acecutoff to ctfcutoff

[leginonbot]

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Author Name: Gabriel Lander (@gclander) Original Redmine Issue: 1273, https://emg.nysbc.org/redmine/issues/1273 Original Date: 2011-04-27 Original Assignee: Amber Herold

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The "--acecutoff" option for makestack was confusing to people, since this option does not only check the ACE confidence values, but whatever ctf estimator was run. Switched it to "--ctfcutoff". r15590

[leginonbot]

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Original Redmine Comment Author Name: Amber Herold (Amber Herold) Original Date: 2011-04-27T16:21:32Z

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Gabe, I took a look at the changes, and noticed the following lines still referencing Ace cutoff in some way. Looks like you are leaving the database column name as aceCutoff, which accounts for a few of the remaining references. Probably best to leave the DB as is. The rest are comments or are displayed to the user, which you may want to change for continuity.

|.file|.line|_.code| |trunk/myamiweb/processing/index.php| line 344| $ctfcutoff=($stackparams['aceCutoff']) ? $stackparams['aceCutoff']100 : '' ;| |trunk/appion/bin/makestack2.py| line 916| help="ACE cut off")| |trunk/appion/bin/imgRejector.py| line 150| ### check that ACE estimation is above confidence threshold| || line 152| apDisplay.printColor("\nrejecting below ACE cutoff: "+apDisplay.short(imgdata['filename'])+" conf="+str(round(conf,3)), "cyan")| |trunk/myamiweb/processing/index.php |line 344| $ctfcutoff=($stackparams['aceCutoff']) ? $stackparams['aceCutoff']100 : '' ;| |trunk/myamiweb/processing/runImgRejector.php (note:checkbox name is still acecheck) |line 164 |ACE Confidence Cutoff
| || line 328 |createImgRejectorForm("ERROR: Ace cutoff must be between 0 & 1");|

[leginonbot]

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Original Redmine Comment Author Name: Gabriel Lander (@gclander) Original Date: 2011-04-27T16:55:08Z

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Thanks for catching that, Amber, I didn't change the database columns "aceCutoff", so I left all those references the same, but I fixed the rest you that you caught. r15595

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Original Redmine Comment Author Name: Amber Herold (Amber Herold) Original Date: 2011-04-27T16:58:55Z

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Looks good!

[leginonbot]

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Original Redmine Comment Author Name: Dmitry Lyumkis (@LyumkisLab) Original Date: 2011-04-27T18:43:48Z

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works for me.

When testing, I also noticed that the page did not increment my stack directory if it existed (i.e. it wanted me to make "stack3" despite it already existing as a directory). This was because the $sessionpathval variable was not ending in a '/'. I addded a one-line check for this.

line 161: $sessionpathval = (substr($sessionpathval, -1) == '/')? $sessionpathval : $sessionpathval.'/';

[leginonbot]

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Original Redmine Comment Author Name: Amber Herold (Amber Herold) Original Date: 2011-04-27T18:52:59Z

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looks good Dmitry, thanks. Closing this out.