Project

General

Profile

Appion/Leginon 3.4

closed

85%

123 issues   (105 closed — 18 open)

Time tracking
Estimated time 0.00 hour
Spent time 0.00 hour
Issues by
Bug

50/64
Feature

54/58
Support

1/1
Related issues
Bug #5368: jpgraph included with myamiweb thinks php7 is invalid version Actions
Bug #5576: motioncor2_ucsf saves both gpuid and gpuids as run parameters Actions
Leginon - Bug #5580: Empty focus sequence gui error Actions
Leginon - Bug #5593: map.php ruler does not work Actions
Leginon - Bug #5598: Film is no longer a valid option for FEI software version 2.9 Actions
Leginon - Bug #5607: Specific multihole template causes image not same shape error in correlation Actions
Leginon - Bug #5618: error log for camera error does not suggest solution Actions
Leginon - Bug #5619: mosaicquiltfinder get error because it does not have preview and reference target selection tool in the panel Actions
Leginon - Bug #5622: tomography sequential scheme should always adjust target Actions
Leginon - Bug #5632: kill application change dictionary size during iteration Actions
Leginon - Bug #5647: nitrogen autofiller may start filling between leginon check and starts its refill. Actions
Leginon - Bug #5762: AutoN2Filler node can not distinguish between slow fill and no fill COMError Actions
Leginon - Bug #5771: Non queue counting slows down web server Actions
Leginon - Bug #5780: mysqli_fetch_row() expects parameter 1 to be mysqli_result, boolean given Actions
Leginon - Bug #5792: ice standard deviation thickness can not be compared with inf Actions
Leginon - Bug #5818: better machine image stats Actions
Leginon - Bug #5828: beam tilt and other projection mode and probe mode dependent tem values need to be called after the modes are set through preset Actions
Leginon - Bug #5840: hidden leginon sessions are shown in the web viewer Actions
Leginon - Bug #5841: dataStatusReport table definition in projectDBSchema.xml fails to apply during web database initialization with mysql 5.7 or mariadb Actions
Leginon - Bug #5869: settings import insert error if the key does not exists any more Actions
Bug #5888: imgRejector2 hide exemplar images Actions
Leginon - Bug #5892: exposure pause time does not change Actions
Leginon - Bug #5921: import_leginon_cal.py and import_leginon_presets.py adds a new administratore user on very old installation Actions
Bug #5922: batch_leginon_path_change.py is broken Actions
Leginon - Bug #5940: Falcon protector blocks beam too often Actions
Leginon - Bug #5957: allow camera aligned DD movies to be aligned again Actions
Leginon - Bug #5963: import_leginon_cal.py only check one tem to be paired if pixelsize exists on that pair Actions
Bug #5964: frame alignment does not allow camera binning Actions
Bug #6021: dd frame alignment extname referenced before defining Actions
Leginon - Bug #6023: k2 super resolution return only a quarter strip Actions
Leginon - Bug #6086: imgreport.php image-shift aberration matrix does not show edited values Actions
Bug #6097: imgRejector2 does not hide ice image that has a broad crystal ring Actions
Bug #6111: cannot choose ctf run or picking run in standard web view Actions
Bug #6113: python filesystem fs needs to be a specific version Actions
Leginon - Bug #6127: rawtransfer.py query for frames name too slow Actions
Leginon - Bug #6131: mosaicclickfinder freeze when user submit targets without any mosaic Actions
Bug #6150: ddstack bad pixel correction error when corrector plan is None Actions
Leginon - Bug #6152: k3 stuck in gain normalized mode even though dmsem.cfg has been changed Actions
Bug #6155: can not get pixel size of aligned and binned super-res image Actions
Leginon - Bug #6184: tomography keep printing out error message about the last tilt did not return properly Actions
Leginon - Bug #6249: myamiweb tomo tracking graph broken Actions
Bug #6251: frame alignment gain correction does not recover from ocassional K2 image dimension issue Actions
Leginon - Bug #6259: k2 loses data from a digitizer channel Actions
Leginon - Bug #6277: error resetting coma correction if the first acquisition failed due to a preset or target adjustment movement error Actions
Bug #6293: motioncor2 frame alignment error for unsuccessful run not explicit Actions
Leginon - Bug #6338: The first image shift target gets different image rotation matrix from the rest when a probe change is involved between the low mag parent preset and the acquiring preset Actions
Leginon - Bug #6411: leginon can not find nano probe phase plate beam tilt rotation calibration if hl preset is in micro probe mode Actions
Leginon - Bug #6430: Navigator iterative move stuck in reacquire check if camera returns no image Actions
Leginon - Bug #6518: Align_ZLP return to target without adjusting the target Actions
Bug #6538: defocus offset correction for beam-image shift are used in myamiweb and Appion as intended defocus. Actions
Leginon - Bug #6539: rawtransfer.py keeps checking duplicated file or frames not having a saved database record and slow down as a result Actions
Leginon - Bug #6728: rawtransfer.py clean up frames in k2 camera too quickly Actions
Leginon - Bug #6763: image report does not show histogram if the image is cached as jpeg file Actions
Leginon - Bug #6812: Error on Align Presets screen when the source preset is the last in the list Actions
Leginon - Bug #6824: summary.php does not always show project name and link Actions
Leginon - Bug #6829: centOS 7 autoInstaller can not read Leginon application xml as web user Actions
Leginon - Bug #7058: schema update breaks if a branch does not have the tagged revision Actions
Bug #7095: missing findEM library requirement on CentOS 7 autoinstaller Actions
Leginon - Bug #7105: download.php can not get sessionid if image has missing information Actions
Leginon - Bug #7109: measuring tool (ruler) not working Actions
Leginon - Bug #7193: centos7 autoinstaller does not run correctly Actions
Leginon - Bug #7557: image-shift abberation calibration does not apply last calibrated stig and defocus when starting Actions
Leginon - Bug #7576: dbschema update failed on new branch Actions
Leginon - Bug #9231: ran into an error where a float was passed instead of an integer for array index in raster.py Actions
Leginon - Feature #2727: support tiff lzw format writing from SerialEMCCD for raw frames from K2 dose fractionation Actions
Leginon - Feature #3764: webviewer for file list selected in imageviewer by catagory or preset Actions
Leginon - Feature #4686: configure tcp connection by ip address Actions
Leginon - Feature #4936: Falcon3 implementation Actions
Leginon - Feature #5401: Numbering the red "acquired" targets Actions
Leginon - Feature #5581: Display in myamiweb target count and time estimate for non queued targets Actions
Leginon - Feature #5583: apply template hole finder to each tile in mini atlas of the square Actions
Leginon - Feature #5629: relax stage at the end of the move Actions
Leginon - Feature #5635: set default stage z position while calculating grid atlas parameters Actions
Leginon - Feature #5642: tranfer done targets from one grid atlas to another of the same grid but different insertion Actions
Leginon - Feature #5666: web tool for managing instrument Actions
Leginon - Feature #5713: Import random defocus range when importing presets Actions
Leginon - Feature #5753: carry NodeSpecData within the node Actions
Leginon - Feature #5786: correct stig on beam-image shift Actions
Leginon - Feature #5789: Defocal series for manual acquisition Actions
Leginon - Feature #5797: debug mode for data transport Actions
Leginon - Feature #5809: configuration test before launching leginon Actions
Leginon - Feature #5814: use gctf to estimate ctf during coma free alignment and related calibration Actions
Leginon - Feature #5815: auto coma correction in beam tilt imager Actions
Leginon - Feature #5831: work around Falcon3 occasional lost of communication Actions
Leginon - Feature #5863: flexable defocus sequence that does not require many presets to be set Actions
Leginon - Feature #5868: export import projection submap as part of the calibration Actions
Leginon - Feature #5872: MSI-Tomography phase plate application Actions
Leginon - Feature #5884: Download beam tilt values estimated by image-shift coma matrix for Relion 3 Actions
Feature #5890: script to unhide all images Actions
Leginon - Feature #5902: Glacios integration Actions
Leginon - Feature #5912: correct defocus change from beam-image shift Actions
Leginon - Feature #5918: reading metadata from Falcon3 Actions
Feature #5919: Show directional graph of astigmatism in ctf report Actions
Leginon - Feature #5923: add data type to batch_leginon_path_change.py to move references Actions
Leginon - Feature #5942: swing tilt order for tomography to reduce over correct in one direction Actions
Feature #5946: Run command through myamiweb directly on processing host Actions
Leginon - Feature #5949: Add a user result page similar to the summary page for Leginon sessions Actions
Leginon - Feature #5958: restrict frames session permission with rawtransfer.py Actions
Leginon - Feature #5962: support Falcon subframe alignment Actions
Leginon - Feature #5972: add gui for editing image-shift coma and other related beam tilt calibrations Actions
Leginon - Feature #6026: simulated GatanSocket.py for testing. Actions
Leginon - Feature #6041: Black stripe monitor added Actions
Leginon - Feature #6069: Microscope names Actions
Feature #6104: Update Motioncor2 wrapper for MotionCor2 1.2 version Actions
Feature #6143: save DD frame alignment trajectory and stats to database Actions
Leginon - Feature #6151: orthogonal distance regression function Actions
Feature #6153: remove aligned images from ddstack run directory if they are committed to database Actions
Leginon - Feature #6199: remove image display in loi Actions
Leginon - Feature #6231: limit viewer session selection in the configuration Actions
Leginon - Feature #6273: General Pause and Continue from a central gui Actions
Leginon - Feature #6344: combine image rotation and scale calibration in one node Actions
Leginon - Feature #6415: Leginon simulation tem and camera that shows a pre-saved images according to the mags Actions
Leginon - Feature #6439: tuple sequence entry for gui Actions
Leginon - Feature #6649: Send a fake error message to slack when Leginon predicts the N2 fill is about to happen on the next check Actions
Leginon - Feature #6714: tia raw format reader Actions
Leginon - Feature #6715: utility to convert tia raw data series to other formats Actions
Feature #6748: Provide native Appion support for Topaz particle picking Actions
Feature #6773: link uploaded tilt series to a parent image through a fake target Actions
Feature #6776: use an existing image of the session to set upload scope and camera imaging condition during upload Actions
Leginon - Feature #6800: stop users from using special charactors in atlas and grid name Actions
Leginon - Feature #6822: gui to allow users to calibrate image-shift aberration correction manually Actions
Leginon - Feature #7011: Enter manually per pixel dose rate from camera during preset dose determination Actions
Leginon - Support #6830: Tool for enabling buffer host Actions