[Paraview] adjusting vertical level setting via paraview python script
Andy Bauer
andy.bauer at kitware.com
Mon Aug 3 13:33:14 EDT 2015
Hi,
Dave is correct in that the reader's output needs to match what the adaptor
is producing and in this case the MPAS NetCDF reader does not match what
the adaptor provides to Catalyst. The way to get around this is to run
Catalyst with a sample Python script that outputs the full data set that
the adaptor provides. For MPAS this is slightly more complex because it
provides several outputs, 10 in fact, depending on how the scientists want
the data (e.g. spherical vs. projected, primal vs. dual grid, single level
vs. multiple levels) for what they're trying to do. The attached script can
be used to write out all 10 of these outputs which is done every 5th output
(this can be changed by changing the outputfrequency value).
The general workflow would be to run MPAS with this script for a small
amount of time steps (maybe also with a smaller input data set). Then use
those outputs to generate the Catalyst script that you want from the GUI.
If this is a bit unclear, I'd recommend going through the Catalyst User's
Guide (
http://www.paraview.org/files/catalyst/docs/ParaViewCatalystUsersGuide_v2.pdf)
for more details.
Regards,
Andy
On Mon, Aug 3, 2015 at 12:20 PM, David E DeMarle <dave.demarle at kitware.com>
wrote:
> Andy Bauer just explained it to me. He'll get back to you soon with a
> detailed explanation and hints about how to get what you want done.
>
> Meanwhile, what is tripping us up is that MPAS's catalyst adaptor is not
> the same thing as ParaViews MPAS reader. The reader has the
> SetVerticalLevel(int) method, but the adaptor probably has an entirely
> different method for doing that.
>
> I don't know firsthand what that method is so we'll have to wait for his
> response.
>
>
>
>
>
> David E DeMarle
> Kitware, Inc.
> R&D Engineer
> 21 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4909
>
> On Thu, Jul 30, 2015 at 4:20 PM, Eatmon Jr., Arnold <aeatmon at lanl.gov>
> wrote:
>
>> # Level2 = paraview.simple.FindSource('X_Y_Z_1LAYER-primal')
>>
>> # Level2.VerticalLevel = 32
>>
>>
>> Layer2 = output00240101_000000nc
>>
>> Layer2.VerticalLevel = 32
>>
>>
>>
>> Also,
>>
>> I tried both of the above both individually with the other commented out
>> and running at the same time, they both return that the attribute
>> VerticalLevel does not exist in that class. It seems to solely exist in
>> paraview.simple.NetCDFreader.
>>
>>
>> From: David E DeMarle <dave.demarle at kitware.com>
>> Date: Thursday, July 30, 2015 at 1:45 PM
>> To: First name Last name <aeatmon at lanl.gov>
>> Subject: Re: [Paraview] adjusting vertical level setting via paraview
>> python script
>>
>> I verified in the GUI that I can change the level and see it take effect,
>> so it should work in principle. You might want to open that file in the
>> paraView GUI and do the same exercise.
>>
>> In your script a couple of bits looks fishy to me and might cause the
>> problem.
>>
>> paraview.simple.NetCDFMPASreader.PointArrayStatus = ['temperature']
>> paraview.simple.NetCDFMPASreader.ShowMultilayerView = 0
>> paraview.simple.NetCDFMPASreader.VerticalLevel = '1' *#use = 1 not = '1'*
>>
>> later
>>
>> paraview.simple.NetCDFMPASreader.VerticalLevel = 1
>>
>> just do it one time
>>
>>
>> I think the above all do something like set propeties of the global
>> netcdmfmpasreader class, not the one specific instance of that class that
>> you care about.
>>
>> # get active source.
>> # Level2 = paraview.simple.GetActiveSource()
>> # Level2.VerticalLevel = 1
>>
>> this is closer, try
>> level2=paraview.simple.FindSource('X_Y_Z_1LAYER-primal')
>>
>> or better yet, since it is defined early on just
>>
>> Layer2 = output00240101_000000nc
>>
>> Either should give you the specific instance and then you can call Layer2.VerticalLevel
>> = 1 on it.
>>
>>
>>
>> David E DeMarle
>> Kitware, Inc.
>> R&D Engineer
>> 21 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-881-4909
>>
>> On Thu, Jul 30, 2015 at 3:12 PM, Eatmon Jr., Arnold <aeatmon at lanl.gov>
>> wrote:
>>
>>> As a followup to my last reply, I’m pasting the script below for
>>> reference because there may be a problem within of which I am not aware.
>>> The script is not too clean, though.
>>>
>>> Also attached is an image of the output where I see the vertical level
>>> still needs to be turned down.
>>>
>>> ——————————————————————————————————————————————————
>>>
>>> from paraview import coprocessing
>>>
>>>
>>>
>>> #--------------------------------------------------------------
>>>
>>> # Code generated from cpstate.py to create the CoProcessor.
>>>
>>> # ParaView 4.3.1 64 bits
>>>
>>>
>>>
>>> # ----------------------- CoProcessor definition -----------------------
>>>
>>>
>>> def CreateCoProcessor():
>>>
>>> def _CreatePipeline(coprocessor, datadescription):
>>>
>>> class Pipeline:
>>>
>>> # state file generated using paraview version 4.3.1
>>>
>>>
>>> # ----------------------------------------------------------------
>>>
>>> # setup views used in the visualization
>>>
>>> # ----------------------------------------------------------------
>>>
>>>
>>> #### disable automatic camera reset on 'Show'
>>>
>>> paraview.simple._DisableFirstRenderCameraReset()
>>>
>>>
>>> # Create a new 'Render View'
>>>
>>> renderView1 = CreateView('RenderView')
>>>
>>> renderView1.ViewSize = [1811, 837]
>>>
>>> renderView1.CenterOfRotation = [0.0, 0.0, 69503.75]
>>>
>>> renderView1.StereoType = 0
>>>
>>> renderView1.CameraPosition = [-41129254.56226203,
>>> -8828710.007515563, 6001602.840730475]
>>>
>>> renderView1.CameraFocalPoint = [0.0, 0.0, 69503.75]
>>>
>>> renderView1.CameraViewUp = [0.06821863148547692,
>>> 0.3176561586160046, 0.9457487949828816]
>>>
>>> renderView1.CameraParallelScale = 10995245.645232411
>>>
>>> renderView1.Background = [0.37254901960784315,
>>> 0.36470588235294116, 0.3411764705882353]
>>>
>>>
>>> # register the view with coprocessor
>>>
>>> # and provide it with information such as the filename to use,
>>>
>>> # how frequently to write the images, etc.
>>>
>>> coprocessor.RegisterView(renderView1,
>>>
>>> filename='image_%t.png', freq=1, fittoscreen=0,
>>> magnification=1, width=1811, height=837, cinema={"camera":"Spherical",
>>> "phi":[-180,-162,-144,-126,-108,-90,-72,-54,-36,-18,0,18,36,54,72,90,108,126,144,162],
>>> "theta":[-180,-162,-144,-126,-108,-90,-72,-54,-36,-18,0,18,36,54,72,90,108,126,144,162]
>>> })
>>>
>>>
>>> # ----------------------------------------------------------------
>>>
>>> # setup the data processing pipelines
>>>
>>> # ---------------------------------------------------------------
>>>
>>>
>>> # create a new 'NetCDF MPAS reader'
>>>
>>> # create a producer from a simulation input
>>>
>>> output00240101_000000nc =
>>> coprocessor.CreateProducer(datadescription, 'X_Y_Z_1LAYER-primal')
>>>
>>>
>>> # ----------------------------------------------------------------
>>>
>>> # setup color maps and opacity mapes used in the visualization
>>>
>>> # note: the Get..() functions create a new object, if needed
>>>
>>> # ----------------------------------------------------------------
>>>
>>>
>>>
>>> # reset view to fit data
>>>
>>> renderView1.ResetCamera()
>>>
>>>
>>> # show data in view
>>>
>>> output00240101_000000ncDisplay = Show(output00240101_000000nc,
>>> renderView1)
>>>
>>>
>>> # Properties modified on output00240101_000000nc
>>>
>>> paraview.simple.NetCDFMPASreader.PointArrayStatus = ['temperature']
>>>
>>> paraview.simple.NetCDFMPASreader.ShowMultilayerView = 0
>>>
>>> paraview.simple.NetCDFMPASreader.VerticalLevel = '1'
>>>
>>>
>>> # Level1 = paraview.simple.ColorByArray()
>>>
>>> # Level1.ColorBy(mpas_data_1pvtuDisplay, ('CELLS', 'temperature'))
>>>
>>>
>>> # set scalar coloring
>>>
>>> ColorBy(output00240101_000000ncDisplay, ('CELLS', 'temperature'))
>>>
>>>
>>> # rescale color and/or opacity maps used to include current data
>>> range
>>>
>>>
>>> output00240101_000000ncDisplay.RescaleTransferFunctionToDataRange(True)
>>>
>>>
>>>
>>> # get color transfer function/color map for 'temperature'
>>>
>>> temperatureLUT = GetColorTransferFunction('temperature')
>>>
>>> temperatureLUT.InterpretValuesAsCategories = 0
>>>
>>> temperatureLUT.Discretize = 0
>>>
>>> temperatureLUT.MapControlPointsToLinearSpace()
>>>
>>> temperatureLUT.UseLogScale = 0
>>>
>>> temperatureLUT.RGBPoints = [-2.0, 0.105882, 0.2, 0.14902, -1.25,
>>> 0.141176, 0.25098, 0.180392, -0.5, 0.172549, 0.301961, 0.211765, 0.25,
>>> 0.211765, 0.34902, 0.243137, 1.0, 0.227451, 0.388235, 0.254902, 1.75,
>>> 0.239216, 0.431373, 0.258824, 2.5, 0.25098, 0.470588, 0.262745, 3.25,
>>> 0.258824, 0.509804, 0.258824, 4.0, 0.294118, 0.54902, 0.27451, 4.75,
>>> 0.333333, 0.580392, 0.294118, 5.5, 0.380392, 0.619608, 0.321569,
>>> 6.250000000000002, 0.431373, 0.658824, 0.34902, 7.0, 0.482353, 0.690196,
>>> 0.380392, 7.750000000000002, 0.52549, 0.729412, 0.388235, 8.5, 0.564706,
>>> 0.760784, 0.380392, 9.250000000000002, 0.631373, 0.788235, 0.411765, 10.0,
>>> 0.694118, 0.819608, 0.443137, 10.75, 0.745098, 0.85098, 0.458824, 11.5,
>>> 0.803922, 0.878431, 0.494118, 12.25, 0.843137, 0.901961, 0.521569, 13.0,
>>> 0.894118, 0.929412, 0.556863, 14.500000000000004, 0.94902, 0.94902,
>>> 0.647059, 16.0, 0.968627, 0.968627, 0.796078, 17.05, 1.0, 0.996078,
>>> 0.901961, 17.2, 0.968627, 1.0, 0.996078, 17.35, 0.901961, 1.0, 0.984314,
>>> 18.1, 0.831373, 0.988235, 0.972549, 19.0, 0.721569, 0.94902, 0.945098,
>>> 19.75, 0.639216, 0.882353, 0.901961, 20.500000000000004, 0.568627,
>>> 0.807843, 0.85098, 21.25, 0.513725, 0.717647, 0.788235, 22.0, 0.447059,
>>> 0.627451, 0.721569, 22.75, 0.388235, 0.541176, 0.65098, 23.5, 0.337255,
>>> 0.462745, 0.580392, 24.25, 0.286275, 0.388235, 0.521569, 25.0, 0.25098,
>>> 0.333333, 0.478431, 25.750000000000004, 0.219608, 0.290196, 0.45098, 26.5,
>>> 0.196078, 0.247059, 0.419608, 27.25, 0.152941, 0.188235, 0.34902, 28.0,
>>> 0.113725, 0.113725, 0.278431]
>>>
>>> temperatureLUT.ColorSpace = 'Lab'
>>>
>>> temperatureLUT.LockScalarRange = 0
>>>
>>> temperatureLUT.NanColor = [0.250004, 0.0, 0.0]
>>>
>>> temperatureLUT.ScalarRangeInitialized = 1.0
>>>
>>>
>>>
>>> # get opacity transfer function/opacity map for 'temperature'
>>>
>>> temperaturePWF = GetOpacityTransferFunction('temperature')
>>>
>>> temperaturePWF.Points = [-2.0, 0.0, 0.5, 0.0, 28.0, 1.0, 0.5, 0.0]
>>>
>>> temperaturePWF.ScalarRangeInitialized = 1
>>>
>>>
>>> # Properties modified on temperatureLUT
>>>
>>> # temperatureLUT.InterpretValuesAsCategories = 0
>>>
>>>
>>>
>>> # paraview.simple.NetCDFMPASreader.ShowMultilayerView = 0
>>>
>>> paraview.simple.NetCDFMPASreader.VerticalLevel = 1
>>>
>>>
>>> # renderView1.ResetCamera()
>>>
>>>
>>> # get active source.
>>>
>>> # Level2 = paraview.simple.GetActiveSource()
>>>
>>> # Level2.VerticalLevel = 1
>>>
>>>
>>>
>>> # ----------------------------------------------------------------
>>>
>>> # setup the visualization in view 'renderView1'
>>>
>>> # ----------------------------------------------------------------
>>>
>>>
>>> # show data from output00240101_000000nc
>>>
>>> output00240101_000000ncDisplay = Show(output00240101_000000nc,
>>> renderView1)
>>>
>>> # trace defaults for the display properties. 356617.92693278694
>>>
>>> output00240101_000000ncDisplay.ColorArrayName = ['CELLS',
>>> 'temperature']
>>>
>>> output00240101_000000ncDisplay.LookupTable = temperatureLUT
>>>
>>> output00240101_000000ncDisplay.ScalarOpacityUnitDistance = 1469170.
>>> 6394257464
>>>
>>>
>>> # show color legend
>>>
>>> output00240101_000000ncDisplay.SetScalarBarVisibility(renderView1,
>>> True)
>>>
>>>
>>> # setup the color legend parameters for each legend in this view
>>>
>>>
>>>
>>> # get color legend/bar for temperatureLUT in view renderView1
>>>
>>> temperatureLUTColorBar = GetScalarBar(temperatureLUT, renderView1)
>>>
>>> temperatureLUTColorBar.Title = 'temperature'
>>>
>>> temperatureLUTColorBar.ComponentTitle = ''
>>>
>>> return Pipeline()
>>>
>>>
>>> class CoProcessor(coprocessing.CoProcessor):
>>>
>>> def CreatePipeline(self, datadescription):
>>>
>>> self.Pipeline = _CreatePipeline(self, datadescription)
>>>
>>>
>>> coprocessor = CoProcessor()
>>>
>>> # these are the frequencies at which the coprocessor updates.
>>>
>>> freqs = {'X_Y_Z_1LAYER-primal': [1]}
>>>
>>> coprocessor.SetUpdateFrequencies(freqs)
>>>
>>> return coprocessor
>>>
>>>
>>> #--------------------------------------------------------------
>>>
>>> # Global variables that will hold the pipeline for each timestep
>>>
>>> # Creating the CoProcessor object, doesn't actually create the ParaView
>>> pipeline.
>>>
>>> # It will be automatically setup when coprocessor.UpdateProducers() is
>>> called the
>>>
>>> # first time.
>>>
>>> coprocessor = CreateCoProcessor()
>>>
>>>
>>> #--------------------------------------------------------------
>>>
>>> # Enable Live-Visualizaton with ParaView
>>>
>>> coprocessor.EnableLiveVisualization(False, 1)
>>>
>>>
>>>
>>> # ---------------------- Data Selection method ----------------------
>>>
>>>
>>> def RequestDataDescription(datadescription):
>>>
>>> "Callback to populate the request for current timestep"
>>>
>>> global coprocessor
>>>
>>> if datadescription.GetForceOutput() == True:
>>>
>>> # We are just going to request all fields and meshes from the
>>> simulation
>>>
>>> # code/adaptor.
>>>
>>> for i in range(datadescription.GetNumberOfInputDescriptions()):
>>>
>>> datadescription.GetInputDescription(i).AllFieldsOn()
>>>
>>> datadescription.GetInputDescription(i).GenerateMeshOn()
>>>
>>> return
>>>
>>>
>>> # setup requests for all inputs based on the requirements of the
>>>
>>> # pipeline.
>>>
>>> coprocessor.LoadRequestedData(datadescription)
>>>
>>>
>>> # ------------------------ Processing method ------------------------
>>>
>>>
>>> def DoCoProcessing(datadescription):
>>>
>>> "Callback to do co-processing for current timestep"
>>>
>>> global coprocessor
>>>
>>>
>>> # Update the coprocessor by providing it the newly generated
>>> simulation data.
>>>
>>> # If the pipeline hasn't been setup yet, this will setup the
>>> pipeline.
>>>
>>> coprocessor.UpdateProducers(datadescription)
>>>
>>>
>>> # Write output data, if appropriate.
>>>
>>> coprocessor.WriteData(datadescription);
>>>
>>>
>>>
>>>
>>> # Write image capture (Last arg: rescale lookup table), if
>>> appropriate.
>>>
>>> coprocessor.WriteImages(datadescription, rescale_lookuptable=False)
>>>
>>>
>>> # Live Visualization, if enabled.
>>>
>>> coprocessor.DoLiveVisualization(datadescription, "localhost", 22222)
>>>
>>>
>>>
>>>
>>> From: David E DeMarle <dave.demarle at kitware.com>
>>> Date: Thursday, July 30, 2015 at 12:32 PM
>>> To: First name Last name <aeatmon at lanl.gov>
>>> Cc: "paraview at paraview.org" <paraview at paraview.org>
>>> Subject: Re: [Paraview] adjusting vertical level setting via paraview
>>> python script
>>>
>>> Regarding the adding attributes error message, it is likely that the
>>> ActiveSource is not an MPAS reader at that point in time.
>>> …GetActiveSource().__class__ should tell your what it is.
>>>
>>> Regarding the level setting - what is yourReader.ShowMultilayerView?
>>> The docs indicated a value of 1 makes VerticalLayer immaterial.
>>>
>>>
>>>
>>> David E DeMarle
>>> Kitware, Inc.
>>> R&D Engineer
>>> 21 Corporate Drive
>>> Clifton Park, NY 12065-8662
>>> Phone: 518-881-4909
>>>
>>> On Thu, Jul 30, 2015 at 9:52 AM, Eatmon Jr., Arnold <aeatmon at lanl.gov>
>>> wrote:
>>>
>>>> I’m one of the DSS interns working under Jim Ahrens for the summer. I
>>>> am using paraviews python script in the HPC and I’m having an issue
>>>> adjusting an attribute of paraview.simple.netcdfmpasreader “VerticalLevel”.
>>>>
>>>> I want to adjust it from the default to one and attempted:
>>>>
>>>> paraview.simple.NetCDFMPASreader.VerticalLevel = 1
>>>> paraview.simple.NetCDFMPASreader.VerticalLevel = ‘1'
>>>> And
>>>> paraview.simple.GetActiveSource().VerticalLevel = 1
>>>>
>>>> The first two operate with no errors doing nothing in the program and
>>>> the last returns an error that the class bars adding attributes to prevent
>>>> errors due to spelling.
>>>>
>>>> How do I adjust the vertical level setting?
>>>>
>>>> Thank you in advance for your assistance.
>>>>
>>>> _______________________________________________
>>>> Powered by www.kitware.com
>>>>
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>>>>
>>>
>>
>
> _______________________________________________
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