Operations on volumes

There are different operations that are frequently required when processing 3d data, both for small volumes (as templates, averages and particle) or tomograms. Dynamo and Matlab itself provide several commands.

Using the functions

In general, volumes need to be read into the worskpace, creating a variable. The operator can then be used onto the variable and then the result is written back into a file. For instance

 a = dread('myFile.mrc'); 
 b= dread('myFile.mrc'); 
 dwrite(b'myFile.mrc'); 

Most processing options accept as input indistinctly a filename or a variable.

Dealing with big tomograms

Reading full tomograms into the worskpace might be a bad idea, leading to overcrowding you RAM memory and freezing your system. In these situations, it is frequently a good approach to let Dynamo divide automatically the tomogram and operate separately on the chunks (we call this "chunk partition" in the documentation). There are two different devices for this task:

Commands oriented to chunk processing

Some tasks already integrate the operation through a chunk partition operated on the fly, for instance the binning of tomograms, which allows the command dpktomo.partition.bin

Partition objects

Technical information For operations that you want to define yourself, you can use the class behind dpktomo.partition.bin

Functionalities

Binning

Command dbin.

Normalization

Command dynamo_normalize_roi .html dynamo_normalize_roi. You can also pass a mask, so that the normalization will ensure zero mean and std=1 inside the mask.

Filters

Commands dynamo_bandpass .html dbandpass, dynamo_median.html dmedian.

Contrast inversion

You can just use the minus operator in Matlab:

 dread file.mrc a 
 b = -a

possibly normalizing again.

Flippling along a direction

You can use the Matlab commad flip

Flipping two directions

You can use the Matlab commad permute to interchange two directions in a volume.

Rotations and shifts

dynamo_rot.html drot,dynamo_move .html dmove

Advanced functions

A (somewhat) GUI version is available as the command dvolume. The command line counterpart is dynamo_particle.html dparticle