TODOs

Todo

skimage in version 0.14 (not officially released yet, supports 3D up- and downsampling. Should replace this class with the skimage functionality once officially available.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/image_sampling.py:docstring of mermaid.image_sampling, line 3.)

Todo

This documentation needs to be updated.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/docs/source/notes/howto_own_registration.rst, line 1.)

Todo

These settings need more explanation. Where are they used?

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/docs/source/notes/settings.rst, line 116.)

Todo

This documentation needs to be updated. For now have a look at testSimpleInterface.py in the demos directory for a simple example on how to compute registrations.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/docs/source/notes/simple_example.rst, line 1.)

Todo

Check what the best way to adapt the tolerances for the pre-defined optimizers; tying it to rel_ftol is not really correct.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/multiscale_optimizer.py:docstring of mermaid.multiscale_optimizer.SingleScaleRegistrationOptimizer, line 3.)

Todo

Add support for multiple parameter groups.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/custom_optimizers.py:docstring of mermaid.custom_optimizers, line 5.)

Todo

Clean up the two implementations (spatial and Fourier of the Gaussian smoothers). In particular, assure that all computions are done in physical coordinates. For now these are just in [-1,1]^d

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/smoother_factory.py:docstring of mermaid.smoother_factory.GaussianSmoother, line 3.)

Todo

Reorganize this package in a more meaningful way.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/utils.py:docstring of mermaid.utils, line 3.)

Todo

Create a CUDA version of these convolutions functions. There is already a CUDA based FFT implementation available which could be built upon. Alternatively, spatial smoothing may be sufficiently fast on the GPU.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/custom_pytorch_extensions.py:docstring of mermaid.custom_pytorch_extensions, line 4.)

Todo

There should be a better check for closeness of points. The implemented one is very crude.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/custom_pytorch_extensions.py:docstring of mermaid.custom_pytorch_extensions.are_indices_close, line 7.)

Todo

The current check seems to fail in pyTorch. However, the gradient appears to be correct. Potentially an issue with the numerical gradient approximiaton.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/custom_pytorch_extensions.py:docstring of mermaid.custom_pytorch_extensions.check_fourier_conv, line 5.)

Todo

Add CUDA implementation. Could be based of the existing 2D CUDA implementation.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/libraries/functions/stn_nd.py:docstring of mermaid.libraries.functions.stn_nd, line 3.)

Todo

Implement CUDA version. There is already a 2D CUDA version available (in the source directory here). But it needs to be extended to 1D and 3D. We also make use of a different convention for images which needs to be accounted for, as we use the BxCxXxYxZ image format and BxdimxXxYxZ for the maps.

(The original entry is located in /home/docs/checkouts/readthedocs.org/user_builds/mermaid/checkouts/latest/mermaid/libraries/modules/stn_nd.py:docstring of mermaid.libraries.modules.stn_nd, line 4.)