Skip to content

add test for recipe localization modules coordinate conventions#1663

Draft
barentine wants to merge 1 commit into
python-microscopy:masterfrom
barentine:recipeloc_coordinates
Draft

add test for recipe localization modules coordinate conventions#1663
barentine wants to merge 1 commit into
python-microscopy:masterfrom
barentine:recipeloc_coordinates

Conversation

@barentine
Copy link
Copy Markdown
Member

I'm PR'ing this as a draft to show a test I think we should have, and to raise as an issue the coordinate convention headache that one might hit if they do a couple of localization processes using recipe modules.
Namely:

  • DetectPoints2D output is in units of pixels, not units of nanometers
  • FitPoints requires input positions to be in units of nanometers
  • Between density mapping and FitPoints one picks up a half-pixel shift.

Would love to hear some thoughts on preferred way to fix some of these @David-Baddeley !
My thought would be to:

  • multiply DetectPoints2D by voxelsize_nm.x and voxelsize_nm.y
  • fix the fixme in visHelpers.rendGauss about im[0,0] centering
  • write a documentation page about coordinate conventions in PYMEVis / PYMEImage

Co-authored-by: Copilot <copilot@github.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant