preferences

changelog.md

@@ -19,6 +19,9 @@
 - Fixed an issue where the dropdowns in the Viewer windows would immediately open and close when using a trackpad
 - glover and spm hrf models now function as intended without crashing. Currently, group analysis is still only supported by fir
 - Revamped the fold channels viewer to not hang the application and to better process multiple participants at once
+- Added a Preferences menu to the navigation bar
+- Currently, there is only one preference allowing to bypass the warning of 2D data
+- Fixed [Issue 8](https://git.research.dezeeuw.ca/tyler/flares/issues/8), [Issue 9](https://git.research.dezeeuw.ca/tyler/flares/issues/9), [Issue 30](https://git.research.dezeeuw.ca/tyler/flares/issues/30), [Issue 31](https://git.research.dezeeuw.ca/tyler/flares/issues/31), [Issue 34](https://git.research.dezeeuw.ca/tyler/flares/issues/34), [Issue 36](https://git.research.dezeeuw.ca/tyler/flares/issues/36)
 
 
 # Version 1.1.7

main.py

@@ -188,11 +188,11 @@ SECTIONS = [
             {"name": "RESAMPLE_FREQ", "default": 1, "type": int, "help": "The frequency the data should be resampled to."},
             
             {"name": "HRF_MODEL", "default": ["fir"], "type": list, "options": ["fir", "glover", "spm", "spm + derivative", "spm + derivative + dispersion", "glover + derivative", "glover + derivative + dispersion"], "exclusive": True, "help": "Specifies the hemodynamic response function."},
-            {"name": "STIM_DUR", "default": 0.5, "type": float, "help": "The length of your stimulus."},
+            {"name": "STIM_DUR", "default": 0.5, "type": float, "help": "The length of your stimulus. If your HRF_MODEL is fir, this dictates how wide a bin should be."},
-            {"name": "DRIFT_MODEL", "default": "cosine", "type": str, "help": "Specifies the desired drift model."},
+            {"name": "DRIFT_MODEL", "default": ["cosine"], "type": list, "options": ["cosine", "polynomial"], "help": "Specifies the desired drift model."},
             {"name": "HIGH_PASS", "default": 0.01, "type": float, "help": "High-pass frequency in case of a cosine model (in Hz)."},
             {"name": "DRIFT_ORDER", "default": 1, "type": int, "help": "Order of the drift model (in case it is polynomial)"},
-            {"name": "FIR_DELAYS", "default": "None", "type": range, "help": "In case of FIR design, yields the array of delays used in the FIR model (in scans)."},
+            {"name": "FIR_DELAYS", "default": "None", "type": range, "depends_on": "HRF_MODEL", "depends_value": "fir", "help": "In case of FIR design, yields the array of delays used in the FIR model (in scans)."},
             {"name": "MIN_ONSET", "default": -24, "type": int, "help": "Minimal onset relative to frame times (in seconds)"},
             {"name": "OVERSAMPLING", "default": 50, "type": int, "help": "Oversampling factor used in temporal convolutions."},
             {"name": "REMOVE_EVENTS", "default": "None", "type": list, "help": "Remove events matching the names provided before generating the Design Matrix"},
@@ -4342,6 +4342,7 @@ class MainApplication(QMainWindow):
         self.folder_paths = []
         self.section_widget = None
         self.first_run = True
+        self.is_2d_bypass = False
         
         self.files_total = 0        # total number of files to process
         self.files_done = set()     # set of file paths done (success or fail)
@@ -4590,6 +4591,13 @@ class MainApplication(QMainWindow):
             if i == 1 or i == 3:  # after the first 2 actions (0,1)
                 options_menu.addSeparator()
 
+        preferences_menu = menu_bar.addMenu("Preferences")
+        preferences_actions = [
+            ("2D Data Bypass", "Ctrl+B", self.is_2d_bypass_func, resource_path("icons/info_24dp_1F1F1F.svg"))
+        ]
+        for name, shortcut, slot, icon in preferences_actions:
+            preferences_menu.addAction(make_action(name, shortcut, slot, icon=icon, checkable=True, checked=False))
+
         terminal_menu = menu_bar.addMenu("Terminal")
         terminal_actions = [
             ("New Terminal", "Ctrl+Alt+T", self.terminal_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
@@ -4670,6 +4678,8 @@ class MainApplication(QMainWindow):
         self.top_left_widget.paste()  # Trigger paste
         self.statusbar.showMessage("Pasted from clipboard")  # Show status message
 
+    def is_2d_bypass_func(self, checked):
+        self.is_2d_bypass = checked
 
     def about_window(self):
         if self.about is None or not self.about.isVisible():
@@ -5290,13 +5300,14 @@ class MainApplication(QMainWindow):
             )
 
             if is_2d:
-                QMessageBox.critical(None, "Error - 2D Data Detected - FLARES", f"Error: 2 dimensional data was found in {i}. "
+                if self.is_2d_bypass == False:
-                                     "It is not possible to process this file. Please update the coordinates "
+                    QMessageBox.critical(None, "Error - 2D Data Detected - FLARES", f"Error: 2 dimensional data was found in {i}. "
-                                     "using the 'Update optodes in snirf file...' option from the Options menu or by pressing 'F6'.")
+                                        "Please update the coordinates using the 'Update optodes in snirf file...' option from the Options menu or by pressing 'F6'. "
-                self.button1.clicked.disconnect(self.cancel_task)
+                                        "You may also select the '2D Data Bypass' option from the Preferences menu to ignore this warning and process anyway. ")
-                self.button1.setText("Process")
+                    self.button1.clicked.disconnect(self.cancel_task)
-                self.button1.clicked.connect(self.on_run_task)
+                    self.button1.setText("Process")
-                return
+                    self.button1.clicked.connect(self.on_run_task)
+                    return
             
         self.files_total = len(snirf_files)
         self.files_done = set()