Fix bugs all around

docs/mqtt_messages.md

@@ -68,13 +68,13 @@ This topic controls the camera and capture. The message allowed is a JSON messag
 ```json
 {
   "action": "image",
-  "sleep": 5,
+  "pump_direction": "FORWARD",
   "volume": 1,
   "nb_frame": 200
 }
 ```
 
-Sleep in seconds and volume in mL.
+Volume is in mL.
 
 This topic can also receive a config update message:
 ```json

hardware.json

@@ -5,6 +5,6 @@
   "pump_steps_per_ml": 507,
   "focus_max_speed": 0.5,
   "pump_max_speed": 30,
-  "stepper_type": "adafruit",
+  "stepper_type": "waveshare",
   "camera_type": "HQ"
 }

scripts/bash/update.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+cd /home/pi/PlanktonScope
+
+git stash
+git pull
+git checkout stash@{0} -- config.json hardware.json 

scripts/planktoscope/imager.py

@@ -160,6 +160,7 @@ class ImagerProcess(multiprocessing.Process):
         self.__img_done = 0
         self.__sleep_before = None
         self.__pump_volume = None
+        self.__pump_direction = "FORWARD"
         self.__img_goal = None
         self.imager_client = None
 
@@ -303,7 +304,12 @@ class ImagerProcess(multiprocessing.Process):
         # Get duration to wait before an image from the different received arguments
         self.__sleep_before = float(last_message["sleep"])
         # Get volume in between two images from the different received arguments
-        self.__pump_volume = float(last_message["volume"])
+        # Minimal volume is 0.1mL
+        self.__pump_volume = max(float(last_message["volume"]), 0.1)
+
+        # Get the pump direction message
+        self.__pump_direction = last_message["pump_direction"]
+
         # Get the number of frames to image from the different received arguments
         self.__img_goal = int(last_message["nb_frame"])
 
@@ -471,6 +477,21 @@ class ImagerProcess(multiprocessing.Process):
                 f"We did not understand the received request {action} - {last_message}"
             )
 
+    def __pump_message(self):
+        """Sends a message to the pump process"""
+        # Pump during a given volume
+        self.imager_client.client.publish(
+            "actuator/pump",
+            json.dumps(
+                {
+                    "action": "move",
+                    "direction": self.__pump_direction,
+                    "volume": self.__pump_volume,
+                    "flowrate": 2,
+                }
+            ),
+        )
+
     def __state_imaging(self):
         # TODO we should make sure here that we are not writing to an existing folder
         # otherwise we might overwrite the metadata.json file
@@ -516,17 +537,9 @@ class ImagerProcess(multiprocessing.Process):
 
         # Set the LEDs as Blue
         planktoscope.light.setRGB(0, 0, 255)
-        self.imager_client.client.publish(
+
-            "actuator/pump",
+        self.__pump_message()
-            json.dumps(
+
-                {
-                    "action": "move",
-                    "direction": "FORWARD",
-                    "volume": self.__pump_volume,
-                    "flowrate": 2,
-                }
-            ),
-        )
         # FIXME We should probably update the global metadata here with the current datetime/position/etc...
 
         # Set the LEDs as Green
@@ -610,18 +623,7 @@ class ImagerProcess(multiprocessing.Process):
                 "status/pump", self.pump_callback
             )
 
-            # Pump during a given volume
+            self.__pump_message()
-            self.imager_client.client.publish(
-                "actuator/pump",
-                json.dumps(
-                    {
-                        "action": "move",
-                        "direction": "BACKWARD",
-                        "volume": self.__pump_volume,
-                        "flowrate": 2,
-                    }
-                ),
-            )
 
             # Set the LEDs as Green
             planktoscope.light.setRGB(0, 255, 0)

scripts/planktoscope/light.py

@@ -92,6 +92,7 @@ def light(state):
 ## Wait message: Green
 ## Actuate message: White
 ## Pumping message: Blue
+## Pumping 2 message: BLue + Green
 
 # This is called if this script is launched directly
 if __name__ == "__main__":

scripts/planktoscope/stepper.py

@@ -16,7 +16,7 @@ logger.info("planktoscope.stepper is loaded")
 
 
 class StepperWaveshare:
-    """A bipolar stepper motor."""
+    """A bipolar stepper motor using the Waveshare HAT."""
 
     def __init__(self, dir_pin, step_pin, enable_pin):
         self.dir_pin = dir_pin
@@ -178,6 +178,7 @@ class StepperProcess(multiprocessing.Process):
     def __init__(self, event):
         super(StepperProcess, self).__init__()
         logger.info("Initialising the stepper process")
+        RPi.GPIO.setup([12, 4], RPi.GPIO.OUT, initial=RPi.GPIO.HIGH)
 
         self.stop_event = event