New User Features » History » Version 2
Amber Herold, 04/23/2010 01:21 PM
1 | 1 | Amber Herold | h1. New User Features |
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6 | h2. General |
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12 | * The settings window gui can all fit in 12" laptop display now |
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22 | h2. Acquisition/Navigator Class |
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25 | The following applies to an acquisition node that uses the navigator to move to its |
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26 | target: |
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27 | * Based on a threshold, Targets can either be aborted or forced to collect when the |
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28 | multiple move failed to reduce further before reaching the goal. |
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31 | * It is possible to improve the targeting accuracy with a combination of stage |
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32 | movement and final image shift. However, this requires specific relationship between |
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33 | the acquiring presets and parent image presets. It works currently only for tomography |
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34 | and depth-first traversal MSI scheme. |
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43 | h2. BeamFixer Class (New) |
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46 | Simple beam shift adjustment to correct unstable beam position in long runs. |
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52 | h2. BeamTiltImager Class (New) |
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55 | Visual aid to coma-tilt alignment. It is used to acquire images of beam tilt |
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56 | difractogram tableau. The user can then click at the location of the tableau where he/she |
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57 | considers as the coma-free and therefore adjust the beam tilt. See Node Description Chapter |
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58 | for details. |
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64 | h2. Corrector Class |
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70 | * A bad pixel region can be specified by clicking the corners and added to the bad |
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71 | pixel plan |
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74 | * 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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77 | * Normalization image of the chosen camera configuration can be displayed. |
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87 | h2. DriftManager Class |
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93 | * A timeout for drift monitoring can now be specified so that if the drift is |
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94 | incorrectly detected due to an empty imaging area, the acquisition of the target will |
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95 | be aborted. |
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105 | h2. DTFinder Class (New) |
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108 | Dynamic template finder is developed for tissue section imaging. An initial template is |
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109 | defined by the user. The subsequent images it receives are then shifted and rotated against |
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110 | the template to find the best match to the section so that the target selected on the |
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111 | template can be transferred on to the new image. |
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117 | h2. FFTMaker Class |
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123 | * Power Spectrum is displayed if processed. |
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126 | * Option for calculating power spectrum but not saved to disk. |
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129 | * Option for calculate a truncated power spectrum to speed up the calculation for |
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130 | large images. |
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140 | h2. GridEntry Class (New) |
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143 | Direct entry of grid information to Leginon database to organize the data acquired. The |
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144 | main use is for simple one-pass grid screening of multiple grids when the robot does not |
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145 | exist. |
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151 | h2. ImageProcessor Class (New) |
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154 | Base class for process images of a completed image target list. Mainly used for |
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155 | development of batch processing of the images acquired such as image stack creation of a |
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156 | tilt series. An example of its use is in filenames.py. |
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162 | h2. ManualAcquisition Class |
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168 | * The acquired image can be sent to FFTMaker. |
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178 | h2. PresetsManager Class |
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184 | * Preset Beam Ajustment Tool allows easier semi-automated adjustment of multiple |
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185 | presets at the same magnification. |
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195 | h2. PixelSizeCalibrator Class |
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201 | * Power spectrum calculated from acquired image is displayed. |
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204 | * Distances measured between diffraction spots are used for an user-interactive |
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205 | pixel size calculation and averaging. |
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215 | h2. Robot2 Class (Replacing Robot) |
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218 | This class replaces Robot Class in all applications. It commnunicates to grid handling |
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219 | robot(s) through database. A few default settings are changed to reflect it and also the |
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220 | more general usage |
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221 | * Simulate Robot Insert/extraction = True |
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224 | * Default Z Position = 0 |
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233 | h2. TargetFilter Class |
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239 | * The images and targets that are filtered are displayed. |
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242 | * User inspection and editing of the filtered targets are allowed. |
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252 | h2. Tomography Class |
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258 | * Allow the model to remain fixed to the initial values. |
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261 | * Separate goniometer models for positive and negative tilts. |
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264 | * Options that are not found useful are removed. |
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274 | h2. TransformManager Class (New) |
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277 | This class will eventually handle the transformation of an old target to a new one for |
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278 | reacquisition after shift, tilt, and/or rotation in the grid plane. The current use is to |
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279 | replace the shift adjustment in Drift Manager. As an option, it can transform targets based |
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280 | on more than just its parent but all direct ancestors which makes the range of shift it can |
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281 | handle much larger than the original drift manager implementation. |
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282 | 2 | Amber Herold | |
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284 | ______ |
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286 | [[pyScope Change|< pyScope Change]] | [[Updated Applications (All)|Updated Applications (All) >]] |
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287 | |||
288 | ______ |