celldetective 1.4.2__py3-none-any.whl → 1.5.0b1__py3-none-any.whl

celldetective/gui/workers.py

@@ -1,140 +1,417 @@
 from multiprocessing import Queue
 from PyQt5.QtWidgets import QPushButton, QVBoxLayout, QHBoxLayout, QLabel, QProgressBar
 from PyQt5.QtCore import QRunnable, QObject, pyqtSignal, QThreadPool, QSize, Qt
-
-from celldetective.gui.base_components import CelldetectiveDialog
-from celldetective.gui.gui_utils import center_window
+from PyQt5.QtGui import QPixmap, QImage
 import math
+import numpy as np
+
+from celldetective.gui.base.components import CelldetectiveDialog
+from celldetective.gui.base.utils import center_window
+from celldetective.log_manager import get_logger
+
+logger = get_logger(__name__)
+
 
 class ProgressWindow(CelldetectiveDialog):
 
-	def __init__(self, process=None, parent_window=None, title="", position_info=True, process_args=None):
-
-		super().__init__()
-		#QDialog.__init__(self)
-
-		self.setWindowTitle(f'{title} Progress')
-		self.__process = process
-		self.parent_window = parent_window
-
-		self.position_info = position_info
-		if self.position_info:
-			self.pos_name = self.parent_window.pos_name
-
-		#self.__btn_run = QPushButton("Start")
-		self.__btn_stp = QPushButton("Cancel")
-		if self.position_info:
-			self.position_label = QLabel(f'Processing position {self.pos_name}...')
-		self.__label   = QLabel("Idle")
-		self.time_left_lbl = QLabel('')
-
-		self.progress_bar = QProgressBar()
-		self.progress_bar.setValue(0)
-
-		self.__runner  = Runner(process=self.__process, progress_bar=self.progress_bar, process_args=process_args, remaining_time_label=self.time_left_lbl)
-		self.pool = QThreadPool.globalInstance()
-		#print("Multithreading with maximum %d threads" % self.pool.maxThreadCount())
-
-		#self.__btn_run.clicked.connect(self.__run_net)
-		self.__btn_stp.clicked.connect(self.__stp_net)
-		self.__runner.signals.finished.connect(self.__on_finished)
-		self.__runner.signals.finished.connect(self.__on_error)
-		self.__runner.signals.update.connect(self.progress_bar.setValue)
-		self.__runner.signals.update_time.connect(self.time_left_lbl.setText)
-
-		self.__btn_stp.setDisabled(True)
-
-		self.layout = QVBoxLayout()
-		if self.position_info:
-			self.layout.addWidget(self.position_label)
-		self.layout.addWidget(self.time_left_lbl)
-		self.layout.addWidget(self.progress_bar)
-		self.btn_layout = QHBoxLayout()
-		self.btn_layout.addWidget(self.__btn_stp)
-		self.btn_layout.addWidget(self.__label)
-		self.layout.addLayout(self.btn_layout)
-
-		self.setLayout(self.layout)
-		self.setFixedSize(QSize(250, 130))
-		self.__run_net()
-		self.setModal(True)
-		center_window(self)
-
-	def closeEvent(self, evnt):
-		# if self._want_to_close:
-		# 	super(MyDialog, self).closeEvent(evnt)
-		# else:
-		evnt.ignore()
-		self.setWindowState(Qt.WindowMinimized)
-
-	def __run_net(self):
-		#self.__btn_run.setDisabled(True)
-		self.__btn_stp.setEnabled(True)
-		self.__label.setText("Running...")
-		self.pool.start(self.__runner)
-
-	def __stp_net(self):
-		self.__runner.close()
-		print('\n Job cancelled... Abort.')
-		self.reject()
-
-	def __on_finished(self):
-		self.__btn_stp.setDisabled(True)
-		self.__label.setText("\nFinished!")
-		self.__runner.close()
-		self.accept()
-
-	def __on_error(self):
-		self.__btn_stp.setDisabled(True)
-		self.__label.setText("\nError")
-		self.__runner.close()
-		self.accept()
+    def __init__(
+        self,
+        process=None,
+        parent_window=None,
+        title="",
+        position_info=True,
+        process_args=None,
+    ):
+
+        super().__init__()
+        # QDialog.__init__(self)
+
+        self.setWindowTitle(f"{title}")
+        self.__process = process
+        self.parent_window = parent_window
+
+        self.position_info = position_info
+        if self.position_info:
+            self.pos_name = getattr(self.parent_window, "pos_name", "Batch")
+
+        # self.__btn_run = QPushButton("Start")
+        self.__btn_stp = QPushButton("Cancel")
+        if self.position_info:
+            self.position_label = QLabel(f"Processing position {self.pos_name}...")
+        self.__label = QLabel("Idle")
+        self.time_left_lbl = QLabel("")
+
+        self.well_time_lbl = QLabel("Well progress:")
+        self.well_progress_bar = QProgressBar()
+        self.well_progress_bar.setValue(0)
+        self.well_progress_bar.setFormat("Total (Wells): %p%")
+
+        self.pos_time_lbl = QLabel("Position progress:")
+        self.pos_progress_bar = QProgressBar()
+        self.pos_progress_bar.setValue(0)
+        self.pos_progress_bar.setFormat("Current Well (Positions): %p%")
+
+        self.frame_time_lbl = QLabel("Frame progress:")
+        self.frame_progress_bar = QProgressBar()
+        self.frame_progress_bar.setValue(0)
+        self.frame_progress_bar.setFormat("Current Position (Frames): %p%")
+
+        self.__runner = Runner(
+            process=self.__process,
+            process_args=process_args,
+        )
+        logger.info("Runner initialized...")
+        self.pool = QThreadPool.globalInstance()
+
+        self.__btn_stp.clicked.connect(self.__stp_net)
+        self.__runner.signals.finished.connect(self.__on_finished)
+        self.__runner.signals.error.connect(self.__on_error)
+
+        self.__runner.signals.update_well.connect(self.well_progress_bar.setValue)
+        self.__runner.signals.update_well_time.connect(self.well_time_lbl.setText)
+
+        self.__runner.signals.update_pos.connect(self.pos_progress_bar.setValue)
+        self.__runner.signals.update_pos_time.connect(self.pos_time_lbl.setText)
+
+        self.__runner.signals.update_frame.connect(self.frame_progress_bar.setValue)
+        self.__runner.signals.update_frame_time.connect(self.frame_time_lbl.setText)
+        self.__runner.signals.update_status.connect(self.__label.setText)
+        self.__runner.signals.update_image.connect(self.update_image)
+
+        self.image_label = QLabel()
+        self.image_label.setFixedSize(250, 250)
+        self.image_label.setAlignment(Qt.AlignCenter)
+        # self.image_label.setScaledContents(True)
+        self.image_label.hide()
+
+        self.__btn_stp.setDisabled(True)
+
+        self.progress_layout = QVBoxLayout()
+        if self.position_info:
+            self.progress_layout.addWidget(self.position_label)
+
+        self.progress_layout.addWidget(self.well_time_lbl)
+        self.progress_layout.addWidget(self.well_progress_bar)
+
+        self.progress_layout.addWidget(self.pos_time_lbl)
+        self.progress_layout.addWidget(self.pos_progress_bar)
+
+        self.progress_layout.addWidget(self.frame_time_lbl)
+        self.progress_layout.addWidget(self.frame_progress_bar)
+
+        self.btn_layout = QHBoxLayout()
+        self.btn_layout.addWidget(self.__btn_stp)
+        self.btn_layout.addWidget(self.__label)
+
+        # Left Column Layout (Bars + Buttons)
+        self.left_layout = QVBoxLayout()
+        self.left_layout.addLayout(self.progress_layout)
+        self.left_layout.addLayout(self.btn_layout)
+
+        # Main Root Layout (Left Column + Image)
+        self.root_layout = QHBoxLayout()
+        self.root_layout.addLayout(self.left_layout)
+        self.root_layout.addWidget(self.image_label)
+
+        self.setLayout(self.root_layout)
+        self.setFixedSize(QSize(400, 220))
+        self.show()
+        self.raise_()
+        self.activateWindow()
+        logger.info("ProgressWindow initialized and shown.")
+        self.__run_net()
+        self.setModal(True)
+        # center_window(self)
+
+    def closeEvent(self, evnt):
+        evnt.ignore()
+        self.setWindowState(Qt.WindowMinimized)
+
+    def __run_net(self):
+        # self.__btn_run.setDisabled(True)
+        self.__btn_stp.setEnabled(True)
+        self.__label.setText("Running...")
+        self.pool.start(self.__runner)
+
+    def __stp_net(self):
+        self.__runner.close()
+        logger.info("\n Job cancelled... Abort.")
+        self.reject()
+
+    def __on_finished(self):
+        self.__btn_stp.setDisabled(True)
+        self.__label.setText("\nFinished!")
+        self.__runner.close()
+        self.accept()
+
+    def __on_error(self, message="Error"):
+        self.__btn_stp.setDisabled(True)
+        self.__label.setText("\nError")
+        self.__runner.close()
+
+        # Show error in a message box to ensure it's seen
+        from PyQt5.QtWidgets import QMessageBox
+
+        msg = QMessageBox()
+        msg.setIcon(QMessageBox.Critical)
+        msg.setText("Process failed")
+        msg.setInformativeText(str(message))
+        msg.setWindowTitle("Error")
+        msg.exec_()
+
+        self.reject()
+
+    def update_image(self, img_data):
+        try:
+            if img_data is None:
+                return
+
+            if self.image_label.isHidden():
+                self.image_label.show()
+                # Expand window width and height to accommodate image
+                self.setFixedSize(QSize(750, 320))
+            # Normalize for display
+            img = img_data.astype(float)
+            img = np.nan_to_num(img)
+
+            min_val = np.min(img)
+            max_val = np.max(img)
+
+            if max_val > min_val:
+                img = (img - min_val) / (max_val - min_val) * 255
+            else:
+                img = np.zeros_like(img)
+
+            img = img.astype(np.uint8)
+            img = np.require(
+                img, np.uint8, "C"
+            )  # Maintain strict C-contiguity for Qt stability
+
+            height, width = img.shape[:2]
+
+            # Grayscale or RGB
+            if img.ndim == 3:
+                # RGB
+                bytes_per_line = 3 * width
+                q_img = QImage(
+                    img.data, width, height, bytes_per_line, QImage.Format_RGB888
+                )
+            else:
+                # Grayscale
+                bytes_per_line = width
+                q_img = QImage(
+                    img.data, width, height, bytes_per_line, QImage.Format_Grayscale8
+                )
+
+            # Use .copy() ensures deep copy of data into QPixmap so we don't depend on volatile memory
+            pixmap = QPixmap.fromImage(q_img.copy())
+            # Scale with Aspect Ratio preserved to avoid cutting or distortion
+            scaled_pixmap = pixmap.scaled(
+                self.image_label.size()
+                - QSize(20, 20),  # Add 10px padding on all sides
+                Qt.KeepAspectRatio,
+                Qt.SmoothTransformation,
+            )
+            self.image_label.setPixmap(scaled_pixmap)
+        except Exception as e:
+            logger.error(f"Image update failed: {e}")
+
 
 class Runner(QRunnable):
 
-	def __init__(self, process=None, progress_bar=None, remaining_time_label=None, process_args=None):
-		QRunnable.__init__(self)
-
-		print(f"{process_args=}")
-		self.progress_bar = progress_bar
-		#self.parent_window = parent_window
-		self.remaining_time_label = remaining_time_label
-		self.__queue = Queue()
-		self.__process = process(self.__queue, process_args=process_args)
-		self.signals = RunnerSignal()
-
-	def run(self):
-		self.__process.start()
-		while True:
-			try:
-				data = self.__queue.get()
-				if len(data)==2:
-					progress, time = data
-					time = int(time)
-					remaining_minutes = time // 60
-					remaining_seconds = int(time % 60)
-					time_left = "About "+str(remaining_minutes)+" min and "+str(remaining_seconds)+" s remaining"
-					if remaining_minutes == 0:
-						time_left = "About "+str(remaining_seconds)+" s remaining"
-					self.signals.update_time.emit(time_left)
-					if isinstance(progress, (float,int)):
-						self.signals.update.emit(math.ceil(progress))
-				if data == "finished":
-					self.signals.finished.emit()
-					break
-				elif data == "error":
-					self.signals.error.emit()
-			except Exception as e:
-				print(e)
-				pass
-
-	def close(self):
-		self.__process.end_process()
+    def __init__(
+        self,
+        process=None,
+        process_args=None,
+    ):
+        QRunnable.__init__(self)
+
+        logger.info(f"{process_args=}")
+        self.__queue = Queue()
+        self.__process = process(self.__queue, process_args=process_args)
+        self.signals = RunnerSignal()
+
+    def run(self):
+        logger.info("Starting Process (runner-side)...")
+        self.__process.start()
+        while True:
+            try:
+                data = self.__queue.get()
+
+                # Handle dictionary for triple progress
+                if isinstance(data, dict):
+                    if "well_progress" in data:
+                        self.signals.update_well.emit(int(data["well_progress"]))
+                    if "well_time" in data:
+                        self.signals.update_well_time.emit(data["well_time"])
+
+                    if "pos_progress" in data:
+                        self.signals.update_pos.emit(int(data["pos_progress"]))
+                    if "pos_time" in data:
+                        self.signals.update_pos_time.emit(data["pos_time"])
+
+                    if "frame_progress" in data:
+                        self.signals.update_frame.emit(int(data["frame_progress"]))
+                    if "frame_time" in data:
+                        self.signals.update_frame_time.emit(data["frame_time"])
+
+                    if "image_preview" in data:
+                        self.signals.update_image.emit(data["image_preview"])
+                    elif "bg_image" in data:  # Backward compatibility
+                        self.signals.update_image.emit(data["bg_image"])
+
+                    if "plot_data" in data:
+                        self.signals.update_plot.emit(data["plot_data"])
+
+                    if "training_result" in data:
+                        self.signals.training_result.emit(data["training_result"])
+
+                    if "status" in data:  # Moved this block out of frame_time check
+                        logger.info(
+                            f"Runner received status: {data['status']}"
+                        )  # New log as per instruction
+                        if data["status"] == "finished":
+                            self.signals.finished.emit()
+                            break
+                        elif data["status"] == "error":
+                            msg = data.get("message", "Unknown error")
+                            logger.error(f"Runner received error: {msg}")
+                            self.signals.error.emit(str(msg))
+                        else:
+                            self.signals.update_status.emit(data["status"])
+
+                # Simple fallback for legacy list [progress, time] -> map to POS progress
+                elif isinstance(data, list) and len(data) == 2:
+                    progress, time = data
+                    self.signals.update_pos.emit(math.ceil(progress))
+
+                elif data == "finished":
+                    self.signals.finished.emit()
+                    break
+                elif data == "error":
+                    self.signals.error.emit("Unknown error")
+
+            except Exception as e:
+                logger.error(e)
+                pass
+
+    def close(self):
+        self.__process.end_process()
 
 
 class RunnerSignal(QObject):
 
-	update = pyqtSignal(int)
-	update_time = pyqtSignal(str)
-	finished = pyqtSignal()
-	error = pyqtSignal()
+    update_well = pyqtSignal(int)
+    update_well_time = pyqtSignal(str)
+
+    update_pos = pyqtSignal(int)
+    update_pos_time = pyqtSignal(str)
+
+    update_frame = pyqtSignal(int)
+    update_frame_time = pyqtSignal(str)
+    update_image = pyqtSignal(object)
+    update_plot = pyqtSignal(dict)
+    training_result = pyqtSignal(dict)
+    update_status = pyqtSignal(str)
+
+    finished = pyqtSignal()
+    error = pyqtSignal(str)
+
+
+class GenericProgressWindow(CelldetectiveDialog):
+
+    def __init__(
+        self,
+        process=None,
+        parent_window=None,
+        title="",
+        process_args=None,
+        label_text="Progress:",
+    ):
+
+        super().__init__()
+
+        self.setWindowTitle(f"{title}")
+        self.__process = process
+        self.parent_window = parent_window
+
+        self.__btn_stp = QPushButton("Cancel")
+        self.__label = QLabel("Idle")
+        self.progress_label = QLabel(label_text)
+
+        self.progress_bar = QProgressBar()
+        self.progress_bar.setValue(0)
+        self.progress_bar.setFormat("%p%")
+
+        self.__runner = Runner(
+            process=self.__process,
+            process_args=process_args,
+        )
+        logger.info("Runner initialized...")
+        self.pool = QThreadPool.globalInstance()
+
+        self.__btn_stp.clicked.connect(self.__stp_net)
+        self.__runner.signals.finished.connect(self.__on_finished)
+        self.__runner.signals.error.connect(self.__on_error)
+        self.__runner.signals.update_status.connect(self.__label.setText)
+
+        # Connect update_pos for generic progress (Runner maps generic list progress to update_pos)
+        self.__runner.signals.update_pos.connect(self.progress_bar.setValue)
+
+        self.__btn_stp.setDisabled(True)
+
+        self.layout = QVBoxLayout()
+        self.layout.addWidget(self.progress_label)
+        self.layout.addWidget(self.progress_bar)
+
+        self.btn_layout = QHBoxLayout()
+        self.btn_layout.addWidget(self.__btn_stp)
+        self.btn_layout.addWidget(self.__label)
+
+        self.layout.addLayout(self.btn_layout)
+
+        self.setLayout(self.layout)
+        self.setFixedSize(QSize(400, 150))
+        self.show()
+        self.raise_()
+        self.activateWindow()
+        logger.info("GenericProgressWindow initialized and shown.")
+        self.__run_net()
+        self.setModal(True)
+
+    def closeEvent(self, evnt):
+        evnt.ignore()
+        self.setWindowState(Qt.WindowMinimized)
+
+    def __run_net(self):
+        self.__btn_stp.setEnabled(True)
+        self.__label.setText("Running...")
+        self.pool.start(self.__runner)
+
+    def __stp_net(self):
+        self.__runner.close()
+        logger.info("\n Job cancelled... Abort.")
+        self.reject()
+
+    def __on_finished(self):
+        self.__btn_stp.setDisabled(True)
+        self.__label.setText("\nFinished!")
+        self.__runner.close()
+        self.accept()
+
+    def __on_error(self, message="Error"):
+        self.__btn_stp.setDisabled(True)
+        self.__label.setText("\nError")
+        self.__runner.close()
+
+        # Show error in a message box to ensure it's seen
+        from PyQt5.QtWidgets import QMessageBox
+
+        msg = QMessageBox()
+        msg.setIcon(QMessageBox.Critical)
+        msg.setText("Process failed")
+        msg.setInformativeText(str(message))
+        msg.setWindowTitle("Error")
+        msg.exec_()
+
+        self.reject()

celldetective/log_manager.py

@@ -0,0 +1,92 @@
+import logging
+import os
+import sys
+
+# from contextlib import contextmanager
+
+# Default formatters
+CONSOLE_FORMAT = "[%(levelname)s] %(message)s"
+FILE_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+
+
+def setup_global_logging(level=logging.INFO, log_file=None):
+    """
+    Sets up the global logger for the application.
+    """
+    root_logger = logging.getLogger("celldetective")
+    root_logger.setLevel(level)
+    root_logger.propagate = False  # Prevent double logging if attached to root
+
+    # Clear existing handlers to avoid duplicates on reload
+    if root_logger.handlers:
+        root_logger.handlers.clear()
+
+    # Console Handler
+    console_handler = logging.StreamHandler(sys.__stdout__)
+    console_handler.setFormatter(logging.Formatter(CONSOLE_FORMAT))
+    root_logger.addHandler(console_handler)
+
+    # Optional Global File Handler
+    if log_file:
+        os.makedirs(os.path.dirname(log_file), exist_ok=True)
+        file_handler = logging.FileHandler(log_file)
+        file_handler.setFormatter(logging.Formatter(FILE_FORMAT))
+        root_logger.addHandler(file_handler)
+
+        for lib in ["trackpy", "btrack", "cellpose", "stardist"]:
+            lib_logger = logging.getLogger(lib)
+            lib_logger.setLevel(logging.INFO)
+            if file_handler not in lib_logger.handlers:
+                lib_logger.addHandler(file_handler)
+
+    # Hook to capture uncaught exceptions
+    def handle_exception(exc_type, exc_value, exc_traceback):
+        if issubclass(exc_type, KeyboardInterrupt):
+            sys.__excepthook__(exc_type, exc_value, exc_traceback)
+            return
+        root_logger.error(
+            "Uncaught exception", exc_info=(exc_type, exc_value, exc_traceback)
+        )
+
+    sys.excepthook = handle_exception
+
+    return root_logger
+
+
+def get_logger(name="celldetective"):
+    """
+    Returns a logger with the specified name, defaulting to the package logger.
+    """
+    return logging.getLogger(name)
+
+
+# @contextmanager
+# def positionlogger(position_path, logger_name="celldetective"):
+#     """
+#     context manager to dynamically route logs to a file within a specific position folder.
+#
+#     args:
+#         position_path (str): path to the position folder.
+#         logger_name (str): name of the logger to attach the handler to.
+#     """
+#     logger = logging.getlogger(logger_name)
+#
+#     # ensure logs/ directory exists in the position folder
+#     log_dir = os.path.join(position_path, "logs")
+#     os.makedirs(log_dir, exist_ok=true)
+#
+#     log_file = os.path.join(log_dir, "process.log")
+#
+#     # create file handler
+#     file_handler = logging.filehandler(log_file)
+#     file_handler.setformatter(logging.formatter(file_format))
+#
+#     # add handler
+#     logger.addhandler(file_handler)
+#
+#     try:
+#         yield logger
+#     finally:
+#         # remove handler to stop logging to this file
+#         file_handler.close()
+#         logger.removehandler(file_handler)