Tags: DeMarcoLab/fibsem
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v0.2.3 Release (#213) * add top/bottom edge, median edge det, trained new model (#201) * bump version * silence perf logging * hotfix: tiled metadata * Add huggingface checkpoint downloads to load_model (#210) * hf checkpoint download * notebook update * rename weights to checkpoint * basic experiment widget * [FEAT] add logging for detection in workflow * added special logging for analytics (move, mill, det) * add fibsem image to DetectedFeatures * Gis time duration (#211) * changed time and put in update button * blank beam setting * cleaning up UI * gis final updates * fix fibsem image * [FEAT] Eucentric move update #197 * less info logging * Tab order (#212) fix tab ordering of UI * add fname logging for det * extra logging for stage / state * hfw milling threshold * fix thread issue temp * fix history from: v0.2-dev-fix-napari-patterns @Rohit-Kannachel (#215) * draw patterns on minimap * cmt * waffle figures * rm env file * add missing stages for protocol * update pattern logic * autoliftout stage positions * add unsafe flat to beam movement * system widget * img and movement widgets * detetction, milling, manipulator * move by coords * fix duplicate key for pattern selection * training upgrade * model configs * training / eval notebooks * threading * interactions toggle * V0.2 dev UI consistency (#219) * system widget * img and movement widgets * detetction, milling, manipulator * add model to demo * fixes --------- Co-authored-by: Patrick Cleeve <patrick.cleeve@monash.edu> * V0.2 dev minimap upgrade (#222) * add all settings to minimap ui * thread tile collection, minimap * tile / stitching progress indicator * tile while collecting * formatting for button * updated undercut * add offset for det distance * fix thermo passes parameter * fix passes / config * added reproject to rotated positions * target identification from repojrected position * auto targeting * fixed logging, updated to json * bump version * imaging button orange * milling button orange * added napari notifications * notification signal imaging * no yielding in movement * no yielding in milling stage * fix move_based on_detection for new det, add point to detect_features * moving pattern update (#221) * moving pattern update * modified to not need an else block * improved logic to remove large else block * fixed stuff and removed comments oops hehe * fixed everything * solved world hunger --------- Co-authored-by: Patrick Cleeve <80024299+patrickcleeve2@users.noreply.github.com> Co-authored-by: Rohit-Kannachel <rohit.kannachel@monash.edu> * add version to ui * actually log final px position * fix px logging * test notebook * model evaluation improvements * refactor edge detection * cfg v4 waffle autolamella * updated wanbd logging * figures * cfg * eval notebook * tescan fixes * data engine image examples * improved eval code * system setup docs * connection * reorganisation * Imaging * eval data baseline * add features to ingore * movement * milling pt 1 * better aug * milling * working dataset aug * cfgs * update training code * eval / aug notebooks * eval plot update * V0.2.4 dev online labelling (#230) * start online labelling * fix saving data * disable sam for embedded labelling * V0.2 dev positions widget (#227) * minimap * append or overwrite positions file * loading positions on start up * system yaml * closing figures before making new ones * add position from external source * minor bug, smaller size --------- Co-authored-by: Patrick Cleeve <patrick.cleeve@monash.edu> * reduce num updates minimap * milling * stage setup * upgrade needle tip det + test masks * testing masks * add vspot weld,change passes to numeric * vertical horseshoe pattern * bug: missing protocol values * add pattern type to protocol from stages * rename serial liftout test images * add additional det features, rename test images * rm plot * add multi points for multi patterns * refactor + add move_based_on_det * beam reset * manipulator * bugs: leaked code from merged branch * detection basic * minor edit * detection 2 * image setup * image patterns 2 * fix: tmp disable images after minimap movement * fix threaded movements * fix * detection * basic milling stages drawing napari * add default serial liftout positions * fix: serial liftout testing * fix: milling passes not set correctly (THERMO) * return flag, legend * rm unused files * edit docs * presets * moved into microscope * update evals * dev: ccd view * serial-test * add point projection to det func * minor fix * hotfix: projected position for demo microscope --------- Co-authored-by: Rohit-Kannachel <111263763+Rohit-Kannachel@users.noreply.github.com> Co-authored-by: LucileNaegele <lucile.naegele@monash.edu> Co-authored-by: Rohit-Kannachel <rohit.kannachel@monash.edu>
v0.2.2 Release (#156) ### Highlights - OpenFIBSEM is now available on PyPI. Use pip to install: `pip install fibsem`. On ThermoFisher systems, OpenFIBSEM will automatically find your Autoscript installation if it installed. On Tescan, please install into the same environment as the Automation API. - Minimap: Added a minimap widget for collecting tiled images, selecting positions and correlation. Provides an overview of the current stage position and the positions of the selected locations. Also provides an integrated correlation user interface. You can use the minimap to select locations for other applications, such as AutoLamella. ### Features - Added a _safe_absolute_stage_movement. This function will tilt flat before performing large movements to prevent collions. - Added cleaning_cross_section and scan_direction to the milling widget user interface. - Rectangle Patterns now sputter a 'passes' parameter. This allows you to explicitly set the number of passes the beam will scan. - Adjusted the milling widget to allow for the selection of multiple milling stages. This allows you to move multiple stages together. - Added automatic logging for alignment data. All alignment data is now logged to a file in the log/crosscorrelation directory. You can change this log directory in the config. - Added a cryo sputter widget for automated sputtering in cryo conditions. - Added two way projection between image and stage coordinates. This allows you to click on an image and move the stage to that location, as well as project a stage coordinate to an image coordinate (currently located in fibsem.imaging._tile). - To move milling stages in the UI, you now need to 'Shift' + 'Left Click' (Was 'Right Click') - To move the stage vertically (eucentric_move), you now need to 'Alt' + 'Left Click' (Was previously an option in the UI). ### Fixes / Updates - Fixed an issue where masks were not calculated for alignment.correct_stage_drift. - Changed the model checkpoint lookup to search the fibsem/segmentation/models directory instead of expecting an absolute path. - Fixed an issue where coordinate system was flipped when moving using a detection. - Fixed an issue where milling protocols were being overwritten when setting the milling stages directly. [USER-INTERFACE] - The milling widget hfw should now update automatically when changing the imaging settings. [USER-INTERFACE] - The user interface won't try to draw the cross hair if no image is available. [USER-INTERFACE] - Explicitly converting the last_image to np.uint8 (was np.uint16) [THERMO] - Explictly settings the manipulator coordinate system when performing movements [THERMO] - Post milling current now set to 30keV: 150 pA instead of 30keV: UHR Imaging [TESCAN] - Fixed milling rate conversions, where the milling rate units were not converted correctly [TESCAN]
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