Project

General

Profile

Appion/Leginon 3.2

closed

88%

136 issues   (121 closed — 15 open)

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

77/87
Feature

39/42
Support

2/2
Task

3/5
Related issues
Leginon - Bug #611: When libCV is missing this is not properly reported Actions
Bug #1806: rpn in clusterParamsForm.inc need to be smaller than ppn Actions
Bug #1832: Cannot hard link to prepared refinement job launcher page Actions
Bug #2845: Appion Loop takes too long to load old images Actions
Leginon - Bug #2896: rct acquisition does not need to check drift if threshold is 0 Actions
Leginon - Bug #2905: myami svn download directory is hardcoded in autoInstallSetup.php Actions
Leginon - Bug #2906: make download sample images in autoinstaller an option Actions
Leginon - Bug #2907: K2 dark image default dimension xy is flipped Actions
Leginon - Bug #2927: lattice extension raster points go off towards the edge of images Actions
Leginon - Bug #2934: dmsem does not control Gatan GIF energy filter slit Actions
Leginon - Bug #2936: Svn rev 18580: DM_VERSION harcoded in pyscope/dmsem.py Actions
Leginon - Bug #2946: DM 2.3.1 frames need up-down flip in comparison to the older version Actions
Leginon - Bug #2962: frame selection for makestack with ddstack also leave out last n frames if ask to leave out first n frames Actions
Bug #2978: can not transfer picks from particle stack to dd aligned images if ddstack is specified but needs to come from more than one ddstack Actions
Leginon - Bug #2982: values of text labels in mrc files includes trailing byte zeros expressed as python string Actions
Leginon - Bug #2987: jeolcom.py does not set eucentric focus properly Actions
Leginon - Bug #3003: can not select existing client choices in session wizard gui on Mac OS 10.9 Actions
Leginon - Bug #3010: pixel size calibration can not be reverted back to earlier values in the gui Actions
Leginon - Bug #3026: jeol automated aperture not always accessable through scripting Actions
Leginon - Bug #3029: need to account for different scale within projection submodes on JEOL scopes Actions
Leginon - Bug #3106: RasterFinder can not submit preview targets Actions
Leginon - Bug #3142: jeolcom scripting not reporting error when it can not move to the requested position in stage z Actions
Leginon - Bug #3144: image reacquired becomes that of the parent if target adjustment with navigator fails to be make to acceptable tolerance Actions
Leginon - Bug #3145: image-beam shift used on Jeol scopes not always used in target adjustment Actions
Leginon - Bug #3154: defocus estimation in power spectrum image uses fixed 2.0 cm Cs value Actions
Leginon - Bug #3157: automated apertures can not be controlled from scripting at NYSBC 3200fsc Actions
Leginon - Bug #3161: jeolconfig.py does not read different level of values consistently among python versions Actions
Leginon - Bug #3244: camera dimension for preset dose measurement for full size K2 camera is not in common configuration Actions
Leginon - Bug #3245: runtime error during hole finder testing are output to terminal, not caught Actions
Leginon - Bug #3253: jem3200 needs to relax beam to keep beam shift stable after intensity adjustment Actions
Leginon - Bug #3254: copying beamshift for all presets at the same mag is a bad idea for Titan Krios and JEM-2100f Actions
Leginon - Bug #3255: preset parameters are not always get properly from scope Actions
Leginon - Bug #3258: grid mosaic shows gaps when camera y axis is shorter than x Actions
Leginon - Bug #3289: jem3200 x y position callback is not where it gets to. Actions
Leginon - Bug #3293: sinedon only saves 2x2 numpy.matrix at first dimension Actions
Leginon - Bug #3314: can not import applications from addapp.php after initial installation Actions
Leginon - Bug #3321: alignzlp settings error Actions
Leginon - Bug #3331: AlignZeroLossPeakPublishEvent not bound to any node error Actions
Leginon - Bug #3374: MosaicClickFinder acquisition target panel settings leads to no where Actions
Leginon - Bug #3375: pixel size calibration linear extrapolation causes large error Actions
Bug #3422: Fix magnification in Appion generated FREALIGN par file Actions
Bug #3555: makeDEAlignedSum.py does not apply alignlabel to aligned image Actions
Bug #3556: deProcessFrames.py needs both in pythonpath and path environment variable Actions
Leginon - Bug #3562: Some target tool settings panels have no values, and therefore should be disabled Actions
Bug #3569: makestack "pixlimit" feature adding black pixels. Actions
Bug #3599: makeDEAlignedSum.py error if not using queue Actions
Leginon - Bug #3614: Save frames is deactivated to the preset if an image is taken in Navigation node and then retrieved from the scope Actions
Bug #3617: nominal option needed to be in web gui to shift large nominal defocus Actions
Leginon - Bug #3625: wxPython not in CentOS 6.7 yum repository Actions
Leginon - Bug #3638: findMagnifications does not set new MagnificationsData in the database Actions
Bug #3645: Available queue does not show up in myamiweb clusterparam form if the user is logged in Actions
Leginon - Bug #3677: why default runMaxLikeAlignment.php to 1 ? Actions
Leginon - Bug #3678: RCT never check drifts Actions
Bug #3691: Autoinstaller fails at install/newDBsetup.php Actions
Leginon - Bug #3692: adjust.php does not return to fftbin order to after Actions
Leginon - Bug #3693: scalebar does not show up at the bottom of the image in web image viewer when image is rectangular Actions
Bug #3738: can't create substack Actions
Leginon - Bug #3739: square finding tool in grid atlas does not do anything Actions
Bug #3758: uploaded signle direction tilt series causes error in preparation step for protomo2aligner Actions
Leginon - Bug #3763: Camera physical pixel size for GatanK2 super-resolution mode is incorrect Actions
Bug #3765: commit doesn't uncheck when testing image in dogpicker Actions
Leginon - Bug #3793: exception caused by image array not returned from camera not handled Actions
Bug #3807: uploaded session not showing up in project page Actions
Bug #3808: uploadImages.py does not set "frame path" field in SessionData Actions
Bug #3811: dd alignment with motioncorr fails with larger movies or larger shifts Actions
Bug #3819: help bubble in particle selection processing page disappeared. Actions
Leginon - Bug #3835: mag selection in Leginon interface not going to the said magnification when the magnification is higher than an overwritten one in low mag mode Actions
Bug #3839: post values not filled in to particle diameter in particle selection runAppionLoop.php forms Actions
Bug #3848: keep non-error extraHTML in smaller font in test result displays Actions
Bug #3873: Image does not always have preset for retrieving scope and camera information Actions
Leginon - Bug #3893: TargetFinder acquisition template settings gui broken after importing application settings from json files Actions
Bug #3931: makeDEAlignedSum.py try to process images with no frames saved Actions
Bug #3933: ctfdata download on individual run does not have confidence_30_10 and other new style confidence Actions
Bug #3935: combining stack containing virtual stack fails to add particles in stackfile Actions
Leginon - Bug #3943: Gatan K2 Summit early return with DM 2.2 returns zero dimension array Actions
Leginon - Bug #3944: jeolcom image shift scale is mag dependent if PLA is used to shift Actions
Bug #3960: CTF estimation resmax parameter get modified in a run mixed with and without bestctf Actions
Bug #3961: particle selection from stackIntoPicks.py off a combined stack from multiple sessions can not be used to create new particle stack Actions
Leginon - Bug #3967: rawtransfer,py rsync method duplicates frame transfer when host frames are not be removed Actions
Leginon - Bug #3986: FEI Titan gave Error on the HalOpticsLensObjMainMiddle board when sending LM preset after SA mag preset Actions
Bug #3995: polishStack.py fails if expperframe and expweight are noneType Actions
Leginon - Bug #3997: export_session_settings.py output mutliple copies of settings from the same node alias or focus sequence Actions
Leginon - Bug #4000: stage position confirmation loops inifinately Actions
Leginon - Bug #4003: The magnification used in projection lens normalization in lowmag range is not the same for all jeol scopes Actions
Bug #4047: ctfind4 stigmatism definition has changed Actions
Leginon - Bug #4246: Filament is turned off between images on JEOL 1400 Actions
Bug #4624: Stack Centering hung up Actions
Feature #2621: expose more dosefgpu_driftcorr options Actions
Feature #2720: Xmipp3 CL2D Actions
Feature #2748: process raw frames from falcon Actions
Feature #2797: Leginon node class logger so that Appion can use functions in them Actions
Leginon - Feature #2811: adjust preset exposure dose by illumination area Actions
Feature #2834: Protomo alignment launching and assessment via Appion Actions
Feature #2841: Create a basic appion layout form for creating a new gui page Actions
Feature #2843: Add a gui for uploadExternalRefine.py Actions
Feature #2847: add DE frame alignment script Actions
Feature #2869: Add an option to cluster parameters form to select which queue to submit a job to Actions
Leginon - Feature #2959: Pause longer for the first image taken on the parent image Actions
Leginon - Feature #2974: open column valve before taking images Actions
Feature #2991: Enable BestDB feature in Appion version of CTFFIND Actions
Feature #2995: Scripts to help user change the session and appion run path Actions
Feature #2996: mrc validation script Actions
Feature #3000: support for SGE cluster type Actions
Leginon - Feature #3011: set JEOL scale in a config file, not in the jeolcom.py module Actions
Leginon - Feature #3012: get tem projection modes and save in database Actions
Leginon - Feature #3014: calibrate jeol TEM3 value scale on viewing screen Actions
Leginon - Feature #3150: default template files to the one in the install leginon directory if the file in the current settings does not exist Actions
Leginon - Feature #3178: option to invert template in MSI-T template hole finder (JAHCFinder) Actions
Leginon - Feature #3184: Restrict projects seen by users at Leginon setup Wizard project selection page Actions
Leginon - Feature #3267: open column valve automatically before acquiring image Actions
Leginon - Feature #3291: manual image beam shift compensation calibrator Actions
Feature #3354: add CTFFIND 4 to the pipeline Actions
Feature #3361: trim off edge after flat field correction in makeDDRawFrameSatack.py Actions
Feature #3441: Add default flags to MakeDDRawFrameStack Actions
Leginon - Feature #3561: use TargetPanel.py to read specific frame from an image stack or a single z slice of a volume Actions
Leginon - Feature #3600: move skip auto target finder settings to basic settings Actions
Feature #3746: Reorganize Appion menu so the working ones are at the top Actions
Leginon - Feature #3751: move instrument configuration to config files Actions
Leginon - Feature #3754: read mode 5 mrc file as unsigned 8-bit integer Actions
Leginon - Feature #3768: check conflict match of database to leginon image path Actions
Feature #3833: Change myamiweb form default for makeDEAlignedSum.py avoid error Actions
Feature #3856: show host name for job submission even when there is only on cluster host Actions
Leginon - Feature #3882: copy flat field reference information into frame directories when doing rawtransfer Actions
Feature #3918: generateMissingStack myamiweb job submission form Actions
Feature #3979: handle FEI Falcon raw format with int16 data using header Actions
Leginon - Feature #3990: Not to repeat drift monitoring after drift has settled Actions
Feature #4011: Create selectObjectPicker.php interface for selecting a particle picker instead of the menuprocessing.php Actions
Feature #4020: do DE images frame alignment using different gain reference Actions
Feature #4424: A way to display total dose (cumulative dose) per tilt. Actions
Leginon - Support #2899: a way to test array passing through tcptransport Actions
Leginon - Support #3989: change CS in phpmyadmin Actions
Leginon - Task #3249: break rawtransfer.py into subclasses for windows and linux Actions
Task #3343: Add protomo and opencv-python to centosAutoInstallation.py Actions
Leginon - Task #3350: normalize jeol1230 to other pyscope modules, especially jeolcom Actions
Leginon - Task #3546: make autoinstalled rctacquisition.py executable Actions
Leginon - Task #3832: new release dbschema update changes for 3.2 Actions