Nabu command line interface

On top of the nabu library, applications can be built for specific purposes. Currently, nabu.appprovides a reconstruction pipeline for full-field data.

Generating a configuration file

Please see the documentation on configuration file.

Running the reconstruction pipeline

The user entry point for running the reconstruction pipeline is the command line nabu.

Running nabu --help gives an overview of the syntax. nabu --version returns the current installed version.

The command line nabu is always used with a configuration file. When you have created a configuration file nabu.conf, then running

nabu nabu.conf

will reconstruct all the volume on the local machine, except if start_z and/or end_z are modified in nabu.conf. In any case, you can overwrite these configuration file values. Fo example:

nabu nabu.conf --slice 500-599

will reconstruct 100 slices: 500, 501, 502, …, 599 included.

Warning

Indexing is zero-based. This means that to reconstruct the first slice, you have to run nabu nabu.conf –slice 0 (or put start_z = 0 in the configuration file)

Examples

Reconstruct a single slice

Reconstruct the first slice:

nabu nabu.conf --slice 0

or equivalently:

nabu nabu.conf --slice first

Reconstruct the middle slice:

nabu nabu.conf --slice middle

Reconstruct the last slice:

nabu nabu.conf --slice last

Reconstruct a range of slices

Reconstruct 300 slices (900, 901, …, 1199 included):

nabu nabu.conf --slice 900-1199

Reconstruct all the volume

If start_z = 0 and end_z = -1 in nabu.conf:

nabu nabu.conf

or equivalently:

nabu nabu.conf --slice all

Tune the computing resources

If other processes are using memory on the local machine, then it is wise to restrict Nabu resources consumption. For this you can use --cpu_mem_fraction and --gpu_mem_fraction. By default these values are 0.9 (i.e 90% of said resources are used by nabu).

nabu nabu.conf --cpu_mem_fraction 0.5 --gpu_mem_fraction 0.6

Define a log file

You can choose in which file the reconstruction messages (logs) are written. By default it is nabu.log.

nabu nabu.conf --logfile my_log_file.log

The verbosity can be tuned in the configuration file in section [about].