MemoryError: 无法为 DIPY 图像配准中具有形状 (344, 344, 127) 和数据类型 float64 的数组分配 115. MiB

Question

I'm trying to do image registration using DIPY (Affine registration in 3d) I tried to run the following code (Actually I tried to reproduce the example code with a different nifti file)

from os.path import join as pjoin
import numpy as np
from dipy.viz import regtools
from dipy.data import fetch_mni_template, read_mni_template
from dipy.data.fetcher import fetch_syn_data, read_syn_data
from dipy.io.image import load_nifti
from dipy.align.imaffine import (transform_centers_of_mass,
                                 AffineMap,
                                 MutualInformationMetric,
                                 AffineRegistration)
from dipy.align.transforms import (TranslationTransform3D,
                                   RigidTransform3D,
                                   AffineTransform3D)

files, folder = fetch_mni_template()
static_data, static_affine = load_nifti(pjoin(folder, 'mni_icbm152_t1_tal_nlin_asym_09a.nii'))
static = np.squeeze(static_data)
static_grid2world = static_affine

files, folder = fetch_syn_data()
moving_data, moving_affine = load_nifti(pjoin(folder, '2018.nii'))
moving = moving_data
moving_grid2world = moving_affine

identity = np.eye(4)
affine_map = AffineMap(identity,
                       static.shape, static_grid2world,
                       moving.shape, moving_grid2world)
print(static.shape)


resampled = affine_map.transform(moving)


regtools.overlay_slices(static, resampled, None, 0,
                        "Static", "Moving", "resampled_0.png")
regtools.overlay_slices(static, resampled, None, 1,
                        "Static", "Moving", "resampled_1.png")
regtools.overlay_slices(static, resampled, None, 2,
                        "Static", "Moving", "resampled_2.png")

c_of_mass = transform_centers_of_mass(static, static_grid2world,
                                      moving, moving_grid2world)

transformed = c_of_mass.transform(moving)
regtools.overlay_slices(static, transformed, None, 0,
                        "Static", "Transformed", "transformed_com_0.png")
regtools.overlay_slices(static, transformed, None, 1,
                        "Static", "Transformed", "transformed_com_1.png")
regtools.overlay_slices(static, transformed, None, 2,
                        "Static", "Transformed", "transformed_com_2.png")

nbins = 32
sampling_prop = None
metric = MutualInformationMetric(nbins, sampling_prop)

level_iters = [10000, 1000, 100]

sigmas = [3.0, 1.0, 0.0]

factors = [4, 2, 1]

affreg = AffineRegistration(metric=metric,
                            level_iters=level_iters,
                            sigmas=sigmas,
                            factors=factors)

transform = TranslationTransform3D()
params0 = None
starting_affine = c_of_mass.affine

translation = affreg.optimize(static, moving, transform, params0,
                              static_grid2world, moving_grid2world,
                              starting_affine=starting_affine)

but im getting the following error

MemoryError: Unable to allocate 115. MiB for an array with shape (344, 344, 127) and data type float64

I couldn't find a solution for this.

Answer 1

I solved this issue by moving from 32 bit version of python to 64 bit version

Thanks, Mani