How to resize and save a slice from a nii file as a PNG image in Python?

  • Topic: Python 
  • Thread starter Thread starter BRN
  • Start date Start date
  • Tags Tags
    File
Join the discussion
Registration is free. Ask a follow-up in this thread, or start your own.
Sign up Log in
3 replies · 3K views
BRN
Messages
107
Reaction score
10
Hello everyone,

I have to extract a slice from a nii files and resize it with dimensions 256x256. Once this is done, I have to save it as a PNG image.

This is my code:

[CODE lang="python" title="slice from nii file"]def img_from_nii(height, width, n_slice, label, in_path, temp_path):

filenames = os.listdir(in_path)

for i in range(len(filenames)):
mri_file = in_path + filenames
img_data = nib.load(mri_file).get_fdata()
img_data = np.transpose(img_data, (2, 1, 0))
slice_2D = Image.fromarray(img_data[:, :, n_slice]).resize((height, width))

resized_slice = plt.matshow(slice_2D, cmap = 'gray', fignum = 0)
plt.axis('off')
plt.gca().set_axis_off()
plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0, hspace = 0, wspace = 0)
plt.margins(0, 0)

plt.savefig(temp_path + label + '_ADNI_' + 'slc' + str(n_slice) + '_' + str(i + 1) + '.png')
plt.close()

print('dataset done!')[/CODE]

The problem is that PNG files are correctly created, but if you check the image size I do not get 256x256. How is it possible?

[CODE lang="python" title="check size"]
im = Image.open('./outputs/ADNI_png_temp/P_ADNI_slc150_3.png')

width, height = im.size

print('width:', width)
print('height:', height)[/CODE]

[CODE title="outputs"]
width: 432
height: 288
[/CODE]

How can I solve?

Thanks.
 
Physics news on Phys.org

Discussion

Have you looked at the images in Paint or something? From memory savefig pads the images the same way show() does.

Doesn't the Image class have a save method? Have you tried that?
 
If as Image class you mean that of Pillow, yes there is the save method, but it does not support 32-bit images and I lose quality.

By opening the image with any reader, I see the image in the correct size 256x256, but I also have two completely empty side bands.

I believe that the save method of Matplotlib does not provide for the cropping.
 
Oops! I forgot to update this post ...:-p

The problem was given by the 'Mathshow ()' function that adds additional spaces around the figure even if the axes are hidden.

I solved this way:
[CODE lang="python" title="slice from nii file ok"]def img_from_nii(height, width, n_slice, label, in_path, temp_path):

filenames = os.listdir(in_path)

for i in range(len(filenames)):
mri_file = in_path + filenames
img_data = nib.load(mri_file).get_fdata()
img_data = np.transpose(img_data, (2, 1, 0))
slice_2D = Image.fromarray(img_data[:, :, n_slice]).resize((height, width), resample = Image.Resampling.LANCZOS)

plt.imsave(temp_path + label + '_ADNI_' + 'slc' + str(n_slice) + '_' + str(i + 1) + '.png', slice_2D)

plt.close()

print('ADNI ' + label + ' dataset done!')[/CODE]