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

2018-01-18 Thread Omid Mahabadi
Thanks Ken. I will try this on other machines. BTW I have version 3.0 of
OpenGL:
$ glxinfo | grep "OpenGL version"
OpenGL version string: 3.0 Mesa 10.5.9

Best regards,
Omid
--
Omid Mahabadi, Ph.D., P.Eng.
President & Geomechanics Specialist
Geomechanica Inc

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On Tue, Jan 16, 2018 at 10:31 AM, Moreland, Kenneth <kmo...@sandia.gov>
wrote:

> Omid,
>
>
>
> The only other thing I can think of is that there is something odd about
> the OpenGL driver/hardware on your system that for some reason is not
> supporting the coincident topology resolution in ParaView. ParaView changed
> its rendering system from OpenGL 1.3 to OpenGL 3.1 in version 5, the
> version that you report seeing the issue.
>
>
>
> Once again, I recommend trying to run ParaView on a completely different
> computer if you can find access to one. You might also try updating the
> OpenGL drivers on your computer. Beyond that, I am out of ideas.
>
>
>
> -Ken
>
>
>
> *From: *Omid Mahabadi <omid.mahab...@geomechanica.com>
> *Date: *Tuesday, January 16, 2018 at 7:58 AM
> *To: *"Moreland, Kenneth" <kmo...@sandia.gov>
> *Cc: *"paraview@paraview.org" <paraview@paraview.org>
>
> *Subject: *[EXTERNAL] Re: [Paraview] ParaView 5.x not showing all objects
> available in Pipeline Browser
>
>
>
> Hi Ken,
>
> Thanks for your feedback and sorry for my late reply. Somehow I didn't get
> this message and only found your reply after searching in my mailbox.
>
>
>
> I tried various values for the Z Shift, increasing it by one order of
> magnitude until reaching a value of 200, restarting in between changes.
> This didn't help.
>
>
>
> I haven't really made any other changes in ParaView settings. I even
> restored to defaults a couple of times. I've been using Linux Mint 17 and
> have also experienced the same issue on Ubuntu 14.04 both 64 bit.
>
>
>
> Thanks
>
>
> Best regards,
>
> Omid
>
>
>
>
>
>
>
> On Wed, Jan 10, 2018 at 12:45 PM, Moreland, Kenneth <kmo...@sandia.gov>
> wrote:
>
> 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 <kmo...@sandia.gov>
> *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 f

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

2018-01-16 Thread Omid Mahabadi
Hi Ken,
Thanks for your feedback and sorry for my late reply. Somehow I didn't get
this message and only found your reply after searching in my mailbox.

I tried various values for the Z Shift, increasing it by one order of
magnitude until reaching a value of 200, restarting in between changes.
This didn't help.

I haven't really made any other changes in ParaView settings. I even
restored to defaults a couple of times. I've been using Linux Mint 17 and
have also experienced the same issue on Ubuntu 14.04 both 64 bit.

Thanks

Best regards,
Omid



On Wed, Jan 10, 2018 at 12:45 PM, Moreland, Kenneth <kmo...@sandia.gov>
wrote:

> 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 <kmo...@sandia.gov>
> *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 <kmo...@sandia.gov>
> 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 aroun

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

2018-01-10 Thread 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 <kmo...@sandia.gov> 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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[Paraview] ParaView 5.x not showing all objects available in Pipeline Browser

2018-01-08 Thread Omid Mahabadi
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


ucs_basic_0.vtu
Description: Binary data


ucs_broken_joint_0.vtu
Description: Binary data
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Re: [Paraview] ParaView Seg Faults when running Animation in a Programmable Filter

2015-01-30 Thread Omid Mahabadi
After a lot of debugging, it turns out the issue is with the SetCells
function of the vtk unstructured grid. Below are the bits of my
Programmable Filter code that are relevant to the seg fault:

output  = self.GetOutputDataObject(0)

cellArray   = vtk.vtkCellArray()
cellTypes   = []

# Create a polygon to display the selected points
polygon = vtk.vtkPolygon()
polygon.GetPoints().DeepCopy(pointArray)
polygon.GetPointIds().SetNumberOfIds(len(coordinates))
for i in range(len(coordinates)):
  polygon.GetPointIds().SetId(i, coordinates[i][0])

# Add the polygon to a list of Cells
cellArray.InsertNextCell(polygon)
cellTypes.append(vtk.VTK_POLYGON)

# Get the cell containing a given cell  add it to the cellArray
selectedCell  = input.GetCell(cellID)  
cellArray.InsertNextCell(selectedCell)
cellTypes.append(vtk.VTK_TETRA)

# SetCells of the output with only the selected analyzed cells
output.SetCells(cellTypes, cellArray)

The last line above seg faults on one of my computers but not on the
other one, both using Linux Mint 15 OS, and similar versions of
ParaView. Any thoughts?


On 15-01-28 07:27 PM, Omid Mahabadi wrote:
 Hi,
 I've been experiencing a very weird seg faults in various versions of
 ParaView (4.1.x, 4.2.0, 4.3.x) when running an animation (streaming
 over time) of my Programmable Filter. I'm not even sure this is a
 ParaView issue, but I'll still share my story in case someone has any
 insights that they can kindly share.

 My Programmable Filter code works fine for the Current time step,
 regardless at which time step I run it (i.e., hit the Apply button of
 the Programmable Filter). However, when I hit the Play button to loop
 over time steps (which appends some information to a CSV file),
 ParaView seg faults after reaching the /3rd time step/. The filter has
 been working for some time and this started to happen all of a sudden,
 without any system update.

 It may be related to a weird combination of hardware, software, and
 drivers. My script works fine on a desktop computer I have but it seg
 faults on my main workstation, which has an AMD/ATI Radeon R9 280x GPU
 running on Linux Mint 15, 64-bit. When I completely removed the AMD
 drivers, it still seg faulted but after reaching the /6th time step/
 after the current one. Then, I launched an Ubuntu 14.04 LTS 64-bit,
 live on a USB flash drive. The script in Programmable Filter worked
 perfectly fine. As a result, I installed the OS, but it acted up
 exactly as the Linux Mint installation.

 The input files are massive vtk unstructured grids (about 800 MB
 each). I created smaller files, but unfortunately I couldn't reproduce
 the error. But I'm fairly sure that the files are not corrupted. As
 such, I can't send out the files that cause the issue. I also
 monitored the memory usage using free -h command while Playing. Here's
 the output for the -/+ buffers/cache line:

  total   used   free
 -/+ buffers/cache:   7.2G   8.4G (Opening the .vtu files)
 -/+ buffers/cache:   7.2G   8.4G
 -/+ buffers/cache:   7.4G   8.2G
 -/+ buffers/cache:   7.6G   8.0G
 -/+ buffers/cache:   7.6G   8.0G
 -/+ buffers/cache:   7.6G   8.0G
 -/+ buffers/cache:   7.9G   7.7G
 -/+ buffers/cache:   8.3G   7.4G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.6G   7.0G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.5G   7.1G
 -/+ buffers/cache:   8.6G   7.0G
 -/+ buffers/cache:   8.9G   6.7G
 -/+ buffers/cache:   9.1G   6.5G
 -/+ buffers/cache:   9.3G   6.3G
 -/+ buffers/cache:   9.4G   6.2G (Seg faults here)
 -/+ buffers/cache:   7.0G   8.6G

 As you can see, my system still had a lot of free memory when the seg
 fault happened and I haven't done anything explicitly to limit memory
 usage by a single process.

 Looking at syslog, this is the error message for the seg fault:

 kernel: [77995.911073] paraview[22483]: segfault at 7f3c8e0398ac
 ip 7f3a47ebe169 sp 7fff9106ab50 error 4 in
 fglrx_dri.so[7f3a479e9000+21e9000]


 Am I missing something here? Is there any other debugging steps I
 should take? Any insights or help will be hugely appreciated.

 Thank you,
 Omid



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-- 
Omid Mahabadi

[Paraview] ParaView Seg Faults when running Animation in a Programmable Filter

2015-01-28 Thread Omid Mahabadi
Hi,
I've been experiencing a very weird seg faults in various versions of
ParaView (4.1.x, 4.2.0, 4.3.x) when running an animation (streaming over
time) of my Programmable Filter. I'm not even sure this is a ParaView
issue, but I'll still share my story in case someone has any insights
that they can kindly share.

My Programmable Filter code works fine for the Current time step,
regardless at which time step I run it (i.e., hit the Apply button of
the Programmable Filter). However, when I hit the Play button to loop
over time steps (which appends some information to a CSV file), ParaView
seg faults after reaching the /3rd time step/. The filter has been
working for some time and this started to happen all of a sudden,
without any system update.

It may be related to a weird combination of hardware, software, and
drivers. My script works fine on a desktop computer I have but it seg
faults on my main workstation, which has an AMD/ATI Radeon R9 280x GPU
running on Linux Mint 15, 64-bit. When I completely removed the AMD
drivers, it still seg faulted but after reaching the /6th time step/
after the current one. Then, I launched an Ubuntu 14.04 LTS 64-bit, live
on a USB flash drive. The script in Programmable Filter worked perfectly
fine. As a result, I installed the OS, but it acted up exactly as the
Linux Mint installation.

The input files are massive vtk unstructured grids (about 800 MB each).
I created smaller files, but unfortunately I couldn't reproduce the
error. But I'm fairly sure that the files are not corrupted. As such, I
can't send out the files that cause the issue. I also monitored the
memory usage using free -h command while Playing. Here's the output for
the -/+ buffers/cache line:

 total   used   free
-/+ buffers/cache:   7.2G   8.4G (Opening the .vtu files)
-/+ buffers/cache:   7.2G   8.4G
-/+ buffers/cache:   7.4G   8.2G
-/+ buffers/cache:   7.6G   8.0G
-/+ buffers/cache:   7.6G   8.0G
-/+ buffers/cache:   7.6G   8.0G
-/+ buffers/cache:   7.9G   7.7G
-/+ buffers/cache:   8.3G   7.4G
-/+ buffers/cache:   8.5G   7.1G
-/+ buffers/cache:   8.6G   7.0G
-/+ buffers/cache:   8.5G   7.1G
-/+ buffers/cache:   8.5G   7.1G
-/+ buffers/cache:   8.5G   7.1G
-/+ buffers/cache:   8.5G   7.1G
-/+ buffers/cache:   8.6G   7.0G
-/+ buffers/cache:   8.9G   6.7G
-/+ buffers/cache:   9.1G   6.5G
-/+ buffers/cache:   9.3G   6.3G
-/+ buffers/cache:   9.4G   6.2G (Seg faults here)
-/+ buffers/cache:   7.0G   8.6G

As you can see, my system still had a lot of free memory when the seg
fault happened and I haven't done anything explicitly to limit memory
usage by a single process.

Looking at syslog, this is the error message for the seg fault:

kernel: [77995.911073] paraview[22483]: segfault at 7f3c8e0398ac ip
7f3a47ebe169 sp 7fff9106ab50 error 4 in
fglrx_dri.so[7f3a479e9000+21e9000]


Am I missing something here? Is there any other debugging steps I should
take? Any insights or help will be hugely appreciated.

Thank you,
Omid

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Re: [Paraview] Programmable filter, looping over time steps and reimporting inputs

2015-01-09 Thread Omid Mahabadi
Thanks Utkarsh for your reply. I've gone through the blog a few times
already but I still don't understand the whole procedure. I even tried
to just run the example in the blog in a Programmable Source but it
doesn't work ('No module named numpy_interface'). Part of the issue
could be that I still don't fully understand the RequestInformation,
RequestUpdateExtent, and RequestData bits of the filter.

The input data that I'm working on in the pipeline (vtk unstructured
grid) already have different time steps. How can I update the values of
the inputs for the different time steps?

Thank you,
Omid
 
On 14-12-16 05:26 PM, Utkarsh Ayachit wrote:
 Check this blog: http://www.kitware.com/blog/home/post/783
 It should give you information on what you need to put in the Scripts
 for various passes of the filter.

 Utkarsh


 On Tue, Dec 16, 2014 at 5:12 PM, Omid Mahabadi
 omid.mahab...@geomechanica.com
 mailto:omid.mahab...@geomechanica.com wrote:

 Hi,
 I'm writing a python script for the Programmable Filter of
 ParaView to do some analysis on my simulation results. The
 simulations results are transient and hence the analysis has to be
 done over time steps (perhaps similar to integrate over time
 filter). All bits of my script are working fine. However, after
 spending a considerable amount of time on fiddling with the
 script, googling, reading mailing lists and the VTK documentation,
 I haven't found a way to loop over time steps AND update the
 input from within the script. I can loop over time steps using:

 from vtk import vtkStreamingDemandDrivenPipeline
 for time in
 outInfo.Get(vtkStreamingDemandDrivenPipeline.TIME_STEPS()):
 #Perform some analysis, for instance subtracting value_v
 for this time from value_v at time zero...

 However, the input data is still from the time step where I first
 applied the script. Of course, when I animate the results, the
 inputs will be updated, but I will need to achieve the same
 results from within my script in the Programmable Filter dialogue.

 How can I update the inputs from within my for loop or how can I
 modify the for loop or my script to achieve that? Can Programmable
 Filter handle my situation? If not, what is the alternative?

 Many thanks,
 Omid

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Omid Mahabadi, Ph.D.
Geomechanica, Inc.
http://www.geomechanica.com/
Tel : +1-647-478-9767
Cell: +1-416-824-2408

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[Paraview] Programmable filter, looping over time steps and reimporting inputs

2014-12-16 Thread Omid Mahabadi
Hi,
I'm writing a python script for the Programmable Filter of ParaView to
do some analysis on my simulation results. The simulations results are
transient and hence the analysis has to be done over time steps (perhaps
similar to integrate over time filter). All bits of my script are
working fine. However, after spending a considerable amount of time on
fiddling with the script, googling, reading mailing lists and the VTK
documentation, I haven't found a way to loop over time steps AND update
the input from within the script. I can loop over time steps using:

from vtk import vtkStreamingDemandDrivenPipeline
for time in outInfo.Get(vtkStreamingDemandDrivenPipeline.TIME_STEPS()):
#Perform some analysis, for instance subtracting value_v for
this time from value_v at time zero...

However, the input data is still from the time step where I first
applied the script. Of course, when I animate the results, the inputs
will be updated, but I will need to achieve the same results from within
my script in the Programmable Filter dialogue.

How can I update the inputs from within my for loop or how can I modify
the for loop or my script to achieve that? Can Programmable Filter
handle my situation? If not, what is the alternative?

Many thanks,
Omid
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