtkFlRenderWindowInteractor to support a user registered callback for interaction events (mouse, keyboard). This was to display current cursor position in world coords on a status line, and to call application logic on "special" key presses. There may be a way to do this with vtkInteractorStyle? but it was quick and effective for me. So this could be a suggested extension to the class. - Extract the core structure as a generic base class for linking windowing libraries with vtk, vtkFlRenderWindowInteractor would be a specific descendant. vtkFlRenderWindowInteractor distribution with ITK - Can the class be contributed to vtk? I know this introduces a dependancy on an external library (FLTK) with possible issues around distributing, building and supporting the vtk distribution. Can it be an optional extra that is included in the distribution (and testing?) but excluded from the usual distribution build? This would save ITKers and other vtk-FLTKers from having to download one more piece to get set up. regards Dave Pont "Charl P. Botha" insight-developers@public.kitware.com Sent by: "Charl P. cc: david.pont@forestresearch.co.nz Botha" Subject: Re: [Insight-users] new VTK 4.0 19/03/2002 21:09 Dear ITKers and Luis, I am quoting most of the previous mail so that David Pont, on whom's code and concept vtkFlRenderWindowInteractor is based, also knows what's being discussed. On Mon, Mar 18, 2002 at 05:24:27PM -0500, Luis Ibanez wrote: > That's great news, thank you for letting us know. > We have found this class very useful. > > BTW we were wondering about the conditions under > we could keep your vtkFlRenderWindowInteractor > class in the ITK distribution. So far we have copied it > in every Example that requires to use VTK and FLTK > keeping the header copyright intact. > > We could ask users to directly download it from your > page in the same way we ask to dowload FLTK or > VTK for those examples that need it. The advantage of > the direct download is that they will always get the latest > version. > > What would you think it is the right way to proceed in > this case ? vtkFlRenderWindowInteractor, being as simple and single-minded as it is, is just about done and there probably won't be all that many releases in the future, unless VTK changes drastically. I would think it more convenient to include the latest version in ITK. However, and I'm no expert on this, the fact that it's under the LGPL might pose problems. In short, one is allowed to link binary applications with it, but if one distributes these, vtkFlRenderWindowInteractor itself must be made available in source form. Also, modifications _directly_ to LGPL'd source must also be LGPL. There might be experts on the ITK list who can comment on this. If the LGPL is going to pose problems, maybe we could dual-license the code. I'm hoping that it can be integrated without problems. Best regards, Charl > > Thanks > > Luis > > ===================================== > Charl P. Botha wrote: > > >Dear ITKers, > > > >I attempted building the ITK examples today and experienced some > >vtkFlRenderWindowInteractor + VTK 4.0 related errors in Examples/FEMMesh/ > >code. Fortunately, the vtkFlRWI code is mine. > > > >This is to announce that version 0.5 of this class is available from > >http://cpbotha.net/vtkFlRenderWindowInteractor.html with the major change > >that it now builds and works with VTK 3.2 and VTK 4.0. Feel free to update > >the version you have in the FEMMesh example. The code is under the LGPL > >license. > > > >Regards, > >Charl > > > >PS. I'm not subscribed to this list. > > > > > -- charl p. botha http://cpbotha.net/ http://visualisation.tudelft.nl/ From lng@insightful.com Thu Mar 21 01:44:23 2002 From: lng@insightful.com (Lydia Ng) Date: Wed, 20 Mar 2002 17:44:23 -0800 Subject: [Insight-users] Anisotropic diffusion ( was RE: ShapeDetection) Message-ID: <635ADAEFC2399148BCCBB4193B6BF3A00AA9DA@se2kexch01.insightful.com> Can someone help Christina as to the differences in the differ favors of anisotropic diffusion? She is hoping to use the anisotropic diffusion to remove texture and enhance MR images of the liver. Cheers, Lydia > -----Original Message----- > From: Christina Lee [mailto:dreamie222@yahoo.com] > Sent: Wednesday, March 20, 2002 2:28 PM > To: Lydia Ng > Subject: RE: ShapeDetection >=20 >=20 >=20 > Hi Lydia, >=20 > How are you? > I think I'll try to preprocess the MR images with > anisotropic diffusion as you suggested. Although I'm > not exactly sure what kind of anistropic diffusion > filter that I need (there seems to be three > -curvature, gradient & vector!?) >=20 > I couldn't find the source code (or the cxx file) for > itkAnisotropicDiffusionImageFilter.h & I did a > thorough search on the files that I downloaded from > the ITK website. Are there DLL or LIB files for the > derived classes that I'm not aware of?=20 >=20 > Hope to hear from you soon. >=20 > Thank you so much for your help! >=20 > Christina > --- Lydia Ng wrote: > > Hi Christina, > >=20 > > The ShapeDetection program is not very sophisticated > > in > > that it only uses image gradient information to > > generate > > an edge potential map. Ideally, the edge potential > > map is > > zero at an "edge" and one in homogenous areas. > >=20 > > A fastmarching algorithm is used to grow out > > a contour from a seed point. The rate of expansion > > of the=20 > > contour is determined by the values in the edge > > potential map.=20 > >=20 > > I think the algorithm is working well for CT=20 > > because the edges are nice and strong. > > I am not familiar with MR images of the liver, but > > if there are > > high gradient textures within the liver then these > > might=20 > > interfere with the expansion of the contour. > >=20 > > The other issue is that the computed edge potential > > map > > is far from ideal. For example, if the boundary > > gradient isn't > > strong, the associated edge potential will be > > some non-zero value and the contour will eventually > > leak=20 > > across the boundary as time goes on. > >=20 > > What kind of output are you getting when you look > > at it at various time crossing thresholds? > >=20 > > I guess you can also try some preprocessing with > > something > > like anisotropic diffusion to get rid of some of the > > texture > > and enhance the boundaries. > >=20 > > - Lydia > >=20 > > > -----Original Message----- > > > From: Christina Lee [mailto:dreamie222@yahoo.com] > > > Sent: Wednesday, February 27, 2002 2:30 PM > > > To: Lydia Ng > > > Subject: ShapeDetection > > >=20 > > >=20 > > >=20 > > > Hi Lydia, > > >=20 > > > How are you?=20 > > > I've been running the ShapeDetection program on > > some > > > MR images (to segment out the liver) & I haven't > > had > > > any luck. The program worked pretty well for the > > CT > > > data but not for the MR data - I wonder if it's > > > because the MR images are more textured. Any > > comments > > > or suggestions? > > > =20 > > > Hope to hear from you soon. > > >=20 > > > Thanks, > > >=20 > > > Christina > > >=20 > > > __________________________________________________ > > > Do You Yahoo!? > > > Yahoo! Greetings - Send FREE e-cards for every > > occasion! > > > http://greetings.yahoo.com > > >=20 >=20 >=20 > __________________________________________________ > Do You Yahoo!? > Yahoo! Movies - coverage of the 74th Academy Awards=AE > http://movies.yahoo.com/ >=20 From luis.ibanez@kitware.com Thu Mar 21 16:33:43 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Thu, 21 Mar 2002 11:33:43 -0500 Subject: [Insight-users] Re: question: ITK Examples References: <000b01c1cff0$81223d50$c73d6fa6@fj> <3C989ED1.9020104@kitware.com> <002601c1d0a0$15770170$c73d6fa6@fj> Message-ID: <3C9A0B67.50800@kitware.com> Hi Fj, About the examples: Not all the examples in ITK use graphic interface. Some of them are expected to be run from the command line. You can run them from a MS-DOS command window or if you have Cygwin installed you can also use your bash shell window. About what you are seeing when you run the examples: - itkEllipsoidInteriorExteriorSpatialFunctionExample - FEM is the MS-DOS windows comming up, running the example and closing. That's perfectly normal. Just run them from an MS-DOS window directly. Just to clarify: ITK doesn't provide any visualization at all. It is not attached to FLTK or VTK either. The reason for this is that everybody want visualization... but with a different tool. So attaching ITK to a particular visualization style will necessarily eliminate a lot of users. ITK should be considered an "Image Processing Engine" that you can use for developping applications. About the Fuzzy connectedness example: most examples have a README file in their respective directory and a web page located at: http://public.kitware.com/Insight/HTML/Examples.htm It is probably that some examples are still missing one or the other. For FuzzyConnectedness you will find two files: Readme.doc Readme.pdf located at : Insight/Examples/FuzzyConnectedness (with the code) -------------------- About the problem with Auxiliary: You can turn Auxiliary "ON" whithout having to install VTK. Just make sure that you set USE_INSTALL_VTK to "OFF" USE_BINARY_VTK to "OFF" The Auxiliary directory provides extra code that help us to create simple applications for the Examples. This directory is *not* considered part of ITK but is very convenient for the purpose of the Examples. Without this directory we will only be able to write examples that run from the Comman line. Auxiliary contains a mix of things, some parts require FLTK, some parts require VTK. If you turn them off selectively they should not be a problem. Luis ========================================= fj wrote: >Hi Luis: >I have extract the ITKSourceWin32Beta again . > when I use cmake to compile ITK and select the BUILD_AUXILIARY is "ON".Then ,when I compile in VC6,there is a error , >detail: > >But when I set BUILD_AUXILIARY is "OFF",there is no error.what is wrong with the auxiliary part?because the installation of vtk?????? > >And when I run the EllipsoidInteriorExteriorSpatialFunction ,The window just flash one time and then nothing happened,and there is some word on the window ,the detail: > >itkEllipsoidInteriorExteriorSpatialFunction example start >new physical sourceImage crated >new physical sourceImage allocated >the window just display those words and then nothing happened. > >when i run the FEM example , >the window is flash so quickly,I can see nothing. > >when I run the Fuzzy Connectedness example ,the example display "input file name",but I do not know the rule of input. >is there a document about use the example?????? >the shape detection example is same as Fuzzyconnectedness example. > >the MultiResMIRegistration and PrincipalAxes and EllipsoidInteriorExteriorSpatialFunction example are same as FEM example. >are there some document about how to handle the example??????? > > > From luis.ibanez@kitware.com Thu Mar 21 16:45:55 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Thu, 21 Mar 2002 11:45:55 -0500 Subject: [Insight-users] Re: question: Problem with vtk\itk References: <000c01c1d0aa$6199ed60$c73d6fa6@fj> Message-ID: <3C9A0E43.1060507@kitware.com> Hi Fj, Auxiliary/vtk Contains code for interfacing ITK and VTK. This is not officially part of the ITK Toolkit. It is provided for convinience for those users who may be interested in using both toolkits together. If you want to take advantage of this code you have to install VTK in your system. If you already have VTK in your machine, what may be missing is to set up the VTK paths correctly. Note that you can use a "Binary" VTK installation or a "Built" installation. The "Binary" is the one that you download as compiled libraries and is intalled in your systems with the Install wizard. The "Built" exist only if you downloaded VTK source code and compile it yourself. In some cases people have both of them so CMake is letting you select which one (if any) you want to use. Once you select: USE_INSTALLED_VTK (ON/OFF) USE_BUILT_VTK (ON/OFF) Then click on the "Advanced" CMake check box and make sure that the following paths are set correctly according to your installation: VTK_BINARY_PATH VTK_INSTALL_PATH Please let us know if you continue experiencing any problems with the installation. Thanks Luis ================================ fj wrote: > Hi Luis: > I have extract the ITKSourceWin32Beta again . > when I use cmake to compile ITK and select the BUILD_AUXILIARY is > "ON".Then ,when I compile in VC6,there is a error , > detail: > > --------------------Configuration: itkCurvatureFlowToVTK - Win32 > Debug-------------------- > Performing Custom Build Step on > E:/TEMP/itk/itk/ITKSourceWin32Beta/Insight/Auxiliary/vtk/CMakeLists.txt > Compiling... > itkCurvatureFlowToVTK.cxx > E:\TEMP\itk\itk\ITKSourceWin32Beta\Insight\Auxiliary\vtk\itkCurvatureFlowToVTK.cxx(24) > : fatal error C1083: Cannot open include file: 'vtkImageImport.h': No > such file or directory > Error executing cl.exe. > > But when I set BUILD_AUXILIARY is "OFF",there is no error.what is > wrong with the auxiliary part?because the installation of vtk?????? > > And when I run the EllipsoidInteriorExteriorSpatialFunction ,The > window just flash one time and then nothing happened,and there is some > word on the window ,the detail: > > itkEllipsoidInteriorExteriorSpatialFunction example start > new physical sourceImage crated > new physical sourceImage allocated > the window just display those words and then nothing happened. > > when i run the FEM example , > the window is flash so quickly,I can see nothing. > > when I run the Fuzzy Connectedness example ,the example display "input > file name",but I do not know the rule of input. > is there a document about use the example?????? > the shape detection example is same as Fuzzyconnectedness example. > > the MultiResMIRegistration and PrincipalAxes and > EllipsoidInteriorExteriorSpatialFunction example are same as FEM example. > are there some document about how to handle the example??????? > > From cates@cs.utah.edu Thu Mar 21 18:31:00 2002 From: cates@cs.utah.edu (Joshua Cates) Date: Thu, 21 Mar 2002 11:31:00 -0700 (MST) Subject: [Insight-users] Anisotropic diffusion ( was RE: ShapeDetection) In-Reply-To: <635ADAEFC2399148BCCBB4193B6BF3A00AA9DA@se2kexch01.insightful.com> Message-ID: Hi Christina, The different varieties of anisotropic diffusion that we have implemented are documented in the header files of the code and are also described on the www.itk.org webpage under the Documentation, Manual Pages section. =20 You will find an overview of the mathematics involved and some references. = =20 Take a look at the documentation for itkAnisotropicDiffusionFunction.h for the most detailed info. I apologize for the missing equations in the online documentation, this was supposed to have been fixed some time ago. Briefy, here is a breakdown of the different filters: Curvature: Less blurring at regions of high curvature. Better for preserving smaller image features but a slower technique. Gradient: Preserves regions with higher gradient magnitude. If you find the curvature variant doesn't give the results you want, try this one. The vector filters are just implementations of the above for vector-valued data, rgb data, etc. They require an images of itk::Vectors. Sounds like for MRI data you probably won't need these. (AnisotropicDiffusionImageFilter is just a base class for the specific types of diffusion and has no functionality in itself. It cannot be instantiated. ) For parameters, start with about 10-15 iterations of the filters using Conductance parameters of 1.0 and TimeStep of 0.125. You can lower the time step value, but values much higher than 0.125 will not produce stable solutions. Let me know if you have any more questions or any suggestions, Josh ______________________________ Josh Cates=09=09=09 School of Computer Science=09 University of Utah Email: cates@cs.utah.edu Phone: (801) 587-7697 URL: www.cs.utk.edu/~cates On Wed, 20 Mar 2002, Lydia Ng wrote: > Can someone help Christina as to the differences > in the differ favors of anisotropic diffusion? >=20 > She is hoping to use the anisotropic diffusion to remove > texture and enhance MR images of the liver. >=20 > Cheers, > Lydia >=20 > > -----Original Message----- > > From: Christina Lee [mailto:dreamie222@yahoo.com] > > Sent: Wednesday, March 20, 2002 2:28 PM > > To: Lydia Ng > > Subject: RE: ShapeDetection > >=20 > >=20 > >=20 > > Hi Lydia, > >=20 > > How are you? > > I think I'll try to preprocess the MR images with > > anisotropic diffusion as you suggested. Although I'm > > not exactly sure what kind of anistropic diffusion > > filter that I need (there seems to be three > > -curvature, gradient & vector!?) > >=20 > > I couldn't find the source code (or the cxx file) for > > itkAnisotropicDiffusionImageFilter.h & I did a > > thorough search on the files that I downloaded from > > the ITK website. Are there DLL or LIB files for the > > derived classes that I'm not aware of?=20 > >=20 > > Hope to hear from you soon. > >=20 > > Thank you so much for your help! > >=20 > > Christina > > --- Lydia Ng wrote: > > > Hi Christina, > > >=20 > > > The ShapeDetection program is not very sophisticated > > > in > > > that it only uses image gradient information to > > > generate > > > an edge potential map. Ideally, the edge potential > > > map is > > > zero at an "edge" and one in homogenous areas. > > >=20 > > > A fastmarching algorithm is used to grow out > > > a contour from a seed point. The rate of expansion > > > of the=20 > > > contour is determined by the values in the edge > > > potential map.=20 > > >=20 > > > I think the algorithm is working well for CT=20 > > > because the edges are nice and strong. > > > I am not familiar with MR images of the liver, but > > > if there are > > > high gradient textures within the liver then these > > > might=20 > > > interfere with the expansion of the contour. > > >=20 > > > The other issue is that the computed edge potential > > > map > > > is far from ideal. For example, if the boundary > > > gradient isn't > > > strong, the associated edge potential will be > > > some non-zero value and the contour will eventually > > > leak=20 > > > across the boundary as time goes on. > > >=20 > > > What kind of output are you getting when you look > > > at it at various time crossing thresholds? > > >=20 > > > I guess you can also try some preprocessing with > > > something > > > like anisotropic diffusion to get rid of some of the > > > texture > > > and enhance the boundaries. > > >=20 > > > - Lydia > > >=20 > > > > -----Original Message----- > > > > From: Christina Lee [mailto:dreamie222@yahoo.com] > > > > Sent: Wednesday, February 27, 2002 2:30 PM > > > > To: Lydia Ng > > > > Subject: ShapeDetection > > > >=20 > > > >=20 > > > >=20 > > > > Hi Lydia, > > > >=20 > > > > How are you?=20 > > > > I've been running the ShapeDetection program on > > > some > > > > MR images (to segment out the liver) & I haven't > > > had > > > > any luck. The program worked pretty well for the > > > CT > > > > data but not for the MR data - I wonder if it's > > > > because the MR images are more textured. Any > > > comments > > > > or suggestions? > > > > =20 > > > > Hope to hear from you soon. > > > >=20 > > > > Thanks, > > > >=20 > > > > Christina > > > >=20 > > > > __________________________________________________ > > > > Do You Yahoo!? > > > > Yahoo! Greetings - Send FREE e-cards for every > > > occasion! > > > > http://greetings.yahoo.com > > > >=20 > >=20 > >=20 > > __________________________________________________ > > Do You Yahoo!? > > Yahoo! Movies - coverage of the 74th Academy Awards=AE > > http://movies.yahoo.com/ > >=20 > _______________________________________________ > Insight-users mailing list > Insight-users@public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users >=20 From David.Rich@trw.com Thu Mar 21 22:01:39 2002 From: David.Rich@trw.com (David Rich) Date: Thu, 21 Mar 2002 17:01:39 -0500 Subject: [Insight-users] MultiResMIRegistration Example Message-ID: This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --=_CE936558.2E4F886D Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable I am trying to test the MultiResMIRegistration example on a couple of = images. However, I do not understand some of the parameters of the input = file. In particular, line 14 specifies the translation scale at each = resolution level. These seemed to affect my output in a strange way, so I = checked into the code: // set the translation scale itk::Point scales; scales.Fill(1.0); for( int j =3D 4; j < 7; j++ ) { scales[j] =3D 1.0 / vnl_math_sqr( m_TranslationScales[0] ); } internalRegistrator->GetOptimizer()->GetTransform()->SetScale( scales ); =20 First, I don't understand why the code reads in 5 different scales and = then only uses the first one. =20 Second, it appears that the scaling fills 3 parameters, 4 through 6. =20 I would appreciate it if somenone could explane what this is supposed to = do. I can't find any other documentation on it. Also, input lines 10 and 11 read in the starting level shrink factor for = each of the two images. Is this the term used for resolution reduction? Thanks for any help. Dave Rich --=_CE936558.2E4F886D Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Description: HTML

I am trying to test the MultiResMIRegistration example = on a=20 couple of images. However, I do not understand some of the parameters= of=20 the input file. In particular, line 14 specifies the translation = scale at=20 each resolution level. These seemed to affect my output in a strange = way,=20 so I checked into the code:

// set the translation scale
=20 itk::Point<double,7> scales;
scales.Fill(1.0);
= for(=20 int j =3D 4; j < 7; j++ )
    {
   = =20 scales[j] =3D 1.0 / vnl_math_sqr( m_TranslationScales[0] );
  = =20 }
=20 internalRegistrator->GetOptimizer()->GetTransform()->SetScale( = scales=20 );

First, I don't understand why the code reads in 5 different scales = and then=20 only uses the first one.

Second, it appears that the scaling fills 3 parameters, 4 = through=20 6.

I would appreciate it if somenone could explane what this is = supposed=20 to do. I can't find any other documentation on it.

Also, input lines 10 and 11 read in the starting level shrink factor = for=20 each of the two images. Is this the term used for resolution=20 reduction?

Thanks for any help.

Dave Rich

--=_CE936558.2E4F886D-- From Siddhartha.Thyagarajan@geind.ge.com Fri Mar 22 03:44:27 2002 From: Siddhartha.Thyagarajan@geind.ge.com (Thyagarajan, Siddhartha (CORP, GEITC)) Date: Fri, 22 Mar 2002 09:14:27 +0530 Subject: [Insight-users] itk to vtk Message-ID: <1988808309E4D51195440008C716B67AA2775E@ban05xbindge.jfwtc.ge.com> I'm wondering if there is a way itk classes can be called in vtk ..and if so how? _____________________________________________________________________ Siddhartha Thyagarajan EMail: Siddhartha.Thyagarajan@geind.ge.com Imaging Technology. Phone: +91-80-8412050 Ext: 3622 GE John F. Welch Technology Center EPIP, Phase II, Hoodi Village, Whitefield Rd., Bangalore 560066, INDIA "THIS E-MAIL MESSAGE ALONG WITH ANY ATTACHMENTS IS INTENDED ONLY FOR THE ADDRESSEE and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are notified that any dissemination, distribution or copy of this communication is strictly Prohibited. If you have received this message by error, please notify us immediately, return the original mail to the sender and delete the message from your system." From wlorens1@nycap.rr.com Fri Mar 22 03:42:34 2002 From: wlorens1@nycap.rr.com (Bill Lorensen) Date: Thu, 21 Mar 2002 22:42:34 -0500 Subject: [Insight-users] itk to vtk In-Reply-To: <1988808309E4D51195440008C716B67AA2775E@ban05xbindge.jfwtc. ge.com> Message-ID: <5.1.0.14.2.20020321224025.024d38c0@pop.nycap.rr.com> Yes there is, although we have not released the code yet. We have designed a set of vtk classes that encapsulate the import/export mechanisms of vtk and itk. Hopefully, we can release this code soon. It needs a bit of cleanup. Bill At 09:14 AM 3/22/02 +0530, Thyagarajan, Siddhartha (CORP, GEITC) wrote: >I'm wondering if there is a way itk classes can be called in vtk ..and if so >how? > >_____________________________________________________________________ >Siddhartha Thyagarajan EMail: >Siddhartha.Thyagarajan@geind.ge.com >Imaging Technology. Phone: +91-80-8412050 Ext: >3622 >GE John F. Welch Technology Center >EPIP, Phase II, Hoodi Village, Whitefield Rd., Bangalore 560066, INDIA > > > > > >"THIS E-MAIL MESSAGE ALONG WITH ANY ATTACHMENTS IS INTENDED ONLY FOR THE >ADDRESSEE and may contain confidential and privileged information. >If the reader of this message is not the intended recipient, >you are notified that any dissemination, distribution or copy of this >communication is strictly Prohibited. >If you have received this message by error, please notify us >immediately, return the original mail to the sender and delete the >message from your system." > >_______________________________________________ >Insight-users mailing list >Insight-users@public.kitware.com >http://public.kitware.com/mailman/listinfo/insight-users From lng@insightful.com Fri Mar 22 04:06:47 2002 From: lng@insightful.com (Lydia Ng) Date: Thu, 21 Mar 2002 20:06:47 -0800 Subject: [Insight-users] MultiResMIRegistration Example Message-ID: 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Two way bindings? It would be quite nice to be able to combine Java and ITK. Jarek From luis.ibanez@kitware.com Fri Mar 22 13:38:06 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Fri, 22 Mar 2002 08:38:06 -0500 Subject: [Insight-users] Re: question: ITK Examples References: <000b01c1cff0$81223d50$c73d6fa6@fj> <3C989ED1.9020104@kitware.com> <002601c1d0a0$15770170$c73d6fa6@fj> <3C9A0B67.50800@kitware.com> <000001c1d155$4cb32a00$c73d6fa6@fj> Message-ID: <3C9B33BE.7080509@kitware.com> Hi Fj, Here is who I did in my own installation: 1) VTK is installed in d:\vtk40 NOTE that the .exe that you need to download is: - vtk40Cpp.exe Which contains both the libraries and headers for development with VC++ 6.0. The libraries are automatically put in a "lib" subdirectory and the headers in an "include" subdirectory. It looks like you installed "vtk40Core.exe" which only contains the .dll and put them in a "bin" subdirectory. 2) In CMake I have selected: VTK_INSTALL_PATH = D:/vtk40 USE_BUILT_VTK=OFF USE_INSTALLED_VTK=ON My guess is that your VTK installation is actually missing the header files....but this is just a guess. Please let us know if this helps. Luis ============================ fj wrote: >when i set the path is E:\vtk\vtk40\vtk40core\bin,still the same error , > >when i set to E:\vtk\vtk40\vtk40core, still the smae error; >--------------------Configuration: itkCurvatureFlowToVTK - Win32 Debug-------------------- >Performing Custom Build Step on E:/TEMP/itk/itk/ITKSourceWin32Beta/Insight/Auxiliary/vtk/CMakeLists.txt >Compiling... >itkCurvatureFlowToVTK.cxx >E:\TEMP\itk\itk\ITKSourceWin32Beta\Insight\Auxiliary\vtk\itkCurvatureFlowToVTK.cxx(24) : fatal error C1083: Cannot open include file: 'vtkImageImport.h': No such file or directory >Error executing cl.exe. > >how to set the VTK_BINARY_PATH and VTK_INSTALL_PATH?????? > > From brad.king@kitware.com Fri Mar 22 14:29:57 2002 From: brad.king@kitware.com (Brad King) Date: Fri, 22 Mar 2002 09:29:57 -0500 (EST) Subject: [Insight-users] Java bindings In-Reply-To: <5.1.0.14.2.20020321231722.01fc9238@pop3.norton.antivirus> Message-ID: Jarek, > Are there plans to add Java bindings to ITK? Two way bindings? It > would be quite nice to be able to combine Java and ITK. The wrapping tool for ITK is CABLE, but it doesn't yet support anything but Tcl bindings. Extending it to support other languages is planned, but it will be a while before any new work is done. -Brad From dkulkarni@uh.edu Fri Mar 22 17:17:20 2002 From: dkulkarni@uh.edu (Dhananjay Kulkarni) Date: Fri, 22 Mar 2002 11:17:20 -0600 Subject: [Insight-users] DICOMM reader Message-ID: HI , I am looking for a DICOM reader as I am working on DICOM files. If possible I need it in C++. Is it available somewhere on the web...(open source). Any help would be greatly appreciated. Thanks, Dhananjay Kulkarni. From will.schroeder@kitware.com Fri Mar 22 19:45:34 2002 From: will.schroeder@kitware.com (Will Schroeder) Date: Fri, 22 Mar 2002 14:45:34 -0500 Subject: [Insight-users] Downtime for itk.org and In-Reply-To: Message-ID: <5.1.0.14.0.20020322144254.026b7640@pop.nycap.rr.com> Hello! Kitware's public web server (which serves itk.org) is in need of an update. We are working towards replacing public.kitware.com with a much more powerful server. The new server has features such as dedicated UPS, RAID-5 disk array, better CPU, more memory, and much more disk space than the old one. We are planning to replace the server soon, but before we do this, we would like to notify all users that there will be downtime. We have not decided on when the replacement will happen, but the new server is almost ready. We will let you know several days in advance. If you have any question, comments, or suggestions, please let us know. Andy Cedilnik (andy.cedilnik@kitware.com) Kitware Inc. From luis.ibanez@kitware.com Sat Mar 23 13:58:45 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Sat, 23 Mar 2002 08:58:45 -0500 Subject: [Insight-users] Re: question: ITK Examples References: <000b01c1cff0$81223d50$c73d6fa6@fj> <3C989ED1.9020104@kitware.com> <002601c1d0a0$15770170$c73d6fa6@fj> <3C9A0B67.50800@kitware.com> <000001c1d155$4cb32a00$c73d6fa6@fj> <3C9B33BE.7080509@kitware.com> <000801c1d20b$464b55a0$c73d6fa6@fj> Message-ID: <3C9C8A15.8090702@kitware.com> Hi fj, It is Ok to install vtk40core.exe and vtk40cpp.exe in a different path. If you install vtk40cpp you don't need vtk40core.exe at all. ( I would remove vtk40core in order to avoid confusions). vtk40Cpp.exe contains all what you need: 1) a lib/vtk directory with all the libraries as static libraries. 2) an include/vtk directory with all the headers. vtk40Core.exe is intended for applications that link dynamically with VTK but not for code development. Let's say that you write your killer application using VTK, when you build it you can link dynamically with VTK dll's; So when you ship your application to a client, the VTK dll's can be appart from your application. That prevents you from producing huge .exe files in which a large percent of the code are the VTK libs themselves. All that makes more sense when you produce your secons killer application :-) because this second one can just "share" the dlls (that's what shared libraries are for, after all...) So you factorize the VTK code from the applications that use it. ---- (comming back to ITK....) When you install vkt40Cpp.exe it asks you for a particular directory where you want to have the /lib/vtk and include/vtk subdirectories. This same directory is the one that you should pass to CMake as : VTK_INSTALLED_PATH then put USE_INSTALLED_VTK to "ON" That should do it ! Please let us know if that works for you. You're very close now, don't give up !! :-) Luis =============================== fj wrote: >Hi Luis : > I have install vtk40core.exe and vtk40cpp.exe in a different folder.is that ok??????? >are the vtk40core and vtk40cpp all in the same path you have used????? > From luis.ibanez@kitware.com Mon Mar 25 14:08:12 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Mon, 25 Mar 2002 09:08:12 -0500 Subject: [Insight-users] Re: another question References: <000001c1d3d0$ae11e070$c73d6fa6@fj> Message-ID: <3C9F2F4C.1000806@kitware.com> Hi Fj, ITK have different kinds of examples. Some of them run on the command line. Some of them have a GUI. The ones that run on the command line have to be executed from the MS-DOS command window or the Cygwin Bash shell window. If you click on them from the file navigator you will only see the MS-DOS window pop-up and disappear right away. Most of the examples that use a GUI require to install FLTK in your machine. FLTK is not required for using the ITK library. It is *only* used by some of the examples. Once you build ITK all the executables for the examples are placed in their corresponding subdirectory. For example, the Morphogenesis example executable will be placed in your binary directory under: myITKBinaryDirectory/Examples/Morphogenesis/Debug/Morphogenesis.exe Note that VC++ always add a subdirectory with the configuration you selected at build time: (Debug, Release, ...etc). For the examples with GUI you can go directly to their binary directories and double click on the icon of the .exe file. It may be simpler to do it from VC++ just to selecting their project as an active project and making: Ctrl+F5 Are you interested in running a particular example ? --------------------------------- In case you want to verify the installation sequence for examples with GUI, here is a detailed description: 1) Install FLTK 2) Run CMake and do the following: 2.1) set BUILD_AUXILIARY = ON 2.2) Click on the "Advanced" checkbox 2.2.1) Select FLTK_LIBRARY="... your path to fltk.lib.. " 2.2.2) Select FLTK_INCLUDE_PATH="..your path to fltk dir " 2.2.3) Select FLTK_FLUID_PATH=" your path to /fluid/fluid.exe..." 2.3) set BUILD_FLTKIMAGEVIEWER = ON 2.4) set BUILD_EXAMPLES = ON 2.5) click on "Configure" until no new red items appear. 2.6) click on "OK" (CMake will generate the projects and quit) 3) Open ITK.dsw with VC++. You should see most of the examples in the list of projects. ------------------------------------- fj wrote: > Hi luis : > > another question .I have install fltk before install itk ,and when I > compile itk I have select the BUILD_Auxiliary "ON". And I have know if > I select the BUILD_Auxiliary "ON", I can get a gui to use to example > .how to start the gui? > > I did not find it in my itk folder(installed folder). > From luis.ibanez@kitware.com Mon Mar 25 14:46:21 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Mon, 25 Mar 2002 09:46:21 -0500 Subject: [Insight-users] Re: question: ITK Examples References: <000b01c1cff0$81223d50$c73d6fa6@fj> <3C989ED1.9020104@kitware.com> <002601c1d0a0$15770170$c73d6fa6@fj> <3C9A0B67.50800@kitware.com> <000001c1d155$4cb32a00$c73d6fa6@fj> <3C9B33BE.7080509@kitware.com> <000801c1d20b$464b55a0$c73d6fa6@fj> <3C9C8A15.8090702@kitware.com> <000801c1d3cd$67ab71d0$c73d6fa6@fj> Message-ID: <3C9F383D.6060308@kitware.com> Hi Fj, There was an error in the CMakeLists.txt file in : Insight/Examples. The option that enables the WatershedSegmenation example was misspelled as "WATERSHED_REGISTRATION" instead of "WATERSHED_SEGMENTATION". It is now fixed on the repository if you want to make a cvs update. Otherwise you can just go and edit the file. in: Insight/Examples/CMakeLists.txt go to line 17, and replace: BUILD_WATERSHED_REGISTRATION by BUILD_WATERSHED_SEGMENTATION and the run CMake. The project : itkWatershedSegmentation should now appear in your VC++ workspace when you load ITK.dsw. Once you get it built, you can run this example from the command line. You will find detailed instructions about how to run this example in the README file located at Insight/Examples/WatershedSegmentation/README and in the web page of the example, located at: http://www.itk.org/HTML/WatershedSegmentationExample.html BTW: most of the examples have descriptions at the web page: http://www.itk.org/HTML/Examples.htm Please let us know if you encounter any problem when trying to run the example. Thanks Luis =========================================== fj wrote: >Hi Luis : > I have successfully install itk(i think).But I still can not use the example. >I have see the readme of FuzzyConnectedness.So I have know the input rule of it . So I can use the example. >But I still can use the watershedsegmentation example . >When I double click the watershedsegmentation.exe in the debug folder,the new window just flash one time ,and some word on it ,and then nothing. >the word in the window is : > >use:watershed input_file output_file_prefix conductance_temp diffusion_iterations lower_threshlod >press any key to continue > >how can i use the example to segment a *.pgm ??????? > >thanks for your help yours fangjing > From Vincent.Daanen@imag.fr Tue Mar 26 13:08:46 2002 From: Vincent.Daanen@imag.fr (Vincent Daanen) Date: Tue, 26 Mar 2002 14:08:46 +0100 Subject: [Insight-users] Compilation of Itk fails on Win2000 Message-ID: <3CA072DE.52851437@mail-timc.imag.fr> Hi, I try to compile itk on a win2000 based box with msvc 6.0 When compiling the IView project, compilation stop with theses errors IViewGUI.cxx (same errors for IViewGUIBase.cxx file) E:\Outils_Dev\fltk-1.1.0b10\FL\math.h(52) : error C2065: 'floor' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(149) : error C2039: 'sqrt' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(149) : error C2065: 'sqrt' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'exp' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'log' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'exp' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'log' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2065: 'exp' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2065: 'log' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vcl\win32/vcl_complex.h(49) : error C2373: 'sqrt' : redefinition; different type modifiers Is this due to a mis configuration within CmakeSetup ? what should I do ? Thanks for help Vince -- Vincent Daanen, Research Engineer- Post Doctoral Position Laboratoire TIMC/IMAG Equipe GMCAO - Universit� Joseph Fourier - CNRS UMR 5525 Facult� de M閐ecine - Domaine de la Merci - 38706 La Tronche cedex - France Tel: +33 (0)4 76 54 95 23 Vincent.Daanen@imag.fr From jjomier@cs.unc.edu Tue Mar 26 16:15:15 2002 From: jjomier@cs.unc.edu (Julien Jomier) Date: Tue, 26 Mar 2002 11:15:15 -0500 Subject: [Insight-users] Compilation of Itk fails on Win2000 References: <3CA072DE.52851437@mail-timc.imag.fr> Message-ID: <002401c1d4e1$6a0d4830$33ff1398@vangogh> Hi Vincent, That seems to be a problem with FLTK: Did you compile FLTK using multithread DLL directive ? (msvc under Projects/Settings/"C/C++") Let me know if that works Julien ----- Original Message ----- From: "Vincent Daanen" To: Sent: Tuesday, March 26, 2002 8:08 AM Subject: [Insight-users] Compilation of Itk fails on Win2000 Hi, I try to compile itk on a win2000 based box with msvc 6.0 When compiling the IView project, compilation stop with theses errors IViewGUI.cxx (same errors for IViewGUIBase.cxx file) E:\Outils_Dev\fltk-1.1.0b10\FL\math.h(52) : error C2065: 'floor' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(149) : error C2039: 'sqrt' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(149) : error C2065: 'sqrt' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'exp' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'log' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'exp' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2039: 'log' : is not a member of '`global namespace'' E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2065: 'exp' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vnl/vnl_math.h(153) : error C2065: 'log' : undeclared identifier E:\Outils_Dev\Insight\Code\Numerics\vxl\vcl\win32/vcl_complex.h(49) : error C2373: 'sqrt' : redefinition; different type modifiers Is this due to a mis configuration within CmakeSetup ? what should I do ? Thanks for help Vince -- Vincent Daanen, Research Engineer- Post Doctoral Position Laboratoire TIMC/IMAG Equipe GMCAO - Universit� Joseph Fourier - CNRS UMR 5525 Facult� de M閐ecine - Domaine de la Merci - 38706 La Tronche cedex - France Tel: +33 (0)4 76 54 95 23 Vincent.Daanen@imag.fr _______________________________________________ Insight-users mailing list Insight-users@public.kitware.com http://public.kitware.com/mailman/listinfo/insight-users From luis.ibanez@kitware.com Wed Mar 27 14:44:50 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Wed, 27 Mar 2002 09:44:50 -0500 Subject: [Insight-users] pragmatic.crd Time Machine Message-ID: <3CA1DAE2.9030102@kitware.com> HI, "pragmatic.crd" is producing 97 warning messages related with a clock synchronization problem: gmake[2]: *** Warning: File `cmake.depends' has modification time in the future (2002-03-27 08:03:21 > 2002-03-27 07:54:20) gmake[2]: warning: Clock skew detected. Your build may be incomplete. The system clock seems to be 9 minutes ahead of the file server. Could it be possible to synchronize this platform ? Thanks Luis From luis.ibanez@kitware.com Wed Mar 27 14:49:15 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Wed, 27 Mar 2002 09:49:15 -0500 Subject: [Insight-users] pragmatic.crd Time Machine References: <3CA1DAE2.9030102@kitware.com> Message-ID: <3CA1DBEB.20106@kitware.com> My apologies, This message was suppossed to be sent to the developers list. Luis ---------------------------------------------- Luis Ibanez wrote: > HI, > > "pragmatic.crd" is producing 97 warning messages > related with a clock synchronization problem: > > > gmake[2]: *** Warning: File `cmake.depends' has modification time in the > future (2002-03-27 08:03:21 > 2002-03-27 07:54:20) > gmake[2]: warning: Clock skew detected. Your build may be incomplete. > > > > The system clock seems to be 9 minutes ahead of the file server. > > > Could it be possible to synchronize this platform ? > > > > Thanks > > > Luis > > > _______________________________________________ > Insight-users mailing list > Insight-users@public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users > From ycllydia@hotmail.com Wed Mar 27 18:04:50 2002 From: ycllydia@hotmail.com (ycl lydia) Date: Wed, 27 Mar 2002 18:04:50 +0000 Subject: [Insight-users] win32 Console application Message-ID: Hi folks I have two questions 1. I made the win32 console application as mention in the document VC_Custom project. I followed exactly the instructions, but I got a list of 102 message errors: Here is a sample d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error C2653: 'vcl_generic_iosfwd_STD' : is not a class or namespace name d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error C2143: syntax error : missing ';' before '&' d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error C2501: 'ostream' : missing storage-class or type specifiers d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error C2059: syntax error : ';' d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error C2653: 'vcl_generic_iosfwd_STD' : is not a class or namespace name d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error C2061: syntax error : identifier 'ostream' Could anyone help ? _________________________________________________________________ MSN Photos est le moyen le plus simple de partager, modifier et imprimer vos photos pr閒閞閑s. http://photos.msn.fr/Support/WorldWide.aspx From ycllydia@hotmail.com Wed Mar 27 18:07:57 2002 From: ycllydia@hotmail.com (ycl lydia) Date: Wed, 27 Mar 2002 18:07:57 +0000 Subject: [Insight-users] another question Message-ID: I compiled itk and it works. The only problem that I have is with the project vtk2itk I have always this message error tk2itk.obj : error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall vtkObject::Print(class std::basic_ostream > &)" (__imp_?Print@vtkObject@@QAEXAAV?$basic_ostream@DU?$char_traits @D@std@@@std@@@Z) did anyone already have the same message?? Lydia _________________________________________________________________ T閘閏hargez MSN Explorer gratuitement � l'adresse http://explorer.msn.fr/intl.asp. From luis.ibanez@kitware.com Wed Mar 27 19:04:55 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Wed, 27 Mar 2002 14:04:55 -0500 Subject: [Insight-users] another question References: Message-ID: <3CA217D7.9060602@kitware.com> Hi Lydia, This particular project is intended to present an example of how to link ITK with VTK. It seems that at linking time it is not finding the appropiate VTK libraries. Could you please run CMake and double check that the PATH's you provided for VTK libraries are correct. Please let us know if that helps or not. Thanks Luis ----------------------------------------------------------- ycl lydia wrote: > I compiled itk and it works. The only problem that I have is with the > project vtk2itk > I have always this message error > tk2itk.obj : error LNK2001: unresolved external symbol > "__declspec(dllimport) public: void __thiscall vtkObject::Print(class > std::basic_ostream > &)" > (__imp_?Print@vtkObject@@QAEXAAV?$basic_ostream@DU?$char_traits > @D@std@@@std@@@Z) > > did anyone already have the same message?? > > Lydia > > _________________________________________________________________ > T閘閏hargez MSN Explorer gratuitement � l'adresse > http://explorer.msn.fr/intl.asp. > > _______________________________________________ > Insight-users mailing list > Insight-users@public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users > > From ycllydia@hotmail.com Wed Mar 27 19:13:06 2002 From: ycllydia@hotmail.com (ycl lydia) Date: Wed, 27 Mar 2002 19:13:06 +0000 Subject: [Insight-users] another question Message-ID: Hi Luis, Thanks Luis for your reply. I don't think that it's a problem of paths, in fact if don't use the flag /D "VTK_USE_ANSI_STDLIB" /GX /Zm1000 in the setting, I have a the following compilation error error C2664: 'Print' : cannot convert parameter 1 from 'class std::basic_ostream >' to 'class ostream &' A reference that is not to 'const' cannot be bound to a non-lvalue But If I use the flag, I have no compilation error but a linkage error, I think this is dur to some iostream library. >From: Luis Ibanez >To: ycl lydia >CC: insight-users@public.kitware.com >Subject: Re: [Insight-users] another question >Date: Wed, 27 Mar 2002 14:04:55 -0500 > > >Hi Lydia, > >This particular project is intended to present an example >of how to link ITK with VTK. > >It seems that at linking time it is not finding the appropiate >VTK libraries. > >Could you please run CMake and double check that the >PATH's you provided for VTK libraries are correct. > >Please let us know if that helps or not. > > >Thanks > > >Luis > >----------------------------------------------------------- > >ycl lydia wrote: > >>I compiled itk and it works. The only problem that I have is with the >>project vtk2itk >>I have always this message error >>tk2itk.obj : error LNK2001: unresolved external symbol >>"__declspec(dllimport) public: void __thiscall vtkObject::Print(class >>std::basic_ostream > &)" >>(__imp_?Print@vtkObject@@QAEXAAV?$basic_ostream@DU?$char_traits >>@D@std@@@std@@@Z) >> >>did anyone already have the same message?? >> >>Lydia >> >>_________________________________________________________________ >>T閘閏hargez MSN Explorer gratuitement � l'adresse >>http://explorer.msn.fr/intl.asp. >> >>_______________________________________________ >>Insight-users mailing list >>Insight-users@public.kitware.com >>http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > >_______________________________________________ >Insight-users mailing list >Insight-users@public.kitware.com >http://public.kitware.com/mailman/listinfo/insight-users _________________________________________________________________ Discutez en ligne avec vos amis, essayez MSN Messenger�: http://messenger.msn.fr From luis.ibanez@kitware.com Wed Mar 27 19:19:05 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Wed, 27 Mar 2002 14:19:05 -0500 Subject: [Insight-users] win32 Console application References: Message-ID: <3CA21B29.7070000@kitware.com> Hi Lydia, VNL is the mathematical library that support among other things the management of matrices and vectors in ITK. This section of the code is heavely tested every day on the Dashboard, so a compilation error on this headers files suggest that your project may be including header files in an unfortunate order or that a configuration option is going wrong. It is hard however to guess just from the error message. Did you created your project using CMake ? or by setting by hand all the options in new VC++ project ? Could you please post your code to the list ? In particular is interesting to see what are the headers you are including. Thanks Luis ========================================================== ycl lydia wrote: > Hi folks > I have two questions > 1. I made the win32 console application as mention in the document > VC_Custom project. I followed exactly the instructions, but I got a > list of 102 message errors: Here is a sample > > d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error > C2653: 'vcl_generic_iosfwd_STD' : is not a class or namespace name > d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error > C2143: syntax error : missing ';' before '&' > d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error > C2501: 'ostream' : missing storage-class or type specifiers > d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error > C2059: syntax error : ';' > d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error > C2653: 'vcl_generic_iosfwd_STD' : is not a class or namespace name > d:\itknew\insight\code\numerics\vxl\vnl\vnl_vector.h(417) : error > C2061: syntax error : identifier 'ostream' > > Could anyone help ? > > > _________________________________________________________________ > MSN Photos est le moyen le plus simple de partager, modifier et > imprimer vos photos pr閒閞閑s. > http://photos.msn.fr/Support/WorldWide.aspx > > _______________________________________________ > Insight-users mailing list > Insight-users@public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users > > From luis.ibanez@kitware.com Wed Mar 27 19:28:05 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Wed, 27 Mar 2002 14:28:05 -0500 Subject: [Insight-users] another question References: Message-ID: <3CA21D45.5040600@kitware.com> Lydia, You're right, the problem is related to an iostream header. By default VTK use the traditional header files for iostrem, like: #include instead of the new ones used by ITK, like #include These two styles are incompatible. In order to use VTK with ITK you need to set VTK_USE_ANSI_STDLIB to "ON" in CMake when building VTK. This tells VTK to use the new standard header files so it can be compatible with ITK. Is the "Print" error message appearing when you compile VTK or when you compile ITK ? Could you post to the list the complete error message to get an idea of the file from which this is originated. Thanks Luis ======================================= ycl lydia wrote: > Hi Luis, > Thanks Luis for your reply. > I don't think that it's a problem of paths, in fact if don't use the > flag /D "VTK_USE_ANSI_STDLIB" /GX /Zm1000 in the setting, I have a the > following compilation error > error C2664: 'Print' : cannot convert parameter 1 from 'class > std::basic_ostream >' to 'class > ostream &' A reference that is not to 'const' cannot be bound to a > non-lvalue > But If I use the flag, I have no compilation error but a linkage > error, I think this is dur to some iostream library. > > >> From: Luis Ibanez >> To: ycl lydia >> CC: insight-users@public.kitware.com >> Subject: Re: [Insight-users] another question >> Date: Wed, 27 Mar 2002 14:04:55 -0500 >> >> >> Hi Lydia, >> >> This particular project is intended to present an example >> of how to link ITK with VTK. >> >> It seems that at linking time it is not finding the appropiate >> VTK libraries. >> >> Could you please run CMake and double check that the >> PATH's you provided for VTK libraries are correct. >> >> Please let us know if that helps or not. >> >> >> Thanks >> >> >> Luis >> >> ----------------------------------------------------------- >> >> ycl lydia wrote: >> >>> I compiled itk and it works. The only problem that I have is with the >>> project vtk2itk >>> I have always this message error >>> tk2itk.obj : error LNK2001: unresolved external symbol >>> "__declspec(dllimport) public: void __thiscall vtkObject::Print(class >>> std::basic_ostream > &)" >>> (__imp_?Print@vtkObject@@QAEXAAV?$basic_ostream@DU?$char_traits >>> @D@std@@@std@@@Z) >>> >>> did anyone already have the same message?? >>> >>> Lydia >>> >>> _________________________________________________________________ >>> T閘閏hargez MSN Explorer gratuitement � l'adresse >>> http://explorer.msn.fr/intl.asp. >>> >>> _______________________________________________ >>> Insight-users mailing list >>> Insight-users@public.kitware.com >>> http://public.kitware.com/mailman/listinfo/insight-users >>> >>> >> >> >> >> _______________________________________________ >> Insight-users mailing list >> Insight-users@public.kitware.com >> http://public.kitware.com/mailman/listinfo/insight-users > > > > _________________________________________________________________ > Discutez en ligne avec vos amis, essayez MSN Messenger : > http://messenger.msn.fr > > _______________________________________________ > Insight-users mailing list > Insight-users@public.kitware.com > http://public.kitware.com/mailman/listinfo/insight-users > > From ycllydia@hotmail.com Wed Mar 27 19:39:15 2002 From: ycllydia@hotmail.com (ycl lydia) Date: Wed, 27 Mar 2002 19:39:15 +0000 Subject: [Insight-users] another question Message-ID: I'm using vtk sine a while now and there is no problem with it. The message appears when I compile itk. I think your explanation is logical, now, I will try to rebuild vtk, I don't remember if I set TK_USE_ANSI_STDLIB to "ON" when I built it the first time. Here is the compete message (D:\itknew\Insight\Unsupported\vtk\vtk2itk.cxx(313) : error C2664: 'Print' : cannot convert parameter 1 from 'class std::basic_ostream >' to 'class ostream &' A reference that is not to 'const' cannot be bound to a non-lvalue) Lydia >From: Luis Ibanez >To: ycl lydia >CC: insight-users@public.kitware.com >Subject: Re: [Insight-users] another question >Date: Wed, 27 Mar 2002 14:28:05 -0500 > > >Lydia, > > >You're right, the problem is related to an iostream header. >By default VTK use the traditional header files for iostrem, >like: > > #include > >instead of the new ones used by ITK, like > > #include > >These two styles are incompatible. > > >In order to use VTK with ITK you need to set > > VTK_USE_ANSI_STDLIB to "ON" > >in CMake when building VTK. This tells VTK to >use the new standard header files so it can be >compatible with ITK. > > >Is the "Print" error message appearing when you >compile VTK or when you compile ITK ? > > >Could you post to the list the complete error message >to get an idea of the file from which this is originated. > > >Thanks > > Luis > > > >======================================= > >ycl lydia wrote: > >>Hi Luis, >>Thanks Luis for your reply. >>I don't think that it's a problem of paths, in fact if don't use the >>flag /D "VTK_USE_ANSI_STDLIB" /GX /Zm1000 in the setting, I have a the >>following compilation error >>error C2664: 'Print' : cannot convert parameter 1 from 'class >>std::basic_ostream >' to 'class >>ostream &' A reference that is not to 'const' cannot be bound to a >>non-lvalue >>But If I use the flag, I have no compilation error but a linkage >>error, I think this is dur to some iostream library. >> >> >>>From: Luis Ibanez >>>To: ycl lydia >>>CC: insight-users@public.kitware.com >>>Subject: Re: [Insight-users] another question >>>Date: Wed, 27 Mar 2002 14:04:55 -0500 >>> >>> >>>Hi Lydia, >>> >>>This particular project is intended to present an example >>>of how to link ITK with VTK. >>> >>>It seems that at linking time it is not finding the appropiate >>>VTK libraries. >>> >>>Could you please run CMake and double check that the >>>PATH's you provided for VTK libraries are correct. >>> >>>Please let us know if that helps or not. >>> >>> >>>Thanks >>> >>> >>>Luis >>> >>>----------------------------------------------------------- >>> >>>ycl lydia wrote: >>> >>>>I compiled itk and it works. The only problem that I have is with the >>>>project vtk2itk >>>>I have always this message error >>>>tk2itk.obj : error LNK2001: unresolved external symbol >>>>"__declspec(dllimport) public: void __thiscall vtkObject::Print(class >>>>std::basic_ostream > &)" >>>>(__imp_?Print@vtkObject@@QAEXAAV?$basic_ostream@DU?$char_traits >>>>@D@std@@@std@@@Z) >>>> >>>>did anyone already have the same message?? >>>> >>>>Lydia >>>> >>>>_________________________________________________________________ >>>>T閘閏hargez MSN Explorer gratuitement � l'adresse >>>>http://explorer.msn.fr/intl.asp. >>>> >>>>_______________________________________________ >>>>Insight-users mailing list >>>>Insight-users@public.kitware.com >>>>http://public.kitware.com/mailman/listinfo/insight-users >>>> >>>> >>> >>> >>> >>>_______________________________________________ >>>Insight-users mailing list >>>Insight-users@public.kitware.com >>>http://public.kitware.com/mailman/listinfo/insight-users >> >> >> >>_________________________________________________________________ >>Discutez en ligne avec vos amis, essayez MSN Messenger : >>http://messenger.msn.fr >> >>_______________________________________________ >>Insight-users mailing list >>Insight-users@public.kitware.com >>http://public.kitware.com/mailman/listinfo/insight-users >> >> > > > _________________________________________________________________ Discutez en ligne avec vos amis, essayez MSN Messenger�: http://messenger.msn.fr From luis.ibanez@kitware.com Thu Mar 28 06:18:56 2002 From: luis.ibanez@kitware.com (Luis Ibanez) Date: Thu, 28 Mar 2002 01:18:56 -0500 Subject: [Insight-users] about TPS and EBS References: <001701c1cd80$71be7620$1223bd89@ee.cuhk.edu.hk> <3C9613F2.80506@kitware.com> <002b01c1cf5e$b31bbee0$1223bd89@ee.cuhk.edu.hk> <3C98BA27.4000405@kitware.com> <002201c1d033$9fc853a0$19c3000a@dingdan> Message-ID: <3CA2B5D0.1030902@kitware.com> Hi Alex, The Code for the ThinPlateSpline and ElasticBodySpline is running much faster now. The bottleneck was at the level of the base class: itkKernelTransform. It was reorganizing the W matrix each time a point was transformed. This reorganization has been moved now to a "ReorganizeW()" method that is called only once at the end of ComputeW(). This method produce: (1) a NDxNL Matrix with the weights to be applied to all the G Kernel matrices, (2) one NDxND Matrix and (3) one ND vector with components of the Affine part of the transformation. ND = Dimensions of points NL = Dimensions of landmarks Note that ITK is N-Dimensional ! This KernelTransforms can be applied to Points in any dimension. We added the third Spline Kernel described in Davis' IEEE-TMI paper: the "Volume" spline where G = r^3 * I. It is in fact quite easy to add new kernels. Just add a new class deriving from KernelSpline and rewrite the G() matrix. An Important point: the KernelSpline transform is templated over the type used for representing the points in space (typically float or double) This type is being used now for the transformation matrices too, which has a fundamental influence in the results of the inversion of the matrix. The vnl_svd method is quite sensitive to the use of float. You can interpret that as : "never use float" ! :-) We will be fixing the intenal matrix type of the KernelTransform to "double" in the short term. If you want to verify how much it changes the results (and have some fun on the way...), just change "double" by "float" in line 46 of Examples/ThinPlateSpline/ThinPlateSplineApplicationBase.cxx recompile and run the demo. In order to execute the Transform, click on the "Map Points" button at the lower right corner of the GUI. Points transformed by VTK are displayed in Green Points transformed by ITK are displayed in Red You can select the ITK and VTK kernels with the Choice button in the upper right of the GUI. Note that the only two equivalent kernels are VTK's "R" with ITK's ThinPlate. The other combinations are not supposed to produce the same results. Clicking on the menu bar option "Time" will display the results of computing time for each one of the method. You can ask for the results at each time by clickin on the "Report" button or you can run in continuous mode by clicking on the checkbox "Continuous". These are the time I got now on Window on debug mode: ITK TPS 0.156 seconds VTK TPS 0.016 seconds Under Linux (in debugging mode too) the times are: ITK TPS 1.37 ITK TPS 1.01 (Windows and linux times are not comparable here) We could probably improve the performance by delegating computation of the weighted sum of kernels to the TPS, EBS and VS subclasses. For example in the TPS and VS the Kernels are diagonal matrices with const elements, so only three multiplications are actually required for multiplying the G matrix by a vector of weights. We perform however nine multiplications because we use the normal matrix product (six of these multiplications are always products by zero...in the TPS and VS cases). Please let us know if these changes help to improve the performance of your code. Thanks Luis --------------- Alex zhang wrote: > Dear Mr Luis： > Thank you very much for your work. > I just wonder that why there should be this much diffence between codes in ITK and VTK. > I have checked the code for TPS and EBS, and I don't think there is special optimization > in VTK TPS, it is also follow the matrix calculation step by step similar with the ITK TPS and EBS,only diffence is that the calculation of the ITK is on a 3N+12 times 3N+12 matrix(svd) > and the VTK TPS is done on three N+4 times N+4 matrices, and I have try svd method in matlab, > there isn't so much time diffence between the SVD of a 3N+12*3N+12 matrix and a N+4*N+4 > matrix. I am wondering about this and hope we can find the reason for this. > > regards, > zhang zhijun > >