Re: [Paraview] generic NetCDFreader support for CellData

2018-05-03 Thread Engelen, J. van (Joeri) 
Thank you Cory,

That indeed worked on the toy example, but when I tried it on my full dataset 
(uploaded here as well) Paraview v5.4.1 had trouble rendering it (only rendered 
part of the outer sides, when activating coloring).
I think it is not the script now giving issues, but the renderer. As I 
experience similar issues previously with celldata loaded from a .VTR file (I 
assumed that that file was corrupted).
It seems to me that when you go beyond a certain amount of cells, Paraview does 
not render its output properly.

Could you test whether it works for you on v5.5?

I uploaded my full dataset here:
https://coeri.stackstorage.com/s/ztga1yLO8mjD1EO

To visualize data properly:
Put a threshold filter and filter out 0.0 (as that is NoData) by putting 
minimum on 0.5, furthermore stretch the z direction by a factor 3000.


From: Cory Quammen [mailto:cory.quam...@kitware.com]
Sent: Thursday, May 03, 2018 4:13 PM
To: Engelen, J. van (Joeri)
Cc: Moreland, Kenneth; paraview@public.kitware.com
Subject: Re: [Paraview] generic NetCDFreader support for CellData

Indeed, my original script is not quite right. Here is a more robust version 
that should copy all point data arrays to cell data arrays:


dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].PointData

outputCd = output.CellData

for array in inputPd:

  print(type(array))

  outputCd.append(array, array.GetName())
I hope that does it. It works in my ParaView 5.5 with the sample data you 
provided (thank you for providing that!).

Best regards,
Cory

On Thu, May 3, 2018 at 7:48 AM Engelen, J. van (Joeri) 
<j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>> wrote:
Thanks everybody for the support,

I followed Ken’s suggestion, which will simplify things, however when I put 
Cory’s original script in the programmable filter no Data Array can be found in 
the output. So I sense there is a (small) bug in the script?
I tried changing the last three lines to the oneliner 
output.GetCellData().SetScalars(inputs[0].GetPointData().GetScalars())
But that did not help.

I have uploaded a small subset of my data here for you to toy around with 
https://coeri.stackstorage.com/s/0vUfQkVyv2MD3Ml. (Note: It helps for 
visualization to stretch the z-axis by a factor 3000).
This perhaps helps you with helping me.


From: Moreland, Kenneth [mailto:kmo...@sandia.gov<mailto:kmo...@sandia.gov>]
Sent: Wednesday, May 02, 2018 7:27 PM
To: Quammen, Cory (External Contacts); Engelen, J. van (Joeri)
Cc: paraview@public.kitware.com<mailto:paraview@public.kitware.com>
Subject: Re: [Paraview] generic NetCDFreader support for CellData

The NetCDF Generic/CF reader has an option named “Output Type” that you can use 
to force the output to a vtkImageData. Then Cory’s original programmable filter 
will work, and you won’t have to deal with the coordinates.

-Ken

From: ParaView 
<paraview-boun...@public.kitware.com<mailto:paraview-boun...@public.kitware.com>>
 on behalf of Cory Quammen 
<cory.quam...@kitware.com<mailto:cory.quam...@kitware.com>>
Date: Wednesday, May 2, 2018 at 11:19 AM
To: "j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>" 
<j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>>
Cc: "paraview@public.kitware.com<mailto:paraview@public.kitware.com>" 
<paraview@public.kitware.com<mailto:paraview@public.kitware.com>>
Subject: [EXTERNAL] Re: [Paraview] generic NetCDFreader support for CellData

On Wed, May 2, 2018 at 11:37 AM Engelen, J. van (Joeri) 
<j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>> wrote:
Thank you Cory,

I sense this solution might work. However, the type of my data is “Rectilinear 
Grid”, not sure if that increases the complexity (dx = 1000, dy = 1000, dz = 1).

Ah. From the documentation: "To define a 
vtkRectilinearGrid<https://www.vtk.org/doc/nightly/html/classvtkRectilinearGrid.html>,
 you must specify the dimensions of the data and provide three arrays of values 
specifying the coordinates along the x-y-z axes". It should be a similar 
script, but you'd have to add an additional X, Y, and Z position at the end of 
those coordinate arrays. So your script would look more like:

dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].GetPointData()

outputCd = output.GetCellData()

outputCd.SetScalars(inputPd.GetScalars())



# Set coordinates

xCoords = inputs[0].GetXCoordinates().NewInstance()

xCoords.DeepCopy(inputs[0].GetXCoordinates())

xCoords.InsertNextValue(1.0) # Should a reasonable x value for your dataset 
larger than previous max x

output.SetXCoordinates(xCoords)



yCoords = inputs[0].GetYCoordinates().NewIn

Re: [Paraview] generic NetCDFreader support for CellData

2018-05-03 Thread Cory Quammen 
Indeed, my original script is not quite right. Here is a more robust
version that should copy all point data arrays to cell data arrays:

dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].PointData

outputCd = output.CellData

for array in inputPd:

  print(type(array))

  outputCd.append(array, array.GetName())

I hope that does it. It works in my ParaView 5.5 with the sample data you
provided (thank you for providing that!).

Best regards,
Cory

On Thu, May 3, 2018 at 7:48 AM Engelen, J. van (Joeri) <j.vanengel...@uu.nl>
wrote:

> Thanks everybody for the support,
>
>
>
> I followed Ken’s suggestion, which will simplify things, however when I
> put Cory’s original script in the programmable filter no Data Array can be
> found in the output. So I sense there is a (small) bug in the script?
>
> I tried changing the last three lines to the oneliner output.GetCellData()
> .SetScalars(inputs[0].GetPointData().GetScalars())
>
> But that did not help.
>
>
>
> I have uploaded a small subset of my data here for you to toy around with
> https://coeri.stackstorage.com/s/0vUfQkVyv2MD3Ml. (Note: It helps for
> visualization to stretch the z-axis by a factor 3000).
>
> This perhaps helps you with helping me.
>
>
>
>
>
> *From:* Moreland, Kenneth [mailto:kmo...@sandia.gov]
> *Sent:* Wednesday, May 02, 2018 7:27 PM
> *To:* Quammen, Cory (External Contacts); Engelen, J. van (Joeri)
> *Cc:* paraview@public.kitware.com
> *Subject:* Re: [Paraview] generic NetCDFreader support for CellData
>
>
>
> The NetCDF Generic/CF reader has an option named “Output Type” that you
> can use to force the output to a vtkImageData. Then Cory’s original
> programmable filter will work, and you won’t have to deal with the
> coordinates.
>
>
>
> -Ken
>
>
>
> *From: *ParaView <paraview-boun...@public.kitware.com> on behalf of Cory
> Quammen <cory.quam...@kitware.com>
> *Date: *Wednesday, May 2, 2018 at 11:19 AM
> *To: *"j.vanengel...@uu.nl" <j.vanengel...@uu.nl>
> *Cc: *"paraview@public.kitware.com" <paraview@public.kitware.com>
> *Subject: *[EXTERNAL] Re: [Paraview] generic NetCDFreader support for
> CellData
>
>
>
> On Wed, May 2, 2018 at 11:37 AM Engelen, J. van (Joeri) <
> j.vanengel...@uu.nl> wrote:
>
> Thank you Cory,
>
>
>
> I sense this solution might work. However, the type of my data is
> “Rectilinear Grid”, not sure if that increases the complexity (dx = 1000,
> dy = 1000, dz = 1).
>
>
>
> Ah. From the documentation: "To define a *vtkRectilinearGrid*
> <https://www.vtk.org/doc/nightly/html/classvtkRectilinearGrid.html>, you
> must specify the dimensions of the data and provide three arrays of values
> specifying the coordinates along the x-y-z axes". It should be a similar
> script, but you'd have to add an additional X, Y, and Z position at the end
> of those coordinate arrays. So your script would look more like:
>
>
>
> dims = inputs[0].GetDimensions()
>
> ext = inputs[0].GetExtent()
>
> output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)
>
> output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)
>
> inputPd = inputs[0].GetPointData()
>
> outputCd = output.GetCellData()
>
> outputCd.SetScalars(inputPd.GetScalars())
>
>
>
> *# Set coordinates*
>
> xCoords = inputs[0].GetXCoordinates().NewInstance()
>
> xCoords.DeepCopy(inputs[0].GetXCoordinates())
>
> xCoords.InsertNextValue(1.0) # Should a reasonable x value for your dataset 
> larger than previous max x
>
> output.SetXCoordinates(xCoords)
>
>
>
> yCoords = inputs[0].GetYCoordinates().NewInstance()
>
> yCoords.DeepCopy(inputs[0].GetYCoordinates())
>
> yCoords.InsertNextValue(1.5) # Should be a reasonable like the x coordinate
>
> output.SetYCoordinates(yCoords)
>
>
>
> zCoords = inputs[0].GetZCoordinates().NewInstance()
>
> zCoords.DeepCopy(inputs[0].GetZCoordinates())
>
> zCoords.InsertNextValue(1.0) # Should be a reasonable like the z coordinate
>
> output.SetZCoordinates(zCoords)
>
>
>
> Some extent information also needs to be supplied, but I'm not entirely
> clear on how to do that correctly.
>
>
>
> A better solution would be to add an option to the reader to take care of
> this for you if that is reasonable for your data.
>
>
>
> Best,
>
> Cory
>
>
>
> Regardless, the script you provided does not give me output and it also
> does not throw an error, so I’m left a bit in the dark here.
>
>
>
>

Re: [Paraview] generic NetCDFreader support for CellData

2018-05-03 Thread Engelen, J. van (Joeri) 
Thanks everybody for the support,

I followed Ken’s suggestion, which will simplify things, however when I put 
Cory’s original script in the programmable filter no Data Array can be found in 
the output. So I sense there is a (small) bug in the script?
I tried changing the last three lines to the oneliner 
output.GetCellData().SetScalars(inputs[0].GetPointData().GetScalars())
But that did not help.

I have uploaded a small subset of my data here for you to toy around with 
https://coeri.stackstorage.com/s/0vUfQkVyv2MD3Ml. (Note: It helps for 
visualization to stretch the z-axis by a factor 3000).
This perhaps helps you with helping me.


From: Moreland, Kenneth [mailto:kmo...@sandia.gov]
Sent: Wednesday, May 02, 2018 7:27 PM
To: Quammen, Cory (External Contacts); Engelen, J. van (Joeri)
Cc: paraview@public.kitware.com
Subject: Re: [Paraview] generic NetCDFreader support for CellData

The NetCDF Generic/CF reader has an option named “Output Type” that you can use 
to force the output to a vtkImageData. Then Cory’s original programmable filter 
will work, and you won’t have to deal with the coordinates.

-Ken

From: ParaView <paraview-boun...@public.kitware.com> on behalf of Cory Quammen 
<cory.quam...@kitware.com>
Date: Wednesday, May 2, 2018 at 11:19 AM
To: "j.vanengel...@uu.nl" <j.vanengel...@uu.nl>
Cc: "paraview@public.kitware.com" <paraview@public.kitware.com>
Subject: [EXTERNAL] Re: [Paraview] generic NetCDFreader support for CellData

On Wed, May 2, 2018 at 11:37 AM Engelen, J. van (Joeri) 
<j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>> wrote:
Thank you Cory,

I sense this solution might work. However, the type of my data is “Rectilinear 
Grid”, not sure if that increases the complexity (dx = 1000, dy = 1000, dz = 1).

Ah. From the documentation: "To define a 
vtkRectilinearGrid<https://www.vtk.org/doc/nightly/html/classvtkRectilinearGrid.html>,
 you must specify the dimensions of the data and provide three arrays of values 
specifying the coordinates along the x-y-z axes". It should be a similar 
script, but you'd have to add an additional X, Y, and Z position at the end of 
those coordinate arrays. So your script would look more like:

dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].GetPointData()

outputCd = output.GetCellData()

outputCd.SetScalars(inputPd.GetScalars())



# Set coordinates

xCoords = inputs[0].GetXCoordinates().NewInstance()

xCoords.DeepCopy(inputs[0].GetXCoordinates())

xCoords.InsertNextValue(1.0) # Should a reasonable x value for your dataset 
larger than previous max x

output.SetXCoordinates(xCoords)



yCoords = inputs[0].GetYCoordinates().NewInstance()

yCoords.DeepCopy(inputs[0].GetYCoordinates())

yCoords.InsertNextValue(1.5) # Should be a reasonable like the x coordinate

output.SetYCoordinates(yCoords)



zCoords = inputs[0].GetZCoordinates().NewInstance()

zCoords.DeepCopy(inputs[0].GetZCoordinates())

zCoords.InsertNextValue(1.0) # Should be a reasonable like the z coordinate

output.SetZCoordinates(zCoords)


Some extent information also needs to be supplied, but I'm not entirely clear 
on how to do that correctly.

A better solution would be to add an option to the reader to take care of this 
for you if that is reasonable for your data.

Best,
Cory

Regardless, the script you provided does not give me output and it also does 
not throw an error, so I’m left a bit in the dark here.

From: Cory Quammen 
[mailto:cory.quam...@kitware.com<mailto:cory.quam...@kitware.com>]
Sent: Wednesday, May 02, 2018 5:01 PM
To: Engelen, J. van (Joeri)
Cc: paraview@public.kitware.com<mailto:paraview@public.kitware.com>
Subject: Re: [Paraview] generic NetCDFreader support for CellData

Joeri,

You can try the "Point Data to Cell Data" filter, but that averages the point 
data and places the results in the cell data. You may wind up with some 
incorrect values using that approach.

Better would be to use a "Progammable Filter" to resize the cartesian grid read 
by the NetCDF reader and treat the point data as cell data. That is a bit 
involved, but not terrible. Set the Script to


dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].GetPointData()

outputCd = output.GetCellData()

outputCd.SetScalars(inputPd.GetScalars())


This assumes that the NetCDF reader is producing a vtkImageData (you can check 
under the Information panel) which would report the Type: of the data set as 
"Image (Uniform Rectilinear Grid).

HTH,
Cory

On Wed, May 2, 2018 at 10:17 AM Engelen, J. van (Joeri) 
<j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>> wrote:
Hi,

Re: [Paraview] generic NetCDFreader support for CellData

2018-05-02 Thread Moreland, Kenneth via ParaView 
The NetCDF Generic/CF reader has an option named “Output Type” that you can use 
to force the output to a vtkImageData. Then Cory’s original programmable filter 
will work, and you won’t have to deal with the coordinates.

-Ken

From: ParaView <paraview-boun...@public.kitware.com> on behalf of Cory Quammen 
<cory.quam...@kitware.com>
Date: Wednesday, May 2, 2018 at 11:19 AM
To: "j.vanengel...@uu.nl" <j.vanengel...@uu.nl>
Cc: "paraview@public.kitware.com" <paraview@public.kitware.com>
Subject: [EXTERNAL] Re: [Paraview] generic NetCDFreader support for CellData

On Wed, May 2, 2018 at 11:37 AM Engelen, J. van (Joeri) 
<j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>> wrote:
Thank you Cory,

I sense this solution might work. However, the type of my data is “Rectilinear 
Grid”, not sure if that increases the complexity (dx = 1000, dy = 1000, dz = 1).

Ah. From the documentation: "To define a 
vtkRectilinearGrid<https://www.vtk.org/doc/nightly/html/classvtkRectilinearGrid.html>,
 you must specify the dimensions of the data and provide three arrays of values 
specifying the coordinates along the x-y-z axes". It should be a similar 
script, but you'd have to add an additional X, Y, and Z position at the end of 
those coordinate arrays. So your script would look more like:

dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].GetPointData()

outputCd = output.GetCellData()

outputCd.SetScalars(inputPd.GetScalars())



# Set coordinates

xCoords = inputs[0].GetXCoordinates().NewInstance()

xCoords.DeepCopy(inputs[0].GetXCoordinates())

xCoords.InsertNextValue(1.0) # Should a reasonable x value for your dataset 
larger than previous max x

output.SetXCoordinates(xCoords)



yCoords = inputs[0].GetYCoordinates().NewInstance()

yCoords.DeepCopy(inputs[0].GetYCoordinates())

yCoords.InsertNextValue(1.5) # Should be a reasonable like the x coordinate

output.SetYCoordinates(yCoords)



zCoords = inputs[0].GetZCoordinates().NewInstance()

zCoords.DeepCopy(inputs[0].GetZCoordinates())

zCoords.InsertNextValue(1.0) # Should be a reasonable like the z coordinate

output.SetZCoordinates(zCoords)


Some extent information also needs to be supplied, but I'm not entirely clear 
on how to do that correctly.


A better solution would be to add an option to the reader to take care of this 
for you if that is reasonable for your data.

Best,
Cory


Regardless, the script you provided does not give me output and it also does 
not throw an error, so I’m left a bit in the dark here.

From: Cory Quammen 
[mailto:cory.quam...@kitware.com<mailto:cory.quam...@kitware.com>]
Sent: Wednesday, May 02, 2018 5:01 PM
To: Engelen, J. van (Joeri)
Cc: paraview@public.kitware.com<mailto:paraview@public.kitware.com>
Subject: Re: [Paraview] generic NetCDFreader support for CellData

Joeri,

You can try the "Point Data to Cell Data" filter, but that averages the point 
data and places the results in the cell data. You may wind up with some 
incorrect values using that approach.

Better would be to use a "Progammable Filter" to resize the cartesian grid read 
by the NetCDF reader and treat the point data as cell data. That is a bit 
involved, but not terrible. Set the Script to


dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].GetPointData()

outputCd = output.GetCellData()

outputCd.SetScalars(inputPd.GetScalars())


This assumes that the NetCDF reader is producing a vtkImageData (you can check 
under the Information panel) which would report the Type: of the data set as 
"Image (Uniform Rectilinear Grid).

HTH,
Cory

On Wed, May 2, 2018 at 10:17 AM Engelen, J. van (Joeri) 
<j.vanengel...@uu.nl<mailto:j.vanengel...@uu.nl>> wrote:
Hi,

I was wondering whether it is possible to read NetCDF files as CellData.

I have categorial data on Cartesian coordinates that I want to visualize. To be 
more specific, the data represents lithologies of the subsurface. So 1 = sand, 
3 = clay, 5 = rock.
The problem is that my file is automatically interpreted as PointData. To 
render this PointData, Paraview than consequently interpolates to achieve cell 
values.
With most variables that is not such a problem, but here it is. If I have sand 
(1) overlying rock (5), Paraview shows me clay (3).

Also, the information available to me was ambiguous,
-this source says it is probably not possible:
https://public.kitware.com/pipermail/paraview/2017-September/040984.html
-this states it is possible return Cell Data information:
https://www.paraview.org/ParaView/Doc/Nightly/www/py-doc/paraview.simple.NetCDFReader.html

I tried converting my d

Re: [Paraview] generic NetCDFreader support for CellData

2018-05-02 Thread Cory Quammen 
On Wed, May 2, 2018 at 11:37 AM Engelen, J. van (Joeri) <j.vanengel...@uu.nl>
wrote:

> Thank you Cory,
>
>
>
> I sense this solution might work. However, the type of my data is
> “Rectilinear Grid”, not sure if that increases the complexity (dx = 1000,
> dy = 1000, dz = 1).
>

Ah. From the documentation: "To define a vtkRectilinearGrid
<https://www.vtk.org/doc/nightly/html/classvtkRectilinearGrid.html>, you
must specify the dimensions of the data and provide three arrays of values
specifying the coordinates along the x-y-z axes". It should be a similar
script, but you'd have to add an additional X, Y, and Z position at the end
of those coordinate arrays. So your script would look more like:

dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].GetPointData()

outputCd = output.GetCellData()

outputCd.SetScalars(inputPd.GetScalars())


# Set coordinates

xCoords = inputs[0].GetXCoordinates().NewInstance()

xCoords.DeepCopy(inputs[0].GetXCoordinates())

xCoords.InsertNextValue(1.0) # Should a reasonable x value for your
dataset larger than previous max x

output.SetXCoordinates(xCoords)


yCoords = inputs[0].GetYCoordinates().NewInstance()

yCoords.DeepCopy(inputs[0].GetYCoordinates())

yCoords.InsertNextValue(1.5) # Should be a reasonable like the x coordinate

output.SetYCoordinates(yCoords)


zCoords = inputs[0].GetZCoordinates().NewInstance()

zCoords.DeepCopy(inputs[0].GetZCoordinates())

zCoords.InsertNextValue(1.0) # Should be a reasonable like the z coordinate

output.SetZCoordinates(zCoords)


Some extent information also needs to be supplied, but I'm not entirely
clear on how to do that correctly.

A better solution would be to add an option to the reader to take care of
this for you if that is reasonable for your data.

Best,
Cory

Regardless, the script you provided does not give me output and it also
> does not throw an error, so I’m left a bit in the dark here.
>

>
> *From:* Cory Quammen [mailto:cory.quam...@kitware.com]
> *Sent:* Wednesday, May 02, 2018 5:01 PM
> *To:* Engelen, J. van (Joeri)
> *Cc:* paraview@public.kitware.com
> *Subject:* Re: [Paraview] generic NetCDFreader support for CellData
>
>
>
> Joeri,
>
>
>
> You can try the "Point Data to Cell Data" filter, but that averages the
> point data and places the results in the cell data. You may wind up with
> some incorrect values using that approach.
>
>
>
> Better would be to use a "Progammable Filter" to resize the cartesian grid
> read by the NetCDF reader and treat the point data as cell data. That is a
> bit involved, but not terrible. Set the Script to
>
>
>
> dims = inputs[0].GetDimensions()
>
> ext = inputs[0].GetExtent()
>
> output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)
>
> output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)
>
> inputPd = inputs[0].GetPointData()
>
> outputCd = output.GetCellData()
>
> outputCd.SetScalars(inputPd.GetScalars())
>
>
>
> This assumes that the NetCDF reader is producing a vtkImageData (you can
> check under the Information panel) which would report the Type: of the data
> set as "Image (Uniform Rectilinear Grid).
>
>
>
> HTH,
>
> Cory
>
>
>
> On Wed, May 2, 2018 at 10:17 AM Engelen, J. van (Joeri) <
> j.vanengel...@uu.nl> wrote:
>
> Hi,
>
>
>
> I was wondering whether it is possible to read NetCDF files as CellData.
>
>
>
> I have categorial data on Cartesian coordinates that I want to visualize.
> To be more specific, the data represents lithologies of the subsurface. So
> 1 = sand, 3 = clay, 5 = rock.
>
> The problem is that my file is automatically interpreted as PointData. To
> render this PointData, Paraview than consequently interpolates to achieve
> cell values.
>
> With most variables that is not such a problem, but here it is. If I have
> sand (1) overlying rock (5), Paraview shows me clay (3).
>
>
>
> Also, the information available to me was ambiguous,
>
> -this source says it is probably not possible:
>
> https://public.kitware.com/pipermail/paraview/2017-September/040984.html
>
> -this states it is possible return Cell Data information:
>
>
> https://www.paraview.org/ParaView/Doc/Nightly/www/py-doc/paraview.simple.NetCDFReader.html
>
>
>
> I tried converting my data from NetCDF to a .vtr file in Python, but this
> resulted in more problems than solutions. (Just gave me very glitched
> rendering).
>
>
>
> So I have two questions:
>
> -Is this possible?
>
> -Are there any workarounds you can think of to get my data a

Re: [Paraview] generic NetCDFreader support for CellData

2018-05-02 Thread Aashish Chaudhary 
is it possible for you to share you data with us?


On Wed, May 2, 2018 at 11:37 AM Engelen, J. van (Joeri) <j.vanengel...@uu.nl>
wrote:

> Thank you Cory,
>
>
>
> I sense this solution might work. However, the type of my data is
> “Rectilinear Grid”, not sure if that increases the complexity (dx = 1000,
> dy = 1000, dz = 1).
>
> Regardless, the script you provided does not give me output and it also
> does not throw an error, so I’m left a bit in the dark here.
>
>
>
> *From:* Cory Quammen [mailto:cory.quam...@kitware.com]
> *Sent:* Wednesday, May 02, 2018 5:01 PM
> *To:* Engelen, J. van (Joeri)
> *Cc:* paraview@public.kitware.com
> *Subject:* Re: [Paraview] generic NetCDFreader support for CellData
>
>
>
> Joeri,
>
>
>
> You can try the "Point Data to Cell Data" filter, but that averages the
> point data and places the results in the cell data. You may wind up with
> some incorrect values using that approach.
>
>
>
> Better would be to use a "Progammable Filter" to resize the cartesian grid
> read by the NetCDF reader and treat the point data as cell data. That is a
> bit involved, but not terrible. Set the Script to
>
>
>
> dims = inputs[0].GetDimensions()
>
> ext = inputs[0].GetExtent()
>
> output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)
>
> output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)
>
> inputPd = inputs[0].GetPointData()
>
> outputCd = output.GetCellData()
>
> outputCd.SetScalars(inputPd.GetScalars())
>
>
>
> This assumes that the NetCDF reader is producing a vtkImageData (you can
> check under the Information panel) which would report the Type: of the data
> set as "Image (Uniform Rectilinear Grid).
>
>
>
> HTH,
>
> Cory
>
>
>
> On Wed, May 2, 2018 at 10:17 AM Engelen, J. van (Joeri) <
> j.vanengel...@uu.nl> wrote:
>
> Hi,
>
>
>
> I was wondering whether it is possible to read NetCDF files as CellData.
>
>
>
> I have categorial data on Cartesian coordinates that I want to visualize.
> To be more specific, the data represents lithologies of the subsurface. So
> 1 = sand, 3 = clay, 5 = rock.
>
> The problem is that my file is automatically interpreted as PointData. To
> render this PointData, Paraview than consequently interpolates to achieve
> cell values.
>
> With most variables that is not such a problem, but here it is. If I have
> sand (1) overlying rock (5), Paraview shows me clay (3).
>
>
>
> Also, the information available to me was ambiguous,
>
> -this source says it is probably not possible:
>
> https://public.kitware.com/pipermail/paraview/2017-September/040984.html
>
> -this states it is possible return Cell Data information:
>
>
> https://www.paraview.org/ParaView/Doc/Nightly/www/py-doc/paraview.simple.NetCDFReader.html
>
>
>
> I tried converting my data from NetCDF to a .vtr file in Python, but this
> resulted in more problems than solutions. (Just gave me very glitched
> rendering).
>
>
>
> So I have two questions:
>
> -Is this possible?
>
> -Are there any workarounds you can think of to get my data as CellData in
> Paraview?
>
>
>
> I’m using Paraview v5.4.1 on Windows 7.
>
>
>
> Kind regards,
> Joeri
>
> ___
> 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://public.kitware.com/mailman/listinfo/paraview
>
>
>
>
> --
>
> Cory Quammen
> Staff R Engineer
> Kitware, Inc.
> ___
> 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://public.kitware.com/mailman/listinfo/paraview
>
___
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:
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Re: [Paraview] generic NetCDFreader support for CellData

2018-05-02 Thread Cory Quammen 
Joeri,

You can try the "Point Data to Cell Data" filter, but that averages the
point data and places the results in the cell data. You may wind up with
some incorrect values using that approach.

Better would be to use a "Progammable Filter" to resize the cartesian grid
read by the NetCDF reader and treat the point data as cell data. That is a
bit involved, but not terrible. Set the Script to

dims = inputs[0].GetDimensions()

ext = inputs[0].GetExtent()

output.SetDimensions(dims[0]+1, dims[1]+1, dims[2]+1)

output.SetExtent(ext[0], ext[1]+1, ext[2], ext[3]+1, ext[4], ext[5]+1)

inputPd = inputs[0].GetPointData()

outputCd = output.GetCellData()

outputCd.SetScalars(inputPd.GetScalars())


This assumes that the NetCDF reader is producing a vtkImageData (you can
check under the Information panel) which would report the Type: of the data
set as "Image (Uniform Rectilinear Grid).

HTH,
Cory

On Wed, May 2, 2018 at 10:17 AM Engelen, J. van (Joeri) 
wrote:

> Hi,
>
>
>
> I was wondering whether it is possible to read NetCDF files as CellData.
>
>
>
> I have categorial data on Cartesian coordinates that I want to visualize.
> To be more specific, the data represents lithologies of the subsurface. So
> 1 = sand, 3 = clay, 5 = rock.
>
> The problem is that my file is automatically interpreted as PointData. To
> render this PointData, Paraview than consequently interpolates to achieve
> cell values.
>
> With most variables that is not such a problem, but here it is. If I have
> sand (1) overlying rock (5), Paraview shows me clay (3).
>
>
>
> Also, the information available to me was ambiguous,
>
> -this source says it is probably not possible:
>
> https://public.kitware.com/pipermail/paraview/2017-September/040984.html
>
> -this states it is possible return Cell Data information:
>
>
> https://www.paraview.org/ParaView/Doc/Nightly/www/py-doc/paraview.simple.NetCDFReader.html
>
>
>
> I tried converting my data from NetCDF to a .vtr file in Python, but this
> resulted in more problems than solutions. (Just gave me very glitched
> rendering).
>
>
>
> So I have two questions:
>
> -Is this possible?
>
> -Are there any workarounds you can think of to get my data as CellData in
> Paraview?
>
>
>
> I’m using Paraview v5.4.1 on Windows 7.
>
>
>
> Kind regards,
> Joeri
> ___
> 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://public.kitware.com/mailman/listinfo/paraview
>


-- 
Cory Quammen
Staff R Engineer
Kitware, Inc.
___
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

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https://public.kitware.com/mailman/listinfo/paraview