Closed jankrepl closed 2 years ago
This PR is based on the following change https://github.com/BlueBrain/atlas-annotation/pull/46/files
See below the standard output when I ran nissl_to_ccfv3.py on my computer.
nissl_to_ccfv3.py
2022-05-24 15:36:10,945 - INFO - nissl-to-ccfv3 - Loading volumes 2022-05-24 15:36:12,040 - INFO - nissl-to-ccfv3 - Start registration... 2022-05-24 15:36:12,040 - INFO - nissl-to-ccfv3 - Compute the registration... 2022-05-24 15:38:35,429 - INFO - nissl-to-ccfv3 - Apply transformation to Moving Volume... 2022-05-24 15:41:18,932 - INFO - nissl-to-ccfv3 - Apply transformation to Nissl Volume... 2022-05-24 15:41:45,489 - INFO - nissl-to-ccfv3 - Saving results...
So overall this script took ~5m30s
Note that while working on this PR I actually wrote a custom remapping logic that was really fast ~3s per volume. However, then I realized that remapping is not needed at all. If we ever need remapping in the future we can go back to it. See below a permalink: https://github.com/BlueBrain/Deep-Atlas/blob/a7d7372dae5b5f6a5177f7b826febe13233b43e0/src/deepatlas/utils.py
~3s per volume
This PR is based on the following change https://github.com/BlueBrain/atlas-annotation/pull/46/files
How fast is it?
See below the standard output when I ran
nissl_to_ccfv3.pyon my computer.So overall this script took ~5m30s
Custom remapping
Note that while working on this PR I actually wrote a custom remapping logic that was really fast
~3s per volume. However, then I realized that remapping is not needed at all. If we ever need remapping in the future we can go back to it. See below a permalink: https://github.com/BlueBrain/Deep-Atlas/blob/a7d7372dae5b5f6a5177f7b826febe13233b43e0/src/deepatlas/utils.py