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Appion/Leginon 3.0.0

closed

redux enabled CentOS 6 version

88%

163 issues   (144 closed — 19 open)

Version300

Appion Version 3.0 includes the following changes:

  1. CentOS 6 compatible - there are major changes to the web server and processing server to be compatible with newer versions of PHP and Python.
  2. New features for Director Detector images including Frame Alignment
  3. Added an automatic masking tool called EM Hole Finder. The EM Hole Finder software computes masks of carbon holes in electron micrographs and is available at https://github.com/hbradlow/em_hole_finder.
  4. Improved CTF reporting tools.
  5. Added SIMPLE abinitio alignment and reconstruction
  6. Added Support for GPU version of FindEM
  7. Added support for the Maskiton image masking tool
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Issues by
Bug

81/98
Feature

58/59
Support

0/1
Task

5/5
Related issues
Leginon - Bug #314: The FFT of rectangular images does not work in the viewer. Actions
Bug #1435: mrc can not read large stack even with memory mapping Actions
Leginon - Bug #1500: RCT feature-finding libCV error Actions
Bug #1503: fftw installation problem for python 2.4 on CentOS 5.x Actions
Bug #1524: applyctf from EMAN 1.9 release causes strip in the corrected image when installed on CentOS 6 Actions
Leginon - Bug #1587: redux makes the web page stuck when a request can not read the image. Actions
Bug #1737: Refactor how we manage publication references Actions
Bug #1817: helicalstep should not be an required option in ParticleBoxLoop Actions
Bug #1820: make apRefineJobFrealign and its gui the way Niko recommends Actions
Bug #1866: import parameters from previous refinement should limit to same package usage Actions
Bug #1872: different icosahedral symmetry convension makes euler angle passing to Frealign difficult Actions
Bug #1873: confict in icosahedral convention and refinement packages Actions
Bug #1875: redux info reading error on png image Actions
Bug #1905: ace2correct does not work correctly on images of rectangular shape Actions
Bug #1916: hard to remake Chimera snapshots in reconUploader Actions
Bug #1960: fscplot.php needs to be updated for Redux Actions
Bug #1962: centerStack.php gives wrong path to script for just show command Actions
Bug #1963: floating point exception in Redux when viewing stack Actions
Bug #2016: How to get CTF data from database Actions
Bug #2032: preg error on processing/index.php Actions
Bug #2038: procsummary.php not working Actions
Bug #2064: SPIDER 18 does not use 'AP MQ' and requires 'AP SH' Actions
Bug #2065: CTF viewer in imageviewer not switching between graphs properly Actions
Bug #2067: CTF fixes on Sept 29, 2012 Actions
Leginon - Bug #2144: RCT node drift limit is zero Actions
Leginon - Bug #2222: image adjust stays at manual settings when switch back to auto Actions
Leginon - Bug #2225: loi.php delays imcache by always trying to view newest image before having the chance to cache Actions
Bug #2277: Quote characters are not handled well in the description for makestack Actions
Bug #2295: Make stack has frequent memory leaks which cause fatal errors Actions
Bug #2299: when an experiment is shared to another user with data processing privilege, the data still can not be processed Actions
Bug #2355: self.selectiondata not set if there is no more images to process in makeDDParticleGIFMovie.py Actions
Bug #2379: various php code does not work due to require vs require_once Actions
Bug #2387: hide prepared refinement does not work Actions
Bug #2396: uploadEMANRefine.py does not handle mirror correctly Actions
Bug #2397: ParticleFile produced by EMAN for reconUploader does not match particle correctly Actions
Bug #2401: imported mask radius for refinement don't give the right mask size in angstrom. Actions
Leginon - Bug #2408: preset with session=NULL Actions
Leginon - Bug #2416: preset import and creation need to avoid appion-derived presets Actions
Leginon - Bug #2417: x and y coordinates in add Extrema as bad pixel are reversed Actions
Bug #2421: viewstack.php sometimes does not show image number Actions
Bug #2422: viewstack.php does not show number of images in class average Imagic file Actions
Bug #2428: multiple failed trials of the same refine job executed from command line all show up as queued Actions
Bug #2429: ready to upload count in processing menu for refinement job is not correct Actions
Leginon - Bug #2433: Too many K2 camera dimensions listed but not a good square one for manual focus Actions
Bug #2438: Number of particles in class no longer displayed when viewing alignment results Actions
Leginon - Bug #2449: Leginon collects garbage if scope filament went off or camera returning blank in target transformation Actions
Bug #2454: "Import Initial orientations" button gets unchecked Actions
Bug #2455: getAllPrimes does not need powers of 4 boxsize rule applied Actions
Leginon - Bug #2458: preset image alignment binning may be invalid for the camera Actions
Bug #2459: when frealign receives euler angles from other packages, the first step should use them to make a reconstruction Actions
Bug #2460: ctf method selection option in prepRefineFrealign.py does not use it in generating params. Actions
Leginon - Bug #2468: beam tilt imager tableau creation does not work with K2 dimension Actions
Leginon - Bug #2469: tomography calcBinning for correlation does not work with full dimension of K2 Actions
Bug #2475: defocus2 not shown in myamiweb imageviewers if angle of astigmatism happens to be 0 degree. Actions
Bug #2476: imgreport.php ctf graphs not always work Actions
Bug #2477: Xmipp refine upload fails for icosohedral symmetry Actions
Leginon - Bug #2480: RCT "Centered Square" reverts z height when queuing is on in Square Centering node Actions
Leginon - Bug #2489: rawtransfer.py is not accurate with multiple dd camera and not efficient with multiple file servers Actions
Bug #2493: Download best ctf reults to emx file not returning best results Actions
Leginon - Bug #2505: Leginon gui imageviewer does not work well with with K2 images Actions
Bug #2506: Makestack fails for older projects created prior to newer CTF database table entries Actions
Bug #2507: catchUpDDAlign.py sum up only 2 aligned frames Actions
Leginon - Bug #2517: Corrector instruments in settings gui does not match what Leginon think it is on when initialized Actions
Leginon - Bug #2525: Submit new sq targets from loaded atlas doesn't processed Actions
Leginon - Bug #2537: need to catch error in z stage correction out of range better. Actions
Leginon - Bug #2542: targets adjustment causes relative target drift on versions of parent image Actions
Bug #2544: graph missing in session summary.php Actions
Leginon - Bug #2550: Rpublishing unprocessed image causes persistent data cannot be modified error Actions
Leginon - Bug #2551: starting leginon with ref session Actions
Bug #2552: prime number decomposition for CTF estimation Actions
Leginon - Bug #2557: new table in database causes sinedon to look for the class in in dataclass definition in python even though the reference is not in python class list Actions
Leginon - Bug #2561: Tomography stage tilt not reset after previous tilt-series aborted Actions
Bug #2570: Pixel error while creating particle stack using Appion Actions
Leginon - Bug #2577: rct feature match fails frequently when come back to zero tilt Actions
Leginon - Bug #2578: tomography predication graph and download has both frame aligned and unaligned images Actions
Bug #2582: makestack phaseFlipAceTwo got too small Cs Actions
Bug #2584: mask image are saved twice due to user error Actions
Bug #2591: Remove SMTP email option from Setup Wizard until we can make it work Actions
Leginon - Bug #2599: Lacey carbon RasterFCFinder gui bug Actions
Leginon - Bug #2603: change recommended production php error reporting Actions
Leginon - Bug #2612: table field defaults not set from xml files through myami setup wizard Actions
Bug #2613: GroEL demo project has no symmetry data nor ApSymmetryData table Actions
Bug #2616: Need timezone info for AutoInstaller Actions
Leginon - Bug #2617: SERIALEMCCD socket connection not opened with 2.30.542.0 Actions
Bug #2619: rawFrameStackReport.php shows all ddstackruns of the project not just the session Actions
Bug #2623: ctfreport does not show any figures Actions
Bug #2629: Autoinstaller is not always launching the web gui Actions
Bug #2650: APPION_PARENT_ADDITION web configuration parameter is not supported by the cluster parameter form Actions
Bug #2651: downloadctf.php does not show new ctf confidence measurments Actions
Bug #2656: refine job base class does not handle flags in iteration param list Actions
Leginon - Bug #2659: Beam stays tilted when low level error occurs in BeamTiltCalibrationClient Actions
Leginon - Bug #2665: target adjusted in the second tilt after drift get stretched perpendicular to the tilt axis Actions
Leginon - Bug #2718: manual acquisition manual focus geometry error when the current image is highly binned Actions
Bug #2735: The 3.0 branch revision was not added to dbschema/updatelib.py when the branch was created, possibly causeing DB update issues. Actions
Bug #2762: Allow a cs value of 0 when uploading images Actions
Bug #2856: weird login bug on particle picking Actions
Bug #2878: Auto masking hidden by HIDE_FEATURE flag in config.php Actions
Leginon - Bug #2918: corrected integrated image returned to Leginon has different mean from the raw when exposure time is low Actions
Feature #666: Add links to redmine wiki help pages to appion pages Actions
Leginon - Feature #1504: direct detector raw frame saving and auto transfering Actions
Feature #1559: make DD frame movies from particle picks Actions
Feature #1740: Add a notice to users in the appion header Actions
Feature #1800: make skip test a separate function Actions
Feature #1809: start a module for image manipulation that needs database Actions
Feature #1836: make it possible to mark a generic Appion job as done Actions
Feature #1845: move apCtf.py into a folder as apCtf/ctfdb.py to allow major expansion of CTF related functions Actions
Feature #1847: Implement next generation CTF display tools Actions
Feature #1867: Make a smarter Appion implementation of CtfFind Actions
Feature #1876: add Xmipp CTF estimation to Appion Actions
Feature #1881: create a new selection menu for CTF programs Actions
Feature #1884: more options for ctf estimation display Actions
Feature #1885: allowing ctffind result to be corrected by ace2correct? Actions
Feature #1918: add Moab Torque subsubmission class Actions
Feature #1922: use multiple qsub to launch multiple frealign to refine chunks of particle Actions
Feature #1958: Next Gen CTF Display for Rectangular Images Actions
Feature #1967: Phase 3 Next Gen CTF Display Tools: CTF resolution Actions
Feature #1983: Make it easy to see where raw data is stored for all sessions in a project Actions
Feature #2012: Better and faster CTF report page Actions
Feature #2030: Add redux config file params to the setup wizard Actions
Feature #2031: Update web troubleshooting tool for centos6 appion 3.0 release Actions
Feature #2043: Create an advanced user status and only hide advanced settings if not an advanced user Actions
Feature #2044: Add Relion single model refinement to appion pipeline Actions
Leginon - Feature #2061: Limit number of bad pixels can be added to corrector plan Actions
Feature #2192: myamiweb interface for DD frame alignment Actions
Leginon - Feature #2203: default image cache using redux Actions
Feature #2207: determine debris on Gatan K2 counted frame image and correct it Actions
Feature #2211: Make corrected frame stack with references from the alternative channel Actions
Feature #2216: Specify reference image to be used in raw frame processing Actions
Feature #2259: Clean up CTF 1d plot window Actions
Leginon - Feature #2263: sinedon query by timestamp range Actions
Feature #2265: Unhide iterative msa/mra alignment Actions
Leginon - Feature #2284: include filename where ice thickness is obtained in the data report Actions
Feature #2319: Add Auto Masking (em_hole_finder) to pipeline Actions
Leginon - Feature #2327: allow custom tilts to be added to the tilt list in tomography Actions
Leginon - Feature #2334: rawtransfer.py Actions
Leginon - Feature #2337: create fftw wisdom plan before starting redux Actions
Feature #2370: Parallel run of DD frame stack making and alignment Actions
Feature #2371: Select frames used in particle stack making by frame drift rate during alignment Actions
Feature #2380: How to get best CTF estimation from database Actions
Leginon - Feature #2394: python script to query across appion and leginon databases Actions
Feature #2399: save gain/dark corrected dd frames on local computer that will be used for gpu frame alignment Actions
Feature #2415: display recon symmetry orientation not model in reconsummary Actions
Feature #2418: choose frames to sum up and upload after dd frame alignment Actions
Feature #2419: option to remove ddstack after aligned sum image is uploaded to database Actions
Feature #2427: eman make3d failure report Actions
Feature #2430: avoid making new refine stack if exists Actions
Leginon - Feature #2466: viewer status for removing images Actions
Feature #2470: Add subdivision of Appion directory beyond sessionname according to Leginon session Actions
Feature #2485: Add "method" to XML file export of ctf data for ctf challenge Actions
Leginon - Feature #2486: add legpause by William Nicholson to myami repository Actions
Feature #2564: Update centosAutoInstallation for 3.0 release Actions
Feature #2588: sorting of averages Actions
Feature #2589: delete SelectionRun Actions
Feature #2590: Make updates to the web troubleshooter for 3.0 release Actions
Leginon - Feature #2620: hide outdated applications without TransformManager Navigator MoveToTargetEvent automatically Actions
Feature #2766: import script to repair FEIs MRC format Actions
Feature #2853: ctffind page update Actions
Support #2378: Need to check installation documentation for setup.py of appion? Actions
Task #1513: CentOS 6 installation of myami 3.0 errors Actions
Leginon - Task #2488: clean up failed development in svn Actions
Leginon - Task #2574: 3.0 default settings Actions
Task #2583: change myamiweb/test/checkwebserver.php for redux Actions
Leginon - Task #2643: dbschema for 3.0 branch Actions