Merge pull request #587 from czbiohub-sf/develop

v0.5.5

ulc_mm_package/QtGUI/oracle.py

@@ -7,6 +7,7 @@
 
 import os
 import sys
+import traceback
 import socket
 import enum
 import logging
@@ -840,9 +841,8 @@ def shutoff(self):
         self.shutoff_done = True
 
     def emergency_shutoff(self):
-        self.logger.warning("Starting emergency oracle shut off.")
-
         if not self.shutoff_done:
+            self.logger.warning("Starting emergency oracle shut off.")
             try:
                 os.remove(LOCKFILE)
                 self.logger.info(f"Removed lockfile ({LOCKFILE}).")
@@ -873,8 +873,9 @@ def main():
 
     app.connect_signal(oracle.scopeop.shutoff)
 
-    def shutoff_excepthook(type, value, traceback):
-        sys.__excepthook__(type, value, traceback)
+    def shutoff_excepthook(type, value, tb):
+        tb_string = "".join(traceback.format_exception(type, value, tb))
+        oracle.logger.warning(f"Oracle shutoff due to exception - {tb_string}")
         try:
             app.shutoff.emit()
             # Pause before shutting off hardware to ensure there are no calls to camera post-shutoff

ulc_mm_package/QtGUI/scope_op.py

@@ -523,7 +523,7 @@ def _end_experiment(self, *args):
 
         runtime = self._get_experiment_runtime()
         if runtime != 0:
-            self.logger.info(f"Net FPS is {self.frame_count/runtime}")
+            self.logger.info(f"Net FPS is {self.frame_count/runtime:.1f}")
 
         self.finishing_experiment.emit(10)
 
@@ -575,14 +575,19 @@ def run_autobrightness(self, img, _timestamp):
             self.logger.info("Slot executed after experiment ended.")
             return
 
-        self.img_signal.disconnect(self.run_autobrightness)
+        try:
+            self.img_signal.disconnect(self.run_autobrightness)
+        except TypeError:
+            self.logger.info(
+                "run_autobrightness: img_signal already disconnected, no signal/slot changes were made."
+            )
 
         try:
             self.autobrightness_routine.send(img)
         except StopIteration as e:
             self.autobrightness_result = e.value
             self.logger.info(
-                f"Autobrightness ✅. Mean pixel val = {self.autobrightness_result}."
+                f"Autobrightness ✅. Mean pixel val = {self.autobrightness_result:.1f}."
             )
             self.last_img = img
             if self.state in {
@@ -638,7 +643,12 @@ def run_cellfinder(self, img, _timestamp):
             self.logger.info("Slot executed after experiment ended")
             return
 
-        self.img_signal.disconnect(self.run_cellfinder)
+        try:
+            self.img_signal.disconnect(self.run_cellfinder)
+        except TypeError:
+            self.logger.info(
+                "run_cellfinder: img_signal already disconnected, no signal/slot changes were made."
+            )
 
         try:
             self.cellfinder_routine.send(img)
@@ -667,7 +677,12 @@ def run_autofocus(self, img, _timestamp):
             self.logger.info("Slot executed after experiment ended.")
             return
 
-        self.img_signal.disconnect(self.run_autofocus)
+        try:
+            self.img_signal.disconnect(self.run_autofocus)
+        except TypeError:
+            self.logger.info(
+                "run_autofocus: img_signal already disconnected, no signal/slot changes were made."
+            )
 
         if not self.autofocus_done:
             if len(self.autofocus_batch) < AF_BATCH_SIZE:
@@ -742,7 +757,12 @@ def run_fastflow(self, img, timestamp):
             self.logger.info("Slot executed after experiment ended.")
             return
 
-        self.img_signal.disconnect(self.run_fastflow)
+        try:
+            self.img_signal.disconnect(self.run_fastflow)
+        except TypeError:
+            self.logger.info(
+                "run_fastflow: img_signal already disconnected, no signal/slot changes were made."
+            )
 
         try:
             img_ds_10x = downsample_image(img, DOWNSAMPLE_FACTOR)
@@ -806,7 +826,12 @@ def run_experiment(self, img, timestamp) -> None:
             self.logger.info("Slot executed after experiment ended.")
             return
 
-        self.img_signal.disconnect(self.run_experiment)
+        try:
+            self.img_signal.disconnect(self.run_experiment)
+        except TypeError:
+            self.logger.info(
+                "run_experiment: img_signal already disconnected, no signal/slot changes were made."
+            )
 
         current_time = perf_counter()
         self.img_metadata["looptime"] = current_time - self.last_time

ulc_mm_package/hardware/hardware_constants.py

@@ -77,7 +77,7 @@
 MPRLS_RST = 10
 MPRLS_PWR = 22
 
-MIN_PRESSURE_DIFF = 400  # In units of hPa
+MIN_PRESSURE_DIFF = 330  # In units of hPa
 # ================ Fan constants ================ #
 FAN_GPIO = 5
 CAM_FAN_1 = 23

ulc_mm_package/hardware/scope_routines.py

@@ -14,14 +14,20 @@
     BrightnessCriticallyLow,
     checkLedWorking,
 )
-from ulc_mm_package.image_processing.flow_control import FlowController
-
+from ulc_mm_package.image_processing.flow_control import (
+    FlowController,
+    CantReachTargetFlowrate,
+)
 from ulc_mm_package.image_processing.cell_finder import (
     CellFinder,
     NoCellsFound,
     LowDensity,
 )
-from ulc_mm_package.hardware.pneumatic_module import PressureLeak, PressureSensorBusy
+from ulc_mm_package.hardware.pneumatic_module import (
+    PressureLeak,
+    PressureSensorBusy,
+    SyringeEndOfTravel,
+)
 from ulc_mm_package.hardware.motorcontroller import Direction, MotorControllerError
 from ulc_mm_package.hardware.hardware_constants import (
     MIN_PRESSURE_DIFF,
@@ -510,9 +516,15 @@ def find_cells_routine(
                     mscope.pneumatic_module.getAmbientPressure()
                     - mscope.pneumatic_module.getPressure()[0]
                 )
-                while curr_pressure_gauge < processing_constants.MAX_VACUUM_PRESSURE:
+                while curr_pressure_gauge < MIN_PRESSURE_DIFF:
                     # Pass in a flow_error=1.0 to pull the syringe down
-                    flow_controller.adjustSyringe(flow_error=1.0)
+                    try:
+                        flow_controller.adjustSyringe(flow_error=1.0)
+                    except (CantReachTargetFlowrate, SyringeEndOfTravel):
+                        self.logger.info(
+                            f"Syringe reached end of travel but current pressure: ({curr_pressure_gauge:.2f} mBar) is less than max allowable ({processing_constants.MAX_VACUUM_PRESSURE:.2f} mBar).\nContinuing with cell finder anyway..."
+                        )
+                        break
                     curr_pressure_gauge = abs(
                         mscope.pneumatic_module.getAmbientPressure()
                         - mscope.pneumatic_module.getPressure()[0]

ulc_mm_package/image_processing/focus_metrics.py

@@ -29,8 +29,8 @@ def radial_average(data):
 
 
 def gradientAverage(img: np.ndarray):
-    """Returns the normalized gradient average (in x and y)"""
-    gx, gy = np.gradient(img) / np.max(img)
+    """Returns the normalized (by mean) gradient average (in x and y)"""
+    gx, gy = np.gradient(img) / np.mean(img)
     return np.average(np.sqrt(gx**2 + gy**2))
 
 
@@ -86,12 +86,22 @@ def get_diff(img: np.ndarray):
     return gy, gx
 
 
+def numba_mean(img: np.ndarray):
+    return np.mean(img)
+
+
 @njit(cache=True)
 def custom_gradient_average(img: np.ndarray):
     # I know these are flipped from what the return statement in `get_diff`
     # but my 'gy' corresponds to np.gradient's 'gx'
     # and rewriting `get_diff` is a bit of a pain and ultimately inconsequential
     # for how we're using it here
+    img_mean = np.mean(img)
+
+    # A guard against any potential division by zero errors
+    img_mean = 1 if img_mean == 0 else img_mean
     gx, gy = get_diff(img)
+    gx = gx / img_mean
+    gy = gy / img_mean
 
     return np.mean(np.sqrt(gx**2 + gy**2))

ulc_mm_package/logger.config

@@ -8,7 +8,7 @@ keys=fileHandler, printHandler
 keys=stringFormatter, printFormatter
 
 [logger_root]
-level=DEBUG
+level=INFO
 handlers=fileHandler, printHandler
 
 [handler_fileHandler]

ulc_mm_package/utilities/lock_utils.py

@@ -1,5 +1,6 @@
 import functools
 
+from threading import Lock
 from typing import Optional
 from contextlib import contextmanager
 
@@ -25,7 +26,7 @@ def wrapper(*args, **kwargs):
 
 
 @contextmanager
-def lock_timeout(lock, timeout: Optional[float] = None):
+def lock_timeout(lock: Lock, timeout: Optional[float] = None):
     """lock context manager w/ timeout
 
     timeout value of 'None' or negative numbers disables timeout
@@ -37,4 +38,5 @@ def lock_timeout(lock, timeout: Optional[float] = None):
     try:
         yield
     finally:
-        lock.release()
+        if lock.locked():
+            lock.release()