napari-tmidas 0.2.0__py3-none-any.whl → 0.2.1__py3-none-any.whl

napari_tmidas/_file_selector.py

@@ -585,7 +585,8 @@ class ProcessingWorker(QThread):
                 filepath = future_to_file[future]
                 try:
                     result = future.result()
-                    if result:
+                    # Only process result if it's not None (folder functions may return None)
+                    if result is not None:
                         processed_files_info.append(result)
                         self.file_processed.emit(result)
                 except (
@@ -611,6 +612,16 @@ class ProcessingWorker(QThread):
 
             print(f"Original image shape: {image.shape}, dtype: {image_dtype}")
 
+            # Check if this is a folder-processing function that shouldn't save individual files
+            function_name = getattr(
+                self.processing_func, "__name__", "unknown"
+            )
+            is_folder_function = (
+                "timepoint" in function_name.lower()
+                or "merge" in function_name.lower()
+                or "folder" in function_name.lower()
+            )
+
             # Apply processing with parameters
             processed_image = self.processing_func(image, **self.param_values)
 
@@ -618,6 +629,19 @@ class ProcessingWorker(QThread):
                 f"Processed image shape before removing singletons: {processed_image.shape}, dtype: {processed_image.dtype}"
             )
 
+            # For folder functions, check if the output is the same as input (indicating no individual file should be saved)
+            if is_folder_function:
+                # If the function returns the original image unchanged, it means it handled saving internally
+                if np.array_equal(processed_image, image):
+                    print(
+                        "Folder function returned unchanged image - skipping individual file save"
+                    )
+                    return None  # Return None to indicate no file should be created
+                else:
+                    print(
+                        "Folder function returned different data - will save individual file"
+                    )
+
             # Remove ALL singleton dimensions from the processed image
             # This will keep only dimensions with size > 1
             processed_image = np.squeeze(processed_image)
@@ -939,9 +963,49 @@ class FileResultsWidget(QWidget):
 
         # Update description
         description = function_info.get("description", "")
-        self.function_description.setText(description)
 
-        # Update parameters
+        # Check if this is a folder-processing function that needs single threading
+        is_folder_function = (
+            "folder" in function_name.lower()
+            or "timepoint" in function_name.lower()
+            or "merge" in function_name.lower()
+            or "folder" in description.lower()
+            or "cellpose" in description.lower()
+            or "careamics" in description.lower()
+            or "trackastra" in description.lower()
+        )
+
+        # Disable threading controls for folder functions
+        if is_folder_function:
+            self.thread_count.setValue(1)
+            self.thread_count.setEnabled(False)
+            self.thread_count.setToolTip(
+                "This function processes entire folders and must run with 1 thread only."
+            )
+
+            # Add warning to description if not already present
+            if (
+                "IMPORTANT:" not in description
+                and "WARNING:" not in description
+            ):
+                description += "\nThis function has to run single-threaded."
+
+            self.function_description.setText(description)
+
+            # Change the description color to make it more prominent
+            self.function_description.setStyleSheet(
+                "QLabel { color: #ff6b00; font-weight: bold; }"
+            )
+        else:
+            # Re-enable threading controls for normal functions
+            self.thread_count.setEnabled(True)
+            self.thread_count.setToolTip(
+                "Number of threads to use for parallel processing"
+            )
+            self.function_description.setStyleSheet("")  # Reset styling
+            self.function_description.setText(description)
+
+        # Get parameters
         parameters = function_info.get("parameters", {})
 
         # Remove old parameters widget if it exists
@@ -1014,6 +1078,23 @@ class FileResultsWidget(QWidget):
         self.batch_button.setEnabled(False)
         self.cancel_button.setEnabled(True)
 
+        # Set thread count based on function properties
+        worker_thread_count = self.thread_count.value()
+
+        # Check if function should run single-threaded
+        if (
+            hasattr(processing_func, "thread_safe")
+            and not processing_func.thread_safe
+        ):
+            worker_thread_count = 1
+            self.viewer.status = (
+                "Processing with a single thread (function is not thread-safe)"
+            )
+        else:
+            self.viewer.status = (
+                f"Processing with {worker_thread_count} threads"
+            )
+
         # Create and start the worker thread
         self.worker = ProcessingWorker(
             self.file_list,
@@ -1024,8 +1105,8 @@ class FileResultsWidget(QWidget):
             output_suffix,
         )
 
-        # Set the thread count from the UI
-        self.worker.thread_count = self.thread_count.value()
+        # Set the thread count from the UI or function attribute
+        self.worker.thread_count = worker_thread_count
 
         # Connect signals
         self.worker.progress_updated.connect(self.update_progress)
@@ -1037,7 +1118,7 @@ class FileResultsWidget(QWidget):
         self.worker.start()
 
         # Update status
-        self.viewer.status = f"Processing {len(self.file_list)} files with {selected_function_name} using {self.thread_count.value()} threads"
+        self.viewer.status = f"Processing {len(self.file_list)} files with {selected_function_name} using {worker_thread_count} threads"
 
     def update_progress(self, value):
         """Update the progress bar"""

napari_tmidas/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.0'
-__version_tuple__ = version_tuple = (0, 2, 0)
+__version__ = version = '0.2.1'
+__version_tuple__ = version_tuple = (0, 2, 1)