Switch to PyQt6 + Python3.13 typing + formatting

Author: i-jey

setup.py

@@ -27,7 +27,7 @@ def readme():
         "matplotlib==3.4.3",
         "numpy==1.21.0",
         "opencv-python",
-        "PyQt5>=5.15.2",
+        "PyQt6>=6.4.0",
         "pypylon==1.7.2",
         "zarr==2.10.1",
         "pigpio==1.78",
@@ -36,7 +36,7 @@ def readme():
         "adafruit-circuitpython-sht31d",
         "argparse",
         "pimoroni-ioexpander",
-        "qimage2ndarray==1.9.0",
+        "qimage2ndarray>=1.10.0",
         "py_cameras @ git+https://github.com/czbiohub/pyCameras@master",
         "pymotors @ git+https://github.com/czbiohub/PyMotors@master",
         "stats_utils @ git+https://github.com/czbiohub-sf/[email protected]",
@@ -55,7 +55,7 @@ def readme():
             "black==23.1.0",
             "mypy==1.0.1",
             "mypy-extensions==1.0.0",
-            "PyQt5-stubs",
+            "PyQt6-stubs",
             "ruff==0.0.253",
         ]
     },

ulc_mm_package/QtGUI/acquisition.py

@@ -7,7 +7,7 @@
 import logging
 import numpy as np
 
-from PyQt5.QtCore import (
+from PyQt6.QtCore import (
     QObject,
     QTimer,
     pyqtSignal,
@@ -40,11 +40,11 @@ def __init__(self):
     @pyqtSlot()
     def create_timers(self):
         self.acquisition_timer = QTimer()
-        self.acquisition_timer.setTimerType(Qt.PreciseTimer)
+        self.acquisition_timer.setTimerType(Qt.TimerType.PreciseTimer)
         self.acquisition_timer.timeout.connect(self.get_img)
 
         self.liveview_timer = QTimer()
-        self.liveview_timer.setTimerType(Qt.PreciseTimer)
+        self.liveview_timer.setTimerType(Qt.TimerType.PreciseTimer)
         self.liveview_timer.timeout.connect(self.send_img)
 
         self.logger.info("Created acquisition and liveview timers.")

ulc_mm_package/QtGUI/clickablelineedit.py

@@ -1,5 +1,5 @@
-from PyQt5.QtCore import pyqtSignal
-from PyQt5.QtWidgets import QLineEdit
+from PyQt6.QtCore import pyqtSignal
+from PyQt6.QtWidgets import QLineEdit
 
 
 class ClickableLineEdit(QLineEdit):

ulc_mm_package/QtGUI/dev_run.py

@@ -5,14 +5,13 @@
 import sys
 import traceback
 import subprocess
-from typing import Dict
 from time import perf_counter, sleep
 
 import cv2
 import numpy as np
-from PyQt5 import QtWidgets, uic  # type: ignore
-from PyQt5.QtCore import Qt, QThread, pyqtSignal, pyqtSlot
-from PyQt5.QtGui import QImage, QPixmap
+from PyQt6 import QtWidgets, uic  # type: ignore
+from PyQt6.QtCore import QThread, pyqtSignal, pyqtSlot
+from PyQt6.QtGui import QImage, QPixmap
 from qimage2ndarray import gray2qimage
 from gpiozero import CPUTemperature
 
@@ -64,8 +63,6 @@
 
 cpu = CPUTemperature()
 
-QtWidgets.QApplication.setAttribute(Qt.AA_EnableHighDpiScaling, True)
-
 # Qt GUI Files
 curr_dir = Path(__file__).parent.resolve()  # Get full path
 os.chdir(curr_dir)
@@ -149,7 +146,7 @@ def _initializeAttributes(self, external_dir: str, mscope: MalariaScope):
             self.autofocus_model = AutoFocus()
         except RuntimeError as e:
             raise RuntimeError(
-                f'got {str(e)}:\n {subprocess.getoutput("lsusb | grep Myriad")}'
+                f"got {str(e)}:\n {subprocess.getoutput('lsusb | grep Myriad')}"
             )
         self.active_autofocus = False
         self.prev_autofocus_time = 0.0
@@ -182,7 +179,7 @@ def run(self):
                     print(e)
                     print(traceback.format_exc())
 
-    def getMetadata(self) -> Dict:
+    def getMetadata(self) -> dict:
         """Required metadata:
         - Measurement type (actual diagnostic experiment or data collection)
         - Sample type / sample name (i.e dataset name)
@@ -466,7 +463,7 @@ def __init__(self, *args, **kwargs):
                 "ERROR! No external harddrive / SSD detected. Press OK to continue, cancel to quit.",
                 cancel=True,
             )
-            if retval == QtWidgets.QMessageBox.Ok:
+            if retval == QtWidgets.QMessageBox.StandardButton.Ok:
                 self.external_dir = None
             else:
                 quit()
@@ -646,10 +643,11 @@ def _displayMessageBox(self, icon, title, text, cancel):
         msgBox.setText(f"{text}")
         if cancel:
             msgBox.setStandardButtons(
-                QtWidgets.QMessageBox.Ok | QtWidgets.QMessageBox.Cancel
+                QtWidgets.QMessageBox.StandardButton.Ok
+                | QtWidgets.QMessageBox.StandardButton.Cancel
             )
         else:
-            msgBox.setStandardButtons(QtWidgets.QMessageBox.Ok)
+            msgBox.setStandardButtons(QtWidgets.QMessageBox.StandardButton.Ok)
         return msgBox.exec()
 
     def txtBoxFocusGotFocus(self):
@@ -700,7 +698,7 @@ def btnSnapHandler(self):
             start_time = self.acquisitionThread.start_time
             num_images = self.acquisitionThread.im_counter
             print(
-                f"{num_images} images taken in {end_time - start_time:.2f}s ({num_images / (end_time-start_time):.2f} fps)"
+                f"{num_images} images taken in {end_time - start_time:.2f}s ({num_images / (end_time - start_time):.2f} fps)"
             )
 
             return
@@ -947,7 +945,7 @@ def btnFullZStackHandler(self):
             cancel=True,
         )
 
-        if retval == QtWidgets.QMessageBox.Ok:
+        if retval == QtWidgets.QMessageBox.StandardButton.Ok:
             self.disableMotorUIElements()
             self.acquisitionThread.runFullZStack()
 
@@ -967,7 +965,7 @@ def btnLocalZStackHandler(self):
             cancel=True,
         )
 
-        if retval == QtWidgets.QMessageBox.Ok:
+        if retval == QtWidgets.QMessageBox.StandardButton.Ok:
             self.disableMotorUIElements()
             self.acquisitionThread.runLocalZStack()
 
@@ -1142,7 +1140,7 @@ def exit(self):
             cancel=True,
         )
 
-        if retval == QtWidgets.QMessageBox.Ok:
+        if retval == QtWidgets.QMessageBox.StandardButton.Ok:
             # Move syringe back and de-energize
             self.pneumatic_module.close()
 
@@ -1171,7 +1169,7 @@ def main():
         app = QtWidgets.QApplication(sys.argv)
         main_window = MalariaScopeGUI()
         main_window.show()
-        app.exec_()
+        app.exec()
     finally:
         main_window.mscope.shutoff()
 

ulc_mm_package/QtGUI/dev_run.ui

@@ -788,7 +788,7 @@
   <customwidget>
    <class>ClickableLineEdit</class>
    <extends>QLineEdit</extends>
-   <header>clickablelineedit.h</header>
+   <header>clickablelineedit</header>
   </customwidget>
  </customwidgets>
  <resources/>

ulc_mm_package/QtGUI/form_gui.py

@@ -6,7 +6,9 @@
 
 import sys
 
-from PyQt5.QtWidgets import (
+from PyQt6.QtCore import QRect, pyqtSignal
+from PyQt6.QtGui import QIcon
+from PyQt6.QtWidgets import (
     QApplication,
     QDialog,
     QGridLayout,
@@ -15,10 +17,7 @@
     QLineEdit,
     QPlainTextEdit,
     QComboBox,
-    QDesktopWidget,
 )
-from PyQt5.QtGui import QIcon
-from PyQt5.QtCore import pyqtSignal
 
 from ulc_mm_package.scope_constants import EXPERIMENT_METADATA_KEYS
 from ulc_mm_package.image_processing.processing_constants import TARGET_FLOWRATE
@@ -60,13 +59,20 @@ def _load_ui(self):
         self.setWindowTitle("Experiment form")
 
         # Get screen parameters
-        self.screen = QDesktopWidget().screenGeometry()
+        screen = QApplication.primaryScreen()
+        if screen is not None:
+            self.screen = screen.geometry()
+            available_geometry = screen.availableGeometry()
+        else:
+            self.screen = QRect(0, 0, 800, 480)
+            available_geometry = self.screen
+
         if self.screen.height() > 480:
             self.setGeometry(0, 0, 675, 500)
 
             # Move window to middle of screen
             window_geometry = self.frameGeometry()
-            centerpoint = QDesktopWidget().availableGeometry().center()
+            centerpoint = available_geometry.center()
             window_geometry.moveCenter(centerpoint)
             self.move(window_geometry.topLeft())
         else:
@@ -196,4 +202,4 @@ def sf(self) -> None:
     print(gui.get_form_input())
 
     gui.show()
-    sys.exit(app.exec_())
+    sys.exit(app.exec())

ulc_mm_package/QtGUI/liveview_gui.py

@@ -4,13 +4,15 @@
 
 import sys
 from functools import partial
-from typing import List, NamedTuple, Dict, Tuple
+from typing import NamedTuple
 from time import strftime, gmtime
 
 from qimage2ndarray import gray2qimage
 import numpy as np
 
-from PyQt5.QtWidgets import (
+from PyQt6.QtCore import Qt, pyqtSlot, pyqtSignal, QSize, QRect
+from PyQt6.QtGui import QPixmap, QIcon
+from PyQt6.QtWidgets import (
     QApplication,
     QMainWindow,
     QGridLayout,
@@ -27,10 +29,7 @@
     QPlainTextEdit,
     QPushButton,
     QScrollBar,
-    QDesktopWidget,
 )
-from PyQt5.QtCore import Qt, pyqtSlot, pyqtSignal, QSize
-from PyQt5.QtGui import QPixmap, QIcon
 
 from ulc_mm_package.image_processing.flow_control import get_flow_error
 
@@ -59,8 +58,8 @@ class ThumbnailDisplay(NamedTuple):
     class_name: str
     class_id: int
     list_widget: QListWidget
-    list_widget_conf_labels: List[QLabel]
-    list_widget_img_labels: List[QLabel]
+    list_widget_conf_labels: list[QLabel]
+    list_widget_img_labels: list[QLabel]
 
 
 class LiveviewGUI(QMainWindow):
@@ -72,7 +71,12 @@ def __init__(self):
         self.target_flowrate = None
 
         # Get screen parameters
-        self.screen = QDesktopWidget().screenGeometry()
+        screen = QApplication.primaryScreen()
+        if screen is not None:
+            self.screen = screen.geometry()
+        else:
+            self.screen = QRect(0, 0, 800, 480)
+
         if self.screen.height() > 480:
             self.big_screen = True
         else:
@@ -225,8 +229,8 @@ def clear_thumbnails(self):
     @pyqtSlot(object)
     def update_thumbnails(
         self,
-        tuple_of_dict_of_thumbnails: Tuple[
-            Dict[int, List[Thumbnail]], Dict[int, List[Thumbnail]]
+        tuple_of_dict_of_thumbnails: tuple[
+            dict[int, list[Thumbnail]], dict[int, list[Thumbnail]]
         ],
     ):
         max_confs = tuple_of_dict_of_thumbnails[0]
@@ -350,14 +354,14 @@ def _load_infopanel_ui(self):
         self.flowrate_val = QLabel("-")
 
         # Set title alignments
-        self.state_lbl.setAlignment(Qt.AlignCenter)
-        self.cell_count_title.setAlignment(Qt.AlignCenter)
-        self.focus_title.setAlignment(Qt.AlignCenter)
-        self.flowrate_title.setAlignment(Qt.AlignCenter)
-        self.tcp_lbl.setAlignment(Qt.AlignCenter)
-        self.end_of_run_progress_bar.setAlignment(Qt.AlignCenter)
+        self.state_lbl.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        self.cell_count_title.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        self.focus_title.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        self.flowrate_title.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        self.tcp_lbl.setAlignment(Qt.AlignmentFlag.AlignCenter)
+        self.end_of_run_progress_bar.setAlignment(Qt.AlignmentFlag.AlignCenter)
         self.end_of_run_progress_bar.setStyleSheet(
-            "QProgressBar::chunk " "{" "background-color: green;" "}"
+            "QProgressBar::chunk {background-color: green;}"
         )
 
         # Setup column size
@@ -429,7 +433,7 @@ def _load_liveview_ui(self):
         # Populate liveview tab
         self.liveview_img = QLabel()
 
-        self.liveview_img.setAlignment(Qt.AlignCenter)
+        self.liveview_img.setAlignment(Qt.AlignmentFlag.AlignCenter)
         self.liveview_img.setMinimumSize(1, 1)
         self.liveview_img.setScaledContents(True)
 
@@ -443,22 +447,27 @@ def _load_thumbnail_ui(self):
 
         # Populate thumbnail tab
         class_labels = [QLabel(c.capitalize()) for c in CLASSES_TO_DISPLAY]
-        [label.setAlignment(Qt.AlignVCenter | Qt.AlignLeft) for label in class_labels]
+        [
+            label.setAlignment(
+                Qt.AlignmentFlag.AlignVCenter | Qt.AlignmentFlag.AlignLeft
+            )
+            for label in class_labels
+        ]
 
-        self.max_and_min_conf_thumbnail_displays: Dict[str, List[ThumbnailDisplay]] = {
+        self.max_and_min_conf_thumbnail_displays: dict[str, list[ThumbnailDisplay]] = {
             "max_conf": [],
             "min_conf": [],
         }
         for k in self.max_and_min_conf_thumbnail_displays.keys():
-            thumbnail_lists: List[ThumbnailDisplay] = []
+            thumbnail_lists: list[ThumbnailDisplay] = []
             for i, c in enumerate(CLASSES_TO_DISPLAY):
                 class_id = CLASS_IDS[i]
                 class_name = c
-                conf_labels: List[QLabel] = []
-                img_labels: List[QLabel] = []
+                conf_labels: list[QLabel] = []
+                img_labels: list[QLabel] = []
 
                 list_widget = QListWidget()
-                list_widget.setFlow(QListView.LeftToRight)
+                list_widget.setFlow(QListView.Flow.LeftToRight)
                 list_widget.setContentsMargins(0, 0, 0, 0)
 
                 for i in range(MAX_THUMBNAILS):
@@ -470,19 +479,21 @@ def _load_thumbnail_ui(self):
                     )
 
                     conf_label = QLabel()
-                    conf_label.setAlignment(Qt.AlignBottom | Qt.AlignHCenter)
+                    conf_label.setAlignment(
+                        Qt.AlignmentFlag.AlignBottom | Qt.AlignmentFlag.AlignHCenter
+                    )
 
                     img_label = QLabel()
                     conf_labels.append(conf_label)
                     img_labels.append(img_label)
 
                     layout.addWidget(conf_label)
                     layout.addWidget(img_label)
-                    layout.setAlignment(Qt.AlignVCenter)
+                    layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
                     w.setLayout(layout)
 
                     v = QListWidgetItem()
-                    v.setFlags(Qt.NoItemFlags)
+                    v.setFlags(Qt.ItemFlag.NoItemFlags)
                     qs = QSize()
                     qs.setHeight(MIN_THUMBNAIL_DISPLAY_SIZE)
                     qs.setWidth(MIN_THUMBNAIL_DISPLAY_SIZE)
@@ -617,4 +628,4 @@ def _load_metadata_ui(self):
 
     gui.showMaximized()
     gui.exit_btn.clicked.connect(gui.close)
-    sys.exit(app.exec_())
+    sys.exit(app.exec())