Re: [Paraview] Paraview and Python related question

[Amit Goel]

Thanks for the help. When I set DYLD now the idle stops working:

fluid:~ armando$ export 
DYLD_LIBRARY_PATH=/Applications/ArmandoApps/paraview.app/Contents/Libraries/:$DYLD_LIBRARY_PATH
fluid:~ armando$ export 
PYTHONPATH=/Applications/ArmandoApps/paraview.app/Contents/Python/vtk:/Applications/ArmandoApps/paraview.app/Contents/Python:$PYTHONPATH
fluid:~ armando$ idle
** IDLE can't import Tkinter.
Your Python may not be configured for Tk. **

I have python and py-tkinter installed using macports and if I open a new 
terminal, idle just works fine.

I am searching on Macports / python and other forums… if anyone on paraview 
list has encountered it before please let me know.

Regards

amit


On Sep 22, 2015, at 1:35 PM, Shawn Waldon 
> wrote:

Hi Amit,

Since you appear to be using OSX, the environment variable you want is 
DYLD_LIBRARY_PATH, not LD_LIBRARY_PATH.

HTH,
Shawn

On Tue, Sep 22, 2015 at 1:32 PM, Amit Goel 
> wrote:
Hi

I downloaded the Paraview app and put it in a folder. Then I tried following 
instructions on this page: 
http://www.paraview.org/ParaView3/Doc/Nightly/www/py-doc/quick-start.html

export 
PYTHONPATH=/Applications/ArmandoApps/paraview.app/Contents/Python:$PYTHONPATH
export 
LD_LIBRARY_PATH=/Applications/ArmandoApps/paraview.app/Contents/Libraries/:$LD_LIBRARY_PATH

and I get this error:

Python 2.7.10 (default, Sep 14 2015, 23:52:44)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
Type "copyright", "credits" or "license()" for more information.
>>> from paraview.simple import *
Error: Could not import vtkCommonComputationalGeometryPython

Traceback (most recent call last):
  File "", line 1, in 
from paraview.simple import *
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/simple.py", 
line 39, in 
import servermanager
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/servermanager.py",
 line 48, in 
import paraview, re, os, os.path, new, sys, atexit, vtk
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/vtk/__init__.py",
 line 7, in 
from vtkCommonCorePython import *
ImportError: No module named vtkCommonCorePython
>>>

When i add vtk subfolder also to PYTHONPATH, I get this error:

ImportError: 
dlopen(/Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so,
 2): Library not loaded: 
@executable_path/../Libraries/libvtkCommonCorePython27D-pv4.3.1.dylib
  Referenced from: 
/Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so
  Reason: image not found

vtkCommonCorePython.so is present in LD_LIBRARY_PATH set earlier.

So question is: Am I following correct instructions ?

I guess there are three scenarios I would be working with in coming days:

1. python code to run default python.app on my local MacOS, read H5Part file 
and visualize it.
2. python code to run compiled python on my cluster
3. python code to run compiled python server on my cluster

I dont know yet what would the difference in 2nd and 3rd point but for now I am 
trying to write a python script that would start python and open a file and 
visualize it.

Any help would be highly appreciated.

Regards

Amit


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[Paraview] problem with particle tracer in release 4.3.1 and 4.4.0

[Perschall Markus (DC/ENE21)]

Hi

for some visualizations of unsteady fluid flow data I used to set particle 
tracer with the following pipeline:

volume data ==> Temporal Interpolator ==> ParticleTracer (with Input:Temporal 
Interpolator, seed source: some Point or Plane).

This worked fine up to Paraview version 4.1.0. However, in both versions 4.3.1 
and 4.4.0 Paraview crashes after setting up the pipeline during the step to 
next timestep. It behaves like this on both Unix and Windows (64bit).
Any comments or hints on this? Do I have to set up the pipeline differently in 
the new versions?
Any help would be highly appreciated

Regards,

Markus




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[Paraview] Pull Downloads only

[Angelini, Richard C (Rick) CIV USARMY RDECOM ARL (US)]

I have to build systems that do not have external network connectivity – is 
there a trick to tell the Superbuild to only pull down the tar balls that it 
needs to build but not actually do the build?




Rick Angelini
USArmy Research Laboratory
CISD/HPC Architectures Team
Phone:  410-278-6266
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Re: [Paraview] 400GB dataset out of memory on 1k cores?

[Anton Shterenlikht]

>From berk.gev...@kitware.com Tue Sep 22 19:18:53 2015
>
>Hmmm. We are not exactly on the same wavelength :-) When you run a
>threshold filter, you indeed get a volume with all the cells of a given
>grain id. However, when you show it as a Surface (the default mode),
>ParaView extracts the outer surface of that volume. Which ends up being
>equivalent to showing all the interfaces between grains. To actually see
>_all_ of the elements, you need volume rendering. Can you send me a small
>dataset so I can demonstrate the difference in some pictures.

Yes yes, you are right of course!
This is what I meant.
I don't want volume rendering, but
the surfaces of all volumes (clusters, blobs) of cells
of certain value.

I put a small xz-compressed dataset here:
http://eis.bris.ac.uk/~mexas/0.txz

This is a raw binary file
with extents 312, 312, 310.
I'm sorry I haven't had the time to make a really small dataset.
Let me know if this is too big.

I read the data as

ext1= 312
ext2= 312
ext3= 310
ffile   = 
from paraview.simple import *
cracks = ImageReader( FilePrefix= ffile )
cracks.DataExtent=[ 0, ext1-1, 0, ext2-1, 0, ext3-1 ]
cracks.DataByteOrder = 'LittleEndian'
cracks.DataScalarType = 'int'

Many thanks for your help

Anton

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Re: [Paraview] Paraview and Python related question

[Shawn Waldon]

Hi Amit,

Since you appear to be using OSX, the environment variable you want is
DYLD_LIBRARY_PATH, not LD_LIBRARY_PATH.

HTH,
Shawn

On Tue, Sep 22, 2015 at 1:32 PM, Amit Goel  wrote:

> Hi
>
> I downloaded the Paraview app and put it in a folder. Then I tried
> following instructions on this page:
> http://www.paraview.org/ParaView3/Doc/Nightly/www/py-doc/quick-start.html
>
> export
> PYTHONPATH=/Applications/ArmandoApps/paraview.app/Contents/Python:$PYTHONPATH
> export
> LD_LIBRARY_PATH=/Applications/ArmandoApps/paraview.app/Contents/Libraries/:$LD_LIBRARY_PATH
>
> and I get this error:
>
> Python 2.7.10 (default, Sep 14 2015, 23:52:44)
> [GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
> Type "copyright", "credits" or "license()" for more information.
> >>> from paraview.simple import *
> Error: Could not import vtkCommonComputationalGeometryPython
>
> Traceback (most recent call last):
>   File "", line 1, in 
> from paraview.simple import *
>   File
> "/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/simple.py",
> line 39, in 
> import servermanager
>   File
> "/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/servermanager.py",
> line 48, in 
> import paraview, re, os, os.path, new, sys, atexit, vtk
>   File
> "/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/vtk/__init__.py",
> line 7, in 
> from vtkCommonCorePython import *
> ImportError: No module named vtkCommonCorePython
> >>>
>
> When i add vtk subfolder also to PYTHONPATH, I get this error:
>
> ImportError:
> dlopen(/Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so,
> 2): Library not loaded:
> @executable_path/../Libraries/libvtkCommonCorePython27D-pv4.3.1.dylib
>   Referenced from:
> /Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so
>   Reason: image not found
>
> vtkCommonCorePython.so is present in LD_LIBRARY_PATH set earlier.
>
> So question is: Am I following correct instructions ?
>
> I guess there are three scenarios I would be working with in coming days:
>
> 1. python code to run default python.app on my local MacOS, read H5Part
> file and visualize it.
> 2. python code to run compiled python on my cluster
> 3. python code to run compiled python server on my cluster
>
> I dont know yet what would the difference in 2nd and 3rd point but for now
> I am trying to write a python script that would start python and open a
> file and visualize it.
>
> Any help would be highly appreciated.
>
> Regards
>
> Amit
>
>
> ___
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>
> Visit other Kitware open-source projects at
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[Paraview] Paraview and Python related question

[Amit Goel]

Hi

I downloaded the Paraview app and put it in a folder. Then I tried following 
instructions on this page: 
http://www.paraview.org/ParaView3/Doc/Nightly/www/py-doc/quick-start.html

export 
PYTHONPATH=/Applications/ArmandoApps/paraview.app/Contents/Python:$PYTHONPATH
export 
LD_LIBRARY_PATH=/Applications/ArmandoApps/paraview.app/Contents/Libraries/:$LD_LIBRARY_PATH

and I get this error:

Python 2.7.10 (default, Sep 14 2015, 23:52:44)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
Type "copyright", "credits" or "license()" for more information.
>>> from paraview.simple import *
Error: Could not import vtkCommonComputationalGeometryPython

Traceback (most recent call last):
  File "", line 1, in 
from paraview.simple import *
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/simple.py", 
line 39, in 
import servermanager
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/servermanager.py",
 line 48, in 
import paraview, re, os, os.path, new, sys, atexit, vtk
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/vtk/__init__.py",
 line 7, in 
from vtkCommonCorePython import *
ImportError: No module named vtkCommonCorePython
>>>

When i add vtk subfolder also to PYTHONPATH, I get this error:

ImportError: 
dlopen(/Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so,
 2): Library not loaded: 
@executable_path/../Libraries/libvtkCommonCorePython27D-pv4.3.1.dylib
  Referenced from: 
/Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so
  Reason: image not found

vtkCommonCorePython.so is present in LD_LIBRARY_PATH set earlier.

So question is: Am I following correct instructions ?

I guess there are three scenarios I would be working with in coming days:

1. python code to run default python.app on my local MacOS, read H5Part file 
and visualize it.
2. python code to run compiled python on my cluster
3. python code to run compiled python server on my cluster

I dont know yet what would the difference in 2nd and 3rd point but for now I am 
trying to write a python script that would start python and open a file and 
visualize it.

Any help would be highly appreciated.

Regards

Amit

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Re: [Paraview] 400GB dataset out of memory on 1k cores?

[Berk Geveci]

Hmmm. We are not exactly on the same wavelength :-) When you run a
threshold filter, you indeed get a volume with all the cells of a given
grain id. However, when you show it as a Surface (the default mode),
ParaView extracts the outer surface of that volume. Which ends up being
equivalent to showing all the interfaces between grains. To actually see
_all_ of the elements, you need volume rendering. Can you send me a small
dataset so I can demonstrate the difference in some pictures.

Best,
-berk

On Tue, Sep 22, 2015 at 11:11 AM, Anton Shterenlikht 
wrote:

> Hi Berk,
>
> sorry for replying via online gmail, it will probably screw up the context.
> I deleted your mail by accident from mbox, so have to resort to this...
>
> Anyway, I haven't tried your script yet, but you are probably correct
> about the threshold.
> I have another script working on the same dataset (see below),
> which runs fine. That script only shows the surface.
>
> You ask "extract the interfaces between the grains, correct?"
> If I understand you right, then no.
> Please see here the expected image from a smaller dataset:
>  http://eis.bris.ac.uk/~mexas/cgpack/201509res/crgb.png
> I want to show all elements of the 3D array (dataset) with
> particular values in particular colours. In my case yellow
> for all cells (array elements) with value 0:
>
> cracks100.ThresholdRange = [ 0, 0 ]
> DataRepresentation3 = Show()
> DataRepresentation3.DiffuseColor = [1.0, 1.0, 0.0]
>
> green for all cells with value -1:
>
> cracks110.ThresholdRange = [ -1, -1 ]
> DataRepresentation4 = Show()
> DataRepresentation4.DiffuseColor = [0.0, 1.0, 0.5]
>
> and semi-transparent purple all cells with value 2:
>
> Threshold1 = Threshold()
> Threshold1.ThresholdRange = [ 2, 2 ]
> DataRepresentation2 = Show()
> DataRepresentation2.DiffuseColor = [ 1, 0, 1 ]
>
> And I'd like to show the cells not as individual points,
> but link adjacent cells into some sort of surface.
>
> I my case green and yellow are cracks on different crystallographic planes,
> and purple are grain boundaries.
>
> Many thanks for your help
>
> Anton
>
> 
>
> The script that runs fine on the same 400GB dataset:
>
> ext1= 4640   # data extent along 1
> ext2= 4650# data extent along 2
> ext3= 4650   # data extent along 3
> infile  = "./large/1000/zg0.raw"   # input file name
> outfile = "g.png"   # output file name
> imsize1 = 1200 # size, in pixels, of the resulting image along 1
> imsize2 = 1200 # size, in pixels, of the resulting image along 2
> minval  = 1   # min colour value
> maxval  = 1.0e6   # max colour value, equal to the number of grains
>
> # End of adjustable parameters
> ##72
>
> # define the centre of rotation (cor)
> cor1 = 0.5 * ext1
> cor2 = 0.5 * ext2
> cor3 = 0.5 * ext3
>
> from paraview.simple import *
>
> reader=ImageReader(FilePrefix= infile )
> reader.DataExtent=[ 0, ext1-1, 0, ext2-1, 0, ext3-1 ]
> reader.DataByteOrder = 'LittleEndian'
> reader.DataScalarType = 'int'
>
> RenderView1 = GetRenderView()
> DataRepresentation1 = Show()
>
> dp = GetDisplayProperties(reader)
> dp.LookupTable = MakeBlueToRedLT(minval,maxval)
> dp.ColorAttributeType = 'POINT_DATA'
> dp.ColorArrayName = 'ImageFile'
> dp.Representation = "Surface"
>
> bar = CreateScalarBar(LookupTable=dp.LookupTable, Title="grain")
> bar.Position=[0.80,0.15]
> GetRenderView().Representations.append(bar)
>
> camera = GetActiveCamera()
> camera.SetViewUp(-1,0,0)
> camera.Azimuth(30)
> camera.Elevation(30)
>
> #camera.SetPosition(0,0,100)
> #camera.Roll(-90)
>
> RenderView1.ResetCamera()
> # make white background, for papers
> #RenderView1.Background = [ 1,1,1]
>
> # gradient background colour
> RenderView1.UseGradientBackground = 1
> RenderView1.Background2 = [0.0, 0.0, 0.16470588235294117]
> RenderView1.Background = [0.3215686274509804, 0.3411764705882353,
> 0.43137254901960786]
>
> RenderView1.CenterAxesVisibility = 0
> RenderView1.OrientationAxesVisibility = 1
> RenderView1.CenterOfRotation = [ cor1, cor2, cor3 ]
> RenderView1.ViewSize = [ imsize1, imsize2 ]
>
> WriteImage( outfile )
>
> Render()
>
>
> On 22/09/2015, Berk Geveci  wrote:
> > Hi Anton,
> >
> > Let's debug this a big. I suspect that the thresholds are the issue here.
> > Does this script work?
> >
> > ext1= 4640   # data extent along 1
> > ext2= 4650   # data extent along 2
> > ext3= 4650   # data extent along 3
> > ffile   = "./large/1000/zf5.raw" # fracture file
> > imsize1 = 1200 # size, in pixels, of the resulting image along 1
> > imsize2 = 1200 # size, in pixels, of the resulting image along 2
> >
> > cor1 = 0.5 * ext1
> > cor2 = 0.5 * ext2
> > cor3 = 0.5 * ext3
> >
> > from paraview.simple import *
> >
> > # the extents start from zero, so need to lower
> > # the upper extents by 1
> > cracks = 

Re: [Paraview] Pull Downloads only

[Utkarsh Ayachit]

Not to my knowledge, but that'd certainly be a good feature to add. In
any case, all the files to download are listed in versions.cmake
(https://gitlab.kitware.com/paraview/paraview-superbuild/blob/master/versions.cmake).

Utkarsh

On Tue, Sep 22, 2015 at 2:39 PM, Angelini, Richard C (Rick) CIV USARMY
RDECOM ARL (US)  wrote:
> I have to build systems that do not have external network connectivity – is
> there a trick to tell the Superbuild to only pull down the tar balls that it
> needs to build but not actually do the build?
>
>
>
> 
> Rick Angelini
> USArmy Research Laboratory
> CISD/HPC Architectures Team
> Phone:  410-278-6266
>
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Re: [Paraview] Custom filter: exposed properties of a Calculator filter

[Cory Quammen]

Jean-Michel,

I am not able to reproduce what you are reporting with 4.3.1 or 4.4.

Did you remember to click the + sign when adding the property? The first
time I tried I forgot to do that, and the Function property was not exposed
in my custom filter. When I did add the property, it was exposed.

HTH,
Cory

On Tue, Sep 22, 2015 at 5:07 AM, Jean-Michel Lucas 
wrote:

> Hi,
>
>
>
> I am trying to create a Custom Filter in ParaView 4.3.1.
>
>
>
> I am having trouble with the exposed properties of a Calculator filter:
> when defining the properties for my custom filter, I am selecting the
> "Function" property and setting the property name for this Calculator.
> However, when using the custom filter, this property name does not appear
> in the Properties panel of the Object Inspector. Is this a known bug or is
> there something I'm missing ?
>
>
>
> Also, is it possible to hide the calculator buttons and only leave the
> blank field ? This was the default behavior in (at least) ParaView 3.12.0.
>
>
>
> Thank you for your help.
>
>
>
> Jean-Michel
>
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>
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>


-- 
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R Engineer
Kitware, Inc.
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Re: [Paraview] Legend and labels

[Cory Quammen]

Hi Jean-Michel,

In response to your questions:

>
> 1) Is it possible to adjust the spacing between the Title Texts and the
> labels ?
>

Unfortunately, no. This is a fixed spacing.

2) Is it possible to adjust the labels' font size ?
>

Yes. To change the labels' font size, open the Color Map Editor and find
the button with the color bar and the letter "e". Clicking on this will
bring up a dialog that lets you change the font size of the labels
(Text/Annotation Font Properties). Note that the font size is more of a
recommendation - ParaView will pick a font size for the label based on size
constraints and the number of digits in the label format.

Cheers,
Cory


>
>
> Thank you in advance for your help.
>
>
>
> Jean-Michel
>
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>


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Kitware, Inc.
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Re: [Paraview] Paraview and Python related question

[Amit Goel]

There is this weird behaviour :

fluid:~ armando$ export DYLD_LIBRARY_PATH=/lib
fluid:~ armando$ idle

idle works just fine even if I point DYLD_LIBRARY_PATH to anything… as in above 
example /lib

But when I set it to paraview:

fluid:~ armando$ export 
DYLD_LIBRARY_PATH=/Applications/ArmandoApps/paraview.app/Contents/Libraries/
fluid:~ armando$ idle
** IDLE can't import Tkinter.
Your Python may not be configured for Tk. **

I get tkinter error.

Any ideas anyone please ?

Regards

amit


On Sep 22, 2015, at 2:03 PM, Amit Goel 
> wrote:

Thanks for the help. When I set DYLD now the idle stops working:

fluid:~ armando$ export 
DYLD_LIBRARY_PATH=/Applications/ArmandoApps/paraview.app/Contents/Libraries/:$DYLD_LIBRARY_PATH
fluid:~ armando$ export 
PYTHONPATH=/Applications/ArmandoApps/paraview.app/Contents/Python/vtk:/Applications/ArmandoApps/paraview.app/Contents/Python:$PYTHONPATH
fluid:~ armando$ idle
** IDLE can't import Tkinter.
Your Python may not be configured for Tk. **

I have python and py-tkinter installed using macports and if I open a new 
terminal, idle just works fine.

I am searching on Macports / python and other forums… if anyone on paraview 
list has encountered it before please let me know.

Regards

amit


On Sep 22, 2015, at 1:35 PM, Shawn Waldon 
> wrote:

Hi Amit,

Since you appear to be using OSX, the environment variable you want is 
DYLD_LIBRARY_PATH, not LD_LIBRARY_PATH.

HTH,
Shawn

On Tue, Sep 22, 2015 at 1:32 PM, Amit Goel 
> wrote:
Hi

I downloaded the Paraview app and put it in a folder. Then I tried following 
instructions on this page: 
http://www.paraview.org/ParaView3/Doc/Nightly/www/py-doc/quick-start.html

export 
PYTHONPATH=/Applications/ArmandoApps/paraview.app/Contents/Python:$PYTHONPATH
export 
LD_LIBRARY_PATH=/Applications/ArmandoApps/paraview.app/Contents/Libraries/:$LD_LIBRARY_PATH

and I get this error:

Python 2.7.10 (default, Sep 14 2015, 23:52:44)
[GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin
Type "copyright", "credits" or "license()" for more information.
>>> from paraview.simple import *
Error: Could not import vtkCommonComputationalGeometryPython

Traceback (most recent call last):
  File "", line 1, in 
from paraview.simple import *
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/simple.py", 
line 39, in 
import servermanager
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/servermanager.py",
 line 48, in 
import paraview, re, os, os.path, new, sys, atexit, vtk
  File 
"/Applications/ArmandoApps/paraview.app/Contents/Python/paraview/vtk/__init__.py",
 line 7, in 
from vtkCommonCorePython import *
ImportError: No module named vtkCommonCorePython
>>>

When i add vtk subfolder also to PYTHONPATH, I get this error:

ImportError: 
dlopen(/Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so,
 2): Library not loaded: 
@executable_path/../Libraries/libvtkCommonCorePython27D-pv4.3.1.dylib
  Referenced from: 
/Applications/ArmandoApps/paraview.app/Contents/Python/vtk/vtkCommonCorePython.so
  Reason: image not found

vtkCommonCorePython.so is present in LD_LIBRARY_PATH set earlier.

So question is: Am I following correct instructions ?

I guess there are three scenarios I would be working with in coming days:

1. python code to run default python.app on my local MacOS, read H5Part file 
and visualize it.
2. python code to run compiled python on my cluster
3. python code to run compiled python server on my cluster

I dont know yet what would the difference in 2nd and 3rd point but for now I am 
trying to write a python script that would start python and open a file and 
visualize it.

Any help would be highly appreciated.

Regards

Amit


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Re: [Paraview] Saving with Solid Color information

[Cory Quammen]

Hi Leonardo,

Are you saving a state file (File -> Save State)? State files are the
mechanism for saving display properties like color. Color information is
not saved with the data if you save the data only (File -> Save Data).

Hope that helps,
Cory

On Mon, Sep 21, 2015 at 4:48 PM, Léo Pessanha 
wrote:

> Hi,
>
> My question is simple, but I can't figure it out an easy way to do it !
>
> I want to save a SourceBox with the Solid Color that I've picked from the
> Select Colors dialog box.
>
> After picking a color and saving the dataset, the Solid Color info is not
> saved.
>
> Is there a way of doing what I want to?
>
> Thanks in advance.
>
> Leonardo Pessanha
> LAMCE/COPPE/UFRJ
>
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[Paraview] Custom filter: exposed properties of a Calculator filter

[Jean-Michel Lucas]

Hi,

 

I am trying to create a Custom Filter in ParaView 4.3.1.

 

I am having trouble with the exposed properties of a Calculator filter: when
defining the properties for my custom filter, I am selecting the "Function"
property and setting the property name for this Calculator. However, when
using the custom filter, this property name does not appear in the
Properties panel of the Object Inspector. Is this a known bug or is there
something I'm missing ?

 

Also, is it possible to hide the calculator buttons and only leave the blank
field ? This was the default behavior in (at least) ParaView 3.12.0.

 

Thank you for your help.

 

Jean-Michel

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[Paraview] Get XMLRectilinearGridReader Data into a numpy array

[no name]

I want to read a VTR file and work with its data. In my case it has 3
Components,

source = XMLRectilinearGridReader(FileName=['test.vtr'])
arrayName = 'M'
arrayComponents = 3
data = source.GetCellDataInformation()
array = data.GetArray(arrayName)
dataRange = array.GetRange(component)
FieldData = source.GetFieldData()
print FieldData

gives me:

vtkPVDataSetAttributesInformation (0EAE6FC0)

Debug: Off

Modified Time: 1066787

Reference Count: 2

Registered Events: (none)

RootOnly: 0

ArrayInformation, number of arrays: 1

Debug: Off

Modified Time: 1068264

Reference Count: 1

Registered Events: (none)

RootOnly: 0

Name: M

DataType: 11

NumberOfComponents: 3

NumberOfTuples: 250

IsPartial: 0

Ranges :

0, 1.53585e+006

-1.53585e+006, 1.53585e+006

-1.53585e+006, 1.53585e+006

-306523, 1.53393e+006

InformationKeys :

vtkAbstractArray::PER_COMPONENT

vtkDataArray::L2_NORM_RANGE


SortArrays: 1

Now I would like to access this data, best case for me would be if I can
use it in numpy, with the

from vtk.util.numpy_support import vtk_to_numpy

methods...

Or should I work with a Programmable Filter Option instead?

Thanks
Richard
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Re: [Paraview] Select which fields to load when loading .vtm multi-block

[Deij-van Rijswijk, Menno]

Anyone?

From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of Deij-van 
Rijswijk, Menno
Sent: vrijdag 18 september 2015 16:06
To: paraview@paraview.org
Subject: [Paraview] Select which fields to load when loading .vtm multi-block

Hi,

I noticed that when I load a .vtm file, I cannot select which data fields to 
load. This requires me to load the entire file into memory, after which the 
Pass Arrays filter allows me to take the required data field forward in the 
pipeline. If I load other formats (e.g. CGNS and .vtu) I can choose which field 
to load.

Maybe I’m missing something obvious? Should there be metadata on the fields in 
the vtm file that is missing?

Thanks and best wishes,


Menno Deij – van Rijswijk


dr. ir. Menno A. Deij-van Rijswijk
Researcher / Software Engineer

Maritime Simulation & Software Group


 
MARIN
 

2, Haagsteeg

E m.d...@marin.nl
P.O. Box 28
T +31 317 49 39 11

6700 AA Wageningen
F +31 317 49 32 45
T  +31 317 49 35 06
The Netherlands
I  www.marin.nl
 
MARIN news: MARIN Report available on App store & Google play
This e-mail may be confidential, privileged and/or protected by copyright. If 
you are not the intended recipient, you should return it to the sender 
immediately and delete your copy from your system.
 
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Re: [Paraview] 400GB dataset out of memory on 1k cores?

[Anton Shterenlikht]

Hi Berk,

sorry for replying via online gmail, it will probably screw up the context.
I deleted your mail by accident from mbox, so have to resort to this...

Anyway, I haven't tried your script yet, but you are probably correct
about the threshold.
I have another script working on the same dataset (see below),
which runs fine. That script only shows the surface.

You ask "extract the interfaces between the grains, correct?"
If I understand you right, then no.
Please see here the expected image from a smaller dataset:
 http://eis.bris.ac.uk/~mexas/cgpack/201509res/crgb.png
I want to show all elements of the 3D array (dataset) with
particular values in particular colours. In my case yellow
for all cells (array elements) with value 0:

cracks100.ThresholdRange = [ 0, 0 ]
DataRepresentation3 = Show()
DataRepresentation3.DiffuseColor = [1.0, 1.0, 0.0]

green for all cells with value -1:

cracks110.ThresholdRange = [ -1, -1 ]
DataRepresentation4 = Show()
DataRepresentation4.DiffuseColor = [0.0, 1.0, 0.5]

and semi-transparent purple all cells with value 2:

Threshold1 = Threshold()
Threshold1.ThresholdRange = [ 2, 2 ]
DataRepresentation2 = Show()
DataRepresentation2.DiffuseColor = [ 1, 0, 1 ]

And I'd like to show the cells not as individual points,
but link adjacent cells into some sort of surface.

I my case green and yellow are cracks on different crystallographic planes,
and purple are grain boundaries.

Many thanks for your help

Anton



The script that runs fine on the same 400GB dataset:

ext1= 4640   # data extent along 1
ext2= 4650# data extent along 2
ext3= 4650   # data extent along 3
infile  = "./large/1000/zg0.raw"   # input file name
outfile = "g.png"   # output file name
imsize1 = 1200 # size, in pixels, of the resulting image along 1
imsize2 = 1200 # size, in pixels, of the resulting image along 2
minval  = 1   # min colour value
maxval  = 1.0e6   # max colour value, equal to the number of grains

# End of adjustable parameters
##72

# define the centre of rotation (cor)
cor1 = 0.5 * ext1
cor2 = 0.5 * ext2
cor3 = 0.5 * ext3

from paraview.simple import *

reader=ImageReader(FilePrefix= infile )
reader.DataExtent=[ 0, ext1-1, 0, ext2-1, 0, ext3-1 ]
reader.DataByteOrder = 'LittleEndian'
reader.DataScalarType = 'int'

RenderView1 = GetRenderView()
DataRepresentation1 = Show()

dp = GetDisplayProperties(reader)
dp.LookupTable = MakeBlueToRedLT(minval,maxval)
dp.ColorAttributeType = 'POINT_DATA'
dp.ColorArrayName = 'ImageFile'
dp.Representation = "Surface"

bar = CreateScalarBar(LookupTable=dp.LookupTable, Title="grain")
bar.Position=[0.80,0.15]
GetRenderView().Representations.append(bar)

camera = GetActiveCamera()
camera.SetViewUp(-1,0,0)
camera.Azimuth(30)
camera.Elevation(30)

#camera.SetPosition(0,0,100)
#camera.Roll(-90)

RenderView1.ResetCamera()
# make white background, for papers
#RenderView1.Background = [ 1,1,1]

# gradient background colour
RenderView1.UseGradientBackground = 1
RenderView1.Background2 = [0.0, 0.0, 0.16470588235294117]
RenderView1.Background = [0.3215686274509804, 0.3411764705882353,
0.43137254901960786]

RenderView1.CenterAxesVisibility = 0
RenderView1.OrientationAxesVisibility = 1
RenderView1.CenterOfRotation = [ cor1, cor2, cor3 ]
RenderView1.ViewSize = [ imsize1, imsize2 ]

WriteImage( outfile )

Render()


On 22/09/2015, Berk Geveci  wrote:
> Hi Anton,
>
> Let's debug this a big. I suspect that the thresholds are the issue here.
> Does this script work?
>
> ext1= 4640   # data extent along 1
> ext2= 4650   # data extent along 2
> ext3= 4650   # data extent along 3
> ffile   = "./large/1000/zf5.raw" # fracture file
> imsize1 = 1200 # size, in pixels, of the resulting image along 1
> imsize2 = 1200 # size, in pixels, of the resulting image along 2
>
> cor1 = 0.5 * ext1
> cor2 = 0.5 * ext2
> cor3 = 0.5 * ext3
>
> from paraview.simple import *
>
> # the extents start from zero, so need to lower
> # the upper extents by 1
> cracks = ImageReader( FilePrefix= ffile )
> cracks.DataExtent=[ 0, ext1-1, 0, ext2-1, 0, ext3-1 ]
> cracks.DataByteOrder = 'LittleEndian'
> cracks.DataScalarType = 'int'
>
> RenderView1 = GetRenderView()
> DataRepresentation1 = Show()
>
> If this works, let's discuss how to avoid using Threshold but get the same
> result. The issue with Threshold is that it creates a volume as an
> unstructured grid, which is heavy-weight. For example, a ~40KB volume (one
> float variable) turns into a ~800KB if I extract all of it as an
> unstructured grid. It seems like all you need is to extract the interfaces
> between the grains, correct?
>
> Best,
> -berk
>
> On Mon, Sep 21, 2015 at 10:50 AM, Anton Shterenlikht 
> wrote:
>
>> >From mexas Mon Sep 21 14:29:16 2015
>> >To: paraview@paraview.org
>> >Subject: 400GB dataset out 

[Paraview] Quadrangles and Q_1,1 basis functions

[Torquil Macdonald Sørensen]

Hi!

I have defined a 2d quadrangle mesh consisting of 2x2 elements, with
Q_1,1 basis functions in GetFEM++, and exported an example function to
ASCII VTK format. The only node at which the example function is nonzero
is the middle one.

When I open the VTK file in Paraview, it looks as if it has used some
kind of triangle interpolation. Instead of its support being the entire
mesh, it has become zero near two opposite domain corners. In
particular, the result should have been 90-degree rotation symmetric
about the centre node.

How do I get Paraview to display this Q_1,1 function correctly, or at
least without it seemingly being interpolated onto a triangular mesh?

I'm using Paraview 4.3.1 and the ASCI VTK file generated by GetFEM++ is:

# vtk DataFile Version 2.0
Exported by getfem++
ASCII
DATASET UNSTRUCTURED_GRID
POINTS 9 float
 0 0 0
 0.5 0 0
 0 0.5 0
 0.5 0.5 0
 1 0 0
 1 0.5 0
 0 1 0
 0.5 1 0
 1 1 0

CELLS 4 20
 4 0 1 3 2
 4 1 4 5 3
 4 2 3 7 6
 4 3 5 8 7

CELL_TYPES 4
 9
 9
 9
 9

POINT_DATA 9


SCALARS scalarField float 1
LOOKUP_TABLE default
 0 0 0 1 0 0 0 0 0

Thanks and best regards
Torquil Sørensen
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Re: [Paraview] Select which fields to load when loading .vtm multi-block

[Berk Geveci]

Hmmm. It doesn't look like there is support for array selection in that
reader. We should add it... Can you make a feature request in the bug
tracker?

Thanks,
-berk

On Tue, Sep 22, 2015 at 6:40 AM, Deij-van Rijswijk, Menno 
wrote:

> Anyone?
>
> From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of
> Deij-van Rijswijk, Menno
> Sent: vrijdag 18 september 2015 16:06
> To: paraview@paraview.org
> Subject: [Paraview] Select which fields to load when loading .vtm
> multi-block
>
> Hi,
>
> I noticed that when I load a .vtm file, I cannot select which data fields
> to load. This requires me to load the entire file into memory, after which
> the Pass Arrays filter allows me to take the required data field forward in
> the pipeline. If I load other formats (e.g. CGNS and .vtu) I can choose
> which field to load.
>
> Maybe I’m missing something obvious? Should there be metadata on the
> fields in the vtm file that is missing?
>
> Thanks and best wishes,
>
>
> Menno Deij – van Rijswijk
>
>
> dr. ir. Menno A. Deij-van Rijswijk
> Researcher / Software Engineer
>
> Maritime Simulation & Software Group
>
>
>
> MARIN
>
>
> 2, Haagsteeg
>
> E m.d...@marin.nl
> P.O. Box 28
> T +31 317 49 39 11
>
> 6700 AA Wageningen
> F +31 317 49 32 45
> T  +31 317 49 35 06
> The Netherlands
> I  www.marin.nl
>
> MARIN news: MARIN Report available on App store & Google play
> This e-mail may be confidential, privileged and/or protected by copyright.
> If you are not the intended recipient, you should return it to the sender
> immediately and delete your copy from your system.
>
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>
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>
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>
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