Re: [Paraview] ParaView 5.x not showing all objects available in Pipeline Browser

[Moreland, Kenneth]

Omid,

Even after applying the Threshold filter, I cannot replicate your problem. I’ve 
tried on both ParaView 5.2 and 5.4. Both work fine for me.

My settings are the default. “Resolve Coincident Topology” is set to “Shift 
z-buffer when rendering lines and points”. “Z Shift” is set to 0.002. (Polygon 
offset should not matter in this mode.) You could try increasing the Z Shift to 
fix the problem. Note that you have to restart ParaView in order for these 
options to take effect.

It is possible that there is some quirk with the rendering system on your 
computer that does not implement the topology resolution. Do you happen to have 
another computer on which you can try to run this? I also noted that if I turn 
on OSPRay rendering, I do get the missing line issue you describe. There might 
be other display/rendering parameters that cause issues. But the defaults 
should be fine, so unless you have done some tinkering you should be OK.

-Ken

From: Omid Mahabadi [mailto:omid.mahab...@geomechanica.com]
Sent: Wednesday, January 10, 2018 9:21 AM
To: Moreland, Kenneth 
Cc: paraview@paraview.org
Subject: [EXTERNAL] Re: [Paraview] ParaView 5.x not showing all objects 
available in Pipeline Browser

Hi Ken,
Thanks for the detailed reply. I could not get anything out of the settings 
dialog as per your suggestion. Did you have a combination of those settings 
that might work for my files?
I can also see the image you sent; that's usually fine. However, I typically 
apply a Threshold filter to the _basic_ files (Scalar: alive; min: 0.1; max: 
1). In this case, the _basic_ object is always drawn in front of the 
_broken_joint_ object.
In addition, I visualize dozens of these files every day so Transforming every 
single object is a bit tedious.
Thank you,
Omid


On Mon, Jan 8, 2018 at 5:56 PM, Moreland, Kenneth 
> wrote:
Omid,

I am unable to replicate your issue in ParaView 5.4.1. When I loaded your data 
and showed the broken_joint data in wireframe, I was clearly able to see the 
lines of broken_joint over the polygons of basic. (See the attached image.)

The problem you are getting is likely caused by z-buffer fighting in the 
rendering. This happens when two objects are the exact same distance from the 
viewer, as I believe is the case in your data. Wanting to draw lines on top of 
polygons is common enough that there are some corrections to help the rendering 
determine what to draw in front. Perhaps by changing the settings on resolving 
coincident topology will resolve your issue. You can find them by opening the 
ParaView settings dialog (Edit → Settings), clicking on the Render View tab, 
and turning on the advanced options. The options you are looking for are 
“Resolve Coincident Topology,” “Polygon Offset Parameters”, and “Z Shift.”

Another, possibly easier, solution it to simply move the lines of the 
broken_joint data closer to the camera. Click the broken_joint object and add 
the Transform filter. Change the Translate parameter to 0, 0, 1 and apply. That 
should shift the wireframe forward enough to see it properly.

-Ken

From: ParaView 
[mailto:paraview-boun...@paraview.org] On 
Behalf Of Omid Mahabadi
Sent: Monday, January 8, 2018 2:30 PM
To: paraview@paraview.org
Subject: [EXTERNAL] [Paraview] ParaView 5.x not showing all objects available 
in Pipeline Browser

Hi,
I use ParaView to visualize data of our simulations using the Unstructured Grid 
data format. Up until ParaView 4.x everything worked fine: we typically 
visualize one set of data files as Surfaces and another as Wireframe. The 
Wireframe dataset refers to "fracture lines" in our simulations.
See below how the simulation looked like in PV version 4.x. You could clearly 
see the line around the boundaries of the model.

[Inline image 1]
However, in PV 5.x the lines are not fully visualized as if they're hidden 
below the other data object:

[Inline image 2]
I've tried a few versions of 5.x but they all behave similarly.
Does anyone know what might be going on here? Is this a bug / removed featured 
from the new version or should I do something different with 5.x? I've noticed 
that this issue does not happen consistently. I've seen the issue on both Linux 
Mint 17.3 (64 bit) and Ubuntu
I've attached two example VTU files. Please visualize the second file as 
Wireframe (_broken_joint). Below are two large VTU files.
https://www.dropbox.com/s/kzt4jq1wbwfua4j/out.zip?dl=0

Can someone else reproduce this issue?

I'd really hope to start using ParaView 5 since it finally has the long-missing 
Reload Files options!
Thank you,
Omid




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Re: [Paraview] [EXTERNAL] ParaView - Variables and different Time Steps

[Scott, W Alan]

Here is an answer from Cory last summer, off list, to one of my customers:  

On Tue, Jul 11, 2017 at 2:50 PM, Cory Quammen  wrote:
> Dear ,
>
> I think the Force Time filter will come in handy here for this use 
> case. It can be used to "freeze" a dataset at a certain timestep.
>
> * Load can.ex2
> * Add a Force Time filter. Set the timestep to the one whose 
> displacement you want to be zero. The output of this filter is the
> can.ex2 dataset "frozen" at the chosen timestep. It will not change as 
> you advance through time.
> * Select both can.ex2 and the ForceTime1 sources in the Pipeline 
> Browser. Note that the original can.ex2 source will update as the 
> timestep changes, but the ForceTime1 source will not change.
> * Add a Python Calculator filter to subtract the displacement in the 
> "frozen" data set from the current timestep in can.ex2. Set the 
> expression to
>
> inputs[0].PointData['DISPL'] - inputs[1].PointData['DISPL']
>
> The order of inputs into the Python Calculator is not well defined, so 
> you may need to swap the indices in inputs[0] and inputs[1] to get the 
> correct sign on the result, but this should work.
> * Finally, add a Plot Selection over Time filter. This filter will run 
> over all time steps, subtracting the data from the current timestep 
> from the data in the "frozen" timestep produced by the Force Time 
> filter, and plot the result in a graph. The first timestep should have 
> a value of 0.
>
> Please let me know if this approach isn't clear or doesn't work.
>
> Best regards,
> Cory
>
>
> On Tue, Jul 11, 2017 at 1:27 PM, Scott, W Alan  wrote:
>> Morning team,
>>
>> , one of my customers, has been working on an issue for a while.  
>> Ken and Andy have replied, but I don’t think we understood, or 
>> answered,  problem.  Here is what he is trying to do, using 
>> can.exo as an example.
>>
>>
>>
>> I assume this will require the Programmable Filter – if so, mind 
>> voodooing up the source?
>>
>>
>>
>> I believe that  basically wants to be able to subtract two 
>> timesteps from each other.  I thought I had an example from a 
>> previous thread, but can’t find it.
>>
>>
>>
>> Thanks!
>>
>>
>>
>> Alan
>>
>>
>>
>>
>>
>>

> -Original Message-
> From: ParaView [mailto:paraview-boun...@paraview.org] On Behalf Of
> Carolin Helbig
> Sent: Wednesday, January 10, 2018 2:57 AM
> To: paraview@paraview.org
> Subject: [EXTERNAL] [Paraview] ParaView - Variables and different Time
> Steps
> 
> Dear ParaView team,
> 
> I read a post at the ParaView website concerning variables and different time
> steps (see https://public.kitware.com/pipermail/paraview/2014-
> May/031054.html). I have a similar problem and I want to access values from
> different time steps using the programmable filter with multiple inputs. I
> unfortunately have no idea how to access other time steps using the
> programmable filter. Could you give me some advice or a hint where I can
> find detailed information about that issue? I would be very happy if you
> could help me.
> 
> Best regards,
> Carolin.
> 
> --
> Dr. Carolin Helbig
> 
> Department Umweltinformatik
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Permoserstraße 15 I
> 04318 Leipzig
> Tel.: +49 341 235 - 1032
> Email: carolin.hel...@ufz.de
> WWW: http://www.ufz.de
>   https://www.ufz.de/index.php?en=31616
> 
> 
> 
> Sitz der Gesellschaft
> Registergericht: Amtsgericht Leipzig
> Handelsregister Nr.: B 4703
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> Geschäftsführer: Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin: Prof. Dr. Heike Graßmann
> 
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Re: [Paraview] ParaView 5.x not showing all objects available in Pipeline Browser

[Omid Mahabadi]

Hi Ken,
Thanks for the detailed reply. I could not get anything out of the settings
dialog as per your suggestion. Did you have a combination of those settings
that might work for my files?

I can also see the image you sent; that's usually fine. However, I
typically apply a Threshold filter to the _basic_ files (Scalar: alive;
min: 0.1; max: 1). In this case, the _basic_ object is always drawn in
front of the _broken_joint_ object.

In addition, I visualize dozens of these files every day so Transforming
every single object is a bit tedious.

Thank you,
Omid


On Mon, Jan 8, 2018 at 5:56 PM, Moreland, Kenneth  wrote:

> Omid,
>
>
>
> I am unable to replicate your issue in ParaView 5.4.1. When I loaded your
> data and showed the broken_joint data in wireframe, I was clearly able to
> see the lines of broken_joint over the polygons of basic. (See the attached
> image.)
>
>
>
> The problem you are getting is likely caused by z-buffer fighting in the
> rendering. This happens when two objects are the exact same distance from
> the viewer, as I believe is the case in your data. Wanting to draw lines on
> top of polygons is common enough that there are some corrections to help
> the rendering determine what to draw in front. Perhaps by changing the
> settings on resolving coincident topology will resolve your issue. You can
> find them by opening the ParaView settings dialog (Edit → Settings),
> clicking on the Render View tab, and turning on the advanced options. The
> options you are looking for are “Resolve Coincident Topology,” “Polygon
> Offset Parameters”, and “Z Shift.”
>
>
>
> Another, possibly easier, solution it to simply move the lines of the
> broken_joint data closer to the camera. Click the broken_joint object and
> add the Transform filter. Change the Translate parameter to 0, 0, 1 and
> apply. That should shift the wireframe forward enough to see it properly.
>
>
>
> -Ken
>
>
>
> *From:* ParaView [mailto:paraview-boun...@paraview.org] *On Behalf Of *Omid
> Mahabadi
> *Sent:* Monday, January 8, 2018 2:30 PM
> *To:* paraview@paraview.org
> *Subject:* [EXTERNAL] [Paraview] ParaView 5.x not showing all objects
> available in Pipeline Browser
>
>
>
> Hi,
>
> I use ParaView to visualize data of our simulations using the Unstructured
> Grid data format. Up until ParaView 4.x everything worked fine: we
> typically visualize one set of data files as Surfaces and another as
> Wireframe. The Wireframe dataset refers to "fracture lines" in our
> simulations.
>
> See below how the simulation looked like in PV version 4.x. You could
> clearly see the line around the boundaries of the model.
>
> [image: Inline image 1]
>
> However, in PV 5.x the lines are not fully visualized as if they're hidden
> below the other data object:
>
> [image: Inline image 2]
>
> I've tried a few versions of 5.x but they all behave similarly.
>
> Does anyone know what might be going on here? Is this a bug / removed
> featured from the new version or should I do something different with 5.x?
> I've noticed that this issue does not happen consistently. I've seen the
> issue on both Linux Mint 17.3 (64 bit) and Ubuntu
>
> I've attached two example VTU files. Please visualize the second file as
> Wireframe (_broken_joint). Below are two large VTU files.
>
> https://www.dropbox.com/s/kzt4jq1wbwfua4j/out.zip?dl=0
>
>
>
> Can someone else reproduce this issue?
>
>
>
> I'd really hope to start using ParaView 5 since it finally has the
> long-missing Reload Files options!
>
> Thank you,
>
> Omid
>
>
>
>
>
>
>
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Re: [Paraview] Given 2D Displacement Field, Visualize Stretch as Geometric Change in Mesh

[Cory Quammen]

Great, thanks for the follow up.

Cory

On Wed, Jan 10, 2018 at 10:58 AM, Charlie Talbot  wrote:
> That seems to work, thank you very much! I had some issues with Paraview 5.0
> (crashed upon python calculation) but this did indeed work after upgrading
> to Paraview 5.4
>
> On Tue, Jan 9, 2018 at 4:02 PM, Charlie Talbot  wrote:
>>
>> Thanks Cory!
>>
>> Knowing the procedure is very helpful.
>>
>> I am not well-versed in paraview, so I am referring to the wiki to see how
>> to use the Python Calculator and execute the other steps.  Will update.
>> Thanks again
>>
>> On Tue, Jan 9, 2018 at 2:48 PM, Cory Quammen 
>> wrote:
>>>
>>> Charlie,
>>>
>>> You can use the Warp by Vector filter to warp the points in your data
>>> set according to a vector field. To get that vector field from your
>>> p_x and p_y scalar arrays, it is convenient to use the Python
>>> Calculator with the expression
>>>
>>> make_vector(p_x, p_y, np.zeros(p_x.shape))
>>>
>>> Apply the Python Calculator filter to your data set, then add a Warp
>>> by Vector filter off the Python Calculator filter. Set the Vectors
>>> property to "result", the default name of the array produced by the
>>> Python Calculator.
>>>
>>> Hope that helps,
>>> Cory
>>>
>>> On Tue, Jan 9, 2018 at 2:02 PM, Charlie Talbot 
>>> wrote:
>>> > Hi, this is my first time posting to paraview-users, and I am wondering
>>> > how
>>> > to visualize displacements by changes in the mesh rather than field
>>> > quantities (for attached file, px and py, displacements in x and y
>>> > coordinates).
>>> >
>>> > Is this possible in paraview?  How so?  Thanks!
>>> >
>>> > ___
>>> > Powered by www.kitware.com
>>> >
>>> > Visit other Kitware open-source projects at
>>> > http://www.kitware.com/opensource/opensource.html
>>> >
>>> > Please keep messages on-topic and check the ParaView Wiki at:
>>> > http://paraview.org/Wiki/ParaView
>>> >
>>> > Search the list archives at: http://markmail.org/search/?q=ParaView
>>> >
>>> > Follow this link to subscribe/unsubscribe:
>>> > https://paraview.org/mailman/listinfo/paraview
>>> >
>>>
>>>
>>>
>>> --
>>> Cory Quammen
>>> Staff R Engineer
>>> Kitware, Inc.
>>
>>
>



-- 
Cory Quammen
Staff R Engineer
Kitware, Inc.
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Re: [Paraview] ParaView - Variables and different Time Steps

[Utkarsh Ayachit]

The easiest way to do such a thing is as follows:

1. Apply Extract TimeSteps filter to your reader/source to choose the
timesteps of interest.
2. Apply Group TimeSteps filter to it to group the timesteps extracted
in (1) into a mutliblock dataset with 1 block for each selected
timestep in order.
3. Now add your programmable filter to (2) and you can access all
timesteps of interest as blocks in your input.

You can skip (1) if you want to use all timesteps, and not just a subset.

Utkarsh

On Wed, Jan 10, 2018 at 4:56 AM, Carolin Helbig  wrote:
> Dear ParaView team,
>
> I read a post at the ParaView website concerning variables and different
> time steps (see
> https://public.kitware.com/pipermail/paraview/2014-May/031054.html). I have
> a similar problem and I want to access values from different time steps
> using the programmable filter with multiple inputs. I unfortunately have no
> idea how to access other time steps using the programmable filter. Could you
> give me some advice or a hint where I can find detailed information about
> that issue? I would be very happy if you could help me.
>
> Best regards,
> Carolin.
>
> --
> Dr. Carolin Helbig
>  Department Umweltinformatik
> Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
> Permoserstraße 15 I 04318 Leipzig
> Tel.: +49 341 235 - 1032
> Email: carolin.hel...@ufz.de
> WWW: http://www.ufz.de
>  https://www.ufz.de/index.php?en=31616
>
>
> Sitz der Gesellschaft
> Registergericht: Amtsgericht Leipzig
> Handelsregister Nr.: B 4703
> Vorsitzender des Aufsichtsrats: MinDirig Wilfried Kraus
> Wissenschaftlicher Geschäftsführer: Prof. Dr. Dr. h.c. Georg Teutsch
> Administrative Geschäftsführerin: Prof. Dr. Heike Graßmann
>
> ___
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> Please keep messages on-topic and check the ParaView Wiki at:
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>
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Re: [Paraview] Compile Error of Paraview on Maverick

[Cory Quammen]

I don't see any errors in the terminal output you've posted. Are there
errors further back in the terminal output history?

Thanks,
Cory

On Wed, Jan 10, 2018 at 12:28 AM, Yangguang Liao  wrote:
> Hi,
>
> Trying to compile Paraview but get such error. I have no idea what is the
> reason.
>
> Here is terminal output:
> [  3%] Built target protobuf
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/dynamic_message.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/extension_set_heavy.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/generated_message_reflection.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/message.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/reflection_ops.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/service.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/text_format.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/unknown_field_set.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/wire_format.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/io/printer.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/io/zero_copy_stream_impl.cc.o
> [  3%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/io/tokenizer.cc.o
> [  4%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/compiler/importer.cc.o
> [  4%] Building CXX object
> ThirdParty/protobuf/vtkprotobuf/src/CMakeFiles/protoc_compiler.dir/google/protobuf/compiler/parser.cc.o
> [  4%] Linking CXX executable ../../../../bin/protoc
> [  4%] Built target protoc_compiler
> make: *** [all] Error 2
>
> Mu compiler is using icc and icpc. have Qt5 installed.
> Thanks!
> --
> Yangguang Liao
> PhD. student of Computer Science Department
> University of California, Davis
>
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-- 
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Staff R Engineer
Kitware, Inc.
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[Paraview] ParaView - Variables and different Time Steps

[Carolin Helbig]

Dear ParaView team,

I read a post at the ParaView website concerning variables and different 
time steps (see 
https://public.kitware.com/pipermail/paraview/2014-May/031054.html). I 
have a similar problem and I want to access values from different time 
steps using the programmable filter with multiple inputs. I 
unfortunately have no idea how to access other time steps using the 
programmable filter. Could you give me some advice or a hint where I can 
find detailed information about that issue? I would be very happy if you 
could help me.


Best regards,
Carolin.

--
Dr. Carolin Helbig
 
Department Umweltinformatik

Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Permoserstraße 15 I 04318 Leipzig
Tel.: +49 341 235 - 1032
Email: carolin.hel...@ufz.de
WWW: http://www.ufz.de
 https://www.ufz.de/index.php?en=31616

 


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Vorsitzender des Aufsichtsrats: MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer: Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin: Prof. Dr. Heike Graßmann  

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