Table

Tables are the basical metadata system in Dynamo. They are just matrices that describe the properties of sets of particles. The property coded on each column is fixed.

A table can be seen as the metadata of a given data folder. The first column in a table is just an integer number (which we call a tag) that identifies a particle. In the data folder, this particle is identified by the name of the file that contains it, i.e.

<myData>/particle_00003.em

would be the particle with tag 3 in the data folder myData. A table will be able to operate on this particle if it has a row whose first column is the integer 3.

As Tables are matrices, Matlab tools (like find,plot,hist) are easily customizable to explore and visualize the contents of a table. Additionally, Dynamo includes many specific utilities. dapropos table will give you a list of basic commands that you can use for table manipulation.

Format convention in a table

Rows correspond to particles, columns correspond to predefined properties. The convention used in the definition of each column of the table can be consulted each time by the command dthelp

Reading and writing tables

Tables are customarily stored as text files with extension '.tbl'.

Tables can be read and write into the matlab worspace with the standard commands dwrite and dread.

For specially long tables, you can use the extension '.tbl', which will write the files in binary format, allowing considerable speedup in I/O.

Visualization of tables

Basic info

A summary of contents in a table can be displayed by dtinfo. Typing the command:

dinfo mytable.tbl

on a table file mytable.tbl you will get the mean and std values for the contents of each column of the table.

Plots through command line

dtplot allows the creation of graphs like: positions of particles in a volume, orientations, distributions of orientations. For instace, you can check if all the particles in a reference (column = 34) have a similar missing wedge orientation (the tilt angle is coded in column 8).

Basic plots through GUI

The basic GUI is dtshow. Typing dtshow table opens a lightweight GUI that allows quick plotting of the contents of the table, and also a GUI access to all the plotting options of dtplot. This GUI is one of options that the dcp GUI offers when exploring the results of an alignment through browsing the generated tables.

GUI for complex plots dtview

dtview is a more complicated browser for table contents, allowing the joint visualization of pairs of properties for particle sets inside a table.

Table manipulation

Creating tables

In general, Dynamo itself creates correctly formatted tables as they are needed. If a table needs to be explicitly created, an easy way to create a blank table compatible with a given data folder is with the command dynamo_table_blank.

Selection of parts of a table

Use dtgrep. It's applicability ranges from just selecting an explicitely defined range of particle tags to the computation of particles pointing in a direction.

Conversion tools for other software packages

dapropos compatibility will print a selection of functions that can be used to import and export particle metadata with the format expected by other packages, as AV3, jsubtomo and XMIPP