Difference between revisions of "Walkthrough on command line based tilt series alignment"

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== Acquisition settings==
 
== Acquisition settings==
<nowiki>u.enter.settingAcquisition.apix(2.7);</nowiki>
+
<tt>u.enter.settingAcquisition.apix(2.7);</tt>
  
 
== Detection settings==
 
== Detection settings==
 +
These here are the actual design decisions when running an alignment workflow:
 +
 
<code>u.enter.settingDetection.beadRadius(16);
 
<code>u.enter.settingDetection.beadRadius(16);
u.enter.settingDetection.detectionBinningFactor(1);
 
 
u.enter.settingDetection.maskRadius(28);</code>
 
u.enter.settingDetection.maskRadius(28);</code>
  
  
u.enter.templateSidelength(64);
+
<tt>u.enter.templateSidelength(64);</tt>
 +
 
 +
The bin level is mainly used to accelerate the detection procedure. Needs to be chosen in a way that a binned gold bead still can be recognisable as such, with a radius of at least 4 pixels.
 +
<tt>u.enter.settingDetection.detectionBinningFactor(1);</tt>
 +
 
  
u.enter.settingComputing.parallelCPUUse(1);
+
== Detection settings==
 +
<tt>u.enter.settingComputing.parallelCPUUse(1); </tt>
  
 
== Changing generic parameters ==
 
== Changing generic parameters ==
Through auto completion on the <tt>area</tt>  
+
Yo can find handles to the parameters of the individuals steps through auto ompletion on the <tt>area</tt>, then <tt>step</tt> items.
<tt>u.area.indexing.step.tiltGapFiller.parameterSet.residualsThreshold(8);</tt>
+
<tt>u.area.indexing.step.tiltGapFiller.parameterSet.residualsThreshold(8);</tt>
  
 
% computing parameters
 
% computing parameters
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= Running the workflow =
 
= Running the workflow =
<tt>u.run.all('noctf',1);</tt>
+
<tt>u.run.all('noctf',1);</tt>

Revision as of 12:56, 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

These here are the actual design decisions when running an alignment workflow:

u.enter.settingDetection.beadRadius(16); u.enter.settingDetection.maskRadius(28);


u.enter.templateSidelength(64);

The bin level is mainly used to accelerate the detection procedure. Needs to be chosen in a way that a binned gold bead still can be recognisable as such, with a radius of at least 4 pixels.

u.enter.settingDetection.detectionBinningFactor(1);


Detection settings

u.enter.settingComputing.parallelCPUUse(1);

Changing generic parameters

Yo can find handles to the parameters of the individuals steps through auto ompletion on the area, then step items.

u.area.indexing.step.tiltGapFiller.parameterSet.residualsThreshold(8);

% computing parameters


Running the workflow

u.run.all('noctf',1);