Problems with npy to nii.gz conversion-CodePudding

I'm trying to convert a .npy image to a nii.gz image, I'm having various problems even though I'm following instructions correctly.

This is the code I'm using:

import numpy as np
import nibabel as nib

file_dir = "D:/teste volumes slicer/"
fileNPY1 = "teste01.npy"
img_array1 = np.load(file_dir   fileNPY1)
print(img_array1.shape)
print(img_array1.dtype)

normal_array = "D:/teste volumes slicer/teste01.npy"
print ("done")
nifti_file = nib.Nifti1Image(normal_array, np.eye(4))

About the image: (332, 360, 360) float64 (this is what we got when we print the shape and dtype) https://ibb.co/mRyTrw7 - image that shows the error and the image's information

The error message: 
Traceback (most recent call last):
  File "d:\teste volumes slicer\conversor.py", line 16, in <module>
    nifti_file = nib.Nifti1Image(normal_array, np.eye(4))
  File "C:\Python39\lib\site-packages\nibabel\nifti1.py", line 1756, in __init__
    super(Nifti1Pair, self).__init__(dataobj,
  File "C:\Python39\lib\site-packages\nibabel\analyze.py", line 918, in __init__
    super(AnalyzeImage, self).__init__(
  File "C:\Python39\lib\site-packages\nibabel\spatialimages.py", line 469, in __init__
    self.update_header()
  File "C:\Python39\lib\site-packages\nibabel\nifti1.py", line 2032, in update_header
    super(Nifti1Image, self).update_header()
  File "C:\Python39\lib\site-packages\nibabel\nifti1.py", line 1795, in update_header
    super(Nifti1Pair, self).update_header()
  File "C:\Python39\lib\site-packages\nibabel\spatialimages.py", line 491, in update_header
    shape = self._dataobj.shape
AttributeError: 'str' object has no attribute 'shape'

CodePudding user response：

The problem with your code is instead of passing your Numpy-array (your image), you are passing the path of the image to the Nifti1Image function.

This is the correct way to convert it:

import numpy as np
import nibabel as nib

file_dir = "D:/teste volumes slicer/"
fileNPY1 = "teste01.npy"
img_array1 = np.load(file_dir   fileNPY1) 
nifti_file = nib.Nifti1Image(img_array1 , np.eye(4))