Daverage - Revision history

Daniel Castaño: /* Syntax */

2017-10-13T13:09:01Z

Syntax

Daniel Castaño: /* Rotation and shift */

2017-10-13T13:08:41Z

Rotation and shift

Daniel Castaño at 13:07, 13 October 2017

2017-10-13T13:07:20Z

Daniel Castaño at 12:47, 13 October 2017

2017-10-13T12:47:32Z

Daniel Castaño at 12:42, 13 October 2017

2017-10-13T12:42:29Z

Daniel Castaño at 12:10, 13 October 2017

2017-10-13T12:10:13Z

Daniel Castaño at 11:41, 13 October 2017

2017-10-13T11:41:01Z

Daniel Castaño at 11:38, 13 October 2017

2017-10-13T11:38:25Z

Daniel Castaño: Created page with " `daverage` is the basic command line option for averaging particles in a data folder using alignment parameters expresed inside a table. == Syntax == The ba..."

2017-10-13T10:33:52Z

Created page with " <tt>daverage</tt> is the basic command line option for averaging particles in a data folder using alignment parameters expresed inside a table. == Syntax == The ba..."

New page

<tt>daverage</tt> is the basic command line option for averaging particles in a [[data folder]] using alignment parameters expresed inside a [[table]].

== Syntax ==

The basic syntax of the command is:

<tt> output = daverage('myData','t','myTable.tbl');</tt>

where <tt>output</tt> is an structure recording several items (including of course the density map). If you want to use a linux-like notation, you can produce a left-hand-side output wuth the flag <tt>ws</tt> (short for ''workspace''), i.e.

<tt> daverage myData -t myTable.tbl -ws output</tt>

== Input==

=== Data folder ===

The location of the particles can be passed through:
* a [[data folder]]
* a [[dBoxes folder | DBox folder]]

=== Table ===

A regular ''Dynamo'' table, than can be passed as file or numeric matrix.

=== Options ===

== Output ==

The output structure has several fields.

== Averaging procedure ==

=== Rotation and shift===

=== Normalization===

=== NaN compensation ===

=== Missing wedge compensation===

← Older revision		Revision as of 13:09, 13 October 2017
Line 10:		Line 10:

	where <tt>output</tt> is an structure recording several items (including of course the density map). If you want to use a linux-like notation, you can produce a left-hand-side output wuth the flag <tt>ws</tt> (short for ''workspace''), i.e.		where <tt>output</tt> is an structure recording several items (including of course the density map). If you want to use a linux-like notation, you can produce a left-hand-side output wuth the flag <tt>ws</tt> (short for ''workspace''), i.e.
−

	<tt> daverage myData -t myTable.tbl -ws output</tt>		<tt> daverage myData -t myTable.tbl -ws output</tt>

@@ Line 50: / Line 50: @@
   <nowiki>shiftsParticle =-myTable(i,4:6);
-eulersParticle =-myTable(i,:7:9);</nowiki>
+eulersParticle =-fliplr(myTable(i,:7:9));</nowiki>
-and the operation can be written as :
+and the operation that creates the aligned particle can be written as :
-  <tt>rotatadParticle = dynamo_shift_rot(particle, shiftsParticle, eulersParticle);</tt>
+  <tt>rotatedParticle = dynamo_shift_rot(particle, shiftsParticle, eulersParticle);</tt>
 ==== Corner effects ====
@@ Line 62: / Line 64: @@
 ''Dynamo'' keeps track of the pixels that are brought from out-of-scope areas:
 # The contribution of such a pixel to the average is zero.
 # These pixels are accumulated into a counter.
-−
 === Normalization===

@@ Line 40: / Line 40: @@
 *   <tt> .fsc_labels: </tt>     <br />   useful information to annotate fsc plots
 *    <tt>.tags:</tt>         <br />      list of tags that did actually contribute to the  averaging procedure.  This is useful to control which is the final result of confronting which data is available, which tags are marked in the table, and also which particles where excluded.
-*   <tt> .nanContributions <br />  map with the number of particles that contributed a NaN value for each pixel.
+*   <tt> .nanContributions</tt>   <br />  map with the number of particles that contributed a NaN value for each pixel.
@@ Line 50: / Line 50: @@
   <nowiki>shiftsParticle =-myTable(i,4:6);
- eulersParticle =-myTable(i,:7:9);</nowiki>
+eulersParticle =-myTable(i,:7:9);</nowiki>
 and the operation can be written as :
@@ Line 74: / Line 74: @@
 Rotation and shiftings bring into the rotated volume a set of undefined values. They are equated to zero during the summation of the aligned particles.
-Thus, if you have N particles, in these sum map some pixels will represent the summation of  ''real'' contributions of N particles, and some will represent the contribution of less particles. In order to compensate this, the default behaviour of ''Dynamo'' is as following: the average intensity is computed by dividing the sum by the number of actual
+Thus, if you have N particles, in these sum map some pixels will represent the summation of  ''real'' contributions of N particles, and some will represent the contribution of less particles. In order to compensate this, the default behaviour of ''Dynamo'' is as follows: the average intensity is computed by dividing in each pixels  the sum intensity (including the zero contributions) by the number of actual contributions.
 === Missing wedge compensation===
 [[Fourier compensation during averaging | Missing wedge compensation]] will be activated whenever the flag <tt>fc</tt>  or <tt>fourier_compansate</tt> is used.

← Older revision		Revision as of 12:47, 13 October 2017
Line 74:		Line 74:
	Rotation and shiftings bring into the rotated volume a set of undefined values. They are equated to zero during the summation of the aligned particles.		Rotation and shiftings bring into the rotated volume a set of undefined values. They are equated to zero during the summation of the aligned particles.

−	~~This means that~~ in ~~this~~ sum, some ~~pixels~~ represent the	+	Thus, if you have N particles, in these sum map some pixels will represent the summation of ''real'' contributions of N particles, and some will represent the contribution of less particles. In order to compensate this, the default behaviour of ''Dynamo'' is as following: the average intensity is computed by dividing the sum by the number of actual
−
−

@@ Line 58: / Line 58: @@
 ==== Corner effects ====
-Rotation causes
+Rotation causes [[Border alignment artifact|undefined values in the corners of a rotated volume]]. By default, when a cube is rotated, the resulting sharp edge is created in the rotated version of the cube. Alternatively, one can switch on the flag <tt>implicitRotationMasking</tt> (to value 1). This will compute the values of the rotated volume only inside an interior sphere, making "almost" invisible the effect of the edges. Only  "almost": shifting acts exacly like rotation, introducing edges inside the rotated volume. As we assume that shifts shouldn't be too large, the effects of the shifts are less evident.
 === Normalization===
@@ Line 68: / Line 72: @@
 === NaN compensation ===
-Rotation and shiftings bring into the rotated volume a set of undefined values.
+Rotation and shiftings bring into the rotated volume a set of undefined values. They are equated to zero during the summation of the aligned particles.
 === Missing wedge compensation===
 [[Fourier compensation during averaging | Missing wedge compensation]] will be activated whenever the flag <tt>fc</tt>  or <tt>fourier_compansate</tt> is used.

@@ Line 12: / Line 12: @@
-<tt> daverage myData -t myTable.tbl -ws output</tt>
+ <tt> daverage myData -t myTable.tbl -ws output</tt>
 == Input==
@@ Line 32: / Line 32: @@
 The output structure has several fields.
-*    .average_raw:      <br />  without compensation for overweighting of fourier pixels
+*   <tt> .average_raw:</tt>      <br />  without compensation for overweighting of fourier pixels
+*   <tt> .average: </tt>          <br />  with compensation for the fourier overweighting
-*    .average:          <br />  with compensation for the fourier overweighting
+*   <tt> .fweight:</tt>           <br /> map of overrrepresentation of fourier components in  the output property <tt>.average_raw</tt>
+*   <tt> .fmask: </tt>           <br />  binary mask denoting available fourier coefficients
-*    .fweight:          <br /> map of overrrepresentation of fourier components in  the output property <tt>.average_raw</tt>
+*   <tt> .variance: </tt>       <br />   variance map
+*   <tt> .fsc: </tt>            <br />   fsc values
-*    .fmask:           <br />  binary mask denoting available fourier coefficients
+*   <tt> .fsc_labels: </tt>     <br />   useful information to annotate fsc plots
+*    <tt>.tags:</tt>         <br />      list of tags that did actually contribute to the  averaging procedure.  This is useful to control which is the final result of confronting which data is available, which tags are marked in the table, and also which particles where excluded.
-*    .variance:       <br />   variance map
+*   <tt> .nanContributions <br />  map with the number of particles that contributed a NaN value for each pixel.

@@ Line 27: / Line 27: @@
 === Options ===
 == Output ==
 The output structure has several fields.