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Appion/Leginon 3.2
closed
88%
136 issues
(
121 closed
—
15 open
)
Time tracking
Estimated time
0
.00
hour
Spent time
0
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hour
Issues by
Tracker
Status
Priority
Author
Assignee
Category
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
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Bug #1832
: Cannot hard link to prepared refinement job launcher page
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Bug #2845
: Appion Loop takes too long to load old images
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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
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Leginon -
Bug #2906
: make download sample images in autoinstaller an option
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Leginon -
Bug #2907
: K2 dark image default dimension xy is flipped
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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
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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
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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
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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
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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
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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
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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
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Feature #2991
: Enable BestDB feature in Appion version of CTFFIND
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Feature #2995
: Scripts to help user change the session and appion run path
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Feature #2996
: mrc validation script
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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
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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
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Feature #3354
: add CTFFIND 4 to the pipeline
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Feature #3361
: trim off edge after flat field correction in makeDDRawFrameSatack.py
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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
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Leginon -
Feature #3600
: move skip auto target finder settings to basic settings
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Feature #3746
: Reorganize Appion menu so the working ones are at the top
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Leginon -
Feature #3751
: move instrument configuration to config files
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Leginon -
Feature #3754
: read mode 5 mrc file as unsigned 8-bit integer
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Leginon -
Feature #3768
: check conflict match of database to leginon image path
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Feature #3833
: Change myamiweb form default for makeDEAlignedSum.py avoid error
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Feature #3856
: show host name for job submission even when there is only on cluster host
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Leginon -
Feature #3882
: copy flat field reference information into frame directories when doing rawtransfer
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Feature #3918
: generateMissingStack myamiweb job submission form
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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
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Feature #4011
: Create selectObjectPicker.php interface for selecting a particle picker instead of the menuprocessing.php
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Feature #4020
: do DE images frame alignment using different gain reference
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Feature #4424
: A way to display total dose (cumulative dose) per tilt.
Actions
Leginon -
Support #2899
: a way to test array passing through tcptransport
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Leginon -
Support #3989
: change CS in phpmyadmin
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Leginon -
Task #3249
: break rawtransfer.py into subclasses for windows and linux
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Task #3343
: Add protomo and opencv-python to centosAutoInstallation.py
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Leginon -
Task #3350
: normalize jeol1230 to other pyscope modules, especially jeolcom
Actions
Leginon -
Task #3546
: make autoinstalled rctacquisition.py executable
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Leginon -
Task #3832
: new release dbschema update changes for 3.2
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