Atlas-Download-Tools
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Custom strategy to determine the slice coordinate in the reference space
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In #40 a very simple logic of determining the refspace coordinate was implemented (inside of download_dataset_parallel). Namely:
- Let the user choose
detection_xy=(x, y)which is a fixed point in the image. Be default it is(0, 0). - Query the Image-To-Reference API (
xy_to_pir) to get the corresponding(p, i, r)(link) - The slice coordinate is then just
pifaxis="coronal"orrifaxis="sagittal".
The above is clearly not ideal. See below some other ideas
- Keep the current algorithm with a dynamic default - finding the middle of the image automatically since it may vary for each section image
- Query all 4 corners of the image using
xy_to_pirand let the slice coordinate be their average - Use the
section_numberprovided by Allen (see #50) together with the slice ?thickness?