Difference between revisions of "Table convention"

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4  : dx            x shift from center (in pixels)
 
4  : dx            x shift from center (in pixels)
 +
 
5  : dy            y shift from center (in pixels)
 
5  : dy            y shift from center (in pixels)
 +
 
6  : dz            z shift from center (in pixels)
 
6  : dz            z shift from center (in pixels)
 +
 
7  : tdrot        euler angle (rotation around z, in degrees)
 
7  : tdrot        euler angle (rotation around z, in degrees)
 +
 
8  : tilt          euler angle (rotation around new x, in degrees)
 
8  : tilt          euler angle (rotation around new x, in degrees)
 +
 
9  : narot        euler angle (rotation around new z, in degrees)
 
9  : narot        euler angle (rotation around new z, in degrees)
 +
 
10  : cc            Cross correlation coefficient
 
10  : cc            Cross correlation coefficient
 +
 
11  : cc2          Cross correlation coefficient after thresholding II
 
11  : cc2          Cross correlation coefficient after thresholding II
 +
 
12  : cpu          processor that aligned the particle
 
12  : cpu          processor that aligned the particle
 +
 
13  : ftype        0: full range; 1: tilt around y ( ... dhelp dtutorial for more options)
 
13  : ftype        0: full range; 1: tilt around y ( ... dhelp dtutorial for more options)
 +
 
14  : ymintilt      minimum angle in the tilt series around tilt axis (i.e. -60)
 
14  : ymintilt      minimum angle in the tilt series around tilt axis (i.e. -60)
 +
 
15  : ymaxtilt      maximum angle in the tilt series around tilt axis (i.e. 60)
 
15  : ymaxtilt      maximum angle in the tilt series around tilt axis (i.e. 60)
 +
 
16  : xmintilt      minimum angle in the tilt series around second tilt axis (i.e. -60)
 
16  : xmintilt      minimum angle in the tilt series around second tilt axis (i.e. -60)
 +
 
17  : xmaxtilt      maximum angle in the tilt series around second x (i.e. 60)
 
17  : xmaxtilt      maximum angle in the tilt series around second x (i.e. 60)
 +
 
18  : fs1          free parameter for fourier sampling #1()
 
18  : fs1          free parameter for fourier sampling #1()
 +
 
19  : fs2          free parameter for fourier sampling #2()
 
19  : fs2          free parameter for fourier sampling #2()
 +
 
20  : tomo          tomogram number  
 
20  : tomo          tomogram number  
 +
 
21  : reg          for arbitrary assignations of regions inside tomograms
 
21  : reg          for arbitrary assignations of regions inside tomograms
 +
 
22  : class        class number  
 
22  : class        class number  
 +
 
23  : annotation    use this field for assigning arbitrary labels
 
23  : annotation    use this field for assigning arbitrary labels
 +
 
24  : x            x coordinate in original volume
 
24  : x            x coordinate in original volume
 +
 
25  : y            y coordinate in original volume
 
25  : y            y coordinate in original volume
 +
 
26  : z            z coordinate in original volume
 
26  : z            z coordinate in original volume
 +
 
27  : dshift        norm of shift vector
 
27  : dshift        norm of shift vector
 +
 
28  : daxis        difference in axis orientation
 
28  : daxis        difference in axis orientation
 +
 
29  : dnarot        difference in narot
 
29  : dnarot        difference in narot
 +
 
30  : dcc          difference in CC
 
30  : dcc          difference in CC
 +
 
31  : otag          original tag (subboxing)
 
31  : otag          original tag (subboxing)
 +
 
32  : npar          number of added particles (compactions) / subunit label (subboxing)
 
32  : npar          number of added particles (compactions) / subunit label (subboxing)
 +
 
34  : ref          reference. Used in multireference projects
 
34  : ref          reference. Used in multireference projects
 +
 
35  : sref          subreference (i.e. generated by Dynamo PCA)
 
35  : sref          subreference (i.e. generated by Dynamo PCA)
 +
 
36  : apix          angstrom per pixel
 
36  : apix          angstrom per pixel
 +
 
37  : def          defocus (in micron)
 
37  : def          defocus (in micron)
 +
 
41  : eig1          "eigencoefficient" #1
 
41  : eig1          "eigencoefficient" #1
 +
 
42  : eig2          "eigencoefficient" #2
 
42  : eig2          "eigencoefficient" #2
 +
 
   
 
   
 
more columns can be added for user-defined properties.
 
more columns can be added for user-defined properties.

Revision as of 17:25, 14 March 2016


As a rule, regular users don't necessarily need to remember the structure of a Dynamo table. However, it might be useful in order to interprete the results of a project, to check if a table has been correctly generated/imported or to diagnose problems.

The column convention used to define a table can be consulted by just typing dthelp, which should produce this output:

1 : tag tag of particle file in data folder

2 : aligned value 1: marks the particle for alignment

3 : averaged value 1: the particle was included in the average

4 : dx x shift from center (in pixels)

5 : dy y shift from center (in pixels)

6 : dz z shift from center (in pixels)

7 : tdrot euler angle (rotation around z, in degrees)

8 : tilt euler angle (rotation around new x, in degrees)

9 : narot euler angle (rotation around new z, in degrees)

10 : cc Cross correlation coefficient

11 : cc2 Cross correlation coefficient after thresholding II

12 : cpu processor that aligned the particle

13 : ftype 0: full range; 1: tilt around y ( ... dhelp dtutorial for more options)

14 : ymintilt minimum angle in the tilt series around tilt axis (i.e. -60)

15 : ymaxtilt maximum angle in the tilt series around tilt axis (i.e. 60)

16 : xmintilt minimum angle in the tilt series around second tilt axis (i.e. -60)

17 : xmaxtilt maximum angle in the tilt series around second x (i.e. 60)

18 : fs1 free parameter for fourier sampling #1()

19 : fs2 free parameter for fourier sampling #2()

20 : tomo tomogram number

21 : reg for arbitrary assignations of regions inside tomograms

22 : class class number

23 : annotation use this field for assigning arbitrary labels

24 : x x coordinate in original volume

25 : y y coordinate in original volume

26 : z z coordinate in original volume

27 : dshift norm of shift vector

28 : daxis difference in axis orientation

29 : dnarot difference in narot

30 : dcc difference in CC

31 : otag original tag (subboxing)

32 : npar number of added particles (compactions) / subunit label (subboxing)

34 : ref reference. Used in multireference projects

35 : sref subreference (i.e. generated by Dynamo PCA)

36 : apix angstrom per pixel

37 : def defocus (in micron)

41 : eig1 "eigencoefficient" #1

42 : eig2 "eigencoefficient" #2


more columns can be added for user-defined properties.

The shortnames can actually used in some programs of Dynamo (as dtgrep and dtplot) to refer to the columns.

Tags

The tags, in column one, are the link between a table and the data folder that is intended to be talked to by the table.

aligned

When a table is passed to a project, you can set to zero the particles in the data folder that you don't want to included into the alignment or classification project. Of course, you can just a table that does not include the particles you want to exclude.

When Dynamo runs a refinement project that operates some particle thresholding from iteration to iteration, the table in the subsequent iteration will not just omit the particles of the previous iteration, but will mark with zero the particles that are not to be aligned in the subsequent iteration.

averaged

This column is never set by the user, but it is typically filled by Dynamo during an alignment project. Dynamo generates several tables during the project (for each reference and for each iteration), and this column allows to track which particle contributed to which reference at which iteration.

dx,dy,dz

The shift parameters, in pixels, measured always from the center of the box.

tdrot,tilt,narot

A set of euler angles.