planktoscope/scripts
2019-12-13 15:00:20 -08:00
..
fan.py Create fan.py 2019-12-13 15:00:20 -08:00
focus.py Update focus.py 2019-12-13 14:40:35 -08:00
image.py Add files via upload 2019-12-13 14:51:50 -08:00
kill_image.sh Update kill_image.sh 2019-12-13 14:20:31 -08:00
killer.sh Add files via upload 2019-12-13 14:51:50 -08:00
light.py Update light.py 2019-12-13 14:13:23 -08:00
pump.py Update pump.py 2019-12-13 14:40:20 -08:00
README.md Add files via upload 2019-12-13 14:51:50 -08:00
recover.py Create recover.py 2019-12-13 12:39:16 -08:00


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

Image

image.py in_path sample_project sample_id acq_id volume flowrate
  • in_path : string - directory to store acquisitions the path has to end with /
  • sample_project : string
  • sample_id : string
  • acq_id : string
  • volume : integer
  • flowrate : float

Example:

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

Light

light.py state
  • state : string

Example:

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

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

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