Difference between revisions of "Averaging of subtomograms"
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== Through the command line == | == Through the command line == | ||
To operate manually averages of particles (given an available [[table|metadata]]), use the {{t|daverage}} command, or its GUI version {{t|dvarage_GUI}}. {{docfunction|dynamo_average|daverage}} | To operate manually averages of particles (given an available [[table|metadata]]), use the {{t|daverage}} command, or its GUI version {{t|dvarage_GUI}}. {{docfunction|dynamo_average|daverage}} | ||
| − | The most important flags are | + | The most important flags are: |
| − | * ''fcompensate'' : if tuned to 1, a | + | |
| + | * ''mask'' : if a mask is provided and the ''normalization'' flag is tuned to 1 (as it is by default), each particle will be normalized to have zero mean and standard deviation 1 inside the passed mask before adding it to the average. | ||
| + | * ''fcompensate'' : if tuned to 1, a [[Fourier compensation during averaging | Fourier compensation step]] will be carried out. | ||
* ''fmin'' : minimum number of particles that need to contribute to a given Fourier component. | * ''fmin'' : minimum number of particles that need to contribute to a given Fourier component. | ||
| − | * ''' | + | * ''implicitRotationMask''. If tuned to 1, the contribution of the particle outside an interior sphere will be discarded to minimize [[Border alignment artifact | rotation artifacts]] <br />default value is one. |
== Inside an alignment project == | == Inside an alignment project == | ||
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There are different project parameters that can be used to modify the default behaviour of the {{t|daverage}} command used inside an alignment project. | There are different project parameters that can be used to modify the default behaviour of the {{t|daverage}} command used inside an alignment project. | ||
*''fCompensationSmoothingMask'' | *''fCompensationSmoothingMask'' | ||
| − | *''implicitRotationMask' | + | *''fCompensationSmoothingMask'' |
| + | *''implicitRotationMask' <br /> default value is zero. | ||
=== Reproducing averaging steps of a project from the command line === | === Reproducing averaging steps of a project from the command line === | ||
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Here, <tt>o</tt> would be the output of the <tt>daverage</tt> command as operated with the flags passed to it by in the project <tt>vpr</tt>. These flags can be obtained explicitely with a second left hand side: | Here, <tt>o</tt> would be the output of the <tt>daverage</tt> command as operated with the flags passed to it by in the project <tt>vpr</tt>. These flags can be obtained explicitely with a second left hand side: | ||
| − | <tt> [o,flags] = dpkproject.pipeline.genericInput2Average(vpr,myTable,'ite',ite); </tt> | + | <tt> [o,flags] = dpkproject.pipeline.genericInput2Average(vpr,myTable,'ite',ite,'justFlags',1); </tt> |
===Parallelism=== | ===Parallelism=== | ||
Revision as of 21:02, 3 December 2017
Averaging of subtomograms means applying an available set of alignment parameters onto a set of data particles and adding them together. Because of the missing wedge, a compensation in the Fourier space is operated during this step.
From the operative point of view, the particles are stored in a data folder, which are indexed by a table.
Contents
Through the command line
To operate manually averages of particles (given an available metadata), use the daverage command, or its GUI version dvarage_GUI. daverage The most important flags are:
- mask : if a mask is provided and the normalization flag is tuned to 1 (as it is by default), each particle will be normalized to have zero mean and standard deviation 1 inside the passed mask before adding it to the average.
- fcompensate : if tuned to 1, a Fourier compensation step will be carried out.
- fmin : minimum number of particles that need to contribute to a given Fourier component.
- implicitRotationMask. If tuned to 1, the contribution of the particle outside an interior sphere will be discarded to minimize rotation artifacts
default value is one.
Inside an alignment project
At the end of each iteration, the refined table generated by Dynamo is used to produce an average, which will be used as starting template in the next iteration.
There are different project parameters that can be used to modify the default behaviour of the daverage command used inside an alignment project.
- fCompensationSmoothingMask
- fCompensationSmoothingMask
- implicitRotationMask'
default value is zero.
Reproducing averaging steps of a project from the command line
It is possible to apply onto a set of particles exactly the same averaging flags that were using during the runtime of a project using the command dpkproject.pipeline.genericInput2Average.
o = dpkproject.pipeline.genericInput2Average(vpr,myTable,'ite',ite);
Here, o would be the output of the daverage command as operated with the flags passed to it by in the project vpr. These flags can be obtained explicitely with a second left hand side:
[o,flags] = dpkproject.pipeline.genericInput2Average(vpr,myTable,'ite',ite,'justFlags',1);
Parallelism
It is possible to select the number of cores that will be used during the averaging. The project parameter is called matlab_workers_average (shortform mwa), and can be modified also in dcp GUI (in the section of environment variables).
This option is available for computations on a single server with several cores. It will not work for the current MPI implementation.
