Overlapping plots

ParaView Support
1

Hi,

I have a working script for generating plots for one file. Now I want to loop over all the files and generate one plot for each of them. Here is the script I am using:

from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
import glob
filenames = glob.glob("../data/*.vtu")

for filename in filenames:
   # create a new 'XML Unstructured Grid Reader'
   testvtu = XMLUnstructuredGridReader(
      FileName=[filename])
   testvtu.PointArrayStatus = ['B [nT]', 'P [nPa]']

   # get active view
   view = GetActiveViewOrCreate('RenderView')
   # uncomment following to set a specific view size
   view.ViewSize = [1352, 754]

   # create a new 'Clip'
   clip1 = Clip(Input=testvtu)
   clip1.ClipType = 'Box'
   clip1.ClipType.Position = [-2.0, -2.0, -2.0]
   clip1.ClipType.Length = [2.0, 4.0, 4.0]

   # create a new 'Contour'
   contour1 = Contour(Input=clip1)
   contour1.ContourBy = ['POINTS', 'B [nT]_Z']
   contour1.Isosurfaces = [0.0]

   # show data in view
   contour1Display = Show(contour1, view)

   # get color transfer function/color map for 'BnT_Z'
   pnPaLUT = GetColorTransferFunction('P [nPa]')

   # trace defaults for the display properties.
   contour1Display.Representation = 'Surface'
   contour1Display.ColorArrayName = ['POINTS', 'P [nPa]']
   contour1Display.LookupTable = pnPaLUT
   contour1Display.OSPRayScaleArray = 'P [nPa]'
   contour1Display.OSPRayScaleFunction = 'PiecewiseFunction'
   contour1Display.ScaleFactor = 0.4
   contour1Display.SelectScaleArray = 'P [nPa]'
   contour1Display.GlyphType = 'Arrow'
   contour1Display.GlyphTableIndexArray = 'P [nPa]'
   contour1Display.GaussianRadius = 0.02
   contour1Display.SetScaleArray = ['POINTS', 'P [nPa]']
   contour1Display.ScaleTransferFunction = 'PiecewiseFunction'
   contour1Display.OpacityArray = ['POINTS', 'P [nPa]']
   contour1Display.OpacityTransferFunction = 'PiecewiseFunction'
   contour1Display.DataAxesGrid = 'GridAxesRepresentation'
   contour1Display.PolarAxes = 'PolarAxesRepresentation'

   # init the 'PiecewiseFunction' selected for 'ScaleTransferFunction'
   contour1Display.ScaleTransferFunction.Points = [0.0, 0.0, 0.5, 0.0, 1.1757813367477812e-38, 1.0, 0.5, 0.0]

   # init the 'PiecewiseFunction' selected for 'OpacityTransferFunction'
   contour1Display.OpacityTransferFunction.Points = [0.0, 0.0, 0.5, 0.0, 1.1757813367477812e-38, 1.0, 0.5, 0.0]

   # show color bar/color legend
   contour1Display.SetScalarBarVisibility(view, True)

   # rescale color and/or opacity maps used to include current data range
   contour1Display.RescaleTransferFunctionToDataRange(True, False)

   # show color bar/color legend
   contour1Display.SetScalarBarVisibility(view, True)

   # get color transfer function/color map for 'PnPa'
   pnPaLUT = GetColorTransferFunction('PnPa')

   # Properties modified on pnPaLUT
   pnPaLUT.AutomaticRescaleRangeMode = 'Never'

   # get opacity transfer function/opacity map for 'PnPa'
   pnPaPWF = GetOpacityTransferFunction('PnPa')

   # Rescale transfer function
   pnPaLUT.RescaleTransferFunction(0.01, 10.0)

   # Rescale transfer function
   pnPaPWF.RescaleTransferFunction(0.01, 10.0)

   # Apply a preset using its name.
   pnPaLUT.ApplyPreset('Viridis (matplotlib)', True)

   # get color legend/bar for pnPaLUT in view
   pnPaLUTColorBar = GetScalarBar(pnPaLUT, view)

   # change scalar bar placement
   pnPaLUTColorBar.WindowLocation = 'AnyLocation'
   pnPaLUTColorBar.Position = [0.83, 0.028]
   pnPaLUTColorBar.ScalarBarLength = 0.33

   # create a new 'Text'
   text1 = Text()
   tmin = int(filename[21:23])
   tsec = int(filename[23:25])
   time = tmin*60 + tsec
   text1.Text = 't = ' + str(time) + 's'
   #text1.Text = filename

   text1Display = Show(text1, view)
   text1Display.WindowLocation = 'UpperLeftCorner'
   text1Display.FontFamily = 'Courier'
   text1Display.FontSize = 10

   # current camera placement for view
   view.CameraPosition = [-6.399978992012728, -0.7675947684358911, 0.007641971283834748]
   view.CameraFocalPoint = [3.220738468431737, 0.07902926244000752, 0.007641971283834748]
   view.CameraViewUp = [0.0, 0.0, 1.0]
   view.CameraParallelScale = 1.384939947024134

   # save screenshot
   SaveScreenshot(
      filename[0:-3]+'png',
      view, ImageResolution=[1352, 754])

   ResetSession()

However, this gave me some overlapped figures like:

cut_mhd_2_t00002345_n00962422
cut_mhd_2_t00002345_n00962422.jpg1352×754 183 KB
cut_mhd_2_t00002434_n00990792
cut_mhd_2_t00002434_n00990792.jpg1352×754 126 KB

I thought ResetSession() might resolve the problem, but it didn’t. So what am I missing here? Should I avoid creating new Text() and Contour(), and reuse the old ones?

Thanks!

2

Sorry, it is quite unclear how this could happen.

Could you share data and steps to reproduce ?

3

It’s weird that ResetSession is not deleting the object. I suspect it is because in order to do a ResetSession the Python interpreter has to disconnect from the ParaView service instance and connect to a new one. Perhaps there is something about a non-interactive loop that is delaying the shutdown and restart of the ParaView service.

Anyway, a way around the problem should be to use the Delete function to delete each of the objects that you create. It’s probably best to delete them in the reverse order that they were created. So something like this at the end of your loop.

    Delete(text1)
    Delete(contour1)
    Delete(clip1)
    Delete(testvtu)

One more thing although you didn’t ask. You might consider doing the contour first and the clip second. The operation should be more efficient that way.

4

Yeah I think this is kind of a bug, and your solution works for me on my Mac, but not on the Linux server. For some unknown reason, it crashed after I first did the contour and then did the clip. At the line of contour1Display = Show(contour1, view), it said:

ERROR: In /admin/build/admin/rpms/frontera/BUILD/ParaView-v5.6.0/VTK/Common/Core/vtkGenericDataArray.txx, line 452
vtkIdTypeArray (0x96eb770): Unable to allocate 241094125 elements of size 8 bytes. 

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
./run_pvbatch_login: line 2: 74488 Aborted

BTW, if I run this script in the GUI python shell, it does not do anything. I don’t know what’s going on there.

5

Here are two sample outputs. Link: https://drive.google.com/file/d/1nP2WmMKzavK3n8EKHQh_V2iR3QG72SbD/view?usp=sharing
https://drive.google.com/file/d/1-0iJyK6AOIRooZifmvgqo-B5bGzMDTGk/view?usp=sharing

Probably you need to modify some directory in the script. I would say it is very obvious with the Text() object. Even without the data, you may be able to reproduce the issue.

6

Apologies for the very late reply to this thread. I just ran across it while searching for the answer to a completely different question. I’m not sure what is causing this error, but I routinely do something very similar to this, so thought I’d share the method that works for me.

After setting up my pipeline in the GUI, I save the state as a python script, then edit it to look something like the following:

import sys
DEST_IMAGE_DIR="/path_to_output_image_directory"
DATA_DIR= "/path_to_input_data"
DATA_FILES = []

total_steps = 300
for i in range(0, total_steps):
	temp_name = "%s/data_step_%04d.vtu" % (DATA_DIR, i)
	DATA_FILES.append(temp_name)

start_frame=int(sys.argv[1])
num_frames=int(sys.argv[2])

renderView1 = CreateView('RenderView')
## set other view parameters

ugrid_data = XMLUnstructuredGridReader(FileName= DATA_FILES[start_frame])

## Set up all of your filters and rendering parameters

## Now loop over the given set of frames, and write out an image for each
for i in range(start_frame, start_frame+num_frames):
    ugrid_data.FileName=DATA_FILES[i]
    IMAGE_FILE_NAME="%s/frame_%04d.png" % (DEST_IMAGE_DIR, i)
    print ("Save: ", IMAGE_FILE_NAME)
    WriteImage(IMAGE_FILE_NAME)

Then, I typically run pvbatch on a cluster, and can submit multiple jobs to work on multiple chunks of frames in parallel:

pvbatch script.py 0 100
pvbatch script.py 100 100
pvbatch script.py 200 100

Hopefully folks find this useful.
Cheers,
joe

7

Thanks for sharing this!

My original feeling was that this might have something to do with Garbage Collection (GC) in Python. I have never encountered such behaviour in C or Fortran. I may be wrong, though.