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Refactor and improve affine handling in the viewer. #7
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Commits on Oct 6, 2021
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Handle affine, reorienting as close to RAS+ as possible
reorder data axes to RAS before passing onto Napari. This avoids potential issues in affine handling: napari/napari#3410 We also now drop the non-diagonal (rotation, shear) components from the affine, since napari does not currently handle these. oi
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use SPL ordering so initial view is axial with the brain upright
patient left will be to the right side of the screen (radiological orientation) verified that for each dimensions, moving the slider to the right moves to S, P or L as expected, depending on the visible dimensions
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Commits on Oct 15, 2021
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Remove erroneous RAS->SPL transform
update reorder_axes to take a specified target orientation instead of assuming RAS Use LPS rather than SPL for now so that affine_plumb[:3, :3] will be diagonal. Once appropriate fixes for perfmuted axes have been made to napari, we can switch to SPL Co-authored-by: Christopher Nauroth-Kreß <56394171+ch-n@users.noreply.github.com>
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simplify the reorientation code
use as_reoriented method as it is more concise and will also update the affine we pass on in the metadata Co-authored-by: Christopher Nauroth-Kreß <56394171+ch-n@users.noreply.github.com>
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