Project

General

Profile

Appion/Leginon 3.5

closed

82%

141 issues   (116 closed — 25 open)

Issues by
Bug

62/79
Feature

50/57
Support

2/2
Task

2/3
Related issues
Bug #7018: Error in Python code when getting presets "From Scope" Actions
Bug #7076: Unstable beam position when preset change involves spot size change on Talos column Actions
Bug #7182: missed merge conflict in rawtransfer.py Actions
Bug #7265: setInstrument exception while moving back from reference target not caught Actions
Bug #7480: MosFlm does not read smv file made by numsmv.py Actions
Bug #7524: settings loading uses node defaultsettings from python code, not admin is_default query when only one item is not set Actions
Bug #7685: Dials does not read binning from smv file Actions
Bug #7689: numpy.float64' object cannot be interpreted as an index error during hole finding Actions
Bug #7706: low dose scripting should not be a requirement Actions
Bug #7719: import_leginon_presets.py may save presets into a session for a different tem so that it does not show up in leginon Actions
Bug #7752: adding field to createSQLTable try to add instead of change default when it is not the same as the original Actions
Bug #7753: multiple indexed field keys caused by xml initialization and sinedon Actions
Bug #7755: J1230 toggle queue timeout to turn off filament Actions
Bug #7798: mariadb server version 10.2 allows timestamp to default to null Actions
Appion - Bug #7812: Download particle data takes too much memory Actions
Bug #7834: Shutter control during acquisition does not work if pre-specimen shutter is set to Shutter number 2 in GMS Actions
Appion - Bug #7943: handle correction plan through motioncor2 Actions
Bug #7963: tomography z0 change maximum is in microns but the default assumes in meters Actions
Bug #8011: pymysql adds duplicated index to table with a new keyname Actions
Bug #8021: myamiweb imageviewer assembles sq preset level image list as grid atlas rather than gr preset in a specific situation Actions
Bug #8027: Feature request: better support for non-square cameras Actions
Appion - Bug #8037: Fresh Appion install with only uploaded images do not show pixel size in myamiweb image viewer Actions
Bug #8058: Databases with utf8mb4 character set do not give queue counting in myamiweb LOI Actions
Bug #8153: autoinstaller not installing fftw3 correctly in the webserver installer part Actions
Bug #8160: K3 camera pixel size incorrect ? Actions
Bug #8193: Some dark references takes longer than trip value for recent dark criteria Actions
Bug #8309: autoinstaller security Actions
Bug #8330: mysocket mapping test fails if the address is not the primary ip of the host Actions
Appion - Bug #8333: ddstack does not handle camera gain-corrected k3 stacks Actions
Bug #8334: Error in attempt to display target area on loaded non-leginon session image in target finders Actions
Bug #8351: semccd frame orientation change in 2019 Actions
Bug #8364: Queue timeout tool creates confusion and problem if used before all queue are submitted Actions
Bug #8387: mysql 8 deprecated current_timestamp as the system default for timestamp type Actions
Bug #8392: k3 camera insertion slower than k2 Actions
Bug #8399: Fix package resolution histogram Actions
Bug #8406: None is not iterable error when creating new reference session Actions
Bug #8455: MosaicQuiltfinder submit tool does not get activated after target list is finished. Actions
Appion - Bug #8457: ctfreport fails to show stats for mysql server version 5.7 and above Actions
Bug #8467: K3 needs to use prepareDarkReference to make dark current correction, and need it more often, too Actions
Bug #8474: mysql 8 requires order by query item to be included in select query Actions
Appion - Bug #8481: ctfgraph query fails on mysql 5.7 and above server Actions
Appion - Bug #8698: imageloader.py failed on mrc stack Actions
Bug #9096: new instrument is inserted if the old entry has hidden field as null in the database Actions
Bug #9107: General Pause does not pause unless already in progress Actions
Bug #9109: lost communication to leginon-remote error is not caught Actions
Bug #9149: import_leginon_cal.py import magnifications in float Actions
Bug #9152: leginon client opened on instrument microscope complain about needing requests Actions
Bug #9166: drift manager freeze on correlation error Actions
Bug #9180: import_leginon_cal.py import magnifications in wrong order Actions
Bug #9187: application xml exported from mariadb can not be imported to mysql Actions
Bug #9195: reduce remote server activities when session not controlled by remote user Actions
Bug #9202: myamiweb does not display atlas if imcache jpeg images are the only ones available Actions
Bug #9230: preset imported by Import_leginon_presets.py do not show up in leginon because it is saved to an old session with more than one tem instrument Actions
Bug #9269: Catch more error sending request error in the middle of the run Actions
Bug #9284: directq.complexMysqlQuery get MySQL server has gone away error if the script loading the module is run for too long Actions
Bug #9286: dmsem setEnergyFilter function is slow to return even if it is already in that state Actions
Bug #9287: remove unnecessary set functions to fei scopes Actions
Bug #9327: myamiweb shows session ends when aligned images are saved, not when it is acquired from the scope Actions
Bug #9348: no attribute imagereadable error while calculating norm reference image while collecting bright/dark image on reference path Actions
Bug #9350: instruments.cfg from the three possible location got combined instead of overwritten Actions
Bug #9417: 64-bit comtypes for tia and feicam is not compatible with pyscope/safearray.py Actions
Bug #9460: can not report column pressure Actions
Bug #9475: camera sensitivity calibration of exact zero causes uncaught ZeroDivisionError Actions
Bug #9476: falcon3 getImage Attribute Error: Data Actions
Bug #9494: poster.php is slow from unnecessary query Actions
Bug #9495: increase timing stats table speed on large session Actions
Bug #9498: Incorrect unit in Buffer cycler trip level setting gui Actions
Bug #9511: catch instrument setting error in queue processor thread set up and clean up Actions
Bug #9527: myami-pymysql fails sinedon.directq connection ping function from trunk Actions
Appion - Bug #9631: imgreport.php getSEMDataFromId call error Actions
Bug #9771: Falcon4 base frame time is not quite right Actions
Bug #9818: web imageviewer stuck in server internal error if a session with no image is loaded. Actions
Bug #9858: imcache pow.jpg binned before power spectrum calculation show artifact and wrong resolution scale on rectangular image. Actions
Bug #10110: slack notification does not work Actions
Bug #10125: rawtransfer.py recursive chown causes slow down with large session Actions
Bug #10230: tomography tilt series adjust target not between the two groups of tilts Actions
Bug #10232: K3 camera saved frame orientation not correctly assigned Actions
Bug #10358: acquisition not waiting for image processing if not displaying image Actions
Bug #10371: rawtransfer.py may transfer frames to the wrong session if both cameras save its timestamped file as the same name Actions
Feature #6444: Diffraction projection mode support Actions
Feature #6652: minimized leginon tutorial for workshops Actions
Feature #7285: stand-alone liquid nitrogen monitor to notify user if autofiller does not fill when leginon is not running Actions
Feature #7468: Avoid K2/K3 dark current reference acquisition with auto nitrogen fill during off-hour Actions
Feature #7491: Port forwarding uisng a linux PC to microscope PC Actions
Feature #7525: record movie through tia gui Actions
Feature #7718: support Gatan Rio 9 camera Actions
Feature #7751: use pymysql in sinedon instead of MySQL-python Actions
Feature #7754: testing mysql reconnect after timeout Actions
Feature #7781: camera length calibration for diffraction mode Actions
Feature #7915: Set JAHC Finder focus standard deviation min threshold Actions
Feature #7954: Off target low mag tracking for tilt series tomography data collection Actions
Feature #7969: Gatan K3 correlated double sampling mode support Actions
Feature #8002: functions to find pattern center and calibrate camera length from a diffraction image of cross-grating replica Actions
Appion - Feature #8036: Allow upload tif movie frames to Appion Actions
Feature #8161: Speed up K2/K3 acquisition by faking returned sum array Actions
Feature #8178: Angled and non-square target area display in Leginon target finder Actions
Feature #8273: auto insert beam stop for any camera acquisition in diffraction mode Actions
Feature #8311: filter acquisition targets with ice thickness threshold and record their stats Actions
Feature #8346: tools for managing diffraction series Actions
Feature #8348: auto transfer and upload of diffraction movie series Actions
Feature #8369: close column valve after idle timed out Actions
Feature #8376: Warn user about how many targetlist they are about to abort with StopQueue tool Actions
Feature #8391: Do K2/K3 defect correction in GMS 3.3.2 and up with pre-counting correction Actions
Feature #8398: increase number of decimal places in A pixel sixe from 2 to 3 Actions
Feature #8404: allow environment variable replacement of path in leginon.cfg parsing Actions
Appion - Feature #8433: allow particle run to hide and unhide from summary table Actions
Feature #8476: Show all target number on grid atlas Actions
Feature #8490: get image data object mrc file shape and readability without reading the array Actions
Feature #8491: Allow user to set the length of idle timeout length in presets manager Actions
Feature #8492: overwrite k2 and k3 default frame flip from dmsem.cfg Actions
Appion - Feature #8615: a way to view dd drift data used in dddriftgraph.php Actions
Feature #8620: set TEMAdvancedScripting version in fei.cfg Actions
Feature #8621: calibrate stage tilt delay and rate Actions
Feature #8622: calibrate camera movie saving delay Actions
Feature #8697: use Django REST framework to exchange data between leginon and remote Actions
Feature #8746: export/import image references Actions
Appion - Feature #8747: Upload particle coordinates from single Relion star file Actions
Feature #8758: set sesssion name prefix in a config file Actions
Feature #8776: option to reacquire image three times with some sleep time before pause Actions
Feature #8801: record offset used in leginon to convert signed integer image format to smv Actions
Feature #9105: add IMAGE_PEDESTRAL to smv diffraction files for DIALS Actions
Feature #9108: return control to remote after terminating by local operator Actions
Feature #9132: use node order to block remote tool from being used when scope is busy on some other tasks Actions
Appion - Feature #9160: move basic xml read/write function from apXml to pyami.xmlfun Actions
Feature #9188: reconnect to leginon-remote if remote server is down in the middle of a session Actions
Feature #9267: add linear regression stats to holeicetoalslice.php Actions
Feature #9276: Accept all blobs as lattice points for targeting Actions
Feature #9285: allow user to download tilts of a tomography series from web viewer. Actions
Feature #9288: function test for camera Actions
Feature #9316: loop drift measurement and save to a file Actions
Appion - Feature #9334: Falcon4 motion correction support Actions
Appion - Feature #9353: reduce leginon image data folder size after pre-processing Actions
Feature #9424: Falcon4 support that saves mrc stack as movie frames Actions
Feature #9454: Change multitarget default to 4 Actions
Feature #10953: Handle Talos 2.7 Flucam gui with extra button shifting beamstop control Actions
Feature #10987: Leginon: speed up ZLP ice thickness Actions
Support #7953: numpy.linalg.lstsq rcond default change warning for 1.14 and above Actions
Support #10135: Problem with Gatan K3 PC setup Actions
Appion - Task #8270: Relion 3 default imported micrographs to be saved under Micrographs not micrographs. ctfdata download needs to match that Actions
Task #8367: clean up failed IdleTimer events and functions Actions
Task #9328: minimize use of tommonikor scripting Actions