Merge pull request #1617 from AllenNeuralDynamics/develop

[production merge] 2025-09-26

Author: alexpiet

src/foraging_gui/Calibration.ui

@@ -451,38 +451,6 @@
              <string/>
             </property>
         </widget>
-        <widget class="QPushButton" name="SaveLeft">
-            <property name="geometry">
-                <rect>
-                    <x>580</x>
-                    <y>20</y>
-                    <width>80</width>
-                    <height>25</height>
-                </rect>
-            </property>
-            <property name="text">
-                <string>Save</string>
-            </property>
-            <property name="checkable">
-                <bool>true</bool>
-            </property>
-        </widget>
-        <widget class="QPushButton" name="SaveRight">
-            <property name="geometry">
-                <rect>
-                    <x>580</x>
-                    <y>55</y>
-                    <width>80</width>
-                    <height>25</height>
-                </rect>
-            </property>
-            <property name="text">
-                <string>Save</string>
-            </property>
-            <property name="checkable">
-                <bool>true</bool>
-            </property>
-        </widget>
     </widget>
     <widget class="QCheckBox" name="multi_value_enable">
         <property name="geometry">
@@ -866,8 +834,6 @@
     <zorder>WeightAfterRight</zorder>
     <zorder>TotalWaterSingleLeft</zorder>
     <zorder>TotalWaterSingleRight</zorder>
-    <zorder>SaveLeft</zorder>
-    <zorder>SaveRight</zorder>
     <zorder>label_21</zorder>
     <zorder>CalibrationType</zorder>
     <zorder>IntervalRight_2</zorder>

src/foraging_gui/Dialogs.py

@@ -572,8 +572,6 @@ def _connectSignalsSlots(self):
             lambda val: self.OpenRightForever.setDisabled(val)
         )
 
-        self.SaveLeft.clicked.connect(lambda: self._SaveValve("Left"))
-        self.SaveRight.clicked.connect(lambda: self._SaveValve("Right"))
         self.StartCalibratingLeft.clicked.connect(self._StartCalibratingLeft)
         self.StartCalibratingRight.clicked.connect(self._StartCalibratingRight)
         self.Continue.clicked.connect(self._Continue)
@@ -896,34 +894,42 @@ def _CalibrateLeftOne(self, repeat=False):
             return
         self.WeightAfterLeft.setText(str(final_tube_weight))
 
-        # Mark measurement as complete, save data, and update figure
-        self.left_measurements[next_index] = True
-        self._Save(
-            valve="Left",
-            valve_open_time=str(current_valve_opentime),
-            valve_open_interval=str(self.params["Interval"]),
-            cycle=str(self.params["Cycle"]),
-            total_water=float(final_tube_weight),
-            tube_weight=float(before_weight),
-        )
-        self._UpdateFigure()
-
-        # Direct user for next steps
-        if np.all(self.left_measurements):
-            self.Warning.setText(
-                "Measurements recorded for all values. Please press Repeat, or Finished"
-            )
-            self.Repeat.setStyleSheet("color: black;background-color : none;")
-            self.Finished.setStyleSheet(
-                "color: white;background-color : mediumorchid;"
+        if self.check_calibration_curve(float(final_tube_weight), float(before_weight)):
+            # Mark measurement as complete, save data, and update figure
+            self.left_measurements[next_index] = True
+            self._Save(
+                valve="Left",
+                valve_open_time=str(current_valve_opentime),
+                valve_open_interval=str(self.params["Interval"]),
+                cycle=str(self.params["Cycle"]),
+                total_water=float(final_tube_weight),
+                tube_weight=float(before_weight),
             )
+            self._UpdateFigure()
+
+            # Direct user for next steps
+            if np.all(self.left_measurements):
+                self.Warning.setText(
+                    "Measurements recorded for all values. Please press Repeat, or Finished"
+                )
+                self.Repeat.setStyleSheet("color: black;background-color : none;")
+                self.Finished.setStyleSheet(
+                    "color: white;background-color : mediumorchid;"
+                )
+            else:
+                self.Warning.setText("Please press Continue, Repeat, or Finished")
+                self.Continue.setStyleSheet(
+                    "color: white;background-color : mediumorchid;"
+                )
+                self.Repeat.setStyleSheet("color: black;background-color : none;")
         else:
-            self.Warning.setText("Please press Continue, Repeat, or Finished")
-            self.Continue.setStyleSheet(
-                "color: white;background-color : mediumorchid;"
+            self.Warning.setText(
+                "Recorded before and after tube weights do not pass checks. Please repeat check."
+                "Value has not been saved."
             )
             self.Repeat.setStyleSheet("color: black;background-color : none;")
 
+
     def _StartCalibratingRight(self):
         """start the calibration loop of right valve"""
 
@@ -1083,31 +1089,59 @@ def _CalibrateRightOne(self, repeat=False):
             return
         self.WeightAfterRight.setText(str(final_tube_weight))
 
-        # Mark measurement as complete, save data, and update figure
-        self.right_measurements[next_index] = True
-        self._Save(
-            valve="Right",
-            valve_open_time=str(current_valve_opentime),
-            valve_open_interval=str(self.params["Interval"]),
-            cycle=str(self.params["Cycle"]),
-            total_water=float(final_tube_weight),
-            tube_weight=float(before_weight),
-        )
-        self._UpdateFigure()
-
-        # Direct user for next steps
-        if np.all(self.right_measurements):
-            self.Warning.setText(
-                "Measurements recorded for all values. Please press Repeat, or Finished"
+        if self.check_calibration_curve(float(final_tube_weight), float(before_weight)):
+            # Mark measurement as complete, save data, and update figure
+            self.right_measurements[next_index] = True
+            self._Save(
+                valve="Right",
+                valve_open_time=str(current_valve_opentime),
+                valve_open_interval=str(self.params["Interval"]),
+                cycle=str(self.params["Cycle"]),
+                total_water=float(final_tube_weight),
+                tube_weight=float(before_weight),
             )
-            self.Repeat.setStyleSheet("color: black;background-color : none;")
+            self._UpdateFigure()
+
+            # Direct user for next steps
+            if np.all(self.right_measurements):
+                self.Warning.setText(
+                    "Measurements recorded for all values. Please press Repeat, or Finished"
+                )
+                self.Repeat.setStyleSheet("color: black;background-color : none;")
+            else:
+                self.Warning.setText("Please press Continue, Repeat, or Finished")
+                self.Continue.setStyleSheet(
+                    "color: white;background-color : mediumorchid;"
+                )
+                self.Repeat.setStyleSheet("color: black;background-color : none;")
         else:
-            self.Warning.setText("Please press Continue, Repeat, or Finished")
-            self.Continue.setStyleSheet(
-                "color: white;background-color : mediumorchid;"
+            self.Warning.setText(
+                "Recorded before and after tube weights do not pass checks. Please repeat check."
+                "Value has not been saved."
             )
             self.Repeat.setStyleSheet("color: black;background-color : none;")
 
+    def check_calibration_curve(self,
+        after_tube_weight: float,
+        init_tube_weight: float) -> bool:
+
+        """
+        Check that values are positive and will not result in negative curve
+
+        :param after_tube_weight: tube weight after calibration
+        :param init_tube_weight: tube weight before calibration
+
+        :returns boolean indicating whether values passed check
+        """
+
+        if not after_tube_weight >= 0 or not init_tube_weight >= 0:
+            return False
+
+        if after_tube_weight <= init_tube_weight:
+            return False
+
+        return True
+
     def _CalibrationStatus(self, opentime, weight_before, i, cycle, interval):
         self.Warning.setText(
             "Measuring left valve: {}s".format(opentime)
@@ -1174,6 +1208,7 @@ def _Save(
             WaterCalibrationResults[date_str][valve][valve_open_time][
                 valve_open_interval
             ][cycle] = [np.round(total_water, 1)]
+
         self.WaterCalibrationResults = WaterCalibrationResults.copy()
 
         # save to the json file
@@ -1187,6 +1222,11 @@ def _Save(
         # update the figure
         self._UpdateFigure()
 
+        # update calibration parameters ui uses
+        self.MainWindow._GetWaterCalibration()
+        FittingResults = self.PlotM.FittingResults
+        self.MainWindow._GetLatestFitting(FittingResults)
+
     def _UpdateFigure(self):
         """plot the calibration result"""
         if self.ToInitializeVisual == 1:  # only run once
@@ -1322,7 +1362,6 @@ def _SpotCheck(self, valve: Literal["Left", "Right"]):
         """
 
         spot_check = getattr(self, f"SpotCheck{valve}")
-        save = getattr(self, f"Save{valve}")
         total_water = getattr(self, f"TotalWaterSingle{valve}")
         pre_weight = getattr(self, f"SpotCheckPreWeight{valve}")
         volume = getattr(self, f"Spot{valve}Volume").text()
@@ -1331,7 +1370,6 @@ def _SpotCheck(self, valve: Literal["Left", "Right"]):
         if self.MainWindow.InitializeBonsaiSuccessfully == 0:
             spot_check.setChecked(False)
             spot_check.setStyleSheet("background-color : none;")
-            save.setStyleSheet("color: black;background-color : none;")
             total_water.setText("")
             pre_weight.setText("")
             return
@@ -1352,7 +1390,6 @@ def _SpotCheck(self, valve: Literal["Left", "Right"]):
                 self.Warning.setText("")
                 pre_weight.setText("")
                 total_water.setText("")
-                save.setStyleSheet("color: black;background-color : none;")
                 return
 
             logging.info(f"starting spot check {valve.lower()}")
@@ -1380,7 +1417,6 @@ def _SpotCheck(self, valve: Literal["Left", "Right"]):
                 self.Warning.setText(f"Spot check {valve.lower()} cancelled")
                 pre_weight.setText("")
                 total_water.setText("")
-                save.setStyleSheet("color: black;background-color : none;")
                 return
             pre_weight.setText(str(empty_tube_weight))
 
@@ -1490,9 +1526,6 @@ def _SpotCheck(self, valve: Literal["Left", "Right"]):
                         valve, error
                     )
                 )
-                save.setStyleSheet(
-                    "color: white;background-color : mediumorchid;"
-                )
                 self.Warning.setText(
                     f"Measuring {valve.lower()} valve: {volume}uL"
                     + "\nEmpty tube weight: {}g".format(empty_tube_weight)

src/foraging_gui/Foraging.py

@@ -1569,12 +1569,17 @@ def _LoadSchedule(self):
 
             # Find the correct week on the schedule
             dividers = schedule[[isinstance(x,str)and('/' in x) for x in schedule['Mouse ID'].values]]
-            today = datetime.now().strftime('%m/%d/%Y')
+            today = datetime.now()
 
             # Multiple weeks on the schedule
             if len(dividers) > 1:
-                first = dividers.iloc[0]['Mouse ID']
-                if datetime.strptime(today, "%m/%d/%Y") < datetime.strptime(first,"%m/%d/%Y"):
+                first = datetime.strptime(dividers.iloc[0]['Mouse ID'], "%m/%d/%Y")
+
+                # switch schedule at Friday 5pm
+                cutoff = first - timedelta(days=3)  # Go back to Friday
+                cutoff = cutoff.replace(hour=17, minute=0, second=0, microsecond=0)  # 5 PM
+
+                if today < cutoff:
                     # Use last weeks schedule
                     schedule = schedule.loc[dividers.index.values[1]:]
                 else:
@@ -4111,8 +4116,17 @@ def _Save(self, ForceSave=0, SaveAs=0, SaveContinue=0, BackupSave=0):
                     with open(self.SaveFile, "w") as outfile:
                         json.dump(Obj2, outfile, indent=4, cls=NumpyEncoder)
                 elif self.SaveFile.endswith(".json"):
-                    with open(self.SaveFile, "w") as outfile:
+                    # Crashses during save can corupt a json file.
+                    # Make tmp file to save to
+                    tmp_file_name = self.SaveFile.split('.json')[0]
+                    tmp_file_name = tmp_file_name + '_tmp.json'
+                    with open(tmp_file_name, "w") as outfile:
                         json.dump(Obj, outfile, indent=4, cls=NumpyEncoder)
+                    # After file is safely saved, remove the old save file
+                    # and rewrite the new one.
+                    if os.path.isfile(self.SaveFile):
+                        os.remove(self.SaveFile)
+                    os.rename(tmp_file_name,self.SaveFile)
 
         # Toggle unsaved data to False
         if BackupSave == 0: