angelolab / ark-analysis / 4528
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Create remapping interface for tiling script (#488)

* Initial commit of tile visualization

* Add interactive remapping visualization draft

* Add button to save remapping

* Encapsulate logic in callback functions and fix save message error

* Suppress mplDeprecation in notebook because RTD complains about it not being a class in tiling_utils

* Remove commented-out tma = False

* Add better type checking for reading in tiling parameters

* Add some testing and a draw_radius argument for circle viz

* Commit everything but the official remapping for now

* Some bug fixes, basic tests, notebook sweeteners, etc.

* Remove the import sys paths

* Add randomization and Moly point insertion procedure after remapping

* Fix TMA from upper-right/bottom-left to upper-left/bottom-right

* Fix documentation for interactive visualization

* Change y-coordinate axis so that it goes from bottom to top ascending

* Update FOV naming conventions

* Add documentation to clarify use of the Save mapping button

* Add new FOV dot visualization method (#490)

* Update the dot size, color scheme to green on hit, and slide size

* Shrink and adjust colors for tile centroids, shrink figure size further

* Change interactive viz notebook comment to reflect new coloring scheme

* When remapping only add the metadata fields if the user specified them

* Remove import sys

* Address renaming conventions and optional randomize/Moly point settings

* Docs and PYCODESTYLE

* More documentation

* Nuke more proposed to manual

* Documentation nitpicks and official tested notebook

* Need to mock ipywidgets for documentation

* More nitpicks

* Nuke more tiles and change auto-generated FOV naming conventions to 1-indexed

* Add tested notebook

* Notebook documentation

* Address code review comments related to TMAs; add more complete testing for both TMAs and non-TMAs

* Fix documentation

* More notebook docum... (continued)

2375 of 2612 relevant lines covered (90.93%)

0.91 hits per line

Jobs
ID Job ID Ran Files Coverage
1 4528.1 (MPLBACKEND=Agg) 0
90.93
 Travis Job 4528.1
Source Files on build 4528
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