Merge branch 'master' into 60-v4-1-0-subject-matter-expert-review

.gitignore

@@ -117,3 +117,5 @@ MATLAB/
 
 # FluEgg results
 results/
+
+error_log.txt

app.py

+import os
 import sys
-from PyQt5.QtWidgets import QApplication
+import traceback
+import logging
+
+from PyQt5.QtWidgets import QApplication, QMessageBox
+from PyQt5.QtCore import Qt
 
 import fluegg
+import fluegggui
 from fluegggui.gui import AppWindow
 
+
 if __name__ == '__main__':
-    # Initialize the UI
-    fluegg.set_logging_level('critical')
-    app = QApplication(sys.argv)
-    w = AppWindow()
-    w.show()
-    sys.exit(app.exec_())
+
+    class FluEggApp:
+
+        def __init__(self):
+
+            log_filename = os.path.join(os.getcwd(), 'error_log.txt')
+
+            formatter = logging.Formatter(
+                '%(asctime)s - %(message)s')
+
+            fh = logging.FileHandler(log_filename, delay=True)
+            fh.setLevel(logging.ERROR)
+            fh.setFormatter(formatter)
+
+            fluegggui.logger.addHandler(fh)
+
+            fluegg.set_logging_level('error')
+            fluegggui.set_logging_level('error')
+
+            sys.excepthook = self.excepthook
+
+            self._app = None
+            self._w = None
+            self._log_file = log_filename
+
+        def excepthook(self, etype, evalue, tb):
+
+            fluegggui.logger.error('Unhandled error occurred')
+
+            for line in traceback.format_exception(etype, evalue, tb):
+                fluegggui.logger.error(line.strip())
+
+            QMessageBox.warning(
+                self._w, 'Unhandled Exception',
+                'An unhandled exception occurred.\n\n' +
+                'See the file\n{}\n'.format(self._log_file) +
+                'for more information.')
+
+        def run_app(self):
+
+            self._app = QApplication(sys.argv)
+            self._w = AppWindow()
+            self._w.show()
+            return self._app.exec_()
+
+    fluegg_app = FluEggApp()
+    app_exit_code = fluegg_app.run_app()
+
+    sys.exit(app_exit_code)