From david.gobbi at gmail.com Tue Nov 1 09:58:05 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Tue, 1 Nov 2016 07:58:05 -0600 Subject: [vtk-developers] Leaks in vtkTkRenderWidget under python In-Reply-To: References: Message-ID: On Mon, Oct 31, 2016 at 3:30 PM, David Gobbi wrote: > On Mon, Oct 31, 2016 at 1:56 PM, Ken Martin > wrote: > >> >> So I recently fixed the leak reporting in VTK and with Will's help >> cleaned up some leaks that had crept in recently. But.. there are some >> leaks in vtkTkRenderWidget tests under Python that I'm a bit stuck on. I >> added some error checking code and the >> >> vtkTkRenderWidget_Destroy(char *memPtr) >> >> is never getting invoked. As I don't know Python, the test example leaves >> me a bit lost as to what should be calling that. If anyone has an idea for >> a fix please go ahead. If not I'll suppress the errors on those four tests >> so the nightlies are clean. etc. >> > > I'll take a look. The trick will be to ensure it isn't destroyed too > soon... > The following MR fixes the leaks by explicitly calling destroy(): http://gitlab.kitware.com/vtk/vtk/merge_requests/2125 It's not an ideal solution, but it's a workable one. - David -------------- next part -------------- An HTML attachment was scrubbed... URL: From ken.martin at kitware.com Tue Nov 1 10:02:48 2016 From: ken.martin at kitware.com (Ken Martin) Date: Tue, 1 Nov 2016 10:02:48 -0400 Subject: [vtk-developers] Leaks in vtkTkRenderWidget under python In-Reply-To: References: Message-ID: Awesome! Thanks so much David! On Tue, Nov 1, 2016 at 9:58 AM, David Gobbi wrote: > On Mon, Oct 31, 2016 at 3:30 PM, David Gobbi > wrote: > >> On Mon, Oct 31, 2016 at 1:56 PM, Ken Martin >> wrote: >> >>> >>> So I recently fixed the leak reporting in VTK and with Will's help >>> cleaned up some leaks that had crept in recently. But.. there are some >>> leaks in vtkTkRenderWidget tests under Python that I'm a bit stuck on. I >>> added some error checking code and the >>> >>> vtkTkRenderWidget_Destroy(char *memPtr) >>> >>> is never getting invoked. As I don't know Python, the test example >>> leaves me a bit lost as to what should be calling that. If anyone has an >>> idea for a fix please go ahead. If not I'll suppress the errors on those >>> four tests so the nightlies are clean. etc. >>> >> >> I'll take a look. The trick will be to ensure it isn't destroyed too >> soon... >> > > The following MR fixes the leaks by explicitly calling destroy(): > http://gitlab.kitware.com/vtk/vtk/merge_requests/2125 > It's not an ideal solution, but it's a workable one. > > - David > -- Ken Martin PhD Chairman & CFO Kitware Inc. 28 Corporate Drive Clifton Park NY 12065 518 371 3971 This communication, including all attachments, contains confidential and legally privileged information, and it is intended only for the use of the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken in reliance on it is prohibited and may be unlawful. If you received this communication in error please notify us immediately and destroy the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ken.martin at kitware.com Tue Nov 1 10:33:08 2016 From: ken.martin at kitware.com (Ken Martin) Date: Tue, 1 Nov 2016 10:33:08 -0400 Subject: [vtk-developers] InvokeEvent test randomly failing quiz Message-ID: OK here is a puzzle. We have a test that is occasionally failing and I suspect it fails due to random python order of deletion of vtk objects. The relevant python code is below. It fails when unregistering a vtkObject and I suspect it is failing when invoking an callback during the unregisterinternal method see the stack trace. So maybe python has deleted the object from its maps but then it gets used in a callback for another object being deleted? Again my python foo is weak but maybe we have to unregister the anyEvent observer before the end of the script? Maybe something else? @vtk.calldata_type(vtk.VTK_OBJECT) def callbackObj(self, caller, event, calldata): self.calldata = calldata def setUp(self): self.vtkObj = vtk.vtkObject() self.vtkObjForCallData = vtk.vtkObject() def test_obj(self): self.vtkObj.AddObserver(vtk.vtkCommand.AnyEvent, self.callbackObj) self.vtkObj.InvokeEvent(vtk.vtkCommand.ModifiedEvent, self.vtkObjForCallData) self.assertEqual(self.calldata, self.vtkObjForCallData) 0x7f98bd3e8770 : ??? [(???) ???:-1] 0x7f98bd19b778 : vtkPythonCommand::Execute(vtkObject*, unsigned long, void*) [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] 0x7f98bcb9fd7e : ??? [(???) ???:-1] 0x7f98bcba000c : vtkObject::UnRegisterInternal(vtkObjectBase*, int) [(libvtkCommonCore-7.1.so.1) ???:-1] 0x7f98bd19f045 : vtkPythonUtil::RemoveObjectFromMap(_object*) [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] 0x7f98bd1a5b30 : PyVTKObject_Delete [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] -------------- next part -------------- An HTML attachment was scrubbed... URL: From utkarsh.ayachit at kitware.com Tue Nov 1 11:19:33 2016 From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit) Date: Tue, 1 Nov 2016 11:19:33 -0400 Subject: [vtk-developers] InvokeEvent test randomly failing quiz In-Reply-To: References: Message-ID: Ken, The issue seems to be that the callback is attempted to be called for vtkCommand::DeleteEvent since the observer is set to respond to "AnyEvent". When the object is being cleaned up as part of the interpreter being destroyed, calling Python commands is indeed problematic and hence the failure. The test can be fixed by changing the observer to only listen to ModifiedEvent instead of AnyEvent. Ideally vtkPythonCommand::Execute can check if the interpreter is being cleaned up, but I am not sure how to do that. Utkarsh On Tue, Nov 1, 2016 at 10:33 AM, Ken Martin wrote: > OK here is a puzzle. We have a test that is occasionally failing and I > suspect it fails due to random python order of deletion of vtk objects. The > relevant python code is below. It fails when unregistering a vtkObject and I > suspect it is failing when invoking an callback during the > unregisterinternal method see the stack trace. So maybe python has deleted > the object from its maps but then it gets used in a callback for another > object being deleted? Again my python foo is weak but maybe we have to > unregister the anyEvent observer before the end of the script? Maybe > something else? > > @vtk.calldata_type(vtk.VTK_OBJECT) > def callbackObj(self, caller, event, calldata): > self.calldata = calldata > > def setUp(self): > self.vtkObj = vtk.vtkObject() > > self.vtkObjForCallData = vtk.vtkObject() > > def test_obj(self): > self.vtkObj.AddObserver(vtk.vtkCommand.AnyEvent, self.callbackObj) > self.vtkObj.InvokeEvent(vtk.vtkCommand.ModifiedEvent, > self.vtkObjForCallData) > self.assertEqual(self.calldata, self.vtkObjForCallData) > > 0x7f98bd3e8770 : ??? [(???) ???:-1] > 0x7f98bd19b778 : vtkPythonCommand::Execute(vtkObject*, unsigned long, void*) > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] > 0x7f98bcb9fd7e : ??? [(???) ???:-1] > 0x7f98bcba000c : vtkObject::UnRegisterInternal(vtkObjectBase*, int) > [(libvtkCommonCore-7.1.so.1) ???:-1] > 0x7f98bd19f045 : vtkPythonUtil::RemoveObjectFromMap(_object*) > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] > 0x7f98bd1a5b30 : PyVTKObject_Delete [(libvtkWrappingPython35Core-7.1.so.1) > ???:-1] > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > From alvaro.sanchez at kitware.com Tue Nov 1 19:17:19 2016 From: alvaro.sanchez at kitware.com (Alvaro Sanchez) Date: Tue, 1 Nov 2016 19:17:19 -0400 Subject: [vtk-developers] UseJitteringOn() has no effect in 7.1.0.rc1 In-Reply-To: References: Message-ID: Hi Elvis, the patch for this in https://gitlab.kitware.com/vtk/vtk/merge_requests/2130 please give it a try and let me know if it helps. Cheers, Alvaro On Wed, Oct 26, 2016 at 11:59 AM, Elvis Stansvik < elvis.stansvik at orexplore.com> wrote: > 2016-10-26 16:27 GMT+02:00 Alvaro Sanchez : > > Hi Elvis, > > > > I found the root cause of this, the noise texture is not being correctly > > sampled in the shader. I will tag you on the MR once the patch is ready > so > > that you can try it out. > > That's great news \o/ Thanks a lot Alvaro. > > Elvis > > > > > Cheers, > > > > On Thu, Oct 20, 2016 at 1:30 AM, Elvis Stansvik > > wrote: > >> > >> 2016-10-20 5:46 GMT+02:00 Alvaro Sanchez : > >> > I ran your test program and I could reproduce the wood-grain artifacts > >> > you > >> > see. It seems to me that the jitter noise might need some tweaking. > I > >> > will > >> > try a few things and investigate further, will let you know my > findings. > >> > >> Thanks Alvaro. > >> > >> Elvis > >> > >> > > >> > > >> > On Wed, Oct 19, 2016 at 8:07 AM, Elvis Stansvik > >> > wrote: > >> >> > >> >> 2016-10-19 14:03 GMT+02:00 Alvaro Sanchez < > alvaro.sanchez at kitware.com>: > >> >> > Hi Elvis, > >> >> > > >> >> > thanks for the test case. Sorry, I did not have time to run it yet > >> >> > but > >> >> > I > >> >> > will have a look at it today. > >> >> > > >> >> > It seems unlikely to me that the small data spacing is affecting > >> >> > jittering. > >> >> > I will come back to you after debugging a bit with your test case. > >> >> > >> >> Alright, no hurry. Thanks a lot for having a look. > >> >> > >> >> Elvis > >> >> > >> >> > > >> >> > Cheers, > >> >> > Alvaro > >> >> > > >> >> > On Wed, Oct 19, 2016 at 1:54 AM, Elvis Stansvik > >> >> > wrote: > >> >> >> > >> >> >> 2016-10-15 11:16 GMT+02:00 Elvis Stansvik > >> >> >> : > >> >> >> > 2016-10-14 15:54 GMT+02:00 Alvaro Sanchez > >> >> >> > : > >> >> >> >> Hi Elvis, > >> >> >> >> > >> >> >> >> the mapper uses a vtkPerlinNoise instance to generate the > jitter > >> >> >> >> noise > >> >> >> >> and > >> >> >> >> as far as I know there are currently no knobs exposed to tweak > >> >> >> >> the > >> >> >> >> amount of > >> >> >> >> ray perturbation. Are you using the GL2 backend? It would > also > >> >> >> >> be > >> >> >> >> good to > >> >> >> >> know what features are active along with ray jittering > (multiple > >> >> >> >> components, > >> >> >> >> etc.), so if you could provide some sample data or code would > be > >> >> >> >> very > >> >> >> >> helpful. > >> >> >> > > >> >> >> > Hi again Alvaro, > >> >> >> > > >> >> >> > Here's a minimal test case including sample data (129 MB): > >> >> >> > > >> >> >> > https://dl.dropboxusercontent. > com/u/22350696/test_grain.tar.gz > >> >> >> > > >> >> >> > Build with: > >> >> >> > > >> >> >> > cmake . > >> >> >> > make > >> >> >> > > >> >> >> > and run with: > >> >> >> > > >> >> >> > ./test_grain rec-0300mm-0400mm.xml > >> >> >> > > >> >> >> > The result should be as in the attached screenshot. > >> >> >> > >> >> >> Anyone had time to run my test case? Are you seeing the same > thing? > >> >> >> > >> >> >> Elvis > >> >> >> > >> >> >> > > >> >> >> > Elvis > >> >> >> > > >> >> >> >> > >> >> >> >> Thanks! > >> >> >> >> Alvaro > >> >> >> >> > >> >> >> >> On Fri, Oct 14, 2016 at 3:47 AM, Elvis Stansvik > >> >> >> >> wrote: > >> >> >> >>> > >> >> >> >>> Hi all, > >> >> >> >>> > >> >> >> >>> I updated our product to use VTK 7.1.0.rc1, as I was > interested > >> >> >> >>> in > >> >> >> >>> trying out vtkGPUVolumeRayCastMapper::UseJitteringOn() to get > >> >> >> >>> rid > >> >> >> >>> of > >> >> >> >>> some woodgrain effects we're suffering from in our volume > >> >> >> >>> rendering > >> >> >> >>> (mostly when the volumes are rendered very opaque). > >> >> >> >>> > >> >> >> >>> But turning the option on seems to have little to no effect. > >> >> >> >>> This > >> >> >> >>> is > >> >> >> >>> the result with the option on: > >> >> >> >>> > >> >> >> >>> https://dl.dropboxusercontent.com/u/22350696/out.ogv > >> >> >> >>> > >> >> >> >>> It looks about the same to me as it does with the option off. > >> >> >> >>> > >> >> >> >>> Are there any knobs for this option? How does it determine how > >> >> >> >>> much > >> >> >> >>> to > >> >> >> >>> perturbate the rays? > >> >> >> >>> > >> >> >> >>> Thanks for any advise. > >> >> >> >>> > >> >> >> >>> Elvis > >> >> >> >>> _______________________________________________ > >> >> >> >>> Powered by www.kitware.com > >> >> >> >>> > >> >> >> >>> Visit other Kitware open-source projects at > >> >> >> >>> http://www.kitware.com/opensource/opensource.html > >> >> >> >>> > >> >> >> >>> Search the list archives at: > >> >> >> >>> http://markmail.org/search/?q=vtk-developers > >> >> >> >>> > >> >> >> >>> Follow this link to subscribe/unsubscribe: > >> >> >> >>> http://public.kitware.com/mailman/listinfo/vtk-developers > >> >> >> >>> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> -- > >> >> >> >> Alvaro Sanchez > >> >> >> >> Kitware, Inc. > >> >> >> >> Senior R&D Engineer > >> >> >> >> 21 Corporate Drive > >> >> >> >> Clifton Park, NY 12065-8662 > >> >> >> >> Phone: 518-881-4901 > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > Alvaro Sanchez > >> >> > Kitware, Inc. > >> >> > Senior R&D Engineer > >> >> > 21 Corporate Drive > >> >> > Clifton Park, NY 12065-8662 > >> >> > Phone: 518-881-4901 > >> > > >> > > >> > > >> > > >> > -- > >> > Alvaro Sanchez > >> > Kitware, Inc. > >> > Senior R&D Engineer > >> > 21 Corporate Drive > >> > Clifton Park, NY 12065-8662 > >> > Phone: 518-881-4901 > > > > > > > > > > -- > > Alvaro Sanchez > > Kitware, Inc. > > Senior R&D Engineer > > 21 Corporate Drive > > Clifton Park, NY 12065-8662 > > Phone: 518-881-4901 > -- Alvaro Sanchez Kitware, Inc. Senior R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4901 -------------- next part -------------- An HTML attachment was scrubbed... URL: From magnus_elden at hotmail.com Wed Nov 2 01:28:57 2016 From: magnus_elden at hotmail.com (Magnus Elden) Date: Wed, 2 Nov 2016 05:28:57 +0000 Subject: [vtk-developers] What I have learned about providing a VR system that is intuitive to use while keeping discomfort to a minimum. In-Reply-To: <1e6d01d234c7$64aea8b0$2e0bfa10$@hotmail.com> References: <1e6d01d234c7$64aea8b0$2e0bfa10$@hotmail.com> Message-ID: Hello! I sent a mail to Kitware and got a reply that I should send this info to the VTK and Paraview developer mailing lists. I would like to start with saying that the following words are based on my personal experience and the feedback I have gotten from the small group of people around me who have tried VR systems. As such, please think about what I have to say and then do your own testing to see what works for your own systems and use cases. I have been working on using Paraview with UE4 to provide a platform for VR to be used as a tool of scientific visualisation. I have been working on this for only half a year, and I started by looking into maybe modifying Paraview to render to OpenVR. However, I was defeated by the fact that I could not for the life of me understand how to use VTK to open xdmf files. I got errors complaining about time all the time. I eventually hacked a python script together to render and create a bunch of slices that I imported to UE4 and I wrote my own volume renderer there. You are basically doing what I am doing for my master's thesis and I believe that having VR support directly integrated into VTK or Paraview is the best way to go for VR visualization for researchers. Since I am not that well versed with the Paraview and VTK systems I was unable to help directly by adding code, especially since I had nobody to really turn to, but I can at least provide some hints based on my experience. First and foremost, when running in a VR environment it is very important for the user that they have a floor and maybe some walls which they can use for reference. Blurring, depth of field and motion blur are also enemies of a good VR experience. The Paraview overlap detection also seemed slightly wonky as I had to re-grab several times. Unlike a standard screen a VR system covers the entire visual field and makes it impossible for the brain to calibrate using peripheral vision. This leads to mismatch between visual cues and the other signals the brain receives. This mismatch leads to the users feeling nausea and other discomforts. This makes the standard systems used for visualizing 3D models and volumes are not optimal. In short, make it feel like you have the model in front of you inside a world you have created. Imagine a hologram in a science fiction film. Finally, from feedback, the handling should be similar to handling objects in real life in order to minimize confusion and make it natural. This means that the model is not necessarily in the center of the space around which the camera rotates. The models can be moved by grabbing with the controllers and scaled in the models local space, not world space, by grabbing the model with both hands. Handling things like cutting planes will also have to be like moving a stick or something else physical we handle in the real world with our hands. The way the cutting plane in Paraview is already working is a very good example of how it can be. Grab the center with your left hand and place it where you want it to be while you grab the rotational "stick" with your right hand and orient it. Quickly I want to answer what I find to be the strengths and weaknesses of both the Paraview, and similar platforms, and game engines like UE4. Paraview is great for volumetric visualisations and quick iterative analysis. Colour encoding and iso-surface generation and all the other powerful tools of Paraview is great for the researchers who can understand the colours, symbols and encoded data. It is not good for creating a interactive, wholesome experience that can be experiences by several users at once. This is where UE4 can shine. As a research tool it is not great, but it is great at presentation. Simplified and processed models can be made to move and interact with any number of concurrent users while showing animations and playing sounds. This allows UE4 to be a great tool to Conway the processed data to those learning or otherwise without the required specialized knowledge. For education and presentation I can see a lot of use for these simplified and processed models. I wrote this because I believe VR can be a great aid for research. I also know that Paraview and similar software are made for the researchers and I want to stress that Paraview should keep that focus. It can be among the best tools a researcher has and as such it should not diminish itself by trying to also be something it is not. I hope that this will lead to Paraview and VTK being used to give even better functionality for the scientific world. Yours, Magnus Elden If you want some info on what I am doing and the state of the volume rendering in VR in UE4, please refer to this forum thread: https://forums.unrealengine.com/showthread.php?119267-Your-thoughts-on-and-comments-to-Volume-Rendering-in-Unreal-Engine-4/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Wed Nov 2 01:48:19 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Tue, 1 Nov 2016 23:48:19 -0600 Subject: [vtk-developers] InvokeEvent test randomly failing quiz In-Reply-To: References: Message-ID: I wasn't able to reproduce the issue, but I think that I found out what causes it. When vtkPythonCommand::Execute() is called, it tries to promote the subject object (i.e. the object being deleted for DeleteEvent) into a Python object. I was able to confirm that this actually happens, and even though I couldn't get it to crash, I'm pretty sure that it puts the program into a bad state. See https://gitlab.kitware.com/vtk/vtk/merge_requests/2131 - David On Tue, Nov 1, 2016 at 9:19 AM, Utkarsh Ayachit wrote: > Ken, > > The issue seems to be that the callback is attempted to be called for > vtkCommand::DeleteEvent since the observer is set to respond to > "AnyEvent". When the object is being cleaned up as part of the > interpreter being destroyed, calling Python commands is indeed > problematic and hence the failure. > > The test can be fixed by changing the observer to only listen to > ModifiedEvent instead of AnyEvent. Ideally vtkPythonCommand::Execute > can check if the interpreter is being cleaned up, but I am not sure > how to do that. > > Utkarsh > > On Tue, Nov 1, 2016 at 10:33 AM, Ken Martin > wrote: > > OK here is a puzzle. We have a test that is occasionally failing and I > > suspect it fails due to random python order of deletion of vtk objects. > The > > relevant python code is below. It fails when unregistering a vtkObject > and I > > suspect it is failing when invoking an callback during the > > unregisterinternal method see the stack trace. So maybe python has > deleted > > the object from its maps but then it gets used in a callback for another > > object being deleted? Again my python foo is weak but maybe we have to > > unregister the anyEvent observer before the end of the script? Maybe > > something else? > > > > @vtk.calldata_type(vtk.VTK_OBJECT) > > def callbackObj(self, caller, event, calldata): > > self.calldata = calldata > > > > def setUp(self): > > self.vtkObj = vtk.vtkObject() > > > > self.vtkObjForCallData = vtk.vtkObject() > > > > def test_obj(self): > > self.vtkObj.AddObserver(vtk.vtkCommand.AnyEvent, > self.callbackObj) > > self.vtkObj.InvokeEvent(vtk.vtkCommand.ModifiedEvent, > > self.vtkObjForCallData) > > self.assertEqual(self.calldata, self.vtkObjForCallData) > > > > 0x7f98bd3e8770 : ??? [(???) ???:-1] > > 0x7f98bd19b778 : vtkPythonCommand::Execute(vtkObject*, unsigned long, > void*) > > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] > > 0x7f98bcb9fd7e : ??? [(???) ???:-1] > > 0x7f98bcba000c : vtkObject::UnRegisterInternal(vtkObjectBase*, int) > > [(libvtkCommonCore-7.1.so.1) ???:-1] > > 0x7f98bd19f045 : vtkPythonUtil::RemoveObjectFromMap(_object*) > > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] > > 0x7f98bd1a5b30 : PyVTKObject_Delete [(libvtkWrappingPython35Core- > 7.1.so.1) > > ???:-1] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Wed Nov 2 16:45:20 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Wed, 2 Nov 2016 21:45:20 +0100 Subject: [vtk-developers] [VTK] [TESTING] Interest in contributing to improve VTK's code coverage Message-ID: Hi, I would like to start contributing to VTK's regression tests and its code coverage improvement. I am familiar to ITK's testing framework, and also have some experience with gitlab, but I am aware that things may slightly differ in VTK. I do not know whether anyone in the list leads the testing task, or whether somebody could guide me through. Thanks ! JON HAITZ -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Wed Nov 2 16:48:12 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Wed, 2 Nov 2016 14:48:12 -0600 Subject: [vtk-developers] InvokeEvent test randomly failing quiz In-Reply-To: References: Message-ID: It looks like the fix didn't work. But now that I know which dashboard is failing, and have seen the whole stack trace, I have a better idea of where the problem might be. I'll give it another shot tonight. - David On Tue, Nov 1, 2016 at 11:48 PM, David Gobbi wrote: > I wasn't able to reproduce the issue, but I think that I found out what > causes it. When vtkPythonCommand::Execute() is called, it tries to promote > the subject object (i.e. the object being deleted for DeleteEvent) into a > Python object. I was able to confirm that this actually happens, and even > though I couldn't get it to crash, I'm pretty sure that it puts the program > into a bad state. > > See https://gitlab.kitware.com/vtk/vtk/merge_requests/2131 > > - David > > On Tue, Nov 1, 2016 at 9:19 AM, Utkarsh Ayachit < > utkarsh.ayachit at kitware.com> wrote: > >> Ken, >> >> The issue seems to be that the callback is attempted to be called for >> vtkCommand::DeleteEvent since the observer is set to respond to >> "AnyEvent". When the object is being cleaned up as part of the >> interpreter being destroyed, calling Python commands is indeed >> problematic and hence the failure. >> >> The test can be fixed by changing the observer to only listen to >> ModifiedEvent instead of AnyEvent. Ideally vtkPythonCommand::Execute >> can check if the interpreter is being cleaned up, but I am not sure >> how to do that. >> >> Utkarsh >> >> On Tue, Nov 1, 2016 at 10:33 AM, Ken Martin >> wrote: >> > OK here is a puzzle. We have a test that is occasionally failing and I >> > suspect it fails due to random python order of deletion of vtk objects. >> The >> > relevant python code is below. It fails when unregistering a vtkObject >> and I >> > suspect it is failing when invoking an callback during the >> > unregisterinternal method see the stack trace. So maybe python has >> deleted >> > the object from its maps but then it gets used in a callback for another >> > object being deleted? Again my python foo is weak but maybe we have to >> > unregister the anyEvent observer before the end of the script? Maybe >> > something else? >> > >> > @vtk.calldata_type(vtk.VTK_OBJECT) >> > def callbackObj(self, caller, event, calldata): >> > self.calldata = calldata >> > >> > def setUp(self): >> > self.vtkObj = vtk.vtkObject() >> > >> > self.vtkObjForCallData = vtk.vtkObject() >> > >> > def test_obj(self): >> > self.vtkObj.AddObserver(vtk.vtkCommand.AnyEvent, >> self.callbackObj) >> > self.vtkObj.InvokeEvent(vtk.vtkCommand.ModifiedEvent, >> > self.vtkObjForCallData) >> > self.assertEqual(self.calldata, self.vtkObjForCallData) >> > >> > 0x7f98bd3e8770 : ??? [(???) ???:-1] >> > 0x7f98bd19b778 : vtkPythonCommand::Execute(vtkObject*, unsigned long, >> void*) >> > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] >> > 0x7f98bcb9fd7e : ??? [(???) ???:-1] >> > 0x7f98bcba000c : vtkObject::UnRegisterInternal(vtkObjectBase*, int) >> > [(libvtkCommonCore-7.1.so.1) ???:-1] >> > 0x7f98bd19f045 : vtkPythonUtil::RemoveObjectFromMap(_object*) >> > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] >> > 0x7f98bd1a5b30 : PyVTKObject_Delete [(libvtkWrappingPython35Core-7 >> .1.so.1) >> > ???:-1] >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From elvis.stansvik at orexplore.com Wed Nov 2 18:17:23 2016 From: elvis.stansvik at orexplore.com (Elvis Stansvik) Date: Wed, 2 Nov 2016 23:17:23 +0100 Subject: [vtk-developers] UseJitteringOn() has no effect in 7.1.0.rc1 In-Reply-To: References: Message-ID: Den 2 nov. 2016 12:17 fm skrev "Alvaro Sanchez" : > > Hi Elvis, > > the patch for this in https://gitlab.kitware.com/vtk/vtk/merge_requests/2130 > > please give it a try and let me know if it helps. Great, thanks a lot. I'll give it a go when I'm back at work tomorrow. Elvis > > Cheers, > Alvaro > > > On Wed, Oct 26, 2016 at 11:59 AM, Elvis Stansvik < elvis.stansvik at orexplore.com> wrote: >> >> 2016-10-26 16:27 GMT+02:00 Alvaro Sanchez : >> > Hi Elvis, >> > >> > I found the root cause of this, the noise texture is not being correctly >> > sampled in the shader. I will tag you on the MR once the patch is ready so >> > that you can try it out. >> >> That's great news \o/ Thanks a lot Alvaro. >> >> Elvis >> >> > >> > Cheers, >> > >> > On Thu, Oct 20, 2016 at 1:30 AM, Elvis Stansvik >> > wrote: >> >> >> >> 2016-10-20 5:46 GMT+02:00 Alvaro Sanchez : >> >> > I ran your test program and I could reproduce the wood-grain artifacts >> >> > you >> >> > see. It seems to me that the jitter noise might need some tweaking. I >> >> > will >> >> > try a few things and investigate further, will let you know my findings. >> >> >> >> Thanks Alvaro. >> >> >> >> Elvis >> >> >> >> > >> >> > >> >> > On Wed, Oct 19, 2016 at 8:07 AM, Elvis Stansvik >> >> > wrote: >> >> >> >> >> >> 2016-10-19 14:03 GMT+02:00 Alvaro Sanchez < alvaro.sanchez at kitware.com>: >> >> >> > Hi Elvis, >> >> >> > >> >> >> > thanks for the test case. Sorry, I did not have time to run it yet >> >> >> > but >> >> >> > I >> >> >> > will have a look at it today. >> >> >> > >> >> >> > It seems unlikely to me that the small data spacing is affecting >> >> >> > jittering. >> >> >> > I will come back to you after debugging a bit with your test case. >> >> >> >> >> >> Alright, no hurry. Thanks a lot for having a look. >> >> >> >> >> >> Elvis >> >> >> >> >> >> > >> >> >> > Cheers, >> >> >> > Alvaro >> >> >> > >> >> >> > On Wed, Oct 19, 2016 at 1:54 AM, Elvis Stansvik >> >> >> > wrote: >> >> >> >> >> >> >> >> 2016-10-15 11:16 GMT+02:00 Elvis Stansvik >> >> >> >> : >> >> >> >> > 2016-10-14 15:54 GMT+02:00 Alvaro Sanchez >> >> >> >> > : >> >> >> >> >> Hi Elvis, >> >> >> >> >> >> >> >> >> >> the mapper uses a vtkPerlinNoise instance to generate the jitter >> >> >> >> >> noise >> >> >> >> >> and >> >> >> >> >> as far as I know there are currently no knobs exposed to tweak >> >> >> >> >> the >> >> >> >> >> amount of >> >> >> >> >> ray perturbation. Are you using the GL2 backend? It would also >> >> >> >> >> be >> >> >> >> >> good to >> >> >> >> >> know what features are active along with ray jittering (multiple >> >> >> >> >> components, >> >> >> >> >> etc.), so if you could provide some sample data or code would be >> >> >> >> >> very >> >> >> >> >> helpful. >> >> >> >> > >> >> >> >> > Hi again Alvaro, >> >> >> >> > >> >> >> >> > Here's a minimal test case including sample data (129 MB): >> >> >> >> > >> >> >> >> > https://dl.dropboxusercontent.com/u/22350696/test_grain.tar.gz >> >> >> >> > >> >> >> >> > Build with: >> >> >> >> > >> >> >> >> > cmake . >> >> >> >> > make >> >> >> >> > >> >> >> >> > and run with: >> >> >> >> > >> >> >> >> > ./test_grain rec-0300mm-0400mm.xml >> >> >> >> > >> >> >> >> > The result should be as in the attached screenshot. >> >> >> >> >> >> >> >> Anyone had time to run my test case? Are you seeing the same thing? >> >> >> >> >> >> >> >> Elvis >> >> >> >> >> >> >> >> > >> >> >> >> > Elvis >> >> >> >> > >> >> >> >> >> >> >> >> >> >> Thanks! >> >> >> >> >> Alvaro >> >> >> >> >> >> >> >> >> >> On Fri, Oct 14, 2016 at 3:47 AM, Elvis Stansvik >> >> >> >> >> wrote: >> >> >> >> >>> >> >> >> >> >>> Hi all, >> >> >> >> >>> >> >> >> >> >>> I updated our product to use VTK 7.1.0.rc1, as I was interested >> >> >> >> >>> in >> >> >> >> >>> trying out vtkGPUVolumeRayCastMapper::UseJitteringOn() to get >> >> >> >> >>> rid >> >> >> >> >>> of >> >> >> >> >>> some woodgrain effects we're suffering from in our volume >> >> >> >> >>> rendering >> >> >> >> >>> (mostly when the volumes are rendered very opaque). >> >> >> >> >>> >> >> >> >> >>> But turning the option on seems to have little to no effect. >> >> >> >> >>> This >> >> >> >> >>> is >> >> >> >> >>> the result with the option on: >> >> >> >> >>> >> >> >> >> >>> https://dl.dropboxusercontent.com/u/22350696/out.ogv >> >> >> >> >>> >> >> >> >> >>> It looks about the same to me as it does with the option off. >> >> >> >> >>> >> >> >> >> >>> Are there any knobs for this option? How does it determine how >> >> >> >> >>> much >> >> >> >> >>> to >> >> >> >> >>> perturbate the rays? >> >> >> >> >>> >> >> >> >> >>> Thanks for any advise. >> >> >> >> >>> >> >> >> >> >>> Elvis >> >> >> >> >>> _______________________________________________ >> >> >> >> >>> Powered by www.kitware.com >> >> >> >> >>> >> >> >> >> >>> Visit other Kitware open-source projects at >> >> >> >> >>> http://www.kitware.com/opensource/opensource.html >> >> >> >> >>> >> >> >> >> >>> Search the list archives at: >> >> >> >> >>> http://markmail.org/search/?q=vtk-developers >> >> >> >> >>> >> >> >> >> >>> Follow this link to subscribe/unsubscribe: >> >> >> >> >>> http://public.kitware.com/mailman/listinfo/vtk-developers >> >> >> >> >>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> Alvaro Sanchez >> >> >> >> >> Kitware, Inc. >> >> >> >> >> Senior R&D Engineer >> >> >> >> >> 21 Corporate Drive >> >> >> >> >> Clifton Park, NY 12065-8662 >> >> >> >> >> Phone: 518-881-4901 >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > Alvaro Sanchez >> >> >> > Kitware, Inc. >> >> >> > Senior R&D Engineer >> >> >> > 21 Corporate Drive >> >> >> > Clifton Park, NY 12065-8662 >> >> >> > Phone: 518-881-4901 >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Alvaro Sanchez >> >> > Kitware, Inc. >> >> > Senior R&D Engineer >> >> > 21 Corporate Drive >> >> > Clifton Park, NY 12065-8662 >> >> > Phone: 518-881-4901 >> > >> > >> > >> > >> > -- >> > Alvaro Sanchez >> > Kitware, Inc. >> > Senior R&D Engineer >> > 21 Corporate Drive >> > Clifton Park, NY 12065-8662 >> > Phone: 518-881-4901 > > > > > -- > Alvaro Sanchez > Kitware, Inc. > Senior R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4901 -------------- next part -------------- An HTML attachment was scrubbed... URL: From andy.bauer at kitware.com Wed Nov 2 22:26:44 2016 From: andy.bauer at kitware.com (Andy Bauer) Date: Wed, 2 Nov 2016 22:26:44 -0400 Subject: [vtk-developers] [VTK] [TESTING] Interest in contributing to improve VTK's code coverage In-Reply-To: References: Message-ID: Hi Jon, VTK is always looking for contributions, especially testing and code coverage improvements. In case you haven't seen it yet, the VTK contributing guide is at https://gitlab.kitware.com/vtk/vtk/blob/master/CONTRIBUTING.md. It's probably fairly similar to what you'd see for ITK. The VTK dashboard is at https://open.cdash.org/index.php?project=VTK and near the very bottom there's a Coverage section if you want to see what parts of the code are well covered and what parts are not. Most of the tests that I add are usually C++ but Python also seems to be a popular option for doing regression testing. If you have questions about any of this, the developers list is a good place to ask! Good luck and welcome to the community! Andy On Wed, Nov 2, 2016 at 4:45 PM, Jon Haitz Legarreta < jhlegarreta at vicomtech.org> wrote: > Hi, > I would like to start contributing to VTK's regression tests and its code > coverage improvement. > > I am familiar to ITK's testing framework, and also have some experience > with gitlab, but I am aware that things may slightly differ in VTK. > > I do not know whether anyone in the list leads the testing task, or > whether somebody could guide me through. > > Thanks ! > > JON HAITZ > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tharun160190 at gmail.com Wed Nov 2 22:53:13 2016 From: tharun160190 at gmail.com (Tharun) Date: Wed, 2 Nov 2016 19:53:13 -0700 (MST) Subject: [vtk-developers] Crashing of visualizer on changing of a large mesh representation to wireframe Message-ID: <1478141593971-5741020.post@n5.nabble.com> I have 20 million faces mesh imported to qvtk widget. Actors are LOD actors. Representing in surface is not a problem with more bigger meshes also but with this 20millionn faces mesh, visualizer crashed on changing to wire frame representation. Any idea on the selective behavior? Thank you in advance -- View this message in context: http://vtk.1045678.n5.nabble.com/Crashing-of-visualizer-on-changing-of-a-large-mesh-representation-to-wireframe-tp5741020.html Sent from the VTK - Dev mailing list archive at Nabble.com. From jhlegarreta at vicomtech.org Thu Nov 3 05:54:19 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Thu, 3 Nov 2016 10:54:19 +0100 Subject: [vtk-developers] [VTK] [TESTING] Interest in contributing to improve VTK's code coverage In-Reply-To: References: Message-ID: Hi, OK, thanks for the answer and the pointers provided Andy. Yes, I'm familiar to the dashboard and its sections. I'll start contributing little by little, and will ask for opinion/help to the list when needed.. Cheers, JON HAITZ -- On 3 November 2016 at 03:26, Andy Bauer wrote: > Hi Jon, > > VTK is always looking for contributions, especially testing and code > coverage improvements. In case you haven't seen it yet, the VTK > contributing guide is at https://gitlab.kitware.com/vtk/vtk/blob/master/ > CONTRIBUTING.md. It's probably fairly similar to what you'd see for ITK. > The VTK dashboard is at https://open.cdash.org/index.php?project=VTK and > near the very bottom there's a Coverage section if you want to see what > parts of the code are well covered and what parts are not. Most of the > tests that I add are usually C++ but Python also seems to be a popular > option for doing regression testing. > > If you have questions about any of this, the developers list is a good > place to ask! > > Good luck and welcome to the community! > Andy > > On Wed, Nov 2, 2016 at 4:45 PM, Jon Haitz Legarreta < > jhlegarreta at vicomtech.org> wrote: > >> Hi, >> I would like to start contributing to VTK's regression tests and its code >> coverage improvement. >> >> I am familiar to ITK's testing framework, and also have some experience >> with gitlab, but I am aware that things may slightly differ in VTK. >> >> I do not know whether anyone in the list leads the testing task, or >> whether somebody could guide me through. >> >> Thanks ! >> >> JON HAITZ >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Search the list archives at: http://markmail.org/search/?q=vtk-developers >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/vtk-developers >> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From elvis.stansvik at orexplore.com Thu Nov 3 08:09:20 2016 From: elvis.stansvik at orexplore.com (Elvis Stansvik) Date: Thu, 3 Nov 2016 13:09:20 +0100 Subject: [vtk-developers] UseJitteringOn() has no effect in 7.1.0.rc1 In-Reply-To: References: Message-ID: 2016-11-02 23:17 GMT+01:00 Elvis Stansvik : > Den 2 nov. 2016 12:17 fm skrev "Alvaro Sanchez" < > alvaro.sanchez at kitware.com>: > > > > Hi Elvis, > > > > the patch for this in https://gitlab.kitware.com/ > vtk/vtk/merge_requests/2130 > > > > please give it a try and let me know if it helps. > > Great, thanks a lot. I'll give it a go when I'm back at work tomorrow. > Got held up with some other things, but going to try it out now. I saw that in the comments you said that this fix could wait until 8.0. No chance of backporting it to 7.1? We're basing our product on 7.1.0.rc1 at the moment, expecting to use 7.1 for our first release, so would love to have the fix in there. Elvis > Elvis > > > > > Cheers, > > Alvaro > > > > > > On Wed, Oct 26, 2016 at 11:59 AM, Elvis Stansvik < > elvis.stansvik at orexplore.com> wrote: > >> > >> 2016-10-26 16:27 GMT+02:00 Alvaro Sanchez : > >> > Hi Elvis, > >> > > >> > I found the root cause of this, the noise texture is not being > correctly > >> > sampled in the shader. I will tag you on the MR once the patch is > ready so > >> > that you can try it out. > >> > >> That's great news \o/ Thanks a lot Alvaro. > >> > >> Elvis > >> > >> > > >> > Cheers, > >> > > >> > On Thu, Oct 20, 2016 at 1:30 AM, Elvis Stansvik > >> > wrote: > >> >> > >> >> 2016-10-20 5:46 GMT+02:00 Alvaro Sanchez >: > >> >> > I ran your test program and I could reproduce the wood-grain > artifacts > >> >> > you > >> >> > see. It seems to me that the jitter noise might need some > tweaking. I > >> >> > will > >> >> > try a few things and investigate further, will let you know my > findings. > >> >> > >> >> Thanks Alvaro. > >> >> > >> >> Elvis > >> >> > >> >> > > >> >> > > >> >> > On Wed, Oct 19, 2016 at 8:07 AM, Elvis Stansvik > >> >> > wrote: > >> >> >> > >> >> >> 2016-10-19 14:03 GMT+02:00 Alvaro Sanchez < > alvaro.sanchez at kitware.com>: > >> >> >> > Hi Elvis, > >> >> >> > > >> >> >> > thanks for the test case. Sorry, I did not have time to run it > yet > >> >> >> > but > >> >> >> > I > >> >> >> > will have a look at it today. > >> >> >> > > >> >> >> > It seems unlikely to me that the small data spacing is affecting > >> >> >> > jittering. > >> >> >> > I will come back to you after debugging a bit with your test > case. > >> >> >> > >> >> >> Alright, no hurry. Thanks a lot for having a look. > >> >> >> > >> >> >> Elvis > >> >> >> > >> >> >> > > >> >> >> > Cheers, > >> >> >> > Alvaro > >> >> >> > > >> >> >> > On Wed, Oct 19, 2016 at 1:54 AM, Elvis Stansvik > >> >> >> > wrote: > >> >> >> >> > >> >> >> >> 2016-10-15 11:16 GMT+02:00 Elvis Stansvik > >> >> >> >> : > >> >> >> >> > 2016-10-14 15:54 GMT+02:00 Alvaro Sanchez > >> >> >> >> > : > >> >> >> >> >> Hi Elvis, > >> >> >> >> >> > >> >> >> >> >> the mapper uses a vtkPerlinNoise instance to generate the > jitter > >> >> >> >> >> noise > >> >> >> >> >> and > >> >> >> >> >> as far as I know there are currently no knobs exposed to > tweak > >> >> >> >> >> the > >> >> >> >> >> amount of > >> >> >> >> >> ray perturbation. Are you using the GL2 backend? It would > also > >> >> >> >> >> be > >> >> >> >> >> good to > >> >> >> >> >> know what features are active along with ray jittering > (multiple > >> >> >> >> >> components, > >> >> >> >> >> etc.), so if you could provide some sample data or code > would be > >> >> >> >> >> very > >> >> >> >> >> helpful. > >> >> >> >> > > >> >> >> >> > Hi again Alvaro, > >> >> >> >> > > >> >> >> >> > Here's a minimal test case including sample data (129 MB): > >> >> >> >> > > >> >> >> >> > https://dl.dropboxusercontent.com/u/ > 22350696/test_grain.tar.gz > >> >> >> >> > > >> >> >> >> > Build with: > >> >> >> >> > > >> >> >> >> > cmake . > >> >> >> >> > make > >> >> >> >> > > >> >> >> >> > and run with: > >> >> >> >> > > >> >> >> >> > ./test_grain rec-0300mm-0400mm.xml > >> >> >> >> > > >> >> >> >> > The result should be as in the attached screenshot. > >> >> >> >> > >> >> >> >> Anyone had time to run my test case? Are you seeing the same > thing? > >> >> >> >> > >> >> >> >> Elvis > >> >> >> >> > >> >> >> >> > > >> >> >> >> > Elvis > >> >> >> >> > > >> >> >> >> >> > >> >> >> >> >> Thanks! > >> >> >> >> >> Alvaro > >> >> >> >> >> > >> >> >> >> >> On Fri, Oct 14, 2016 at 3:47 AM, Elvis Stansvik > >> >> >> >> >> wrote: > >> >> >> >> >>> > >> >> >> >> >>> Hi all, > >> >> >> >> >>> > >> >> >> >> >>> I updated our product to use VTK 7.1.0.rc1, as I was > interested > >> >> >> >> >>> in > >> >> >> >> >>> trying out vtkGPUVolumeRayCastMapper::UseJitteringOn() to > get > >> >> >> >> >>> rid > >> >> >> >> >>> of > >> >> >> >> >>> some woodgrain effects we're suffering from in our volume > >> >> >> >> >>> rendering > >> >> >> >> >>> (mostly when the volumes are rendered very opaque). > >> >> >> >> >>> > >> >> >> >> >>> But turning the option on seems to have little to no > effect. > >> >> >> >> >>> This > >> >> >> >> >>> is > >> >> >> >> >>> the result with the option on: > >> >> >> >> >>> > >> >> >> >> >>> https://dl.dropboxusercontent.com/u/22350696/out.ogv > >> >> >> >> >>> > >> >> >> >> >>> It looks about the same to me as it does with the option > off. > >> >> >> >> >>> > >> >> >> >> >>> Are there any knobs for this option? How does it determine > how > >> >> >> >> >>> much > >> >> >> >> >>> to > >> >> >> >> >>> perturbate the rays? > >> >> >> >> >>> > >> >> >> >> >>> Thanks for any advise. > >> >> >> >> >>> > >> >> >> >> >>> Elvis > >> >> >> >> >>> _______________________________________________ > >> >> >> >> >>> Powered by www.kitware.com > >> >> >> >> >>> > >> >> >> >> >>> Visit other Kitware open-source projects at > >> >> >> >> >>> http://www.kitware.com/opensource/opensource.html > >> >> >> >> >>> > >> >> >> >> >>> Search the list archives at: > >> >> >> >> >>> http://markmail.org/search/?q=vtk-developers > >> >> >> >> >>> > >> >> >> >> >>> Follow this link to subscribe/unsubscribe: > >> >> >> >> >>> http://public.kitware.com/mailman/listinfo/vtk-developers > >> >> >> >> >>> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> > >> >> >> >> >> -- > >> >> >> >> >> Alvaro Sanchez > >> >> >> >> >> Kitware, Inc. > >> >> >> >> >> Senior R&D Engineer > >> >> >> >> >> 21 Corporate Drive > >> >> >> >> >> Clifton Park, NY 12065-8662 > >> >> >> >> >> Phone: 518-881-4901 > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > > >> >> >> > -- > >> >> >> > Alvaro Sanchez > >> >> >> > Kitware, Inc. > >> >> >> > Senior R&D Engineer > >> >> >> > 21 Corporate Drive > >> >> >> > Clifton Park, NY 12065-8662 > >> >> >> > Phone: 518-881-4901 > >> >> > > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > Alvaro Sanchez > >> >> > Kitware, Inc. > >> >> > Senior R&D Engineer > >> >> > 21 Corporate Drive > >> >> > Clifton Park, NY 12065-8662 > >> >> > Phone: 518-881-4901 > >> > > >> > > >> > > >> > > >> > -- > >> > Alvaro Sanchez > >> > Kitware, Inc. > >> > Senior R&D Engineer > >> > 21 Corporate Drive > >> > Clifton Park, NY 12065-8662 > >> > Phone: 518-881-4901 > > > > > > > > > > -- > > Alvaro Sanchez > > Kitware, Inc. > > Senior R&D Engineer > > 21 Corporate Drive > > Clifton Park, NY 12065-8662 > > Phone: 518-881-4901 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alvaro.sanchez at kitware.com Thu Nov 3 08:20:13 2016 From: alvaro.sanchez at kitware.com (Alvaro Sanchez) Date: Thu, 3 Nov 2016 08:20:13 -0400 Subject: [vtk-developers] UseJitteringOn() has no effect in 7.1.0.rc1 In-Reply-To: References: Message-ID: If I can get it reviewed today I could get it into 7.1 still, I will do my best. On Thu, Nov 3, 2016 at 8:09 AM, Elvis Stansvik wrote: > 2016-11-02 23:17 GMT+01:00 Elvis Stansvik : > >> Den 2 nov. 2016 12:17 fm skrev "Alvaro Sanchez" < >> alvaro.sanchez at kitware.com>: >> > >> > Hi Elvis, >> > >> > the patch for this in https://gitlab.kitware.com/vt >> k/vtk/merge_requests/2130 >> > >> > please give it a try and let me know if it helps. >> >> Great, thanks a lot. I'll give it a go when I'm back at work tomorrow. >> > Got held up with some other things, but going to try it out now. > > I saw that in the comments you said that this fix could wait until 8.0. No > chance of backporting it to 7.1? We're basing our product on 7.1.0.rc1 at > the moment, expecting to use 7.1 for our first release, so would love to > have the fix in there. > > Elvis > >> Elvis >> >> > >> > Cheers, >> > Alvaro >> > >> > >> > On Wed, Oct 26, 2016 at 11:59 AM, Elvis Stansvik < >> elvis.stansvik at orexplore.com> wrote: >> >> >> >> 2016-10-26 16:27 GMT+02:00 Alvaro Sanchez > >: >> >> > Hi Elvis, >> >> > >> >> > I found the root cause of this, the noise texture is not being >> correctly >> >> > sampled in the shader. I will tag you on the MR once the patch is >> ready so >> >> > that you can try it out. >> >> >> >> That's great news \o/ Thanks a lot Alvaro. >> >> >> >> Elvis >> >> >> >> > >> >> > Cheers, >> >> > >> >> > On Thu, Oct 20, 2016 at 1:30 AM, Elvis Stansvik >> >> > wrote: >> >> >> >> >> >> 2016-10-20 5:46 GMT+02:00 Alvaro Sanchez < >> alvaro.sanchez at kitware.com>: >> >> >> > I ran your test program and I could reproduce the wood-grain >> artifacts >> >> >> > you >> >> >> > see. It seems to me that the jitter noise might need some >> tweaking. I >> >> >> > will >> >> >> > try a few things and investigate further, will let you know my >> findings. >> >> >> >> >> >> Thanks Alvaro. >> >> >> >> >> >> Elvis >> >> >> >> >> >> > >> >> >> > >> >> >> > On Wed, Oct 19, 2016 at 8:07 AM, Elvis Stansvik >> >> >> > wrote: >> >> >> >> >> >> >> >> 2016-10-19 14:03 GMT+02:00 Alvaro Sanchez < >> alvaro.sanchez at kitware.com>: >> >> >> >> > Hi Elvis, >> >> >> >> > >> >> >> >> > thanks for the test case. Sorry, I did not have time to run >> it yet >> >> >> >> > but >> >> >> >> > I >> >> >> >> > will have a look at it today. >> >> >> >> > >> >> >> >> > It seems unlikely to me that the small data spacing is >> affecting >> >> >> >> > jittering. >> >> >> >> > I will come back to you after debugging a bit with your test >> case. >> >> >> >> >> >> >> >> Alright, no hurry. Thanks a lot for having a look. >> >> >> >> >> >> >> >> Elvis >> >> >> >> >> >> >> >> > >> >> >> >> > Cheers, >> >> >> >> > Alvaro >> >> >> >> > >> >> >> >> > On Wed, Oct 19, 2016 at 1:54 AM, Elvis Stansvik >> >> >> >> > wrote: >> >> >> >> >> >> >> >> >> >> 2016-10-15 11:16 GMT+02:00 Elvis Stansvik >> >> >> >> >> : >> >> >> >> >> > 2016-10-14 15:54 GMT+02:00 Alvaro Sanchez >> >> >> >> >> > : >> >> >> >> >> >> Hi Elvis, >> >> >> >> >> >> >> >> >> >> >> >> the mapper uses a vtkPerlinNoise instance to generate the >> jitter >> >> >> >> >> >> noise >> >> >> >> >> >> and >> >> >> >> >> >> as far as I know there are currently no knobs exposed to >> tweak >> >> >> >> >> >> the >> >> >> >> >> >> amount of >> >> >> >> >> >> ray perturbation. Are you using the GL2 backend? It >> would also >> >> >> >> >> >> be >> >> >> >> >> >> good to >> >> >> >> >> >> know what features are active along with ray jittering >> (multiple >> >> >> >> >> >> components, >> >> >> >> >> >> etc.), so if you could provide some sample data or code >> would be >> >> >> >> >> >> very >> >> >> >> >> >> helpful. >> >> >> >> >> > >> >> >> >> >> > Hi again Alvaro, >> >> >> >> >> > >> >> >> >> >> > Here's a minimal test case including sample data (129 MB): >> >> >> >> >> > >> >> >> >> >> > https://dl.dropboxusercontent >> .com/u/22350696/test_grain.tar.gz >> >> >> >> >> > >> >> >> >> >> > Build with: >> >> >> >> >> > >> >> >> >> >> > cmake . >> >> >> >> >> > make >> >> >> >> >> > >> >> >> >> >> > and run with: >> >> >> >> >> > >> >> >> >> >> > ./test_grain rec-0300mm-0400mm.xml >> >> >> >> >> > >> >> >> >> >> > The result should be as in the attached screenshot. >> >> >> >> >> >> >> >> >> >> Anyone had time to run my test case? Are you seeing the same >> thing? >> >> >> >> >> >> >> >> >> >> Elvis >> >> >> >> >> >> >> >> >> >> > >> >> >> >> >> > Elvis >> >> >> >> >> > >> >> >> >> >> >> >> >> >> >> >> >> Thanks! >> >> >> >> >> >> Alvaro >> >> >> >> >> >> >> >> >> >> >> >> On Fri, Oct 14, 2016 at 3:47 AM, Elvis Stansvik >> >> >> >> >> >> wrote: >> >> >> >> >> >>> >> >> >> >> >> >>> Hi all, >> >> >> >> >> >>> >> >> >> >> >> >>> I updated our product to use VTK 7.1.0.rc1, as I was >> interested >> >> >> >> >> >>> in >> >> >> >> >> >>> trying out vtkGPUVolumeRayCastMapper::UseJitteringOn() >> to get >> >> >> >> >> >>> rid >> >> >> >> >> >>> of >> >> >> >> >> >>> some woodgrain effects we're suffering from in our volume >> >> >> >> >> >>> rendering >> >> >> >> >> >>> (mostly when the volumes are rendered very opaque). >> >> >> >> >> >>> >> >> >> >> >> >>> But turning the option on seems to have little to no >> effect. >> >> >> >> >> >>> This >> >> >> >> >> >>> is >> >> >> >> >> >>> the result with the option on: >> >> >> >> >> >>> >> >> >> >> >> >>> https://dl.dropboxusercontent.com/u/22350696/out.ogv >> >> >> >> >> >>> >> >> >> >> >> >>> It looks about the same to me as it does with the option >> off. >> >> >> >> >> >>> >> >> >> >> >> >>> Are there any knobs for this option? How does it >> determine how >> >> >> >> >> >>> much >> >> >> >> >> >>> to >> >> >> >> >> >>> perturbate the rays? >> >> >> >> >> >>> >> >> >> >> >> >>> Thanks for any advise. >> >> >> >> >> >>> >> >> >> >> >> >>> Elvis >> >> >> >> >> >>> _______________________________________________ >> >> >> >> >> >>> Powered by www.kitware.com >> >> >> >> >> >>> >> >> >> >> >> >>> Visit other Kitware open-source projects at >> >> >> >> >> >>> http://www.kitware.com/opensource/opensource.html >> >> >> >> >> >>> >> >> >> >> >> >>> Search the list archives at: >> >> >> >> >> >>> http://markmail.org/search/?q=vtk-developers >> >> >> >> >> >>> >> >> >> >> >> >>> Follow this link to subscribe/unsubscribe: >> >> >> >> >> >>> http://public.kitware.com/mailman/listinfo/vtk-developers >> >> >> >> >> >>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> >> >> Alvaro Sanchez >> >> >> >> >> >> Kitware, Inc. >> >> >> >> >> >> Senior R&D Engineer >> >> >> >> >> >> 21 Corporate Drive >> >> >> >> >> >> Clifton Park, NY 12065-8662 >> >> >> >> >> >> Phone: 518-881-4901 >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > -- >> >> >> >> > Alvaro Sanchez >> >> >> >> > Kitware, Inc. >> >> >> >> > Senior R&D Engineer >> >> >> >> > 21 Corporate Drive >> >> >> >> > Clifton Park, NY 12065-8662 >> >> >> >> > Phone: 518-881-4901 >> >> >> > >> >> >> > >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > Alvaro Sanchez >> >> >> > Kitware, Inc. >> >> >> > Senior R&D Engineer >> >> >> > 21 Corporate Drive >> >> >> > Clifton Park, NY 12065-8662 >> >> >> > Phone: 518-881-4901 >> >> > >> >> > >> >> > >> >> > >> >> > -- >> >> > Alvaro Sanchez >> >> > Kitware, Inc. >> >> > Senior R&D Engineer >> >> > 21 Corporate Drive >> >> > Clifton Park, NY 12065-8662 >> >> > Phone: 518-881-4901 >> > >> > >> > >> > >> > -- >> > Alvaro Sanchez >> > Kitware, Inc. >> > Senior R&D Engineer >> > 21 Corporate Drive >> > Clifton Park, NY 12065-8662 >> > Phone: 518-881-4901 >> > > -- Alvaro Sanchez Kitware, Inc. Senior R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4901 -------------- next part -------------- An HTML attachment was scrubbed... URL: From elvis.stansvik at orexplore.com Thu Nov 3 08:26:35 2016 From: elvis.stansvik at orexplore.com (Elvis Stansvik) Date: Thu, 3 Nov 2016 13:26:35 +0100 Subject: [vtk-developers] UseJitteringOn() has no effect in 7.1.0.rc1 In-Reply-To: References: Message-ID: 2016-11-03 13:20 GMT+01:00 Alvaro Sanchez : > If I can get it reviewed today I could get it into 7.1 still, I will do > my best. > Thanks a lot, and if you can't make it, then I guess we can always backport it ourselves and keep it as a patch in the Debian package we're building. Elvis > > On Thu, Nov 3, 2016 at 8:09 AM, Elvis Stansvik < > elvis.stansvik at orexplore.com> wrote: > >> 2016-11-02 23:17 GMT+01:00 Elvis Stansvik : >> >>> Den 2 nov. 2016 12:17 fm skrev "Alvaro Sanchez" < >>> alvaro.sanchez at kitware.com>: >>> > >>> > Hi Elvis, >>> > >>> > the patch for this in https://gitlab.kitware.com/vt >>> k/vtk/merge_requests/2130 >>> > >>> > please give it a try and let me know if it helps. >>> >>> Great, thanks a lot. I'll give it a go when I'm back at work tomorrow. >>> >> Got held up with some other things, but going to try it out now. >> >> I saw that in the comments you said that this fix could wait until 8.0. >> No chance of backporting it to 7.1? We're basing our product on 7.1.0.rc1 >> at the moment, expecting to use 7.1 for our first release, so would love to >> have the fix in there. >> >> Elvis >> >>> Elvis >>> >>> > >>> > Cheers, >>> > Alvaro >>> > >>> > >>> > On Wed, Oct 26, 2016 at 11:59 AM, Elvis Stansvik < >>> elvis.stansvik at orexplore.com> wrote: >>> >> >>> >> 2016-10-26 16:27 GMT+02:00 Alvaro Sanchez >> >: >>> >> > Hi Elvis, >>> >> > >>> >> > I found the root cause of this, the noise texture is not being >>> correctly >>> >> > sampled in the shader. I will tag you on the MR once the patch is >>> ready so >>> >> > that you can try it out. >>> >> >>> >> That's great news \o/ Thanks a lot Alvaro. >>> >> >>> >> Elvis >>> >> >>> >> > >>> >> > Cheers, >>> >> > >>> >> > On Thu, Oct 20, 2016 at 1:30 AM, Elvis Stansvik >>> >> > wrote: >>> >> >> >>> >> >> 2016-10-20 5:46 GMT+02:00 Alvaro Sanchez < >>> alvaro.sanchez at kitware.com>: >>> >> >> > I ran your test program and I could reproduce the wood-grain >>> artifacts >>> >> >> > you >>> >> >> > see. It seems to me that the jitter noise might need some >>> tweaking. I >>> >> >> > will >>> >> >> > try a few things and investigate further, will let you know my >>> findings. >>> >> >> >>> >> >> Thanks Alvaro. >>> >> >> >>> >> >> Elvis >>> >> >> >>> >> >> > >>> >> >> > >>> >> >> > On Wed, Oct 19, 2016 at 8:07 AM, Elvis Stansvik >>> >> >> > wrote: >>> >> >> >> >>> >> >> >> 2016-10-19 14:03 GMT+02:00 Alvaro Sanchez < >>> alvaro.sanchez at kitware.com>: >>> >> >> >> > Hi Elvis, >>> >> >> >> > >>> >> >> >> > thanks for the test case. Sorry, I did not have time to run >>> it yet >>> >> >> >> > but >>> >> >> >> > I >>> >> >> >> > will have a look at it today. >>> >> >> >> > >>> >> >> >> > It seems unlikely to me that the small data spacing is >>> affecting >>> >> >> >> > jittering. >>> >> >> >> > I will come back to you after debugging a bit with your test >>> case. >>> >> >> >> >>> >> >> >> Alright, no hurry. Thanks a lot for having a look. >>> >> >> >> >>> >> >> >> Elvis >>> >> >> >> >>> >> >> >> > >>> >> >> >> > Cheers, >>> >> >> >> > Alvaro >>> >> >> >> > >>> >> >> >> > On Wed, Oct 19, 2016 at 1:54 AM, Elvis Stansvik >>> >> >> >> > wrote: >>> >> >> >> >> >>> >> >> >> >> 2016-10-15 11:16 GMT+02:00 Elvis Stansvik >>> >> >> >> >> : >>> >> >> >> >> > 2016-10-14 15:54 GMT+02:00 Alvaro Sanchez >>> >> >> >> >> > : >>> >> >> >> >> >> Hi Elvis, >>> >> >> >> >> >> >>> >> >> >> >> >> the mapper uses a vtkPerlinNoise instance to generate the >>> jitter >>> >> >> >> >> >> noise >>> >> >> >> >> >> and >>> >> >> >> >> >> as far as I know there are currently no knobs exposed to >>> tweak >>> >> >> >> >> >> the >>> >> >> >> >> >> amount of >>> >> >> >> >> >> ray perturbation. Are you using the GL2 backend? It >>> would also >>> >> >> >> >> >> be >>> >> >> >> >> >> good to >>> >> >> >> >> >> know what features are active along with ray jittering >>> (multiple >>> >> >> >> >> >> components, >>> >> >> >> >> >> etc.), so if you could provide some sample data or code >>> would be >>> >> >> >> >> >> very >>> >> >> >> >> >> helpful. >>> >> >> >> >> > >>> >> >> >> >> > Hi again Alvaro, >>> >> >> >> >> > >>> >> >> >> >> > Here's a minimal test case including sample data (129 MB): >>> >> >> >> >> > >>> >> >> >> >> > https://dl.dropboxusercontent >>> .com/u/22350696/test_grain.tar.gz >>> >> >> >> >> > >>> >> >> >> >> > Build with: >>> >> >> >> >> > >>> >> >> >> >> > cmake . >>> >> >> >> >> > make >>> >> >> >> >> > >>> >> >> >> >> > and run with: >>> >> >> >> >> > >>> >> >> >> >> > ./test_grain rec-0300mm-0400mm.xml >>> >> >> >> >> > >>> >> >> >> >> > The result should be as in the attached screenshot. >>> >> >> >> >> >>> >> >> >> >> Anyone had time to run my test case? Are you seeing the same >>> thing? >>> >> >> >> >> >>> >> >> >> >> Elvis >>> >> >> >> >> >>> >> >> >> >> > >>> >> >> >> >> > Elvis >>> >> >> >> >> > >>> >> >> >> >> >> >>> >> >> >> >> >> Thanks! >>> >> >> >> >> >> Alvaro >>> >> >> >> >> >> >>> >> >> >> >> >> On Fri, Oct 14, 2016 at 3:47 AM, Elvis Stansvik >>> >> >> >> >> >> wrote: >>> >> >> >> >> >>> >>> >> >> >> >> >>> Hi all, >>> >> >> >> >> >>> >>> >> >> >> >> >>> I updated our product to use VTK 7.1.0.rc1, as I was >>> interested >>> >> >> >> >> >>> in >>> >> >> >> >> >>> trying out vtkGPUVolumeRayCastMapper::UseJitteringOn() >>> to get >>> >> >> >> >> >>> rid >>> >> >> >> >> >>> of >>> >> >> >> >> >>> some woodgrain effects we're suffering from in our volume >>> >> >> >> >> >>> rendering >>> >> >> >> >> >>> (mostly when the volumes are rendered very opaque). >>> >> >> >> >> >>> >>> >> >> >> >> >>> But turning the option on seems to have little to no >>> effect. >>> >> >> >> >> >>> This >>> >> >> >> >> >>> is >>> >> >> >> >> >>> the result with the option on: >>> >> >> >> >> >>> >>> >> >> >> >> >>> https://dl.dropboxusercontent.com/u/22350696/out.ogv >>> >> >> >> >> >>> >>> >> >> >> >> >>> It looks about the same to me as it does with the option >>> off. >>> >> >> >> >> >>> >>> >> >> >> >> >>> Are there any knobs for this option? How does it >>> determine how >>> >> >> >> >> >>> much >>> >> >> >> >> >>> to >>> >> >> >> >> >>> perturbate the rays? >>> >> >> >> >> >>> >>> >> >> >> >> >>> Thanks for any advise. >>> >> >> >> >> >>> >>> >> >> >> >> >>> Elvis >>> >> >> >> >> >>> _______________________________________________ >>> >> >> >> >> >>> Powered by www.kitware.com >>> >> >> >> >> >>> >>> >> >> >> >> >>> Visit other Kitware open-source projects at >>> >> >> >> >> >>> http://www.kitware.com/opensource/opensource.html >>> >> >> >> >> >>> >>> >> >> >> >> >>> Search the list archives at: >>> >> >> >> >> >>> http://markmail.org/search/?q=vtk-developers >>> >> >> >> >> >>> >>> >> >> >> >> >>> Follow this link to subscribe/unsubscribe: >>> >> >> >> >> >>> http://public.kitware.com/mail >>> man/listinfo/vtk-developers >>> >> >> >> >> >>> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> >>> >> >> >> >> >> -- >>> >> >> >> >> >> Alvaro Sanchez >>> >> >> >> >> >> Kitware, Inc. >>> >> >> >> >> >> Senior R&D Engineer >>> >> >> >> >> >> 21 Corporate Drive >>> >> >> >> >> >> Clifton Park, NY 12065-8662 >>> >> >> >> >> >> Phone: 518-881-4901 >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > >>> >> >> >> > -- >>> >> >> >> > Alvaro Sanchez >>> >> >> >> > Kitware, Inc. >>> >> >> >> > Senior R&D Engineer >>> >> >> >> > 21 Corporate Drive >>> >> >> >> > Clifton Park, NY 12065-8662 >>> >> >> >> > Phone: 518-881-4901 >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > >>> >> >> > -- >>> >> >> > Alvaro Sanchez >>> >> >> > Kitware, Inc. >>> >> >> > Senior R&D Engineer >>> >> >> > 21 Corporate Drive >>> >> >> > Clifton Park, NY 12065-8662 >>> >> >> > Phone: 518-881-4901 >>> >> > >>> >> > >>> >> > >>> >> > >>> >> > -- >>> >> > Alvaro Sanchez >>> >> > Kitware, Inc. >>> >> > Senior R&D Engineer >>> >> > 21 Corporate Drive >>> >> > Clifton Park, NY 12065-8662 >>> >> > Phone: 518-881-4901 >>> > >>> > >>> > >>> > >>> > -- >>> > Alvaro Sanchez >>> > Kitware, Inc. >>> > Senior R&D Engineer >>> > 21 Corporate Drive >>> > Clifton Park, NY 12065-8662 >>> > Phone: 518-881-4901 >>> >> >> > > > -- > Alvaro Sanchez > Kitware, Inc. > Senior R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4901 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Thu Nov 3 09:21:31 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Thu, 3 Nov 2016 07:21:31 -0600 Subject: [vtk-developers] InvokeEvent test randomly failing quiz In-Reply-To: References: Message-ID: Okay, I think that I've found the problem. The crash occurs when there is a mismatch between the calldata_type set for the callback, and the type of the actual calldata object passed at event invocation. In TestInvokeEvent.py, when the DeleteEvent is invoked, the calldata is a vtkObject, so when the callback has been set to expect something else, there's a crash. In other words, the test crashes simply because the callbacks are receiving events that the test's author didn't anticipate. So Ken's earlier MR that modified the test is probably going in the right direction. Since the callbacks in that test are expecting specific calldata types, they should be made to observe only the specific events that they expect. I also think that TestInvokeEvent.py shouldn't use ModifiedEvent as the event to watch for. For each calldata type, it should use an event type that usually uses calldata of that type. For reference: https://gitlab.kitware.com/vtk/vtk/merge_requests/2135 - David On Wed, Nov 2, 2016 at 2:48 PM, David Gobbi wrote: > It looks like the fix didn't work. But now that I know which dashboard is > failing, and have seen the whole stack trace, I have a better idea of where > the problem might be. I'll give it another shot tonight. > > - David > > On Tue, Nov 1, 2016 at 11:48 PM, David Gobbi > wrote: > >> I wasn't able to reproduce the issue, but I think that I found out what >> causes it. When vtkPythonCommand::Execute() is called, it tries to promote >> the subject object (i.e. the object being deleted for DeleteEvent) into a >> Python object. I was able to confirm that this actually happens, and even >> though I couldn't get it to crash, I'm pretty sure that it puts the program >> into a bad state. >> >> See https://gitlab.kitware.com/vtk/vtk/merge_requests/2131 >> >> - David >> >> On Tue, Nov 1, 2016 at 9:19 AM, Utkarsh Ayachit < >> utkarsh.ayachit at kitware.com> wrote: >> >>> Ken, >>> >>> The issue seems to be that the callback is attempted to be called for >>> vtkCommand::DeleteEvent since the observer is set to respond to >>> "AnyEvent". When the object is being cleaned up as part of the >>> interpreter being destroyed, calling Python commands is indeed >>> problematic and hence the failure. >>> >>> The test can be fixed by changing the observer to only listen to >>> ModifiedEvent instead of AnyEvent. Ideally vtkPythonCommand::Execute >>> can check if the interpreter is being cleaned up, but I am not sure >>> how to do that. >>> >>> Utkarsh >>> >>> On Tue, Nov 1, 2016 at 10:33 AM, Ken Martin >>> wrote: >>> > OK here is a puzzle. We have a test that is occasionally failing and I >>> > suspect it fails due to random python order of deletion of vtk >>> objects. The >>> > relevant python code is below. It fails when unregistering a vtkObject >>> and I >>> > suspect it is failing when invoking an callback during the >>> > unregisterinternal method see the stack trace. So maybe python has >>> deleted >>> > the object from its maps but then it gets used in a callback for >>> another >>> > object being deleted? Again my python foo is weak but maybe we have to >>> > unregister the anyEvent observer before the end of the script? Maybe >>> > something else? >>> > >>> > @vtk.calldata_type(vtk.VTK_OBJECT) >>> > def callbackObj(self, caller, event, calldata): >>> > self.calldata = calldata >>> > >>> > def setUp(self): >>> > self.vtkObj = vtk.vtkObject() >>> > >>> > self.vtkObjForCallData = vtk.vtkObject() >>> > >>> > def test_obj(self): >>> > self.vtkObj.AddObserver(vtk.vtkCommand.AnyEvent, >>> self.callbackObj) >>> > self.vtkObj.InvokeEvent(vtk.vtkCommand.ModifiedEvent, >>> > self.vtkObjForCallData) >>> > self.assertEqual(self.calldata, self.vtkObjForCallData) >>> > >>> > 0x7f98bd3e8770 : ??? [(???) ???:-1] >>> > 0x7f98bd19b778 : vtkPythonCommand::Execute(vtkObject*, unsigned long, >>> void*) >>> > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] >>> > 0x7f98bcb9fd7e : ??? [(???) ???:-1] >>> > 0x7f98bcba000c : vtkObject::UnRegisterInternal(vtkObjectBase*, int) >>> > [(libvtkCommonCore-7.1.so.1) ???:-1] >>> > 0x7f98bd19f045 : vtkPythonUtil::RemoveObjectFromMap(_object*) >>> > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] >>> > 0x7f98bd1a5b30 : PyVTKObject_Delete [(libvtkWrappingPython35Core-7 >>> .1.so.1) >>> > ???:-1] >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Thu Nov 3 09:49:46 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Thu, 3 Nov 2016 07:49:46 -0600 Subject: [vtk-developers] InvokeEvent test randomly failing quiz In-Reply-To: References: Message-ID: A small correction to my discussion below: for DeleteEvent the calldata is a NULL pointer, not a vtkObject pointer. The crash occurred when this NULL pointer was cast and dereferenced because the callback was expecting something else. On Thu, Nov 3, 2016 at 7:21 AM, David Gobbi wrote: > Okay, I think that I've found the problem. The crash occurs when there is > a mismatch between the calldata_type set for the callback, and the type of > the actual calldata object passed at event invocation. > > In TestInvokeEvent.py, when the DeleteEvent is invoked, the calldata is a > vtkObject, so when the callback has been set to expect something else, > there's a crash. In other words, the test crashes simply because the > callbacks are receiving events that the test's author didn't anticipate. > > So Ken's earlier MR that modified the test is probably going in the right > direction. Since the callbacks in that test are expecting specific > calldata types, they should be made to observe only the specific events > that they expect. > > I also think that TestInvokeEvent.py shouldn't use ModifiedEvent as the > event to watch for. For each calldata type, it should use an event type > that usually uses calldata of that type. > > For reference: > https://gitlab.kitware.com/vtk/vtk/merge_requests/2135 > > - David > > On Wed, Nov 2, 2016 at 2:48 PM, David Gobbi wrote: > >> It looks like the fix didn't work. But now that I know which dashboard >> is failing, and have seen the whole stack trace, I have a better idea of >> where the problem might be. I'll give it another shot tonight. >> >> - David >> >> On Tue, Nov 1, 2016 at 11:48 PM, David Gobbi >> wrote: >> >>> I wasn't able to reproduce the issue, but I think that I found out what >>> causes it. When vtkPythonCommand::Execute() is called, it tries to promote >>> the subject object (i.e. the object being deleted for DeleteEvent) into a >>> Python object. I was able to confirm that this actually happens, and even >>> though I couldn't get it to crash, I'm pretty sure that it puts the program >>> into a bad state. >>> >>> See https://gitlab.kitware.com/vtk/vtk/merge_requests/2131 >>> >>> - David >>> >>> On Tue, Nov 1, 2016 at 9:19 AM, Utkarsh Ayachit < >>> utkarsh.ayachit at kitware.com> wrote: >>> >>>> Ken, >>>> >>>> The issue seems to be that the callback is attempted to be called for >>>> vtkCommand::DeleteEvent since the observer is set to respond to >>>> "AnyEvent". When the object is being cleaned up as part of the >>>> interpreter being destroyed, calling Python commands is indeed >>>> problematic and hence the failure. >>>> >>>> The test can be fixed by changing the observer to only listen to >>>> ModifiedEvent instead of AnyEvent. Ideally vtkPythonCommand::Execute >>>> can check if the interpreter is being cleaned up, but I am not sure >>>> how to do that. >>>> >>>> Utkarsh >>>> >>>> On Tue, Nov 1, 2016 at 10:33 AM, Ken Martin >>>> wrote: >>>> > OK here is a puzzle. We have a test that is occasionally failing and I >>>> > suspect it fails due to random python order of deletion of vtk >>>> objects. The >>>> > relevant python code is below. It fails when unregistering a >>>> vtkObject and I >>>> > suspect it is failing when invoking an callback during the >>>> > unregisterinternal method see the stack trace. So maybe python has >>>> deleted >>>> > the object from its maps but then it gets used in a callback for >>>> another >>>> > object being deleted? Again my python foo is weak but maybe we have to >>>> > unregister the anyEvent observer before the end of the script? Maybe >>>> > something else? >>>> > >>>> > @vtk.calldata_type(vtk.VTK_OBJECT) >>>> > def callbackObj(self, caller, event, calldata): >>>> > self.calldata = calldata >>>> > >>>> > def setUp(self): >>>> > self.vtkObj = vtk.vtkObject() >>>> > >>>> > self.vtkObjForCallData = vtk.vtkObject() >>>> > >>>> > def test_obj(self): >>>> > self.vtkObj.AddObserver(vtk.vtkCommand.AnyEvent, >>>> self.callbackObj) >>>> > self.vtkObj.InvokeEvent(vtk.vtkCommand.ModifiedEvent, >>>> > self.vtkObjForCallData) >>>> > self.assertEqual(self.calldata, self.vtkObjForCallData) >>>> > >>>> > 0x7f98bd3e8770 : ??? [(???) ???:-1] >>>> > 0x7f98bd19b778 : vtkPythonCommand::Execute(vtkObject*, unsigned >>>> long, void*) >>>> > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] >>>> > 0x7f98bcb9fd7e : ??? [(???) ???:-1] >>>> > 0x7f98bcba000c : vtkObject::UnRegisterInternal(vtkObjectBase*, int) >>>> > [(libvtkCommonCore-7.1.so.1) ???:-1] >>>> > 0x7f98bd19f045 : vtkPythonUtil::RemoveObjectFromMap(_object*) >>>> > [(libvtkWrappingPython35Core-7.1.so.1) ???:-1] >>>> > 0x7f98bd1a5b30 : PyVTKObject_Delete [(libvtkWrappingPython35Core-7 >>>> .1.so.1) >>>> > ???:-1] >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From berk.geveci at kitware.com Thu Nov 3 11:01:49 2016 From: berk.geveci at kitware.com (Berk Geveci) Date: Thu, 3 Nov 2016 11:01:49 -0400 Subject: [vtk-developers] Caching library In-Reply-To: <4d73-5814e600-1c3-a4f59f0@56547606> References: <4d73-5814e600-1c3-a4f59f0@56547606> Message-ID: This would be a potentially very useful addition, as long as it was done in a way that followed the correct VTK patterns. You will probably create a custom vtkExecutive subclass (probably a subclass of vtkCompositeDataPipeline) to do this. We have an external module functionality that can be used to host this externally but optionally pull it into a VTK build. Bill Lorensen is the expert there and can provide some guidance I hope. C++11 should not be an issue. VTK will require C++11 in the next version coming in the beginning of 2018. It is currently possible to enable C++11 enable support and everything compiles & works. Best, -berk On Sat, Oct 29, 2016 at 2:09 PM, Bc. Lukas HRUDA wrote: > Hello, > We are aware that many VTK filtres are implemented so that when input > values of two successive calls are the same, the filter performs the > calculation only once (during the first call). However, what if the > repetitive pattern is a more complex? For example, the pattern could be 1, > 1, 1, 2, 2, 1, 1, 2, 2, 1, 2, 1, in which case you probably agree with me > that it would be very benefitial to calculate the output for input 1 once > and for input 2 once. > Of course in general we don't know the pattern in advance and the set of > possible inputs can be very large. > > I am a student at the University of West Bohemia, Faculty of Applied > Science, Department of Computer Science, Czech Republic. > As a part of my bachelor thesis I have designed and implemented a small > library that can be used for caching results of time consuming calculations > in such cases. > The library was integrated and tested in a visualisation application for > medical data which is based on VTK. > The library aims to reduce number of repeated calculations that take > noticeable time (what is considered noticeable may differ from case to > case, in some cases it can be 1 second, in other cases it can be 30 > milliseconds). > The library's system works in a way that when the programmer runs any > calculation through it, it remembers the input and output and if a > calculation with the same input is run through it againt later, it does not > start the calculation and returns the remembered result instead. > The library does this whole process itself without programmers > interaction, it just needs to be properly initialized. > It is very generic, so it can be used for caching almost any type of data. > > Me and the supervisor of my bachelor thesis thought that this library > could be useful for you and we decided that we would like to integrate it > into the VTK. > It can be used to significantly speed up visualisations where any time > consuming calculation may occur more than once. > > Would you be interested to have our library integrated in VTK, perhaps as > an optional modul, so that VTK programmers could use it to speed up their > filters or whole applications? Please note that the library uses variadic > templates so it needs C++11 to compile. > If you have any questions about the library I will be glad to answer them. > > Best regards > Lukas Hruda > > > > > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zack.galbreath at kitware.com Thu Nov 3 12:09:40 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Thu, 3 Nov 2016 12:09:40 -0400 Subject: [vtk-developers] open.cdash.org upgrade Friday 2016.11.04 12pm EDT Message-ID: I will update open.cdash.org tomorrow, Friday November 4th, at 12pm (noon) EDT. I'll reply to message when I begin the upgrade, and again when it completes. This update involves some changes to CDash's database layout, so I expect it may take an hour or so to complete. The site should still be accessible during this time. Assuming this upgrade doesn't reveal any major new bugs, we plan on releasing CDash v2.4 soon. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.demarle at kitware.com Thu Nov 3 20:38:41 2016 From: dave.demarle at kitware.com (David E DeMarle) Date: Thu, 3 Nov 2016 20:38:41 -0400 Subject: [vtk-developers] announce: vtk 7.1.0 release candidate 2 is ready Message-ID: Hello, The next release candidate in the VTK 7.1 release cycle is ready for you to try. Thank you everyone who tried and provided feedback and updates based on rc1. As usual you can find the source, data, and vtkpython binary packages here: http://www.vtk.org/download/#candidate Please try this version of VTK and report any issues the the gitlab issue tracker so that we can try to address them before VTK 7.1.0 final in a few weeks time. The changes from rc1 are as follows: David C. Lonie (2): Prevent crash in HiddenLineRemovalPass. Reset extents pointer in SurfaceLICComposite. David Gobbi (2): 16870: Fix origin when TransformInputSamplingOff() is used. Add a simple Cxx test for vtkImageReslice Ken Martin (6): fix ios getpixeldata calls rebassed fix for front buffer draw pixels not showing better handling of how to get an OpenGL context win32 try fix for offscreen rendering on Windows memory leak in ExtractHierarchicalBins fix memory leax in vtkPlotParallelCoordinates Michael Fogleman (1): use vtkMath::IsNan Sankhesh Jhaveri (13): Clamp volume component weights to between 0.0 and 1.0 More changes with regards to doxygen documentation in smart volume mapper Provided ivar getter function for vector mode Modify behavior of average intensity projected volume rendering Improve documentation for volume mapper classes Validity of render checks for volume mappers Add missing doxygen decorator Improve volume shader code Added tests for multi-component additive and average intensity volumes Fix documentation for shading in volume rendering Added volume test for different blend modes Minor volume shader optimization Fix unused variable warning Sean McBride (1): Removed doxygen deprecation comment on vtkImageData methods Shawn Waldon (2): Disable TBB's implicit linking with #pragmas Update Xdmf3 tests for python3 Will Schroeder (2): Fixed memory leak Fixed memory leak David E DeMarle Kitware, Inc. R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4909 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zack.galbreath at kitware.com Fri Nov 4 11:59:12 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Fri, 4 Nov 2016 11:59:12 -0400 Subject: [vtk-developers] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: Message-ID: Starting the upgrade now. On Thu, Nov 3, 2016 at 12:09 PM, Zack Galbreath wrote: > I will update open.cdash.org tomorrow, Friday November 4th, at 12pm > (noon) EDT. I'll reply to message when I begin the upgrade, and again when > it completes. > > This update involves some changes to CDash's database layout, so I expect > it may take an hour or so to complete. The site should still be accessible > during this time. > > Assuming this upgrade doesn't reveal any major new bugs, we plan on > releasing CDash v2.4 soon. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alvaro.sanchez at kitware.com Fri Nov 4 12:09:54 2016 From: alvaro.sanchez at kitware.com (Alvaro Sanchez) Date: Fri, 4 Nov 2016 12:09:54 -0400 Subject: [vtk-developers] UseJitteringOn() has no effect in 7.1.0.rc1 In-Reply-To: References: Message-ID: The patch was merged so the fix will be included in 7.1 final (not RC2 though). Jittering will now be turned off by default since it depends on the specific case whether it makes things better or not, so make sure you enable it manually (just like you were already). It is also possible to customize the noise function, check out the JitteringCustom test case. On Thu, Nov 3, 2016 at 8:26 AM, Elvis Stansvik wrote: > 2016-11-03 13:20 GMT+01:00 Alvaro Sanchez : > >> If I can get it reviewed today I could get it into 7.1 still, I will do >> my best. >> > > Thanks a lot, and if you can't make it, then I guess we can always > backport it ourselves and keep it as a patch in the Debian package we're > building. > > Elvis > > >> >> On Thu, Nov 3, 2016 at 8:09 AM, Elvis Stansvik < >> elvis.stansvik at orexplore.com> wrote: >> >>> 2016-11-02 23:17 GMT+01:00 Elvis Stansvik >>> : >>> >>>> Den 2 nov. 2016 12:17 fm skrev "Alvaro Sanchez" < >>>> alvaro.sanchez at kitware.com>: >>>> > >>>> > Hi Elvis, >>>> > >>>> > the patch for this in https://gitlab.kitware.com/vt >>>> k/vtk/merge_requests/2130 >>>> > >>>> > please give it a try and let me know if it helps. >>>> >>>> Great, thanks a lot. I'll give it a go when I'm back at work tomorrow. >>>> >>> Got held up with some other things, but going to try it out now. >>> >>> I saw that in the comments you said that this fix could wait until 8.0. >>> No chance of backporting it to 7.1? We're basing our product on 7.1.0.rc1 >>> at the moment, expecting to use 7.1 for our first release, so would love to >>> have the fix in there. >>> >>> Elvis >>> >>>> Elvis >>>> >>>> > >>>> > Cheers, >>>> > Alvaro >>>> > >>>> > >>>> > On Wed, Oct 26, 2016 at 11:59 AM, Elvis Stansvik < >>>> elvis.stansvik at orexplore.com> wrote: >>>> >> >>>> >> 2016-10-26 16:27 GMT+02:00 Alvaro Sanchez < >>>> alvaro.sanchez at kitware.com>: >>>> >> > Hi Elvis, >>>> >> > >>>> >> > I found the root cause of this, the noise texture is not being >>>> correctly >>>> >> > sampled in the shader. I will tag you on the MR once the patch is >>>> ready so >>>> >> > that you can try it out. >>>> >> >>>> >> That's great news \o/ Thanks a lot Alvaro. >>>> >> >>>> >> Elvis >>>> >> >>>> >> > >>>> >> > Cheers, >>>> >> > >>>> >> > On Thu, Oct 20, 2016 at 1:30 AM, Elvis Stansvik >>>> >> > wrote: >>>> >> >> >>>> >> >> 2016-10-20 5:46 GMT+02:00 Alvaro Sanchez < >>>> alvaro.sanchez at kitware.com>: >>>> >> >> > I ran your test program and I could reproduce the wood-grain >>>> artifacts >>>> >> >> > you >>>> >> >> > see. It seems to me that the jitter noise might need some >>>> tweaking. I >>>> >> >> > will >>>> >> >> > try a few things and investigate further, will let you know my >>>> findings. >>>> >> >> >>>> >> >> Thanks Alvaro. >>>> >> >> >>>> >> >> Elvis >>>> >> >> >>>> >> >> > >>>> >> >> > >>>> >> >> > On Wed, Oct 19, 2016 at 8:07 AM, Elvis Stansvik >>>> >> >> > wrote: >>>> >> >> >> >>>> >> >> >> 2016-10-19 14:03 GMT+02:00 Alvaro Sanchez < >>>> alvaro.sanchez at kitware.com>: >>>> >> >> >> > Hi Elvis, >>>> >> >> >> > >>>> >> >> >> > thanks for the test case. Sorry, I did not have time to run >>>> it yet >>>> >> >> >> > but >>>> >> >> >> > I >>>> >> >> >> > will have a look at it today. >>>> >> >> >> > >>>> >> >> >> > It seems unlikely to me that the small data spacing is >>>> affecting >>>> >> >> >> > jittering. >>>> >> >> >> > I will come back to you after debugging a bit with your test >>>> case. >>>> >> >> >> >>>> >> >> >> Alright, no hurry. Thanks a lot for having a look. >>>> >> >> >> >>>> >> >> >> Elvis >>>> >> >> >> >>>> >> >> >> > >>>> >> >> >> > Cheers, >>>> >> >> >> > Alvaro >>>> >> >> >> > >>>> >> >> >> > On Wed, Oct 19, 2016 at 1:54 AM, Elvis Stansvik >>>> >> >> >> > wrote: >>>> >> >> >> >> >>>> >> >> >> >> 2016-10-15 11:16 GMT+02:00 Elvis Stansvik >>>> >> >> >> >> : >>>> >> >> >> >> > 2016-10-14 15:54 GMT+02:00 Alvaro Sanchez >>>> >> >> >> >> > : >>>> >> >> >> >> >> Hi Elvis, >>>> >> >> >> >> >> >>>> >> >> >> >> >> the mapper uses a vtkPerlinNoise instance to generate >>>> the jitter >>>> >> >> >> >> >> noise >>>> >> >> >> >> >> and >>>> >> >> >> >> >> as far as I know there are currently no knobs exposed to >>>> tweak >>>> >> >> >> >> >> the >>>> >> >> >> >> >> amount of >>>> >> >> >> >> >> ray perturbation. Are you using the GL2 backend? It >>>> would also >>>> >> >> >> >> >> be >>>> >> >> >> >> >> good to >>>> >> >> >> >> >> know what features are active along with ray jittering >>>> (multiple >>>> >> >> >> >> >> components, >>>> >> >> >> >> >> etc.), so if you could provide some sample data or code >>>> would be >>>> >> >> >> >> >> very >>>> >> >> >> >> >> helpful. >>>> >> >> >> >> > >>>> >> >> >> >> > Hi again Alvaro, >>>> >> >> >> >> > >>>> >> >> >> >> > Here's a minimal test case including sample data (129 MB): >>>> >> >> >> >> > >>>> >> >> >> >> > https://dl.dropboxusercontent >>>> .com/u/22350696/test_grain.tar.gz >>>> >> >> >> >> > >>>> >> >> >> >> > Build with: >>>> >> >> >> >> > >>>> >> >> >> >> > cmake . >>>> >> >> >> >> > make >>>> >> >> >> >> > >>>> >> >> >> >> > and run with: >>>> >> >> >> >> > >>>> >> >> >> >> > ./test_grain rec-0300mm-0400mm.xml >>>> >> >> >> >> > >>>> >> >> >> >> > The result should be as in the attached screenshot. >>>> >> >> >> >> >>>> >> >> >> >> Anyone had time to run my test case? Are you seeing the >>>> same thing? >>>> >> >> >> >> >>>> >> >> >> >> Elvis >>>> >> >> >> >> >>>> >> >> >> >> > >>>> >> >> >> >> > Elvis >>>> >> >> >> >> > >>>> >> >> >> >> >> >>>> >> >> >> >> >> Thanks! >>>> >> >> >> >> >> Alvaro >>>> >> >> >> >> >> >>>> >> >> >> >> >> On Fri, Oct 14, 2016 at 3:47 AM, Elvis Stansvik >>>> >> >> >> >> >> wrote: >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> Hi all, >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> I updated our product to use VTK 7.1.0.rc1, as I was >>>> interested >>>> >> >> >> >> >>> in >>>> >> >> >> >> >>> trying out vtkGPUVolumeRayCastMapper::UseJitteringOn() >>>> to get >>>> >> >> >> >> >>> rid >>>> >> >> >> >> >>> of >>>> >> >> >> >> >>> some woodgrain effects we're suffering from in our >>>> volume >>>> >> >> >> >> >>> rendering >>>> >> >> >> >> >>> (mostly when the volumes are rendered very opaque). >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> But turning the option on seems to have little to no >>>> effect. >>>> >> >> >> >> >>> This >>>> >> >> >> >> >>> is >>>> >> >> >> >> >>> the result with the option on: >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> https://dl.dropboxusercontent >>>> .com/u/22350696/out.ogv >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> It looks about the same to me as it does with the >>>> option off. >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> Are there any knobs for this option? How does it >>>> determine how >>>> >> >> >> >> >>> much >>>> >> >> >> >> >>> to >>>> >> >> >> >> >>> perturbate the rays? >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> Thanks for any advise. >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> Elvis >>>> >> >> >> >> >>> _______________________________________________ >>>> >> >> >> >> >>> Powered by www.kitware.com >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> Visit other Kitware open-source projects at >>>> >> >> >> >> >>> http://www.kitware.com/opensource/opensource.html >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> Search the list archives at: >>>> >> >> >> >> >>> http://markmail.org/search/?q=vtk-developers >>>> >> >> >> >> >>> >>>> >> >> >> >> >>> Follow this link to subscribe/unsubscribe: >>>> >> >> >> >> >>> http://public.kitware.com/mail >>>> man/listinfo/vtk-developers >>>> >> >> >> >> >>> >>>> >> >> >> >> >> >>>> >> >> >> >> >> >>>> >> >> >> >> >> >>>> >> >> >> >> >> -- >>>> >> >> >> >> >> Alvaro Sanchez >>>> >> >> >> >> >> Kitware, Inc. >>>> >> >> >> >> >> Senior R&D Engineer >>>> >> >> >> >> >> 21 Corporate Drive >>>> >> >> >> >> >> Clifton Park, NY 12065-8662 >>>> >> >> >> >> >> Phone: 518-881-4901 >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > >>>> >> >> >> > -- >>>> >> >> >> > Alvaro Sanchez >>>> >> >> >> > Kitware, Inc. >>>> >> >> >> > Senior R&D Engineer >>>> >> >> >> > 21 Corporate Drive >>>> >> >> >> > Clifton Park, NY 12065-8662 >>>> >> >> >> > Phone: 518-881-4901 >>>> >> >> > >>>> >> >> > >>>> >> >> > >>>> >> >> > >>>> >> >> > -- >>>> >> >> > Alvaro Sanchez >>>> >> >> > Kitware, Inc. >>>> >> >> > Senior R&D Engineer >>>> >> >> > 21 Corporate Drive >>>> >> >> > Clifton Park, NY 12065-8662 >>>> >> >> > Phone: 518-881-4901 >>>> >> > >>>> >> > >>>> >> > >>>> >> > >>>> >> > -- >>>> >> > Alvaro Sanchez >>>> >> > Kitware, Inc. >>>> >> > Senior R&D Engineer >>>> >> > 21 Corporate Drive >>>> >> > Clifton Park, NY 12065-8662 >>>> >> > Phone: 518-881-4901 >>>> > >>>> > >>>> > >>>> > >>>> > -- >>>> > Alvaro Sanchez >>>> > Kitware, Inc. >>>> > Senior R&D Engineer >>>> > 21 Corporate Drive >>>> > Clifton Park, NY 12065-8662 >>>> > Phone: 518-881-4901 >>>> >>> >>> >> >> >> -- >> Alvaro Sanchez >> Kitware, Inc. >> Senior R&D Engineer >> 21 Corporate Drive >> Clifton Park, NY 12065-8662 >> Phone: 518-881-4901 >> > > -- Alvaro Sanchez Kitware, Inc. Senior R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4901 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zack.galbreath at kitware.com Fri Nov 4 12:27:07 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Fri, 4 Nov 2016 12:27:07 -0400 Subject: [vtk-developers] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: Message-ID: The upgrade is complete. The only issue I've noticed is that old coverage files are not being displayed properly. Newly submitted ones are, though, so I suppose this problem will resolve itself tomorrow. Please do not hesitate to contact me if you notice anything else that seems to be amiss. On Fri, Nov 4, 2016 at 11:59 AM, Zack Galbreath wrote: > Starting the upgrade now. > > On Thu, Nov 3, 2016 at 12:09 PM, Zack Galbreath < > zack.galbreath at kitware.com> wrote: > >> I will update open.cdash.org tomorrow, Friday November 4th, at 12pm >> (noon) EDT. I'll reply to message when I begin the upgrade, and again when >> it completes. >> >> This update involves some changes to CDash's database layout, so I expect >> it may take an hour or so to complete. The site should still be accessible >> during this time. >> >> Assuming this upgrade doesn't reveal any major new bugs, we plan on >> releasing CDash v2.4 soon. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From elvis.stansvik at orexplore.com Fri Nov 4 13:22:50 2016 From: elvis.stansvik at orexplore.com (Elvis Stansvik) Date: Fri, 4 Nov 2016 18:22:50 +0100 Subject: [vtk-developers] UseJitteringOn() has no effect in 7.1.0.rc1 In-Reply-To: References: Message-ID: Den 4 nov. 2016 5:09 em skrev "Alvaro Sanchez" : > > The patch was merged so the fix will be included in 7.1 final (not RC2 though). Jittering will now be turned off by default since it depends on the specific case whether it makes things better or not, so make sure you enable it manually (just like you were already). It is also possible to customize the noise function, check out the JitteringCustom test case. Yes, was following the MR closely :) Didn't know it was on by default before. Many thanks for handling this so quickly, and thanks also to the reviewers. Have a nice weekend! Elvis > > On Thu, Nov 3, 2016 at 8:26 AM, Elvis Stansvik < elvis.stansvik at orexplore.com> wrote: >> >> 2016-11-03 13:20 GMT+01:00 Alvaro Sanchez : >>> >>> If I can get it reviewed today I could get it into 7.1 still, I will do my best. >> >> >> Thanks a lot, and if you can't make it, then I guess we can always backport it ourselves and keep it as a patch in the Debian package we're building. >> >> Elvis >> >>> >>> >>> On Thu, Nov 3, 2016 at 8:09 AM, Elvis Stansvik < elvis.stansvik at orexplore.com> wrote: >>>> >>>> 2016-11-02 23:17 GMT+01:00 Elvis Stansvik : >>>>> >>>>> Den 2 nov. 2016 12:17 fm skrev "Alvaro Sanchez" < alvaro.sanchez at kitware.com>: >>>>> > >>>>> > Hi Elvis, >>>>> > >>>>> > the patch for this in https://gitlab.kitware.com/vtk/vtk/merge_requests/2130 >>>>> > >>>>> > please give it a try and let me know if it helps. >>>>> >>>>> Great, thanks a lot. I'll give it a go when I'm back at work tomorrow. >>>> >>>> Got held up with some other things, but going to try it out now. >>>> >>>> I saw that in the comments you said that this fix could wait until 8.0. No chance of backporting it to 7.1? We're basing our product on 7.1.0.rc1 at the moment, expecting to use 7.1 for our first release, so would love to have the fix in there. >>>> >>>> Elvis >>>>> >>>>> Elvis >>>>> >>>>> > >>>>> > Cheers, >>>>> > Alvaro >>>>> > >>>>> > >>>>> > On Wed, Oct 26, 2016 at 11:59 AM, Elvis Stansvik < elvis.stansvik at orexplore.com> wrote: >>>>> >> >>>>> >> 2016-10-26 16:27 GMT+02:00 Alvaro Sanchez < alvaro.sanchez at kitware.com>: >>>>> >> > Hi Elvis, >>>>> >> > >>>>> >> > I found the root cause of this, the noise texture is not being correctly >>>>> >> > sampled in the shader. I will tag you on the MR once the patch is ready so >>>>> >> > that you can try it out. >>>>> >> >>>>> >> That's great news \o/ Thanks a lot Alvaro. >>>>> >> >>>>> >> Elvis >>>>> >> >>>>> >> > >>>>> >> > Cheers, >>>>> >> > >>>>> >> > On Thu, Oct 20, 2016 at 1:30 AM, Elvis Stansvik >>>>> >> > wrote: >>>>> >> >> >>>>> >> >> 2016-10-20 5:46 GMT+02:00 Alvaro Sanchez < alvaro.sanchez at kitware.com>: >>>>> >> >> > I ran your test program and I could reproduce the wood-grain artifacts >>>>> >> >> > you >>>>> >> >> > see. It seems to me that the jitter noise might need some tweaking. I >>>>> >> >> > will >>>>> >> >> > try a few things and investigate further, will let you know my findings. >>>>> >> >> >>>>> >> >> Thanks Alvaro. >>>>> >> >> >>>>> >> >> Elvis >>>>> >> >> >>>>> >> >> > >>>>> >> >> > >>>>> >> >> > On Wed, Oct 19, 2016 at 8:07 AM, Elvis Stansvik >>>>> >> >> > wrote: >>>>> >> >> >> >>>>> >> >> >> 2016-10-19 14:03 GMT+02:00 Alvaro Sanchez < alvaro.sanchez at kitware.com>: >>>>> >> >> >> > Hi Elvis, >>>>> >> >> >> > >>>>> >> >> >> > thanks for the test case. Sorry, I did not have time to run it yet >>>>> >> >> >> > but >>>>> >> >> >> > I >>>>> >> >> >> > will have a look at it today. >>>>> >> >> >> > >>>>> >> >> >> > It seems unlikely to me that the small data spacing is affecting >>>>> >> >> >> > jittering. >>>>> >> >> >> > I will come back to you after debugging a bit with your test case. >>>>> >> >> >> >>>>> >> >> >> Alright, no hurry. Thanks a lot for having a look. >>>>> >> >> >> >>>>> >> >> >> Elvis >>>>> >> >> >> >>>>> >> >> >> > >>>>> >> >> >> > Cheers, >>>>> >> >> >> > Alvaro >>>>> >> >> >> > >>>>> >> >> >> > On Wed, Oct 19, 2016 at 1:54 AM, Elvis Stansvik >>>>> >> >> >> > wrote: >>>>> >> >> >> >> >>>>> >> >> >> >> 2016-10-15 11:16 GMT+02:00 Elvis Stansvik >>>>> >> >> >> >> : >>>>> >> >> >> >> > 2016-10-14 15:54 GMT+02:00 Alvaro Sanchez >>>>> >> >> >> >> > : >>>>> >> >> >> >> >> Hi Elvis, >>>>> >> >> >> >> >> >>>>> >> >> >> >> >> the mapper uses a vtkPerlinNoise instance to generate the jitter >>>>> >> >> >> >> >> noise >>>>> >> >> >> >> >> and >>>>> >> >> >> >> >> as far as I know there are currently no knobs exposed to tweak >>>>> >> >> >> >> >> the >>>>> >> >> >> >> >> amount of >>>>> >> >> >> >> >> ray perturbation. Are you using the GL2 backend? It would also >>>>> >> >> >> >> >> be >>>>> >> >> >> >> >> good to >>>>> >> >> >> >> >> know what features are active along with ray jittering (multiple >>>>> >> >> >> >> >> components, >>>>> >> >> >> >> >> etc.), so if you could provide some sample data or code would be >>>>> >> >> >> >> >> very >>>>> >> >> >> >> >> helpful. >>>>> >> >> >> >> > >>>>> >> >> >> >> > Hi again Alvaro, >>>>> >> >> >> >> > >>>>> >> >> >> >> > Here's a minimal test case including sample data (129 MB): >>>>> >> >> >> >> > >>>>> >> >> >> >> > https://dl.dropboxusercontent.com/u/22350696/test_grain.tar.gz >>>>> >> >> >> >> > >>>>> >> >> >> >> > Build with: >>>>> >> >> >> >> > >>>>> >> >> >> >> > cmake . >>>>> >> >> >> >> > make >>>>> >> >> >> >> > >>>>> >> >> >> >> > and run with: >>>>> >> >> >> >> > >>>>> >> >> >> >> > ./test_grain rec-0300mm-0400mm.xml >>>>> >> >> >> >> > >>>>> >> >> >> >> > The result should be as in the attached screenshot. >>>>> >> >> >> >> >>>>> >> >> >> >> Anyone had time to run my test case? Are you seeing the same thing? >>>>> >> >> >> >> >>>>> >> >> >> >> Elvis >>>>> >> >> >> >> >>>>> >> >> >> >> > >>>>> >> >> >> >> > Elvis >>>>> >> >> >> >> > >>>>> >> >> >> >> >> >>>>> >> >> >> >> >> Thanks! >>>>> >> >> >> >> >> Alvaro >>>>> >> >> >> >> >> >>>>> >> >> >> >> >> On Fri, Oct 14, 2016 at 3:47 AM, Elvis Stansvik >>>>> >> >> >> >> >> wrote: >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> Hi all, >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> I updated our product to use VTK 7.1.0.rc1, as I was interested >>>>> >> >> >> >> >>> in >>>>> >> >> >> >> >>> trying out vtkGPUVolumeRayCastMapper::UseJitteringOn() to get >>>>> >> >> >> >> >>> rid >>>>> >> >> >> >> >>> of >>>>> >> >> >> >> >>> some woodgrain effects we're suffering from in our volume >>>>> >> >> >> >> >>> rendering >>>>> >> >> >> >> >>> (mostly when the volumes are rendered very opaque). >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> But turning the option on seems to have little to no effect. >>>>> >> >> >> >> >>> This >>>>> >> >> >> >> >>> is >>>>> >> >> >> >> >>> the result with the option on: >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> https://dl.dropboxusercontent.com/u/22350696/out.ogv >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> It looks about the same to me as it does with the option off. >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> Are there any knobs for this option? How does it determine how >>>>> >> >> >> >> >>> much >>>>> >> >> >> >> >>> to >>>>> >> >> >> >> >>> perturbate the rays? >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> Thanks for any advise. >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> Elvis >>>>> >> >> >> >> >>> _______________________________________________ >>>>> >> >> >> >> >>> Powered by www.kitware.com >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> Visit other Kitware open-source projects at >>>>> >> >> >> >> >>> http://www.kitware.com/opensource/opensource.html >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> Search the list archives at: >>>>> >> >> >> >> >>> http://markmail.org/search/?q=vtk-developers >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >>> Follow this link to subscribe/unsubscribe: >>>>> >> >> >> >> >>> http://public.kitware.com/mailman/listinfo/vtk-developers >>>>> >> >> >> >> >>> >>>>> >> >> >> >> >> >>>>> >> >> >> >> >> >>>>> >> >> >> >> >> >>>>> >> >> >> >> >> -- >>>>> >> >> >> >> >> Alvaro Sanchez >>>>> >> >> >> >> >> Kitware, Inc. >>>>> >> >> >> >> >> Senior R&D Engineer >>>>> >> >> >> >> >> 21 Corporate Drive >>>>> >> >> >> >> >> Clifton Park, NY 12065-8662 >>>>> >> >> >> >> >> Phone: 518-881-4901 >>>>> >> >> >> > >>>>> >> >> >> > >>>>> >> >> >> > >>>>> >> >> >> > >>>>> >> >> >> > -- >>>>> >> >> >> > Alvaro Sanchez >>>>> >> >> >> > Kitware, Inc. >>>>> >> >> >> > Senior R&D Engineer >>>>> >> >> >> > 21 Corporate Drive >>>>> >> >> >> > Clifton Park, NY 12065-8662 >>>>> >> >> >> > Phone: 518-881-4901 >>>>> >> >> > >>>>> >> >> > >>>>> >> >> > >>>>> >> >> > >>>>> >> >> > -- >>>>> >> >> > Alvaro Sanchez >>>>> >> >> > Kitware, Inc. >>>>> >> >> > Senior R&D Engineer >>>>> >> >> > 21 Corporate Drive >>>>> >> >> > Clifton Park, NY 12065-8662 >>>>> >> >> > Phone: 518-881-4901 >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > -- >>>>> >> > Alvaro Sanchez >>>>> >> > Kitware, Inc. >>>>> >> > Senior R&D Engineer >>>>> >> > 21 Corporate Drive >>>>> >> > Clifton Park, NY 12065-8662 >>>>> >> > Phone: 518-881-4901 >>>>> > >>>>> > >>>>> > >>>>> > >>>>> > -- >>>>> > Alvaro Sanchez >>>>> > Kitware, Inc. >>>>> > Senior R&D Engineer >>>>> > 21 Corporate Drive >>>>> > Clifton Park, NY 12065-8662 >>>>> > Phone: 518-881-4901 >>>> >>>> >>> >>> >>> >>> -- >>> Alvaro Sanchez >>> Kitware, Inc. >>> Senior R&D Engineer >>> 21 Corporate Drive >>> Clifton Park, NY 12065-8662 >>> Phone: 518-881-4901 >> >> > > > > -- > Alvaro Sanchez > Kitware, Inc. > Senior R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4901 -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcus.hanwell at kitware.com Fri Nov 4 14:36:56 2016 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Fri, 4 Nov 2016 14:36:56 -0400 Subject: [vtk-developers] [vtkusers] HiDPI not working on VTK 7.1.0 rc2 In-Reply-To: <581C7ED9.90003@bluequartz.net> References: <581C7ED9.90003@bluequartz.net> Message-ID: On Fri, Nov 4, 2016 at 8:28 AM, Michael Jackson wrote: > I just tried the HiDPI support on VTK 7.1.0-rc2 and I get the usual VTK > rendering canvas that is half the size of the widget that it is embedded > into. > > We are using Qt 5.6.2 on macOS 10.10.5. I compiled my original pull request > (way back in Aug 2016) and that patch gives me a full size canvas. But when > compiling the latest VTK 7.1.0-rc2 I get the half size canvas. I thought the > branch was merged on Sept 28 2016 but I guess I got busy and never actually > tested it on a retina screen. > > Most likely I am doing something wrong in the initialization in my code but > just in case can anyone else confirm with Qt 5.6.x that they can actually > get a Retina/HiDPI canvas? > Bob has a retinal Mac that I can do some testing on, this is likely to end up being after Supercomputing, but I would like to follow up on this. We had it working when you visited, and I am hoping to get this enabled in Tomviz at some point soon. It would be great to hear from Sean and/or David. To the best of my recollection an alternate approach was developed, and that was merged. It had several other changes in addition to what was proposed originally. I can look at cherry-picking the patch we developed when you were out, and going over what may have not made it into current master if this isn't working. Posting this to developers as it feels like more of a development issue to me, I got busy and didn't get around to testing master once it was merged (and don't have easy access to a retinal machine, but I can walk across to Bob's office to borrow one). I will see about getting Tomviz set up there, and attempt to enable retinal in the Qt API for the application which is also based on Qt 5.6+ From marcus.hanwell at kitware.com Fri Nov 4 15:14:15 2016 From: marcus.hanwell at kitware.com (Marcus D. Hanwell) Date: Fri, 4 Nov 2016 15:14:15 -0400 Subject: [vtk-developers] [vtkusers] HiDPI not working on VTK 7.1.0 rc2 In-Reply-To: <581CD914.1090001@bluequartz.net> References: <581C7ED9.90003@bluequartz.net> <581CD914.1090001@bluequartz.net> Message-ID: On Fri, Nov 4, 2016 at 2:53 PM, Michael Jackson wrote: > > Marcus D. Hanwell wrote: >> >> On Fri, Nov 4, 2016 at 8:28 AM, Michael Jackson >> wrote: >>> >>> I just tried the HiDPI support on VTK 7.1.0-rc2 and I get the usual VTK >>> rendering canvas that is half the size of the widget that it is embedded >>> into. >>> >>> We are using Qt 5.6.2 on macOS 10.10.5. I compiled my original pull >>> request >>> (way back in Aug 2016) and that patch gives me a full size canvas. But >>> when >>> compiling the latest VTK 7.1.0-rc2 I get the half size canvas. I thought >>> the >>> branch was merged on Sept 28 2016 but I guess I got busy and never >>> actually >>> tested it on a retina screen. >>> >>> Most likely I am doing something wrong in the initialization in my code >>> but >>> just in case can anyone else confirm with Qt 5.6.x that they can actually >>> get a Retina/HiDPI canvas? >>> >> Bob has a retinal Mac that I can do some testing on, this is likely to >> end up being after Supercomputing, but I would like to follow up on >> this. We had it working when you visited, and I am hoping to get this >> enabled in Tomviz at some point soon. It would be great to hear from >> Sean and/or David. To the best of my recollection an alternate >> approach was developed, and that was merged. It had several other >> changes in addition to what was proposed originally. >> >> I can look at cherry-picking the patch we developed when you were out, >> and going over what may have not made it into current master if this >> isn't working. Posting this to developers as it feels like more of a >> development issue to me, I got busy and didn't get around to testing >> master once it was merged (and don't have easy access to a retinal >> machine, but I can walk across to Bob's office to borrow one). >> >> I will see about getting Tomviz set up there, and attempt to enable >> retinal in the Qt API for the application which is also based on Qt >> 5.6+ > > You can always just use the screen res hack to enable HiDPI modes on the 30" > monitor. This is how I am testing here at the office. Better than nothing. > True, but I would like access to a real retinal display to assess the user interface when we move over. From jhlegarreta at vicomtech.org Mon Nov 7 02:02:55 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Mon, 7 Nov 2016 08:02:55 +0100 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: Hi, thanks for the upgrade Zach. Coverage reports seem not to be working yet. Although the coverage figures seem to be computed/updated, the file reports do not show which lines are being exercised, and just show an empty line. Thanks, JON HAITZ On 5 November 2016 at 02:02, Bradley Lowekamp wrote: > Thanks for the upgrade! All seems ok for my usage today. I also > appreciate the separated graphs with the correct axis label. > > Brad > > On Nov 4, 2016, at 12:27 PM, Zack Galbreath > wrote: > > The upgrade is complete. > > The only issue I've noticed is that old coverage files are not being > displayed properly. Newly submitted ones are, though, so I suppose this > problem will resolve itself tomorrow. > > Please do not hesitate to contact me if you notice anything else that > seems to be amiss. > > > > On Fri, Nov 4, 2016 at 11:59 AM, Zack Galbreath < > zack.galbreath at kitware.com> wrote: > >> Starting the upgrade now. >> >> On Thu, Nov 3, 2016 at 12:09 PM, Zack Galbreath < >> zack.galbreath at kitware.com> wrote: >> >>> I will update open.cdash.org tomorrow, Friday November 4th, at 12pm >>> (noon) EDT. I'll reply to message when I begin the upgrade, and again when >>> it completes. >>> >>> This update involves some changes to CDash's database layout, so I >>> expect it may take an hour or so to complete. The site should still be >>> accessible during this time. >>> >>> Assuming this upgrade doesn't reveal any major new bugs, we plan on >>> releasing CDash v2.4 soon. >>> >> >> > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Kitware offers ITK Training Courses, for more information visit: > http://kitware.com/products/protraining.php > > Please keep messages on-topic and check the ITK FAQ at: > http://www.itk.org/Wiki/ITK_FAQ > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/insight-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zack.galbreath at kitware.com Mon Nov 7 09:30:06 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Mon, 7 Nov 2016 09:30:06 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: Hi Jon, Thanks for noticing that this issue was still not resolved. I just purged the cache of coverage files on open.cdash.org, so line-by-line coverage should be properly displayed once this data is resubmitted tonight. I'll double check this tomorrow morning. On Mon, Nov 7, 2016 at 2:02 AM, Jon Haitz Legarreta < jhlegarreta at vicomtech.org> wrote: > Hi, > thanks for the upgrade Zach. > > Coverage reports seem not to be working yet. Although the coverage figures > seem to be computed/updated, the file reports do not show which lines are > being exercised, and just show an empty line. > > Thanks, > JON HAITZ > > > > > On 5 November 2016 at 02:02, Bradley Lowekamp wrote: > >> Thanks for the upgrade! All seems ok for my usage today. I also >> appreciate the separated graphs with the correct axis label. >> >> Brad >> >> On Nov 4, 2016, at 12:27 PM, Zack Galbreath >> wrote: >> >> The upgrade is complete. >> >> The only issue I've noticed is that old coverage files are not being >> displayed properly. Newly submitted ones are, though, so I suppose this >> problem will resolve itself tomorrow. >> >> Please do not hesitate to contact me if you notice anything else that >> seems to be amiss. >> >> >> >> On Fri, Nov 4, 2016 at 11:59 AM, Zack Galbreath < >> zack.galbreath at kitware.com> wrote: >> >>> Starting the upgrade now. >>> >>> On Thu, Nov 3, 2016 at 12:09 PM, Zack Galbreath < >>> zack.galbreath at kitware.com> wrote: >>> >>>> I will update open.cdash.org tomorrow, Friday November 4th, at 12pm >>>> (noon) EDT. I'll reply to message when I begin the upgrade, and again when >>>> it completes. >>>> >>>> This update involves some changes to CDash's database layout, so I >>>> expect it may take an hour or so to complete. The site should still be >>>> accessible during this time. >>>> >>>> Assuming this upgrade doesn't reveal any major new bugs, we plan on >>>> releasing CDash v2.4 soon. >>>> >>> >>> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Kitware offers ITK Training Courses, for more information visit: >> http://kitware.com/products/protraining.php >> >> Please keep messages on-topic and check the ITK FAQ at: >> http://www.itk.org/Wiki/ITK_FAQ >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/insight-developers >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zack.galbreath at kitware.com Mon Nov 7 09:34:44 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Mon, 7 Nov 2016 09:34:44 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: On Fri, Nov 4, 2016 at 9:02 PM, Bradley Lowekamp wrote: > Thanks for the upgrade! All seems ok for my usage today. I also > appreciate the separated graphs with the correct axis label. > Glad to you like it! Off the top of my head, another improvement we made is to the "Test Overview" page. Instead of simply showing an alphabetical list of all tests that failed, it now shows you how frequently each test failed or timed out. This is more useful for tracking down unreliable tests. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Mon Nov 7 10:44:58 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 7 Nov 2016 10:44:58 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: Seems like compile errors are not being listed... https://open.cdash.org/viewBuildError.php?buildid=4630324 On Mon, Nov 7, 2016 at 9:34 AM, Zack Galbreath wrote: > On Fri, Nov 4, 2016 at 9:02 PM, Bradley Lowekamp wrote: >> >> Thanks for the upgrade! All seems ok for my usage today. I also >> appreciate the separated graphs with the correct axis label. > > > Glad to you like it! > > Off the top of my head, another improvement we made is to the "Test > Overview" page. Instead of simply showing an alphabetical list of all tests > that failed, it now shows you how frequently each test failed or timed out. > This is more useful for tracking down unreliable tests. > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > -- Unpaid intern in BillsBasement at noware dot com From zack.galbreath at kitware.com Mon Nov 7 11:10:26 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Mon, 7 Nov 2016 11:10:26 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: On Mon, Nov 7, 2016 at 10:44 AM, Bill Lorensen wrote: > Seems like compile errors are not being listed... > https://open.cdash.org/viewBuildError.php?buildid=4630324 Looks okay to me. Might be a stale cache on your end? Let me know if I'm missing something. ? > > On Mon, Nov 7, 2016 at 9:34 AM, Zack Galbreath > wrote: > > On Fri, Nov 4, 2016 at 9:02 PM, Bradley Lowekamp > wrote: > >> > >> Thanks for the upgrade! All seems ok for my usage today. I also > >> appreciate the separated graphs with the correct axis label. > > > > > > Glad to you like it! > > > > Off the top of my head, another improvement we made is to the "Test > > Overview" page. Instead of simply showing an alphabetical list of all > tests > > that failed, it now shows you how frequently each test failed or timed > out. > > This is more useful for tracking down unreliable tests. > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Search the list archives at: http://markmail.org/search/?q= > vtk-developers > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/vtk-developers > > > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: build_errors.png Type: image/png Size: 470063 bytes Desc: not available URL: From bill.lorensen at gmail.com Mon Nov 7 11:29:18 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 7 Nov 2016 11:29:18 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: On my ubuntu system, works on firefox, not on Chrome On Mon, Nov 7, 2016 at 11:10 AM, Zack Galbreath wrote: > On Mon, Nov 7, 2016 at 10:44 AM, Bill Lorensen > wrote: > >> Seems like compile errors are not being listed... >> https://open.cdash.org/viewBuildError.php?buildid=4630324 > > > Looks okay to me. Might be a stale cache on your end? Let me know if I'm > missing something. > > > > ? > > > > > > > >> >> On Mon, Nov 7, 2016 at 9:34 AM, Zack Galbreath >> wrote: >> > On Fri, Nov 4, 2016 at 9:02 PM, Bradley Lowekamp >> wrote: >> >> >> >> Thanks for the upgrade! All seems ok for my usage today. I also >> >> appreciate the separated graphs with the correct axis label. >> > >> > >> > Glad to you like it! >> > >> > Off the top of my head, another improvement we made is to the "Test >> > Overview" page. Instead of simply showing an alphabetical list of all >> tests >> > that failed, it now shows you how frequently each test failed or timed >> out. >> > This is more useful for tracking down unreliable tests. >> > >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Search the list archives at: http://markmail.org/search/?q= >> vtk-developers >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/vtk-developers >> > >> > >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> > > -- Unpaid intern in BillsBasement at noware dot com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: build_errors.png Type: image/png Size: 470063 bytes Desc: not available URL: From david.gobbi at gmail.com Mon Nov 7 11:56:03 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Mon, 7 Nov 2016 09:56:03 -0700 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: I had the same problem (I'm using Chrome), and clearing the cache fixed it. Simply reloading the page didn't help, I had to clear the cache. I wonder if this problem could be avoided if each major upgrade changed the names of whichever resources are being cached. - David On Mon, Nov 7, 2016 at 9:10 AM, Zack Galbreath wrote: > On Mon, Nov 7, 2016 at 10:44 AM, Bill Lorensen > wrote: > >> Seems like compile errors are not being listed... >> https://open.cdash.org/viewBuildError.php?buildid=4630324 > > > Looks okay to me. Might be a stale cache on your end? Let me know if I'm > missing something. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Mon Nov 7 12:07:01 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Mon, 7 Nov 2016 12:07:01 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: Thanks David. Clearing the cache did it for me. On Mon, Nov 7, 2016 at 11:56 AM, David Gobbi wrote: > I had the same problem (I'm using Chrome), and clearing the cache fixed it. > Simply reloading the page didn't help, I had to clear the cache. > > I wonder if this problem could be avoided if each major upgrade > changed the names of whichever resources are being cached. > > - David > > > On Mon, Nov 7, 2016 at 9:10 AM, Zack Galbreath > wrote: >> >> On Mon, Nov 7, 2016 at 10:44 AM, Bill Lorensen >> wrote: >>> >>> Seems like compile errors are not being listed... >>> https://open.cdash.org/viewBuildError.php?buildid=4630324 >> >> >> Looks okay to me. Might be a stale cache on your end? Let me know if I'm >> missing something. > > -- Unpaid intern in BillsBasement at noware dot com From zack.galbreath at kitware.com Mon Nov 7 12:10:15 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Mon, 7 Nov 2016 12:10:15 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: On Mon, Nov 7, 2016 at 11:56 AM, David Gobbi wrote: > I wonder if this problem could be avoided if each major upgrade > changed the names of whichever resources are being cached. > We already do this ("cache busting") for our Javascript code. Before the next upgrade I'll look into doing something similar for our HTML templates. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sean at rogue-research.com Mon Nov 7 13:58:35 2016 From: sean at rogue-research.com (Sean McBride) Date: Mon, 7 Nov 2016 14:58:35 -0400 Subject: [vtk-developers] [vtkusers] HiDPI not working on VTK 7.1.0 rc2 In-Reply-To: References: <581C7ED9.90003@bluequartz.net> Message-ID: <20161107185835.473800880@mail.rogue-research.com> On Fri, 4 Nov 2016 14:36:56 -0400, Marcus D. Hanwell said: >On Fri, Nov 4, 2016 at 8:28 AM, Michael Jackson > wrote: >> I just tried the HiDPI support on VTK 7.1.0-rc2 and I get the usual VTK >> rendering canvas that is half the size of the widget that it is embedded >> into. >> >> We are using Qt 5.6.2 on macOS 10.10.5. I compiled my original pull request >> (way back in Aug 2016) and that patch gives me a full size canvas. But when >> compiling the latest VTK 7.1.0-rc2 I get the half size canvas. I thought the >> branch was merged on Sept 28 2016 but I guess I got busy and never actually >> tested it on a retina screen. >> >> Most likely I am doing something wrong in the initialization in my code but >> just in case can anyone else confirm with Qt 5.6.x that they can actually >> get a Retina/HiDPI canvas? >> >Bob has a retinal Mac that I can do some testing on, this is likely to >end up being after Supercomputing, but I would like to follow up on >this. We had it working when you visited, and I am hoping to get this >enabled in Tomviz at some point soon. It would be great to hear from >Sean and/or David. To the best of my recollection an alternate >approach was developed, and that was merged. It had several other >changes in addition to what was proposed originally. We merged my PR: and not Mike's: IIRC mine was a superset of Mike's, unless we screwed something up somewhere. I was always of the view that the changes were necessary but not sufficient. I'm swamped this week preparing for the SfN conference, but can look more next week... Cheers, -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From zack.galbreath at kitware.com Tue Nov 8 09:02:54 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Tue, 8 Nov 2016 09:02:54 -0500 Subject: [vtk-developers] [ITK-dev] open.cdash.org upgrade Friday 2016.11.04 12pm EDT In-Reply-To: References: <61F71A78-0415-4827-AAE7-D331F5FF09FC@mail.nih.gov> Message-ID: On Mon, Nov 7, 2016 at 9:30 AM, Zack Galbreath wrote: > I just purged the cache of coverage files on open.cdash.org, so > line-by-line coverage should be properly displayed once this data is > resubmitted tonight. I'll double check this tomorrow morning. > It looks like this is fixed now. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arankin at robarts.ca Tue Nov 8 14:56:26 2016 From: arankin at robarts.ca (Adam Rankin) Date: Tue, 8 Nov 2016 19:56:26 +0000 Subject: [vtk-developers] VTK without vtksys Message-ID: <30e0a7e31c6648349e8578ccc862219b@dag2.robarts.ca> Hello all, I am trying to build VTK for UWP, and I will fully admit to not knowing the linkages/structure of modules and their dependency on vtksys (aside that the VTK CMake output lists it as a dependency). Is it a crazy notion to write a vtksys alternative library that builds against the UWP? I guess what I'm looking for is someone to say, "Sure it's possible, it would take me a month." Or "Sure, it's possible, see you in a year." Sorry for the vague question, Adam -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Tue Nov 8 15:58:55 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Tue, 8 Nov 2016 13:58:55 -0700 Subject: [vtk-developers] VTK without vtksys In-Reply-To: <30e0a7e31c6648349e8578ccc862219b@dag2.robarts.ca> References: <30e0a7e31c6648349e8578ccc862219b@dag2.robarts.ca> Message-ID: Hi Adam, It's not a crazy notion. Even though kwsys has lots of Windows API calls, finding them all is straightforward (they're all marked with #if's) and adding another #if clause for UWP calls shouldn't be difficult. I know nothing about UWP, however, I'm just working on the assumption that, as far as the generic system calls in kwsys goes, it mirrors the old Windows API fairly closely. - David On Tue, Nov 8, 2016 at 12:56 PM, Adam Rankin wrote: > Hello all, > > > > I am trying to build VTK for UWP, and I will fully admit to not knowing > the linkages/structure of modules and their dependency on vtksys (aside > that the VTK CMake output lists it as a dependency). > > > > Is it a crazy notion to write a vtksys alternative library that builds > against the UWP? > > > > I guess what I?m looking for is someone to say, ?Sure it?s possible, it > would take me a month.? Or ?Sure, it?s possible, see you in a year.? > > > > Sorry for the vague question, > > > > Adam > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Tue Nov 8 16:18:53 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Tue, 8 Nov 2016 14:18:53 -0700 Subject: [vtk-developers] VTK without vtksys In-Reply-To: References: <30e0a7e31c6648349e8578ccc862219b@dag2.robarts.ca> Message-ID: As a follow-up, there are lots of Windows API calls in VTK outside of kwsys. In particular, Rendering/OpenGL and Rendering/OpenGL2 would probably require a large number of changes. Ken Martin and others did a lot of work on Android and iOS changes, the situation with UWP might be parallel with those. On Tue, Nov 8, 2016 at 1:58 PM, David Gobbi wrote: > Hi Adam, > > It's not a crazy notion. Even though kwsys has lots of Windows API calls, > finding them all is straightforward (they're all marked with #if's) and > adding another #if clause for UWP calls shouldn't be difficult. I know > nothing about UWP, however, I'm just working on the assumption that, as far > as the generic system calls in kwsys goes, it mirrors the old Windows API > fairly closely. > > - David > > > On Tue, Nov 8, 2016 at 12:56 PM, Adam Rankin wrote: > >> Hello all, >> >> >> >> I am trying to build VTK for UWP, and I will fully admit to not knowing >> the linkages/structure of modules and their dependency on vtksys (aside >> that the VTK CMake output lists it as a dependency). >> >> >> >> Is it a crazy notion to write a vtksys alternative library that builds >> against the UWP? >> >> >> >> I guess what I?m looking for is someone to say, ?Sure it?s possible, it >> would take me a month.? Or ?Sure, it?s possible, see you in a year.? >> >> >> >> Sorry for the vague question, >> >> >> >> Adam >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From arankin at robarts.ca Tue Nov 8 16:21:07 2016 From: arankin at robarts.ca (Adam Rankin) Date: Tue, 8 Nov 2016 21:21:07 +0000 Subject: [vtk-developers] VTK without vtksys In-Reply-To: References: <30e0a7e31c6648349e8578ccc862219b@dag2.robarts.ca> Message-ID: <083b4497e3a34122b4e2468b2dcaf822@dag2.robarts.ca> Hi David, Thanks for the insight. I will look into vtksys and do an analysis. With regards to rendering, I admit my selfishness and say that I will have those disabled, as I am working to get VTK up and running on the HoloLens as an infrastructure project. Thanks so much! Adam From: David Gobbi [mailto:david.gobbi at gmail.com] Sent: Tuesday, November 8, 2016 4:19 PM To: Adam Rankin Cc: vtk-developers Subject: Re: [vtk-developers] VTK without vtksys As a follow-up, there are lots of Windows API calls in VTK outside of kwsys. In particular, Rendering/OpenGL and Rendering/OpenGL2 would probably require a large number of changes. Ken Martin and others did a lot of work on Android and iOS changes, the situation with UWP might be parallel with those. On Tue, Nov 8, 2016 at 1:58 PM, David Gobbi > wrote: Hi Adam, It's not a crazy notion. Even though kwsys has lots of Windows API calls, finding them all is straightforward (they're all marked with #if's) and adding another #if clause for UWP calls shouldn't be difficult. I know nothing about UWP, however, I'm just working on the assumption that, as far as the generic system calls in kwsys goes, it mirrors the old Windows API fairly closely. - David On Tue, Nov 8, 2016 at 12:56 PM, Adam Rankin > wrote: Hello all, I am trying to build VTK for UWP, and I will fully admit to not knowing the linkages/structure of modules and their dependency on vtksys (aside that the VTK CMake output lists it as a dependency). Is it a crazy notion to write a vtksys alternative library that builds against the UWP? I guess what I?m looking for is someone to say, ?Sure it?s possible, it would take me a month.? Or ?Sure, it?s possible, see you in a year.? Sorry for the vague question, Adam -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Tue Nov 8 16:31:11 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Tue, 8 Nov 2016 14:31:11 -0700 Subject: [vtk-developers] VTK without vtksys In-Reply-To: <083b4497e3a34122b4e2468b2dcaf822@dag2.robarts.ca> References: <30e0a7e31c6648349e8578ccc862219b@dag2.robarts.ca> <083b4497e3a34122b4e2468b2dcaf822@dag2.robarts.ca> Message-ID: Aha. So I guess the OpenGL code isn't much use to you except as a reference :) - David On Tue, Nov 8, 2016 at 2:21 PM, Adam Rankin wrote: > Hi David, > > > > Thanks for the insight. I will look into vtksys and do an analysis. > > > > With regards to rendering, I admit my selfishness and say that I will have > those disabled, as I am working to get VTK up and running on the HoloLens > as an infrastructure project. > > > > Thanks so much! > > Adam > > > > *From:* David Gobbi [mailto:david.gobbi at gmail.com] > *Sent:* Tuesday, November 8, 2016 4:19 PM > *To:* Adam Rankin > *Cc:* vtk-developers > *Subject:* Re: [vtk-developers] VTK without vtksys > > > > As a follow-up, there are lots of Windows API calls in VTK outside of > kwsys. In particular, Rendering/OpenGL and Rendering/OpenGL2 would probably > require a large number of changes. Ken Martin and others did a lot of work > on Android and iOS changes, the situation with UWP might be parallel with > those. > > > > > > On Tue, Nov 8, 2016 at 1:58 PM, David Gobbi wrote: > > Hi Adam, > > > > It's not a crazy notion. Even though kwsys has lots of Windows API calls, > finding them all is straightforward (they're all marked with #if's) and > adding another #if clause for UWP calls shouldn't be difficult. I know > nothing about UWP, however, I'm just working on the assumption that, as far > as the generic system calls in kwsys goes, it mirrors the old Windows API > fairly closely. > > > > - David > > > > > > On Tue, Nov 8, 2016 at 12:56 PM, Adam Rankin wrote: > > Hello all, > > > > I am trying to build VTK for UWP, and I will fully admit to not knowing > the linkages/structure of modules and their dependency on vtksys (aside > that the VTK CMake output lists it as a dependency). > > > > Is it a crazy notion to write a vtksys alternative library that builds > against the UWP? > > > > I guess what I?m looking for is someone to say, ?Sure it?s possible, it > would take me a month.? Or ?Sure, it?s possible, see you in a year.? > > > > Sorry for the vague question, > > > > Adam > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.demarle at kitware.com Wed Nov 9 06:22:20 2016 From: dave.demarle at kitware.com (David E DeMarle) Date: Wed, 9 Nov 2016 06:22:20 -0500 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: Andrew, does this still appear to be the case in the 7.1 release branch? If so mind filing a quick issue on gitlab with the 7.1 milestone tag? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Wed Nov 9 06:24:28 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Wed, 9 Nov 2016 12:24:28 +0100 Subject: [vtk-developers] [VTK] Build shared libs overlapping with Verdict's flag? Message-ID: Hi there, I'd dare to say that there is some kind of overlap/confusion in the BUILD_SHARED_LIBS flag used by VTK and vtkverdict in master. Please, correct me if I'm wrong, but both the flag belonging to the whole VTK (CMakeLists.txt:180) and that one corresponding to verdict (ThirdParty/verdict/vtkverdict/CMakeLists.txt:18) have the same name. In fact, the tooltip shown by CMake over BUILD_SHARED_LIBS in the general BUILD group reads "Build Verdict with shared libraries.", which I guess should refer to VTK instead. On the other hand, the VTK_BUILD_SHARED_LIBS variable is set to the BUILD_SHARED_LIBS value. Now, if this is a bug, I'd be willing to submit a patch. The thing is that I ignore whether Verdict being built with shared libraries should directly inherit from VTK's BUILD_SHARED_LIBS or whether they should be two distinct options. Any suggestion would be highly appreciated. Thanks, JON HAITZ -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.demarle at kitware.com Wed Nov 9 06:36:30 2016 From: dave.demarle at kitware.com (David E DeMarle) Date: Wed, 9 Nov 2016 06:36:30 -0500 Subject: [vtk-developers] Fwd: [vtkusers] vtk 7.1.0rc1 generate problems In-Reply-To: <1408136758.949796.1476973006854@mail.yahoo.com> References: <1408136758.949796.1476973006854.ref@mail.yahoo.com> <1408136758.949796.1476973006854@mail.yahoo.com> Message-ID: Sankhesh, Could you take a look at this? Perhaps Leonid's build doesn't have ViewsQt on or it does but the variable is set late in CMake so Examples/Infovis doesn't see it or something strange like that? thanks David E DeMarle Kitware, Inc. R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4909 ---------- Forwarded message ---------- From: Leonid Dulman via vtkusers Date: Thu, Oct 20, 2016 at 10:16 AM Subject: [vtkusers] vtk 7.1.0rc1 generate problems To: Vtkdev , VTK Users Hi How I can solved these problems ? Configuring done CMake Error: Qt5::moc target not found EasyView_automoc CMake Error: Qt5::moc target not found CustomLinkView_automoc CMake Error: Qt5::moc target not found StatsView_automoc Generating done Thank you _______________________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensou rce/opensource.html Please keep messages on-topic and check the VTK FAQ at: http://www.vtk.org/Wiki/VTK_FAQ Search the list archives at: http://markmail.org/search/?q=vtkusers Follow this link to subscribe/unsubscribe: http://public.kitware.com/mailman/listinfo/vtkusers -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.demarle at kitware.com Wed Nov 9 08:17:20 2016 From: dave.demarle at kitware.com (David E DeMarle) Date: Wed, 9 Nov 2016 08:17:20 -0500 Subject: [vtk-developers] Fwd: [vtkusers] vtk 7.1.0rc1 generate problems In-Reply-To: <433011352.531124.1478691619835@mail.yahoo.com> References: <1408136758.949796.1476973006854.ref@mail.yahoo.com> <1408136758.949796.1476973006854@mail.yahoo.com> <433011352.531124.1478691619835@mail.yahoo.com> Message-ID: nvm Sanhkesh Examples/Infovis appears to be working. Thanks for testing out the RC's Leonid! David E DeMarle Kitware, Inc. R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4909 On Wed, Nov 9, 2016 at 6:40 AM, Leonid Dulman wrote: > Thank you. I solved this problems and built VTK 7.1.0rc2 with Qt 5.8.0beta > > > ------------------------------ > *From:* David E DeMarle > *To:* Sankhesh Jhaveri ; Leonid Dulman < > leonid_dulman at yahoo.co.uk>; vtkdev ; Chuck Atkins > > *Sent:* Wednesday, November 9, 2016 1:36 PM > *Subject:* Fwd: [vtkusers] vtk 7.1.0rc1 generate problems > > Sankhesh, > > Could you take a look at this? Perhaps Leonid's build doesn't have ViewsQt > on or it does but the variable is set late in CMake so Examples/Infovis > doesn't see it or something strange like that? > > thanks > > David E DeMarle > Kitware, Inc. > R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4909 > > ---------- Forwarded message ---------- > From: *Leonid Dulman via vtkusers* > Date: Thu, Oct 20, 2016 at 10:16 AM > Subject: [vtkusers] vtk 7.1.0rc1 generate problems > To: Vtkdev , VTK Users > > > Hi > How I can solved these problems ? > > Configuring done > CMake Error: Qt5::moc target not found EasyView_automoc > CMake Error: Qt5::moc target not found CustomLinkView_automoc > CMake Error: Qt5::moc target not found StatsView_automoc > Generating done > > Thank you > > ______________________________ _________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/opensou > rce/opensource.html > > Please keep messages on-topic and check the VTK FAQ at: http://www.vtk.org/Wiki/VTK_FA > Q > > Search the list archives at: http://markmail.org/search/?q= vtkusers > > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mail man/listinfo/vtkusers > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.amaclean at gmail.com Wed Nov 9 17:18:06 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Thu, 10 Nov 2016 09:18:06 +1100 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: Hi Guys, For me this still appears to be the case. Try running the attached test code. In Windows and Linux, TestWIFPNGRGB.png are the same. In Windows TestWIFPNGRGBA.png has a transparent background, whilst in KUbuntu no image is produced just a transparent background. Are you able to replicate this behaviour? Andrew On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle wrote: > Andrew, does this still appear to be the case in the 7.1 release branch? > If so mind filing a quick issue on gitlab with the 7.1 milestone tag? > -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TestWIFPNGWiteRead.py Type: text/x-python Size: 5401 bytes Desc: not available URL: From ken.martin at kitware.com Thu Nov 10 09:24:13 2016 From: ken.martin at kitware.com (Ken Martin) Date: Thu, 10 Nov 2016 09:24:13 -0500 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: That example is reading RGBA from a buffer that you have not set to have alpha bitplanes. I do not know what OpenGL does in that case. Maybe the resulting alpha is undefined. There are a few options here 1) set alpha bitplanes to 8 so that you get alpha 2) see if this is a regression related to VTK and try to find and fix it 3) wait until I revamp the window code on Linux at which point I will be forcing all windows to have alpha bitplanes. From what I understand RGB buffers (3 byte alignment) do not really make sense these days and we should not be using them. They are a legacy from when raster memory was so limited that saving the alpha bit planes was a big deal. 4) just change the default alpha bitplanes value to in VTK right now instead of waiting for the windowing cleanup On Wed, Nov 9, 2016 at 5:18 PM, Andrew Maclean wrote: > Hi Guys, > For me this still appears to be the case. Try running the attached test > code. > In Windows and Linux, TestWIFPNGRGB.png are the same. > In Windows TestWIFPNGRGBA.png has a transparent background, whilst in > KUbuntu no image is produced just a transparent background. > Are you able to replicate this behaviour? > > Andrew > > On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle > wrote: > >> Andrew, does this still appear to be the case in the 7.1 release branch? >> If so mind filing a quick issue on gitlab with the 7.1 milestone tag? >> > > > > -- > ___________________________________________ > Andrew J. P. Maclean > > ___________________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > > -- Ken Martin PhD Chairman & CFO Kitware Inc. 28 Corporate Drive Clifton Park NY 12065 518 371 3971 This communication, including all attachments, contains confidential and legally privileged information, and it is intended only for the use of the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken in reliance on it is prohibited and may be unlawful. If you received this communication in error please notify us immediately and destroy the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.demarle at kitware.com Thu Nov 10 09:24:40 2016 From: dave.demarle at kitware.com (David E DeMarle) Date: Thu, 10 Nov 2016 09:24:40 -0500 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: In the RGBA version the blue background _should_ be invisible. The question in my mind is why doesn't your Linux build not show anything in the foreground? Can you share the png's made by your ubuntu build? On my Mac for example, for both GL1 and GL2, RGB has a blue background, RGBA's is transparent. That is expected. The image contents are the same at every pixel except that the RGBA'a alpha channel has value 255 for foreground and 0 for background pixels. David E DeMarle Kitware, Inc. R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4909 On Wed, Nov 9, 2016 at 5:18 PM, Andrew Maclean wrote: > Hi Guys, > For me this still appears to be the case. Try running the attached test > code. > In Windows and Linux, TestWIFPNGRGB.png are the same. > In Windows TestWIFPNGRGBA.png has a transparent background, whilst in > KUbuntu no image is produced just a transparent background. > Are you able to replicate this behaviour? > > Andrew > > On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle > wrote: > >> Andrew, does this still appear to be the case in the 7.1 release branch? >> If so mind filing a quick issue on gitlab with the 7.1 milestone tag? >> > > > > -- > ___________________________________________ > Andrew J. P. Maclean > > ___________________________________________ > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.amaclean at gmail.com Thu Nov 10 15:11:32 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Fri, 11 Nov 2016 07:11:32 +1100 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: David, What you are seeing in the Mac is what I see in Windows and what I would expect. On Kubuntu 16.10 I get the attached RGBA image - trasnparent with a few scattered pixels. if I comment out def testWIFRGB(self): in the code, I get an RGBA with a blue background (I expected a transparent one). In other words it's the same as the RGB image. Interestingly, when I was running Unbuntu I got this image instead of the Kubuntu version. Attached is the output from running the program in Kubuntu 16.10. Andrew On Fri, Nov 11, 2016 at 1:24 AM, David E DeMarle wrote: > In the RGBA version the blue background _should_ be invisible. The > question in my mind is why doesn't your Linux build not show anything in > the foreground? Can you share the png's made by your ubuntu build? > > On my Mac for example, for both GL1 and GL2, RGB has a blue background, > RGBA's is transparent. > That is expected. The image contents are the same at every pixel except > that the RGBA'a alpha channel has value 255 for foreground and 0 for > background pixels. > > > David E DeMarle > Kitware, Inc. > R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4909 > > On Wed, Nov 9, 2016 at 5:18 PM, Andrew Maclean > wrote: > >> Hi Guys, >> For me this still appears to be the case. Try running the attached >> test code. >> In Windows and Linux, TestWIFPNGRGB.png are the same. >> In Windows TestWIFPNGRGBA.png has a transparent background, whilst in >> KUbuntu no image is produced just a transparent background. >> Are you able to replicate this behaviour? >> >> Andrew >> >> On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle < >> dave.demarle at kitware.com> wrote: >> >>> Andrew, does this still appear to be the case in the 7.1 release branch? >>> If so mind filing a quick issue on gitlab with the 7.1 milestone tag? >>> >> >> >> >> -- >> ___________________________________________ >> Andrew J. P. Maclean >> >> ___________________________________________ >> > > -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TestWIFPNGRGB.png Type: image/png Size: 4358 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TestWIFPNGRGBA.png Type: image/png Size: 425 bytes Desc: not available URL: From andrew.amaclean at gmail.com Thu Nov 10 16:00:19 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Fri, 11 Nov 2016 08:00:19 +1100 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: An additional thing. I am using the master as of 2016-11-10 08:08:56 and I ran ctest and have one failure 1425:vtkRenderingCoreCxx-TestPickTextActor out of 1670 tests. So the VTK master is good. Andrew On Fri, Nov 11, 2016 at 7:11 AM, Andrew Maclean wrote: > David, > > What you are seeing in the Mac is what I see in Windows and what I would > expect. > > On Kubuntu 16.10 I get the attached RGBA image - trasnparent with a few > scattered pixels. > > if I comment out def testWIFRGB(self): in the code, I get an RGBA with a > blue background (I expected a transparent one). In other words it's the > same as the RGB image. Interestingly, when I was running Unbuntu I got this > image instead of the Kubuntu version. > > Attached is the output from running the program in Kubuntu 16.10. > > Andrew > > On Fri, Nov 11, 2016 at 1:24 AM, David E DeMarle > wrote: > >> In the RGBA version the blue background _should_ be invisible. The >> question in my mind is why doesn't your Linux build not show anything in >> the foreground? Can you share the png's made by your ubuntu build? >> >> On my Mac for example, for both GL1 and GL2, RGB has a blue background, >> RGBA's is transparent. >> That is expected. The image contents are the same at every pixel except >> that the RGBA'a alpha channel has value 255 for foreground and 0 for >> background pixels. >> >> >> David E DeMarle >> Kitware, Inc. >> R&D Engineer >> 21 Corporate Drive >> Clifton Park, NY 12065-8662 >> Phone: 518-881-4909 >> >> On Wed, Nov 9, 2016 at 5:18 PM, Andrew Maclean > > wrote: >> >>> Hi Guys, >>> For me this still appears to be the case. Try running the attached >>> test code. >>> In Windows and Linux, TestWIFPNGRGB.png are the same. >>> In Windows TestWIFPNGRGBA.png has a transparent background, whilst in >>> KUbuntu no image is produced just a transparent background. >>> Are you able to replicate this behaviour? >>> >>> Andrew >>> >>> On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle < >>> dave.demarle at kitware.com> wrote: >>> >>>> Andrew, does this still appear to be the case in the 7.1 release >>>> branch? If so mind filing a quick issue on gitlab with the 7.1 milestone >>>> tag? >>>> >>> >>> >>> >>> -- >>> ___________________________________________ >>> Andrew J. P. Maclean >>> >>> ___________________________________________ >>> >> >> > > > -- > ___________________________________________ > Andrew J. P. Maclean > > ___________________________________________ > -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.amaclean at gmail.com Thu Nov 10 20:06:57 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Fri, 11 Nov 2016 12:06:57 +1100 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: Hi All, I had to switch the display manager back to lightdm (in order to log into Ubuntu). Look at what I get when running either Kubuntu or Ubuntu. For both Kubuntu and Ubuntu, for the TestWIFPNGRGBA_*.png files, I would have expected a 1/4 sphere with a transparent background. Instead Kubuntu has a transparent background with a few pixels that are not transparent, whilst Ubuntu has a 1/4 sphere with a non-transparent background. I have a GTX980 card and the OpenGL version is 4.5.0 NVIDIA 367.57 On Fri, Nov 11, 2016 at 7:11 AM, Andrew Maclean wrote: > David, > > What you are seeing in the Mac is what I see in Windows and what I would > expect. > > On Kubuntu 16.10 I get the attached RGBA image - trasnparent with a few > scattered pixels. > > if I comment out def testWIFRGB(self): in the code, I get an RGBA with a > blue background (I expected a transparent one). In other words it's the > same as the RGB image. Interestingly, when I was running Unbuntu I got this > image instead of the Kubuntu version. > > Attached is the output from running the program in Kubuntu 16.10. > > Andrew > > On Fri, Nov 11, 2016 at 1:24 AM, David E DeMarle > wrote: > >> In the RGBA version the blue background _should_ be invisible. The >> question in my mind is why doesn't your Linux build not show anything in >> the foreground? Can you share the png's made by your ubuntu build? >> >> On my Mac for example, for both GL1 and GL2, RGB has a blue background, >> RGBA's is transparent. >> That is expected. The image contents are the same at every pixel except >> that the RGBA'a alpha channel has value 255 for foreground and 0 for >> background pixels. >> >> >> David E DeMarle >> Kitware, Inc. >> R&D Engineer >> 21 Corporate Drive >> Clifton Park, NY 12065-8662 >> Phone: 518-881-4909 >> >> On Wed, Nov 9, 2016 at 5:18 PM, Andrew Maclean > > wrote: >> >>> Hi Guys, >>> For me this still appears to be the case. Try running the attached >>> test code. >>> In Windows and Linux, TestWIFPNGRGB.png are the same. >>> In Windows TestWIFPNGRGBA.png has a transparent background, whilst in >>> KUbuntu no image is produced just a transparent background. >>> Are you able to replicate this behaviour? >>> >>> Andrew >>> >>> On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle < >>> dave.demarle at kitware.com> wrote: >>> >>>> Andrew, does this still appear to be the case in the 7.1 release >>>> branch? If so mind filing a quick issue on gitlab with the 7.1 milestone >>>> tag? >>>> >>> >>> >>> >>> -- >>> ___________________________________________ >>> Andrew J. P. Maclean >>> >>> ___________________________________________ >>> >> >> > > > -- > ___________________________________________ > Andrew J. P. Maclean > > ___________________________________________ > -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TestWIFPNGRGB.png Type: image/png Size: 4358 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TestWIFPNGRGBA_Kububuntu.png Type: image/png Size: 431 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TestWIFPNGRGBA_Ubuntu.png Type: image/png Size: 4697 bytes Desc: not available URL: From andrew.amaclean at gmail.com Fri Nov 11 01:57:53 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Fri, 11 Nov 2016 17:57:53 +1100 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: Hi all ... again. I just tested Ken's suggestion of setting alpha bitplanes to 8 in the default settings for vtkRenderWindow and all tests pass as before. On my Kubuntu setup I get 1673/1673 tests passing. With respect to the python test, if I comment out def testWIFRGB(self) in Kubuntu I get an image with a transparent background as expected. In Kubuntu 16.10 I suspect there is some issue with Plasma when in interactive mode as I get a lot of window resets. So perhaps this is the way to go at this stage, just change line 62 in vtkRenderWindow.cxx to: this->AlphaBitPlanes = 8; and maybe add a test. I suspect that the only a few linux users may notice something if they have inadvertently used vtkWindowToImageFilter.SetInputBufferTypeToRGBA() when they meant to use vtkWindowToImageFilter.SetInputBufferTypeToRGB() . What do people think? If everyone is pressed for time, I could probably do something on Monday as my weekend starts tomorrow. Regards Andrew On Fri, Nov 11, 2016 at 12:06 PM, Andrew Maclean wrote: > Hi All, > > I had to switch the display manager back to lightdm (in order to log into > Ubuntu). Look at what I get when running either Kubuntu or Ubuntu. > > For both Kubuntu and Ubuntu, for the TestWIFPNGRGBA_*.png files, I would > have expected a 1/4 sphere with a transparent background. Instead Kubuntu > has a transparent background with a few pixels that are not transparent, > whilst Ubuntu has a 1/4 sphere with a non-transparent background. > > I have a GTX980 card and the OpenGL version is 4.5.0 NVIDIA 367.57 > > > On Fri, Nov 11, 2016 at 7:11 AM, Andrew Maclean > wrote: > >> David, >> >> What you are seeing in the Mac is what I see in Windows and what I would >> expect. >> >> On Kubuntu 16.10 I get the attached RGBA image - trasnparent with a few >> scattered pixels. >> >> if I comment out def testWIFRGB(self): in the code, I get an RGBA with a >> blue background (I expected a transparent one). In other words it's the >> same as the RGB image. Interestingly, when I was running Unbuntu I got this >> image instead of the Kubuntu version. >> >> Attached is the output from running the program in Kubuntu 16.10. >> >> Andrew >> >> On Fri, Nov 11, 2016 at 1:24 AM, David E DeMarle < >> dave.demarle at kitware.com> wrote: >> >>> In the RGBA version the blue background _should_ be invisible. The >>> question in my mind is why doesn't your Linux build not show anything in >>> the foreground? Can you share the png's made by your ubuntu build? >>> >>> On my Mac for example, for both GL1 and GL2, RGB has a blue background, >>> RGBA's is transparent. >>> That is expected. The image contents are the same at every pixel except >>> that the RGBA'a alpha channel has value 255 for foreground and 0 for >>> background pixels. >>> >>> >>> David E DeMarle >>> Kitware, Inc. >>> R&D Engineer >>> 21 Corporate Drive >>> Clifton Park, NY 12065-8662 >>> Phone: 518-881-4909 >>> >>> On Wed, Nov 9, 2016 at 5:18 PM, Andrew Maclean < >>> andrew.amaclean at gmail.com> wrote: >>> >>>> Hi Guys, >>>> For me this still appears to be the case. Try running the attached >>>> test code. >>>> In Windows and Linux, TestWIFPNGRGB.png are the same. >>>> In Windows TestWIFPNGRGBA.png has a transparent background, whilst in >>>> KUbuntu no image is produced just a transparent background. >>>> Are you able to replicate this behaviour? >>>> >>>> Andrew >>>> >>>> On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle < >>>> dave.demarle at kitware.com> wrote: >>>> >>>>> Andrew, does this still appear to be the case in the 7.1 release >>>>> branch? If so mind filing a quick issue on gitlab with the 7.1 milestone >>>>> tag? >>>>> >>>> >>>> >>>> >>>> -- >>>> ___________________________________________ >>>> Andrew J. P. Maclean >>>> >>>> ___________________________________________ >>>> >>> >>> >> >> >> -- >> ___________________________________________ >> Andrew J. P. Maclean >> >> ___________________________________________ >> > > > > -- > ___________________________________________ > Andrew J. P. Maclean > > ___________________________________________ > -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From padraig.looney at gmail.com Sat Nov 12 08:10:30 2016 From: padraig.looney at gmail.com (padraig) Date: Sat, 12 Nov 2016 13:10:30 +0000 Subject: [vtk-developers] vtkNIFTIImageReader coordinates Message-ID: I have noticed some inconsistencies in how NIFTI images are handled in VTK, ITK, and NiBabel. ITK and NiBabel are in agreement with each other and differ with VTK on the position of the volume. The VTK output for a file is below. vtkNIFTIImageReader (0x1de67d0) Debug: Off Modified Time: 91 Reference Count: 2 Registered Events: (none) Executive: 0x1de7720 ErrorCode: Success Information: 0x1de6ad0 AbortExecute: Off Progress: 1 Progress Text: (None) FileName: /home/padraig/Desktop/59674/Seeding/I0000003_59674_sn.nii FileNames: 0 FilePrefix: (none) FilePattern: %s.%d FileNameSliceOffset: 0 FileNameSliceSpacing: 1 DataScalarType: unsigned char NumberOfScalarComponents: 1 File Dimensionality: 3 File Lower Left: On Swap Bytes: Off DataIncrements: (1, 1) DataExtent: (0, 223, 0, 152, 0, 51) DataSpacing: (0.9195, 1.40018, 2.89048) DataOrigin: (0, 0, 0) HeaderSize: 352 Internal File Name: (none) TimeAsVector: Off TimeDimension: 1 TimeSpacing: 1 RescaleSlope: 1 RescaleIntercept: 0 QFac: -1 QFormMatrix: -1 0 0 102.536 0 -1 0 106.413 0 0 1 -117.265 0 0 0 1 SFormMatrix: -1 0 -0 102.536 0 -1 -0 106.413 0 0 1 -117.265 0 0 0 1 NIFTIHeader: PlanarRGB: Off the qform given by nibabel is >>> ni_ob.get_qform() array([[ -0.91949999, 0. , 0. , 102.53600311], [ 0. , -1.40017998, 0. , 106.41300201], [ 0. , 0. , 2.89048004, 30.14909935], [ 0. , 0. , 0. , 1. ]]) ITK has the origin at [-102.536, -106.413, 30.1491] -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Sat Nov 12 09:10:51 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Sat, 12 Nov 2016 07:10:51 -0700 Subject: [vtk-developers] vtkNIFTIImageReader coordinates In-Reply-To: References: Message-ID: Hi Padraig, Can you show us the raw qform and sform fields from the NIFTI header itself? In VTK, you can do this as follows: >>> print(reader.GetNIFTIHeader()) The difference you see between nibabel, ITK, and VTK has to do with differences in the way these packages deal with the pixdim and the qfac of the nifti file. If you print the Direction from the ITK image you might find that it differs from nibabel, too. For VTK, you can read all the gory details here: http://gitlab.kitware.com/vtk/vtk/blob/v7.0.0/IO/Image/vtkNIFTIImageReader.cxx#L738 - David On Sat, Nov 12, 2016 at 6:10 AM, padraig wrote: > I have noticed some inconsistencies in how NIFTI images are handled in > VTK, ITK, and NiBabel. ITK and NiBabel are in agreement with each other and > differ with VTK on the position of the volume. The VTK output for a file is > below. > > vtkNIFTIImageReader (0x1de67d0) > Debug: Off > Modified Time: 91 > Reference Count: 2 > Registered Events: (none) > Executive: 0x1de7720 > ErrorCode: Success > Information: 0x1de6ad0 > AbortExecute: Off > Progress: 1 > Progress Text: (None) > FileName: /home/padraig/Desktop/59674/Seeding/I0000003_59674_sn.nii > FileNames: 0 > FilePrefix: (none) > FilePattern: %s.%d > FileNameSliceOffset: 0 > FileNameSliceSpacing: 1 > DataScalarType: unsigned char > NumberOfScalarComponents: 1 > File Dimensionality: 3 > File Lower Left: On > Swap Bytes: Off > DataIncrements: (1, 1) > DataExtent: (0, 223, 0, 152, 0, 51) > DataSpacing: (0.9195, 1.40018, 2.89048) > DataOrigin: (0, 0, 0) > HeaderSize: 352 > Internal File Name: (none) > TimeAsVector: Off > TimeDimension: 1 > TimeSpacing: 1 > RescaleSlope: 1 > RescaleIntercept: 0 > QFac: -1 > QFormMatrix: -1 0 0 102.536 0 -1 0 106.413 0 0 1 -117.265 0 0 0 1 > SFormMatrix: -1 0 -0 102.536 0 -1 -0 106.413 0 0 1 -117.265 0 0 0 1 > NIFTIHeader: > PlanarRGB: Off > > the qform given by nibabel is > > >>> ni_ob.get_qform() > array([[ -0.91949999, 0. , 0. , 102.53600311], > [ 0. , -1.40017998, 0. , 106.41300201], > [ 0. , 0. , 2.89048004, 30.14909935], > [ 0. , 0. , 0. , 1. ]]) > > > ITK has the origin at > > [-102.536, -106.413, 30.1491] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From padraig.looney at gmail.com Sat Nov 12 09:42:51 2016 From: padraig.looney at gmail.com (padraig) Date: Sat, 12 Nov 2016 14:42:51 +0000 Subject: [vtk-developers] vtkNIFTIImageReader coordinates In-Reply-To: References: Message-ID: <6e2e7899-e38a-75f4-f0bc-d95f563505ee@gmail.com> Hi David, vtkNIFTIImageHeader (0x3346680) Debug: Off Modified Time: 85 Reference Count: 1 Registered Events: (none) DimInfo: 0x0 Dim: 3 224 153 52 1 1 1 1 PixDim: -1 0.9195 1.40018 2.89048 0 0 0 0 VoxOffset:352 IntentP1: 0 IntentP2: 0 IntentP3: 0 IntentCode: 0 DataType: 2 BitPix: 8 SliceStart: 0 SclSlope: 1 SclInter: 0 SliceEnd: 0 SliceCode: 0 XYZTUnits: 0x2 CalMax: 0 CalMin: 0 SliceDuration: 0 TOffset: 0 Descrip: "" AuxFile: "" QFormCode: 2 SFormCode: 1 QuaternB: 0 QuaternC: 0 QuaternD: 1 QOffsetX: 102.536 QOffsetY: 106.413 QOffsetZ: 30.1491 SRowX: -0.9195 0 -0 102.536 SRowY: 0 -1.40018 -0 106.413 SRowZ: 0 0 -2.89048 30.1491 IntentName: "" Magic: "n+1" The direction in ITK is 1 0 0 0 1 0 0 0 -1 I don't know how to see the direction in nibabel On 12/11/16 14:10, David Gobbi wrote: > Hi Padraig, > > Can you show us the raw qform and sform fields from the NIFTI header > itself? In VTK, you can do this as follows: > > >>> print(reader.GetNIFTIHeader()) > > The difference you see between nibabel, ITK, and VTK has to do with > differences in the way these packages deal with the pixdim and the > qfac of the nifti file. If you print the Direction from the ITK image > you might find that it differs from nibabel, too. > > For VTK, you can read all the gory details here: > > http://gitlab.kitware.com/vtk/vtk/blob/v7.0.0/IO/Image/vtkNIFTIImageReader.cxx#L738 > > - David > > > On Sat, Nov 12, 2016 at 6:10 AM, padraig > wrote: > > I have noticed some inconsistencies in how NIFTI images are > handled in VTK, ITK, and NiBabel. ITK and NiBabel are in agreement > with each other and differ with VTK on the position of the volume. > The VTK output for a file is below. > > vtkNIFTIImageReader (0x1de67d0) > Debug: Off > Modified Time: 91 > Reference Count: 2 > Registered Events: (none) > Executive: 0x1de7720 > ErrorCode: Success > Information: 0x1de6ad0 > AbortExecute: Off > Progress: 1 > Progress Text: (None) > FileName: /home/padraig/Desktop/59674/Seeding/I0000003_59674_sn.nii > FileNames: 0 > FilePrefix: (none) > FilePattern: %s.%d > FileNameSliceOffset: 0 > FileNameSliceSpacing: 1 > DataScalarType: unsigned char > NumberOfScalarComponents: 1 > File Dimensionality: 3 > File Lower Left: On > Swap Bytes: Off > DataIncrements: (1, 1) > DataExtent: (0, 223, 0, 152, 0, 51) > DataSpacing: (0.9195, 1.40018, 2.89048) > DataOrigin: (0, 0, 0) > HeaderSize: 352 > Internal File Name: (none) > TimeAsVector: Off > TimeDimension: 1 > TimeSpacing: 1 > RescaleSlope: 1 > RescaleIntercept: 0 > QFac: -1 > QFormMatrix: -1 0 0 102.536 0 -1 0 106.413 0 0 1 -117.265 0 0 0 1 > SFormMatrix: -1 0 -0 102.536 0 -1 -0 106.413 0 0 1 -117.265 0 0 0 1 > NIFTIHeader: > PlanarRGB: Off > > the qform given by nibabel is > > >>> ni_ob.get_qform() > array([[ -0.91949999, 0. , 0. , 102.53600311], > [ 0. , -1.40017998, 0. , 106.41300201], > [ 0. , 0. , 2.89048004, 30.14909935], > [ 0. , 0. , 0. , 1. ]]) > > > ITK has the origin at > > [-102.536, -106.413, 30.1491] > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Sat Nov 12 10:39:13 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Sat, 12 Nov 2016 08:39:13 -0700 Subject: [vtk-developers] vtkNIFTIImageReader coordinates In-Reply-To: <6e2e7899-e38a-75f4-f0bc-d95f563505ee@gmail.com> References: <6e2e7899-e38a-75f4-f0bc-d95f563505ee@gmail.com> Message-ID: Hi Padraig, The "direction" or "orientation" is the 3x3 portion of the 4x4 matrix, after dividing out the scale. So if ITK is giving a direction like the following, it means that ITK allows the direction to include a mirror-flip (in this case, it's a flip along the z-axis): 1 0 0 0 1 0 0 0 -1 The vtkNIFTIImageReader doesn't allow a mirror flip in the QFormMatrix, so instead it re-orders the nifti slices in memory to undo the flip. When it does this, it also has to adjust the 4th column of the QFormMatrix since the 4th column now indicates the position of the last slice in the file, instead of the first slice in the file. The difference in position between the first slice and the last slice is (n - 1)*sz, where n is the number of slices and sz is the slice spacing. For your image, we can add (n - 1)*sz to -117.265 in order to get 30.149: -117.265 + (52 - 1)*2.89048 = 30.149 This accounts for the discrepancy. - David On Sat, Nov 12, 2016 at 7:42 AM, padraig wrote: > Hi David, > > > vtkNIFTIImageHeader (0x3346680) > Debug: Off > Modified Time: 85 > Reference Count: 1 > Registered Events: (none) > DimInfo: 0x0 > Dim: 3 224 153 52 1 1 1 1 > PixDim: -1 0.9195 1.40018 2.89048 0 0 0 0 > VoxOffset:352 > IntentP1: 0 > IntentP2: 0 > IntentP3: 0 > IntentCode: 0 > DataType: 2 > BitPix: 8 > SliceStart: 0 > SclSlope: 1 > SclInter: 0 > SliceEnd: 0 > SliceCode: 0 > XYZTUnits: 0x2 > CalMax: 0 > CalMin: 0 > SliceDuration: 0 > TOffset: 0 > Descrip: "" > AuxFile: "" > QFormCode: 2 > SFormCode: 1 > QuaternB: 0 > QuaternC: 0 > QuaternD: 1 > QOffsetX: 102.536 > QOffsetY: 106.413 > QOffsetZ: 30.1491 > SRowX: -0.9195 0 -0 102.536 > SRowY: 0 -1.40018 -0 106.413 > SRowZ: 0 0 -2.89048 30.1491 > IntentName: "" > Magic: "n+1" > > The direction in ITK is > > > 1 0 0 > 0 1 0 > 0 0 -1 > I don't know how to see the direction in nibabel > > > On 12/11/16 14:10, David Gobbi wrote: > > Hi Padraig, > > Can you show us the raw qform and sform fields from the NIFTI header > itself? In VTK, you can do this as follows: > > >>> print(reader.GetNIFTIHeader()) > > The difference you see between nibabel, ITK, and VTK has to do with > differences in the way these packages deal with the pixdim and the qfac of > the nifti file. If you print the Direction from the ITK image you might > find that it differs from nibabel, too. > > For VTK, you can read all the gory details here: > > http://gitlab.kitware.com/vtk/vtk/blob/v7.0.0/IO/Image/ > vtkNIFTIImageReader.cxx#L738 > > - David > > > On Sat, Nov 12, 2016 at 6:10 AM, padraig wrote: > >> I have noticed some inconsistencies in how NIFTI images are handled in >> VTK, ITK, and NiBabel. ITK and NiBabel are in agreement with each other and >> differ with VTK on the position of the volume. The VTK output for a file is >> below. >> >> vtkNIFTIImageReader (0x1de67d0) >> Debug: Off >> Modified Time: 91 >> Reference Count: 2 >> Registered Events: (none) >> Executive: 0x1de7720 >> ErrorCode: Success >> Information: 0x1de6ad0 >> AbortExecute: Off >> Progress: 1 >> Progress Text: (None) >> FileName: /home/padraig/Desktop/59674/Seeding/I0000003_59674_sn.nii >> FileNames: 0 >> FilePrefix: (none) >> FilePattern: %s.%d >> FileNameSliceOffset: 0 >> FileNameSliceSpacing: 1 >> DataScalarType: unsigned char >> NumberOfScalarComponents: 1 >> File Dimensionality: 3 >> File Lower Left: On >> Swap Bytes: Off >> DataIncrements: (1, 1) >> DataExtent: (0, 223, 0, 152, 0, 51) >> DataSpacing: (0.9195, 1.40018, 2.89048) >> DataOrigin: (0, 0, 0) >> HeaderSize: 352 >> Internal File Name: (none) >> TimeAsVector: Off >> TimeDimension: 1 >> TimeSpacing: 1 >> RescaleSlope: 1 >> RescaleIntercept: 0 >> QFac: -1 >> QFormMatrix: -1 0 0 102.536 0 -1 0 106.413 0 0 1 -117.265 0 0 0 1 >> SFormMatrix: -1 0 -0 102.536 0 -1 -0 106.413 0 0 1 -117.265 0 0 0 1 >> NIFTIHeader: >> PlanarRGB: Off >> >> the qform given by nibabel is >> >> >>> ni_ob.get_qform() >> array([[ -0.91949999, 0. , 0. , 102.53600311], >> [ 0. , -1.40017998, 0. , 106.41300201], >> [ 0. , 0. , 2.89048004, 30.14909935], >> [ 0. , 0. , 0. , 1. ]]) >> >> >> ITK has the origin at >> >> [-102.536, -106.413, 30.1491] >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From padraig.looney at gmail.com Sun Nov 13 11:50:16 2016 From: padraig.looney at gmail.com (padraig) Date: Sun, 13 Nov 2016 16:50:16 +0000 Subject: [vtk-developers] vtkNIFTIImageReader coordinates In-Reply-To: References: <6e2e7899-e38a-75f4-f0bc-d95f563505ee@gmail.com> Message-ID: Hi David, I am still confused by this. Volumes that ITK tells me have the same bounds, VTK displays in Paraview as not having the same bounds. Consider this header from vtkNIFTIImageHeader (0x221e6b0) Debug: Off Modified Time: 85 Reference Count: 1 Registered Events: (none) DimInfo: 0x0 Dim: 3 224 153 52 1 1 1 1 PixDim: 1 0.9195 1.40018 2.89048 0 0 0 0 VoxOffset:352 IntentP1: 0 IntentP2: 0 IntentP3: 0 IntentCode: 0 DataType: 2 BitPix: 8 SliceStart: 0 SclSlope: 1 SclInter: 0 SliceEnd: 0 SliceCode: 0 XYZTUnits: 0x2 CalMax: 0 CalMin: 0 SliceDuration: 0 TOffset: 0 Descrip: "" AuxFile: "" QFormCode: 2 SFormCode: 1 QuaternB: 0 QuaternC: 0 QuaternD: 1 QOffsetX: 102.536 QOffsetY: 106.413 QOffsetZ: 30.1491 SRowX: -0.9195 0 0 102.536 SRowY: 0 -1.40018 0 106.413 SRowZ: 0 0 2.89048 30.1491 IntentName: "" Magic: "n+1" That is the same as the affine from nibabel array([[ -0.91949999, 0. , 0. , 102.53600311], [ 0. , -1.40017998, 0. , 106.41300201], [ 0. , 0. , 2.89048004, 30.14909935], [ 0. , 0. , 0. , 1. ]]) If you look at the SForm matrix below shouldn't the bounds be X: (224-1)*-0.9195 + 102.536 = -102.51249999999999 Y: (153-1)*-1.40018 + 106.413 =--106.41436 Z: (52-1)*2.89048 + 30.1491 = 177.56358 In ITK I have checked the physical coordinates of the image and found the bounds to be, as expected from the above, [-102.536, -106.413, 30.1491][102.512, 106.414, 177.564] In VTK I have checked the centre and origin with vtkNew niiReader; niiReader->SetFileName(str); niiReader->Update(); int size[3]; double center[3], spacing[3], bounds[6]; niiReader->GetOutput()->GetDimensions(size); niiReader->GetOutput()->GetCenter(center); niiReader->GetOutput()->GetBounds(bounds); std::vector bounds_vec(&bounds[0],&bounds[6]); std::cout << bounds[0] << " " << bounds[1] << " " << bounds[2] << " " << bounds[3] << " " << bounds[4] << " " << bounds[5] << std::endl; niiReader->GetOutput()->GetSpacing(spacing); double center1[3] = { center[0], center[1], center[2] }; double center2[3] = { center[0], center[1], center[2] }; std::cout << center[0] << " " << center[1] << " " << center[2] << std::endl; std::cout << size[0] << " " << size[1] << " " << size[2] << std::endl; and get 0 205.048 0 212.827 0 147.414 102.524 106.414 73.7072 224 153 52 On 12/11/16 15:39, David Gobbi wrote: > Hi Padraig, > > The "direction" or "orientation" is the 3x3 portion of the 4x4 matrix, > after dividing out the scale. > > So if ITK is giving a direction like the following, it means that ITK > allows the direction to include a mirror-flip (in this case, it's a > flip along the z-axis): > > 1 0 0 > 0 1 0 > 0 0 -1 > > The vtkNIFTIImageReader doesn't allow a mirror flip in the > QFormMatrix, so instead it re-orders the nifti slices in memory to > undo the flip. When it does this, it also has to adjust the 4th column > of the QFormMatrix since the 4th column now indicates the position of > the last slice in the file, instead of the first slice in the file. > The difference in position between the first slice and the last slice > is (n - 1)*sz, where n is the number of slices and sz is the slice > spacing. For your image, we can add (n - 1)*sz to -117.265 in order > to get 30.149: > > -117.265 + (52 - 1)*2.89048 = 30.149 > > This accounts for the discrepancy. > > - David > > On Sat, Nov 12, 2016 at 7:42 AM, padraig > wrote: > > Hi David, > > > vtkNIFTIImageHeader (0x3346680) > Debug: Off > Modified Time: 85 > Reference Count: 1 > Registered Events: (none) > DimInfo: 0x0 > Dim: 3 224 153 52 1 1 1 1 > PixDim: -1 0.9195 1.40018 2.89048 0 0 0 0 > VoxOffset:352 > IntentP1: 0 > IntentP2: 0 > IntentP3: 0 > IntentCode: 0 > DataType: 2 > BitPix: 8 > SliceStart: 0 > SclSlope: 1 > SclInter: 0 > SliceEnd: 0 > SliceCode: 0 > XYZTUnits: 0x2 > CalMax: 0 > CalMin: 0 > SliceDuration: 0 > TOffset: 0 > Descrip: "" > AuxFile: "" > QFormCode: 2 > SFormCode: 1 > QuaternB: 0 > QuaternC: 0 > QuaternD: 1 > QOffsetX: 102.536 > QOffsetY: 106.413 > QOffsetZ: 30.1491 > SRowX: -0.9195 0 -0 102.536 > SRowY: 0 -1.40018 -0 106.413 > SRowZ: 0 0 -2.89048 30.1491 > IntentName: "" > Magic: "n+1" > > The direction in ITK is > > > 1 0 0 > 0 1 0 > 0 0 -1 > > I don't know how to see the direction in nibabel > > > On 12/11/16 14:10, David Gobbi wrote: >> Hi Padraig, >> >> Can you show us the raw qform and sform fields from the NIFTI >> header itself? In VTK, you can do this as follows: >> >> >>> print(reader.GetNIFTIHeader()) >> >> The difference you see between nibabel, ITK, and VTK has to do >> with differences in the way these packages deal with the pixdim >> and the qfac of the nifti file. If you print the Direction from >> the ITK image you might find that it differs from nibabel, too. >> >> For VTK, you can read all the gory details here: >> >> http://gitlab.kitware.com/vtk/vtk/blob/v7.0.0/IO/Image/vtkNIFTIImageReader.cxx#L738 >> >> >> - David >> >> >> On Sat, Nov 12, 2016 at 6:10 AM, padraig >> > wrote: >> >> I have noticed some inconsistencies in how NIFTI images are >> handled in VTK, ITK, and NiBabel. ITK and NiBabel are in >> agreement with each other and differ with VTK on the position >> of the volume. The VTK output for a file is below. >> >> vtkNIFTIImageReader (0x1de67d0) >> Debug: Off >> Modified Time: 91 >> Reference Count: 2 >> Registered Events: (none) >> Executive: 0x1de7720 >> ErrorCode: Success >> Information: 0x1de6ad0 >> AbortExecute: Off >> Progress: 1 >> Progress Text: (None) >> FileName: >> /home/padraig/Desktop/59674/Seeding/I0000003_59674_sn.nii >> FileNames: 0 >> FilePrefix: (none) >> FilePattern: %s.%d >> FileNameSliceOffset: 0 >> FileNameSliceSpacing: 1 >> DataScalarType: unsigned char >> NumberOfScalarComponents: 1 >> File Dimensionality: 3 >> File Lower Left: On >> Swap Bytes: Off >> DataIncrements: (1, 1) >> DataExtent: (0, 223, 0, 152, 0, 51) >> DataSpacing: (0.9195, 1.40018, 2.89048) >> DataOrigin: (0, 0, 0) >> HeaderSize: 352 >> Internal File Name: (none) >> TimeAsVector: Off >> TimeDimension: 1 >> TimeSpacing: 1 >> RescaleSlope: 1 >> RescaleIntercept: 0 >> QFac: -1 >> QFormMatrix: -1 0 0 102.536 0 -1 0 106.413 0 0 1 -117.265 0 >> 0 0 1 >> SFormMatrix: -1 0 -0 102.536 0 -1 -0 106.413 0 0 1 -117.265 >> 0 0 0 1 >> NIFTIHeader: >> PlanarRGB: Off >> >> the qform given by nibabel is >> >> >>> ni_ob.get_qform() >> array([[ -0.91949999, 0. , 0. , 102.53600311], >> [ 0. , -1.40017998, 0. , >> 106.41300201], >> [ 0. , 0. , 2.89048004, 30.14909935], >> [ 0. , 0. , 0. , 1. ]]) >> >> >> ITK has the origin at >> >> [-102.536, -106.413, 30.1491] >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.gobbi at gmail.com Sun Nov 13 16:26:21 2016 From: david.gobbi at gmail.com (David Gobbi) Date: Sun, 13 Nov 2016 14:26:21 -0700 Subject: [vtk-developers] vtkNIFTIImageReader coordinates In-Reply-To: References: <6e2e7899-e38a-75f4-f0bc-d95f563505ee@gmail.com> Message-ID: Hi Padraig, What you are seeing is one of the big (very big) differences between ITK images and VTK images. It comes about because in ITK, the direction cosines are stored in the image class, but in VTK, they are not, and they must instead be stored in a separate matrix. You're probably wondering why this matters at all, since your image has direction cosines of ((1,0,0),(0,1,0),(0,0,1)). Hopefully I'll be able to provide an explanation that isn't too muddy. In ITK, the transformation from the (I,J,K) indices of each voxel to the (x,y,z) coordinates is as follows: let q = (I,J,K) let p = (x,y,z) p = R*S*q + o where R is ITK's Direction matrix, S is the "scale" matrix (a diagonal matrix made from the Spacing), and "o" is ITK's Origin. Since vtkImageData does not have a Direction matrix, but most medical image formats do have a Direction, it is necessary for VTK medical image readers to produce a vtkMatrix4x4 in addition to the vtkImageData. In VTK, the equivalent equation is: p = R*(S*q + o) Or we can expand this, p = R*S*q + R*o See how the ITK Origin and the VTK Origin mean different things? The ITK origin is rotated with respect to the VTK origin. In fact, the way that VTK defines the image "Origin" is incompatible with NIFTI (and with DICOM, too). So, the vtkNIFTIImageReader always sets the VTK image Origin to (0,0,0). Then, it stores an ITK-style Origin as the 4th column of the SFormMatrix and the QFormMatrix. That's an advantage of using a 4x4 matrix: it can store both a rotation and an offset. When we introduce this matrix "M" and set the VTK image Origin to (0,0,0), p = M*S*q Of course, now we have to make p and q into (I, J, K, 1) and (x, y, z, 1) in order to use the 4x4 matrix. I'll let you work out the rest of the details. In order to properly compute the bounds of an oriented image in VTK, you have to compute the coordinates of the four corners and then multiply them by the matrix M (i.e. by the SFormMatrix). In your case, since the "orientation" is identity, you could simply add the offset. If you're wondering why the reader doesn't set the VTK image Origin to be equal to the offset for axial images, it's to avoid inconsistency between the way the reader treats axial images as compared to sagittal or coronal. For Paraview, you'll have to find a way to get Paraview to use the SFormMatrix (or the QFormMatrix) that is provided by the reader. Unfortunately, I don't know enough about Paraview to help with that... hopefully one of the Paraview users around here can help. - David On Sun, Nov 13, 2016 at 9:50 AM, padraig wrote: > Hi David, > > > I am still confused by this. Volumes that ITK tells me have the same > bounds, VTK displays in Paraview as not having the same bounds. > > Consider this header from > > vtkNIFTIImageHeader (0x221e6b0) > Debug: Off > Modified Time: 85 > Reference Count: 1 > Registered Events: (none) > DimInfo: 0x0 > Dim: 3 224 153 52 1 1 1 1 > PixDim: 1 0.9195 1.40018 2.89048 0 0 0 0 > VoxOffset:352 > IntentP1: 0 > IntentP2: 0 > IntentP3: 0 > IntentCode: 0 > DataType: 2 > BitPix: 8 > SliceStart: 0 > SclSlope: 1 > SclInter: 0 > SliceEnd: 0 > SliceCode: 0 > XYZTUnits: 0x2 > CalMax: 0 > CalMin: 0 > SliceDuration: 0 > TOffset: 0 > Descrip: "" > AuxFile: "" > QFormCode: 2 > SFormCode: 1 > QuaternB: 0 > QuaternC: 0 > QuaternD: 1 > QOffsetX: 102.536 > QOffsetY: 106.413 > QOffsetZ: 30.1491 > SRowX: -0.9195 0 0 102.536 > SRowY: 0 -1.40018 0 106.413 > SRowZ: 0 0 2.89048 30.1491 > IntentName: "" > Magic: "n+1" > > That is the same as the affine from nibabel > > > array([[ -0.91949999, 0. , 0. , 102.53600311], > [ 0. , -1.40017998, 0. , 106.41300201], > [ 0. , 0. , 2.89048004, 30.14909935], > [ 0. , 0. , 0. , 1. ]]) > > > If you look at the SForm matrix below shouldn't the bounds be > > X: (224-1)*-0.9195 + 102.536 = -102.51249999999999 > > Y: (153-1)*-1.40018 + 106.413 =--106.41436 > Z: (52-1)*2.89048 + 30.1491 = 177.56358 > > > In ITK I have checked the physical coordinates of the image and found the > bounds to be, as expected from the above, > > [-102.536, -106.413, 30.1491][102.512, 106.414, 177.564] > > In VTK I have checked the centre and origin with > > vtkNew niiReader; > niiReader->SetFileName(str); > niiReader->Update(); > int size[3]; > double center[3], spacing[3], bounds[6]; > niiReader->GetOutput()->GetDimensions(size); > niiReader->GetOutput()->GetCenter(center); > niiReader->GetOutput()->GetBounds(bounds); > std::vector bounds_vec(&bounds[0],&bounds[6]); > std::cout << bounds[0] << " " << bounds[1] << " " << bounds[2] << " " > << bounds[3] << " " << bounds[4] << " " << bounds[5] << std::endl; > niiReader->GetOutput()->GetSpacing(spacing); > double center1[3] = { center[0], center[1], center[2] }; > double center2[3] = { center[0], center[1], center[2] }; > std::cout << center[0] << " " << center[1] << " " << center[2] << > std::endl; > std::cout << size[0] << " " << size[1] << " " << size[2] << std::endl; > > and get > > 0 205.048 0 212.827 0 147.414 > 102.524 106.414 73.7072 > 224 153 52 > > > On 12/11/16 15:39, David Gobbi wrote: > > Hi Padraig, > > The "direction" or "orientation" is the 3x3 portion of the 4x4 matrix, > after dividing out the scale. > > So if ITK is giving a direction like the following, it means that ITK > allows the direction to include a mirror-flip (in this case, it's a flip > along the z-axis): > > 1 0 0 > 0 1 0 > 0 0 -1 > > The vtkNIFTIImageReader doesn't allow a mirror flip in the QFormMatrix, so > instead it re-orders the nifti slices in memory to undo the flip. When it > does this, it also has to adjust the 4th column of the QFormMatrix since > the 4th column now indicates the position of the last slice in the file, > instead of the first slice in the file. The difference in position between > the first slice and the last slice is (n - 1)*sz, where n is the number of > slices and sz is the slice spacing. For your image, we can add (n - 1)*sz > to -117.265 in order to get 30.149: > > -117.265 + (52 - 1)*2.89048 = 30.149 > > This accounts for the discrepancy. > > - David > > On Sat, Nov 12, 2016 at 7:42 AM, padraig wrote: > >> Hi David, >> >> >> vtkNIFTIImageHeader (0x3346680) >> Debug: Off >> Modified Time: 85 >> Reference Count: 1 >> Registered Events: (none) >> DimInfo: 0x0 >> Dim: 3 224 153 52 1 1 1 1 >> PixDim: -1 0.9195 1.40018 2.89048 0 0 0 0 >> VoxOffset:352 >> IntentP1: 0 >> IntentP2: 0 >> IntentP3: 0 >> IntentCode: 0 >> DataType: 2 >> BitPix: 8 >> SliceStart: 0 >> SclSlope: 1 >> SclInter: 0 >> SliceEnd: 0 >> SliceCode: 0 >> XYZTUnits: 0x2 >> CalMax: 0 >> CalMin: 0 >> SliceDuration: 0 >> TOffset: 0 >> Descrip: "" >> AuxFile: "" >> QFormCode: 2 >> SFormCode: 1 >> QuaternB: 0 >> QuaternC: 0 >> QuaternD: 1 >> QOffsetX: 102.536 >> QOffsetY: 106.413 >> QOffsetZ: 30.1491 >> SRowX: -0.9195 0 -0 102.536 >> SRowY: 0 -1.40018 -0 106.413 >> SRowZ: 0 0 -2.89048 30.1491 >> IntentName: "" >> Magic: "n+1" >> >> The direction in ITK is >> >> >> 1 0 0 >> 0 1 0 >> 0 0 -1 >> I don't know how to see the direction in nibabel >> >> >> On 12/11/16 14:10, David Gobbi wrote: >> >> Hi Padraig, >> >> Can you show us the raw qform and sform fields from the NIFTI header >> itself? In VTK, you can do this as follows: >> >> >>> print(reader.GetNIFTIHeader()) >> >> The difference you see between nibabel, ITK, and VTK has to do with >> differences in the way these packages deal with the pixdim and the qfac of >> the nifti file. If you print the Direction from the ITK image you might >> find that it differs from nibabel, too. >> >> For VTK, you can read all the gory details here: >> >> http://gitlab.kitware.com/vtk/vtk/blob/v7.0.0/IO/Image/vtkNI >> FTIImageReader.cxx#L738 >> >> - David >> >> >> On Sat, Nov 12, 2016 at 6:10 AM, padraig >> wrote: >> >>> I have noticed some inconsistencies in how NIFTI images are handled in >>> VTK, ITK, and NiBabel. ITK and NiBabel are in agreement with each other and >>> differ with VTK on the position of the volume. The VTK output for a file is >>> below. >>> >>> vtkNIFTIImageReader (0x1de67d0) >>> Debug: Off >>> Modified Time: 91 >>> Reference Count: 2 >>> Registered Events: (none) >>> Executive: 0x1de7720 >>> ErrorCode: Success >>> Information: 0x1de6ad0 >>> AbortExecute: Off >>> Progress: 1 >>> Progress Text: (None) >>> FileName: /home/padraig/Desktop/59674/Seeding/I0000003_59674_sn.nii >>> FileNames: 0 >>> FilePrefix: (none) >>> FilePattern: %s.%d >>> FileNameSliceOffset: 0 >>> FileNameSliceSpacing: 1 >>> DataScalarType: unsigned char >>> NumberOfScalarComponents: 1 >>> File Dimensionality: 3 >>> File Lower Left: On >>> Swap Bytes: Off >>> DataIncrements: (1, 1) >>> DataExtent: (0, 223, 0, 152, 0, 51) >>> DataSpacing: (0.9195, 1.40018, 2.89048) >>> DataOrigin: (0, 0, 0) >>> HeaderSize: 352 >>> Internal File Name: (none) >>> TimeAsVector: Off >>> TimeDimension: 1 >>> TimeSpacing: 1 >>> RescaleSlope: 1 >>> RescaleIntercept: 0 >>> QFac: -1 >>> QFormMatrix: -1 0 0 102.536 0 -1 0 106.413 0 0 1 -117.265 0 0 0 1 >>> SFormMatrix: -1 0 -0 102.536 0 -1 -0 106.413 0 0 1 -117.265 0 0 0 1 >>> NIFTIHeader: >>> PlanarRGB: Off >>> >>> the qform given by nibabel is >>> >>> >>> ni_ob.get_qform() >>> array([[ -0.91949999, 0. , 0. , 102.53600311], >>> [ 0. , -1.40017998, 0. , 106.41300201], >>> [ 0. , 0. , 2.89048004, 30.14909935], >>> [ 0. , 0. , 0. , 1. ]]) >>> >>> >>> ITK has the origin at >>> >>> [-102.536, -106.413, 30.1491] >>> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.amaclean at gmail.com Sun Nov 13 21:17:57 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Mon, 14 Nov 2016 13:17:57 +1100 Subject: [vtk-developers] Possible problem creating test.png.md5 files. Message-ID: I follow the instructions in: https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md However I am not getting any message such as: Linked Some/Module/Testing/Data/Baseline/MyTest.png.md5 to ExternalData MD5/.... The png files remain in the /Rendering/Core/Testing/Data/Baseline and no md5 file is created. I have tried in both Windows and Ubuntu. My VTK_DATA_STORE is set up as a sibling. My setup was working a while back. Andrew -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ben.boeckel at kitware.com Mon Nov 14 10:00:51 2016 From: ben.boeckel at kitware.com (Ben Boeckel) Date: Mon, 14 Nov 2016 10:00:51 -0500 Subject: [vtk-developers] Possible problem creating test.png.md5 files. In-Reply-To: References: Message-ID: <20161114150051.GA3424@megas.kitware.com> On Mon, Nov 14, 2016 at 13:17:57 +1100, Andrew Maclean wrote: > I follow the instructions in: > https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md > > However I am not getting any message such as: > Linked Some/Module/Testing/Data/Baseline/MyTest.png.md5 to ExternalData > MD5/.... > The png files remain in the /Rendering/Core/Testing/Data/Baseline and no > md5 file is created. A test needs to reference the image in its arguments for CMake to see the file. Is the test that is supposed to see the file marked as NO_VALID or similar? --Ben From luis.vieira at vektore.com Mon Nov 14 10:12:59 2016 From: luis.vieira at vektore.com (Luis Vieira) Date: Mon, 14 Nov 2016 10:12:59 -0500 Subject: [vtk-developers] Image Analysis Message-ID: <22fe01d23e89$963e1b60$c2ba5220$@vektore.com> Hello vtkusers, Anybody knows the new version of these components? vtkpxAnalyzeImageSource vtkpxOrthoImageSlice vtkpxImageSlice vtkpxObliqueSlice vtkpxVolume vtkImageShiftScale vtkpxAnalyzeImageWriter Thank you, Luis Vieira, Consultant, Software Engineer Vektore Exploration Consulting Corporation ca.linkedin.com/in/joaoluisvieira luis.vieira at vektore.com www.vektore.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From jhlegarreta at vicomtech.org Mon Nov 14 12:15:25 2016 From: jhlegarreta at vicomtech.org (Jon Haitz Legarreta) Date: Mon, 14 Nov 2016 18:15:25 +0100 Subject: [vtk-developers] Fwd: [VTK] Build shared libs overlapping with Verdict's flag? In-Reply-To: References: Message-ID: Hi there, here is the MR for a possible fix to the issue: https://gitlab.kitware.com/vtk/vtk/merge_requests/2160 JON HAITZ ---------- Forwarded message ---------- From: Jon Haitz Legarreta Date: 9 November 2016 at 12:24 Subject: [VTK] Build shared libs overlapping with Verdict's flag? To: "vtk-developers at vtk.org" Hi there, I'd dare to say that there is some kind of overlap/confusion in the BUILD_SHARED_LIBS flag used by VTK and vtkverdict in master. Please, correct me if I'm wrong, but both the flag belonging to the whole VTK (CMakeLists.txt:180) and that one corresponding to verdict (ThirdParty/verdict/vtkverdict/CMakeLists.txt:18) have the same name. In fact, the tooltip shown by CMake over BUILD_SHARED_LIBS in the general BUILD group reads "Build Verdict with shared libraries.", which I guess should refer to VTK instead. On the other hand, the VTK_BUILD_SHARED_LIBS variable is set to the BUILD_SHARED_LIBS value. Now, if this is a bug, I'd be willing to submit a patch. The thing is that I ignore whether Verdict being built with shared libraries should directly inherit from VTK's BUILD_SHARED_LIBS or whether they should be two distinct options. Any suggestion would be highly appreciated. Thanks, JON HAITZ -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.amaclean at gmail.com Mon Nov 14 17:52:15 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Tue, 15 Nov 2016 09:52:15 +1100 Subject: [vtk-developers] Possible problem creating test.png.md5 files. In-Reply-To: <20161114150051.GA3424@megas.kitware.com> References: <20161114150051.GA3424@megas.kitware.com> Message-ID: Thanks Ben, I had NO_RT set but the problem was that I was wanted to use two test images in the one script. So I have no split the script and everything works Ok. Thanks for the pointer. Because when I removed NO_RT I realised what was wrong. Regards Andrew On Tue, Nov 15, 2016 at 2:00 AM, Ben Boeckel wrote: > On Mon, Nov 14, 2016 at 13:17:57 +1100, Andrew Maclean wrote: > > I follow the instructions in: > > https://gitlab.kitware.com/vtk/vtk/blob/master/ > Documentation/dev/git/data.md > > > > However I am not getting any message such as: > > Linked Some/Module/Testing/Data/Baseline/MyTest.png.md5 to ExternalData > > MD5/.... > > The png files remain in the /Rendering/Core/Testing/Data/Baseline and no > > md5 file is created. > > A test needs to reference the image in its arguments for CMake to see > the file. Is the test that is supposed to see the file marked as > NO_VALID or similar? > > --Ben > -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.amaclean at gmail.com Mon Nov 14 21:38:19 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Tue, 15 Nov 2016 13:38:19 +1100 Subject: [vtk-developers] CDash not displaying test/difference images. Message-ID: For example, look at: https://open.cdash.org/testDetails.php?test=499737797&build=4641242 Maybe the problem is here is just a bad link, for example, the address of the first image is: https://open.cdash.org/displayImage.php?imgid=560914 I have tested this on the Google Chrome and Edge browsers. Also there is a weird error message whenever images do not match, namely: "Error regular expression found in output. Regex=[(
|^)ERROR: ]" You can see this on the first link above. Regards Andrew -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ken.martin at kitware.com Tue Nov 15 10:43:30 2016 From: ken.martin at kitware.com (Ken Martin) Date: Tue, 15 Nov 2016 10:43:30 -0500 Subject: [vtk-developers] CDash not displaying test/difference images. In-Reply-To: References: Message-ID: I'm seeing the same issue. Images on failed tests are not showing up. On Mon, Nov 14, 2016 at 9:38 PM, Andrew Maclean wrote: > For example, look at: https://open.cdash.org/testDetails.php?test= > 499737797&build=4641242 > Maybe the problem is here is just a bad link, for example, the address of > the first image is: https://open.cdash.org/displayImage.php?imgid=560914 > > I have tested this on the Google Chrome and Edge browsers. > > Also there is a weird error message whenever images do not match, namely: > "Error regular expression found in output. Regex=[(
|^)ERROR: ]" > > You can see this on the first link above. > > Regards > Andrew > > -- > ___________________________________________ > Andrew J. P. Maclean > > ___________________________________________ > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > > -- Ken Martin PhD Chairman & CFO Kitware Inc. 28 Corporate Drive Clifton Park NY 12065 518 371 3971 This communication, including all attachments, contains confidential and legally privileged information, and it is intended only for the use of the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken in reliance on it is prohibited and may be unlawful. If you received this communication in error please notify us immediately and destroy the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Nov 15 12:33:24 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 15 Nov 2016 12:33:24 -0500 Subject: [vtk-developers] [vtkusers] VTK downoad not accessible In-Reply-To: References: Message-ID: I see the same issue. I have cc'ed the developers list. On Tue, Nov 15, 2016 at 12:24 PM, Guru Krishnan wrote: > I am trying to download VTK 6.3 using the link > http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz but I get a 403 > forbidden / Permission denied message. Can you please fix it? > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the VTK FAQ at: > http://www.vtk.org/Wiki/VTK_FAQ > > Search the list archives at: http://markmail.org/search/?q=vtkusers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtkusers > -- Unpaid intern in BillsBasement at noware dot com From zack.galbreath at kitware.com Tue Nov 15 14:55:47 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Tue, 15 Nov 2016 14:55:47 -0500 Subject: [vtk-developers] CDash not displaying test/difference images. In-Reply-To: References: Message-ID: On Mon, Nov 14, 2016 at 9:38 PM, Andrew Maclean wrote: > For example, look at: https://open.cdash.org/testDetails.php?test= > 499737797&build=4641242 > Maybe the problem is here is just a bad link, for example, the address of > the first image is: https://open.cdash.org/displayImage.php?imgid=560914 > > I have tested this on the Google Chrome and Edge browsers. > > Also there is a weird error message whenever images do not match, namely: > "Error regular expression found in output. Regex=[(
|^)ERROR: ]" > > You can see this on the first link above. > Thanks for letting us know. I'm looking into what might be causing this. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zack.galbreath at kitware.com Tue Nov 15 15:16:03 2016 From: zack.galbreath at kitware.com (Zack Galbreath) Date: Tue, 15 Nov 2016 15:16:03 -0500 Subject: [vtk-developers] CDash not displaying test/difference images. In-Reply-To: References: Message-ID: On Tue, Nov 15, 2016 at 2:55 PM, Zack Galbreath wrote: > Thanks for letting us know. I'm looking into what might be causing this. > This should be fixed now. Please let us know if you find any images that still aren't rendering correctly. -------------- next part -------------- An HTML attachment was scrubbed... URL: From shawn.waldon at kitware.com Tue Nov 15 15:23:26 2016 From: shawn.waldon at kitware.com (Shawn Waldon) Date: Tue, 15 Nov 2016 15:23:26 -0500 Subject: [vtk-developers] [vtkusers] VTK downoad not accessible In-Reply-To: References: Message-ID: Hi Bill & Guru, I forwarded it to the sysadmins and it should be fixed now. I can access the download again. Shawn On Tue, Nov 15, 2016 at 12:33 PM, Bill Lorensen wrote: > I see the same issue. I have cc'ed the developers list. > > > On Tue, Nov 15, 2016 at 12:24 PM, Guru Krishnan > wrote: > > I am trying to download VTK 6.3 using the link > > http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz but I get a 403 > > forbidden / Permission denied message. Can you please fix it? > > > > > > _______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Please keep messages on-topic and check the VTK FAQ at: > > http://www.vtk.org/Wiki/VTK_FAQ > > > > Search the list archives at: http://markmail.org/search/?q=vtkusers > > > > Follow this link to subscribe/unsubscribe: > > http://public.kitware.com/mailman/listinfo/vtkusers > > > > > > -- > Unpaid intern in BillsBasement at noware dot com > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From bill.lorensen at gmail.com Tue Nov 15 15:50:32 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Tue, 15 Nov 2016 15:50:32 -0500 Subject: [vtk-developers] [vtkusers] VTK downoad not accessible In-Reply-To: References: Message-ID: Great, works for me now... On Tue, Nov 15, 2016 at 3:23 PM, Shawn Waldon wrote: > Hi Bill & Guru, > > I forwarded it to the sysadmins and it should be fixed now. I can access > the download again. > > Shawn > > On Tue, Nov 15, 2016 at 12:33 PM, Bill Lorensen > wrote: >> >> I see the same issue. I have cc'ed the developers list. >> >> >> On Tue, Nov 15, 2016 at 12:24 PM, Guru Krishnan >> wrote: >> > I am trying to download VTK 6.3 using the link >> > http://www.vtk.org/files/release/6.3/VTK-6.3.0.tar.gz but I get a 403 >> > forbidden / Permission denied message. Can you please fix it? >> > >> > >> > _______________________________________________ >> > Powered by www.kitware.com >> > >> > Visit other Kitware open-source projects at >> > http://www.kitware.com/opensource/opensource.html >> > >> > Please keep messages on-topic and check the VTK FAQ at: >> > http://www.vtk.org/Wiki/VTK_FAQ >> > >> > Search the list archives at: http://markmail.org/search/?q=vtkusers >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/vtkusers >> > >> >> >> >> -- >> Unpaid intern in BillsBasement at noware dot com >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Search the list archives at: http://markmail.org/search/?q=vtk-developers >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/vtk-developers >> > -- Unpaid intern in BillsBasement at noware dot com From ben.boeckel at kitware.com Wed Nov 16 11:46:44 2016 From: ben.boeckel at kitware.com (Ben Boeckel) Date: Wed, 16 Nov 2016 11:46:44 -0500 Subject: [vtk-developers] New buildbot machines Message-ID: <20161116164644.GA17252@megas.kitware.com> Hi all, We have new VTK dashboard machines and here's the breakdown: mun: Windows 7 machine which has taken over nemesis' VTK builds eeloo: Linux machine which has taken over megas' VTK builds Both have nVidia cards and are using their drivers. There may be tests which are failing and need excluded since the test exclusion lists have been cleared for both machines. Thanks, --Ben From mathieu.westphal at kitware.com Thu Nov 17 04:37:11 2016 From: mathieu.westphal at kitware.com (Mathieu Westphal) Date: Thu, 17 Nov 2016 10:37:11 +0100 Subject: [vtk-developers] In Parallel, how to check if data is distributed across nodes. In-Reply-To: References: Message-ID: Hi All Trying again here with this question. How can a filter check if an input data is distributed accross nodes in Parallel ? I tried to check for CAN_HANDLE_PIECE_REQUEST in my filter RequestInformation, but without success (with ParaView). Regards, Mathieu Westphal On Thu, Sep 1, 2016 at 9:59 AM, Mathieu Westphal < mathieu.westphal at kitware.com> wrote: > Hello > > I would like to know if there is way to to check if the input of the > filter is distributed accross nodes > > In my case I have two filter, a typical pipeline looks like this > > - Input > |- Filter 1 > |- Filter2 > |- Filter 2 > > Input is not parallel aware, so its output will be replicated across > nodes, while filter 1 is, so Filter 1 output can be ditributed across nodes > in parallel. > > How could filter2 know if its input is distributed or not ? > I tried to check for CAN_HANDLE_PIECE_REQUEST but without success (with > ParaView). > > Thanks a lot > > Mathieu Westphal > -------------- next part -------------- An HTML attachment was scrubbed... URL: From utkarsh.ayachit at kitware.com Thu Nov 17 10:03:37 2016 From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit) Date: Thu, 17 Nov 2016 10:03:37 -0500 Subject: [vtk-developers] In Parallel, how to check if data is distributed across nodes. In-Reply-To: References: Message-ID: A filter can't, without explicitly communicating among ranks to know the number of cells/points on each rank. On Thu, Nov 17, 2016 at 4:37 AM, Mathieu Westphal wrote: > Hi All > > Trying again here with this question. > > How can a filter check if an input data is distributed accross nodes in > Parallel ? > I tried to check for CAN_HANDLE_PIECE_REQUEST in my filter > RequestInformation, but without success (with ParaView). > > Regards, > > Mathieu Westphal > > On Thu, Sep 1, 2016 at 9:59 AM, Mathieu Westphal > wrote: >> >> Hello >> >> I would like to know if there is way to to check if the input of the >> filter is distributed accross nodes >> >> In my case I have two filter, a typical pipeline looks like this >> >> - Input >> |- Filter 1 >> |- Filter2 >> |- Filter 2 >> >> Input is not parallel aware, so its output will be replicated across >> nodes, while filter 1 is, so Filter 1 output can be ditributed across nodes >> in parallel. >> >> How could filter2 know if its input is distributed or not ? >> I tried to check for CAN_HANDLE_PIECE_REQUEST but without success (with >> ParaView). >> >> Thanks a lot >> >> Mathieu Westphal > > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > > From andrew.amaclean at gmail.com Fri Nov 18 00:11:53 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Fri, 18 Nov 2016 16:11:53 +1100 Subject: [vtk-developers] PNGWriter now writing out a black background after 17 Oct. In-Reply-To: References: Message-ID: I have done a merge request for this, marked as WIP: https://gitlab.kitware.com/vtk/vtk/merge_requests/2161 Regards Andrew On Fri, Nov 11, 2016 at 5:57 PM, Andrew Maclean wrote: > Hi all ... again. > I just tested Ken's suggestion of setting alpha bitplanes to 8 in the > default settings for vtkRenderWindow and all tests pass as before. On my > Kubuntu setup I get 1673/1673 tests passing. > > With respect to the python test, if I comment out def testWIFRGB(self) in > Kubuntu I get an image with a transparent background as expected. In > Kubuntu 16.10 I suspect there is some issue with Plasma when in interactive > mode as I get a lot of window resets. > > So perhaps this is the way to go at this stage, just change line 62 in > vtkRenderWindow.cxx to: > this->AlphaBitPlanes = 8; > and maybe add a test. > > I suspect that the only a few linux users may notice something if they > have inadvertently used vtkWindowToImageFilter.SetInputBufferTypeToRGBA() > when they meant to use vtkWindowToImageFilter.SetInputBufferTypeToRGB() . > > What do people think? > > If everyone is pressed for time, I could probably do something on Monday > as my weekend starts tomorrow. > > Regards > Andrew > > > On Fri, Nov 11, 2016 at 12:06 PM, Andrew Maclean < > andrew.amaclean at gmail.com> wrote: > >> Hi All, >> >> I had to switch the display manager back to lightdm (in order to log into >> Ubuntu). Look at what I get when running either Kubuntu or Ubuntu. >> >> For both Kubuntu and Ubuntu, for the TestWIFPNGRGBA_*.png files, I would >> have expected a 1/4 sphere with a transparent background. Instead Kubuntu >> has a transparent background with a few pixels that are not transparent, >> whilst Ubuntu has a 1/4 sphere with a non-transparent background. >> >> I have a GTX980 card and the OpenGL version is 4.5.0 NVIDIA 367.57 >> >> >> On Fri, Nov 11, 2016 at 7:11 AM, Andrew Maclean < >> andrew.amaclean at gmail.com> wrote: >> >>> David, >>> >>> What you are seeing in the Mac is what I see in Windows and what I would >>> expect. >>> >>> On Kubuntu 16.10 I get the attached RGBA image - trasnparent with a few >>> scattered pixels. >>> >>> if I comment out def testWIFRGB(self): in the code, I get an RGBA with a >>> blue background (I expected a transparent one). In other words it's the >>> same as the RGB image. Interestingly, when I was running Unbuntu I got this >>> image instead of the Kubuntu version. >>> >>> Attached is the output from running the program in Kubuntu 16.10. >>> >>> Andrew >>> >>> On Fri, Nov 11, 2016 at 1:24 AM, David E DeMarle < >>> dave.demarle at kitware.com> wrote: >>> >>>> In the RGBA version the blue background _should_ be invisible. The >>>> question in my mind is why doesn't your Linux build not show anything in >>>> the foreground? Can you share the png's made by your ubuntu build? >>>> >>>> On my Mac for example, for both GL1 and GL2, RGB has a blue background, >>>> RGBA's is transparent. >>>> That is expected. The image contents are the same at every pixel except >>>> that the RGBA'a alpha channel has value 255 for foreground and 0 for >>>> background pixels. >>>> >>>> >>>> David E DeMarle >>>> Kitware, Inc. >>>> R&D Engineer >>>> 21 Corporate Drive >>>> Clifton Park, NY 12065-8662 >>>> Phone: 518-881-4909 >>>> >>>> On Wed, Nov 9, 2016 at 5:18 PM, Andrew Maclean < >>>> andrew.amaclean at gmail.com> wrote: >>>> >>>>> Hi Guys, >>>>> For me this still appears to be the case. Try running the attached >>>>> test code. >>>>> In Windows and Linux, TestWIFPNGRGB.png are the same. >>>>> In Windows TestWIFPNGRGBA.png has a transparent background, whilst in >>>>> KUbuntu no image is produced just a transparent background. >>>>> Are you able to replicate this behaviour? >>>>> >>>>> Andrew >>>>> >>>>> On Wed, Nov 9, 2016 at 10:22 PM, David E DeMarle < >>>>> dave.demarle at kitware.com> wrote: >>>>> >>>>>> Andrew, does this still appear to be the case in the 7.1 release >>>>>> branch? If so mind filing a quick issue on gitlab with the 7.1 milestone >>>>>> tag? >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> ___________________________________________ >>>>> Andrew J. P. Maclean >>>>> >>>>> ___________________________________________ >>>>> >>>> >>>> >>> >>> >>> -- >>> ___________________________________________ >>> Andrew J. P. Maclean >>> >>> ___________________________________________ >>> >> >> >> >> -- >> ___________________________________________ >> Andrew J. P. Maclean >> >> ___________________________________________ >> > > > > -- > ___________________________________________ > Andrew J. P. Maclean > > ___________________________________________ > -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From mario at emmenlauer.de Sat Nov 19 11:53:58 2016 From: mario at emmenlauer.de (Mario Emmenlauer) Date: Sat, 19 Nov 2016 17:53:58 +0100 Subject: [vtk-developers] disabling png Message-ID: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> I've just tracked down an issue for quite a while and found that VTK brings its own PNG library! This is causing my quite a head- ache. I've googled and read the CMakeLists.txt, but could not find how to disable it. Can you please help? How to disable VTK's internal libpng? Thanks for your help, Mario From utkarsh.ayachit at kitware.com Sat Nov 19 12:13:08 2016 From: utkarsh.ayachit at kitware.com (Utkarsh Ayachit) Date: Sat, 19 Nov 2016 12:13:08 -0500 Subject: [vtk-developers] disabling png In-Reply-To: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> References: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> Message-ID: You can tell VTK to use system PNG. Set VTK_USE_SYSTEM_PNG CMake variable to ON. Utkarsh On Sat, Nov 19, 2016 at 11:53 AM, Mario Emmenlauer wrote: > > I've just tracked down an issue for quite a while and found that > VTK brings its own PNG library! This is causing my quite a head- > ache. I've googled and read the CMakeLists.txt, but could not find > how to disable it. Can you please help? > > How to disable VTK's internal libpng? > > Thanks for your help, > > Mario > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > From mario at emmenlauer.de Sat Nov 19 12:31:58 2016 From: mario at emmenlauer.de (Mario Emmenlauer) Date: Sat, 19 Nov 2016 18:31:58 +0100 Subject: [vtk-developers] disabling png In-Reply-To: References: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> Message-ID: Dear Utkarsh, oh my, thanks a lot, exactly what I need! Great! And there are a bunch more VTK_USE_SYSTEM_XXX options that I did not find before, great! Cheers, Mario On 19.11.2016 18:13, Utkarsh Ayachit wrote: > You can tell VTK to use system PNG. Set VTK_USE_SYSTEM_PNG CMake variable to ON. > > Utkarsh > > On Sat, Nov 19, 2016 at 11:53 AM, Mario Emmenlauer wrote: >> >> I've just tracked down an issue for quite a while and found that >> VTK brings its own PNG library! This is causing my quite a head- >> ache. I've googled and read the CMakeLists.txt, but could not find >> how to disable it. Can you please help? >> >> How to disable VTK's internal libpng? >> >> Thanks for your help, >> >> Mario >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html >> >> Search the list archives at: http://markmail.org/search/?q=vtk-developers >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/vtk-developers >> > Viele Gruesse, Mario Emmenlauer -- BioDataAnalysis GmbH, Mario Emmenlauer Tel. Buero: +49-89-74677203 Balanstr. 43 mailto: memmenlauer * biodataanalysis.de D-81669 M?nchen http://www.biodataanalysis.de/ From bill.lorensen at gmail.com Sat Nov 19 12:40:17 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Sat, 19 Nov 2016 12:40:17 -0500 Subject: [vtk-developers] disabling png In-Reply-To: References: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> Message-ID: Just be careful with these system libraries. Sne th9ird party packages change their api's, so we can really only guarantee results with those that we include with vtk. On Sat, Nov 19, 2016 at 12:31 PM, Mario Emmenlauer wrote: > > Dear Utkarsh, > > oh my, thanks a lot, exactly what I need! Great! And there are a > bunch more VTK_USE_SYSTEM_XXX options that I did not find before, > great! > > Cheers, > > Mario > > > On 19.11.2016 18:13, Utkarsh Ayachit wrote: >> You can tell VTK to use system PNG. Set VTK_USE_SYSTEM_PNG CMake variable to ON. >> >> Utkarsh >> >> On Sat, Nov 19, 2016 at 11:53 AM, Mario Emmenlauer wrote: >>> >>> I've just tracked down an issue for quite a while and found that >>> VTK brings its own PNG library! This is causing my quite a head- >>> ache. I've googled and read the CMakeLists.txt, but could not find >>> how to disable it. Can you please help? >>> >>> How to disable VTK's internal libpng? >>> >>> Thanks for your help, >>> >>> Mario >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html >>> >>> Search the list archives at: http://markmail.org/search/?q=vtk-developers >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/vtk-developers >>> >> > > > > Viele Gruesse, > > Mario Emmenlauer > > > -- > BioDataAnalysis GmbH, Mario Emmenlauer Tel. Buero: +49-89-74677203 > Balanstr. 43 mailto: memmenlauer * biodataanalysis.de > D-81669 M?nchen http://www.biodataanalysis.de/ > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > -- Unpaid intern in BillsBasement at noware dot com From mario at emmenlauer.de Sat Nov 19 13:28:06 2016 From: mario at emmenlauer.de (Mario Emmenlauer) Date: Sat, 19 Nov 2016 19:28:06 +0100 Subject: [vtk-developers] disabling png In-Reply-To: References: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> Message-ID: What you say makes perfect sense! But actually I just realized that VTK offers quite a bit more functionality than I use, and some of this comes (for me) at the price of dll-hell (or the equivalent on Linux :-) ). I guess what I'm really looking for would be VTK_DISABLE_IMAGE_READERS for hdf5, netcdf, tiff, png, ogg, json and similar, leaving mostly the rendering and interactors etc and their dependencies in place. I found options to disable Tk, Java, Python. Are there options to further strip down VTK, or tune it to specific use cases? All the best, Mario On 19.11.2016 18:40, Bill Lorensen wrote: > Just be careful with these system libraries. Sne th9ird party packages > change their api's, so we can really only guarantee results with those > that we include with vtk. > > > On Sat, Nov 19, 2016 at 12:31 PM, Mario Emmenlauer wrote: >> >> Dear Utkarsh, >> >> oh my, thanks a lot, exactly what I need! Great! And there are a >> bunch more VTK_USE_SYSTEM_XXX options that I did not find before, >> great! >> >> Cheers, >> >> Mario >> >> >> On 19.11.2016 18:13, Utkarsh Ayachit wrote: >>> You can tell VTK to use system PNG. Set VTK_USE_SYSTEM_PNG CMake variable to ON. >>> >>> Utkarsh >>> >>> On Sat, Nov 19, 2016 at 11:53 AM, Mario Emmenlauer wrote: >>>> >>>> I've just tracked down an issue for quite a while and found that >>>> VTK brings its own PNG library! This is causing my quite a head- >>>> ache. I've googled and read the CMakeLists.txt, but could not find >>>> how to disable it. Can you please help? >>>> >>>> How to disable VTK's internal libpng? >>>> >>>> Thanks for your help, >>>> >>>> Mario >>>> _______________________________________________ >>>> Powered by www.kitware.com >>>> >>>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html >>>> >>>> Search the list archives at: http://markmail.org/search/?q=vtk-developers >>>> >>>> Follow this link to subscribe/unsubscribe: >>>> http://public.kitware.com/mailman/listinfo/vtk-developers From bill.lorensen at gmail.com Sat Nov 19 14:04:30 2016 From: bill.lorensen at gmail.com (Bill Lorensen) Date: Sat, 19 Nov 2016 14:04:30 -0500 Subject: [vtk-developers] disabling png In-Reply-To: References: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> Message-ID: You can build your app my selecting which components you need from a built VTK. For example, I have an app that just uses these components: find_package(VTK COMPONENTS vtkFiltersGeneral vtkFiltersGeometry vtkIOGeometry vtkIOImage vtkIOLegacy vtkImagingStatistics vtkInteractionWidgets vtkRenderingOpenGL2 ) You can also build a VTK that is stripped down. I'm not sure which use case you have... On Sat, Nov 19, 2016 at 1:28 PM, Mario Emmenlauer wrote: > > What you say makes perfect sense! But actually I just realized that VTK > offers quite a bit more functionality than I use, and some of this comes > (for me) at the price of dll-hell (or the equivalent on Linux :-) ). > > I guess what I'm really looking for would be VTK_DISABLE_IMAGE_READERS > for hdf5, netcdf, tiff, png, ogg, json and similar, leaving mostly the > rendering and interactors etc and their dependencies in place. I found > options to disable Tk, Java, Python. Are there options to further strip > down VTK, or tune it to specific use cases? > > All the best, > > Mario > > > > > On 19.11.2016 18:40, Bill Lorensen wrote: >> Just be careful with these system libraries. Sne th9ird party packages >> change their api's, so we can really only guarantee results with those >> that we include with vtk. >> >> >> On Sat, Nov 19, 2016 at 12:31 PM, Mario Emmenlauer wrote: >>> >>> Dear Utkarsh, >>> >>> oh my, thanks a lot, exactly what I need! Great! And there are a >>> bunch more VTK_USE_SYSTEM_XXX options that I did not find before, >>> great! >>> >>> Cheers, >>> >>> Mario >>> >>> >>> On 19.11.2016 18:13, Utkarsh Ayachit wrote: >>>> You can tell VTK to use system PNG. Set VTK_USE_SYSTEM_PNG CMake variable to ON. >>>> >>>> Utkarsh >>>> >>>> On Sat, Nov 19, 2016 at 11:53 AM, Mario Emmenlauer wrote: >>>>> >>>>> I've just tracked down an issue for quite a while and found that >>>>> VTK brings its own PNG library! This is causing my quite a head- >>>>> ache. I've googled and read the CMakeLists.txt, but could not find >>>>> how to disable it. Can you please help? >>>>> >>>>> How to disable VTK's internal libpng? >>>>> >>>>> Thanks for your help, >>>>> >>>>> Mario >>>>> _______________________________________________ >>>>> Powered by www.kitware.com >>>>> >>>>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html >>>>> >>>>> Search the list archives at: http://markmail.org/search/?q=vtk-developers >>>>> >>>>> Follow this link to subscribe/unsubscribe: >>>>> http://public.kitware.com/mailman/listinfo/vtk-developers > > -- Unpaid intern in BillsBasement at noware dot com From mario at emmenlauer.de Sat Nov 19 19:31:03 2016 From: mario at emmenlauer.de (Mario Emmenlauer) Date: Sun, 20 Nov 2016 01:31:03 +0100 Subject: [vtk-developers] disabling png In-Reply-To: References: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> Message-ID: <012c511f-e4bb-1ff0-4252-f9b0529572f2@emmenlauer.de> Dear Bill, thanks for the nice reply! But my use case is different, I want to avoid bringing certain third-party libraries into VTK. An example is libpng, I have a specific (patched) version that my application needs to use. My version is not interface compatible with VTK's internal version, so I can't just tell cmake to link my (system) version. However when I let VTK use its internal version, my app eventually crashes after showing an error that its compiled against a different libpng version than its linked against. So it seems VTK 'pollutes' my dll space. Can I somehow just disable everything related to libpng in VTK? And same for NetCDF and HDF5? So far I've tested removing the source directories, and my mileage is surprisingly good, but its quite a bit hackish... Cheers, Mario On 19.11.2016 20:04, Bill Lorensen wrote: > You can build your app my selecting which components you need from a built VTK. > For example, I have an app that just uses these components: > find_package(VTK COMPONENTS > vtkFiltersGeneral > vtkFiltersGeometry > vtkIOGeometry > vtkIOImage > vtkIOLegacy > vtkImagingStatistics > vtkInteractionWidgets > vtkRenderingOpenGL2 > ) > > You can also build a VTK that is stripped down. I'm not sure which use > case you have... > > > On Sat, Nov 19, 2016 at 1:28 PM, Mario Emmenlauer wrote: >> >> What you say makes perfect sense! But actually I just realized that VTK >> offers quite a bit more functionality than I use, and some of this comes >> (for me) at the price of dll-hell (or the equivalent on Linux :-) ). >> >> I guess what I'm really looking for would be VTK_DISABLE_IMAGE_READERS >> for hdf5, netcdf, tiff, png, ogg, json and similar, leaving mostly the >> rendering and interactors etc and their dependencies in place. I found >> options to disable Tk, Java, Python. Are there options to further strip >> down VTK, or tune it to specific use cases? >> >> All the best, >> >> Mario >> >> >> >> >> On 19.11.2016 18:40, Bill Lorensen wrote: >>> Just be careful with these system libraries. Sne th9ird party packages >>> change their api's, so we can really only guarantee results with those >>> that we include with vtk. >>> >>> >>> On Sat, Nov 19, 2016 at 12:31 PM, Mario Emmenlauer wrote: >>>> >>>> Dear Utkarsh, >>>> >>>> oh my, thanks a lot, exactly what I need! Great! And there are a >>>> bunch more VTK_USE_SYSTEM_XXX options that I did not find before, >>>> great! >>>> >>>> Cheers, >>>> >>>> Mario >>>> >>>> >>>> On 19.11.2016 18:13, Utkarsh Ayachit wrote: >>>>> You can tell VTK to use system PNG. Set VTK_USE_SYSTEM_PNG CMake variable to ON. >>>>> >>>>> Utkarsh >>>>> >>>>> On Sat, Nov 19, 2016 at 11:53 AM, Mario Emmenlauer wrote: >>>>>> >>>>>> I've just tracked down an issue for quite a while and found that >>>>>> VTK brings its own PNG library! This is causing my quite a head- >>>>>> ache. I've googled and read the CMakeLists.txt, but could not find >>>>>> how to disable it. Can you please help? >>>>>> >>>>>> How to disable VTK's internal libpng? >>>>>> >>>>>> Thanks for your help, >>>>>> >>>>>> Mario >>>>>> _______________________________________________ >>>>>> Powered by www.kitware.com >>>>>> >>>>>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html >>>>>> >>>>>> Search the list archives at: http://markmail.org/search/?q=vtk-developers >>>>>> >>>>>> Follow this link to subscribe/unsubscribe: >>>>>> http://public.kitware.com/mailman/listinfo/vtk-developers From DLRdave at aol.com Sun Nov 20 11:32:16 2016 From: DLRdave at aol.com (David Cole) Date: Sun, 20 Nov 2016 11:32:16 -0500 Subject: [vtk-developers] disabling png In-Reply-To: <012c511f-e4bb-1ff0-4252-f9b0529572f2@emmenlauer.de> References: <24a41bcd-21cd-7348-b37f-d7c91f32ae35@emmenlauer.de> <012c511f-e4bb-1ff0-4252-f9b0529572f2@emmenlauer.de> Message-ID: If you set the CMake cache variable VTK_USE_SYSTEM_PNG to ON when you are configuring VTK, it should avoid pulling in the built-in VTK png library. And the VTK stuff that depends on the png library should be able to use your patched one just fine unless you have significantly altered the api to the library in some way with your patch. There are also several other VTK_USE_SYSTEM_* variables for the third party libraries. HTH, David C. On Sat, Nov 19, 2016 at 7:31 PM, Mario Emmenlauer wrote: > > Dear Bill, thanks for the nice reply! But my use case is different, I want > to avoid bringing certain third-party libraries into VTK. An example is > libpng, I have a specific (patched) version that my application needs to > use. My version is not interface compatible with VTK's internal version, > so I can't just tell cmake to link my (system) version. However when I > let VTK use its internal version, my app eventually crashes after showing > an error that its compiled against a different libpng version than its > linked against. So it seems VTK 'pollutes' my dll space. > > Can I somehow just disable everything related to libpng in VTK? And same for > NetCDF and HDF5? So far I've tested removing the source directories, and my > mileage is surprisingly good, but its quite a bit hackish... > > Cheers, > > Mario > > > > > On 19.11.2016 20:04, Bill Lorensen wrote: >> You can build your app my selecting which components you need from a built VTK. >> For example, I have an app that just uses these components: >> find_package(VTK COMPONENTS >> vtkFiltersGeneral >> vtkFiltersGeometry >> vtkIOGeometry >> vtkIOImage >> vtkIOLegacy >> vtkImagingStatistics >> vtkInteractionWidgets >> vtkRenderingOpenGL2 >> ) >> >> You can also build a VTK that is stripped down. I'm not sure which use >> case you have... >> >> >> On Sat, Nov 19, 2016 at 1:28 PM, Mario Emmenlauer wrote: >>> >>> What you say makes perfect sense! But actually I just realized that VTK >>> offers quite a bit more functionality than I use, and some of this comes >>> (for me) at the price of dll-hell (or the equivalent on Linux :-) ). >>> >>> I guess what I'm really looking for would be VTK_DISABLE_IMAGE_READERS >>> for hdf5, netcdf, tiff, png, ogg, json and similar, leaving mostly the >>> rendering and interactors etc and their dependencies in place. I found >>> options to disable Tk, Java, Python. Are there options to further strip >>> down VTK, or tune it to specific use cases? >>> >>> All the best, >>> >>> Mario >>> >>> >>> >>> >>> On 19.11.2016 18:40, Bill Lorensen wrote: >>>> Just be careful with these system libraries. Sne th9ird party packages >>>> change their api's, so we can really only guarantee results with those >>>> that we include with vtk. >>>> >>>> >>>> On Sat, Nov 19, 2016 at 12:31 PM, Mario Emmenlauer wrote: >>>>> >>>>> Dear Utkarsh, >>>>> >>>>> oh my, thanks a lot, exactly what I need! Great! And there are a >>>>> bunch more VTK_USE_SYSTEM_XXX options that I did not find before, >>>>> great! >>>>> >>>>> Cheers, >>>>> >>>>> Mario >>>>> >>>>> >>>>> On 19.11.2016 18:13, Utkarsh Ayachit wrote: >>>>>> You can tell VTK to use system PNG. Set VTK_USE_SYSTEM_PNG CMake variable to ON. >>>>>> >>>>>> Utkarsh >>>>>> >>>>>> On Sat, Nov 19, 2016 at 11:53 AM, Mario Emmenlauer wrote: >>>>>>> >>>>>>> I've just tracked down an issue for quite a while and found that >>>>>>> VTK brings its own PNG library! This is causing my quite a head- >>>>>>> ache. I've googled and read the CMakeLists.txt, but could not find >>>>>>> how to disable it. Can you please help? >>>>>>> >>>>>>> How to disable VTK's internal libpng? >>>>>>> >>>>>>> Thanks for your help, >>>>>>> >>>>>>> Mario >>>>>>> _______________________________________________ >>>>>>> Powered by www.kitware.com >>>>>>> >>>>>>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html >>>>>>> >>>>>>> Search the list archives at: http://markmail.org/search/?q=vtk-developers >>>>>>> >>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>> http://public.kitware.com/mailman/listinfo/vtk-developers > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers > From dave.demarle at kitware.com Wed Nov 23 12:21:17 2016 From: dave.demarle at kitware.com (David E DeMarle) Date: Wed, 23 Nov 2016 10:21:17 -0700 Subject: [vtk-developers] announce: 7.1.0 is cooked, out of the oven, and ready for carving Message-ID: Read all about it here: https://blog.kitware.com/vtk-7-1-0/ David E DeMarle Kitware, Inc. R&D Engineer 21 Corporate Drive Clifton Park, NY 12065-8662 Phone: 518-881-4909 -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.amaclean at gmail.com Wed Nov 23 16:49:12 2016 From: andrew.amaclean at gmail.com (Andrew Maclean) Date: Thu, 24 Nov 2016 08:49:12 +1100 Subject: [vtk-developers] Problems with the test computers Message-ID: eelo - 1426 failed 926 passed. It seems no tests involving image comparisons are tested. dash3, bigmac, dashlin1 and trey: I suspect that they are not updating the image files. I am picking this up in: https://gitlab.kitware.com/vtk/vtk/merge_requests/2190#note_200773 See the dashboard at: https://open.cdash.org/index.php?compare1=63&filtercount=2&field1=buildname%2Fstring&project=VTK&field2=buildstarttime%2Fdate&showfilters=0&limit=100&compare2=83&value1=f92d9ff9&showfeed=0&value2=20161122T230628 These four machines seem to be comparing the test image against the original reference image. On my machine the difference image when using the original reference image is attached. I would appreciate it if someone could look at these computers and see what reference (valid) image is being used. To help them I attach the original valid image and the new valid image and their respective md5-stamp files. You can see that the new valid image has a faint outer ring and a total of three concentric circles whilst original valid image has no outer ring and two extra concentric circles. Additionally, the original valid image seems to have more pronounced rasterization. Thanks Andrew -- ___________________________________________ Andrew J. P. Maclean ___________________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: TestSphereWidgetZoomInOut.diff.png Type: image/png Size: 4031 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: New_TestSphereWidgetZoomInOut.zip Type: application/zip Size: 20679 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Original_TestSphereWidgetZoomInOut.zip Type: application/zip Size: 22025 bytes Desc: not available URL: From elvis.stansvik at orexplore.com Thu Nov 24 03:04:13 2016 From: elvis.stansvik at orexplore.com (Elvis Stansvik) Date: Thu, 24 Nov 2016 09:04:13 +0100 Subject: [vtk-developers] [vtkusers] announce: 7.1.0 is cooked, out of the oven, and ready for carving In-Reply-To: References: Message-ID: 2016-11-23 18:21 GMT+01:00 David E DeMarle : > Read all about it here: > https://blog.kitware.com/vtk-7-1-0/ > > Great news! A big thanks to everyone involved. Looks like an impressive release. I shall update our Ubuntu package straight away. Cheers, Elvis David E DeMarle > Kitware, Inc. > R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4909 > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Please keep messages on-topic and check the VTK FAQ at: > http://www.vtk.org/Wiki/VTK_FAQ > > Search the list archives at: http://markmail.org/search/?q=vtkusers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtkusers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From elvis.stansvik at orexplore.com Thu Nov 24 04:10:12 2016 From: elvis.stansvik at orexplore.com (Elvis Stansvik) Date: Thu, 24 Nov 2016 10:10:12 +0100 Subject: [vtk-developers] [vtkusers] announce: 7.1.0 is cooked, out of the oven, and ready for carving In-Reply-To: References: Message-ID: 2016-11-23 18:21 GMT+01:00 David E DeMarle : > Read all about it here: > https://blog.kitware.com/vtk-7-1-0/ > > Just a question: vtkOpenGLGPUVolumeRayCastMapper::SetNoiseGenerator was added by Alvaro in https://gitlab.kitware.com/vtk/vtk/merge_requests/2130 but is not listed as an added function at http://www.vtk.org/Wiki/VTK/API_Changes_7_0_0_to_7_1_0#Public_methods_added_in_version_v7.1.0 Is this list maintained manually or generated? If it is generated, perhaps something needs to be fixed in the generation? Elvis David E DeMarle > Kitware, Inc. > R&D Engineer > 21 Corporate Drive > Clifton Park, NY 12065-8662 > Phone: 518-881-4909 > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Please keep messages on-topic and check the VTK FAQ at: > http://www.vtk.org/Wiki/VTK_FAQ > > Search the list archives at: http://markmail.org/search/?q=vtkusers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtkusers > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ken.martin at kitware.com Thu Nov 24 07:46:49 2016 From: ken.martin at kitware.com (Ken Martin) Date: Thu, 24 Nov 2016 07:46:49 -0500 Subject: [vtk-developers] [vtkusers] announce: 7.1.0 is cooked, out of the oven, and ready for carving In-Reply-To: References: Message-ID: That feature was added after the 7.1 release process was well along so it probably did not make it into the 7.1 release. On Thu, Nov 24, 2016 at 3:18 AM, Andrea Gavana wrote: > Hi David & All, > > On 23 November 2016 at 18:21, David E DeMarle wrote: > >> Read all about it here: >> https://blog.kitware.com/vtk-7-1-0/ >> > > > Thank you for the release. I have tried to use the cool feature described > here: > > https://blog.kitware.com/rendering-tubes-and-spheres-in-vtk/ > > Using the just released VTK 7.1 and its Python bindings (I'm using VTK > through Python). However, when I add these two lines to one of my scripts > (property is a vtkProperty): > > property.SetVertexVisibility(1) > property.SetVertexColor(0.5, 1.0, 0.8) > > > I get the following: > > AttributeError: 'vtkRenderingOpenGL2Python.vtkOpenGLProperty' object has > no attribute 'SetVertexVisibility' > > Also, doing a dir(vtkProperty) there is no mention of SetVertexVisibility > or any other "Vertex" method whatsoever. > > Maybe I am missing something obvious... > > Thank you. > > Andrea. > > > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/ > opensource/opensource.html > > Please keep messages on-topic and check the VTK FAQ at: > http://www.vtk.org/Wiki/VTK_FAQ > > Search the list archives at: http://markmail.org/search/?q=vtkusers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtkusers > > -- Ken Martin PhD Chairman & CFO Kitware Inc. 28 Corporate Drive Clifton Park NY 12065 518 371 3971 This communication, including all attachments, contains confidential and legally privileged information, and it is intended only for the use of the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken in reliance on it is prohibited and may be unlawful. If you received this communication in error please notify us immediately and destroy the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From badshah400 at aim.com Thu Nov 24 09:24:42 2016 From: badshah400 at aim.com (Atri Bhattacharya) Date: Thu, 24 Nov 2016 15:24:42 +0100 Subject: [vtk-developers] Problems building with cmake 3.3 Message-ID: <1479997482.13683.3.camel@aim.com> Hi! Congratulations and thanks for another exciting release of vtk! I am a packager of vtk for openSUSE [1], and I find that vtk 7.1 fails to build, e.g. on openSUSE 13.2 (hd5 1.8.13, cmake 3.0.2), openSUSE Leap 42.1 (hdf5 1.8.15, cmake 3.3.2), but builds fine on openSUSE Leap 42.2 (hdf5 1.8.15, cmake 3.5.2) and later. The error I see on the older systems is along the lines of: ``` [??245s] -- [1;4;34mConfiguring proj library:[0m? [??245s] --? [??245s] -- PROJ_CORE_TARGET?????????????????????????= vtkproj4? [??245s] -- PROJ_CORE_TARGET_OUTPUT_NAME?????????????= vtkproj4? [??245s] -- PROJ_LIBRARIES???????????????????????????= vtkproj4? [??246s] CMake Error at CMake/NewCMake/FindHDF5.cmake:483 (find_program): [??246s]???find_program does not support NAMES_PER_DIR [??246s] Call Stack (most recent call first): [??246s]???CMake/FindHDF5.cmake:7 (include) [??246s]???CMake/vtkModuleMacros.cmake:858 (find_package) [??246s]???ThirdParty/hdf5/CMakeLists.txt:1 (vtk_module_third_party) ``` Any way we could continue to provide vtk 7.1 for these older installations, or should we simply stop upgrading vtk for these? Thanks for any help, suggestions, etc. Best wishes. [1] My efforts to build vtk 7.1 are here: https://build.opensuse.org/package/show/home:badshah400:branches:science/vtk which, upon success, I will submit to the official pkgs, which are provided through https://build.opensuse.org/package/show/science/vtk From ken.martin at kitware.com Thu Nov 24 10:29:42 2016 From: ken.martin at kitware.com (Ken Martin) Date: Thu, 24 Nov 2016 10:29:42 -0500 Subject: [vtk-developers] [vtkusers] announce: 7.1.0 is cooked, out of the oven, and ready for carving In-Reply-To: References: Message-ID: You read it correctly, :-) I ***think*** the ability to render points as spheres and lines as tubes is in there but what didn't make it is the ability to render the vertices (i.e. the points used by the cells.). But if you turn on RenderPointsAsSpheres, SetPointSize and SetRepresentationToPoints I think you will get spheres, it is just not as nice an option as rendering a unique list of points referenced by the cells which is what the VertexVisibility does. It just unfortunately was developed right as the release process was going on. On Thu, Nov 24, 2016 at 8:38 AM, Andrea Gavana wrote: > Hi David & All, > > > On 24 November 2016 at 13:46, Ken Martin wrote: > >> That feature was added after the 7.1 release process was well along so it >> probably did not make it into the 7.1 release. >> >> > > Ah, OK, thank you for the clarification. I must have misread the > "RENDERING" section of the announcement in the VTK blog then. > > Andrea. > > > > >> On Thu, Nov 24, 2016 at 3:18 AM, Andrea Gavana >> wrote: >> >>> Hi David & All, >>> >>> On 23 November 2016 at 18:21, David E DeMarle wrote: >>> >>>> Read all about it here: >>>> https://blog.kitware.com/vtk-7-1-0/ >>>> >>> >>> >>> Thank you for the release. I have tried to use the cool feature >>> described here: >>> >>> https://blog.kitware.com/rendering-tubes-and-spheres-in-vtk/ >>> >>> Using the just released VTK 7.1 and its Python bindings (I'm using VTK >>> through Python). However, when I add these two lines to one of my scripts >>> (property is a vtkProperty): >>> >>> property.SetVertexVisibility(1) >>> property.SetVertexColor(0.5, 1.0, 0.8) >>> >>> >>> I get the following: >>> >>> AttributeError: 'vtkRenderingOpenGL2Python.vtkOpenGLProperty' object >>> has no attribute 'SetVertexVisibility' >>> >>> Also, doing a dir(vtkProperty) there is no mention of >>> SetVertexVisibility or any other "Vertex" method whatsoever. >>> >>> Maybe I am missing something obvious... >>> >>> Thank you. >>> >>> Andrea. >>> >>> >>> _______________________________________________ >>> Powered by www.kitware.com >>> >>> Visit other Kitware open-source projects at >>> http://www.kitware.com/opensource/opensource.html >>> >>> Please keep messages on-topic and check the VTK FAQ at: >>> http://www.vtk.org/Wiki/VTK_FAQ >>> >>> Search the list archives at: http://markmail.org/search/?q=vtkusers >>> >>> Follow this link to subscribe/unsubscribe: >>> http://public.kitware.com/mailman/listinfo/vtkusers >>> >>> >> >> >> -- >> Ken Martin PhD >> Chairman & CFO >> Kitware Inc. >> 28 Corporate Drive >> Clifton Park NY 12065 >> 518 371 3971 >> >> This communication, including all attachments, contains confidential and >> legally privileged information, and it is intended only for the use of the >> addressee. Access to this email by anyone else is unauthorized. If you are >> not the intended recipient, any disclosure, copying, distribution or any >> action taken in reliance on it is prohibited and may be unlawful. If you >> received this communication in error please notify us immediately and >> destroy the original message. Thank you. >> > > -- Ken Martin PhD Chairman & CFO Kitware Inc. 28 Corporate Drive Clifton Park NY 12065 518 371 3971 This communication, including all attachments, contains confidential and legally privileged information, and it is intended only for the use of the addressee. Access to this email by anyone else is unauthorized. If you are not the intended recipient, any disclosure, copying, distribution or any action taken in reliance on it is prohibited and may be unlawful. If you received this communication in error please notify us immediately and destroy the original message. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gerald.Lodron at joanneum.at Tue Nov 29 02:18:29 2016 From: Gerald.Lodron at joanneum.at (Lodron, Gerald) Date: Tue, 29 Nov 2016 07:18:29 +0000 Subject: [vtk-developers] Correct choice of data type Message-ID: Hello What would be the correct data type for a ordered Point Cloud like data from a 3D range sensor. Would it be a Rectilinear Grid? Currently I use vtkPolydata but this data is not ordered as on images. Is it possible to specify "nodata" values in that datatype? When I set values in vtkPolydata to QNan I get crashes.... PS: I want to use the data set in paraview.... Best regards, gerald ------------------------------------------------------------------------------------ Gerald Lodron Researcher of Machine Vision Applications Group DIGITAL - Institute for Information and Communication Technologies JOANNEUM RESEARCH Forschungsgesellschaft mbH Steyrergasse 17, 8010 Graz, AUSTRIA phone: +43-316-876-1751 general fax: +43-316-876-1751 web: http://www.joanneum.at/digital e-mail: gerald.lodron at joanneum.at -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.froger.ml at mailoo.org Tue Nov 29 15:28:01 2016 From: david.froger.ml at mailoo.org (David Froger) Date: Tue, 29 Nov 2016 21:28:01 +0100 Subject: [vtk-developers] segfault with vtkLineIntegralConvolution2D Message-ID: <148045128132.2559.17890052110366946280@mael> Hello VTK devs, I'm looking for help/advices to solve https://gitlab.kitware.com/vtk/vtk/issues/16920 . Does vtkPainterCommunicator needs to inherit vtkObject, as I'm trying to do? If so, I now have errors: ERROR: In /home/vagrant/VTK-7.1.0/Common/Core/vtkObject.cxx, line 156 vtkObject (0x18f7140): Trying to delete object with non-zero reference count. Generic Warning: In /home/vagrant/VTK-7.1.0/Common/Core/vtkObjectBase.cxx, line 93 Trying to delete object with non-zero reference count. I understand the error message (C++ deletes an object whose reference count is not zero), but I don't know where is come from, and how to solve it. (I tried to put vtkSmartPointers in place of vtkPainterCommunicator*). Anyway, if vtkPainterCommunicator does not need to inherit vtkObject, the problem does not need to be solved... Another problem is the VTK robot that detect trailing whitespace, that a commit already solved. Thanks, David From burlen.loring at gmail.com Tue Nov 29 17:33:43 2016 From: burlen.loring at gmail.com (Burlen Loring) Date: Tue, 29 Nov 2016 14:33:43 -0800 Subject: [vtk-developers] segfault with vtkLineIntegralConvolution2D In-Reply-To: <148045128132.2559.17890052110366946280@mael> References: <148045128132.2559.17890052110366946280@mael> Message-ID: I took a quick look, vtkPainterCommunicator is a class that is not wrapped, and it seems that commit 4d127b1d introduced the bug. // ETX and // BTX were removed from the Set/Get methods you mention and a number of others in the class. I don't think vtkPainterCommunicator should necessarily be promoted to a vtkObject, the comments in the Set/Get methods explain why it was not one in the first place. IMO, probably best to simply exclude these methods from wrapping, if that's still an option. Burlen On 11/29/2016 12:28 PM, David Froger wrote: > Hello VTK devs, > > I'm looking for help/advices to solve > https://gitlab.kitware.com/vtk/vtk/issues/16920 . > > Does vtkPainterCommunicator needs to inherit vtkObject, as I'm trying to do? > > If so, I now have errors: > > ERROR: In /home/vagrant/VTK-7.1.0/Common/Core/vtkObject.cxx, line 156 > vtkObject (0x18f7140): Trying to delete object with non-zero reference count. > > Generic Warning: In /home/vagrant/VTK-7.1.0/Common/Core/vtkObjectBase.cxx, > line 93 > Trying to delete object with non-zero reference count. > > > I understand the error message (C++ deletes an object whose reference count is > not zero), but I don't know where is come from, and how to solve it. (I tried to > put vtkSmartPointers in place of vtkPainterCommunicator*). Anyway, if > vtkPainterCommunicator does not need to inherit vtkObject, the problem does not > need to be solved... > > Another problem is the VTK robot that detect trailing whitespace, that a commit > already solved. > > Thanks, > David > _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html > > Search the list archives at: http://markmail.org/search/?q=vtk-developers > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/vtk-developers >