v0.7.1

ulc_mm_package/QtGUI/form_gui.py

@@ -6,7 +6,6 @@
 
 import sys
 
-
 from PyQt5.QtWidgets import (
     QApplication,
     QDialog,
@@ -19,10 +18,11 @@
     QDesktopWidget,
 )
 from PyQt5.QtGui import QIcon
-from PyQt5.QtCore import pyqtSignal
+from PyQt5.QtCore import pyqtSignal, QDate, QTime
 
 from ulc_mm_package.scope_constants import EXPERIMENT_METADATA_KEYS
 from ulc_mm_package.image_processing.processing_constants import TARGET_FLOWRATE
+from PyQt5.QtWidgets import QDateEdit, QTimeEdit
 from ulc_mm_package.QtGUI.gui_constants import (
     ICON_PATH,
     SITE_LIST,
@@ -48,6 +48,15 @@ def closeEvent(self, event):
         else:
             event.accept()
 
+    def _validate_temperature(self):
+        text = self.sample_storage_temp.text()
+        if not text.endswith(("C", "F", "c", "f")) or not text[:-1].isdigit():
+            self.sample_storage_temp.setStyleSheet("border: 1px solid red;")
+            self.start_btn.setEnabled(False)
+        else:
+            self.sample_storage_temp.setStyleSheet("")
+            self.start_btn.setEnabled(True)
+
     def _load_ui(self):
         self.setWindowTitle("Experiment form")
 
@@ -78,15 +87,35 @@ def _load_ui(self):
         # Labels
         self.operator_lbl = QLabel("Operator ID")
         self.participant_lbl = QLabel("Non-identifying participant ID")
+        self.sample_collection_date_lbl = QLabel("Sample collection date")
+        self.sample_collection_time_lbl = QLabel("Sample collection time")
+        self.sample_storage_temp_lbl = QLabel("Sample storage temperature (°C or °F)")
         self.flowcell_lbl = QLabel("Flowcell ID")
         self.notes_lbl = QLabel("Other notes")
         self.site_lbl = QLabel("Site")
         self.sample_lbl = QLabel("Sample type")
-        self.msg_lbl = QLabel("Please fill out experiment data.")
 
         # Text boxes
         self.operator_val = QLineEdit()
         self.participant_val = QLineEdit()
+
+        # Sample collection date
+        self.sample_collection_date = QDateEdit(QDate.currentDate())
+        self.sample_collection_date.setCalendarPopup(True)
+        self.sample_collection_date.setDisplayFormat("yyyy-MMM-dd")
+
+        # Sample collection time
+        self.sample_collection_time = QTimeEdit(QTime.currentTime())
+        self.sample_collection_time.setDisplayFormat("hh:mm AP")
+        self.sample_collection_time.setCalendarPopup(True)
+
+        # Sample storage temperature
+        self.sample_storage_temp = QLineEdit()
+        self.sample_storage_temp.setPlaceholderText(
+            "Enter temperature (e.g. 25C or 77F)"
+        )
+        self.sample_storage_temp.textChanged.connect(self._validate_temperature)
+
         self.flowcell_val = QLineEdit()
         self.notes_val = QPlainTextEdit()
 
@@ -107,31 +136,51 @@ def _load_ui(self):
         # Place widgets
         self.main_layout.addWidget(self.operator_lbl, 0, 0)
         self.main_layout.addWidget(self.participant_lbl, 1, 0)
-        self.main_layout.addWidget(self.flowcell_lbl, 2, 0)
-        self.main_layout.addWidget(self.site_lbl, 4, 0)
-        self.main_layout.addWidget(self.sample_lbl, 5, 0)
-        self.main_layout.addWidget(self.notes_lbl, 6, 0)
-        self.main_layout.addWidget(self.exit_btn, 8, 0)
+        self.main_layout.addWidget(self.sample_collection_date_lbl, 2, 0)
+        self.main_layout.addWidget(self.sample_collection_time_lbl, 3, 0)
+        self.main_layout.addWidget(self.sample_storage_temp_lbl, 4, 0)
+        self.main_layout.addWidget(self.flowcell_lbl, 5, 0)
+        self.main_layout.addWidget(self.site_lbl, 6, 0)
+        self.main_layout.addWidget(self.sample_lbl, 7, 0)
+        self.main_layout.addWidget(self.notes_lbl, 8, 0)
+        self.main_layout.addWidget(self.exit_btn, 9, 0)
 
         self.main_layout.addWidget(self.operator_val, 0, 1)
         self.main_layout.addWidget(self.participant_val, 1, 1)
-        self.main_layout.addWidget(self.flowcell_val, 2, 1)
-        self.main_layout.addWidget(self.site_val, 4, 1)
-        self.main_layout.addWidget(self.sample_val, 5, 1)
-        self.main_layout.addWidget(self.notes_val, 6, 1)
-        self.main_layout.addWidget(self.start_btn, 8, 1)
-
-        self.main_layout.addWidget(self.msg_lbl, 7, 0, 1, 2)
+        self.main_layout.addWidget(self.sample_collection_date, 2, 1)
+        self.main_layout.addWidget(self.sample_collection_time, 3, 1)
+        self.main_layout.addWidget(self.sample_storage_temp, 4, 1)
+        self.main_layout.addWidget(self.flowcell_val, 5, 1)
+        self.main_layout.addWidget(self.site_val, 6, 1)
+        self.main_layout.addWidget(self.sample_val, 7, 1)
+        self.main_layout.addWidget(self.notes_val, 8, 1)
+        self.main_layout.addWidget(self.start_btn, 9, 1)
 
         # Set the focus order
         self.operator_val.setFocus()
         self.start_btn.setDefault(True)
 
     def get_form_input(self) -> dict:
+        # Determine the sample age from the current time and the sample collection time
+        current_date = QDate.currentDate()
+        current_time = QTime.currentTime()
+
+        sample_date = self.sample_collection_date.date()
+        sample_time = self.sample_collection_time.time()
+
+        date_diff_in_hours = sample_date.daysTo(current_date) * 24
+        time_diff_in_hours = sample_time.secsTo(current_time) / 3600
+
+        sample_age_hours = round(date_diff_in_hours + time_diff_in_hours, 2)
+
         form_metadata = {
             "operator_id": self.operator_val.text(),
             "participant_id": self.participant_val.text(),
             "flowcell_id": self.flowcell_val.text(),
+            "sample_collection_date": self.sample_collection_date.text(),
+            "sample_collection_time": self.sample_collection_time.text(),
+            "sample_age_hours": sample_age_hours,
+            "sample_storage_temp": self.sample_storage_temp.text(),
             "target_flowrate": (
                 TARGET_FLOWRATE.name.capitalize(),
                 TARGET_FLOWRATE.value,
@@ -156,6 +205,7 @@ def reset_parameters(self) -> None:
 if __name__ == "__main__":
     app = QApplication(sys.argv)
     gui = FormGUI()
+    gui.exit_btn.clicked.connect(gui.close)
 
     print(gui.get_form_input())
 

ulc_mm_package/QtGUI/scope_op.py

@@ -869,7 +869,7 @@ def run_experiment(self, img, timestamp) -> None:
             return
 
         # Record timestamp before running routines
-        self.img_metadata["timestamp"] = timestamp
+        self.img_metadata["timestamp"] = round(timestamp, 2)
         self.img_metadata["im_counter"] = f"{self.frame_count:0{self.digits}d}"
 
         t0 = perf_counter()
@@ -1002,33 +1002,51 @@ def run_experiment(self, img, timestamp) -> None:
         self.img_metadata["motor_pos"] = self.mscope.motor.getCurrentPosition()
         try:
             pressure, status = self.mscope.pneumatic_module.getPressure()
-            (
-                self.img_metadata["pressure_hpa"],
-                self.img_metadata["pressure_status_flag"],
-            ) = (pressure, status)
+            self.img_metadata["pressure_hpa"] = (
+                round(pressure, 2) if pressure is not None else pressure
+            )
         except PressureSensorStaleValue as e:
             ## TODO???
             self.logger.error(f"Stale pressure sensor value - {e}")
 
-        self.img_metadata["led_pwm_val"] = self.mscope.led.pwm_duty_cycle
-        self.img_metadata[
-            "syringe_pos"
-        ] = self.mscope.pneumatic_module.getCurrentDutyCycle()
-        self.img_metadata["flowrate"] = self.flowrate
-        self.img_metadata["focus_error"] = raw_focus_err
-        self.img_metadata["filtered_focus_error"] = filtered_focus_err
+        self.img_metadata["led_pwm_val"] = round(self.mscope.led.pwm_duty_cycle, 4)
+        self.img_metadata["syringe_pos"] = round(
+            self.mscope.pneumatic_module.getCurrentDutyCycle(), 4
+        )
+        self.img_metadata["flowrate"] = (
+            round(self.flowrate, 4) if self.flowrate is not None else self.flowrate
+        )
+        self.img_metadata["focus_error"] = (
+            round(raw_focus_err, 4) if raw_focus_err is not None else raw_focus_err
+        )
+        self.img_metadata["filtered_focus_error"] = (
+            round(filtered_focus_err, 4)
+            if filtered_focus_err is not None
+            else filtered_focus_err
+        )
         self.img_metadata["focus_adjustment"] = focus_adjustment
-        self.img_metadata["classic_sharpness_ratio"] = sharpness_ratio_rel_peak
-        self.img_metadata["mean_pixel_val"] = curr_mean_pixel_val
+        self.img_metadata["classic_sharpness_ratio"] = (
+            round(sharpness_ratio_rel_peak, 4)
+            if sharpness_ratio_rel_peak is not None
+            else sharpness_ratio_rel_peak
+        )
+        self.img_metadata["mean_pixel_val"] = (
+            round(curr_mean_pixel_val, 4)
+            if curr_mean_pixel_val is not None
+            else curr_mean_pixel_val
+        )
 
         if self.frame_count % TH_PERIOD_NUM == 0:
             try:
                 (
                     temperature,
                     humidity,
                 ) = self.mscope.ht_sensor.get_temp_and_humidity()
-                self.img_metadata["humidity"] = humidity
-                self.img_metadata["temperature"] = temperature
+                self.img_metadata["humidity"] = round(humidity, 4)
+                self.img_metadata["temperature"] = round(temperature, 2)
+                self.img_metadata["camera_temperature"] = round(
+                    self.mscope.camera._getTemperature(), 2
+                )
             except Exception as e:
                 # some error has occurred, but the TH sensor isn't critical, so just warn
                 # and move on

ulc_mm_package/scope_constants.py

@@ -145,6 +145,10 @@ def IMG_HEIGHT(self) -> int:
 EXPERIMENT_METADATA_KEYS = [
     "operator_id",
     "participant_id",
+    "sample_collection_date",
+    "sample_collection_time",
+    "sample_age_hours",
+    "sample_storage_temp",
     "flowcell_id",
     "target_flowrate",
     "site",
@@ -166,7 +170,6 @@ def IMG_HEIGHT(self) -> int:
     "timestamp",
     "motor_pos",
     "pressure_hpa",
-    "pressure_status_flag",
     "led_pwm_val",
     "syringe_pos",
     "flowrate",