Overview¶

Automo creates and/or executes processing operation commands based on the configuration file (default to be automo.ini) and the parameter setting file (default to be automo_params.csv). You can specify the path to both files when running automo_process_dir and automo_create_commands.

Configuration file¶

automo.ini contains the settings that define the behavior of Automo as well as the processing procesures to be taken for different types of tomography data. Below is the content of a sample file (also available in the macros folder):

[settings]
default_h5_fname    = data.h5
[robos]
tomo_180            = automo_preview, automo_center, automo_search_center, automo_recon
tomo_360        = automo_preview_360, automo_center_360, automo_search_center, automo_recon_360
tomosaic        = automo_tomosaic_create_meta, automo_tomosaic_reorg, automo_tomosaic_preview, automo_tomosaic_center, automo_tomosaic_recon
std             = preview, center, recon
[robos_move]
tomo_180            = new_folder
tomo_360        = new_folder
tomosaic        = existing_folder
std             = new_folder
[robos_rename]
tomo_180            = False
tomo_360        = False
tomosaic        = False
std             = True

The robos section specifies the workflow that Automo should adopt for each of the three types of tomography data (the std entry is for the exception case where Automo fails to recognize the data files as any of the three categories):

tomo_180: single field-of-view tomography
tomo_360: off-centered 360-degree tomography
tomosaic: mosaic tomography using the Tomosaic acquisition scheme

The data type is automatically detected according to the naming pattern of the HDF5 files. It is thus necessary to keep a consistent naming style as listed in the table below:

Data type	Naming pattern
`tomo_180`	`_180_.h5` (must contain `_180_`)
`tomo_360`	`_360_.h5` (must contain `_360_`)
`tomosaic`	`_y_?_x_?_.h5` (indices start from 0)

Automo will execute commands (for tomo_180 and tomo_360) or create bash command scripts (for tomosaic) following the order at which operations are listed. The name of the operations, such as automo_preview, or automo_tomosaic_reorg, must match the name of the processing scripts contained in the macros directory.

When running automo_process_dir in the folder containing all HDF5 data files collected in a beamtime, the robos_move section tells Automo whether to move a file into a new directory named exactly after the basename of the file (new_folder) or to move it into an existing folder named after the prefix of the filename (existing folder; useful for tomosaic). It is recommended to keep the default settings as shown in the sample file above.

The robos_rename section specifies whether Automo should rename the moved HDF5 file according to the setting in settings/default_h5_fname. Keep this setting as False for tomosaic unless specifically needed.

Parameter file¶

automo_params.csv contains the parameter settings for all operations. The parameters of the same operation must stay in the same line with names and values separated by a semicolon (;). The file should follow the format of

operation_name; param_1_name; param_1_value; param_2_name; param_2_value; ...

If an optional parameter is not provided in the csv file, it will use the default value. Please refer to the docstring of an operation script (for example, automo_tomosaic_center --help) to get help on the names and meanings of all its parameters. As in the case of the ini file, operation_name’s must match operation scripts contained in the macros folder.