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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Thanks for the tips Eric, I will look into these techniques although for a Paraview scripting newbie this is quickly getting in over my head!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Meanwhile I started on another approach, which may also benefit from the techniques you have pointed me to. I saved a LUT from the Paraview GUI (Edit Color
Map | Choose Preset | Export) and used this as an example to help me write a custom LUT for each scalar and save it in an xml file. I can then Import the LUT into Paraview, but only in interactive mode, I'd really like to be able to script it all so I can
automatically generate an image for each scalar. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">I took things further than just a compressed range and constructed a LUT for each scalar based on histogram equalisation of the scalar data. This works great
and will be a more general solution for data with arbitrary distributions. But how to automate it all ! I Also must poke around and check there is a filter in Paraview (or vtk) already that does histogram equalization. The topic is covered in the vtk book,
and would seem to be a useful visualisation trick. A quick peek on Google suggests 'maybe' in ITK… so I may be doing this myself after all.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">I am making progress and your tips may well be good pieces for my jigsaw.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"> regards, Dave<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
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<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:
"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;
font-family:"Tahoma","sans-serif""> Eric E. Monson [mailto:emonson@cs.duke.edu]
<br>
<b>Sent:</b> Thursday, 15 April 2010 5:43 a.m.<br>
<b>To:</b> David Pont<br>
<b>Cc:</b> paraview@paraview.org<br>
<b>Subject:</b> Re: [Paraview] Lookup Table Range<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hey Dave,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">If you want to retrieve the attribute data to make the calculations then you can call<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">servermanager.Fetch()<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">to pull from the server to the client. You can see examples on:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="http://www.cmake.org/Wiki/ParaView/Python_Scripting">http://www.cmake.org/Wiki/ParaView/Python_Scripting</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">If your data is very large, though, it might be tough to do this. If you look at the above page it talks about passing algorithms as the optional arguments, like vtkMinMax, which will process the data on the server and send a result to
the client. I'm not sure all of what would be involved (probably making a plugin that you can load with your custom class), but you may be able to make a quantile filter in place of vtkMinMax and pass that to Fetch(). <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Another thing I've done is to use a Python Programmable Filter (PPF) to do something similar to what vtkMinMax is doing: Calculate statistics on my data set and output a single point which has the calculated attributes (such as mean of
all input attributes). Maybe you could just output a two-point polydata from your PPF in which each point contains the 5 and 95 percentiles for every attribute, and then Fetch that data to set the LUT ranges?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hope this helps,<o:p></o:p></p>
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<div>
<p class="MsoNormal">-Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">------------------------------------------------------<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Eric E Monson<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Duke Visualization Technology Group<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Apr 13, 2010, at 1:00 AM, David Pont wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<div>
<div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am developing a python script to visualise point data (unstructured grid) with a large number of scalar values for each point.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">My problem is some of the scalar data is a bit noisy, i.e. a histogram of the values has a long tail at one or both ends, which effectively reduces the useful range of color
in the visualisation. I would like to determine the 5 and 95 percentiles for each data array and use these as the range for the LUT. And I would like to do this from my python script. I can't figure out how to get at the underlying point data, as it would
then be very easily to calculate a restricted range.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">See my current script below.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Thanks in advance for any help, Dave<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">####################################################<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">from paraview.simple import *<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">sm = servermanager<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">sm.Connect()<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">INPUTFILES = ("Esk all trees v2.txt_1.vtk", "Esk all trees v2.txt_2.vtk", "Esk all trees v2.txt_3.vtk")<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""># create reader for legacy VTK files<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">reader = LegacyVTKReader(FileNames=INPUTFILES[2])<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#create and configure view window<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Show()<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">view = GetActiveView()<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#set the background color<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#view.Background = [1,1,1] #white<o:p></o:p></span></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#set window size<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">view.ViewSize = [800, 600]<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">view.UseOffscreenRenderingForScreenshots = True<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""># set basic display properties<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">dp = GetDisplayProperties()<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#set representation<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">dp.Representation = "Points"<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#dp.Representation = "Surface"<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#set point size<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">dp.PointSize = 2<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">dp.MapScalars = True<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">dp.InterpolateScalarsBeforeMapping = True<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""># create a legend<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">bar = servermanager.rendering.ScalarBarWidgetRepresentation(registrationGroup='scalar_bars', registrationName="ScalarBarWidgetRepresentation1")<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#bar.LabelColor = [1.0, 1.0, 1.0]<o:p></o:p></span></p>
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<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">#bar.TitleColor = [1.0, 1.0, 1.0]<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">bar.TitleFontSize = 10<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">bar.LabelFontSize = 10<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">view.Representations.append(bar)<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""># render and save image for each scalar array in the point data<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">for a in reader.PointData :<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> print a.GetName()<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> r = a.GetRange()<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> dp.LookupTable = MakeBlueToRedLT(r[0], r[1])<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> dp.ColorAttributeType = 'POINT_DATA'<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> dp.ColorArrayName = a.GetName()<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> bar.Title = a.GetName()<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> bar.LookupTable = dp.LookupTable<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> Render()<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> #save screenshot<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> WriteImage( "v%s.jpg" % (a.GetName()) )<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div class="MsoNormal" align="center" style="text-align:center">
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