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>
  
== ADetection settings==
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== Detection settings==
<nowiki>u.enter.settingDetection.beadRadius(16);
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<code>u.enter.settingDetection.beadRadius(16);
 
u.enter.settingDetection.detectionBinningFactor(1);
 
u.enter.settingDetection.detectionBinningFactor(1);
u.enter.settingDetection.maskRadius(28);</nowiki>
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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


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);