Add new FOV dot visualization method #490
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Addressed:
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ngreenwald
requested changes
Jan 6, 2022
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@ngreenwald did you run it after you clicked I don't think We might need to split the notebook up into different parts for the most streamlined experience. However, because all the last section does is renaming, I was hesitant to make that trivial action a separate notebook. |
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Yup, this was after saving
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@ngreenwald OK I see, I assumed that every JSON tile file would contain an |
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@ngreenwald can you see if the new patch works? |
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Yup, it works now |
ngreenwald
requested changes
Jan 6, 2022
ngreenwald
approved these changes
Jan 8, 2022
ngreenwald
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Jan 14, 2022
* 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 documentation * Try another doc fix * Fix definition of TMA in doc * More nitpicky documentation stuff * More documentation fixes * Remove import sys * Documentation * Remapping TMA documentation * Nuke moly_run, change to moly_region * More notebook documentation * Move tma setting to top of example_fov_grid_generate.ipynb * Capitalize fov in tiling_utils * Improve error messages * Nuke more runs to regions * Change tma back to true in example_fov_grid_generate.ipynb * Doc fix * Documentation clarification * For test_read_tiling_param, add a test for input of the wrong type * More run to region conversions in the test file * My OCD is acting up * Remove duplicate files * Fix another comment * Do not need to copy metadata keys over * Split into non-TMA and TMA-specific tiling notebooks (with remapping done in the latter too); changed non_tma to tiled_region in code * Doc fixes * Abstract metadata key-value copying out * Documentation * Fix TMA/non-TMA * Address some code review comments * Fix more tests * Address final code review comments * Remove redundant FOV name to centroid dict * update names Co-authored-by: ngreenwald <noahfgreenwald@gmail.com>
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What is the purpose of this PR?
Previously, we highlighted the names of each FOV on top of their corresponding circle for the interactive remapping visualization. This is problematic because:
With this in mind, we remove the text on each FOV and instead use a green circle to highlight which are selected. This works because FOVs follow a specific numbering scheme such that it's easy to resolve which one names which.
How did you implement your changes
On the initial draw, change the way the circles are colored so that the highlighted pair is green.
On the dropdown-menu updates, make a similar change.