planktoscope/scripts/README.md
2019-12-13 14:20:48 -08:00

1.5 KiB


Focusing

focus.py nb_step orientation
  • nb_step : integer (from 1 to 100000) - number of step to perform by the stage (about 31um/step)
  • orientation : string - orientation of the focus either up or down

Example:

python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up

Pumping

pump.py volume flowrate action
  • volume : integer
  • flowrate : float
  • action : string

Example:

python3.7 $HOME/PlanktonScope/scripts/pump.py 1 10 suck

Killing Focus or Pump event

killer.sh event_to_kill.py
  • event_to_kill.py : string

Example:

bash $HOME/PlanktonScope/scripts/killer.sh pump.py

Image

image.py sample_project sample_id acq_id volume flowrate

-sample_project : string

  • sample_id : string
  • acq_id : string
  • volume : integer
  • flowrate : float

Example:

python3.7 $HOME/PlanktonScope/scripts/pump.py tara_pacific station_125 exp_1 24 3.2

Kill Image

kill_image.sh image.py sample_project sample_id acq_id
  • sample_project : string
  • sample_id : string
  • acq_id : string

Example:

bash $HOME/PlanktonScope/scripts/killer.sh image.py tara_pacific station_125 exp_1

Light

light.py state
  • state : string

Example:

python3.7 $HOME/PlanktonScope/scripts/light.py on