[ITK] [ITK-users] PyBuffer memory consumption

[Harnish, Roy]

Hi Again,

I've played with it more and have another example that shows differences in memory usage depending on the interplay between calls to numpy.ones() and converter.GetImageFromArray(inputNumpyVolume):

import itk
import numpy as np
import resource
import matplotlib.pyplot as plt

ImageType = itk.Image[itk.D, 3]
converter = itk.PyBuffer[ImageType]

# adding +1 to numpy created once
inputNumpyVolume = np.ones([100,100,100])
M = []
n = 10
for i in range(n):

  inputNumpyVolume += 1
  inputVolume = converter.GetImageFromArray(inputNumpyVolume)
  M.append(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)

X = range(n)
plt.plot(X,M,'o', color='red')

# creating new numpy volume each time
M = []
for i in range(n):

  inputNumpyVolume = np.ones([100,100,100])
  inputVolume = converter.GetImageFromArray(inputNumpyVolume)
  M.append(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)

X = [x + n for x in range(n)]
plt.plot(X,M,'o', color='green')

# creating new numpy volume but not calling converter.GetImageFromArray(inputNumpyVolume)
M = []
for i in range(n):

  inputNumpyVolume = np.ones([100,100,100])
  M.append(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)

X = [x + 2*n for x in range(n)]
plt.plot(X,M,'o', color='blue')

plt.savefig("PyBufferMem.png")
plt.show()

Thanks for taking a look.

Roy
________________________________
From: Insight-users [insight-users-bounces at itk.org] on behalf of Harnish, Roy [Roy.Harnish at ucsf.edu]
Sent: Thursday, September 01, 2016 2:39 PM
To: insight-users at itk.org
Subject: [ITK-users] PyBuffer memory consumption

Hi,

I'm resurrecting a thread that I ran across trying to debug what looks to be a memory leak when using PyBuffer:

https://itk.org/pipermail/insight-users/2009-May/030386.html

If I repeatedly assign the output of itk.PyBuffer[ImageType].GetImageFromArray() to the same python variable name, more and more memory is consumed by the process. Wondering if anyone knows how to get this memory released? Here's some example code based on the linked thread that should reproduce the problem:

import itk
import numpy as np
import resource

M = []

for i in range(200):

  M.append(resource.getrusage(resource.RUSAGE_SELF).ru_maxrss)

  ImageType = itk.Image[itk.D, 3]
  converter = itk.PyBuffer[ImageType]

  inputNumpyVolume = np.ones((100, 100, 100))
  inputVolume = converter.GetImageFromArray(inputNumpyVolume)
#  inputVolume.Delete()

print M

Any suggestions much appreciated.

Roy
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