typos and pylance

file_ext_registration.py

@@ -16,6 +16,7 @@ from typing import Optional, Tuple
 # External library imports
 from src.shared.shareddata import APP_NAME, PLATFORM_NAME
 
+
 ELEVATION_FLAG = "--register_file_association_elevated"
 
 
@@ -25,7 +26,6 @@ def register_file_association(ext: Optional[str] = None,
     bundle_id: Optional[str] = None,
     force_admin: bool = False,
 ) -> Tuple[bool, str]:
-    
     """
     Registers a custom file extension across Windows, Linux, and macOS.
     Handles non-admin Windows users by falling back to local user registry.

flares.py

@@ -25,7 +25,7 @@ from copy import deepcopy
 import multiprocessing as mp
 from itertools import compress
 from queue import Empty, Queue
-from typing import Any, Optional, Sequence, cast, Literal, Union
+from typing import Any, Optional, Sequence, cast, Literal, Union, List
 
 # External library imports
 import matplotlib.pyplot as plt
@@ -6274,10 +6274,21 @@ def _single_subject_epoch_coherence(
 # ============================================================================
 
 def run_group_functional_connectivity_betas(
-    haemo_dict, selected_paths, event_name, n_lines, vmin,
+    haemo_dict: dict[str, BaseRaw],
-    *, drift_model="cosine", drift_order=1, hrf_model="glover",
+    selected_paths: List[str],
-    apply_gsr=True, alpha=0.05, min_participants=3, resample_freq=4.0,
+    event_name: Optional[str],
+    n_lines: int,
+    vmin: float,
+    *,
+    drift_model: str = "cosine",
+    drift_order: int = 1,
+    hrf_model: str = "glover",
+    apply_gsr: bool = True,
+    alpha: float = 0.05,
+    min_participants: int = 3,
+    resample_freq: float = 4.0,
 ) -> None:
+    
     subject_results = []
     for path in selected_paths:
         raw = haemo_dict.get(path)
@@ -6311,7 +6322,7 @@ def run_group_functional_connectivity_betas(
 
 
 def run_group_functional_connectivity_epochs(
-    epochs_dict: dict[str | Path, Epochs],
+    epochs_dict: dict[str, Epochs],
     selected_paths: list[str],
     event_name: str | None,
     n_lines: int,

flares_updater.py

@@ -14,15 +14,14 @@ import time
 import shlex
 import psutil
 import shutil
-import platform
 import subprocess
 from typing import Union
 from pathlib import Path
 from datetime import datetime
 
+# External library imports
+from src.shared.shareddata import APP_NAME, PLATFORM_NAME
 
-PLATFORM_NAME = platform.system().lower()
-APP_NAME = "flares"
 
 if PLATFORM_NAME == 'darwin':
     _log_path = os.path.join(os.path.dirname(sys.executable), f"../../../{APP_NAME}_updater.log")
@@ -189,7 +188,6 @@ def main():
         update_folder = sys.argv[1]
         main_exe = sys.argv[2]
 
-        # Interesting naming convention
         main_exe_path = Path(main_exe).resolve()
         app_dir = main_exe_path.parent                         
         bundle_dir = main_exe_path.parents[2]                 

project_manager.py

@@ -21,9 +21,9 @@ from PySide6.QtWidgets import QMessageBox, QVBoxLayout, QFileDialog, QLabel, QDi
 from PySide6.QtCore import QThread, Signal, Qt, QTimer
 from PySide6.QtGui import QAction
 
-from mne.io import read_raw_snirf
+from mne.io import read_raw_snirf # type: ignore
-from mne.preprocessing.nirs import source_detector_distances
+from mne.preprocessing.nirs import source_detector_distances # type: ignore
-from mne_nirs.channels import get_short_channels  # type: ignore
+from mne_nirs.channels import get_short_channels # type: ignore
 
 from src.shared.flaresbasewidget import ProgressBubble
 from src.shared.shareddata import APP_NAME, CURRENT_VERSION, PLATFORM_NAME, DATA_SCHEMA

pylance_progress

@@ -1,7 +1,7 @@
-src\analysis\participantfoldchannels.py  157
+src\analysis\participantfoldchannels.py  158
 src\shared\flaresbasewidget.py  1001+
-src\window\updateevents.py  151
+src\window\updateevents.py  83
 flares.py  1001+
 main_unit_tests.py  153
-main.py  709
+main.py  705
-project_manager.py 407
+project_manager.py 405

src/analysis/exporttocsv.py

@@ -9,7 +9,6 @@ License: GPL-3.0
 
 # Built-in imports
 import os
-from pathlib import Path
 from typing import Any
 
 # External library imports
@@ -27,7 +26,7 @@ from src.shared.shareddata import APP_NAME
 class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
     def __init__(
         self, 
-        haemo_dict: dict[str | Path, BaseRaw], 
+        haemo_dict: dict[str, BaseRaw], 
         cha_dict: dict[str, DataFrame],
         df_ind_dict: dict[str, DataFrame],
         design_matrix_dict: dict[str, DataFrame],

src/analysis/intergroupbrainimage.py

@@ -7,8 +7,7 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
-# Built-in Imports
+# Built-in imports
-from pathlib import Path
 from typing import Any, cast
 
 # External library imports
@@ -69,7 +68,7 @@ DESCRIPTION = """\n1. Group Contrast 2D/3D (plot_2d_3d_contrasts_between_groups)
 class InterGroupBrainImageWidget(InterGroupUIMixin, FlaresBaseWidget):
     def __init__(
         self,
-        haemo_dict: dict[str | Path, BaseRaw], 
+        haemo_dict: dict[str, BaseRaw], 
         df_ind_dict: dict[str, DataFrame],
         design_matrix_dict: dict[str, DataFrame],
         contrast_results_dict: dict[str, dict[str, Any]],

src/analysis/intergroupstats.py

@@ -8,7 +8,6 @@ License: GPL-3.0
 """
 
 # Built-in imports
-from pathlib import Path
 from typing import Any, cast
 
 # External library imports
@@ -147,7 +146,7 @@ class InterGroupStatsWidget(InterGroupUIMixin, FlaresBaseWidget):
 
     def __init__(
         self, 
-        haemo_dict: dict[str | Path, BaseRaw], 
+        haemo_dict: dict[str, BaseRaw], 
         cha_dict: dict[str, DataFrame],
         df_ind_dict: dict[str, DataFrame],
         design_matrix_dict: dict[str, DataFrame],

src/analysis/intragroupbrainimage.py

@@ -7,8 +7,7 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
-# Built-in Imports
+# Built-in imports
-from pathlib import Path
 from typing import Any, cast
 
 # External library imports
@@ -79,7 +78,7 @@ DESCRIPTION = """0. FIR Model Results (plot_fir_model_results)
 class IntraGroupBrainImageWidget(IntraGroupUIMixin, FlaresBaseWidget):
     def __init__(
         self,
-        haemo_dict: dict[str | Path, BaseRaw], 
+        haemo_dict: dict[str, BaseRaw], 
         cha_dict: dict[str, DataFrame],
         df_ind_dict: dict[str, DataFrame],
         design_matrix_dict: dict[str, DataFrame],

src/analysis/intragroupfunctionalconnectivity.py

@@ -8,7 +8,6 @@ License: GPL-3.0
 """
 
 # Built-in imports
-from pathlib import Path
 from typing import Any, cast
 
 # External library imports
@@ -61,7 +60,7 @@ DESCRIPTION = """0. Beta-Series Correlation (run_group_functional_connectivity_b
 class IntraGroupFunctionalConnectivityWidget(IntraGroupUIMixin, FlaresBaseWidget):
     def __init__(
         self,
-        haemo_dict: dict[str | Path, BaseRaw],
+        haemo_dict: dict[str, BaseRaw],
         epochs_dict: dict[str, Epochs],
         group_dict: dict[str, str],
     ) -> None:
@@ -99,7 +98,11 @@ class IntraGroupFunctionalConnectivityWidget(IntraGroupUIMixin, FlaresBaseWidget
                 min_participants = params.get("min_participants", 3)
 
                 run_group_functional_connectivity_betas(
-                    self.haemo_dict, selected_file_paths, selected_event, n_lines, vmin,
+                    self.haemo_dict,
+                    selected_file_paths,
+                    selected_event,
+                    n_lines,
+                    vmin,
                     drift_model=drift_model,
                     drift_order=drift_order,
                     hrf_model=hrf_model,

src/analysis/intragroupstats.py

@@ -8,7 +8,6 @@ License: GPL-3.0
 """
 
 # Built-in imports
-from pathlib import Path
 from typing import Any, cast
 
 # External library imports
@@ -159,7 +158,7 @@ DESCRIPTION = """0. ROI vs. Zero (run_roi_second_level_analysis)
 class IntraGroupStatsWidget(IntraGroupUIMixin, FlaresBaseWidget):
     def __init__(
         self, 
-        haemo_dict: dict[str | Path, BaseRaw], 
+        haemo_dict: dict[str, BaseRaw], 
         cha_dict: dict[str, DataFrame],
         df_ind_dict: dict[str, DataFrame],
         design_matrix_dict: dict[str, DataFrame],
@@ -240,6 +239,10 @@ class IntraGroupStatsWidget(IntraGroupUIMixin, FlaresBaseWidget):
                 if correction_method == "None":
                     correction_method = None
 
+                if not selected_event:
+                    print("Warning: No event condition selected for ROI analysis.")
+                    continue
+
                 if df_group.empty:
                     print("No ROI data (df_ind) found for selected participants.")
                     continue
@@ -265,7 +268,6 @@ class IntraGroupStatsWidget(IntraGroupUIMixin, FlaresBaseWidget):
                     else:
                         all_cha_filtered = all_cha
 
-
                 run_roi_second_level_analysis(
                     df_roi_all=df_filtered,
                     condition=selected_event,
@@ -303,7 +305,6 @@ class IntraGroupStatsWidget(IntraGroupUIMixin, 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),

src/analysis/participantbrain.py

@@ -8,7 +8,6 @@ License: GPL-3.0
 """
 
 # Built-in imports
-from pathlib import Path
 from typing import Any, cast
 
 # External library imports
@@ -69,7 +68,7 @@ PARAMETERIZED_INDEXES: dict[int, list[dict[str, Any]]] = {
 class ParticipantBrainViewerWidget(ParticipantUIMixin, FlaresBaseWidget):
     def __init__(
         self, 
-        haemo_dict: dict[str | Path, BaseRaw], 
+        haemo_dict: dict[str, BaseRaw], 
         cha_dict: dict[str, DataFrame],
     ) -> None:
         

src/analysis/participantfoldchannels.py

@@ -748,7 +748,7 @@ class ProcessOrchestrator(QObject):
 
     def __init__(self,
         selected_files,
-        haemo_dict: dict[str | Path, BaseRaw],
+        haemo_dict: dict[str, BaseRaw],
         worker_func
     ):
         

src/analysis/participantfunctionalconnectivity.py

@@ -7,8 +7,7 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
-# Built-in Imports
+# Built-in imports
-from pathlib import Path
 from typing import Any, cast
 
 # External library imports
@@ -81,7 +80,7 @@ DESCRIPTION = """0. Spectral Coherence (functional_connectivity_spectral_epochs)
 class ParticipantFunctionalConnectivityWidget(ParticipantUIMixin, FlaresBaseWidget):
     def __init__(
         self,
-        haemo_dict: dict[str | Path, BaseRaw],
+        haemo_dict: dict[str, BaseRaw],
         epochs_dict: dict[str, Epochs],
     ) -> None:
         

src/analysis/participantimage.py

@@ -7,7 +7,7 @@ Author: Tyler de Zeeuw
 License: GPL-3.0
 """
 
-# Built-in Imports
+# Built-in imports
 import os.path as op
 from pathlib import Path
 from datetime import datetime
@@ -26,7 +26,7 @@ from src.shared.shareddata import APP_NAME
 class ParticipantImageViewerWidget(FlaresBaseWidget):
     def __init__(
         self, 
-        haemo_dict: dict[str, BaseRaw], 
+        haemo_dict: dict[str, BaseRaw],
         fig_bytes_dict: dict[str, dict[str, bytes]]
     ) -> None:
         

src/window/terminal.py

@@ -13,7 +13,7 @@ from pathlib import Path
 from typing import Any, Callable
 
 # External library imports
-from PySide6.QtWidgets import QWidget, QVBoxLayout, QTextEdit, QLineEdit
+from PySide6.QtWidgets import QWidget, QVBoxLayout, QTextEdit, QLineEdit, QMainWindow
 from PySide6.QtCore import QProcess, Qt, QThread, Signal
 
 from file_ext_registration import register_file_association, is_windows_admin
@@ -124,7 +124,7 @@ class TerminalWindow(QWidget):
 
     def cmd_update(self, *args: Any) -> str:
         main_win = self.parent()
-        if not isinstance(main_win, QWidget):
+        if not isinstance(main_win, QMainWindow):
             return "[Error] Main window context not found."
         
         self.updater = UpdateManager(

src/window/updateevents.py

@@ -10,12 +10,9 @@ License: GPL-3.0
 import os
 import json
 from enum import Enum, auto
-from datetime import datetime
+from typing import Any, List, Optional, cast
-from typing import Optional
 
 # External library imports
-import numpy as np
-
 from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel, QLineEdit, QPushButton, QComboBox, QHBoxLayout, QMessageBox, QFileDialog
 from PySide6.QtCore import Qt
 
@@ -255,15 +252,13 @@ class UpdateEventsWindow(QWidget):
             except (json.JSONDecodeError, FileNotFoundError, KeyError) as e:
                 QMessageBox.warning(self, "Error", f"Failed to parse BORIS file:\n{e}")
                 
-    def extract_boris_observation_keys(self, data):
+    def extract_boris_observation_keys(self, data: dict[str, Any]) -> List[str]:
         if "observations" not in data:
             raise KeyError("Missing 'observations' key in BORIS file.")
 
-        observations = data["observations"]
+        observations = cast(dict[str, Any], data["observations"])
-        if not isinstance(observations, dict):
-            raise TypeError("'observations' must be a dictionary.")
-
         return list(observations.keys())
+
     
     def on_observation_selected(self):
         selected_obs = self.combo_suffix.currentText()
@@ -454,7 +449,7 @@ class UpdateEventsWindow(QWidget):
                 save_path += ".json"
 
             # Build JSON dict
-            json_data = {
+            json_data: dict[str, Any] = {
                 "observation": selected_obs,
                 "snirf_anchor": {"label": snirf_label, "time": snirf_anchor_time},
                 "boris_anchor": {"label": boris_label, "time": boris_anchor_time},
@@ -471,73 +466,73 @@ class UpdateEventsWindow(QWidget):
                 QMessageBox.critical(self, "Error", f"Failed to write JSON:\n{e}")
 
 
-    def update_optode_positions(self, file_a, file_b, save_path):
+    # def update_optode_positions(self, file_a, file_b, save_path):
                 
-        fiducials = {}
+    #     fiducials = {}
-        ch_positions = {}
+    #     ch_positions = {}
 
-        # Read the lines from the optode file
+    #     # Read the lines from the optode file
-        with open(file_b, 'r') as f:
+    #     with open(file_b, 'r') as f:
-            for line in f:
+    #         for line in f:
-                if line.strip():
+    #             if line.strip():
-                    # Split by the semicolon and convert to meters
+    #                 # Split by the semicolon and convert to meters
-                    ch_name, coords_str = line.split(":")
+    #                 ch_name, coords_str = line.split(":")
-                    coords = np.array(list(map(float, coords_str.strip().split()))) * 0.001
+    #                 coords = np.array(list(map(float, coords_str.strip().split()))) * 0.001
 
-                    # The key we have is a fiducial
+    #                 # The key we have is a fiducial
-                    if ch_name.lower() in ['lpa', 'nz', 'rpa']:
+    #                 if ch_name.lower() in ['lpa', 'nz', 'rpa']:
-                        fiducials[ch_name.lower()] = coords
+    #                     fiducials[ch_name.lower()] = coords
 
-                    # The key we have is a source or detector
+    #                 # The key we have is a source or detector
-                    else:
+    #                 else:
-                        ch_positions[ch_name.upper()] = coords
+    #                     ch_positions[ch_name.upper()] = coords
 
-        # Create montage with updated coords in head space
+    #     # Create montage with updated coords in head space
-        initial_montage = make_dig_montage(ch_pos=ch_positions, nasion=fiducials.get('nz'), lpa=fiducials.get('lpa'), rpa=fiducials.get('rpa'), coord_frame='head') # type: ignore
+    #     initial_montage = make_dig_montage(ch_pos=ch_positions, nasion=fiducials.get('nz'), lpa=fiducials.get('lpa'), rpa=fiducials.get('rpa'), coord_frame='head') # type: ignore
 
-        # Read the SNIRF file, set the montage, and write it back
+    #     # Read the SNIRF file, set the montage, and write it back
-        # TODO: Bad! read_raw_snirf doesnt release memory properly! Should be spawned in a seperate process and killed once completed
+    #     # TODO: Bad! read_raw_snirf doesnt release memory properly! Should be spawned in a seperate process and killed once completed
-        raw = read_raw_snirf(file_a, preload=True)
+    #     raw = read_raw_snirf(file_a, preload=True)
-        raw.set_montage(initial_montage)
+    #     raw.set_montage(initial_montage)
-        write_raw_snirf(raw, save_path)
+    #     write_raw_snirf(raw, save_path)
 
 
-    def _apply_events_to_snirf(self, raw, new_annotations, save_path):
+    # def _apply_events_to_snirf(self, raw, new_annotations, save_path):
-        raw.set_annotations(new_annotations)
+    #     raw.set_annotations(new_annotations)
-        write_raw_snirf(raw, save_path)
+    #     write_raw_snirf(raw, save_path)
         
-    def _write_event_mapping_json(
+    # def _write_event_mapping_json(
-        self,
+    #     self,
-        file_a,
+    #     file_a,
-        file_b,
+    #     file_b,
-        selected_obs,
+    #     selected_obs,
-        snirf_anchor,
+    #     snirf_anchor,
-        boris_anchor,
+    #     boris_anchor,
-        time_shift,
+    #     time_shift,
-        mapped_events,
+    #     mapped_events,
-        save_path
+    #     save_path
-    ):
+    # ):
 
-        payload = {
+    #     payload = {
-            "source": {
+    #         "source": {
-                "called_from": self.caller,
+    #             "called_from": self.caller,
-                "snirf_file": os.path.basename(file_a),
+    #             "snirf_file": os.path.basename(file_a),
-                "boris_file": os.path.basename(file_b),
+    #             "boris_file": os.path.basename(file_b),
-                "observation": selected_obs
+    #             "observation": selected_obs
-            },
+    #         },
-            "alignment": {
+    #         "alignment": {
-                "snirf_anchor": snirf_anchor,
+    #             "snirf_anchor": snirf_anchor,
-                "boris_anchor": boris_anchor,
+    #             "boris_anchor": boris_anchor,
-                "time_shift_seconds": time_shift
+    #             "time_shift_seconds": time_shift
-            },
+    #         },
-            "events": mapped_events,
+    #         "events": mapped_events,
-            "created_at": datetime.utcnow().isoformat() + "Z"
+    #         "created_at": datetime.utcnow().isoformat() + "Z"
-        }
+    #     }
 
-        with open(save_path, "w", encoding="utf-8") as f:
+    #     with open(save_path, "w", encoding="utf-8") as f:
-            json.dump(payload, f, indent=2)
+    #         json.dump(payload, f, indent=2)
 
-        return save_path
+    #     return save_path
 
 
 
@@ -747,11 +742,11 @@ class UpdateEventsBlazesWindow(QWidget):
                 self.combo_events.setEnabled(False)
                 
 
-    def extract_json_observation_strings(self, data):
+    def extract_json_observation_strings(self, data: dict[str, Any]) -> List[str]:
         if "events" not in data:
             raise KeyError("Missing 'events' key in JSON file.")
 
-        event_strings = []
+        event_strings: List[str] = []
 
         # The new format is a flat list chronologically ordered
         for event in data["events"]:
@@ -772,7 +767,7 @@ class UpdateEventsBlazesWindow(QWidget):
     
     def go_action(self) -> None:
         file_a = self.line_edit_file_a.text()
-        file_b = self.line_edit_file_b.text()
+        _ = self.line_edit_file_b.text()
         suffix = APP_NAME
     
         if not hasattr(self, "json_data") or self.combo_events.count() == 0 or self.combo_snirf_events.count() == 0:

src/window/viewerlauncher.py

@@ -8,7 +8,6 @@ License: GPL-3.0
 """
 
 # Built-in imports
-from pathlib import Path
 from typing import Any, Callable, Type
 
 # External library imports
@@ -36,7 +35,7 @@ from src.shared.shareddata import APP_NAME
 class ViewerLauncherWidget(QWidget):
     def __init__(
         self,
-        haemo_dict: dict[str | Path, BaseRaw],
+        haemo_dict: dict[str, BaseRaw],
         epochs_dict: dict[str, Epochs],
         cha_dict: dict[str, DataFrame],
         df_ind_dict: dict[str, DataFrame],