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Appion/Leginon 2.2.0

closed

Focus on Extensibility

90%

240 issues   (218 closed — 22 open)

Appion/Leginon 2.2

Appion/Leginon 2.2 will focus on the Extensibility of Appion.
The goal is to make it easy for outside labs to add new processing modules to the Image Pipeline.

Time tracking
Estimated time 48.00 hours
Spent time 6.00 hours
Issues by
Bug

157/172
Feature

53/57
Support

2/2
Task

6/8
Test Case

0/1
Related issues
Bug #30: Cannot choose a output directory for all pages Actions
Bug #41: Standardize the web interface of Appion Actions
Bug #179: viewstack.php bug, does not display last image Actions
Bug #194: Amplitude correction files path is hard coded in the myami code Actions
Bug #195: envelope image does not take into account pixel size changes Actions
Bug #208: image viewer not displaying different particle picking runs Actions
Leginon - Bug #210: Try to remove 'import *' from all python code Actions
Bug #276: Users that cannot login to web server cannot login to myamiweb/processing Actions
Bug #354: Upload image for new session cannot be launched from web Actions
Bug #439: checking web user has copy and past permissions Actions
Bug #443: postproc.php has hard-coded link to appion directory change to config.php Actions
Bug #461: Need to find a way to solve the permission issue Actions
Bug #505: Alignment stacks ready ti upload that should not exist Actions
Bug #532: default_cluster.php is a nightmare to configure Actions
Bug #568: Web tools index page need to check all the databases Actions
Bug #645: exclude/include functionality in viewstack.php Actions
Bug #682: post processing amplitude correction fails Actions
Bug #743: Appion documentation logic through image viewer docs Actions
Bug #774: The back button on updateproject.php does not work Actions
Bug #839: Nasty error message when trying to test template finder show command Actions
Bug #862: Mising help in xmipp maxlike launch page Actions
Bug #883: Ace 2 does not properly write the MRC header file Actions
Bug #943: apIMAGIC.py library Actions
Bug #946: Need better error checking in uploadTemplate.php Actions
Bug #948: Add note in UploadStack Actions
Bug #957: Can't choose output directory. Actions
Leginon - Bug #959: queue timeout option not working with grid atlas Actions
Bug #963: FindEM/Template picking crashing on rectangular images Actions
Bug #965: Error check for array size in FindEM Actions
Bug #984: Check for config.php in leginon.inc uses hardcoded Base URL Actions
Leginon - Bug #990: missing image file causes getimg.php to hang Actions
Bug #991: remove recursive session search in getSessions Actions
Bug #1001: cannot undo exemplar images Actions
Bug #1024: appionScript setRunDir does not work Actions
Bug #1025: appion params['session'] should be replaced by ['sessionname'] Actions
Leginon - Bug #1036: beam tilt correction for image shift didn't get applied Actions
Leginon - Bug #1037: store references in special session Actions
Bug #1046: RuntimeError in Frealign Actions
Leginon - Bug #1048: GIF switches to EFTEM mode, has different magnifications Actions
Leginon - Bug #1049: pixel size calibration not associated with high tension Actions
Leginon - Bug #1050: save frames option got back from regular ccd camera is assgned to None Actions
Bug #1069: Cluster Job Status not updating properly Actions
Bug #1081: Frealiagn job launcher not working Actions
Bug #1084: There are unknown errors (in refine*.txt) for this job, you should resubmit?? Actions
Bug #1086: Frealign prep bug Actions
Bug #1087: Difficult to tell when a Guppy job is queued, running or stalled/dead. Actions
Bug #1090: Extra dmf command in get files from dmf (after EMAN run on garibaldi) that is not needed Actions
Bug #1109: can not unhide an image from web viewer in standard installation Actions
Bug #1143: Tilt Picker should not have the option to run directly from the web page Actions
Bug #1171: The date/time that is displayed for completed dog runs is refering to the wrong table Actions
Leginon - Bug #1180: hole finder exception in trying to pick to one hole for focusing but started with none anyway Actions
Leginon - Bug #1181: strange holefinder.py edge-template correlation failure Actions
Leginon - Bug #1202: Drift graph has a hard-coded pixel and binning size Actions
Leginon - Bug #1203: Unreasonabily and meaningless high drift rate make the graph scaled so that the information is lost Actions
Bug #1208: Ctf summary report on python side unable to get images from database. Actions
Bug #1213: mysql.inc SQLupdate does not handle NULL correctly Actions
Leginon - Bug #1218: queue time estimation does not include focusing time Actions
Leginon - Bug #1219: queue time estimate takes too long if the queue is large Actions
Leginon - Bug #1235: projectexperimentId is used for getting SessionInfo if passed in array Actions
Bug #1239: silly to let anyone download anything if they know where it is Actions
Leginon - Bug #1240: tomography dose display in viewer not correct Actions
Bug #1245: subtomomaker.py uses wrong full tomogram binning Actions
Bug #1267: Auto Installer - can't open image viewer for demo images Actions
Bug #1275: runJpegMaker showing cluster selection list even though it does not allow submission from the web Actions
Bug #1281: emanJobGen.php default runname counting is not safe Actions
Bug #1282: emanJobGen.php outfullpath comes out wrong in the job file Actions
Bug #1283: checkRefineJobs.php detects missing job file at appiondir when remote cluster is used for processing Actions
Bug #1286: Discontinue use of Eman boxer within Appion Actions
Leginon - Bug #1292: Removed 'import Image' from pyami.resultcache Actions
Bug #1294: Divsion by zero error in runMakeStack2.php Actions
Bug #1295: protomo azimuth Actions
Bug #1301: defocus series conversion is wrong in uploadimage.php Actions
Leginon - Bug #1311: instruments.cfg needed on leginon processing server even though it will connect to real scope client Actions
Leginon - Bug #1376: Grab extrema pixel to correction plan does not handle Dead and hot pixel well enough Actions
Bug #1407: Select Stack form displaying a row for stacks with no particles Actions
Leginon - Bug #1417: wx.Color depreciated in wxpython 2.9 Actions
Bug #1418: cl2d Actions
Leginon - Bug #1421: mouse event attribute m_x and m_y depreciated in wxpython 2.9 Actions
Bug #1424: Frealign refine job copy paste error: trying to create Eman object rather than frealign. Actions
Bug #1433: selectPreparedRecon not working for Safari and Chrome Actions
Leginon - Bug #1443: need to prevent resubmit targets under the same atlas name in MosaicTargetMaker (aliased Grid Targeting) Actions
Bug #1460: DOgPicker test mode deos not work anymore??? Actions
Bug #1461: Post processing is not working anymore Actions
Bug #1470: Frealign prep dtype float32 error Actions
Bug #1475: error in outer mask radius in projection matching refinement Actions
Bug #1482: spider consuming all the resources Actions
Bug #1487: AMI group members cannot process other AMI members data Actions
Bug #1514: single refine menu shows 1 completed run with new project Actions
Bug #1515: refine reconstruction menu completed run is pointing to stackhierachy.php Actions
Bug #1516: findem64.exe does not work on CentOS 6 Actions
Bug #1521: download particledata gives imageid in trunk, rather than filename as in 2.1 Actions
Bug #1522: autoinstaller does not complete EMAN installation Actions
Bug #1527: xmipp installation instruction and does not work on CentOS 6 Actions
Bug #1532: selectPreparedRecon.php gives 1x when imported parameters from a previous recon are null Actions
Bug #1533: uploaded EMAN eulers are incorrect Actions
Bug #1542: Helical Processing menu should not appear if there is no stack? Actions
Bug #1555: appionLoop2 has its own setupRunDir Actions
Bug #1558: stackIntoPicks does not transfer rotation angles Actions
Leginon - Bug #1560: ctf estimation used in beam-tilt coma calibration fails Actions
Bug #1562: Ensure all popup help messages are accurate after recon refinement Actions
Bug #1565: runXmippCL2D.py error on 2 processor Actions
Leginon - Bug #1569: defocus of the second of two autofocus sequence with the same preset and defocus adjustment is not set Actions
Bug #1574: upload ML Alignment run into DB problem Actions
Bug #1674: ApContourPointData is scaled at the binned image Actions
Bug #1677: tomomaker exclude list gui make better sense to start from 1 Actions
Bug #1678: Protomo 2 should not be the default tomo alignment method since it is not completed Actions
Leginon - Bug #1684: autofocusgraph does not show graph if focus has not failed Actions
Bug #1694: download.php is redirected to myami home without downloading file Actions
Bug #1696: Display error information to the user in reconsummary.php Actions
Bug #1697: Display current experiment ID when user gets error message that processing is not allowed. Actions
Bug #1698: Add exception handling for missing file in apXmipp.py Actions
Bug #1699: appion setup.py default propogates files in /usr/bin Actions
Bug #1710: limit nproc passed from apGenericJob.py Actions
Leginon - Bug #1711: myamiweb/tomo does not show images after adding label to image in r1642 Actions
Bug #1714: ctf graph and defocus/ace difference plots don't show up in summary page for the session Actions
Bug #1715: readImagic does not use smaller particle iteration number for larger particle image Actions
Bug #1716: Web pages take too long to when executing commands through ssh Actions
Bug #1717: Add appionlibdir to the configuration wizard Actions
Bug #1718: refactor to use new path class Actions
Bug #1720: time to load getproject.php is too long Actions
Bug #1724: ctffind graph does not show up in the viewer if it is the best or only ctf estimation down on an image Actions
Bug #1729: remove commented out check for sinedon.cfg in processing.inc Actions
Bug #1730: clean up ssh.inc Actions
Bug #1732: Add publication reference boxes to single and multi model refinement pages Actions
Bug #1735: Traced objects with small number of vertices are distorted Actions
Bug #1736: Update the Data Collection Info reported for exemplars with new methods Actions
Leginon - Bug #1739: raw frame saving gui cleanup Actions
Bug #1742: Uploadimage.php not working due to require vs require_once Actions
Bug #1744: Remove CS value from the config wizard Actions
Leginon - Bug #1747: nodes in Calibrations application do not get reverted to admin or another session Actions
Bug #1754: Download stack redirects to web tools home page Actions
Bug #1755: upload stack does not work if uploading from a file that the web server does not have access to Actions
Leginon - Bug #1764: pixel counts not always proportional to the square of binning value Actions
Bug #1768: Errors running check.sh in new installation Actions
Bug #1772: Warning in setup wizard for undefined errMsg variable Actions
Bug #1775: expid vs expId cause test image for runDogPicker.php to fail Actions
Bug #1780: Citation not showing up in uploadRecon.php Actions
Bug #1781: Need to indicate units on Max Memory in setup wizard processing host config Actions
Leginon - Bug #1783: leginon.cfg, sinedon.cfg, and instruments.cfg are often lost when installation changes Actions
Bug #1786: Update config file install instructions Actions
Leginon - Bug #1790: get_magnification on existing TEM corrupts the database Actions
Leginon - Bug #1792: methods.log permission error on leginon installed from autoinstaller Actions
Bug #1793: Sometimes there are multiple names for a single host, which causes appion to choke Actions
Leginon - Bug #1795: manual focus tool in focuser should not use the first preset in preset order Actions
Bug #1797: Update auto installer for version 2.2.0 release Actions
Bug #1802: uploadmodel.php directed from selectModelForm.php is broken Actions
Bug #1803: prepRefineForm.php loses modelid once an iteration is selected as initial orientation for frealign Actions
Bug #1805: runRctVolume.php does not have help on valid volume of mask radius Actions
Leginon - Bug #1812: example text in leginon.cfg.template still uses username Actions
Bug #1814: runDogPicker.php puts --ddstartframe=1 in appion script Actions
Bug #1816: prepRefineFrealign.py does not produce mrc stack if remake stack Actions
Bug #1821: Refine form default values not loading properly Actions
Bug #1822: checkRefineJobs.php shows uploaded recons as ready to upload if the upload is run through job submission Actions
Bug #1825: upload MaxLike Align loses job information when submitted Actions
Bug #1835: checkAppionJob.php does not abort job if logged in Actions
Bug #1842: remove "allow frealign to determine ctf" from refine prep page Actions
Leginon - Bug #1843: too many schema update script for appion only Actions
Leginon - Bug #1844: recent decamera changes to merge to 2.2 Actions
Leginon - Bug #1856: dbschema update misses updates needed upon check out branch change Actions
Bug #1857: tifffile.py causes syntex error during install with python version earlier than 2.6 Actions
Leginon - Bug #1858: dbupgrade.py does not allow column name with space Actions
Leginon - Bug #1886: loggedmethod error for gatan.Gatan Actions
Bug #1891: refinement upload always has mirror Actions
Bug #1957: files_to_send are sent to the default remote_rundir even though it is changed in myamiweb Actions
Bug #1990: picking bug at FSU Actions
Bug #2026: Hide frealign for 2.2 release Actions
Bug #2080: templateCorrelator crash Actions
Leginon - Bug #2147: centos autoinstall scripts in 2.2 Actions
Bug #2289: myamiweb/processing/download.php is not working to download mrc volumes Actions
Bug #2320: Mask radius for refinements confuse pixels and angstroms Actions
Bug #2366: Particle Clustering is not committing to Database Actions
Bug #2556: Cannot view aligned particles after topology alignment in longboard/gammamyamiweb Actions
Feature #14: Remove select project box in getproject page. Actions
Feature #15: Reorganize the last column in the view project page. Actions
Leginon - Feature #214: target queue editor Actions
Leginon - Feature #217: Leginon image viewer should cache the FFT images as well. Actions
Leginon - Feature #225: Allow averaging of multiple focus measurements. Actions
Leginon - Feature #226: Feature to measure focus change in a random direction. Actions
Leginon - Feature #287: Move the default CS variable from Processing_config to the Leginon Database instrument config Actions
Feature #397: prepFrealign should take specified parameter file in addition to database values Actions
Feature #422: Need to be able to dynamically define max number of procs per node for each processing host Actions
Feature #493: Ed's iteration alignment Actions
Leginon - Feature #654: import preset by searching for session that uses an application Actions
Feature #676: Instead of installing appion scripts into bin, use the appion wrapper Actions
Feature #692: Implement showOrSubmitCommand() for as many Appion functions as possible Actions
Feature #787: Allow importing of old tilt alignment parameters in new tilt alignments Actions
Feature #912: apFile.py - removeDir Actions
Feature #913: XMIPP normalize stack Actions
Feature #944: topologyAlignment Actions
Leginon - Feature #952: New Grid baking node and application Actions
Feature #992: Print version and revision number in troubleshooting page Actions
Feature #1020: Use an object relational mapper for PHP Actions
Feature #1032: subStack.py exclude file Actions
Feature #1047: mean & std dev option Actions
Feature #1053: make it possible to ban a user from myamiweb without deleting the user Actions
Feature #1054: Use Zend input validation library. Actions
Leginon - Feature #1061: option to park at high magnification preset after acquiring acquiring an image for a target Actions
Feature #1098: use configuration file to get default appion base directory Actions
Feature #1137: running appion script in another appion script Actions
Feature #1146: Embedding image, media and gallery viewer in to Appion. Actions
Feature #1147: Need a solution for submitting jobs on each cluster in a uniform way Actions
Feature #1153: upgrade prototype.js to newest version Actions
Feature #1211: Script to test 3rd party package installation Actions
Feature #1212: Add instructions to web server troubleshooter for running scripts and version info Actions
Leginon - Feature #1237: Hide some users from Leginon wizard page Actions
Feature #1279: Enhance Project Summary Page Actions
Feature #1284: Auto Installer - install 3rd party packages Actions
Leginon - Feature #1285: Additions to statistics report page Actions
Leginon - Feature #1296: Write DB schema update scripts for new statistics table Actions
Feature #1302: simplify appion instrument insertion during image upload Actions
Leginon - Feature #1303: allow tomography index.php to be reached by specified tilt series Actions
Feature #1304: Software Registration Key Request form Actions
Leginon - Feature #1305: better display of instrument.py getData function exception Actions
Leginon - Feature #1308: cs input from instruments,cfg to database InstrumentData Actions
Feature #1324: Recon Refactoring - GUI Actions
Feature #1363: prepFrealign.py needs Actions
Feature #1404: padding and rotation options in synthetic data creation Actions
Feature #1413: make gain correction on dd raw frame mrc images into mrc stack Actions
Leginon - Feature #1416: allow extra pause time between acquisition of the same target with different presets Actions
Feature #1427: add support for each processing host to have it's own wrapper path Actions
Feature #1456: Remove "get Files from DMF" button on refinement page Actions
Leginon - Feature #1467: make GridEntry class works with manual acquisition Actions
Feature #1511: Update Config file template and config wizard to reflect new way of configuring clusters Actions
Feature #1537: complete the frealign refinement uploader Actions
Leginon - Feature #1550: Revert settings to that of a specific session Actions
Feature #1557: break up makestack2.py to extract particledata from images and making stack Actions
Leginon - Feature #1570: beeps when user verification is requested in target finders Actions
Feature #1695: Adds a button to force a queued job to done Actions
Leginon - Feature #1818: save dd info.txt into database in case it is deleted later by the user Actions
Support #1079: data15 full Actions
Support #1756: Update documentation on $PROCESSING_HOSTS[] in config.php Actions
Task #675: Document appion wrapper config in install guide Actions
Task #742: Appion Author Contribution Actions
Task #1517: new installation instruction for myami 2.2 Actions
Task #1589: Appion code freeze in effect Actions
Task #1779: Add appion.cfg installtion to Leginon and upgrade wiki's Actions
Task #1837: dbschema update for release 2.2 Actions
Leginon - Task #1838: default setting making and clean up for Leginon 2.2 Actions
Leginon - Task #1839: Hide incomplete feature GUI controls in 2.2 release Actions
Test Case #1593: alignSubStack.php Actions