Leginon System version 1 6 » History » Revision 2
Revision 1 (Amber Herold, 04/13/2010 01:19 PM) → Revision 2/5 (Amber Herold, 04/14/2010 03:25 PM)
h1. Leginon System version 1.6 # [[pyScope Change]] # [[New User Features]] # [[Updated Applications (All)]] # [[New Project Web Tool Features]] # [[New dbemtool Web Tool Features (1.5.1)]] # [[Bug Fixes]] # [[Recommended Application Preference Changes when updated from version 1.5]] # [[Known Bugs]] Version 1.6 contains enhancement that is not available in version 1.5 and release of a series of Robot Screening application. Most significant changes are the split of Drift Manager functions to Transform Manager which handles the transformation of targets using any level of ancestry rather than one in the original Drift Manager. This allows an expansion of method that is meant to improve targeting accuracy. There are also significant improvement in Tomography node and its operation. h2. pyScope Change With increasing number of instrument conflict, a configuration file is now required to specify the instrument available on a host. h2. New User Features h2. General * The settings window gui can all fit in 12" laptop display now h2. Acquisition/Navigator Class The following applies to an acquisition node that uses the navigator to move to its target: * Based on a threshold, Targets can either be aborted or forced to collect when the multiple move failed to reduce further before reaching the goal. * It is possible to improve the targeting accuracy with a combination of stage movement and final image shift. However, this requires specific relationship between the acquiring presets and parent image presets. It works currently only for tomography and depth-first traversal MSI scheme. h2. BeamFixer Class (New) Simple beam shift adjustment to correct unstable beam position in long runs. h2. BeamTiltImager Class (New) Visual aid to coma-tilt alignment. It is used to acquire images of beam tilt difractogram tableau. The user can then click at the location of the tableau where he/she considers as the coma-free and therefore adjust the beam tilt. See Node Description Chapter for details. h2. Corrector Class * A bad pixel region can be specified by clicking the corners and added to the bad pixel plan * Extreme intensity pixels can be found by a click on this tool!http://emg.nysbc.org/software/leginon/images/icons/stagelocations.png! * Normalization image of the chosen camera configuration can be displayed. h2. DriftManager Class * A timeout for drift monitoring can now be specified so that if the drift is incorrectly detected due to an empty imaging area, the acquisition of the target will be aborted. h2. DTFinder Class (New) Dynamic template finder is developed for tissue section imaging. An initial template is defined by the user. The subsequent images it receives are then shifted and rotated against the template to find the best match to the section so that the target selected on the template can be transferred on to the new image. h2. FFTMaker Class * Power Spectrum is displayed if processed. * Option for calculating power spectrum but not saved to disk. * Option for calculate a truncated power spectrum to speed up the calculation for large images. h2. GridEntry Class (New) Direct entry of grid information to Leginon database to organize the data acquired. The main use is for simple one-pass grid screening of multiple grids when the robot does not exist. h2. ImageProcessor Class (New) Base class for process images of a completed image target list. Mainly used for development of batch processing of the images acquired such as image stack creation of a tilt series. An example of its use is in filenames.py. h2. ManualAcquisition Class * The acquired image can be sent to FFTMaker. h2. PresetsManager Class * Preset Beam Ajustment Tool allows easier semi-automated adjustment of multiple presets at the same magnification. h2. PixelSizeCalibrator Class * Power spectrum calculated from acquired image is displayed. * Distances measured between diffraction spots are used for an user-interactive pixel size calculation and averaging. h2. Robot2 Class (Replacing Robot) This class replaces Robot Class in all applications. It commnunicates to grid handling robot(s) through database. A few default settings are changed to reflect it and also the more general usage * Simulate Robot Insert/extraction = True * Default Z Position = 0 h2. TargetFilter Class * The images and targets that are filtered are displayed. * User inspection and editing of the filtered targets are allowed. h2. Tomography Class * Allow the model to remain fixed to the initial values. * Separate goniometer models for positive and negative tilts. * Options that are not found useful are removed. h2. TransformManager Class (New) This class will eventually handle the transformation of an old target to a new one for reacquisition after shift, tilt, and/or rotation in the grid plane. The current use is to replace the shift adjustment in Drift Manager. As an option, it can transform targets based on more than just its parent but all direct ancestors which makes the range of shift it can handle much larger than the original drift manager implementation. h2. Updated Applications (All) h2. Manual Power spectrum can be automatically calucated from the acquired image and displayed in its own node to allow easy inspection. h2. Calibrations New binding required by Navigation node. h2. MSI New binding required by Navigation node. Drift management is divided between Drift Monitor and Target Adjustment. A Preview and a Beam Fixing node are now standard in all MSI applications h2. Robot-related applications Robot2 class that uses database as midpoint to communicate bettween leginon and the robot controller replaces Robot class h2. New Project Web Tool Features h2. Grid entry for Robot Trays (1.1) This is used to enter grid information for robot trays. h2. Appion processing database creation (1.2) This is used to create and link the project to a new database ready for Appion usage. h2. New dbemtool Web Tool Features (1.5.1) h2. Hide or exemplify an image in the viewers Images can be one of the three status: Normal, Hidden, or Exemplar. Clicking on the hide button above the displayed image where it is available moves the image from its current list. In other words, to hide an image from any of the normal preset list, click on "hide" while display a normal image. This image will now display only if "hidden" is selected from the preset list. Clicking on "hide" above an image displayed in the hidden list removes it from the "hidden" list and return it back to the normal list. Images put in the "exemplar" list will also be shown in the normal list. h2. The mrc images are cached as jpegs in the viewers The cache system allows faster access to the same image next time. h2. More options for image display intensity adjustment You can manually define min/max of the display range in absolute number or relative percentage, as well as in standard deviation unit based on the statistics of the image. The manually determined values are saved for individual image displayed in the same panel until the page is closed. h2. Queue counter in LOI It updates the number of unprocessed queue targets and estimate how much time it will still take to finish them. h2. Queue deletion tool in 3-way and LOI viewers Click on this tool<inlinegraphic fileref="http://emg.nysbc.org/software/leginon/images/images/deq_bt_off.gif" format="GIF"/> above a displayed image pops up a window where you can remove targets derived from that and all its descendent images. In other words. if you have put in the queue targets from 10 holes, each selected from the same square image, you will delete all theses targets if you perform queue deletion on the square image. Please use this carefully. h2. Hole template and 2-way viewers You can see your custom hole templates saved and used in the past leginon sessions in the hole template viewer. 2-way viewer gives you a bigger view of the parent images than the 3-way viewer. h2. Model parameter display in the tomography viewer The model paramters can be displayed for diagnosis by activating the check box. h2. Deletion candidate marking in the tomography viewer The "Mark for deletion" button saves the selected tilt series in the leginon database in a table that the system administrator can look up and delete from the file server in a later time. h2. Appion processing function possible with installation If you install Appion's processing server programs, the processing tag direct you to its menu page. h2. Bug Fixes h2. GUI * Tomography node settings is set in a scrolled window so that it is possible to fit it in a smaller display such as 12" screen of laptop computers * Goniometer Modeler settings are automatically set. . h2. Recommended Application Preference Changes when updated from version 1.5 h2. Adjust Target For Drift Check Box is now a choice If you checked "adjust target for drift" in any node of Acquisition class, it should be changed to select "one" ancestor. A python script "update16.py" is provided for a complete update of such setting in all related nodes. If the drift is so large that the different versions of the parent images can not be correlated, you should change the choice from "one" to "all" ancestors. h2. Known Bugs * (New for v1.5) Resuming image acquisition from Square Targeting after Leginon restart may cause reacquisition of children of the unfinished target list on 32-bit Linux machine. Dictionary ordering problem of MySQL query, No temporary solution. * (New for v1.5) DataAccessError may show up when a user starts new application if default is loaded to an existing database. Temporary solution: See <link linkend="bad_default_reference">Operation Trouble Shooting</link> on the subject. * (New for 1.3) Navigator multiple move option does not work properly in MSI imaging sequence with image shift as the move type. Temporary solution: Always use preset manager when move type is image shift. * Web viewer may not display all targets on the parent image since target is transferred to a different version. No temporary solution. * Kill Application may not kill all process cleanly and may cause problem in connecting to TEM or camera when a new application is reloaded. Temporary solution: Close leginon and clients and restart. * Simulate Target use the current image shift as the target shift on top of its preset shift. Therefore, the acquired image may carry an additional image shift if there is an offset created from previouis acquisition. Temporary solution: Always use Presets Manager to send the preset to be used in simulation first before usinging Simulate Targets tool. * Some, although fewer, User Notification "processing " icons do not disappear but stay pointing up after the node is done. Temporary solution: None. * When running on LINUX system, Preset selection in /Presets Manager/Importing Presets from Another Session/ add a selection when mouse is left-clicked rather than toggle the selection as in convention. Temporary solution: Hold down to Ctrl key to select and deselect multiple presets. Shift key still means selecting all between the two clicks. Note: This problem is caused by some bug in wxPython for LINUX. * Web 3way Image viewer does not always show in yellow the revised (i.e. after drift correction) current target in the parent image. Temporary solution: None. * Starting Manual Focus directly by clicking on the tool does not use preset but still check for the preset assigned for the focuser node.