Scripts README

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Romain Bazile 2020-10-06 12:24:08 +02:00
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_________________ # Python scripts of the PlanktoScope
### Focusing
##### focus.py `nb_step` `orientation`
- `nb_step` : **integer** (from 1 to 100000) - number of step to perform by the stage (about 31um/step) This directory contains the various scripts needed for the PlanktoScope to run properly.
- `orientation` : **string** - orientation of the focus either `up` or `down`
Example: You should start your exploration with the file `main.py` as this is the file started by Node-Red.
python3.7 $HOME/PlanktonScope/scripts/focus.py 650 up The `planktoscope` directory contains the various modules loaded at runtime:
_________________ - `imager_state_machine.py` is the state machine class of the imager process.
### Pumping - `imager.py` is the process that runs the camera and the streaming server for the liveview.
##### pump.py `volume` `flowrate` `action` - `light.py` manages the state of the light messages displayed by the Yahboom HAT.
- `mqtt.py` is the class managing the mqtt dialogue with Mosquitto and Node-Red.
- `volume` : **integer** - `segmenter.py` is the process that controls the segmentation.
- `flowrate` : **float** - `stepper.py` is the process that manages the stepper motors and their movements.
- `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** - `on` OR `off`
Example:
python3.7 $HOME/PlanktonScope/scripts/light.py on
_________________
### Fan
##### fan.py `state`
- `state` : **string** - `on` OR `off`
Example:
python3.7 $HOME/PlanktonScope/scripts/fan.py on