For those interested, I will give here my script how to extract the
minimum value and its location in a serie of time steps, write it to
file and put spheres on the local minimum. <br><br>Since my knowledge of
VTK is quite limited, I didn't know how to access the data, so I use
some tricking to get it. Probably a much cleaner way of doing this is
possible. Be free to give suggestions<br>
<br>
In order to get the locations from the ProgrammableFilter, my trick is
to write all the data with CSVWriter to separate files, and then loop
over the time step and read each file which containt the vtkTable data.
This can porbably as well obtained directory from the
ProgrammableFilter, but how ?<br>
<br>
Also, I wonder if it is necessary to use the ProgramableFilter in the
first place, because I am using pvbatch. So I am calling a python script
from a python script. The reason was that this allow to create a
vtkTable, but again, this can be done better I guess. <br>
<br>
Anyway, any comments are welcome. I am also still learning this batch
programming in paraview. anyway, the version below works and I am quite
satisfied about the result<br>
<br>
Regards <br>
<br>
Eelco<br>
<br><br><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">try: paraview.simple</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">except: from paraview.simple import *</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">import os # file i/o tools</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">import sys # system tools</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">import re # regular expressions</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">import subprocess</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">import pv # load my own parafoam routines</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">import math</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">from optparse import OptionParser</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">paraview.simple._DisableFirstRenderCameraReset()</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">sm=servermanager</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">sm.Connect()</span><br><span style="color: rgb(51, 51, 255);">view = CreateRenderView()</span><br><i style="color: rgb(51, 51, 255);"><br>U_pxy_z0_600_t0 = LegacyVTKReader( FileNames=[ List of filename ])</i><br>
<br><i><span style="color: rgb(51, 51, 255);">Calculator2 = Calculator()</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">Calculator2.AttributeMode = 'point_data'</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">Calculator2.Function = 'U_Z'</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">Calculator2.ResultArrayName = 'U_Z'<br><br> # define the programmable filter here to extract the minimum and position<br>
UzMinProgFilter=ProgrammableFilter()<br> UzMinProgFilter.OutputDataSetType='vtkTable'<br> UzMinProgFilter.PythonPath = ''<br> UzMinProgFilter.RequestInformationScript = ''<br> UzMinProgFilter.Script = "\<br>
input=inputs[0]\n\<br> output=self.GetTableOutput()\n\<br> Uzdata = input.PointData['U_Z']\n\<br> uzmin = Uzdata[0]\n\<br> numPoints = input.GetNumberOfPoints()\n\<br> pts = vtk.vtkPoints()\n\<br>
for i in range(numPoints):\n\<br> uz=Uzdata[i]\n\<br> if uz < uzmin:\n\<br> minpos = input.GetPoint(i)\n\<br> uzmin = uz\n\<br> vtkTable_xpmin=vtk.vtkFloatArray()\n\<br>
vtkTable_xpmin.InsertNextValue(minpos[0])\n\<br> vtkTable_xpmin.SetName('xpmin')\n\<br> vtkTable_ypmin=vtk.vtkFloatArray()\n\<br> vtkTable_ypmin.InsertNextValue(minpos[1])\n\<br> vtkTable_ypmin.SetName('ypmin')\n\<br>
vtkTable_zpmin=vtk.vtkFloatArray()\n\<br> vtkTable_zpmin.InsertNextValue(minpos[2])\n\<br> vtkTable_zpmin.SetName('zpmin')\n\<br> vtkTable_uzmin=vtk.vtkFloatArray()\n\<br> vtkTable_uzmin.InsertNextValue(uzmin)\n\<br>
vtkTable_uzmin.SetName('uzmin')\n\<br> output.AddColumn(vtkTable_xpmin)\n\<br> output.AddColumn(vtkTable_ypmin)\n\<br> output.AddColumn(vtkTable_zpmin)\n\<br> output.AddColumn(vtkTable_uzmin)\n\<br>
"<br><br><br> csvfile="Minima.csv"<br> print "Writing all minima to CSV file: ",csvfile<br> writer_all=CSVWriter(UzMinProgFilter,FileName=csvfile,WriteAllTimeSteps=1)<br> writer_all.UpdatePipeline()<br>
<br><br></span></i><span style="color: rgb(51, 51, 255);">cnt=0</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> print "Writing images:"</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> for time in timesteps:</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> # reading info from file cnt</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> csvfile="Minima%d%s" % (cnt,'.csv')</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> fp=open(csvfile,"r")</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> lineList=fp.readlines()</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> fp.close()</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> xp,yp,zp,uz=lineList[-1].split(',')</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> position=[float(xp),float(yp),float(zp)]</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> print "Put sphere at ",position</span><br style="color: rgb(51, 51, 255);">
<br style="color: rgb(51, 51, 255);">
<br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> MinSphere=Sphere()</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> MinSphere.Radius=0.001</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> MinSphere.Center=position</span><br style="color: rgb(51, 51, 255);">
<br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> rep_sphere = Show(MinSphere,view)</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);"> rep_sphere.DiffuseColor = [0.0, 0.0, 0.0]</span><br>
<br style="color: rgb(51, 102, 255);">
<br><br><div class="gmail_quote">On Fri, Mar 4, 2011 at 5:10 PM, Eelco van Vliet <span dir="ltr"><<a href="mailto:eelcovv@gmail.com">eelcovv@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi David, <br><br>Many thanks for you suggestions. I was away for a while but had some time to look at this points this week again. The using the Python calculator brought me on the trail of using The Programmable Pythonscript filter. <br>
<br>My quest: I want to extrate the minimum value and its position for a time series of VTK files and write the data for all the time step to one single file. <br><br>With the advice so for, I now have the following construction. <br>
<br>First I read a series of VTK files representating the velocity over a cross section<br><br style="color: rgb(51, 51, 255);"><i style="color: rgb(51, 51, 255);">U_pxy_z0_600_t0 = LegacyVTKReader( FileNames=[ List of filename ])</i><br>
<br>Then I extract the U_z velocity component<br><br style="color: rgb(51, 51, 255);"><i><span style="color: rgb(51, 51, 255);">Calculator2 = Calculator()</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">Calculator2.AttributeMode = 'point_data'</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">Calculator2.Function = 'U_Z'</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">Calculator2.ResultArrayName = 'U_Z'<br><br><br></span></i>Then I create a Programmable Filter<br>
<br><span style="color: rgb(51, 51, 255);">ProgrammableFilter2 = ProgrammableFilter()</span><br style="color: rgb(51, 51, 255);"><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">ProgrammableFilter2.RequestUpdateExtentScript = ''</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">ProgrammableFilter2.PythonPath = ''</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">ProgrammableFilter2.RequestInformationScript = ''</span><br style="color: rgb(51, 51, 255);">
<span style="color: rgb(51, 51, 255);">ProgrammableFilter2.OutputDataSetType = 'vtkTable'</span><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255);">ProgrammableFilter2.Script = 'blabla' <br>
<br><br></span>For the script of the Programmable filter, I am now doing the following<br><br>
<table style="margin: 4px; color: rgb(51, 51, 255);">
<tbody><tr>
<td style="border: medium none;">
<p style="margin: 0px; text-indent: 0px;">input=inputs[0]</p>
<p style="margin: 0px; text-indent: 0px;">Uzdata= input.PointData['U_Z']</p>
<p style="margin: 0px; text-indent: 0px;">numPoints = input.GetNumberOfPoints()</p>
<p style="margin: 0px; text-indent: 0px;">uzmin=Uzdata[0]</p>
<p style="margin: 0px; text-indent: 0px;">for i in range(numPoints):</p>
<p style="margin: 0px; text-indent: 0px;"> uz=Uzdata[i]</p>
<p style="margin: 0px; text-indent: 0px;"> if uz<uzmin:</p>
<p style="margin: 0px; text-indent: 0px;"> minpos=input.GetPoint(i)</p>
<p style="margin: 0px; text-indent: 0px;"> uzmin=uz</p>
<p style="margin: 0px; text-indent: 0px;"></p>
<p style="margin: 0px; text-indent: 0px;">print "uzmin: ",uzmin,min(Uzdata)</p>
<p style="margin: 0px; text-indent: 0px;">print "minpos: ",minpos</p>
<p style="margin: 0px; text-indent: 0px;"></p>
<p style="margin: 0px; text-indent: 0px;">output.RowData.append(uzmin, 'uzmin')</p></td></tr></tbody></table><br><i><br></i>At this point I am stuck. First of all, the minpos variable is a tuple, and I don't know how to apend this to the output.RowData, because it needs to be and vtkArray. What is the way to convert a tuple into a vtkArray?<br>
<br>Second of all: if I step over the time step and see correctly the minpos and uzmin value updated in the spreadsheet viewer. However, how can I collect all the values into one array and then write to a single file ? Or should I just write the data of each time step to a seperate file ?<br>
<br>Hopefully someone can give me some advice on how to approach this issue. <br><br>Many thanks in advance!<br><br>Regards, <br><font color="#888888"><br>Eelco <br></font><div><div></div><div class="h5"><br><br><div class="gmail_quote">
On Fri, Feb 11, 2011 at 10:28 PM, David E DeMarle <span dir="ltr"><<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I suggest replacing the Calculator and DescriptiveStatistics filters<br>
with one python programmable filter (or python calculator if you are<br>
using 3.10). That way the data type isn't changed and Fetch will do<br>
what you expect it to - produce a standard vtkDataSet with 1<br>
point/cell.<br>
<br>
The python calculator expression to get an average x,y,and Z point location is:<br>
hstack([<br>
[global_mean(inputs[0].Points[:,0])],<br>
[global_mean(inputs[0].Points[:,1])],<br>
[global_mean(inputs[0].Points[:,2])]<br>
])<br>
<br>
If you then Fetch it's output and get the min (or equivalently max or<br>
just deliver the whole thing and just look at any of the points) you<br>
will get the average X Y and Z coordinates in a 3 component array<br>
names Result.<br>
<div><br>
David E DeMarle<br>
Kitware, Inc.<br>
R&D Engineer<br>
28 Corporate Drive<br>
Clifton Park, NY 12065-8662<br>
Phone: <a href="tel:518-371-3971" target="_blank">518-371-3971</a> x109<br>
<br>
<br>
<br>
</div><div><div></div><div>On Fri, Feb 11, 2011 at 10:34 AM, Eelco van Vliet <<a href="mailto:eelcovv@gmail.com" target="_blank">eelcovv@gmail.com</a>> wrote:<br>
> Hi David,<br>
><br>
> Thanks for you suggestion, I got much closer to what I want, but not quite<br>
> yet. I have the feeling I need one slight extra hint :)<br>
><br>
> To obtain the position of a minimun value I now do the script below: I get<br>
> the mimimum value first with MinMax, then I Threshold the original data on a<br>
> range between min and 0.9*min (the minimum values are negative), then I use<br>
> the calculator to get the x and y position of this range, and then I use the<br>
> DescriptiveStatitics filter to get the average mean of the position. I can<br>
> even use Fetch again to obtain the data, but now the very last step: how to<br>
> I get the mean data itself ? Sorry, I just don't understand how that<br>
> data.objects exactly work, and there is not much assessible documentation on<br>
> it.<br>
><br>
> I hope you can give me one last hint<br>
><br>
> Regards<br>
><br>
> Eelco<br>
><br>
> mm=MinMax(Uzcomponent)<br>
> mm.Operation="MIN"<br>
> mindata=sm.Fetch(Uzcomponent,mm,mm)<br>
> mindata.GetPointData().GetNumberOfArrays()<br>
> a0 = mindata.GetPointData().GetArray(1)<br>
> uzname=a0.GetName()<br>
> uzmin=a0.GetTuple1(0)<br>
> print "minimum of %s found: %g\n "%(uzname,uzmin)<br>
><br>
> Threshold1 = Threshold(Uzcomponent)<br>
> Threshold1.Scalars=['POINTS',uzname]<br>
> Threshold1.ThresholdRange=[uzmin,0.9*uzmin]<br>
><br>
> CalcPos = Calculator()<br>
> CalcPos.AttributeMode = 'point_data'<br>
> CalcPos.Function = 'iHat*coordsX+jHat*coordsY+kHat*coordsZ'<br>
> CalcPos.ResultArrayName = 'MinPos'<br>
><br>
> DescriptiveStatistics1 = DescriptiveStatistics()<br>
> DescriptiveStatistics1.VariablesofInterest = ['MinPos']<br>
> statistics=sm.Fetch(DescriptiveStatistics1)<br>
><br>
><br>
><br>
><br>
> On Thu, Feb 10, 2011 at 7:00 PM, David E DeMarle <<a href="mailto:dave.demarle@kitware.com" target="_blank">dave.demarle@kitware.com</a>><br>
> wrote:<br>
>><br>
>> The min max filter unfortunately doesn't keep track of which tuple and<br>
>> processor it found the min in so you can't get back to the particular<br>
>> point or cell it came from.<br>
>><br>
>> Instead of using fetch and minmax, try using a values selection. Set<br>
>> the value to be that minimum value. Once you extract the selection and<br>
>> fetch it to the client, you get a copy of the actuall cell(s)/point(s)<br>
>> that have the minimum value and you can query them directly for their<br>
>> spatial location.<br>
>><br>
>> David E DeMarle<br>
>> Kitware, Inc.<br>
>> R&D Engineer<br>
>> 28 Corporate Drive<br>
>> Clifton Park, NY 12065-8662<br>
>> Phone: <a href="tel:518-371-3971" target="_blank">518-371-3971</a> x109<br>
>><br>
>><br>
>><br>
>> On Thu, Feb 10, 2011 at 12:13 PM, Eelco van Vliet <<a href="mailto:eelcovv@gmail.com" target="_blank">eelcovv@gmail.com</a>><br>
>> wrote:<br>
>> > Dear Paraviewers,<br>
>> ><br>
>> > I would like to extract the location of a minimum value from a data set<br>
>> > in<br>
>> > pvbatch<br>
>> ><br>
>> > I were able to find the value of the minimum with<br>
>> ><br>
>> ><br>
>> ><br>
>> ><br>
>> > mm=MinMax(Uzcomponent)<br>
>> > mm.Operation="MIN"<br>
>> > mindata=sm.Fetch(Uzcomponent,mm,mm)<br>
>> > mindata.GetPointData().GetNumberOfArrays()<br>
>> > a0 = mindata.GetPointData().GetArray(1)<br>
>> > a1 = mindata.GetScalar()<br>
>> > print "name 1: ", a0.GetName()<br>
>> > print "tuple1: ", a0.GetTuple1(0)<br>
>> ><br>
>> > Here, a0.GetTyple1 give me the value of the minimum<br>
>> ><br>
>> > However: How do I find the location of this value ?<br>
>> ><br>
>> > Any hint appriciate!<br>
>> ><br>
>> > Regards<br>
>> ><br>
>> > Eelco<br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
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>> ><br>
>> > Visit other Kitware open-source projects at<br>
>> > <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> ><br>
>> > Please keep messages on-topic and check the ParaView Wiki at:<br>
>> > <a href="http://paraview.org/Wiki/ParaView" target="_blank">http://paraview.org/Wiki/ParaView</a><br>
>> ><br>
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>> ><br>
>> ><br>
><br>
><br>
</div></div></blockquote></div><br>
</div></div></blockquote></div><br>