Usage

To publish experiment log information to a google page:

$ tomolog run --file-name /local/data/2022-03/Peters/B4_Pb_03_c_10keV_892.h5 --presentation-url https://docs.google.com/presentation/d/128c8JYiJ5EjbQhAtegYYetwDUVZILQjZ5fUIoWuR_aI/edit#slide=id.p

For help:

$ tomolog run -h
usage: tomolog run [-h] [--beamline {None,2-bm,7-bm,32-id}] [--doc-dir DOC_DIR] [--file-name PATH] [--max MAX] [--min MIN] [--parent-folder-id PARENT_FOLDER_ID]
                   [--presentation-url PRESENTATION_URL] [--queue QUEUE] [--config FILE] [--config-update] [--idx IDX] [--idy IDY] [--idz IDZ] [--logs-home FILE]
                   [--magnification MAGNIFICATION] [--pixel-size PIXEL_SIZE] [--save-format {tiff,h5}] [--token-home FILE] [--verbose] [--zoom ZOOM]

optional arguments:
  -h, --help            show this help message and exit
  --beamline {None,2-bm,7-bm,32-id}
                        When set adds the beamline name as a prefix to the slack channel name (default: None)
  --doc-dir DOC_DIR     sphinx/readthedocs documentation directory where the meta data table extracted from the hdf5 file should be saved, e.g. docs/source/... (default: .)
  --file-name PATH      Name of the hdf file (default: .)
  --max MAX             Maximum threshold value for reconstruction visualization (default: 0.0)
  --min MIN             Minimum threshold value for reconstruction visualization (default: 0.0)
  --parent-folder-id PARENT_FOLDER_ID
                        Google public folder ID. Create a public forlder on the google app drive and extract it from the share link: https://drive.google.com/drive/folders/<parent-
                        folder-id>?... (default: None)
  --presentation-url PRESENTATION_URL
                        Google presention. Create a public google slide presentation. (default: None)
  --queue QUEUE         set to separate dropbox files in case or running multiple instance of tomolog-cli (default: 0)
  --config FILE         File name of configuration file (default: /Users/decarlo/logs/tomolog.conf)
  --config-update       When set, the content of the config file is updated using the current params values (default: False)
  --idx IDX             Id of x slice for reconstruction visualization (default: -1)
  --idy IDY             Id of y slice for reconstruction visualization (default: -1)
  --idz IDZ             Id of z slice for reconstruction visualization (default: -1)
  --logs-home FILE      Log file directory (default: /Users/decarlo/logs)
  --magnification MAGNIFICATION
                        Lens magnification. Overwrite value to be used in case in missing from the hdf file (default: -1)
  --pixel-size PIXEL_SIZE
                        Detector pixel size. Overwrite value to be used in case in missing from the hdf file (default: -1)
  --save-format {tiff,h5}
                        Reconstruction save format (default: tiff)
  --token-home FILE     Token file directory (default: /Users/decarlo/tokens)
  --verbose             Verbose output (default: False)
  --zoom ZOOM           zoom for reconstruction, e.g. [1,2,4] (default: [1,2,4])

For other options:

$ tomolog -h
usage: tomolog [-h] [--config FILE]  ...

optional arguments:
  -h, --help     show this help message and exit
  --config FILE  File name of configuration file

Commands:

    init         Create configuration file
    run          Run data logging to google slides
    status       Show the tomolog status