preparation for 1.5.1

2026-07-17 23:59:42 -07:00
parent 0680718398
commit 2b019c1bc0
11 changed files with 350 additions and 59 deletions
@@ -1,3 +1,39 @@
+# Version 1.5.1
+
+- Open a folder is now minimally BIDS compatible. It will recursively go through all folders, but not load external metadata
+- Renamed options in the Viewer Launcher window to better denote what actions they can perform
+- 2 new analysis options have been added in the viewer launcher window: Inter-Group Stats and Cross-Group Stats
+- Each of these analysis options have lots of text explaining what they do when their respective windows are opened
+- The parameter input dialog in the analysis windows will now be able to scroll down when lots of parameters are required
+- When a project is saved, it automatically will populate into the Recent Projects menu. Fixes [Issue 86](https://git.research.dezeeuw.ca/tyler/flares/issues/86)
+- The description when clicking "Why are these useful?" underneath the per-file parameters is no longer placeholder text. Fixes [Issue 85](https://git.research.dezeeuw.ca/tyler/flares/issues/85)
+- Added a new parameter section "Region of Interest". It has one parameter of "JSON_LOCATION", a json file containing Region of Interest data
+- Temporarily removed the parameter REMOVE_EVENTS due to its functionality being removed because of a memory leak
+- Fixed participant metadata remaing in the background when the participant was removed. Fixes [Issue 82](https://git.research.dezeeuw.ca/tyler/flares/issues/82)
+- Fixed processing remaining active hidden in the background when the "Clear" button was pushed. Fixes [Issue 81](https://git.research.dezeeuw.ca/tyler/flares/issues/81)
+- Now when "Clear" is pushed while data is processing, a popup will appear ensuring that the user understands that pushing "Clear" will stop processing
+- Reset to Default Configuration will now properly reset all of the parameters to their default values. [Issue 90](https://git.research.dezeeuw.ca/tyler/flares/issues/90)
+- A confirmation popup will now display once the application has been reset to default in addition to the status bar message
+- Changed the improper display text of "Cross Validation" to now properly read as "Coefficient of Variation"
+- Changed the parameters "CV" and "CV_THRESHOLD" to now be "COEFF_VAR and COEFF_VAR_THRESHOLD"
+- Changed the improper display text of "Mean Absolute Deviation" to now properly read as "Median Absolute Deviation"
+- Changed the parameters "SHORT_CHANNEL", "SHORT_CHANNEL_THRESH", and "LONG_CHANNEL_THRESH" to now be "SHORT_CHANNELS", "SHORT_CHANNELS_THRESHOLD", and "LONG_CHANNELS_THRESHOLD"
+- Changed the parameter section "Channel Variance" to now be "Sensor Dropout" to better reflect the action it performs, not the method employed to calculate it
+- Changed the parameters "CHANNEL_VAR" and "CHANNEL_THRESH" to now be "SENSOR_DROPOUT" and "SENSOR_DROPOUT_VARIANCE_THRESHOLD"
+- Changed the messaged displayed when the application crashes to better reflect what occured
+- Changed the processing stages 25-27 and updates their messages to better reflect their actions that they now perforn
+- Changed stage 25 from "Generate Channel Significance" to "Generate Channel Results"
+- Changed stage 26 from "Generate Channel, Region of Interest, and Contrast Results" to "Generate Region of Interest Results"
+- Changed stage 27 from "Compute Contrast Results" to "Generate Contrast Results"
+- Changed backend code to only load required methods and not load all methods every time
+- Fixed string parameters not going blue and bold when their value was different than default
+- Fixed all parameters not going blue and bold when a save file is loaded containing values that differ from default
+- Fixed a crucial bug where short channels were not being processed and filtered the same way as long channels before being used as regressors
+- Fixed a crucial bug where short channels were being presented to the design matrix as normal long channels
+- Fixed a crucial bug where long channels could be interpolated from short channels. Short channels are still potentially interpolated from long channels. See [this link](https://git.research.dezeeuw.ca/tyler/flares/issues/80) for more information regarding this issue.
+- Added a welcome message when the terminal is opened, resized the terminal, and added more commands
+
+
 # Version 1.5.0

 - This release introduces a new configuration file that may break existing installs. If your application does not update correctly, please download fresh from [this link.](https://git.research.dezeeuw.ca/tyler/flares/releases/)
@@ -1,3 +1,39 @@
+# Version 1.5.1
+
+- Open a folder is now minimally BIDS compatible. It will recursively go through all folders, but not load external metadata
+- Renamed options in the Viewer Launcher window to better denote what actions they can perform
+- 2 new analysis options have been added in the viewer launcher window: Inter-Group Stats and Cross-Group Stats
+- Each of these analysis options have lots of text explaining what they do when their respective windows are opened
+- The parameter input dialog in the analysis windows will now be able to scroll down when lots of parameters are required
+- When a project is saved, it automatically will populate into the Recent Projects menu. Fixes [Issue 86](https://git.research.dezeeuw.ca/tyler/flares/issues/86)
+- The description when clicking "Why are these useful?" underneath the per-file parameters is no longer placeholder text. Fixes [Issue 85](https://git.research.dezeeuw.ca/tyler/flares/issues/85)
+- Added a new parameter section "Region of Interest". It has one parameter of "JSON_LOCATION", a json file containing Region of Interest data
+- Temporarily removed the parameter REMOVE_EVENTS due to its functionality being removed because of a memory leak
+- Fixed participant metadata remaing in the background when the participant was removed. Fixes [Issue 82](https://git.research.dezeeuw.ca/tyler/flares/issues/82)
+- Fixed processing remaining active hidden in the background when the "Clear" button was pushed. Fixes [Issue 81](https://git.research.dezeeuw.ca/tyler/flares/issues/81)
+- Now when "Clear" is pushed while data is processing, a popup will appear ensuring that the user understands that pushing "Clear" will stop processing
+- Reset to Default Configuration will now properly reset all of the parameters to their default values. [Issue 90](https://git.research.dezeeuw.ca/tyler/flares/issues/90)
+- A confirmation popup will now display once the application has been reset to default in addition to the status bar message
+- Changed the improper display text of "Cross Validation" to now properly read as "Coefficient of Variation"
+- Changed the parameters "CV" and "CV_THRESHOLD" to now be "COEFF_VAR and COEFF_VAR_THRESHOLD"
+- Changed the improper display text of "Mean Absolute Deviation" to now properly read as "Median Absolute Deviation"
+- Changed the parameters "SHORT_CHANNEL", "SHORT_CHANNEL_THRESH", and "LONG_CHANNEL_THRESH" to now be "SHORT_CHANNELS", "SHORT_CHANNELS_THRESHOLD", and "LONG_CHANNELS_THRESHOLD"
+- Changed the parameter section "Channel Variance" to now be "Sensor Dropout" to better reflect the action it performs, not the method employed to calculate it
+- Changed the parameters "CHANNEL_VAR" and "CHANNEL_THRESH" to now be "SENSOR_DROPOUT" and "SENSOR_DROPOUT_VARIANCE_THRESHOLD"
+- Changed the messaged displayed when the application crashes to better reflect what occured
+- Changed the processing stages 25-27 and updates their messages to better reflect their actions that they now perforn
+- Changed stage 25 from "Generate Channel Significance" to "Generate Channel Results"
+- Changed stage 26 from "Generate Channel, Region of Interest, and Contrast Results" to "Generate Region of Interest Results"
+- Changed stage 27 from "Compute Contrast Results" to "Generate Contrast Results"
+- Changed backend code to only load required methods and not load all methods every time
+- Fixed string parameters not going blue and bold when their value was different than default
+- Fixed all parameters not going blue and bold when a save file is loaded containing values that differ from default
+- Fixed a crucial bug where short channels were not being processed and filtered the same way as long channels before being used as regressors
+- Fixed a crucial bug where short channels were being presented to the design matrix as normal long channels
+- Fixed a crucial bug where long channels could be interpolated from short channels. Short channels are still potentially interpolated from long channels. See [this link](https://git.research.dezeeuw.ca/tyler/flares/issues/80) for more information regarding this issue.
+- Added a welcome message when the terminal is opened, resized the terminal, and added more commands
+
+
 # Version 1.5.0

 - This release introduces a new configuration file that may break existing installs. If your application does not update correctly, please download fresh from [this link.](https://git.research.dezeeuw.ca/tyler/flares/releases/)
@@ -967,19 +967,29 @@ def interpolate_fNIRS_bads_weighted_average(raw, max_dist=0.03, min_neighbors=2)
        if hbo_names[i] != hbr_names[i]:
            raise RuntimeError(f"Channel pairs do not match: {hbo_names[i]} vs {hbr_names[i]}")

+    all_distances = source_detector_distances(raw.info)
+    pair_distances = all_distances[hbo_picks]
+
    # Identify bad pairs if either channel in pair is bad
    bad_pairs = []
    good_pairs = []
+    n_short_excluded = 0
    for i, base in enumerate(hbo_names):
        hbo_ch = raw.ch_names[hbo_picks[i]]
        hbr_ch = raw.ch_names[hbr_picks[i]]
-        if (hbo_ch in raw.info['bads']) or (hbr_ch in raw.info['bads']):
+        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:
            bad_pairs.append(i)
+        elif is_short:
+            n_short_excluded += 1
        else:
            good_pairs.append(i)
-
+ 
    print(f"Total pairs: {len(hbo_names)}")
-    print(f"Good pairs: {len(good_pairs)}")
+    print(f"Good LONG pairs (eligible donors): {len(good_pairs)}")
+    print(f"Good SHORT pairs (excluded from donor pool): {n_short_excluded}")
    print(f"Bad pairs to interpolate: {len(bad_pairs)}")

    if len(bad_pairs) == 0:
@@ -1488,8 +1498,9 @@ def epochs_calculations(raw_haemo, events, event_dict):

 def make_design_matrix(raw_haemo):

-    events_to_remove = REMOVE_EVENTS
-        
+    # events_to_remove = REMOVE_EVENTS
+    events_to_remove = ""
+
    filtered_annotations = [ann for ann in raw_haemo.annotations if ann['description'] not in events_to_remove]
    
    new_annot = Annotations(
@@ -2742,7 +2753,7 @@ def load_snirf(file_path: str) -> tuple[BaseRaw, Figure]:
    
    # Read the snirf file
    raw = read_raw_snirf(file_path, preload=True, verbose=VERBOSITY) # type: ignore
-    raw.load_data(verbose=VERBOSITY) # type: ignore
+    #raw.load_data(verbose=VERBOSITY) # type: ignore  redundant since preload is set to true

    # TODO: Why was this commented again?
    # Maybe this should be a bypass parameter?
@@ -3217,7 +3228,6 @@ def run_cross_group_second_level_analysis(df_roi_all, file_paths_a, file_paths_b
    ax.set_xlabel('Region of Interest (ROI)', fontsize=12)
    ax.set_title(f"Cross-Group Comparison: {group_a_name} vs {group_b_name}\n({target_chroma.upper()} - {selected_event})", fontsize=13, fontweight='bold', pad=15)
    plt.tight_layout()
-    plt.show()

    # 4. Channel-by-Channel Group-Contrast Topography Map (Zero Hardcoding)
    if df_cha_all is not None and raw_haemo is not None:
@@ -3231,7 +3241,7 @@ def run_cross_group_second_level_analysis(df_roi_all, file_paths_a, file_paths_b
                (df_cha_all['Chroma'] == target_chroma) & 
                (df_cha_all['Condition'] == selected_event)
            ].copy()
-            con_summary['clean_ID'] = con_summary['ID'].apply(clean_subject_id)
+            con_summary['clean_ID'] = con_summary['ID']
            
            raw_picked = raw_haemo.copy().pick(picks=target_chroma)
            
@@ -3254,7 +3264,8 @@ def run_cross_group_second_level_analysis(df_roi_all, file_paths_a, file_paths_b
                    'ch_name': ch,
                    'Coef.': mean_diff,  # Represents Mean A - Mean B
                    't': t_stat,
-                    'P>|t|': p_val       # For threshold masking
+                    'P>|t|': p_val,
+                    'Chroma': target_chroma,        # For threshold masking
                })
                
            con_model_df = pd.DataFrame(contrast_data)
@@ -5401,6 +5412,8 @@ def process_participant(file_path, progress_callback=None):
        if k in globals() and k != "REQUIRED_KEYS"
    }

+    print(config_dict)
+
    # Step 1: Preprocessing
    raw = load_snirf(file_path)
    fig_raw = raw.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="Loaded Raw", show=False)
@@ -5417,7 +5430,7 @@ def process_participant(file_path, progress_callback=None):

    # Step 3: Verify Optode Placement
    if OPTODE_PLACEMENT:
-        fig_optodes = raw.plot_sensors(show_names=SHOW_OPTODE_NAMES, to_sphere=True, show=False) # type: ignore
+        fig_optodes = raw.plot_sensors(show_names=SHOW_OPTODE_NAMES, to_sphere=True, show=False, verbose=VERBOSITY) # type: ignore
        fig_individual["Plot Sensors"] = fig_optodes
    if progress_callback: progress_callback(3)
    logger.info("Step 3 Completed.")
@@ -5426,7 +5439,7 @@ def process_participant(file_path, progress_callback=None):
    if SHORT_CHANNELS and not FOLDING_BYP:
        #NOTE: Have to split again later but since needed for heart rate, this will stay at step 4. Will split later again.
        _short_chans = get_short_channels(raw, max_dist=SHORT_CHANNELS_THRESHOLD) # JUST FOR PLOTTING THEM SEPERATELY
-        fig_short_chans = _short_chans.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="Short Channels Only", show=False)
+        fig_short_chans = _short_chans.plot(duration=raw.times[-1], n_channels=raw.info['nchan'], title="Short Channels Only", show=False, verbose=VERBOSITY)
        fig_individual["Short Channels Raw Data"] = fig_short_chans
    raw = get_long_channels(raw, min_dist=0, max_dist=LONG_CHANNELS_THRESHOLD)
    if progress_callback: progress_callback(4)
@@ -43,7 +43,7 @@ from src.window.updateoptodes import UpdateOptodesWindow
 from src.window.userguide import UserGuideWindow
 from src.window.viewerlauncher import ViewerLauncherWidget
 from src.window.welcome import WelcomeDialog
-from src.shared.flaresbasewidget import ParamSection
+from src.shared.flaresbasewidget import FilePickerWidget, ParamSection
 from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PIPELINE_STAGES, PLATFORM_NAME
 from updater import finish_update_if_needed, UpdateManager, LocalPendingUpdateCheckThread

@@ -91,7 +91,7 @@ SECTIONS = [
        "title": "Trimming",
        "params": [
            {"name": "TRIM", "default": True, "type": bool, "help": "Should the start of the files be trimmed?"},
-            {"name": "SECONDS_TO_KEEP", "default": 5, "type": float, "depends_on": "TRIM", "help": "Seconds to keep at the beginning of all loaded snirf files before the first annotation/event occurs. Calculation is done seperatly on all loaded snirf files. Setting this to 0 will have the first annotation/event be at time point 0. Only used if TRIM is set to True."},
+            {"name": "SECONDS_TO_KEEP", "default": 5.0, "type": float, "depends_on": "TRIM", "help": "Seconds to keep at the beginning of all loaded snirf files before the first annotation/event occurs. Calculation is done seperatly on all loaded snirf files. Setting this to 0 will have the first annotation/event be at time point 0. Only used if TRIM is set to True."},
        ]
    },
    {
@@ -257,7 +257,8 @@ SECTIONS = [
            {"name": "FIR_DELAYS", "default": 15, "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"},
+            # TODO: Re-implement this without causing a memory leak
+            # {"name": "REMOVE_EVENTS", "default": "None", "type": list, "help": "Remove events matching the names provided before generating the Design Matrix"},
            {"name": "SHORT_CHANNEL_REGRESSION", "default": True, "type": bool, "depends_on": "SHORT_CHANNEL", "help": "Should short channel regression be used to create the design matrix? This will use the 'signal' from the short channel and regress it out of all other channels."},
        ]
    },
@@ -272,7 +273,7 @@ SECTIONS = [
    {
        "title": "Region of Interest",
        "params": [
-            {"name": "JSON_LOCATION", "default": "", "type": str, "help": "Location of the JSON file containing region of interest results for significance calculations."},
+            {"name": "JSON_LOCATION", "default": "", "type": "json_file", "help": "Location of the JSON file containing region of interest results for significance calculations."},
        ]
    },
    {
@@ -505,7 +506,7 @@ class MainApplication(QMainWindow):
        self.missing_events_bypass = False
        self.analysis_clearing_bypass = False
        self.folding_bypass = False
-        self.json_location = r"C:\Users\tyler\Desktop\research\flares\regions.json"
+        self.json_location = ""


        # Initialization to ensure that saving can occur
@@ -525,15 +526,13 @@ class MainApplication(QMainWindow):
        self.files_failed = set()   # set of failed file paths
        self.files_results = {}     # dict for successful results (if needed)

-        self.platform_suffix = "-" + PLATFORM_NAME
-
        self.updater = UpdateManager(
            main_window=self,
            api_url=API_URL,
            api_url_sec=API_URL_SECONDARY,
            current_version=CURRENT_VERSION,
            platform_name=PLATFORM_NAME,
-            platform_suffix=self.platform_suffix,
+            platform_suffix="-" + PLATFORM_NAME,
            app_name=APP_NAME
        )

@@ -546,7 +545,7 @@ class MainApplication(QMainWindow):
        self.installEventFilter(self)

        # Start local pending update check thread
-        self.local_check_thread = LocalPendingUpdateCheckThread(CURRENT_VERSION, self.platform_suffix, PLATFORM_NAME, APP_NAME)
+        self.local_check_thread = LocalPendingUpdateCheckThread(CURRENT_VERSION, "-" + PLATFORM_NAME, PLATFORM_NAME, APP_NAME)
        self.local_check_thread.pending_update_found.connect(self.updater.on_pending_update_found)
        self.local_check_thread.no_pending_update.connect(self.updater.on_no_pending_update)
        self.local_check_thread.start()
@@ -617,7 +616,7 @@ class MainApplication(QMainWindow):

        label_desc = QLabel('<a href="#">Why are these useful?</a>')
        label_desc.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
-        label_desc.linkActivated.connect(lambda: QMessageBox.information(None, "Info", "Parameter Info..."))
+        label_desc.linkActivated.connect(lambda: QMessageBox.information(None, f"Info - {APP_NAME.upper()} ", "Age: Used in determing the participants PPF.\nGender: Not currently used or implemented.\nGroup: Used to split participants into groups for comparisons between them."))
        right_column_layout.addWidget(label_desc)
        right_column_layout.addStretch()
        self.right_column_widget.hide()
@@ -835,6 +834,23 @@ class MainApplication(QMainWindow):
        and resets the memory heap.
        """

+        if hasattr(self, "result_process") and self.result_process and self.result_process.is_alive():
+            msg = QMessageBox(self)
+            msg.setWindowTitle(f"Confirm Clear - {APP_NAME.upper()}")
+            msg.setText("Data processing is currently active in the background. "
+                        "Clearing now will forcefully kill all tasks and lose current progress.\n\n"
+                        "Are you sure you want to proceed?")
+            
+            msg.setStandardButtons(QMessageBox.StandardButton.Ok | QMessageBox.StandardButton.Cancel)
+            msg.setDefaultButton(QMessageBox.StandardButton.Cancel)
+
+            response = msg.exec()
+
+            if response == QMessageBox.StandardButton.Ok:
+                self.cancel_task()
+            else:
+                return
+            
        self.top_left_widget.clear()

        if hasattr(self, "last_clicked_bubble"):
@@ -898,6 +914,16 @@ class MainApplication(QMainWindow):

        self.metadata_cache = {}

+        self.file_metadata = {}
+
+        if hasattr(self, "meta_fields"):
+            for field in self.meta_fields.values():
+                field.blockSignals(True)
+                field.clear()
+                field.blockSignals(False)
+
+        self.current_file = None
+
        if hasattr(self, "selected_paths"): self.selected_paths = []
        if hasattr(self, "selected_path"): self.selected_path = None

@@ -1176,9 +1202,20 @@ class MainApplication(QMainWindow):
                file_cfg.read_string(DEFAULT_CONFIG)

            self.sync_app_with_config()
+            self.update_sections(0)
+
+            QTimer.singleShot(100, self._show_reset_success_dialog)
+            
+
+    def _show_reset_success_dialog(self):
+        """Helper method triggered after the UI has completely finished redrawing."""
+        QMessageBox.information(
+            self,
+            "Reset Successful",
+            "All application settings have been successfully restored to their default values."
+        )
+        self.statusbar.showMessage("All settings have been reset to their default values.", 5000)

-            self.statusbar.showMessage("All settings have been reset to their default values.", 5000)
-        

    def sync_app_with_config(self):
        """Reads values from file_cfg and updates both internal variables and UI checkmarks."""
@@ -1418,6 +1455,8 @@ class MainApplication(QMainWindow):

            project_data = sanitize(project_data)

+            self.add_to_recent_projects(os.path.normpath(filename))
+
            self.saving_overlay = SavingOverlay(self)
            self.saving_overlay.resize(self.size())  # Cover the main window
            self.saving_overlay.show()
@@ -1582,6 +1621,12 @@ class MainApplication(QMainWindow):
                    widget.blockSignals(False)
                    widget.update()

+                elif isinstance(widget, FilePickerWidget):
+                    widget.blockSignals(True)
+                    widget.setText(str(value))  # Updates the internal QLineEdit text safely
+                    widget.blockSignals(False)
+                    widget.update()
+
                # QComboBox (bool, list)
                elif isinstance(widget, QComboBox):
                    widget.blockSignals(True)
@@ -1599,10 +1644,19 @@ class MainApplication(QMainWindow):
                    widget.blockSignals(False)
                    widget.update()

+                if hasattr(section_widget, 'check_if_changed'):
+                    if isinstance(widget, (QLineEdit, FilePickerWidget)):
+                        section_widget.check_if_changed(name, widget.text())
+                    elif isinstance(widget, QComboBox):
+                        section_widget.check_if_changed(name, widget.currentText())
+                    elif isinstance(widget, QSpinBox):
+                        section_widget.check_if_changed(name, widget.value())
+
            # After restoring, make sure dependencies are updated
            if hasattr(section_widget, 'update_dependencies'):
                section_widget.update_dependencies()

+        #TODO: Update blue bold text too

    # def show_files_as_bubbles(self, folder_paths):

@@ -1659,7 +1713,6 @@ class MainApplication(QMainWindow):
        current_ui_config = {}
        try:
            for section in self.param_sections:
-                # This calls the get_param_values() method you shared earlier
                section_values = section.get_param_values()
                current_ui_config.update(section_values)
            return current_ui_config
@@ -1839,6 +1892,19 @@ class MainApplication(QMainWindow):
            self.top_left_widget.clear()
            self.right_column_widget.hide()

+            target_path = bubble.file_path
+
+            if hasattr(self, 'file_metadata'):
+                self.file_metadata.pop(target_path, None)
+
+            if getattr(self, 'current_file', None) == target_path:
+                self.current_file = None
+                if hasattr(self, 'meta_fields'):
+                    for field in self.meta_fields.values():
+                        field.blockSignals(True)
+                        field.clear()
+                        field.blockSignals(False)
+
            parent_layout = bubble.parent().layout()
            if parent_layout is not None:
                parent_layout.removeWidget(bubble)
@@ -2055,11 +2121,14 @@ class MainApplication(QMainWindow):
        if self.folding_bypass:
            all_params['FOLDING_BYP'] = True

+        self.json_location = all_params['JSON_LOCATION']
+
        collected_data = {
            "SNIRF_FILES": snirf_files,
            "PARAMS": all_params,  # add this line
            "METADATA": self.get_all_metadata(),  # optionally add metadata if needed
        }
+
        # Start processing
        if current_process().name == 'MainProcess':
            self.result_queue = Queue()
@@ -40,12 +40,6 @@ PARAMETERIZED_INDEXES = {
            "default": "hbo",
            "type": str,
        },
-        {
-            "key": "roi_config",
-            "label": "Location of the ROI config file",
-            "default": r"C:\Users\tyler\Desktop\research\flares\regions.json",
-            "type": str,
-        },
        {
            "key": "threshold_topo",
            "label": "threshold_topo: TBD",
@@ -81,14 +75,14 @@ PARAMETERIZED_INDEXES = {
        {
            "key": "roi_a",
            "label": "ROI A (e.g. contralateral region name from regions.json)",
-            "default": "",
-            "type": str,
+            "default": [],
+            "type": list,
        },
        {
            "key": "roi_b",
            "label": "ROI B (e.g. ipsilateral region name from regions.json)",
-            "default": "",
-            "type": str,
+            "default": [],
+            "type": list,
        }
    ],
    2: [
@@ -116,17 +110,11 @@ PARAMETERIZED_INDEXES = {
            "default": "hbo",
            "type": str,
        },
-        {
-            "key": "roi_config",
-            "label": "Location of the ROI config file",
-            "default": r"C:\Users\tyler\Desktop\research\flares\regions.json",
-            "type": str,
-        },
        {
            "key": "contrast_name",
            "label": "Name of the contrast to use",
-            "default": "",
-            "type": str,
+            "default": [],
+            "type": list,
        },
    ],
 }
@@ -148,7 +136,7 @@ DESCRIPTION = """0. Raw ROI Comparison (run_cross_group_second_level_analysis)


 class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
-    def __init__(self, haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict):
+    def __init__(self, haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, json_location):
        super().__init__("CrossGroupStats")
        self.setWindowTitle(f"Cross-Group Stats Viewer - {APP_NAME.upper()}")
        self.haemo_dict = haemo_dict
@@ -157,12 +145,13 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
        self.design_matrix_dict = design_matrix_dict
        self.contrast_results_dict = contrast_results_dict
        self.group_dict = group_dict
+        self.json_location = json_location

        self.setup_cross_group_ui(["0 (Raw ROI Comparison)", "1 (Laterality Comparison)", "2 (Contrast Comparison)",], placeholder_text=DESCRIPTION)
        

    def process_request(self):
-        request = self.get_common_request_data(PARAMETERIZED_INDEXES)
+        request = self.get_common_request_data(PARAMETERIZED_INDEXES, self.json_location, self.contrast_results_dict)
        if request is None:
            return

@@ -195,7 +184,6 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
                min_subjects = params.get("min_subjects", 3)
                correction_method = params.get("correction_method", "fdr_bh")
                target_chroma = params.get("target_chroma", "hbo")
-                roi_config = params.get("roi_config", r"C:\Users\tyler\Desktop\research\flares\regions.json")
                threshold_topo = params.get("threshold_topo", False)

                run_cross_group_second_level_analysis(
@@ -211,7 +199,7 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
                    correction_method=correction_method,
                    target_chroma=target_chroma,
                    selected_event=selected_event,
-                    roi_config=roi_config,
+                    roi_config=self.json_location,
                    threshold_topo=threshold_topo  # Shows the raw difference map (Unthresholded)
                )
            elif idx == 1:
@@ -273,11 +261,10 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
                min_subjects = params.get("min_subjects", 3)
                correction_method = params.get("correction_method", "fdr_bh")
                target_chroma = params.get("target_chroma", "hbo")
-                roi_config = params.get("roi_config", r"C:\Users\tyler\Desktop\research\flares\regions.json")
                contrast_name = params.get("contrast_name", "")
 
                if not contrast_name:
-                    print("A contrast name must be specified (e.g. '2.0_vs_3.0').")
+                    print("A contrast name must be specified.")
                    continue
 
                # Build each group's channel-level contrast dataframe
@@ -311,7 +298,7 @@ class CrossGroupStatsWidget(CrossGroupUIMixin, FlaresBaseWidget):
                    df_contrasts_a=df_contrasts_a,
                    df_contrasts_b=df_contrasts_b,
                    contrast_name=contrast_name,
-                    roi_json_path=roi_config,
+                    roi_json_path=self.json_location,
                    group_a_name=self.group_a_dropdown.currentText(),
                    group_b_name=self.group_b_dropdown.currentText(),
                    target_chroma=target_chroma,
@@ -271,7 +271,7 @@ class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
                    print("Both ROI A and ROI B must be specified.")
                    continue
                
-
+                print(min_subjects)
                run_roi_paired_contrast_analysis(
                    df_roi_all=df_group,
                    roi_pairs=(roi_a, roi_b),
@@ -290,7 +290,7 @@ class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
                min_subjects = params.get("min_subjects", 5)
                correction_method = params.get("correction_method", "fdr_bh")
                target_chroma = params.get("target_chroma", "hbo")
-                contrast_name = params.get("contrast_name", "2.0_vs_3.0")
+                contrast_name = params.get("contrast_name", "")
                weighted = params.get("weighted", True)
                graph_bounds = params.get("graph_bounds", 0.0)

@@ -239,6 +239,55 @@ class FullClickComboBox(QComboBox):
        return super().eventFilter(obj, event)


+
+from PySide6.QtWidgets import QWidget, QHBoxLayout, QLineEdit, QPushButton, QFileDialog
+from PySide6.QtCore import Signal
+
+class FilePickerWidget(QWidget):
+    # This custom signal lets our container mimic a standard QLineEdit
+    textChanged = Signal(str)
+
+    def __init__(self, default_val="", file_filter="JSON Files (*.json);;All Files (*)", parent=None):
+        super().__init__(parent)
+        
+        # Inline layout to hold line edit and button side-by-side
+        layout = QHBoxLayout(self)
+        layout.setContentsMargins(0, 0, 0, 0)
+        layout.setSpacing(5)
+        
+        self.line_edit = QLineEdit()
+        self.line_edit.setText(str(default_val))
+        self.line_edit.setPlaceholderText("Select file path...")
+        # Forward internal text updates out through our custom component signal
+        self.line_edit.textChanged.connect(self.textChanged.emit)
+        
+        self.browse_btn = QPushButton("Browse...")
+        self.browse_btn.clicked.connect(self.open_file_dialog)
+        
+        layout.addWidget(self.line_edit)
+        layout.addWidget(self.browse_btn)
+        
+        self.file_filter = file_filter
+
+    def open_file_dialog(self):
+        # Open PySide6 native file browser
+        file_path, _ = QFileDialog.getOpenFileName(
+            self, 
+            "Select Configuration File", 
+            self.line_edit.text(), 
+            self.file_filter
+        )
+        if file_path:
+            self.line_edit.setText(file_path)
+
+    # Mimic standard text getter/setter behaviors so parent systems remain unbothered
+    def text(self):
+        return self.line_edit.text()
+
+    def setText(self, text):
+        self.line_edit.setText(text)
+
+
 class ParamSection(QWidget):
    """
    A widget section that dynamically creates labeled input fields from parameter metadata.
@@ -339,9 +388,15 @@ class ParamSection(QWidget):
                else:
                    widget.setValue(15) # Default fallback
                widget.valueChanged.connect(lambda val, p=param["name"]: self.check_if_changed(p, val))
+            elif param["type"] == "json_file":
+                # Create our custom dual-element compound layout widget
+                widget = FilePickerWidget(default_val=default_val, file_filter="JSON Files (*.json)")
+                # Your existing tracking signals connect seamlessly!
+                widget.textChanged.connect(lambda val, p=param["name"]: self.check_if_changed(p, val))
            else: 
                widget = QLineEdit()
                widget.setText(str(default_val))
+                widget.textChanged.connect(lambda val, p=param["name"]: self.check_if_changed(p, val))

            if "depends_on" in param:
                self.dependencies.append({
@@ -567,6 +622,8 @@ class ParamSection(QWidget):
                    values[name] = range(widget.value())
                else:
                    values[name] = range(15) # Fallback
+            elif expected_type == "json_file":
+                values[name] = widget.text()
            else:
                raw_text = widget.text()
                try:
@@ -1236,7 +1293,7 @@ class CrossGroupUIMixin:

        return file_paths
    
-    def get_common_request_data(self, parameterized_indexes):
+    def get_common_request_data(self, parameterized_indexes, json_location=None, contrast_dfs=None):
        selected_event = self.event_dropdown.currentText()
        if selected_event == "<None Selected>":
            selected_event = None
@@ -1274,6 +1331,65 @@ class CrossGroupUIMixin:
            if idx in parameterized_indexes
        }

+        dynamic_rois = []
+        
+        # 1. Check for the JSON file and parse ROI names
+        if os.path.exists(json_location):
+            try:
+                with open(json_location, 'r', encoding='utf-8') as f:
+                    regions_data = json.load(f)
+                    
+                    # Extract "name" from each region under "regions_of_interest"
+                    regions_list = regions_data.get("regions_of_interest", [])
+                    dynamic_rois = [region["name"] for region in regions_list if "name" in region]
+                    
+            except Exception as e:
+                # Safe log if JSON is corrupted or unreadable
+                print(f"Error reading ROI configurations from {json_location}: {e}")
+                
+        # Fallback to prevent UI crashes if JSON file doesn't exist or is empty
+        if not dynamic_rois:
+            dynamic_rois = ["Option 1", "Option 2"]
+
+        dynamic_contrasts = []
+        if contrast_dfs:
+            contrast_set = set()
+            for fp in all_selected_paths:
+                # Get the contrasts dictionary associated with this file path
+                file_contrasts = contrast_dfs.get(fp, {})
+                for contrast_name in file_contrasts.keys():
+                    # If no event is selected, display all contrasts.
+                    # If an event is selected, only keep contrasts containing the event name as a substring.
+                    if selected_event is None or selected_event in contrast_name:
+                        contrast_set.add(contrast_name)
+                        
+            # Sort them cleanly for the UI
+            dynamic_contrasts = sorted(list(contrast_set))
+
+        # 2. Loop through the active parameters needing input and intercept 'roi_a' and 'roi_b'
+        for idx, params_list in indexes_needing_params.items():
+            for param_info in params_list:
+                if param_info["key"] == "roi_a":
+                    # Inject options list dynamically
+                    param_info["options"] = dynamic_rois
+                    # Default to the very first item
+                    param_info["default"] = dynamic_rois[0] if dynamic_rois else ""
+
+                elif param_info["key"] == "roi_b":
+                    # Inject the same options list
+                    param_info["options"] = dynamic_rois
+                    # Default to the first item not taken (index 1), with safety fallbacks
+                    if len(dynamic_rois) > 1:
+                        param_info["default"] = dynamic_rois[1]
+                    elif len(dynamic_rois) == 1:
+                        param_info["default"] = dynamic_rois[0]
+                    else:
+                        param_info["default"] = ""
+
+                elif param_info["key"] == "contrast_name":
+                    param_info["options"] = dynamic_contrasts
+                    param_info["default"] = dynamic_contrasts[0] if dynamic_contrasts else ""
+
        param_values = {}
        if indexes_needing_params:
            dialog = ParameterInputDialog(indexes_needing_params, parent=self)
@@ -43,9 +43,9 @@ PIPELINE_STAGES = [
    "Design Matrix",
    "General Linear Model",
    "Generate GLM Results",
-    "Generate Channel Significance",
-    "Generate Channel, Region of Interest, and Contrast Results",
-    "Compute Contrast Results",
+    "Generate Channel Results",
+    "Generate Region of Interest Results",
+    "Generate Contrast Results",
    "Finishing Up"
 ]

@@ -9,14 +9,16 @@ License: GPL-3.0
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QTextEdit, QLineEdit
 from PySide6.QtCore import Qt

-from src.shared.shareddata import APP_NAME, CURRENT_VERSION
+from src.shared.shareddata import API_URL, API_URL_SECONDARY, APP_NAME, CURRENT_VERSION, PLATFORM_NAME
+from src.window.about import AboutWindow
+from updater import LocalPendingUpdateCheckThread, UpdateManager


 class TerminalWindow(QWidget):
    def __init__(self, parent=None):
        super().__init__(parent, Qt.WindowType.Window)
        self.setWindowTitle(f"Terminal - {APP_NAME.upper()}")
-
+        self.resize(320, 180)
        self.output_area = QTextEdit()
        self.output_area.setReadOnly(True)

@@ -32,8 +34,16 @@ class TerminalWindow(QWidget):
            "hello": self.cmd_hello,
            "help": self.cmd_help,
            "version": self.cmd_version,
+            "about": self.cmd_about,
+            "update": self.cmd_update,
        }

+        self.output_area.append(f"Welcome to {APP_NAME.upper()}. You are running version {CURRENT_VERSION}.")
+        self.output_area.append("Type 'help' for a list of available commands.\n")
+
+        self.input_line.setFocus()
+
+
    def handle_command(self):
        command_text = self.input_line.text()
        self.input_line.clear()
@@ -65,4 +75,27 @@ class TerminalWindow(QWidget):
        return f"Available commands: {', '.join(self.commands.keys())}"
    
    def cmd_version(self, *args):
-        return f"{CURRENT_VERSION}"
+        return f"{APP_NAME.upper()} is running version {CURRENT_VERSION}."
+    
+    def cmd_about(self, *args):
+        self.about = AboutWindow(self)
+        self.about.show()
+
+    def cmd_update(self, *args):
+        main_win = self.parent()
+        if main_win is None:
+            return "[Error] Main window context not found."
+        
+        self.updater = UpdateManager(
+            main_window=main_win,
+            api_url=API_URL,
+            api_url_sec=API_URL_SECONDARY,
+            current_version=CURRENT_VERSION,
+            platform_name=PLATFORM_NAME,
+            platform_suffix="-" + PLATFORM_NAME,
+            app_name=APP_NAME
+        )
+        self.output_area.append("Checking for updates...")
+        
+        self.updater.manual_check_for_updates()
+        return "See status bar for update information."
@@ -37,7 +37,7 @@ class ViewerLauncherWidget(QWidget):
            ("Participant Functional Connectivity Viewer [BETA]", ParticipantFunctionalConnectivityWidget, [haemo_dict, epochs_dict], True),
            ("Inter-Group Functional Connectivity Viewer [BETA]", InterGroupFunctionalConnectivityWidget, [haemo_dict, group_dict, config_dict], True),
            ("Inter-Group Stats Viewer", InterGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, json_location], True),
-            ("Cross-Group Stats Viewer", CrossGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
+            ("Cross-Group Stats Viewer", CrossGroupStatsWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict, json_location], True),
            ("Inter-Group Brain and Image Viewer", InterGroupBrainImageWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
            ("Cross-Group Brain and Image Viewer", CrossGroupBrainImageWidget, [haemo_dict, df_ind_dict, design_matrix_dict, contrast_results_dict, group_dict], True),
            ("Export To CSV Viewer", ExportToCSVWidget, [haemo_dict, cha_dict, df_ind_dict, design_matrix_dict, group_dict, contrast_results_dict], True)
@@ -0,0 +1 @@
+update