pylance standardization

src/analysis/exporttocsv.py

@@ -1,6 +1,7 @@
 """
 Filename: exporttocsv.py
 Description: Logic for the Export To CSV analysis window
+Note: Compliant with pylance strict type checking
 
 Author: Tyler de Zeeuw
 License: GPL-3.0
@@ -8,39 +9,51 @@ License: GPL-3.0
 
 # Built-in imports
 import os
+from pathlib import Path
+from typing import Any
 
 # External library imports
-import numpy as np
-import pandas as pd
+from pandas import DataFrame
+
+from mne.io.base import BaseRaw
 
 from PySide6.QtWidgets import QFileDialog, QMessageBox
 
+from flares import sparks_csv_export
 from src.shared.flaresbasewidget import CSVUIMixin, FlaresBaseWidget
 from src.shared.shareddata import APP_NAME
 
 
 class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
-    def __init__(self, haemo_dict, cha_dict, df_ind, design_matrix, group, contrast_results_dict):
+    def __init__(
+        self, 
+        haemo_dict: dict[str | Path, BaseRaw], 
+        cha_dict: dict[str, DataFrame],
+        df_ind_dict: dict[str, DataFrame],
+        design_matrix_dict: dict[str, DataFrame],
+        contrast_results_dict: dict[str, dict[str, Any]],
+        group_dict: dict[str, str],
+    ) -> None:
+        
         super().__init__("ExportToCSV")
         self.setWindowTitle(f"Export To CSV Viewer - {APP_NAME.upper()}")
         self.haemo_dict = haemo_dict
         self.cha_dict = cha_dict
-        self.df_ind = df_ind
-        self.design_matrix = design_matrix
-        self.group = group
-        self.contrast_results_dict = contrast_results_dict
+        # self.df_ind = df_ind_dict
+        # self.design_matrix = design_matrix_dict
+        # self.contrast_results_dict = contrast_results_dict
+        # self.group = group_dict
         
         self.setup_csv_ui(["0 (Export Data to CSV)", "1 (CSV for SPARKS)",])
         
     
     def process_request(self):
-        # TODO: Move this into flares for the call?
         selected_display_names = self._get_checked_items(self.participant_dropdown)
-        selected_file_paths = []
+        selected_file_paths: list[str] = []
         for display_name in selected_display_names:
             for fp, short_label in self.participant_map.items():
                 expected_display = f"{short_label} ({os.path.basename(fp)})"
-                if display_name == expected_display:
+                if display_name == expected_display: 
                     selected_file_paths.append(fp)
                     break
 
@@ -52,7 +65,6 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
             QMessageBox.warning(self, "Selection Missing", "Please select at least one participant and one export type.")
             return
 
-        # 2. ASK ONCE: Select Output Directory
         output_dir = QFileDialog.getExistingDirectory(self, "Select Output Folder for CSV Exports")
         
         if not output_dir:
@@ -78,29 +90,11 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
                             cha.to_csv(save_path)
                             success_count += 1
 
-
                     elif idx == 1:
                             # SPARKS Export
                             save_path = os.path.join(output_dir, f"{base_filename}_sparks.csv")
-                            if haemo_obj is not None:
-                                raw = haemo_obj
-                                data, times = raw.get_data(return_times=True)
-                                ann_col = np.full(times.shape, "", dtype=object)
-
-                                if raw.annotations is not None and len(raw.annotations) > 0:
-                                    for onset, duration, desc in zip(
-                                        raw.annotations.onset,
-                                        raw.annotations.duration,
-                                        raw.annotations.description
-                                    ):
-                                        mask = (times >= onset) & (times < onset + duration)
-                                        ann_col[mask] = desc
-
-                                df = pd.DataFrame(data.T, columns=raw.ch_names)
-                                df.insert(0, "annotation", ann_col)
-                                df.insert(0, "time", times)
-                                df.to_csv(save_path, index=False)
-                                success_count += 1
+                            sparks_csv_export(haemo_obj, save_path)
+                            success_count += 1
                         
                     else:
                         print(f"No method defined for index {idx}")
@@ -119,5 +113,4 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
             #         mode=EventUpdateMode.WRITE_JSON,
             #         caller="Video Alignment Tool"
             #     )
-            #     win.show()
-
+            #     win.show()