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Leginon System version 1 6 » History » Version 1

Amber Herold, 04/13/2010 01:19 PM

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