Leginon System version 1 6 » History » Version 1
Amber Herold, 04/13/2010 01:19 PM
1 | 1 | Amber Herold | |
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2 | h1. Leginon System version 1.6 |
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3 | |||
4 | |||
5 | |||
6 | Version 1.6 contains enhancement that is not available in version 1.5 and release of a |
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7 | series of Robot Screening application. Most significant changes are the split of Drift Manager |
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8 | functions to Transform Manager which handles the transformation of targets using any level of |
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9 | ancestry rather than one in the original Drift Manager. This allows an expansion of method that |
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10 | is meant to improve targeting accuracy. There are also significant improvement in Tomography |
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11 | node and its operation. |
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12 | |||
13 | |||
14 | |||
15 | h2. pyScope Change |
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16 | |||
17 | |||
18 | |||
19 | With increasing number of instrument conflict, a configuration file is now required to |
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20 | specify the instrument available on a host. |
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21 | |||
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23 | |||
24 | |||
25 | |||
26 | h2. New User Features |
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27 | |||
28 | |||
29 | |||
30 | |||
31 | h2. General |
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32 | |||
33 | |||
34 | |||
35 | |||
36 | |||
37 | * The settings window gui can all fit in 12" laptop display now |
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38 | |||
39 | |||
40 | |||
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42 | |||
43 | |||
44 | |||
45 | |||
46 | |||
47 | h2. Acquisition/Navigator Class |
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48 | |||
49 | |||
50 | The following applies to an acquisition node that uses the navigator to move to its |
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51 | target: |
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52 | * Based on a threshold, Targets can either be aborted or forced to collect when the |
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53 | multiple move failed to reduce further before reaching the goal. |
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54 | |||
55 | |||
56 | * It is possible to improve the targeting accuracy with a combination of stage |
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57 | movement and final image shift. However, this requires specific relationship between |
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58 | the acquiring presets and parent image presets. It works currently only for tomography |
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59 | and depth-first traversal MSI scheme. |
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60 | |||
61 | |||
62 | |||
63 | |||
64 | |||
65 | |||
66 | |||
67 | |||
68 | h2. BeamFixer Class (New) |
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69 | |||
70 | |||
71 | Simple beam shift adjustment to correct unstable beam position in long runs. |
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72 | |||
73 | |||
74 | |||
75 | |||
76 | |||
77 | h2. BeamTiltImager Class (New) |
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78 | |||
79 | |||
80 | Visual aid to coma-tilt alignment. It is used to acquire images of beam tilt |
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81 | difractogram tableau. The user can then click at the location of the tableau where he/she |
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82 | considers as the coma-free and therefore adjust the beam tilt. See Node Description Chapter |
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83 | for details. |
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84 | |||
85 | |||
86 | |||
87 | |||
88 | |||
89 | h2. Corrector Class |
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90 | |||
91 | |||
92 | |||
93 | |||
94 | |||
95 | * A bad pixel region can be specified by clicking the corners and added to the bad |
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96 | pixel plan |
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97 | |||
98 | |||
99 | * 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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100 | |||
101 | |||
102 | * Normalization image of the chosen camera configuration can be displayed. |
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103 | |||
104 | |||
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106 | |||
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108 | |||
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111 | |||
112 | h2. DriftManager Class |
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113 | |||
114 | |||
115 | |||
116 | |||
117 | |||
118 | * A timeout for drift monitoring can now be specified so that if the drift is |
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119 | incorrectly detected due to an empty imaging area, the acquisition of the target will |
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120 | be aborted. |
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121 | |||
122 | |||
123 | |||
124 | |||
125 | |||
126 | |||
127 | |||
128 | |||
129 | |||
130 | h2. DTFinder Class (New) |
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131 | |||
132 | |||
133 | Dynamic template finder is developed for tissue section imaging. An initial template is |
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134 | defined by the user. The subsequent images it receives are then shifted and rotated against |
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135 | the template to find the best match to the section so that the target selected on the |
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136 | template can be transferred on to the new image. |
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137 | |||
138 | |||
139 | |||
140 | |||
141 | |||
142 | h2. FFTMaker Class |
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143 | |||
144 | |||
145 | |||
146 | |||
147 | |||
148 | * Power Spectrum is displayed if processed. |
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149 | |||
150 | |||
151 | * Option for calculating power spectrum but not saved to disk. |
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152 | |||
153 | |||
154 | * Option for calculate a truncated power spectrum to speed up the calculation for |
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155 | large images. |
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156 | |||
157 | |||
158 | |||
159 | |||
160 | |||
161 | |||
162 | |||
163 | |||
164 | |||
165 | h2. GridEntry Class (New) |
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166 | |||
167 | |||
168 | Direct entry of grid information to Leginon database to organize the data acquired. The |
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169 | main use is for simple one-pass grid screening of multiple grids when the robot does not |
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170 | exist. |
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171 | |||
172 | |||
173 | |||
174 | |||
175 | |||
176 | h2. ImageProcessor Class (New) |
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177 | |||
178 | |||
179 | Base class for process images of a completed image target list. Mainly used for |
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180 | development of batch processing of the images acquired such as image stack creation of a |
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181 | tilt series. An example of its use is in filenames.py. |
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182 | |||
183 | |||
184 | |||
185 | |||
186 | |||
187 | h2. ManualAcquisition Class |
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188 | |||
189 | |||
190 | |||
191 | |||
192 | |||
193 | * The acquired image can be sent to FFTMaker. |
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194 | |||
195 | |||
196 | |||
197 | |||
198 | |||
199 | |||
200 | |||
201 | |||
202 | |||
203 | h2. PresetsManager Class |
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204 | |||
205 | |||
206 | |||
207 | |||
208 | |||
209 | * Preset Beam Ajustment Tool allows easier semi-automated adjustment of multiple |
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210 | presets at the same magnification. |
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211 | |||
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216 | |||
217 | |||
218 | |||
219 | |||
220 | h2. PixelSizeCalibrator Class |
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221 | |||
222 | |||
223 | |||
224 | |||
225 | |||
226 | * Power spectrum calculated from acquired image is displayed. |
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227 | |||
228 | |||
229 | * Distances measured between diffraction spots are used for an user-interactive |
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230 | pixel size calculation and averaging. |
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231 | |||
232 | |||
233 | |||
234 | |||
235 | |||
236 | |||
237 | |||
238 | |||
239 | |||
240 | h2. Robot2 Class (Replacing Robot) |
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241 | |||
242 | |||
243 | This class replaces Robot Class in all applications. It commnunicates to grid handling |
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244 | robot(s) through database. A few default settings are changed to reflect it and also the |
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245 | more general usage |
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246 | * Simulate Robot Insert/extraction = True |
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247 | |||
248 | |||
249 | * Default Z Position = 0 |
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250 | |||
251 | |||
252 | |||
253 | |||
254 | |||
255 | |||
256 | |||
257 | |||
258 | h2. TargetFilter Class |
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259 | |||
260 | |||
261 | |||
262 | |||
263 | |||
264 | * The images and targets that are filtered are displayed. |
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265 | |||
266 | |||
267 | * User inspection and editing of the filtered targets are allowed. |
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268 | |||
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271 | |||
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274 | |||
275 | |||
276 | |||
277 | h2. Tomography Class |
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278 | |||
279 | |||
280 | |||
281 | |||
282 | |||
283 | * Allow the model to remain fixed to the initial values. |
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284 | |||
285 | |||
286 | * Separate goniometer models for positive and negative tilts. |
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287 | |||
288 | |||
289 | * Options that are not found useful are removed. |
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290 | |||
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292 | |||
293 | |||
294 | |||
295 | |||
296 | |||
297 | |||
298 | |||
299 | h2. TransformManager Class (New) |
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300 | |||
301 | |||
302 | This class will eventually handle the transformation of an old target to a new one for |
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303 | reacquisition after shift, tilt, and/or rotation in the grid plane. The current use is to |
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304 | replace the shift adjustment in Drift Manager. As an option, it can transform targets based |
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305 | on more than just its parent but all direct ancestors which makes the range of shift it can |
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306 | handle much larger than the original drift manager implementation. |
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307 | |||
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310 | |||
311 | |||
312 | |||
313 | |||
314 | h2. Updated Applications (All) |
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315 | |||
316 | |||
317 | |||
318 | |||
319 | h2. Manual |
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320 | |||
321 | |||
322 | |||
323 | Power spectrum can be automatically calucated from the acquired image and displayed in |
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324 | its own node to allow easy inspection. |
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325 | |||
326 | |||
327 | |||
328 | |||
329 | |||
330 | h2. Calibrations |
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331 | |||
332 | |||
333 | |||
334 | New binding required by Navigation node. |
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335 | |||
336 | |||
337 | |||
338 | |||
339 | |||
340 | h2. MSI |
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341 | |||
342 | |||
343 | |||
344 | New binding required by Navigation node. Drift management is divided between Drift |
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345 | Monitor and Target Adjustment. A Preview and a Beam Fixing node are now standard in all MSI |
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346 | applications |
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347 | |||
348 | |||
349 | |||
350 | |||
351 | |||
352 | h2. Robot-related applications |
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353 | |||
354 | |||
355 | |||
356 | Robot2 class that uses database as midpoint to communicate bettween leginon and the |
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357 | robot controller replaces Robot class |
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358 | |||
359 | |||
360 | |||
361 | |||
362 | |||
363 | |||
364 | |||
365 | h2. New Project Web Tool Features |
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366 | |||
367 | |||
368 | |||
369 | |||
370 | h2. Grid entry for Robot Trays (1.1) |
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371 | |||
372 | |||
373 | |||
374 | This is used to enter grid information for robot trays. |
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375 | |||
376 | |||
377 | |||
378 | |||
379 | |||
380 | h2. Appion processing database creation (1.2) |
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381 | |||
382 | |||
383 | |||
384 | This is used to create and link the project to a new database ready for Appion usage. |
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385 | |||
386 | |||
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388 | |||
389 | |||
390 | |||
391 | |||
392 | |||
393 | h2. New dbemtool Web Tool Features (1.5.1) |
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394 | |||
395 | |||
396 | |||
397 | |||
398 | h2. Hide or exemplify an image in the viewers |
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399 | |||
400 | |||
401 | |||
402 | Images can be one of the three status: Normal, Hidden, or Exemplar. Clicking on the hide |
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403 | button above the displayed image where it is available moves the image from its current |
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404 | list. In other words, to hide an image from any of the normal preset list, click on "hide" |
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405 | while display a normal image. This image will now display only if "hidden" is selected from |
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406 | the preset list. Clicking on "hide" above an image displayed in the hidden list removes it |
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407 | from the "hidden" list and return it back to the normal list. Images put in the "exemplar" |
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408 | list will also be shown in the normal list. |
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409 | |||
410 | |||
411 | |||
412 | |||
413 | |||
414 | h2. The mrc images are cached as jpegs in the viewers |
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415 | |||
416 | |||
417 | |||
418 | The cache system allows faster access to the same image next time. |
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419 | |||
420 | |||
421 | |||
422 | |||
423 | |||
424 | h2. More options for image display intensity adjustment |
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425 | |||
426 | |||
427 | |||
428 | You can manually define min/max of the display range in absolute number or relative |
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429 | percentage, as well as in standard deviation unit based on the statistics of the image. The |
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430 | manually determined values are saved for individual image displayed in the same panel until |
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431 | the page is closed. |
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432 | |||
433 | |||
434 | |||
435 | |||
436 | |||
437 | h2. Queue counter in LOI |
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438 | |||
439 | |||
440 | |||
441 | It updates the number of unprocessed queue targets and estimate how much time it will |
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442 | still take to finish them. |
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443 | |||
444 | |||
445 | |||
446 | |||
447 | |||
448 | h2. Queue deletion tool in 3-way and LOI viewers |
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449 | |||
450 | |||
451 | |||
452 | Click on this tool<inlinegraphic |
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453 | fileref="http://emg.nysbc.org/software/leginon/images/images/deq_bt_off.gif" |
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454 | format="GIF"/> above a displayed image pops up a window where you can remove targets |
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455 | derived from that and all its descendent images. In other words. if you have put in the |
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456 | queue targets from 10 holes, each selected from the same square image, you will delete all |
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457 | theses targets if you perform queue deletion on the square image. Please use this |
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458 | carefully. |
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459 | |||
460 | |||
461 | |||
462 | |||
463 | |||
464 | h2. Hole template and 2-way viewers |
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465 | |||
466 | |||
467 | |||
468 | You can see your custom hole templates saved and used in the past leginon sessions in |
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469 | the hole template viewer. 2-way viewer gives you a bigger view of the parent images than the |
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470 | 3-way viewer. |
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471 | |||
472 | |||
473 | |||
474 | |||
475 | |||
476 | h2. Model parameter display in the tomography viewer |
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477 | |||
478 | |||
479 | |||
480 | The model paramters can be displayed for diagnosis by activating the check box. |
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481 | |||
482 | |||
483 | |||
484 | |||
485 | |||
486 | h2. Deletion candidate marking in the tomography viewer |
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487 | |||
488 | |||
489 | |||
490 | The "Mark for deletion" button saves the selected tilt series in the leginon database in |
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491 | a table that the system administrator can look up and delete from the file server in a later |
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492 | time. |
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493 | |||
494 | |||
495 | |||
496 | |||
497 | |||
498 | h2. Appion processing function possible with installation |
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499 | |||
500 | |||
501 | |||
502 | If you install Appion's processing server programs, the processing tag direct you to its |
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503 | menu page. |
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504 | |||
505 | |||
506 | |||
507 | |||
508 | |||
509 | |||
510 | |||
511 | h2. Bug Fixes |
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512 | |||
513 | |||
514 | |||
515 | |||
516 | h2. GUI |
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517 | |||
518 | |||
519 | |||
520 | |||
521 | * Tomography node settings is set in a scrolled window so that it is possible to fit |
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522 | it in a smaller display such as 12" screen of laptop computers |
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523 | |||
524 | |||
525 | * Goniometer Modeler settings are automatically set. |
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526 | |||
527 | |||
528 | . |
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529 | |||
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531 | |||
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533 | |||
534 | |||
535 | |||
536 | h2. Recommended Application Preference Changes when updated from version 1.5 |
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537 | |||
538 | |||
539 | |||
540 | |||
541 | h2. Adjust Target For Drift Check Box is now a choice |
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542 | |||
543 | |||
544 | |||
545 | If you checked "adjust target for drift" in any node of Acquisition class, it should be |
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546 | changed to select "one" ancestor. A python script "update16.py" is provided for a complete |
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547 | update of such setting in all related nodes. If the drift is so large that the different |
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548 | versions of the parent images can not be correlated, you should change the choice from "one" |
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549 | to "all" ancestors. |
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550 | |||
551 | |||
552 | |||
553 | |||
554 | |||
555 | |||
556 | |||
557 | h2. Known Bugs |
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558 | |||
559 | |||
560 | |||
561 | |||
562 | |||
563 | * (New for v1.5) Resuming image acquisition from Square Targeting after Leginon |
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564 | restart may cause reacquisition of children of the unfinished target list on 32-bit |
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565 | Linux machine. |
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566 | |||
567 | |||
568 | Dictionary ordering problem of MySQL query, No temporary solution. |
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569 | |||
570 | |||
571 | * (New for v1.5) DataAccessError may show up when a user starts new application if |
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572 | default is loaded to an existing database. |
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573 | |||
574 | |||
575 | Temporary solution: See <link linkend="bad_default_reference">Operation Trouble |
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576 | Shooting</link> on the subject. |
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577 | |||
578 | |||
579 | * (New for 1.3) Navigator multiple move option does not work properly in MSI imaging |
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580 | sequence with image shift as the move type. |
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581 | |||
582 | |||
583 | Temporary solution: Always use preset manager when move type is image shift. |
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584 | |||
585 | |||
586 | * Web viewer may not display all targets on the parent image since target is |
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587 | transferred to a different version. |
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588 | |||
589 | |||
590 | No temporary solution. |
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591 | |||
592 | |||
593 | * Kill Application may not kill all process cleanly and may cause problem in |
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594 | connecting to TEM or camera when a new application is reloaded. |
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595 | |||
596 | |||
597 | Temporary solution: Close leginon and clients and restart. |
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598 | |||
599 | |||
600 | * Simulate Target use the current image shift as the target shift on top of its preset |
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601 | shift. Therefore, the acquired image may carry an additional image shift if there is an |
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602 | offset created from previouis acquisition. |
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603 | |||
604 | |||
605 | Temporary solution: Always use Presets Manager to send the preset to be used in |
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606 | simulation first before usinging Simulate Targets tool. |
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607 | |||
608 | |||
609 | * Some, although fewer, User Notification "processing " icons do not disappear but |
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610 | stay pointing up after the node is done. |
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611 | |||
612 | |||
613 | Temporary solution: None. |
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614 | |||
615 | |||
616 | * When running on LINUX system, Preset selection in /Presets Manager/Importing Presets |
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617 | from Another Session/ add a selection when mouse is left-clicked rather than toggle the |
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618 | selection as in convention. |
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619 | |||
620 | |||
621 | Temporary solution: Hold down to Ctrl key to select and deselect multiple presets. |
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622 | Shift key still means selecting all between the two clicks. |
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623 | |||
624 | |||
625 | Note: This problem is caused by some bug in wxPython for LINUX. |
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626 | |||
627 | |||
628 | * Web 3way Image viewer does not always show in yellow the revised (i.e. after drift |
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629 | correction) current target in the parent image. |
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630 | |||
631 | |||
632 | Temporary solution: None. |
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633 | |||
634 | |||
635 | * Starting Manual Focus directly by clicking on the tool does not use preset but still |
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636 | check for the preset assigned for the focuser node. |