VisNow issueshttps://gitlab.com/visnow.org/VisNow/-/issues2020-11-20T11:40:35Zhttps://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/151line probe2020-11-20T12:15:31ZKerstin Kantiemkerstin.kantiem@gmail.comline probe(develop)
test field -> line probe -> viewer 3D
Choose 3D.
Add a probe.
Try to choose a different graph component.
The same in 2D.
11:21:09,417 WT-EventQueue-1 ERROR sNowExceptionHandler.uncaughtException 1526: Uncaught exceptio...(develop)
test field -> line probe -> viewer 3D
Choose 3D.
Add a probe.
Try to choose a different graph component.
The same in 2D.
11:21:09,417 WT-EventQueue-1 ERROR sNowExceptionHandler.uncaughtException 1526: Uncaught exception occurred in thread Thread[AWT-EventQueue-1,6,main]
java.lang.NullPointerException
at pl.edu.icm.visnow.lib.utils.graphing.ComponentDisplayController$ComponentRenderer.getTableCellRendererComponent(ComponentDisplayController.java:125)
at javax.swing.JTable$AccessibleJTable.getAccessibleChild(JTable.java:7037)
at javax.swing.JTable$AccessibleJTable.getAccessibleAt(JTable.java:7424)
at javax.swing.JTable$AccessibleJTable.valueChanged(JTable.java:6939)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:164)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:211)
at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:405)
at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:415)
at javax.swing.DefaultListSelectionModel.setSelectionInterval(DefaultListSelectionModel.java:459)
at javax.swing.JTable.changeSelectionModel(JTable.java:2392)
at javax.swing.JTable.changeSelection(JTable.java:2459)
at javax.swing.plaf.basic.BasicTableUI$Handler.adjustSelection(BasicTableUI.java:1115)
at javax.swing.plaf.basic.BasicTableUI$Handler.mousePressed(BasicTableUI.java:1038)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280)
at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:279)
at java.awt.Component.processMouseEvent(Component.java:6536)
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:4532)
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$6.dispatchEvent(AtkWrapper.java:715)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
11:21:09,454 WT-EventQueue-1 ERROR sNowExceptionHandler.uncaughtException 1526: Uncaught exception occurred in thread Thread[AWT-EventQueue-1,6,main]
java.lang.NullPointerException
at pl.edu.icm.visnow.lib.utils.graphing.ComponentDisplayController$ComponentRenderer.getTableCellRendererComponent(ComponentDisplayController.java:125)
at javax.swing.JTable$AccessibleJTable.getAccessibleChild(JTable.java:7037)
at javax.swing.JTable$AccessibleJTable.getAccessibleAt(JTable.java:7424)
at javax.swing.JTable$AccessibleJTable.valueChanged(JTable.java:6939)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184)
at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:154)
at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:685)
at javax.swing.plaf.basic.BasicTableUI$Handler.setValueIsAdjusting(BasicTableUI.java:955)
at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1166)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
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/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/149Stationary flow visualization issues2021-05-18T09:03:39ZBartosz Boruckibabor@icm.edu.plStationary flow visualization issues1) In "planar slice" mode stationary flow visualization doesn't work on some fields - no streamlines are generated.
On test field + vortex all is fine, while on MRI flow field (/workspace2/tetniak_przeplywy/przeplywy/philips_flow_cropped...1) In "planar slice" mode stationary flow visualization doesn't work on some fields - no streamlines are generated.
On test field + vortex all is fine, while on MRI flow field (/workspace2/tetniak_przeplywy/przeplywy/philips_flow_cropped.vns) it does not work.
2) Why planar slice size/crop resets on every rotate? Bug or feature. It is quite annoying when you already have a good positioning and jus need to slightly correct the rotation.
3) In "plane" mode and "line" mode changing of axis causes disabling of axis settings GUI
4) Legend - is visible by default while legend checkbox is off, checkbox toggle does not repaint viewer.Krzysztof NowinskiKrzysztof Nowinskihttps://gitlab.com/visnow.org/VisNow/-/issues/148Lack of units in component calculator for subcomponents of a vector component2019-09-03T11:40:16ZBartosz Boruckibabor@icm.edu.plLack of units in component calculator for subcomponents of a vector componentUnits are ignored when sub-components of a vector component are used - e.g. momentum.0.
To reproduce load bluntfin.vnf from sample data connect to calculator and run command "out = momentum.0".
This does not influence coords (e.g. coords...Units are ignored when sub-components of a vector component are used - e.g. momentum.0.
To reproduce load bluntfin.vnf from sample data connect to calculator and run command "out = momentum.0".
This does not influence coords (e.g. coords.0 or x variables).Piotr WendykierPiotr Wendykierhttps://gitlab.com/visnow.org/VisNow/-/issues/147Stationary flow visualization module ignores current time2019-08-14T09:35:32ZJedrzej M NowosielskiStationary flow visualization module ignores current time![Screenshot_from_2019-08-13_14-47-52](/uploads/f1cf36f32ccbbd9987f71c1322c1d0b3/Screenshot_from_2019-08-13_14-47-52.png)![Screenshot_from_2019-08-13_14-47-52](/uploads/f1cf36f32ccbbd9987f71c1322c1d0b3/Screenshot_from_2019-08-13_14-47-52.png)https://gitlab.com/visnow.org/VisNow/-/issues/146Add unit support to axes 3D2019-09-08T19:40:11ZBartosz Boruckibabor@icm.edu.plAdd unit support to axes 3DAxes 3D should show units in axes if CoordsUnits are set in the field.Axes 3D should show units in axes if CoordsUnits are set in the field.Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/145Physical and geometric extents in DICOM reader2019-08-19T10:21:22ZJedrzej M NowosielskiPhysical and geometric extents in DICOM reader1. Unclear relation between physical and geometric extents in regular field produced by DICOM reader.
2. Changing unit in DICOM reader results in changing only geometric extents, physical extents remain the same.
Example of achilles ten...1. Unclear relation between physical and geometric extents in regular field produced by DICOM reader.
2. Changing unit in DICOM reader results in changing only geometric extents, physical extents remain the same.
Example of achilles tendon MRI is attached![Screenshot_from_2019-08-09_17-01-09](/uploads/ea5b0541fc99d346a3db19fc74ae1f38/Screenshot_from_2019-08-09_17-01-09.png)Bartosz 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/143DICOM reader fails for images with reversed orientation vector2019-08-13T14:54:30ZBartosz Boruckibabor@icm.edu.plDICOM reader fails for images with reversed orientation vectorFor some specific cases where the image orientation vector is reversed, a reversed ordering of extents is computed causing exception on field extents setting.
```
11:14:33,598 DICOM reader[1] ERROR main.ModuleElement.killFromModule ...For some specific cases where the image orientation vector is reversed, a reversed ordering of extents is computed causing exception on field extents setting.
```
11:14:33,598 DICOM reader[1] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onLocalActive
java.lang.IllegalArgumentException: end1 < start1 || end2 < start2
at pl.edu.icm.jscic.utils.ScalarMath.linearMappingCoefficients(ScalarMath.java:195)
at pl.edu.icm.jscic.FieldSchema.setPreferredExtents(FieldSchema.java:252)
at pl.edu.icm.jscic.Field.setPreferredExtents(Field.java:433)
at pl.edu.icm.visnow.lib.basic.readers.medreaders.ReadDICOM.ReadDICOMCore.readSingleDicomFile(ReadDICOMCore.java:692)
at pl.edu.icm.visnow.lib.basic.readers.medreaders.ReadDICOM.ReadDICOMCore.readDicomFromFileList(ReadDICOMCore.java:489)
at pl.edu.icm.visnow.lib.basic.readers.medreaders.ReadDICOM.ReadDICOMCore.update(ReadDICOMCore.java:112)
at pl.edu.icm.visnow.lib.basic.readers.medreaders.ReadDICOM.ReadDICOM.onActive(ReadDICOM.java:138)
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)
11:14:33,599 DICOM reader[1] WARN main.ModuleElement.setActive 331: java.lang.IllegalArgumentException: end1 < start1 || end2 < start2
```
Use the attached DCM file to reproduce (WARNING! Rotate viewer to see something as the image plane is perpendicular to screen :))
[MR-MONO2-16-knee](/uploads/08cd618a7960ca7b2f482989781e1b91/MR-MONO2-16-knee)Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://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/141regular field slice crashes for truly large fields2019-08-02T09:39:23ZBartosz Boruckibabor@icm.edu.plregular field slice crashes for truly large fieldsFor truly large 3D regular fields (nNodes > 2147483647) regular field slice produces an empty field (no components) and crashes with exception:
`regular field slice[2] ERROR main.ModuleElement.killFromModule 476: An error occ...For truly large 3D regular fields (nNodes > 2147483647) regular field slice produces an empty field (no components) and crashes with exception:
`regular field slice[2] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onActive
java.lang.IllegalArgumentException: Fields without components are not supported!
INTERRUPTED while loading Image
at pl.edu.icm.visnow.lib.types.VNField.<init>(VNField.java:60)
at pl.edu.icm.visnow.lib.types.VNRegularField.<init>(VNRegularField.java:54)
at pl.edu.icm.visnow.lib.basic.mappers.RegularFieldSlice.RegularFieldSlice.onActive(RegularFieldSlice.java:189)
at pl.edu.icm.visnow.engine.main.ModuleElement.setActive(ModuleElement.java:336)
at pl.edu.icm.visnow.engine.main.ModuleElement.onActionMessage(ModuleElement.java:283)
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)
16:22:10,104 field slice[2] WARN main.ModuleElement.setActive 340: java.lang.IllegalArgumentException: Fields without components are not supported!
`
To recreate - create any truly large 3D field (e.g. test regular field 3D with size set to 1500), connect to regular field slice.
Reason: SliceRegularField line 127 is casting nNodes to int causing overflow.Bartosz Boruckibabor@icm.edu.plBartosz Boruckibabor@icm.edu.plhttps://gitlab.com/visnow.org/VisNow/-/issues/140Exception in crop/downsize regular field2019-08-02T08:45:43ZPiotr WendykierException in crop/downsize regular field`
java.lang.IllegalArgumentException: tData == null || tData.isEmpty() || tData.getType() != timeData.getType() || tData.length() != getNElements() * getVectorLength()
at pl.edu.icm.jscic.dataarrays.DataArray.setTimeData(DataArray.java:...`
java.lang.IllegalArgumentException: tData == null || tData.isEmpty() || tData.getType() != timeData.getType() || tData.length() != getNElements() * getVectorLength()
at pl.edu.icm.jscic.dataarrays.DataArray.setTimeData(DataArray.java:2149)
at pl.edu.icm.visnow.lib.utils.field.subset.FieldSample.regularSample(FieldSample.java:226)
at pl.edu.icm.visnow.lib.basic.filters.CropDown.CropDown.onActive(CropDown.java:226)
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)
`
It happens when one tries to downsample (by 2 in each direction) the following field:
![image](/uploads/feff67d9ca3367dcd4ff78f7408359f3/image.png)
Zipped vns file is available at https://office365uksw-my.sharepoint.com/:f:/g/personal/p_wendykier_uksw_edu_pl/EkpNdwOtuEVFoU16PMEh8SwBCWlNV9jo6FEGnEtBN1SgHA?e=vfgawXPiotr WendykierPiotr Wendykierhttps://gitlab.com/visnow.org/VisNow/-/issues/139Image reader does not support large datasets2019-11-04T14:35:08ZPiotr WendykierImage reader does not support large datasetsHere is the line where the overflow can occur: https://gitlab.com/ICM-VisLab/VisNow/blob/develop/src/pl/edu/icm/visnow/lib/utils/ImageUtils.java#L1361Here is the line where the overflow can occur: https://gitlab.com/ICM-VisLab/VisNow/blob/develop/src/pl/edu/icm/visnow/lib/utils/ImageUtils.java#L1361Piotr WendykierPiotr Wendykierhttps://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/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/136Cannot save VisNow's network2019-06-27T11:12:29ZPiotr RegulskiCannot save VisNow's networkOn save .vna an error occurs:
java.lang.NoClassDefFoundError: org/xmlpull/v1/XmlPullParserException
at com.thoughtworks.xstream.XStream.<init>(XStream.java:369)
at pl.edu.icm.visnow.engine.core.Parameters.writeXML(Parameters.java:232)
...On save .vna an error occurs:
java.lang.NoClassDefFoundError: org/xmlpull/v1/XmlPullParserException
at com.thoughtworks.xstream.XStream.<init>(XStream.java:369)
at pl.edu.icm.visnow.engine.core.Parameters.writeXML(Parameters.java:232)
at pl.edu.icm.visnow.application.io.VNWriter.writeModule(VNWriter.java:162)
at pl.edu.icm.visnow.application.io.VNWriter.tryWriteApplication(VNWriter.java:121)
at pl.edu.icm.visnow.application.io.VNWriter.writeApplication(VNWriter.java:80)
at pl.edu.icm.visnow.application.application.Application.betaSaveAs(Application.java:348)
at pl.edu.icm.visnow.system.framework.MainMenu.betaSave(MainMenu.java:319)
at pl.edu.icm.visnow.system.framework.MainWindow.jMenuItem2ActionPerformed(MainWindow.java:828)
at pl.edu.icm.visnow.system.framework.MainWindow.access$1000(MainWindow.java:67)
at pl.edu.icm.visnow.system.framework.MainWindow$11.actionPerformed(MainWindow.java:416)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
at javax.swing.AbstractButton.doClick(AbstractButton.java:356)
at javax.swing.plaf.basic.BasicMenuItemUI$Actions.actionPerformed(BasicMenuItemUI.java:802)
at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1663)
at javax.swing.JComponent.processKeyBinding(JComponent.java:2882)
at javax.swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:699)
at javax.swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:706)
at javax.swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:706)
at javax.swing.JMenuBar.processKeyBinding(JMenuBar.java:677)
at javax.swing.KeyboardManager.fireBinding(KeyboardManager.java:307)
at javax.swing.KeyboardManager.fireKeyboardAction(KeyboardManager.java:293)
at javax.swing.JComponent.processKeyBindingsForAllComponents(JComponent.java:2974)
at javax.swing.JComponent.processKeyBindings(JComponent.java:2966)
at javax.swing.JComponent.processKeyEvent(JComponent.java:2845)
at java.awt.Component.processEvent(Component.java:6310)
at java.awt.Container.processEvent(Container.java:2236)
at java.awt.Component.dispatchEventImpl(Component.java:4889)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954)
at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(DefaultKeyboardFocusManager.java:806)
at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(DefaultKeyboardFocusManager.java:1074)
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:945)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:771)
at java.awt.Component.dispatchEventImpl(Component.java:4760)
at java.awt.Container.dispatchEventImpl(Container.java:2294)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4711)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
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:76)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:731)
at java.awt.EventQueue$4.run(EventQueue.java:729)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
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)
Caused by: java.lang.ClassNotFoundException: org.xmlpull.v1.XmlPullParserException
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 60 morePiotr WendykierPiotr Wendykierhttps://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/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/133flow visualization exception on 2D room.cas dataset2020-01-03T21:25:44ZBartosz Boruckibabor@icm.edu.plflow visualization exception on 2D room.cas datasetRead the attached dataset (room). Connect to flow visualization.
`
14:09:10,325 isualization[2] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onLocalActive
java.lang.ArrayIndexOutOfBoundsException...Read the attached dataset (room). Connect to flow visualization.
`
14:09:10,325 isualization[2] ERROR main.ModuleElement.killFromModule 476: An error occured in function: onLocalActive
java.lang.ArrayIndexOutOfBoundsException: 4
at pl.edu.icm.jscic.IrregularField.getFieldCoords(IrregularField.java:781)
at pl.edu.icm.visnow.lib.utils.pointProbe.GeometricPointProbe.probePosition(GeometricPointProbe.java:96)
at pl.edu.icm.visnow.lib.utils.pointProbe.GeometricPointProbe.updateProbe(GeometricPointProbe.java:108)
at pl.edu.icm.visnow.lib.utils.pointProbe.GeometricPointProbe$1.parameterChanged(GeometricPointProbe.java:63)
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.geometries.interactiveGlyphs.InteractiveGlyphParams.setCoords(InteractiveGlyphParams.java:239)
at pl.edu.icm.visnow.geometries.interactiveGlyphs.InteractiveGlyph.setField(InteractiveGlyph.java:224)
at pl.edu.icm.visnow.lib.utils.pointProbe.GeometricPointProbe.setInData(GeometricPointProbe.java:128)
at pl.edu.icm.visnow.lib.utils.flowVisualizationUtils.SeedPoints.setCurrentRawSeedField(SeedPoints.java:372)
at pl.edu.icm.visnow.lib.utils.flowVisualizationUtils.SeedPoints.setInField(SeedPoints.java:342)
at pl.edu.icm.visnow.lib.basic.mappers.FlowVisualization.FlowVisualization.onActive(FlowVisualization.java:488)
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)
`
[room.cas](/uploads/4b937dc6c380ba781e1c47158b0e2e8b/room.cas)
[room.dat](/uploads/daff41999db75fe7de25b6ef4d076a6c/room.dat)Krzysztof NowinskiKrzysztof Nowinski