Chores

[joelyancey]

AlignEM-SWIFT improvements that can be done without too much trouble list inspired by June visit to Harris Lab at UT Austin (in no particular order).

[ ] = to do [-] = being worked on; or, may need to be revisited [x] = done

[-] only propagate SWIM settings to finer scales at alignment time [x] propagate changes up, but never down, in scale level. [x] show current branch in application title bar [x] match signals sometimes not updating with change in stack Z-index [ ] be able to select arbitrary image to act as reference for any image, i.e. could have a damaged section that can itself be aligned manually, but which makes for a worse reference for another as the image preceding it would [ ] add auto-saves between multiprocessing steps [ ] add 'Rebuild/Regenerate Zarr' only functionality (i.e. regnerate Zarr based on previously generated TIFFs) [x] while scale image pyramid is being generated, project manager table should display a placeholder row in the table, i.e. "Generating..." [x] table needs fix for sudden loss of thumbnail in situation where custom grid regions alignment method is used. the problem is related to the SNR components length and column-sequential loading of row data [x] option to specify 0-index image as calibration grid image upon project creation [x] import calibration grid image into project at project creation time [ ] import calibration grid image after project creation [x] display calibration grid image in project manager [-] the application should be restart-able from the interface, without command-line interaction [ ] add realtime CPU % with per-core breakdown [ ] up/down arrow keys should Zoom in & out on SNR plot, mirroring the behavior in Neuroglancer [ ] add an obvious notice to users stating that Zarr creation may take a while (or make Zarr copy-conversion not be the bottleneck) [x] change 'Quick Swim' text to 'Regenerate Match Signals'. [ ] project deletion should use Python subprocess module to run in the background [ ] file system browser does not sort alphabetically on TACC [ ] in documentation, note that sometimes the node itself is the problem, and occasionally the only solution is to start a new DCV session. [ ] chained multiprocessing tasks should be more modular and robust. Be able to run any multiprocessing task independently. [ ] display exceptions somewhere in the interface, and make the text copy-able for use in bug reports [x] fix yellow-on-white visibility issue of list view in manual mode [ ] fix karg/targ fails to display issue [x] '...' should always get 'done-ed' in process monitor. gives impression that the application is hanging. [x] central logging [x] open GitHub issue tracker in the interface [ ] add quick settings for things like UI update timeout [ ] start layer index at 1 in the control panel (maybe.. some dissenting views were heard) [x] enable scale change in manual mode, also exit manual mode if finer scale is not yet aligned [x] Track the changed state of cumulative affines and present this to the user [x] add a red warning label for sections that have generated alignments which are out of sync with project data [ ] add glossary entry for "generated" as in "generated alignment" or "re-generate" [ ] be able to drag 'match regions' boxes around, instead of deleting and replacing. Also be able to change the order of the match region boxes so when deleting one box, your order is not messed up [Ashley] [x] issue with manual point data sometimes not in sync with local data in Neuroglancer viewer object after context-menu deletion of points [Dhivya] [ ] Add explanatory message to Output Settings groupbox [ ] while table is loading, should be able to page neuroglancer (was not paging in manual mode) [x] fix color display of list view widgets for manual regions/points in manual mode [ ] display Warning (and SNR plot flag) for manual settings do not comport with generated alignment [ ] display Warning (and SNR plot flag) for too few manual regions/points selected [ ] display Warning (and SNR plot flag) for section after a manually aligned defective section should be realigned [ ] display Warning for scale data out of sync [x] remove copying of match regions to reference of next section, bug identified by Ashley and Kristen says better without [x] space bar to jump to Neuroglancer 3DEM view [ ] enter key to blend [ ] hovering a data point in SNR plot should change color of its reference [ ] hovering a data point in the SNR plot should have a tooltip or HUD message stating which alignment method was used to produce that SNR [ ] show Warnings in manual alignment mode as well [ ] add Warning using hashing for project table out-of-sync with data [ ] in manual alignment, delete key should delete selected points in list [ ] issue with zoom in generated alignment, sometimes not connected correctly or updating [ ] precision center point ('x') in painted annotations on thumbnails [x] default match region size should be larger than 128 (256?) [ ] add a label explaining control panel as a whole [x] match signal 0 not showing 'No Signal' [ ] undo button (or previous section button) [x] in MA mode rename 'Reset' button to 'Clear\nRegions' or something else better [ ] Table: skipped sections in red, and other easy usability enhancements [x] point order in manual region selection can become out of sync with colors, i.e. prompted to select a region of a certain color, but the region's order in the ordered dict data structure does not correspond to the order in the other list view [ ] "Lock" toggle to block any accidental changes to data of a scale [ ] separate GUI knobs or controls for each term in 'shape factor' of affine. consult Art/Tom about this. [x] 'clear' buttons in manual region selection in stead of 'Reset' button which is unclear... better button placement [x] False display of 'Complete!' in MA mode despite resetting manual regions [x] hash cumulative affines to generate warnings when generated alignment is out of sync with cumulative. [x] add 'Fix All' button to re-generate alignments for sections with erroneous hashes. [x] add overlay with red text on thumbnail for skipped sections [ ] space bar to jump to previous tab instead of jump to 3DEM (?) [ ] global project notes, toggle between project notes and section notes [ ] global project notes should appear below or above project table, section notes should display in table column [ ] Kristen: which PART/REGION is global alignment?

[joelyancey]

Added convenient access to GitHub issue tracker for submitting bug reports (requires logging into GitHub)

[lyndskirk16]

The first item in your list marked as "done" is still having issues (match signals sometimes not updating with change in stack Z-index). I notice this primarily when I skip a swim window in the custom grid, and the corresponding match region displays the match image from the most recent image in z. See screenshot below