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
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
Danger
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
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
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].