start of plugin support?

flares.py

@@ -105,7 +105,7 @@ from mne_nirs.statistics._glm_level_first import RegressionResults  # type: igno
 from mne_connectivity.viz import plot_connectivity_circle # type: ignore
 from mne_connectivity import envelope_correlation, spectral_connectivity_epochs, spectral_connectivity_time # type: ignore
 
-from src.shared.shareddata import PLATFORM_NAME, resource_path
+from src.shared.shareddata import PLATFORM_NAME, resource_path, get_app_dir
 
 
 
@@ -162,42 +162,7 @@ QC_METRIC_LABELS = {
     "total_processing_seconds": "Processing Time (s)",
 }
 
-
-ROI_MAP = {
-    'ROI_OccipitoParietal_BA18_19_7': [
-        'S1_D1', 'S1_D2', 'S4_D3'
-    ],
-    'ROI_SuperiorParietal_BA7_5': [
-        'S2_D1', 'S3_D1', 'S2_D2', 'S2_D4', 'S4_D4'
-    ],
-    'ROI_TPJ_AngularGyrus_BA39_19_40': [
-        'S4_D2', 'S5_D3', 'S4_D5', 'S5_D5'
-    ],
-    # --- SPLIT BA40 REGIONS ---
-    'ROI_Posterior_BA40_Parietal': [
-        'S6_D4', 'S6_D5'
-    ],
-    'ROI_Anterior_BA40_Sensorimotor': [
-        'S10_D5', 'S8_D5'
-    ],
-    # --------------------------
-    'ROI_Supramarginal_Inferior_BA40_6': [
-        'S6_D6'
-    ],
-    'ROI_VentralSomatosensory_BA1_2_3_43_48': [
-        'S8_D6', 'S9_D6'
-    ],
-    'ROI_Sensorimotor_BA1_2_3_4_6': [
-        'S6_D8', 'S10_D8'
-    ],
-    'ROI_DLPFC_FEF_BA6_8_9': [
-        'S7_D7', 'S7_D8'
-    ],
-    'ROI_Broca_VLPFC_BA6_44_45_4': [
-        'S9_D7', 'S10_D7'
-    ]
-}
-
+ROI_MAP = {} # TODO: Should be grabbed from the json file
 
 DOWNSAMPLE: bool
 DOWNSAMPLE_FREQUENCY: int
@@ -345,24 +310,20 @@ FEATURE_2: bool = False
 script_dir = os.path.dirname(os.path.abspath(__file__))
 os.chdir(script_dir)
 
+
 # Configure logging to file with timestamps and realtime flush
 if PLATFORM_NAME == 'darwin':
-    logging.basicConfig(
-        filename=os.path.join(os.path.dirname(sys.executable), "../../../fnirs_analysis.log"),  # Needed to get out of the bundled application
-        level=logging.INFO,
-        format='%(asctime)s - %(processName)s - %(levelname)s - %(message)s',
-        datefmt='%Y-%m-%d %H:%M:%S',
-        filemode='a'
-    )
-
+    log_path = os.path.abspath(os.path.join(os.path.dirname(sys.executable), "../../../fnirs_analysis.log"))
 else:
-    logging.basicConfig(
-        filename='fnirs_analysis.log',
-        level=logging.INFO,
-        format='%(asctime)s - %(processName)s - %(levelname)s - %(message)s',
-        datefmt='%Y-%m-%d %H:%M:%S',
-        filemode='a'
-    )
+    log_path = os.path.join(get_app_dir(), "fnirs_analysis.log")
+
+logging.basicConfig(
+    filename=log_path,
+    level=logging.INFO,
+    format='%(asctime)s - %(processName)s - %(levelname)s - %(message)s',
+    datefmt='%Y-%m-%d %H:%M:%S',
+    filemode='a'
+)
 
 logger = logging.getLogger()
 
@@ -514,7 +475,8 @@ def process_multiple_participants(file_paths, file_params, file_metadata,
     success_count = {"value": 0}
     failed_stages = {"value": []}
     qc_rows: list[dict[str, Any]] = []
-    qc_summary_path="qc_summary.xlsx"
+    if qc_summary_path is None:
+        qc_summary_path = os.path.join(get_app_dir(), "qc_summary.xlsx")
 
     def elapsed_heartbeat():
         # Ticks once a second so the GUI can show a live-updating timer,