VisNow issueshttps://gitlab.com/visnow.org/VisNow/-/issues2019-03-28T12:09:08Zhttps://gitlab.com/visnow.org/VisNow/-/issues/116orthoviewer3D resize problems2019-03-28T12:09:08ZBartosz Boruckibabor@icm.edu.plorthoviewer3D resize problemsOrthoViewer3D is not resizing the canvases properly when the window is resized on MacOS.
Similarly to previous problems with FieldViewer3D - fix it the same way with split panel events.OrthoViewer3D is not resizing the canvases properly when the window is resized on MacOS.
Similarly to previous problems with FieldViewer3D - fix it the same way with split panel events.Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/119port color in plugin2019-09-18T17:14:04ZKrzysztof Nowinskiport color in pluginIf a plugin has own port type specified in types.xml exception "Could not find color for a port. Add port type to the types.xml file." is raisedIf a plugin has own port type specified in types.xml exception "Could not find color for a port. Add port type to the types.xml file." is raisedhttps://gitlab.com/visnow.org/VisNow/-/issues/120read/write irregular field2019-04-29T10:17:43ZBartosz Boruckibabor@icm.edu.plread/write irregular fieldtest cells module, irregular field output write as VNF (ASCII or binary).
Then read it with VNF reader. An error is thrown:
`ERROR: error in data file: bad number format /Users/babor/Work/tmp/out5.txt; in function /Users/babor/Work/tmp/...test cells module, irregular field output write as VNF (ASCII or binary).
Then read it with VNF reader. An error is thrown:
`ERROR: error in data file: bad number format /Users/babor/Work/tmp/out5.txt; in function /Users/babor/Work/tmp/out5.txt line 37
ERROR: error in data file: bad number format /Users/babor/Work/tmp/out5.txt; in function /Users/babor/Work/tmp/out5.txt line 40
ERROR: error in data file: bad number format /Users/babor/Work/tmp/out5.txt; in function /Users/babor/Work/tmp/out5.txt line 43
ERROR: error in data file: bad number format /Users/babor/Work/tmp/out5.txt; in function /Users/babor/Work/tmp/out5.txt line 46
ERROR: error in data file: bad number format /Users/babor/Work/tmp/out5.txt; in function /Users/babor/Work/tmp/out5.txt line 48
`https://gitlab.com/visnow.org/VisNow/-/issues/125Anisotropic denoiser crash on MacOS Mojave / Windows2019-06-10T12:19:50ZBartosz Boruckibabor@icm.edu.plAnisotropic denoiser crash on MacOS Mojave / Windows[cuda_error.txt](/uploads/433c1ab867a8753230d2dcc9a71e02d8/cuda_error.txt)
Anisotropic denoiser module cannot be created on MacOS Mojave.
This seems due to the lack of GPU access / CUDA support on MacOS 10.14 Mojave.
See https://devt...[cuda_error.txt](/uploads/433c1ab867a8753230d2dcc9a71e02d8/cuda_error.txt)
Anisotropic denoiser module cannot be created on MacOS Mojave.
This seems due to the lack of GPU access / CUDA support on MacOS 10.14 Mojave.
See https://devtalk.nvidia.com/default/topic/1042279/cuda-10-and-macos-10-14/ for details.
However, this should not cause the module to crash as CPU backend should work properly.
There are at least two places to fix this issue - one global in VisNow checking CUDA availability, second in the very module trying to load CUDA-based libraries.Piotr WendykierPiotr Wendykierhttps://gitlab.com/visnow.org/VisNow/-/issues/127stationary flow visualization2019-08-08T12:52:15ZKerstin Kantiemkerstin.kantiem@gmail.comstationary flow visualizationWhen 'auto' is switched off actualization takes place but should not.When 'auto' is switched off actualization takes place but should not.https://gitlab.com/visnow.org/VisNow/-/issues/130Error in short data read from DICOM2019-08-12T13:38:34ZKrzysztof NowinskiError in short data read from DICOM15 bit short DICOM data are read in as signed - some problems with the sign bit? see attached DICOM image[20190605_UKSW_xy0500.dcm](/uploads/09876f87e6f2947e7f079f92b3eefe83/20190605_UKSW_xy0500.dcm)15 bit short DICOM data are read in as signed - some problems with the sign bit? see attached DICOM image[20190605_UKSW_xy0500.dcm](/uploads/09876f87e6f2947e7f079f92b3eefe83/20190605_UKSW_xy0500.dcm)Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/132planar slice exception on large regular field2019-07-25T12:07:12ZBartosz Boruckibabor@icm.edu.plplanar slice exception on large regular fieldPlanar slice does not support large regular fields.
`
13:50:34,454 planar slice[2] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onLocalActive
java.lang.NullPointerException
at pl.edu.icm.visnow...Planar slice does not support large regular fields.
`
13:50:34,454 planar slice[2] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onLocalActive
java.lang.NullPointerException
at pl.edu.icm.visnow.lib.utils.slicing.BasicPlanarSlice.dirComponent(BasicPlanarSlice.java:284)
at pl.edu.icm.visnow.lib.utils.slicing.BasicPlanarSlice.updateSlice(BasicPlanarSlice.java:172)
at pl.edu.icm.visnow.lib.utils.slicing.BasicPlanarSlice$1.parameterChanged(BasicPlanarSlice.java:114)
at pl.edu.icm.visnow.geometries.interactiveGlyphs.InteractiveGlyphParams.fireParameterChanged(InteractiveGlyphParams.java:771)
at pl.edu.icm.visnow.geometries.interactiveGlyphs.InteractiveGlyphParams.setAxis(InteractiveGlyphParams.java:391)
at pl.edu.icm.visnow.lib.utils.slicing.BasicPlanarSlice.setInData(BasicPlanarSlice.java:340)
at pl.edu.icm.visnow.lib.basic.mappers.PlanarSlice.PlanarSlice.onActive(PlanarSlice.java:510)
at pl.edu.icm.visnow.engine.core.ModuleCore.onLocalActive(ModuleCore.java:586)
at pl.edu.icm.visnow.engine.main.ModuleElement.setActive(ModuleElement.java:327)
at pl.edu.icm.visnow.engine.main.ModuleElement.onActionMessage(ModuleElement.java:281)
at pl.edu.icm.visnow.engine.element.Element.nextMessage(Element.java:213)
at pl.edu.icm.visnow.engine.element.Element.run(Element.java:175)
at java.lang.Thread.run(Thread.java:748)
`
To recreate: test field -> 3D -> set resolution to 1000 -> connect planar sliceKrzysztof NowinskiKrzysztof Nowinskihttps://gitlab.com/visnow.org/VisNow/-/issues/134Fluent reader fail for files larger than 2GB2019-06-18T09:01:44ZBartosz Boruckibabor@icm.edu.plFluent reader fail for files larger than 2GBWhile trying to read a file larger than 2GB with ANSYS Fluent reader there is an exception:
`
10:50:04,327 luent reader[1] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onLocalActive
java.lang.Ill...While trying to read a file larger than 2GB with ANSYS Fluent reader there is an exception:
`
10:50:04,327 luent reader[1] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onLocalActive
java.lang.IllegalArgumentException: Size exceeds Integer.MAX_VALUE
at sun.nio.ch.FileChannelImpl.map(FileChannelImpl.java:836)
at pl.edu.icm.visnow.lib.basic.readers.ReadFluent.MemoryFileImageInputStream.<init>(MemoryFileImageInputStream.java:27)
at pl.edu.icm.visnow.lib.basic.readers.ReadFluent.FluentReader.openDataFile(FluentReader.java:331)
at pl.edu.icm.visnow.lib.basic.readers.ReadFluent.FluentReader.requestInformation(FluentReader.java:119)
at pl.edu.icm.visnow.lib.basic.readers.ReadFluent.ReadFluent.onActive(ReadFluent.java:163)
at pl.edu.icm.visnow.engine.core.ModuleCore.onLocalActive(ModuleCore.java:586)
at pl.edu.icm.visnow.engine.main.ModuleElement.setActive(ModuleElement.java:327)
at pl.edu.icm.visnow.engine.main.ModuleElement.onActionMessage(ModuleElement.java:281)
at pl.edu.icm.visnow.engine.element.Element.nextMessage(Element.java:213)
at pl.edu.icm.visnow.engine.element.Element.run(Element.java:175)
at java.lang.Thread.run(Thread.java:745)
`
The reason is the FileChannel/MappedByteBuffer in MemoryFileImageInputStream do not allow sizes larger than MAX_INT. Need to reposition the mapped region for larger files.
Test on file /workspace0/babor/data/fluent/Savoinus3D/SAa.casBartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/135spatial crop module fails to recognize trueNSpace for 2D inputs. Rectangle cr...2019-06-20T15:02:47ZKrzysztof Nowinskispatial crop module fails to recognize trueNSpace for 2D inputs. Rectangle crop fails for the "fully inside" and "on boundary" choices.Krzysztof NowinskiKrzysztof Nowinskihttps://gitlab.com/visnow.org/VisNow/-/issues/137Dicom Reader Erroneous detection of short data2019-09-23T11:51:36ZPiotr RegulskiDicom Reader Erroneous detection of short dataComponent type is set to int instead of short. Min max are invalid.
![Przechwytywanie](/uploads/0b0e7634c5ff91cf1809414e659583ee/Przechwytywanie.JPG)
Both dicom files to be checked:
[DCT0363.dcm](/uploads/96dca8345bc97e1f8190b17c0839...Component type is set to int instead of short. Min max are invalid.
![Przechwytywanie](/uploads/0b0e7634c5ff91cf1809414e659583ee/Przechwytywanie.JPG)
Both dicom files to be checked:
[DCT0363.dcm](/uploads/96dca8345bc97e1f8190b17c08397c19/DCT0363.dcm)
[20190605_UKSW_xy0484.dcm](/uploads/d4abb3ea1cfa736633b0d7a0647abe64/20190605_UKSW_xy0484.dcm)Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/138CUDA anisotropic denoiser on large fields2020-05-19T10:03:28ZKrzysztof NowinskiCUDA anisotropic denoiser on large fieldsCUDA anisotropic denoiser requires 3*sizeof(float)*nNodes in CUDA memory for input, anisotropy field and output. In effect, fields of the size over graphic memory size/12 cannot be denoised by CUDA(Aniso denoiser fails silently)CUDA anisotropic denoiser requires 3*sizeof(float)*nNodes in CUDA memory for input, anisotropy field and output. In effect, fields of the size over graphic memory size/12 cannot be denoised by CUDA(Aniso denoiser fails silently)https://gitlab.com/visnow.org/VisNow/-/issues/142open menus error with no current application2019-08-02T09:38:43ZBartosz Boruckibabor@icm.edu.plopen menus error with no current applicationWhile using open menus (file->open test data / file->open data file) while there's no valid application/tab active (e.g. while start page is active, or no applications are open) there's an exception on getCurrentApplication returning nul...While using open menus (file->open test data / file->open data file) while there's no valid application/tab active (e.g. while start page is active, or no applications are open) there's an exception on getCurrentApplication returning null.
https://gitlab.com/ICM-VisLab/VisNow/merge_requests/122#note_197618680Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/144Generalize frames support as time/dimension/component choice in DICOM reader2019-08-09T09:53:51ZBartosz Boruckibabor@icm.edu.plGeneralize frames support as time/dimension/component choice in DICOM readerNow in DICOM reader the selection of how to treat dicom frames is limited to single slice/multiple frames with option to read frames as time or as 3rd dimension. For volumes frames are read as components.
This should be generalized and...Now in DICOM reader the selection of how to treat dicom frames is limited to single slice/multiple frames with option to read frames as time or as 3rd dimension. For volumes frames are read as components.
This should be generalized and moved to main module GUI. The choice should be - read frames as: time / dimension / components (time should be default, dimension only valid for 2D fields with fallback to time).Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/150Units in modify components/coordinates2019-08-27T09:59:18ZKrzysztof NowinskiUnits in modify components/coordinatesComponent operations do not pass units with vector norm/vector split/ vector combineComponent operations do not pass units with vector norm/vector split/ vector combinehttps://gitlab.com/visnow.org/VisNow/-/issues/152Presentation tab2020-11-20T11:40:35ZKerstin Kantiemkerstin.kantiem@gmail.comPresentation tabtest field -> viewer 3D
Take a new instance of test field. Choose 3D. The structure is regular. No extern faces is selected by default, but you are able to choose min/max i/j/k. Probably this always was in this way, however, when select...test field -> viewer 3D
Take a new instance of test field. Choose 3D. The structure is regular. No extern faces is selected by default, but you are able to choose min/max i/j/k. Probably this always was in this way, however, when selecting some face it would be better when selected faces would appear.
Select some face. Change to inside of box. That is ok.
Change to selected faces - there is no face, however earlier we selected a face and in the menu it is still selected. Ones again choose inside of box. That is ok. Now select again selected faces - we see the box from outside. Sometimes the outside box appears immediately. I don't see the rule for it.https://gitlab.com/visnow.org/VisNow/-/issues/155Component calculator documentation is outdated2019-11-09T00:29:34ZBartosz Boruckibabor@icm.edu.plComponent calculator documentation is outdatedAfter modifying component calculator GUI the documentation needs to be updated.After modifying component calculator GUI the documentation needs to be updated.Kerstin Kantiemkerstin.kantiem@gmail.comKerstin Kantiemkerstin.kantiem@gmail.comhttps://gitlab.com/visnow.org/VisNow/-/issues/160Read Image geometry table annoyance2020-01-03T19:34:34ZKrzysztof NowinskiRead Image geometry table annoyanceAdding units or modifying geometry in the Read Image module:
select x coordinate unit, write e.g. mm in the table cell, hit enter (routine method of accepting change in the cell and proceed to the cell below.) Result is unexpected: re-re...Adding units or modifying geometry in the Read Image module:
select x coordinate unit, write e.g. mm in the table cell, hit enter (routine method of accepting change in the cell and proceed to the cell below.) Result is unexpected: re-read without units, edited cell is reset to default "1"https://gitlab.com/visnow.org/VisNow/-/issues/165planar slice2020-03-17T13:59:57ZKerstin Kantiemkerstin.kantiem@gmail.complanar sliceVTK file reader -> planar slice -> viewer 3D
Read the file hemispheric_white_matter.vtk.vtk.vtk in /home/kerstin/workspace/Kerstin-Kantiem/Dokumenty/Data/DICOM_Slicer/dataset2_Head/MRHead_Scene/Data. In planar slice press 'add slice are...VTK file reader -> planar slice -> viewer 3D
Read the file hemispheric_white_matter.vtk.vtk.vtk in /home/kerstin/workspace/Kerstin-Kantiem/Dokumenty/Data/DICOM_Slicer/dataset2_Head/MRHead_Scene/Data. In planar slice press 'add slice area'.
14:30:22,680 WT-EventQueue-1 ERROR sNowExceptionHandler.uncaughtException 1516: Uncaught exception occurred in thread Thread[AWT-EventQueue-1,6,main]
java.lang.NullPointerException
at pl.edu.icm.visnow.lib.utils.slicing.SliceDisplay.updateImage(SliceDisplay.java:406)
at pl.edu.icm.visnow.lib.utils.slicing.SliceDisplay.<init>(SliceDisplay.java:145)
at pl.edu.icm.visnow.lib.utils.slicing.MultiSliceDisplay.addDisplay(MultiSliceDisplay.java:89)
at pl.edu.icm.visnow.lib.basic.mappers.PlanarSlice.PlanarSlice$5.parameterChanged(PlanarSlice.java:187)
at pl.edu.icm.visnow.engine.core.Parameters.fireParameterChanged(Parameters.java:503)
at pl.edu.icm.visnow.engine.core.Parameters.set(Parameters.java:207)
at pl.edu.icm.visnow.engine.core.Parameters.set(Parameters.java:131)
at pl.edu.icm.visnow.lib.basic.mappers.PlanarSlice.GUI.addAreaButtonActionPerformed(GUI.java:544)
at pl.edu.icm.visnow.lib.basic.mappers.PlanarSlice.GUI.access$200(GUI.java:47)
at pl.edu.icm.visnow.lib.basic.mappers.PlanarSlice.GUI$3.actionPerformed(GUI.java:158)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6539)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
at java.awt.Component.processEvent(Component.java:6304)
at java.awt.Container.processEvent(Container.java:2239)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2297)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
at java.awt.Container.dispatchEventImpl(Container.java:2283)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
at java.awt.EventQueue$4.run(EventQueue.java:733)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
at org.GNOME.Accessibility.AtkWrapper$6.dispatchEvent(AtkWrapper.java:715)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)https://gitlab.com/visnow.org/VisNow/-/issues/166vtk file reader2020-03-17T13:44:36ZKerstin Kantiemkerstin.kantiem@gmail.comvtk file readerRead the file hemispheric_white_matter.vtk.vtk.vtk from /home/kerstin/workspace/Kerstin-Kantiem/Dokumenty/Data/DICOM_Slicer/dataset2_Head/MRHead_Scene/Data.
There appears the comment:
13:39:50,985 file reader[1] ERROR vtk.VTKNative...Read the file hemispheric_white_matter.vtk.vtk.vtk from /home/kerstin/workspace/Kerstin-Kantiem/Dokumenty/Data/DICOM_Slicer/dataset2_Head/MRHead_Scene/Data.
There appears the comment:
13:39:50,985 file reader[1] ERROR vtk.VTKNativeCore.LoadCells 298: VTK cell type 6 not supported, trying to triangulate...https://gitlab.com/visnow.org/VisNow/-/issues/171gl version issues2020-05-05T10:28:41ZKrzysztof Nowinskigl version issuesOn Ubuntu 20.04 LTS nVidia/Intel graphics switchable:
on nVidia
[trace1](/uploads/852278a042efd9bfd16f47d82773ad39/trace1)
on Intel
[trace2](/uploads/5052955b09feaad25d5c28f34ed56eb9/trace2)On Ubuntu 20.04 LTS nVidia/Intel graphics switchable:
on nVidia
[trace1](/uploads/852278a042efd9bfd16f47d82773ad39/trace1)
on Intel
[trace2](/uploads/5052955b09feaad25d5c28f34ed56eb9/trace2)