[Paraview] generic NetCDFreader support for CellData

Thu May 3 10:12:50 EDT 2018

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.vanengelen1 at 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:kmorel at sandia.gov]
> *Sent:* Wednesday, May 02, 2018 7:27 PM
> *To:* Quammen, Cory (External Contacts); Engelen, J. van (Joeri)
> *Cc:* paraview at 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-bounces at public.kitware.com> on behalf of Cory
> Quammen <cory.quammen at kitware.com>
> *Date: *Wednesday, May 2, 2018 at 11:19 AM
> *To: *"j.vanengelen1 at uu.nl" <j.vanengelen1 at uu.nl>
> *Cc: *"paraview at public.kitware.com" <paraview at 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.vanengelen1 at 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.quammen at kitware.com]
> *Sent:* Wednesday, May 02, 2018 5:01 PM
> *To:* Engelen, J. van (Joeri)
> *Cc:* paraview at 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.vanengelen1 at 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
>
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>
>
> --
>
> Cory Quammen
> Staff R&D Engineer
> Kitware, Inc.
>
>
>
>
> --
>
> Cory Quammen
> Staff R&D Engineer
> Kitware, Inc.
>

-- 
Cory Quammen
Staff R&D Engineer
Kitware, Inc.
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