Difference between revisions of "Walkthrough on command line based tilt series alignment"
Line 19: | Line 19: | ||
== Acquisition settings== | == Acquisition settings== | ||
− | < | + | <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.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 == | ||
− | + | 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 | ||
Line 39: | Line 45: | ||
= 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
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
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);