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New User Features » History » Version 2

Amber Herold, 04/23/2010 01:21 PM

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h1. 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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[[pyScope Change|< pyScope Change]] | [[Updated Applications (All)|Updated Applications (All) >]]
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