cell finder bug fix

Author: NicholasBratvold

ulc_mm_package/hardware/real/pneumatic_module.py

@@ -223,8 +223,8 @@ def isMovePossible(self, move_dir: SyringeDirection) -> bool:
         # Cannot move the syringe down
         elif (
             self.duty_cycle - self.min_step_size < self.min_duty_cycle
-            or self.mpr.ambient_pressure - self.mpr.prev_pressure > MAX_VACUUM_PRESSURE
-        ) and move_dir == SyringeDirection.DOWN:
+            and move_dir == SyringeDirection.DOWN
+        ):
             return False
 
         return True

ulc_mm_package/hardware/scope_routines.py

@@ -14,6 +14,7 @@
     BrightnessCriticallyLow,
     checkLedWorking,
 )
+from ulc_mm_package.image_processing.flow_control import FlowController
 
 from ulc_mm_package.image_processing.cell_finder import (
     CellFinder,
@@ -201,7 +202,11 @@ def count_parasitemia(
     def count_parasitemia_periodic_wrapper(
         self,
         mscope: MalariaScope,
-    ) -> Generator[List[AsyncInferenceResult], Tuple[np.ndarray, Optional[int]], None,]:
+    ) -> Generator[
+        List[AsyncInferenceResult],
+        Tuple[np.ndarray, Optional[int]],
+        None,
+    ]:
         while True:
             img, counts = yield mscope.cell_diagnosis_model.get_asyn_results()
             mscope.cell_diagnosis_model(img, counts)
@@ -478,6 +483,7 @@ def find_cells_routine(
         # Maximum number of times to run check for cells routine before aborting
         max_attempts = 3
         cell_finder = CellFinder()
+        flow_controller = FlowController(mscope.pneumatic_module)
         img = yield
 
         # Initial check for cells, return current motor position if cells found
@@ -503,11 +509,9 @@ def find_cells_routine(
             # in which case, cells are already present, we just need to sweep the motor to find them
             if not (skip_syringe_pull):
                 start = perf_counter()
-                mscope.pneumatic_module.setDutyCycle(
-                    mscope.pneumatic_module.getMinDutyCycle()
-                )
 
                 while perf_counter() - start < pull_time:
+                    flow_controller.adjustSyringe(-1)
                     img = yield
                 mscope.pneumatic_module.setDutyCycle(
                     mscope.pneumatic_module.getMaxDutyCycle()

ulc_mm_package/image_processing/flow_control.py

@@ -191,7 +191,7 @@ def control_flow(
                 self.prev_adjustment_stamp = self.counter
 
                 try:
-                    self._adjustSyringe(flow_error)
+                    self.adjustSyringe(flow_error)
                     syringe_successfully_adjusted = True
                 except CantReachTargetFlowrate:
                     syringe_successfully_adjusted = False
@@ -203,7 +203,7 @@ def control_flow(
         else:
             return (None, None, None)
 
-    def _adjustSyringe(self, flow_error: float):
+    def adjustSyringe(self, flow_error: float):
         """Adjusts the syringe based on the flow error.
 
         Parameters
@@ -237,6 +237,7 @@ def _adjustSyringe(self, flow_error: float):
             except SyringeEndOfTravel:
                 raise CantReachTargetFlowrate(self.flowrate)
 
+
     def stop(self):
         self.fre.stop()
         self.fre.reset()