Hello Paraviewers,
(sorry for this long email but I wanted to give some pieces of code and the
different things I tried before using the mailing list)
I have a 3D field of a vector and I would like to create different renderings
at different parts of it. So, I play with ExctractSubset, Programmable filters
and Calculators to build my viz. I do this with some python scripts and pvbatch.
Here is the pipeline I created:
XDMFReader
l
l--ExctractSubset1
l l---------------Calculator1--- Volume rendering
l--ExctractSubset2
l---------------Calculator2
l-------------Programable
filter---- Volume rendering
where I use ExctractSubset to cut my domain into two parts, Calculator to
compute the magnitude of its input and the Programmable filter to set the value
of some region of its input to zero (kind of mask for my VR).
I get the following message when I do the last Render() ( and then
WriteImage()):
ERROR: In
/home/ucl/tfl/sbackaer/local/build/ParaView/ParaViewCore/VTKExtensions/vtkKdTreeGenerator.cxx,
line 168
vtkKdTreeGenerator (0x1229df20): RegionIDs cannot be 0.
(one per core)
and then a Seg fault
_________________________________________________________________
[hmem02:60782] *** Process received signal ***
[hmem02:60782] Signal: Segmentation fault (11)
[hmem02:60782] Signal code: (128)
[hmem02:60782] Failing at address: (nil)
[hmem02:60782] [ 0] /lib64/libpthread.so.0() [0x3344e0f4c0]
[hmem02:60782] [ 1]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkVolumeRendering.so.pv3.12(_Z52vtkVolumeRayCastSpaceLeapingImageFilterMinMaxExecuteIfEvP39vtkVolumeRayCastSpaceLeapingImageFilterP12vtkImageDataS3_PiT_+0x693)
[0x7fde08a7712f]
[hmem02:60782] [ 2]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkVolumeRendering.so.pv3.12(_ZN39vtkVolumeRayCastSpaceLeapingImageFilter19ThreadedRequestDataEP14vtkInformationPP20vtkInformationVectorS3_PPP12vtkImageDataS7_Pii+0x2e7)
[0x7fde08a7030d]
[hmem02:60782] [ 3]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkFiltering.so.pv3.12(_Z40vtkThreadedImageAlgorithmThreadedExecutePv+0x3cb)
[0x7fde01db2b8b]
[hmem02:60782] [ 4]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkCommon.so.pv3.12(_ZN16vtkMultiThreader19SingleMethodExecuteEv+0x627)
[0x7fde010fcf77]
[hmem02:60782] [ 5]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkFiltering.so.pv3.12(_ZN25vtkThreadedImageAlgorithm11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x521)
[0x7fde01db30bb]
[hmem02:60782] [ 6]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkVolumeRendering.so.pv3.12(_ZN39vtkVolumeRayCastSpaceLeapingImageFilter11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x49)
[0x7fde08a714e3]
[hmem02:60782] [ 7]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkFiltering.so.pv3.12(_ZN17vtkImageAlgorithm14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x7b)
[0x7fde01bc2935]
...
____________________________________________________________
If I try to apply the volume rendering on the Calculator2 output instead of
Prog filter, but still with it in the pipe, everything works.
I checked that the programmable filter produces a correct output with
GetPointDataInformation(): in both cases, same object and correct values like
range, bounds, extents...
Here is the part of my code that should be the source of my problem: if I
change DataRepresentation6 = Show(pfilter) to DataRepresentation6 = Show(Ucalc)
and correct field name below, it works... (sub2 is the output of a
ExtractSubset)
=============================================================
...
Ucalc = Calculator(Input=sub2)
Ucalc.AttributeMode = 'point_data'
Ucalc.Function = 'mag(w)'
Ucalc.ResultArrayName = 'upper_norm'
Ucalc.UpdatePipeline()
di=Ucalc.GetDataInformation()
print di.GetExtent(), " --> ", di.GetBounds(), "(nb points= ",
di.GetNumberOfPoints(), "- Memory= ", di.GetMemorySize(),
")"pdi=di.GetPointDataInformation()
print pdi
print pdi.GetArrayInformation(0).GetName(), "mag range: ",
pdi.GetArrayInformation(0).GetComponentRange(-1)
print""
pfilter=ProgrammableFilter(Input=Ucalc)
pfilter.Script="""
pdi=self.GetInput()
upper_norm=pdi.GetPointData().GetArray(1)
pdo=self.GetOutput()
npt=pdo.GetNumberOfPoints()
new_w = vtk.vtkFloatArray()
new_w.SetName("new_upper_norm")
new_w.SetNumberOfComponents(1)
new_w.SetNumberOfTuples(npt)
pdo.GetPointData().AddArray(new_w)
for i in range(0, npt):
coord = pdo.GetPoint(i)
x, y, z = coord[:3]
r=math.sqrt(math.pow(x,2)+math.pow(y,2))
if (r>=55.0) and (y<0.0):
new_w.SetValue(i, 0.0)
else:
new_w.SetValue(i,upper_norm.GetValue(i))
"""
pfilter.UpdatePipeline()
di=pfilter.GetDataInformation()
print di.GetExtent(), " --> ", di.GetBounds(), "(nb points= ",
di.GetNumberOfPoints(), "- Memory= ", di.GetMemorySize(), ")"
pdi=di.GetPointDataInformation()
print pdi
print pdi.GetArrayInformation(0).GetName(), "mag range: ",
pdi.GetArrayInformation(0).GetComponentRange(-1)
print""
DataRepresentation6 = Show(pfilter)
a2_Result_PVLookupTable = GetLookupTableForArray( "new_upper_norm", 1,
NanColor=[0.25, 0.0, 0.0], RGBPoints=[0.0, 0.230, 0.299, 0.754, 1.0, 0.706,
0.016, 0.149], VectorMode='Magnitude', ColorSpace='Diverging',
ScalarRangeInitialized=1.0 )
DataRepresentation6.EdgeColor = [0.0, 0.0, 0.50000762951094835]
DataRepresentation6.ScalarOpacityFunction = CreatePiecewiseFunction(
Points=[0.0, 0.0, 2.9, 0.05, 3.0, 1.0] ) #divide x by 14
DataRepresentation6.ColorArrayName = 'new_upper_norm'
DataRepresentation6.ScalarOpacityUnitDistance = 1.0
DataRepresentation6.LookupTable = a2_Result_PVLookupTable
DataRepresentation6.Representation = 'Volume'
...
Render()
WriteImage...
=============================================================
I tried with another pipeline, same code, only different order/input:
XDMFReader
l---------------Calculator2
l-------------Programable filter---- Volume
rendering
with the code:
=============================================================
...
calc = Calculator(Input=field3D)
calc.AttributeMode = 'point_data'
calc.Function = 'mag(w)'
calc.ResultArrayName = 'norm'
calc.UpdatePipeline()
pfilter=ProgrammableFilter(Input=calc)
pfilter.Script="""
pdi=self.GetInput()
mag_w=pdi.GetPointData().GetArray(1)
pdo=self.GetOutput()
npt=pdo.GetNumberOfPoints()
new_w = vtk.vtkFloatArray()
new_w.SetName("new_norm")
new_w.SetNumberOfComponents(1)
new_w.SetNumberOfTuples(npt)
pdo.GetPointData().AddArray(new_w)
for i in range(0, npt):
coord = pdo.GetPoint(i)
x, y, z = coord[:3]
r=math.sqrt(math.pow(x,2)+math.pow(y,2))
if (r>=55.0) and (y>0.0):
new_w.SetValue(i, 0.0)
else:
new_w.SetValue(i,mag_w.GetValue(i))
"""
pfilter.UpdatePipeline()
a1_Result_PVLookupTable = GetLookupTableForArray( "new_norm", 1,
NanColor=[0.25, 0.0, 0.0], RGBPoints=[0.0, 0.230, 0.299, 0.754, 1.0, 0.706,
0.016, 0.149], VectorMode='Magnitude', ColorSpace='Diverging',
ScalarRangeInitialized=1.0 )
DataRepresentation5 = Show(pfilter)
DataRepresentation5.EdgeColor = [0.0, 0.0, 0.50000762951094835]
DataRepresentation5.ScalarOpacityFunction = CreatePiecewiseFunction(
Points=[0.0, 0.0, 4.0, 1.0] ) #divide x-scale by 3.0
DataRepresentation5.ColorArrayName = 'new_norm'
DataRepresentation5.ScalarOpacityUnitDistance = 1.0
DataRepresentation5.LookupTable = a1_Result_PVLookupTable
DataRepresentation5.Representation = 'Volume'
...
=============================================================
I get also (one per core)
ERROR: In
/home/ucl/tfl/sbackaer/local/build/ParaView/ParaViewCore/VTKExtensions/vtkKdTreeGenerator.cxx,
line 168
vtkKdTreeGenerator (0x145ea500): RegionIDs cannot be 0.
and
_______________________________________________________________
[hmem02:61777] *** Process received signal ***
[hmem02:61777] Signal: Segmentation fault (11)
[hmem02:61777] Signal code: (128)
[hmem02:61777] Failing at address: (nil)
[hmem02:61776] *** Process received signal ***
[hmem02:61776] Signal: Segmentation fault (11)
[hmem02:61776] Signal code: (128)
[hmem02:61776] Failing at address: (nil)
[hmem02:61780] *** Process received signal ***
[hmem02:61780] Signal: Segmentation fault (11)
[hmem02:61780] Signal code: (128)
[hmem02:61780] Failing at address: (nil)
[hmem02:61778] *** Process received signal ***
[hmem02:61775] *** Process received signal ***
[hmem02:61775] Signal: Segmentation fault (11)
[hmem02:61775] Signal code: (128)
[hmem02:61775] Failing at address: (nil)
[hmem02:61778] Signal: Segmentation fault (11)
[hmem02:61778] Signal code: (128)
[hmem02:61778] Failing at address: (nil)
[hmem02:61779] *** Process received signal ***
[hmem02:61781] *** Process received signal ***
[hmem02:61779] Signal: Segmentation fault (11)
[hmem02:61779] Signal code: (128)
[hmem02:61779] Failing at address: (nil)
[hmem02:61781] Signal: Segmentation fault (11)
[hmem02:61781] Signal code: (128)
[hmem02:61781] Failing at address: (nil)
[hmem02:61777] [ 0] /lib64/libpthread.so.0() [0x3344e0f4c0]
[hmem02:61777] [ 1]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkVolumeRendering.so.pv3.12(_Z52vtkVolumeRayCastSpaceLeapingImageFilterMinMaxExecuteIfEvP39vtkVolumeRayCastSpaceLeapingImageFilterP12vtkImageDataS3_PiT_+0x693)
[0x7f7b02f4112f]
[hmem02:61777] [ 2]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkVolumeRendering.so.pv3.12(_ZN39vtkVolumeRayCastSpaceLeapingImageFilter19ThreadedRequestDataEP14vtkInformationPP20vtkInformationVectorS3_PPP12vtkImageDataS7_Pii+0x2e7)
[0x7f7b02f3a30d]
[hmem02:61777] [ 3]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkFiltering.so.pv3.12(_Z40vtkThreadedImageAlgorithmThreadedExecutePv+0x3cb)
[0x7f7afc27cb8b]
[hmem02:61777] [ 4]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkCommon.so.pv3.12(_ZN16vtkMultiThreader19SingleMethodExecuteEv+0x627)
[0x7f7afb5c6f77]
[hmem02:61777] [ 5]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkFiltering.so.pv3.12(_ZN25vtkThreadedImageAlgorithm11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x521)
[0x7f7afc27d0bb]
[hmem02:61777] [ 6]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkVolumeRendering.so.pv3.12(_ZN39vtkVolumeRayCastSpaceLeapingImageFilter11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x49)
[0x7f7b02f3b4e3]
[hmem02:61777] [ 7]
/home/ucl/tfl/sbackaer/local/build/ParaView-build/bin/libvtkFiltering.so.pv3.12(_ZN17vtkImageAlgorithm14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x7b)
[0x7f7afc08c935]
_______________________________________________________________
BUT with this pipeline
XDMFReader
l-------------Programable filter
l---------------Calculator2 ---- Volume rendering
=============================================================
...
pfilter=ProgrammableFilter(Input=field3D)
pfilter.Script="""
pdi=self.GetInput()
w=pdi.GetPointData().GetArray(0)
pdo=self.GetOutput()
npt=pdo.GetNumberOfPoints()
new_w = vtk.vtkFloatArray()
new_w.SetName("new_w")
new_w.SetNumberOfComponents(3)
new_w.SetNumberOfTuples(npt)
pdo.GetPointData().AddArray(new_w)
for i in range(0, npt):
coord = pdo.GetPoint(i)
x, y, z = coord[:3]
r=math.sqrt(math.pow(x,2)+math.pow(y,2))
if (r>=55.0) and (y>0.0):
new_w.SetTuple3(i, 0.0,0.0,0.0)
else:
lw = w.GetTuple3(i)
new_w.SetTuple3(i,lw[0],lw[1],lw[2])
"""
pfilter.UpdatePipeline()
calc = Calculator(Input=pfilter)
calc.AttributeMode = 'point_data'
calc.Function = 'mag(new_w)'
calc.ResultArrayName = 'norm'
calc.UpdatePipeline()
a1_Result_PVLookupTable = GetLookupTableForArray( "norm", 1, NanColor=[0.25,
0.0, 0.0], RGBPoints=[0.0, 0.230, 0.299, 0.754, 1.0, 0.706, 0.016, 0.149],
VectorMode='Magnitude', ColorSpace='Diverging', ScalarRangeInitialized=1.0 )
SetActiveSource(calc)
DataRepresentation5 = Show()
DataRepresentation5.EdgeColor = [0.0, 0.0, 0.50000762951094835]
DataRepresentation5.ScalarOpacityFunction = CreatePiecewiseFunction(
Points=[0.0, 0.0, 4.0, 1.0] ) #divide x-scale by 3.0
DataRepresentation5.ColorArrayName = 'norm'
DataRepresentation5.ScalarOpacityUnitDistance = 1.0
DataRepresentation5.LookupTable = a1_Result_PVLookupTable
DataRepresentation5.Representation = 'Volume'
...
=============================================================
I get the message (one per core)
ERROR: In
/home/ucl/tfl/sbackaer/local/build/ParaView/ParaViewCore/VTKExtensions/vtkKdTreeGenerator.cxx,
line 168
vtkKdTreeGenerator (0x14ba2440): RegionIDs cannot be 0.
but no seg fault and the image is correct!
I checked every output of the different pipelines with GetDataInformation(),
GetPointDataInformation()... all outputs were right.
My first problem is basically that I do not know what "RegionID cannot be 0"
means!
The problem is related somehow to the Volume Rendering...
I get the same issue and same messages with the two different versions 3.12 and
3.14.
Does anyone have any clue? I am a bit lost!
I can provide the results of GetDataInformation(), GetPointDataInformation(),
give my complete codes or try anything else...
Best,
Stephane
_______________________________________________
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