1x1

Author: i-jey

ulc_mm_package/QtGUI/acquisition.py

@@ -18,6 +18,7 @@
 from py_cameras import PyCamerasError
 
 from ulc_mm_package.hardware.scope import MalariaScope
+from ulc_mm_package.image_processing.focus_metrics import downsample_image
 from ulc_mm_package.scope_constants import ACQUISITION_PERIOD
 
 
@@ -92,5 +93,6 @@ def get_img(self):
             self.logger.error(f"Failed to grab image: {e}.")
 
     def send_img(self):
-        self.update_liveview.emit(self.img)
+        img_ds = downsample_image(self.img, 2)
+        self.update_liveview.emit(img_ds)
         self.update_infopanel.emit()

ulc_mm_package/QtGUI/scope_op.py

@@ -517,11 +517,11 @@ def _init_classic_focus(self, *args):
         try:
             if self.classic_focus_routine is None:
                 self.classic_focus_routine = self.routines.classic_focus_routine(
-                    downsample_image(self.last_img, 10)
+                    downsample_image(self.last_img, DOWNSAMPLE_FACTOR)
                 )
             else:
                 self.routines.classic_focus._check_and_update_metric(
-                    downsample_image(self.last_img, 10)
+                    downsample_image(self.last_img, DOWNSAMPLE_FACTOR)
                 )
         except Exception as e:
             self.logger.error(
@@ -780,7 +780,8 @@ def run_autofocus(self, img, _timestamp):
 
         if not self.autofocus_done:
             if len(self.autofocus_batch) < AF_BATCH_SIZE:
-                self.autofocus_batch.append(img)
+                img_ds = downsample_image(img, 2)
+                self.autofocus_batch.append(img_ds)
 
                 if self.running:
                     self.img_signal.connect(self.run_autofocus)
@@ -856,9 +857,10 @@ def run_fastflow(self, img, timestamp):
             )
 
         try:
-            img_ds_10x = downsample_image(img, DOWNSAMPLE_FACTOR)
+            img_ds = downsample_image(img, DOWNSAMPLE_FACTOR)
+            print(f"Starting fast flow - sending img of shape {img_ds.shape}")
             self.flowrate, syringe_can_move = self.fastflow_routine.send(
-                (img_ds_10x, timestamp)
+                (img_ds, timestamp)
             )
 
             if self.flowrate is not None:
@@ -953,9 +955,10 @@ def run_experiment(self, img, timestamp) -> None:
         t1 = perf_counter()
         self._update_metadata_if_verbose("update_img_count", t1 - t0)
 
+        img_ds_2x = downsample_image(img, 2)
         t0 = perf_counter()
         prev_yogo_results = self.routines.count_parasitemia(
-            self.mscope, YOGO.crop_img(img), self.frame_count
+            self.mscope, YOGO.crop_img(img_ds_2x), self.frame_count
         )
         t1 = perf_counter()
 
@@ -1007,7 +1010,7 @@ def run_experiment(self, img, timestamp) -> None:
                 raw_focus_err,
                 filtered_focus_err,
                 focus_adjustment,
-            ) = self.PSSAF_routine.send(img)
+            ) = self.PSSAF_routine.send(img_ds_2x)
         except MotorControllerError as e:
             if not SIMULATION:
                 self.logger.error(
@@ -1039,11 +1042,11 @@ def run_experiment(self, img, timestamp) -> None:
         # ------------------------------------
         t0 = perf_counter()
         # Downsample image for use in flowrate + classic image focus metric
-        img_ds_10x = downsample_image(img, 10)
+        img_ds = downsample_image(img, DOWNSAMPLE_FACTOR)
         try:
             # Returns the ratio of the current sharpness metric over the best seen
             # so far
-            sharpness_ratio_rel_peak = self.classic_focus_routine.send(img_ds_10x)
+            sharpness_ratio_rel_peak = self.classic_focus_routine.send(img_ds)
         except OOF as e:
             self.logger.warning(
                 f"Strayed too far away from focus, transitioning to cell-finder. {e}"
@@ -1055,7 +1058,7 @@ def run_experiment(self, img, timestamp) -> None:
         # Run flow control routine
         # ------------------------------------
         try:
-            self.flowrate, _ = self.flowcontrol_routine.send((img_ds_10x, timestamp))
+            self.flowrate, _ = self.flowcontrol_routine.send((img_ds, timestamp))
         except Exception as e:
             self.logger.error(f"Unexpected flow control exception - {e}")
             self.flowrate = -1

ulc_mm_package/hardware/scope_routines.py

@@ -271,6 +271,7 @@ def flow_control_routine(
         while True:
             img, timestamp = yield flow_val, syringe_can_move
 
+            print(f"Flow control received img of shape: {img.shape}")
             # Get the flow value, difference from target flow, and whether the syringe can move
             # If syringe_can_move is False, a CantReachTargetFlowrate exception was raised, meaning
             # the syringe can't move further and the target flowrate has not been reached.

ulc_mm_package/image_processing/flowrate.py

@@ -20,7 +20,6 @@ def __init__(
         self,
         img_height: int = CAMERA_SELECTION.IMG_HEIGHT // DOWNSAMPLE_FACTOR,
         img_width: int = CAMERA_SELECTION.IMG_WIDTH // DOWNSAMPLE_FACTOR,
-        scale_factor: int = DOWNSAMPLE_FACTOR,
     ):
         """A class for estimating the flow rate of cells using a 2D cross-correlation.
         The class holds two images at a time in `frame_a` and `frame_b`. To use this class,
@@ -58,6 +57,7 @@ def __init__(
         self.img_height, self.img_width = img_height, img_width
 
         # for multi-proc
+        print(f"FRE expects: {img_height}, {img_width}")
         self.multiproc_interface = msr.MultiProcFunc.from_arg_definitions(
             get_flowrate_with_cross_correlation,
             work_fn_inputs=[

ulc_mm_package/scope_constants.py

@@ -39,7 +39,7 @@
 CONFIGURATION_FILE = curr_dir / "configs" / f"{socket.gethostname()}-config.ini"
 
 # ================ For flowcontrol and classc image focus ================ #
-DOWNSAMPLE_FACTOR = 10
+DOWNSAMPLE_FACTOR = 20
 
 # ================ Summary PDF constants ================ #
 DEBUG_REPORT = int(