Difference between revisions of "Walkthrough on command line based tilt series alignment"
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(Created page with "This is the command line based version of the GUI based alignment walkthrough = Create the workflow =...") |
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<nowiki>u.enter.settingAcquisition.apix(2.7);</nowiki> | <nowiki>u.enter.settingAcquisition.apix(2.7);</nowiki> | ||
− | == | + | == Detection settings== |
− | < | + | <code>u.enter.settingDetection.beadRadius(16); |
u.enter.settingDetection.detectionBinningFactor(1); | u.enter.settingDetection.detectionBinningFactor(1); | ||
− | u.enter.settingDetection.maskRadius(28);</ | + | u.enter.settingDetection.maskRadius(28);</code> |
Revision as of 12:51, 27 August 2019
This is the command line based version of the GUI based alignment walkthrough
Contents
Create the workflow
name = 'hivCommandLine'; folder = 'workflows'; u = dtsa(name,'--nogui','-path',folder,'fp',1);
Here, we instruct Dynamo to skip opening the GUI. We also create the workflow in a different folder.
Entering the data
The u object contains several areas to interact with the workflow. They can be found by autocompletion using the tab key.
Basic data
u.enter.tiltSeries(fileWorkshop); u.enter.tiltAngles(-57:3:60); u.enter.discardedTiltIndices([1,2,40]);
Acquisition settings
u.enter.settingAcquisition.apix(2.7);
Detection settings
u.enter.settingDetection.beadRadius(16);
u.enter.settingDetection.detectionBinningFactor(1);
u.enter.settingDetection.maskRadius(28);
u.enter.templateSidelength(64);
u.enter.settingComputing.parallelCPUUse(1);
Changing generic parameters
Through auto completion on the area u.area.indexing.step.tiltGapFiller.parameterSet.residualsThreshold(8);
% computing parameters
Running the workflow
u.run.all('noctf',1);