Averaging of subtomograms - Revision history

Daniel Castaño: /* Through the command line */

2017-12-06T16:09:17Z

Through the command line

Daniel Castaño: /* Through the command line */

2017-12-06T16:04:38Z

Through the command line

Daniel Castaño: /* Through the command line */

2017-12-06T16:04:15Z

Through the command line

Daniel Castaño: /* Through the command line */

2017-12-06T15:32:19Z

Through the command line

Daniel Castaño at 14:02, 4 December 2017

2017-12-04T14:02:05Z

Daniel Castaño at 12:02, 4 December 2017

2017-12-04T12:02:37Z

Daniel Castaño: /* Inside an alignment project */

2017-12-04T12:02:21Z

Inside an alignment project

Daniel Castaño: /* Through the command line */

2017-12-04T11:51:22Z

Through the command line

Daniel Castaño at 11:50, 4 December 2017

2017-12-04T11:50:02Z

Daniel Castaño at 11:49, 4 December 2017

2017-12-04T11:49:40Z

@@ Line 10: / Line 10: @@
   <tt> o = daverage( data,'t',table); </tt>
-in Matlab-like syntax, or
+in Matlab-like syntax, or:
   <tt> o = daverage(data,'t',table);</tt>
@@ Line 17: / Line 17: @@
 * <tt>'average_raw'</tt>: the average of the particles, ''without'' any [[Fourier compensation during averaging | Fourier compensation.]]
 * <tt>'fweight'</tt>:   count of contributions for each Fourier coefficient.
-*<tt>'average'</tt>:  <tt>'average_raw'</tt> compensated through <tt>'fweight'</tt>.
+* <tt>'average'</tt>:  <tt>'average_raw'</tt> compensated through <tt>'fweight'</tt>.
 The most important additional  flags are:

@@ Line 6: / Line 6: @@
 == Through the command line ==
-To operate manually averages of particles (given an available [[table|metadata]]), use the  <tt>[[daverage]]</tt> command, or its GUI version {{t|dvarage_GUI}}. {{docfunction|dynamo_average|daverage}}, with the basic syntax:
+To operate manually averages of particles (given an available [[table|metadata]]), use the  <tt>[[daverage]]</tt> command, or its GUI version {{t|daverage_GUI}}. {{docfunction|dynamo_average|daverage}}, with the basic syntax:
   <tt> o = daverage( data,'t',table); </tt>

@@ Line 6: / Line 6: @@
 == 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}}, with the basic syntax:
+To operate manually averages of particles (given an available [[table|metadata]]), use the  <tt>[[daverage]]</tt> command, or its GUI version {{t|dvarage_GUI}}. {{docfunction|dynamo_average|daverage}}, with the basic syntax:
   <tt> o = daverage( data,'t',table); </tt>

@@ Line 25: / Line 25: @@
 *<tt>'implicitRotationMasking'</tt>. 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 1.
 '''Fourier compensation flags'''
-*<tt>'fcompensate'</tt> : if tuned to 1, a [[Fourier compensation during averaging | Fourier compensation step]] will be carried out.
+*<tt>'fcompensate'</tt> : if tuned to 1, a [[Fourier compensation during averaging | Fourier compensation step]] will be carried out. <br /> default value is zero. No missing wedge compensation.
 *<tt>'fmin'</tt>  : minimum  number of particles that need to contribute to a given Fourier component.
 *<tt>'fminFraction</tt>  : if switched to a value between 0 and 1, selects the minimum fraction of particles that should contribute to a fourier component to admit it during averaging. <br />- default: empty. Elimination of underrepresented fourier components is driven by the value of parameter <tt>'fmin'</tt>.

@@ Line 22: / Line 22: @@
 '''General flags'''
-*<tt>'nmask'</tt>:  if a mask is provided and the ''norm'' 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. <br />- default value is empty (no normalization).
+*<tt>'nmask'</tt>:  if a mask is provided and the ''norm'' flag is tuned to 1 (as it is by default), each particle will be normalized to have zero mean and standard deviation 1 inside this mask before adding it to the average. <br />- default value is empty (no normalization).
 *<tt>'implicitRotationMasking'</tt>. 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 1.
 '''Fourier compensation flags'''

@@ Line 56: / Line 56: @@
   <tt> [o,flags] = dpkproject.pipeline.genericInput2Average(vpr,myTable,'ite',ite,'justFlags',1); </tt>
-===Parallelism===
+===Parallelization===
 It is possible to select the number of cores that will be used during the ''averaging''.  The project parameter is called <tt>matlab_workers_average</tt> (shortform <tt>mwa</tt>), 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.

@@ Line 38: / Line 38: @@
 At the end of each iteration, the {{t|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 {{t|daverage}} command used inside an alignment project.
-*<tt>'implicitRotationMask'</tt>   <br /> default value is zero: this will introduce sharp edges contributing to the average, but will allow checking the features outside of the spherical mask.
+*<tt>'implicitRotationMaskings'</tt>   <br /> default value is zero: this will introduce sharp edges contributing to the average, but will allow checking the features outside of the spherical mask.
 *<tt>'fourierMinimumFractionForAverage'</tt>  <br /> default value is -1: use all Fourier coefficients during [[Fourier compensation during averaging | missing wedge compensation]].

@@ Line 22: / Line 22: @@
 '''General flags'''
-*<tt>'nmask'</tt>:  if a mask is provided and the ''norm'' 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.
+*<tt>'nmask'</tt>:  if a mask is provided and the ''norm'' 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. <br />- default value is empty (no normalization).
-*<tt>'implicitRotationMasking'</tt>. 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.
+*<tt>'implicitRotationMasking'</tt>. 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 1.
 '''Fourier compensation flags'''
 *<tt>'fcompensate'</tt> : if tuned to 1, a [[Fourier compensation during averaging | Fourier compensation step]] will be carried out.
 *<tt>'fmin'</tt>  : minimum  number of particles that need to contribute to a given Fourier component.
-*<tt>'fminFraction</tt>  : if switched to a value between 0 and 1, selects the minimum fraction of particles that should contribute to a fourier component to admit it during averaging. <br /> default: empty. Elimination of underrepresented fourier components is driven by the value of parameter <tt>'fmin'</tt>.
+*<tt>'fminFraction</tt>  : if switched to a value between 0 and 1, selects the minimum fraction of particles that should contribute to a fourier component to admit it during averaging. <br />- default: empty. Elimination of underrepresented fourier components is driven by the value of parameter <tt>'fmin'</tt>.
 '''Smooth masking for Fourier compensation'''
 This family of flags is provided for fine tuning of the behaviour of the Fourier compensation: they drive the imposition of a mask on the raw average before computing its Fourier transform for division with the <tt>'fweight'</tt>. Note that with the default values of the parameters, this step is ''not'' operated.
-*<tt>'fCompensationSmoothingMask'</tt>. If a file or cube is matrix, the raw average will be multiplied with this mask before Fourier compensation. <br /> -default: no mask.
+*<tt>'fCompensationSmoothingMask'</tt>. If a file or cube is matrix, the raw average will be multiplied with this mask before Fourier compensation. <br /> - default: no mask.
-*<tt>'fCompensationSmoothingRadius'</tt>. if a non-zero value is passed, it will generate a spherical mask that will be imposed onto the raw average.   <br /> -default: 0, no spherical mask.
+*<tt>'fCompensationSmoothingRadius'</tt>. if a non-zero value is passed, it will generate a spherical mask that will be imposed onto the raw average.   <br /> - default: 0, no spherical mask.
-*<tt>'fCompensationSmoothingDecay'</tt>. If a spherical mask is used (i.e., if <tt>'fCompensationSmoothingRadius'</tt> is not zero), this sphere will have a smooth gaussian decay of <tt>'fCompensationSmoothingDecay'</tt> pixels from 1 to 0.  <br /> -default value: 4 pixels.
+*<tt>'fCompensationSmoothingDecay'</tt>. If a spherical mask is used (i.e., if <tt>'fCompensationSmoothingRadius'</tt> is not zero), this sphere will have a smooth gaussian decay of <tt>'fCompensationSmoothingDecay'</tt> pixels from 1 to 0.  <br /> - default value: 4 pixels.
-−
 == Inside an alignment project ==