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Appion/Leginon 3.6

open

93%

168 issues   (157 closed — 11 open)

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90/94
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63/66
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4/6
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Related issues
Bug #8111: Align_ZLP does not send scope to check preset during testing Actions
Bug #9633: dbcopy maps all other sessions literally Actions
Bug #9795: logger saving to database has thread id number too large to record as int(20) Actions
Bug #9918: Multi-color jpg files are not displayed on myamiweb Actions
Bug #9965: pause time are not applied to autofocus sequence in focuser Actions
Bug #10065: settings initialization fails if a new item is added in the referenced settings class Actions
Bug #10094: The current targetlist is skipped if restarting leginon after autofocus is completed. Actions
Bug #10123: fail to reportTargetListDone Actions
Bug #10221: Some config files are read Actions
Bug #10231: diffrtransfer.py handles mount point name glacios* as if it is gunlength option Actions
Bug #10244: rawtransfer.py loses files because rsync thread returns before it has finished transfer Actions
Bug #10375: handle camera settings as 'None' better in corrector node Actions
Bug #10467: Autosquare finding on very large grid atlas mosaic takes too much unnecessary resource Actions
Bug #10548: blob display broken when some blob has inf or nan as mean Actions
Bug #10769: consecutive click of abort one and abort queue results in the latter not applied in tomography Actions
Bug #10921: square autofinder do not give consistent targets back with the same settings when run repeatly Actions
Bug #10974: WindowsError in starting fei instruments after Titan 3.8.1 software upgrade Actions
Bug #11011: leginon runs out of alphabet suffix after 26 sessions in the same day Actions
Bug #11027: No processing wheel turning during grid loading in tem controller Actions
Bug #11194: correctorclient does not give good error log when reference session is not accessible Actions
Bug #11291: arraystats fails when numextension is not available Actions
Bug #11332: tomography backlash correction cause more shift than without on some scopes Actions
Bug #11450: arraystats fails when array is not number Actions
Bug #11452: multihole template angle not working as expected Actions
Bug #11496: session list in myamiweb/getproject.php not unique when session names are duplicated Actions
Bug #11654: myamiweb slow query from unspecified filename nor session Actions
Bug #11695: auto defocus reset defocus at the preset value if the measured correction is outside the correction limit Actions
Bug #11696: jahcfinder not return convolved targets outside the square boundary on rectangular image Actions
Bug #11745: Target beam size circle division by zero Actions
Bug #11762: ScopeEMData and CameraEMData do not get new session assignment when autoscreen change session Actions
Bug #11791: autofinder of the mosaic image starts before the last tile is added to the mosaic image display Actions
Bug #11796: camera update recommended error Actions
Bug #11815: reference session creation image path should be based on the current session path Actions
Bug #11852: imagetargetlist got put in DoneImageTargetList after processing preview targets Actions
Bug #11944: left over mysql-python calls in testing and gui Actions
Bug #11992: Use highest mean intensity in a quarter size of the image to calculate aperture-limited scattering ice thickness Actions
Bug #12027: Ptolemy icethickness not shown in myamiweb graphs Actions
Bug #12046: make dbschema/tools installed as bin and executable Actions
Bug #12052: talos and glacios normalize all lens even though changes involves only image shift and defocus Actions
Bug #12099: defect map saved for motioncor2 save a row as defect when it should be a column Actions
Bug #12100: defect map retrieved from image is using most recent correction plan, not from the image Actions
Bug #12172: can not change back BufferHostData buffer bass path if used buffer_host_setup.py to change it to something else. Actions
Bug #12213: Include PYSCOPE_CFG_PATH environment variable in fei.cfg path test for autoit aperture selection Actions
Bug #12214: Some AutoItScript installation does not include AutoItConstants as default Actions
Bug #12242: focuser simulated target crashes if preset order has an invalid preset even though it is not required to acquire final image Actions
Bug #12259: full workflow autoscreen does not proceed to next grid if no square targets are found. Actions
Bug #12260: targetfinder waits for targetlist to be done if aborted from webviewer and leginon is restarted Actions
Bug #12261: grid atlas targets aborted from webviewer can not submit new targets Actions
Bug #12296: pixel size does not show in myamiweb on old database Actions
Bug #12298: eer image use frames field becomes too long to save in database. Actions
Bug #12338: extend lattice feature in JAHCFinder is not compatible with accept all blobs without lattice fitting Actions
Bug #12339: autoit function affected by computer responding slowly Actions
Bug #12418: MosaicScoreFinder example targets not changing threshold area range settings Actions
Appion - Bug #12483: DogPicker can not find any peaks. Actions
Bug #12521: Template-correlated acquisition does not avoid holes used in focusing Actions
Bug #12571: Raster finder raster angle mapped incorrectly when filtering with polygon Actions
Bug #12580: merge score blobs between tiles in grid atlas Actions
Bug #12604: autoscreen does not carry example session's grid atlas label Actions
Bug #12615: queue abort handling problem Actions
Bug #12616: sorttarget web tool show targets from targetlist that are completed Actions
Bug #12625: run application dialog takes a long time to load when there are many sessions ran by the same user Actions
Bug #12639: abort queue dialog wxPython error Actions
Bug #12687: autofocus does not return to pre-aberration-corrected beam tilt/stig after beam-tilt based autofocus that requested image-shift aberration correction Actions
Bug #12688: autoscreen returns to the last user settings not example session settings Actions
Bug #12749: unnecessary duplication of preset setting to tomo at the end of remove alpha backlash Actions
Bug #12764: autoscreen uses example session's user in the new session instead of the ldap user leginon.cfg Actions
Bug #12773: autoscreen send notification activation message to slack too often Actions
Bug #12774: autoscreen sends a message about has been idle for 0.0 minutes Actions
Bug #12775: The next application launched after autoscreen starts off and close column valve automatically if just kill and run the same application Actions
Bug #12820: J1230 fail to set scope Actions
Bug #12823: ReferenceCopier in rawtransfer.py needs to access permanent storage to both read image array and simple metadata Actions
Bug #12824: settings initializes on based on the most recent session regardless of user Actions
Bug #12844: import sinedon does not work without existing pyami.cfg Actions
Bug #12849: autoscreen failed when leginondb has null user Actions
Bug #12871: reference import not using leginon.cfg [references] definition Actions
Bug #12873: reference import/export fails from not having both bright and dark reference associated with norm Actions
Bug #12939: focus at (0.5,0.5) of lattice points does not work when all blobs are accepted Actions
Bug #12997: reference sessions are not hidden Actions
Bug #13030: run application dialog error if recent history include hidden applications Actions
Bug #13060: new user settings come from the last user that used the node class and alias, not administrator Actions
Bug #13212: failed os.getuid prevents leginon session creation Actions
Bug #13239: separate advanced scripting connection makes instance of super function failed. Actions
Bug #13351: reduce autoscreen memory usage Actions
Bug #13383: import xml application file through python does not use sinedon engine specification Actions
Bug #13394: use preset in session query by tem Actions
Bug #13450: rawtransfer.py does not change ownership of the frames files when rsync is used Actions
Bug #13470: gain correction problem on K3 without GIF in Leginon 3.6 Actions
Bug #13569: Grid images with no squares found result in Ptolemy error and an empty file Actions
Bug #13741: export targets does not export with just one image Actions
Bug #13746: c2 aperture size got saved under diffraction tem when that is created after normal scope Actions
Bug #13751: grid loading in autoscreen Fail auto loading Actions
Bug #13823: An all null user is added to database when a SettingsData is referenced by another SettingsData Actions
Bug #13860: autoscreen fails to send gr preset to set TEM Actions
Bug #16172: Hardcoded values in myamiweb/slurmHost.py can't be changed via config Actions
Feature #9489: check intensity at the reference target before trying to align zlp Actions
Feature #9759: Filter recent leginon sessions in setupwizard by session prefix Actions
Feature #9760: filter application names in application history Actions
Feature #9775: allow cached jpg images to be used to adjust contrast Actions
Feature #9915: live reordering of targets in the same target list Actions
Feature #9981: option to support mode change for files generated by diffrtransfer.py Actions
Feature #10034: use example targets to set square finder settings Actions
Feature #10131: set stage limit in pyscope tem classes Actions
Feature #10152: Use ptolemy to find squares Actions
Feature #10239: multiply targets on grid atlas autosquare finder to cover the square Actions
Feature #10240: example of node without gui for development Actions
Feature #10252: change filenames so that aplhanumerical listed order matches collection order Actions
Feature #10280: allow tomography backlash correction pause time on the first image adjustable Actions
Feature #10313: submit grid atlas auto targets through autoscreen.py Actions
Feature #10342: increase ht7800 beam-image shift range Actions
Feature #10378: add prefix in front of timestamped frame name from camera Actions
Feature #10612: Use precalibrated ctf estimate for tomography defocus setting Actions
Feature #10613: limit the storage path from which export reference is searching Actions
Feature #10630: TVIPS F216 support Actions
Feature #10885: Falcon4 eer support Actions
Feature #10948: get beamstop position through AutoIt Actions
Feature #10986: Speed up super res and counted images by calculating stats on decimated image Actions
Feature #11007: allow scope selection in loi Actions
Feature #11010: send a test slack notification when it is activated Actions
Feature #11026: Order grid loader gui in tem controller with first grid at the bottom Actions
Feature #11031: turn on timeout and error notification during autoscreening Actions
Feature #11049: filter ptolemy results on square finding using top scorer Actions
Feature #11184: hole findering using ptolemy med2high Actions
Feature #11259: shrink images used for correlation if they are too big Actions
Feature #11272: option to retract automated objective aperture during auto grid insertion in TEM controller node Actions
Feature #11348: initiate cold feg flashing Actions
Feature #11516: Use icetargetfinder as parent class of other auto hole finders Actions
Feature #11517: allow user to download SerialEM-style mdoc from myamiweb Actions
Feature #11676: save json files for atlas matching Actions
Feature #11753: link grid in grid server with session using session comment field as identification string in autoscreening Actions
Feature #11763: default to not submit focus targets if there is no acquisition target selected Actions
Feature #11770: Export essentials for refresh leginon database in one script Actions
Feature #11807: Scripts to export target metadata produced by its child images Actions
Feature #11878: auto launch appion scripts for new session based on those run on an old one Actions
Feature #11984: transfer frames in batch of sessions Actions
Feature #12011: option for sorting targets on Mosaic atlas to minimize traveling Actions
Feature #12022: display database host and databasename in launcher and manager to help confirm which database they are connected to Actions
Feature #12066: handle dark subtraction and gain correction separately Actions
Feature #12084: support eer frame alignment on motioncor2 Actions
Feature #12177: save 8x8 stats image on Falcon Actions
Feature #12193: tools for changing buffer frame path Actions
Feature #12248: all project assignment in autoscreen Actions
Feature #12382: check settings used in a session from python script Actions
Feature #12424: Make Edge Hole Finder a subclass of JAHCFinder Actions
Feature #12433: center focus half-way between the lattice unit vectors in lattice hole finders Actions
Feature #12450: a way to force storage engine when create tables in myamiweb Actions
Feature #12451: myamiweb install page change for storage engine specification Actions
Feature #12529: make RasterFinder a subclass of IceTargetFinder so we can reuse ice filter and display. Actions
Feature #12541: allow user to select how MosaicScoreTargetFinder filter blobs with scores Actions
Feature #12810: Group square blobs found in auto finder by equal delta value so the sampling has better value distribution Actions
Feature #12822: more specific about config file behavior Actions
Feature #12851: allow append full path in buffer frame path Actions
Feature #12877: save uid and gid when creating leginon session so that rawtransfer.py does not need to use session image path to determining them. Actions
Feature #12879: export holefinder ice filter stats of the ones that are bad Actions
Feature #12993: ellipse and rectangular image panel tool to filter blobs for auto square finding Actions
Feature #12995: TFS Selectris support Actions
Feature #12996: allow user to pause autoscreen before submitting auto square finder targets. Actions
Feature #13029: Falcon4EC behind energy filter Actions
Feature #13119: allow rejected rawtransfer.py movies to be moved to a hidden folder instead of being deleted Actions
Feature #13281: combine all import/export scripts for refreshing database Actions
Feature #13421: export bufferhostdata settings from one database and import them to a new database Actions
Support #11985: use test script to check comtypes safearray.py replacement Actions
Support #12019: remove mapping test in mysocket Actions
Support #12348: more Hitachi focus lens Actions
Support #12739: scoretargetfinder too verbal about failed score finding script run Actions
Support #13104: create default for dbschema Actions
Support #13742: update checkPackages.py Actions
Task #10875: run square finding as multiprocess process Actions
Task #12144: myami-3.6 release Actions