The same issues are observed for singe tensor tracts

I tracked this issue to the change in the vtkMRMLModelDisplayableManager made by Nicole:
http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Libs/MRML/DisplayableManager/vtkMRMLModelDisplayableManager.cxx?r1=23021&r2=23083

Nicole, your change in vtkMRMLModelDisplayableManager broke the coloring of fibers, see note 0000001 from Lauren above.

I'll look into issues 0000001 and 0000004.
Lauren: do you have a sample data set that you can attach to this bug?

Nicole, you can see the coloring issue on any fiber data 1 or 2 tensors (I uploaded a small 1-tensor dataset). If you switch between different tensor properties the color stays red. If you revert your change the colors are correct.
I will upload a 2-tensor data that has this issue when you switch between tensor and scalar property.

Having trouble reproducing various issues:

• loading both .vtk files into Slicer via Add Data, each only has one display node, they were loaded as Model nodes (they're not showing up in the Tractography Display module)
• in the Models module, 2_fibers only has one scalar overlay, 'tensors'
• Models module: glyphs_orig has 1, 2, norm, FA, FA2 and switching between them with the default Data scalar range setting seems to be working correctly.

What steps am I missing?

Nicole you have to load them as fiber bundles.

And go to tractography display under diffusion.

Thanks! Got it now. I don't work with the Slicer tractography functions very much.

This check in should fix the first issue, I checked for fiber bundle display nodes and if present used the old system:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23118

For the fourth issue, where is the scalar range not updating? I see it updating in the Models, Display, Scalars, Active Scalar Range label.

This bug report only refers to issues in tractography display. No one uses models display for tracts. Hope this helps.

For the scalar range update problem, are you referring to the Auto W/L section of the advanced display in the tractography display? If not, can you tell me where you're not seeing it update?

If you switch back and forth what is displayed (for example FA then something from the scalars in the vtk file) the W/L and the scalar display will do random strange things. At times only all-red tracts will be displayed. Just try displaying all the options and switching between them for a bit.

After my check in, Julien's update for VTK6 and his fix of breaking my fix, I can't reproduce the all red tracts despite trying all the different scalars, and flipping between them and
My sense is that this is now a tractography display problem, the scalar ranges are updating properly when I double checked in the Models module, but I don't know how the W/L is calculated in the tractography display gui. I can see that it's not recalculating W/L when I switch the scalar value drop down. There may be a missing observation or pipeline update, but Alex would be the best person to check into it now.

It seems that the major regression has been fixed. I still see problems:
Issue 1. "color by scalar" not updating fiber colors when changing the scalar
Issue 3. Eigenvectors The major and middle eigenvectors are parallel, also their scaling is incorrect. The minor one, it’s not clear if it is correct but it might be. For UKF, the second and third eigenvalues are forced equal, so the scaling of the medium and minor eigenvectors should be the same. This is reproducible in Slicer 4.2 and looks like an old bug.

Fixed Issue 3 above.
At revision: 23147

Nicole, back to you with issue 1 above. It has to do with displaying scalars.
If you load glyphs_orig.vtk as fibers, go to Models module, check "Include Fibers" box, you should see the scalars in the GUI there. Changing between scalars has no effect on display.

Debugging this, wrote some python code to inspect the scalars/chart the arrays:

g = getNode('glyphs_orig')
numDisp = g.GetNumberOfDisplayNodes()
for n in range(numDisp):
disp = g.GetNthDisplayNode(n)
print n,': scalar visib =',disp.GetScalarVisibility(),', active scalar = ',disp.GetActiveScalarName(), ', active tensor = ',disp.GetActiveTensorName()

pd = g.GetPolyData()
ptdata = pd.GetPointData()
numArrays = ptdata.GetNumberOfArrays()
for n in range(numArrays):
ar = ptdata.GetArray(n)
print n,' range = ',ar.GetRange()
dn = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
dn.SetName(ar.GetName())
dna = dn.GetArray()
numTuples = ar.GetNumberOfTuples()
dna.SetNumberOfTuples(numTuples)
for i in range(numTuples):
dna.SetComponent(i, 0, float(i))
dna.SetComponent(i, 1, ar.GetTuple(i)[0])
dna.SetComponent(i, 2, 0.0)

Looks like the problem is in the UpdatePolyDataPipeline method of vtkMRMLFiberBundleDisplayNode and subclasses:

• vtkMRMLFiberBundleDisplayNode doesn't call
  this->Superclass::UpdatePolyDataPipeline();
  which is where the scalar range is being updated on the display node (more testing needed, might not be necessary)
• all the subclasses have very similar UpdatePolyDataPipeline in that they all make this call:
  this->GetInputPolyData()->GetScalarRange(range);
  instead of:
  range = this->GetOutputPolyData()->GetPointData()->GetArray(this->GetActiveScalarName())->GetRange()
  The scalar range on the poly data doesn't seem to change as the active scalar array changes, so it was getting set once and not reset to the proper value. This led to the scalar range on the display node not updating, and the model displayable manager is using that for the fiber bundles as per my last change to try and fix this. I'm not sure why nothing was changing in the 3d viewer, but with this change, it seems to work.

I'll have to make changes to the three subclasses to fix the scalar range calculation. Will post a github link for review.

Also: I get an assert crash when flipping between various scalar options:

ASSERT: "d->equal(d->Slider->minimumValue(), d->MinimumSpinBox->value())" in file /Users/nicole/Slicer4-svn/Slicer-build-debug/CTK/Libs/Widgets/ctkRangeWidget.cpp, line 312

Load glyphs_orig.vtk as a fiber bundle
Tractography Display
Advanced display
Tubes visible
Of Scalar Value (default is FA2)
Change of scalar value to norm
Change of scalar value to 1

Partial stack trace:
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 libsystem_kernel.dylib 0x00007fff8e308212 __pthread_kill + 10
1 libsystem_c.dylib 0x00007fff8f7b6b54 pthread_kill + 90
2 libsystem_c.dylib 0x00007fff8f7fadce abort + 143
3 QtCore 0x00000001198249c5 qt_message_output(QtMsgType, char const) + 117
4 QtCore 0x0000000119824ba7 qt_message(QtMsgType, char const, __va_list_tag) + 183
5 QtCore 0x0000000119824d6a qFatal(char const, ...) + 170
6 libCTKWidgets.0.1.dylib 0x000000010f087f44 ctkRangeWidget::setRange(double, double) + 788 (ctkRangeWidget.cpp:312)
7 libqMRMLWidgets.dylib 0x000000010e9e7e27 qMRMLRangeWidget::updateRange() + 87 (qMRMLRangeWidget.cxx:136)
8 libqMRMLWidgets.dylib 0x000000010e9e7dbc qMRMLRangeWidget::updateSpinBoxRange(double, double) + 172 (qMRMLRangeWidget.cxx:129)
9 libqMRMLWidgets.dylib 0x000000010ea642b2 qMRMLRangeWidget::qt_metacall(QMetaObject::Call, int, void) + 274 (moc_qMRMLRangeWidget.cxx:98)
10 QtCore 0x000000011987ae26 QMetaObject::activate(QObject, QMetaObject const, int, void) + 710
11 libCTKWidgets.0.1.dylib 0x000000010f0db6c5 ctkDoubleRangeSlider::rangeChanged(double, double) + 85 (moc_ctkDoubleRangeSlider.cxx:275)
12 libCTKWidgets.0.1.dylib 0x000000010f021e7a ctkDoubleRangeSlider::setRange(double, double) + 634 (ctkDoubleRangeSlider.cpp:341)
13 libCTKWidgets.0.1.dylib 0x000000010f087dc3 ctkRangeWidget::setRange(double, double) + 403 (ctkRangeWidget.cpp:309)
14 libqSlicerTractographyDisplayModuleWidgets.dylib 0x00000001338bd5af qSlicerTractographyDisplayWidget::updateScalarRange() + 351 (qSlicerTractographyDisplayWidget.cxx:661)
15 libqSlicerTractographyDisplayModuleWidgets.dylib 0x00000001338bc8f5 qSlicerTractographyDisplayWidget::updateWidgetFromMRML() + 2821 (qSlicerTractographyDisplayWidget.cxx:790)
16 libqSlicerTractographyDisplayModuleWidgets.dylib 0x00000001338c3bcb qSlicerTractographyDisplayWidget::qt_metacall(QMetaObject::Call, int, void) + 795 (moc_qSlicerTractographyDisplayWidget.cxx:148)
17 QtCore 0x000000011987ae26 QMetaObject::activate(QObject, QMetaObject const, int, void) + 710
18 libCTKVisualizationVTKCore.0.1.dylib 0x0000000112339f1d ctkVTKConnection::emitExecute(vtkObject, void, unsigned long, void) + 125 (moc_ctkVTKConnection.cxx:106)
19 libCTKVisualizationVTKCore.0.1.dylib 0x0000000112322603 ctkVTKConnectionPrivate::execute(vtkObject, unsigned long, void, void) + 915 (ctkVTKConnection.cpp:409)
20 libCTKVisualizationVTKCore.0.1.dylib 0x0000000112320759 ctkVTKConnectionPrivate::DoCallback(vtkObject, unsigned long, void, void) + 105 (ctkVTKConnection.cpp:369)
21 libvtkCommon.5.10.dylib 0x0000000125825a94 vtkCallbackCommand::Execute(vtkObject, unsigned long, void) + 84 (vtkCallbackCommand.cxx:43)
22 libMRMLCore.dylib 0x00000001156e5dcf vtkEventBroker::InvokeObservation(vtkObservation, unsigned long, void) + 255 (vtkEventBroker.cxx:842)
23 libMRMLCore.dylib 0x00000001156e563c vtkEventBroker::ProcessEvent(vtkObservation, vtkObject, unsigned long, void) + 188 (vtkEventBroker.cxx:688)
24 libMRMLCore.dylib 0x00000001156e672b vtkEventBroker::Callback(vtkObject, unsigned long, void, void) + 507 (vtkEventBroker.cxx:914)
25 libvtkCommon.5.10.dylib 0x0000000125825a94 vtkCallbackCommand::Execute(vtkObject, unsigned long, void) + 84 (vtkCallbackCommand.cxx:43)
26 libvtkCommon.5.10.dylib 0x000000012593143c vtkSubjectHelper::InvokeEvent(unsigned long, void, vtkObject) + 2460 (vtkObject.cxx:620)
27 libvtkCommon.5.10.dylib 0x00000001259319e2 vtkObject::InvokeEvent(unsigned long, void) + 66 (vtkObject.cxx:789)
28 libvtkCommon.5.10.dylib 0x0000000125931bc2 vtkObject::Modified() + 66 (vtkObject.cxx:856)
29 libMRMLCLI.dylib 0x00000001155fc463 vtkMRMLNode::InvokePendingModifiedEvent() + 67 (vtkMRMLNode.h:381)
30 libMRMLCLI.dylib 0x00000001155f826c vtkMRMLNode::EndModify(int) + 60 (vtkMRMLNode.h:228)
31 libMRMLCore.dylib 0x00000001157b14f9 vtkMRMLModelDisplayNode::SetActiveScalarName(char const*) + 121 (vtkMRMLModelDisplayNode.cxx:154)
32 libqSlicerTractographyDisplayModuleWidgets.dylib 0x00000001338bd24f qSlicerTractographyDisplayWidget::onColorByScalarChanged(int) + 271 (qSlicerTractographyDisplayWidget.cxx:369)
33 libqSlicerTractographyDisplayModuleWidgets.dylib 0x00000001338c3a12 qSlicerTractographyDisplayWidget::qt_metacall(QMetaObject::Call, int, void) + 354 (moc_qSlicerTractographyDisplayWidget.cxx:130)
34 QtCore 0x000000011987ae26 QMetaObject::activate(QObject, QMetaObject const, int, void) + 710
35 QtGui 0x0000000118f5c1f0 QComboBox::currentIndexChanged(int) + 48
36 QtGui 0x0000000118f5dbcc QComboBoxPrivate::_q_emitCurrentIndexChanged(QModelIndex const&) + 44
37 QtGui 0x0000000118f6085e QComboBoxPrivate::setCurrentIndex(QModelIndex const&) + 254
38 QtGui 0x0000000118f60c95 QComboBoxPrivate::_q_itemSelected(QModelIndex const&) + 69
39 QtGui 0x0000000118f659da QComboBox::qt_metacall(QMetaObject::Call, int, void) + 714
40 libCTKVisualizationVTKWidgets.0.1.dylib 0x000000010eede173 ctkVTKDataSetArrayComboBox::qt_metacall(QMetaObject::Call, int, void) + 51 (moc_ctkVTKDataSetArrayComboBox.cxx:99)

Please take a look at these changes and let me know if they make sense:

https://github.com/naucoin/Slicer/commit/068c624ac1fe1ffe0c881b006caf6bfc665f9535

Alex - please review and update the bug report.

Sorry, was traveling last week. Looks good to me.

Fix for the scalar range on the tracts checked in as svn 23324:
http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23324

I think that fixes all but the crash that I found, will make that another bug report and assign to Alex.

Closing resolved issues that have not been updated in more than 3 months.