drag+drop support

changelog.md

@@ -1,11 +1,14 @@
 # Version 1.7.1
 
 - Added support for Plugins! Plugins can be downloaded from the official repository or from custom ones. Support for creating a plugin can be found on the wiki
+- Files and folders can now be dragged and dropped into the loaded files area to be loaded instead of relying on the file menu
+- Fixed an issue where shadow snirf files would attempt to be loaded by the application. Fixes [Issue 92](https://git.research.dezeeuw.ca/tyler/flares/issues/92)
 - Fixed an issue where the application could not automatically update between versions 1.5.1 to 1.7.1. Sorry! 1.7.1 upgrading onward should be fixed and more robust
 - Fixed an issue where some log files would not generate, or would generate in an incorrect location
 - Fixed an issue where updating events in a snirf file would not release memory properly
 - Fixed an issue where loading multiple files in quick succession could cause some of the files to never finish loading
 - Fixed an issue where loading a saved project, pushing clear, and re-opening snirf files would cause them to appear incorrectly in the loaded files area
+- Fixed a crucial bug where short channels were still being sent to the donor pool to assist in interpolating long channels from. Fixes [Issue 80](https://git.research.dezeeuw.ca/tyler/flares/issues/80)
 
 
 # Version 1.7.0

flares.py

@@ -1115,10 +1115,10 @@ def interpolate_fNIRS_bads_weighted_average(raw, max_dist=0.03, min_neighbors=2,
         is_bad = (hbo_ch in raw.info['bads']) or (hbr_ch in raw.info['bads'])
         is_short = pair_distances[i] < short_channels_threshold
 
-        if is_bad:
+        if is_short:
-            bad_pairs.append(i)
-        elif is_short:
             n_short_excluded += 1
+        elif is_bad:
+            bad_pairs.append(i)
         else:
             good_pairs.append(i)
  
@@ -1182,7 +1182,7 @@ def interpolate_fNIRS_bads_weighted_average(raw, max_dist=0.03, min_neighbors=2,
                                      constrained_layout=True)
     if n_bad == 1: axes = [axes] # Handle single subplot case
     
-    axes_flat = np.asarray(axes).get_data().flatten() if hasattr(axes, 'get_data') else np.asarray(axes).ravel()
+    axes_flat = np.asarray(axes).ravel()
     for j in range(n_bad, len(axes_flat)):
         if j >= n_bad:
             axes_flat[j].axis('off')
@@ -1222,9 +1222,6 @@ def interpolate_fNIRS_bads_weighted_average(raw, max_dist=0.03, min_neighbors=2,
     print("Bads cleared:", raw.info['bads'])
     raw.info['bads'] = []
 
-    for ch in raw.info['bads']:
-        print(f"Channel {ch} still marked as bad.")
-
     fig_raw_after = raw.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="After interpolation", show=False)
 
     return raw, fig_raw_after, fig_compare

main.py

@@ -22,6 +22,10 @@ from datetime import datetime
 from functools import partial
 from multiprocessing import Process, current_process, freeze_support, Queue, set_start_method
 
+# Fix for plotting on linux
+if sys.platform.startswith("linux"):
+    os.environ["QT_QPA_PLATFORM"] = "xcb"
+
 # External library imports
 import psutil
 
@@ -535,6 +539,49 @@ class ThemeChangeWatcher(QObject):
         self.main_window.update_theme()
 
 
+class DropScrollArea(QScrollArea):
+    """QScrollArea that accepts .snirf file and folder drops."""
+    
+    def __init__(self, on_files_dropped_callback, parent=None):
+        super().__init__(parent)
+        self.on_files_dropped_callback = on_files_dropped_callback
+        self.setAcceptDrops(True)
+        # ScrollAreas require setting acceptDrops on their viewport as well
+        self.viewport().setAcceptDrops(True)
+
+    def dragEnterEvent(self, event) -> None:
+        if event.mimeData().hasUrls():
+            event.acceptProposedAction()
+        else:
+            event.ignore()
+
+    def dropEvent(self, event) -> None:
+        if not event.mimeData().hasUrls():
+            return
+
+        dropped_paths = [
+            url.toLocalFile() for url in event.mimeData().urls() if url.isLocalFile()
+        ]
+
+        files_to_load = []
+        for path_str in dropped_paths:
+            p = Path(path_str)
+            if p.is_file() and p.suffix.lower() == ".snirf":
+                files_to_load.append(os.path.normpath(str(p)))
+            elif p.is_dir():
+                files_to_load.extend(
+                    os.path.normpath(str(f)) for f in p.rglob("*.snirf")
+                )
+
+        if files_to_load:
+            self.on_files_dropped_callback(files_to_load)
+        else:
+            QMessageBox.information(
+                self,
+                "No Valid Files",
+                "None of the dropped items were .snirf files or directories containing .snirf files.",
+            )
+
 class MainApplication(QMainWindow):
     """
     Main application window that creates and sets up the UI.
@@ -715,7 +762,9 @@ class MainApplication(QMainWindow):
         self.bubble_layout = QGridLayout(self.bubble_container)
         self.bubble_layout.setAlignment(Qt.AlignmentFlag.AlignTop)
 
-        self.scroll_area = QScrollArea()
+        self.scroll_area = DropScrollArea(
+            on_files_dropped_callback=self.project_manager.load_dropped_files
+        )
         self.scroll_area.setWidgetResizable(True)
         self.scroll_area.setWidget(self.bubble_container)
         self.scroll_area.setMinimumHeight(200)

project_manager.py

@@ -108,21 +108,116 @@ class ProjectManager:
     # =========================================================================
     # File & Folder Opening Dialogs
     # =========================================================================
+
+    def is_valid_snirf(self, path: str) -> bool:
+        """Fast header check to verify HDF5/SNIRF signature and ignore corrupt/shadow files."""
+        try:
+            if os.path.getsize(path) < 8:
+                return False
+            with open(path, "rb") as f:
+                return f.read(8) == b"\x89HDF\r\n\x1a\n"
+        except Exception:
+            return False
+        
     def open_file_dialog(self) -> None:
         """Opens dialog to pick a single .snirf file."""
         file_path, _ = QFileDialog.getOpenFileName(
             self.app, "Open File", "", "SNIRF Files (*.snirf);;All Files (*)"
         )
-        if file_path:
+        if not file_path:
-            self._load_files_into_pipeline([os.path.normpath(file_path)])
+            return
+
+        norm_path = os.path.normpath(file_path)
+        filename = os.path.basename(norm_path)
+
+        # 1. Check specifically for macOS shadow files
+        if filename.startswith("._"):
+            QMessageBox.warning(
+                self.app,
+                "Invalid SNIRF File",
+                f"'{filename}' is a macOS system shadow file (Apple Double resource fork), not a actual data file."
+            )
+            return
+
+        # 2. Check for general header validity / corruption
+        if not self.is_valid_snirf(norm_path):
+            QMessageBox.warning(
+                self.app,
+                "Invalid SNIRF File",
+                f"'{filename}' is not a valid SNIRF file or has a corrupted header."
+            )
+            return
+
+        self._load_files_into_pipeline([norm_path])
 
     def open_folder_dialog(self)-> None:
         """Recursively finds all .snirf files in a selected directory."""
         folder_path = QFileDialog.getExistingDirectory(self.app, "Select Folder", "")
-        if folder_path:
+        if not folder_path:
-            snirf_files = [os.path.normpath(str(f)) for f in Path(folder_path).rglob("*.snirf")]
+            return
-            self._load_files_into_pipeline(snirf_files)
 
+        # Automatically filter out shadow files and invalid headers in batch mode
+        snirf_files = [
+            os.path.normpath(str(f))
+            for f in Path(folder_path).rglob("*.snirf")
+            if self.is_valid_snirf(str(f))
+        ]
+
+        if not snirf_files:
+            QMessageBox.information(
+                self.app,
+                "No Valid Files",
+                "No valid .snirf files were found in the selected directory."
+            )
+            return
+
+    def load_dropped_files(self, file_paths: List[str]) -> None:
+        """Public entry point for handling files or folders dropped onto the UI."""
+        if not file_paths:
+            return
+
+        # 1. Single file drop: Give explicit feedback like open_file_dialog
+        if len(file_paths) == 1:
+            norm_path = os.path.normpath(file_paths[0])
+            filename = os.path.basename(norm_path)
+
+            if filename.startswith("._"):
+                QMessageBox.warning(
+                    self.app,
+                    "Invalid SNIRF File",
+                    f"'{filename}' is a macOS system shadow file (Apple Double resource fork), not an actual data file."
+                )
+                return
+
+            if not self.is_valid_snirf(norm_path):
+                QMessageBox.warning(
+                    self.app,
+                    "Invalid SNIRF File",
+                    f"'{filename}' is not a valid SNIRF file or has a corrupted header."
+                )
+                return
+
+            valid_files = [norm_path]
+
+        # 2. Batch drop: Silently filter out shadow/corrupt files like open_folder_dialog
+        else:
+            valid_files = [
+                os.path.normpath(p)
+                for p in file_paths
+                if self.is_valid_snirf(os.path.normpath(p))
+            ]
+
+            if not valid_files:
+                QMessageBox.information(
+                    self.app,
+                    "No Valid Files",
+                    "None of the dropped items were valid .snirf files."
+                )
+                return
+
+        # Delegate to internal pipeline
+        self._load_files_into_pipeline(valid_files)
+        
     def _load_files_into_pipeline(self, file_paths: List[str]) -> None:
         """Loads .snirf files into UI using chunked batches and background workers."""
         app = self.app
@@ -146,8 +241,11 @@ class ProjectManager:
         if not hasattr(app, "metadata_cache"):
             app.metadata_cache = {}
 
-        # Filter out files already in the UI to avoid duplicates
+        # Filter out duplicates AND non-SNIRF files (including macOS ._ shadow files)
-        new_files = [p for p in file_paths if p not in app.selected_paths]
+        new_files = [
+            p for p in file_paths 
+            if p not in app.selected_paths and self.is_valid_snirf(p)
+        ]
         if not new_files:
             return