Command Line Interface

In addition to the QT-based graphical user interface, LLSpy includes a command line interface (CLI).

If the program has been installed using conda install -c talley -c conda-forge llspy, or by using setuptools (i.e. running pip install . in the top level llspy directory, where setup.py resides) then an executable will be created that can be triggered by typing lls at the command prompt. Alternatively, the CLI can be directly executed by running python llspy/bin/llspy_cli.py at the command prompt. (For this documentation, it is assumed that the program was installed using conda install and run with lls).

$ lls --help
Usage: lls [OPTIONS] COMMAND [ARGS]...

  LLSpy

  This is the command line interface for the LLSpy library, to facilitate
  processing of lattice light sheet data using cudaDeconv and other tools.

Options:
  --version          Show the version and exit.
  -c, --config PATH  Config file to use instead of the system config.
  -h, --help         Show this message and exit.

Commands:
  camera    Camera correction calibration
  compress  Compression & decompression of LLSdir
  config    Manipulate the system configuration for LLSpy
  decon     Deskew and deconvolve data in LLSDIR.
  deskew    Deskewing only (no decon) of LLS data
  gui       Launch the Graphical User Interface.
  info      Get info on LLSDIR.
  reg       Channel registration

You can configure the program either by providing a configuration .ini in the command using the --config flag, or by setting the system configuration using the llspy config command. Minimally, you will want to establish the OTF directory by typing:

$ lls config --set otfDir /path/to/OTFs/

To get a full list of keys available for configuration, type:

$ lls config --info

To print the current system configuration, type:

$ lls config --print

Note: System configuration values will be superceeded by key-value pairs included in config.ini files provided at the command prompt with --config, and all configuration values will be superceeded by those privided directly using option flags in the decon command.

You can use --help to get more information on any specific subcommand. Many are still under development. The bulk of the program functionality resides in the decon subcommand.

$ lls decon --help
Usage: lls decon [OPTIONS] LLSDIR

  Deskew and deconvolve data in LLSDIR.

Options:
  -c, --config PATH              Overwrite defaults with values in specified
                                 file.
  --otfDir DIRECTORY             Directory with otfs. OTFs should be named
                                 (e.g.): 488_otf.tif
  -b, --background INT           Background to subtract. -1 = autodetect.
                                 [default: -1]
  -i, --iters [INT: 0-30]        Number of RL-deconvolution iterations
                                 [default: 10]
  -R, --rotate                   rotate image to coverslip coordinates after
                                 deconvolution  [default: False]
  -S, --saveDeskewed             Save raw deskwed files, in addition to
                                 deconvolved.  [default: False]
  --cropPad INT                  additional edge pixels to keep when
                                 autocropping  [default: 50]
  -w, --width [INT: 0-3000]      Width of image after deskewing. 0 = full
                                 frame.[default: autocrop based on image
                                 content]
  -s, --shift [INT: -1500-1500]  Shift center when cropping  [default: 0]
  -m, --rMIP <BOOL BOOL BOOL>    Save max-intensity projection after
                                 deskewing along x, y, or z axis.  Takes 3
                                 binary numbers separated by spaces.
                                 [default: False, False, False]
  -M, --MIP <BOOL BOOL BOOL>     Save max-intensity projection after
                                 deconvolution along x, y, or z axis. Takes 3
                                 binary numbers separated by spaces  [default:
                                 False, False, True]
  --mergemips / --sepmips        Combine MIP files into single hyperstack (or
                                 not).  [default: True]
  --uint16 / --uint32            Save results as 16 (default) or 32- bit
  -p, --bleachCorrect            Perform bleach correction on timelapse data
                                 [default: False]
  --trimX <LEFT RIGHT>           Number of X pixels to trim off raw data
                                 before processing  [default: 0, 0]
  --trimY <TOP BOT>              Number of Y pixels to trim off raw data
                                 before processing  [default: 0, 0]
  --trimZ <FIRST LAST>           Number of Z pixels to trim off raw data
                                 before processing  [default: 0, 0]
  -f, --correctFlash             Correct Flash pixels before processing.
                                 [default: False]
  -F, --medianFilter             Correct raw data with selective median
                                 filter. Note: this occurs after flash
                                 correction (if requested).  [default: False]
  --keepCorrected                Process even if the folder already has a
                                 processingLog JSON file, (otherwise skip)
  -z, --compress                 Compress raw files after processing
                                 [default: False]
  -r, --reprocess                Process even if the folder already has a
                                 processingLog JSON file, (otherwise skip)
  --batch                        batch process folder: Recurse through all
                                 subfolders with a Settings.txt file
  --yes / --no                   autorespond to prompts
  -h, --help                     Show this message and exit.