Table of Contents

Usage examples of VT tools¶

from timagetk.io import imread
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

tmp_path = _image_from_url('https://zenodo.org/record/7151866/files/p58-t0-imgSeg.inr.gz',
                           hash_value='3e9259e801c39ec5f8f235deeb8e936c', hash_method='md5')

image = imread(tmp_path)

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from vt.cellproperties import cellProperties
from vt import vtCellProperties

Using cellProperties¶

cp = cellProperties(image.to_vtimage())

volumes = cp.volume()

print(len(volumes))

dir(cp)

['__class__',
 '__delattr__',
 '__dict__',
 '__dir__',
 '__doc__',
 '__eq__',
 '__format__',
 '__ge__',
 '__getattribute__',
 '__gt__',
 '__hash__',
 '__init__',
 '__init_subclass__',
 '__le__',
 '__lt__',
 '__module__',
 '__ne__',
 '__new__',
 '__reduce__',
 '__reduce_ex__',
 '__repr__',
 '__setattr__',
 '__sizeof__',
 '__str__',
 '__subclasshook__',
 '__weakref__',
 'barycenter',
 'contactsurface',
 'covariance',
 'eigenvalue',
 'eigenvector',
 'print',
 'properties',
 'surface',
 'volume',
 'write']

Using vtCellProperties¶

vtcp = vtCellProperties(image.to_vtimage())

labels = vtcp.getLabels()
print(len(labels))

volumes = {l: vtcp.getVolume(l) for l in labels}

print(len(volumes))

print(f"List of methods from `vtCellProperties`: {[m for m in dir(vtcp) if not m.startswith('__')]}")

List of methods from `vtCellProperties`: ['getBarycenter', 'getCovariance', 'getEigenvalues', 'getEigenvectors', 'getLabels', 'getNeighborsLabels', 'getNeighborsSurfaces', 'getSurface', 'getVolume', 'print', 'write']

Using handmade test array¶

import numpy as np
from timagetk.components.labelled_image import LabelledImage
from vt import vtCellProperties

image = LabelledImage(np.ones((10,10,10), dtype='uint16'), voxelsize=[0.5, 0.5, 0.5], not_a_label=0)
zsh, ysh, xsh = (5, 10, 10)  # the shape of label `2`, ZYX sorted
image[:zsh, :ysh, :xsh] = 2

WARNING  [timagetk.components.spatial_image] Undefined parameter ``axes_order``, using default: ZYX

WARNING  [timagetk.components.spatial_image] Undefined parameter ``origin``, using default: [0, 0, 0]

WARNING  [timagetk.components.spatial_image] Undefined parameter ``unit``, using default: 1e-06

vtcp = vtCellProperties(image.to_vtimage())

Labels¶

labels = vtcp.getLabels()
print(labels)

[1 2]

Volumes¶

volume = vtcp.getVolume(2)
print(volume)  # should be equal to: 'zsh * ysh * xsh'

np.prod((zsh, ysh, xsh))

Areas¶

area = vtcp.getSurface(2)
print(area)  # should be equal to: '(ysh-1) * (xsh-1)'

75.08695983886719

np.prod((ysh-1, xsh-1))