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Appion/Leginon 3.1.0

closed

92%

81 issues   (75 closed — 6 open)

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Bug

44/49
Feature

31/32
Related issues
Bug #906: manual tilt picker crashes after first image Actions
Bug #993: IMAGIC MRA writes giant log file in brute force mode Actions
Bug #1055: Add helicalstep parameter in runManualPicker.php Actions
Bug #1322: misleading ctf correction method choice Actions
Bug #1479: radio button broken in refinement prep Actions
Bug #1687: runMaskMaker.php run test not working Actions
Bug #1951: peak finder failing Actions
Leginon - Bug #2229: Leginon freezes when accessing certain nodes when main is run on Windows Actions
Leginon - Bug #2381: Flat field correction is affected by the intensity Actions
Bug #2579: export of ctf data Actions
Bug #2635: refinements on garibaldi - issue 1 - saving command Actions
Bug #2645: Form validator no-quote check should allow the first and last chars to be quote, but nothing in between Actions
Bug #2657: new appionloop form dose not give any preset selection when there is no en preset Actions
Bug #2658: converting IMAGIC to mrc image using imagic_to_mrc() produces header issue for Relion Actions
Leginon - Bug #2660: target handling exception still reported as done in status Actions
Leginon - Bug #2675: target adjustment through navigator does not pre-expose even though preset includes it. Actions
Leginon - Bug #2691: timing of falcon/orius pair camera insertion Actions
Leginon - Bug #2694: camera switching is at the end of pre image acquisition pause Actions
Bug #2705: make stack launch page needs popup help for CTF resolution cutoff Actions
Leginon - Bug #2712: eucentric point determination by stage tilt does not work well when there is big jump in tilt direction change Actions
Leginon - Bug #2722: cannot convert float NaN to integer in image panel display of invalid image Actions
Leginon - Bug #2724: de12 getImage TypeError Actions
Leginon - Bug #2774: newer PIL fork (pillow) does not allow "import Image". It requires "from PIL import Image" Actions
Leginon - Bug #2779: ShowModal needs to be used on wx 3.0 Actions
Leginon - Bug #2794: simulating target on simulator got a real image back Actions
Leginon - Bug #2808: Leginon should not do gain dark correction on Falcon and Ceta camera images Actions
Leginon - Bug #2823: instruments are named by their base class name Actions
Leginon - Bug #2861: Eagle camera is now known as BM-Eagle in TIA Actions
Leginon - Bug #2866: new user gets queuing-wait for processing error Actions
Leginon - Bug #2874: save_frames __getattr__ error Actions
Leginon - Bug #2876: Too many permutation of image and frame orientation Actions
Leginon - Bug #2884: updatecom.py error when a typelib is not found Actions
Leginon - Bug #2887: Exposure node settings default not loading during initialization Actions
Leginon - Bug #2892: redux cache str to text stream error Actions
Leginon - Bug #2901: K2 and Falcon per frame dose measured in presets manager is not based on base frame rate Actions
Leginon - Bug #2913: myamiweb tomography tilt series download not correct Actions
Bug #2917: makegoodaverage.py uploadScroptData error Actions
Leginon - Bug #2932: Order of setting microscope parameters are not optimized Actions
Leginon - Bug #2940: user may try to acquire image while navigator send preset is still going on Actions
Leginon - Bug #2941: beam shift aligner in presets manager sets beam shift back to that of the original value when opened the second time Actions
Leginon - Bug #2942: FEI scopes does not normalize LM to SA mag change Actions
Leginon - Bug #2951: error in calculating raster spacing and angle with image shift as move type in raster finder Actions
Leginon - Bug #2952: beam size is shown as a move type in Raster Finder raster spacing angle calculator Actions
Leginon - Bug #2961: mrc mmap error Actions
Leginon - Bug #2969: getReferenceSession error Actions
Leginon - Bug #3009: DC_SetBrush unknown brush style error froze upon grid atlas loading or drawing polygon on images Actions
Leginon - Bug #3251: align zlp and reference class can not be bypassed Actions
Leginon - Bug #3949: images are not saved to images path which is set at leginon.cfg Actions
Bug #4357: Use frame aligned images for tomo tilt series alignment Actions
Feature #144: Unable to Remove a user as Administrator Actions
Feature #1056: Nonorthogonal boxes for helical insert in Manual Picker Actions
Feature #1175: Fix Xmipp 3d refinement Actions
Feature #1287: allow an end iteration to be specified in recon upload. Actions
Feature #1777: specify ctfrunid in making stack Actions
Feature #1880: create and display particle projection matching for at least some of the particles when running frealign Actions
Feature #2090: way to update pixel size of an mrc file Actions
Feature #2156: K2 frame process Actions
Feature #2230: Speed up particle stack making without pre-manipulation on selected frame range on ddstack Actions
Leginon - Feature #2254: Support Falcon camera Actions
Feature #2369: display stage position in imgreport.php Actions
Leginon - Feature #2520: Krios liquid nitrogen refill pause Actions
Feature #2622: allow making aligned ddstack from unaligned ddstack for testing different options Actions
Feature #2628: Show label of the selectField in forms on top of the selection box Actions
Feature #2646: Move publication list and showReference() to basic Form for all to use Actions
Leginon - Feature #2679: pre-exposure or melting using gun blanker in combination with projection shutter (post specimen) Actions
Feature #2680: Add comment to job files listing the processing host that the job file was created for Actions
Leginon - Feature #2702: Tomography needs independent z0 custom values for the two tilt directions Actions
Leginon - Feature #2725: add DE20 Actions
Feature #2729: create a STAR format file reader/writer Actions
Leginon - Feature #2780: save and set rotation center in beam tilt imager toolbar Actions
Leginon - Feature #2781: K2 system defect correction Actions
Leginon - Feature #2791: prevent users from deactivate queuing when the last acquisition node is not waiting Actions
Leginon - Feature #2792: Display the image size and orientation predicted to be acquired during target selection Actions
Leginon - Feature #2809: Talos integration Actions
Leginon - Feature #2812: Display illuminated area of the next acquisiton node in target finder ImageViewer Actions
Leginon - Feature #2816: allow preset selection and send to scope in navigation node Actions
Leginon - Feature #2818: Automatically refresh atlas when the node is chosen. Actions
Leginon - Feature #2831: read/write mrc files according to 2014 standard Actions
Leginon - Feature #2842: recheck image intensity mean if out of range Actions
Leginon - Feature #2868: 3.1 applications and default settings Actions
Leginon - Feature #3020: rct feature matching using opencv Actions