VT-Python - Memory management¶

import sys
import numpy as np
import vt
from timagetk.io.image import _image_from_url

/builds/J-gEBwyb/0/mosaic/timagetk/src/timagetk/components/labelled_image.py:31: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html
  from tqdm.autonotebook import tqdm

Load a test image¶

tmp_path = _image_from_url('https://zenodo.org/record/7149218/files/090223-p58-flo-top.lsm',
                           hash_value='5548917d3d1490200d0d56cbb31c0d35', hash_method='md5')
img = vt.vtImage(tmp_path)

Print a summary of the loaded image:¶

print(img)

vtImage : { 
 type    : unsigned char, 
 shape  : [460, 460, 59], 
 spacing : [0.200320, 0.200320, 1.000000], 
 }

Accessing the reference count of a python object:¶

As Python does NOT have pointers and use reference counts for memory management you may need to know its value for a given object. It is accessible as follow:

sys.getrefcount(img)

Tutorial to understand the difference between C++ & Python: https://realpython.com/pointers-in-python/

Official documentation for sys.getrefcount: https://docs.python.org/3.7/library/sys.html#sys.getrefcount

Check `vt.Image` object memory address¶

Official documentation for the built-in method id: https://docs.python.org/3.7/library/functions.html#id

id(img)

140154180116976

sys.getrefcount(img)

id(img)

140154180116976

=> Same address… this is good!

sys.getrefcount(img)

=> The refcount value of the img object is changing (decrease) without any modification… this is weird no ?

id(img)

140154180116976

sys.getrefcount(img)

id(img)

140154180116976

sys.getrefcount(img)

Check the memory address of `.to_array()` method¶

The .to_array() method is supposed to return a pointer, we expect the address to be the same!

id(img.to_array())

140154173393296

id(img.to_array())

140154173392624

=> Not the same… this is NOT good!

#arr = img.copy_to_array()

=> Calling img.copy_to_array() after img.to_array() result in a crash !!!

Check the memory address of `.copy_to_array()` method¶

The .copy_to_array() method is supposed to return a numpy.ndarray, we expect the address to change uppon method call!

img = vt.vtImage(tmp_path)

id(img.copy_to_array())

140154173393392

id(img.copy_to_array())

140154173393104

np.testing.assert_array_equal(img.copy_to_array(), img.copy_to_array())

=> As expected, the addresses are different, but the arrays are the same!

Test with python object definition:¶

arr = img.copy_to_array()

type(arr)

numpy.ndarray

sys.getrefcount(arr)

id(arr)

140154172812048

id(arr)

140154172812048

=> As expected, the returned address for a given object is constant!

np.testing.assert_array_equal(arr, img.copy_to_array())

sys.getrefcount(arr)

=> As expected, the reference count for the NumPy array object arr is equal to 2. (+1 for the temporary exrta reference to arr by sys.getrefcount as explained in the official documentation).

Test with array modification:¶

id(arr)

140154172812048

arr[0, 0, 0] = 12
id(arr)

140154172812048

=> As expected the addresses are the same!

Accessing an object size in bytes:¶

Official documentation for sys.getsizeof: https://docs.python.org/3.7/library/sys.html#sys.getsizeof

sys.getsizeof(img.copy_to_array())

12484544

sys.getsizeof(arr)

12484544

=> As expected the object have the same size!

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