tueimage/gryds

A Python package for geometric transformations of images for data augmentation in deep learning

gryds's Issues

Get exact location of sampling grid points

Is there a way to get the exact location of sampling grid points so I can display the grid before and after BSpline deformation superimposed on the image?

cupy import crash

Hi there,

after having installed cupy gryds won't import anymore. I have a Windows 10 machine with Python 3.6, Cuda 10.0, cupy-cuda100 and gryds.
Here is the error message:

Traceback (most recent call last):
File "gryds_test.py", line 2, in
import gryds
File "", line 971, in _find_and_load
File "", line 955, in _find_and_load_unlocked
File "", line 656, in _load_unlocked
File "", line 626, in load_backward_compatible
File "C:\winpython\python\lib\site-packages\gryds-0.0.1-py3.6.egg\gryds_init.py", line 9, in
File "", line 971, in _find_and_load
File "", line 955, in _find_and_load_unlocked
File "", line 656, in _load_unlocked
File "", line 626, in load_backward_compatible
File "C:\winpython\python\lib\site-packages\gryds-0.0.1-py3.6.egg\gryds\interpolators_init.py", line 14, in
File "", line 971, in _find_and_load
File "", line 955, in find_and_load_unlocked
File "", line 656, in load_unlocked
File "", line 626, in load_backward_compatible
File "C:\winpython\python\lib\site-packages\gryds-0.0.1-py3.6.egg\gryds\interpolators\cuda.py", line 9, in
File "C:\winpython\python\lib\site-packages\cupyx_init.py", line 2, in
from cupyx.rsqrt import rsqrt # NOQA
File "C:\winpython\python\lib\site-packages\cupyx\rsqrt.py", line 1, in
from cupy.core.core import create_ufunc
File "C:\winpython\python\lib\site-packages\cupy_init.py", line 11, in
from cupy import core # NOQA
File "C:\winpython\python\lib\site-packages\cupy\core_init.py", line 1, in
from cupy.core import core # NOQA
File "cupy\core\carray.pxi", line 50, in init cupy.core.core
AttributeError: type object 'cupy.core.core.Indexer' has no attribute 'reduce_cython'

Any recommendations on how to make it work?

errlog.txt

How to get inverse grid

Hi, Thanks for sharing this excellent work! I'm trying to generate corresponding flat and warped images with forward transformation grid. Are there any way to get backward grid that recovering generated warped images to origin flat image?

how to get corresponding landmarks using existing BSpline deformation grid

Thanks for sharing! We want to apply existing BSpline deformation grid to some landmarks of source image, how can we get corresponding points after this deformation grid.

Is there any IO for nearest interpolation?

We want to perform augmentation on the image label. Therefore, it requires the nearest interpolation. We wonder whether there is the IO for this operation.

How to embedding the transformation into deep neural layers

Hi Koen,

   I have read your some papers about bspline transformation for medical image analysis. However, I'm still not sure how to change the bspline transformation operations into a neural network layer for training together. Can you show me how to do that? I sent emails to your student address, but it failed. I think you changed your email address.

Thanks a lot.

Yours sincerely,
Shuchao