mainly whitespace, but also some generic qol improvements
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tyler committed
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@@ -12,6 +12,7 @@ import os
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from typing import Any
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# External library imports
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from mne import Epochs
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from pandas import DataFrame
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from mne.io.base import BaseRaw
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@@ -25,8 +26,9 @@ from src.shared.shareddata import APP_NAME
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class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
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def __init__(
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self,
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haemo_dict: dict[str, BaseRaw],
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self,
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haemo_dict: dict[str, BaseRaw],
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epochs_dict: dict[str, Epochs],
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cha_dict: dict[str, DataFrame],
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df_ind_dict: dict[str, DataFrame],
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design_matrix_dict: dict[str, DataFrame],
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@@ -36,10 +38,11 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
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fir_feature_dict: dict[str, dict[str, Any]],
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qc_dict: dict[str, dict[str, Any]],
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) -> None:
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super().__init__("ExportToCSV")
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self.setWindowTitle(f"Export To CSV Viewer - {APP_NAME.upper()}")
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self.haemo_dict = haemo_dict
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self.epochs_dict = epochs_dict
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self.cha_dict = cha_dict
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self.df_ind_dict = df_ind_dict
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self.design_matrix = design_matrix_dict
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@@ -48,20 +51,19 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
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self.config_dict = config_dict
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self.fir_feature_dict = fir_feature_dict
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self.qc_dict = qc_dict
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self.setup_csv_ui(["0 (Export Data to CSV)", "1 (CSV for SPARKS)", "2 (Export Configuration to CSV)", "3 (Paragraph of Configuration)", "4 (Export FIR Waveform Features to CSV)",
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"5 (Export Quality Control Metrics to CSV)",
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"6 (Export Master Consolidated Matrix [All Participants into 1 CSV])"
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"5 (Export Quality Control Metrics to CSV)", "6 (Export Master Consolidated Matrix [All Participants into 1 CSV])"
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])
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def process_request(self):
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selected_display_names = self._get_checked_items(self.participant_dropdown)
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selected_file_paths: list[str] = []
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for display_name in selected_display_names:
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for fp, short_label in self.participant_map.items():
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expected_display = f"{short_label} ({os.path.basename(fp)})"
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if display_name == expected_display:
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if display_name == expected_display:
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selected_file_paths.append(fp)
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break
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@@ -74,7 +76,7 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
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return
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output_dir = QFileDialog.getExistingDirectory(self, "Select Output Folder for CSV Exports")
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if not output_dir:
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print("Export cancelled: No folder selected.")
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return
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@@ -120,78 +122,78 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
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magic_string = self.gen_magic_str(first_params)
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self.placeholder_label.setText(magic_string)
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# elif idx == 4:
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# # FIR Waveform Features Export
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# fir_data = self.fir_feature_dict.get(file_path)
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# if fir_data and isinstance(fir_data, dict):
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# names = fir_data.get("feature_names", [])
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# vals = fir_data.get("features", [])
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# chans = fir_data.get("feature_channels", [])
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elif idx == 4:
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# FIR Waveform Features Export
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fir_data = self.fir_feature_dict.get(file_path)
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if fir_data:
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names = fir_data.get("feature_names", [])
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vals = fir_data.get("features", [])
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chans = fir_data.get("feature_channels", [])
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# fir_df = DataFrame({
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# "Feature_Name": names,
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# "Channel": chans if len(chans) == len(names) else ["N/A"] * len(names),
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# "Value": vals
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# })
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# save_path = os.path.join(output_dir, f"{base_filename}_fir_features.csv")
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# fir_df.to_csv(save_path, index=False)
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# success_count += 1
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fir_df = DataFrame({
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"Feature_Name": names,
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"Channel": chans if len(chans) == len(names) else ["N/A"] * len(names),
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"Value": vals
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})
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save_path = os.path.join(output_dir, f"{base_filename}_fir_features.csv")
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fir_df.to_csv(save_path, index=False)
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success_count += 1
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# elif idx == 5:
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# # Quality Control (QC) Metrics Export
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# qc_data = self.qc_dict.get(file_path)
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# if qc_data and isinstance(qc_data, dict):
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# qc_df = DataFrame(list(qc_data.items()), columns=["Metric", "Value"])
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# save_path = os.path.join(output_dir, f"{base_filename}_qc_metrics.csv")
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# qc_df.to_csv(save_path, index=False)
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# success_count += 1
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elif idx == 5:
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# Quality Control (QC) Metrics Export
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qc_data = self.qc_dict.get(file_path)
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if qc_data and isinstance(qc_data, dict):
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qc_df = DataFrame(list(qc_data.items()), columns=["Metric", "Value"])
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save_path = os.path.join(output_dir, f"{base_filename}_qc_metrics.csv")
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qc_df.to_csv(save_path, index=False)
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success_count += 1
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# elif idx == 6:
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# # Master Consolidated Matrix (1 single CSV combining all selected participants)
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# save_path = os.path.join(output_dir, f"{APP_NAME}_master_consolidated.csv")
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# if not os.path.exists(save_path):
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# master_rows: list[dict[str, Any]] = []
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# for fp in selected_file_paths:
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# abs_path = os.path.abspath(fp)
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# grp = self.group_dict.get(fp, "Unknown")
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# row: dict[str, Any] = {"Participant": abs_path, "Group": grp}
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elif idx == 6:
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# Master Consolidated Matrix (1 single CSV combining all selected participants)
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save_path = os.path.join(output_dir, f"{APP_NAME}_master_consolidated.csv")
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if not os.path.exists(save_path):
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master_rows: list[dict[str, Any]] = []
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for fp in selected_file_paths:
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abs_path = os.path.abspath(fp)
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grp = self.group_dict.get(fp, "Unknown")
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row: dict[str, Any] = {"Participant": abs_path, "Group": grp}
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# # QC Metrics
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# qc_info = self.qc_dict.get(fp, {})
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# if isinstance(qc_info, dict):
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# for mk, mv in qc_info.items():
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# row[f"QC_{mk}"] = mv
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# QC Metrics
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qc_info = self.qc_dict.get(fp, {})
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if isinstance(qc_info, dict):
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for mk, mv in qc_info.items():
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row[f"QC_{mk}"] = mv
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# # FIR Features
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# fir_info = self.fir_feature_dict.get(fp, {})
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# print("1")
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# if isinstance(fir_info, dict):
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# print("2")
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# f_names = fir_info.get("feature_names", [])
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# f_vals = fir_info.get("features", [])
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# print("3")
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# if len(f_names) == len(f_vals):
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# print("4")
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# for fn, fv in zip(f_names, f_vals):
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# row[f"FIR_{fn}"] = fv
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# FIR Features
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fir_info = self.fir_feature_dict.get(fp, {})
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print("1")
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if isinstance(fir_info, dict):
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print("2")
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f_names = fir_info.get("feature_names", [])
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f_vals = fir_info.get("features", [])
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print("3")
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if len(f_names) == len(f_vals):
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print("4")
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for fn, fv in zip(f_names, f_vals):
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row[f"FIR_{fn}"] = fv
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# master_rows.append(row)
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master_rows.append(row)
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# if master_rows:
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# df_master = DataFrame(master_rows)
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# df_master.to_csv(save_path, index=False)
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# success_count += 1
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if master_rows:
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df_master = DataFrame(master_rows)
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df_master.to_csv(save_path, index=False)
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success_count += 1
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else:
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print(f"No method defined for index {idx}")
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except Exception as e:
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print(f"Failed to export {file_path} (Type {idx}): {e}")
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# 4. Final Notification
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if success_count > 0:
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QMessageBox.information(self, "Export Complete", f"Successfully saved {success_count} CSV files to:\n{output_dir}")
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# # If SPARKS export was included, show the Event Window once at the end
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# if 1 in selected_indexes:
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# win = UpdateEventsWindow(
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@@ -203,62 +205,62 @@ class ExportToCSVWidget(CSVUIMixin, FlaresBaseWidget):
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def gen_magic_str(self, all_params: dict[str, str]) -> str:
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magic_str = "To start, the data was loaded into the application. "
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if all_params['DOWNSAMPLE']:
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magic_str += f"The data was downsampled to {all_params['DOWNSAMPLE_FREQUENCY']}hz. "
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else:
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magic_str += "The data was not downsampled and was retained at its original sampling frequency. "
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if all_params['TRIM']:
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magic_str += f"The data was then trimmed to only keep {all_params['SECONDS_TO_KEEP']} seconds before the first event, as the earlier data with no events would not be needed. "
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else:
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magic_str += "The data was not trimmed and was retained at its original length. "
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if all_params['OPTODE_PLACEMENT']:
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magic_str += f"A visualization check of the optode locations in 3D space was performed to ensure that they were at the correct location. "
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if all_params['SHORT_CHANNELS']:
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magic_str += f"A short channel(s) was specified with the maximum length of a short channel being {all_params['SHORT_CHANNELS_THRESHOLD']} metres. Channels that were over this distance but under {all_params['LONG_CHANNELS_THRESHOLD']} metres were retained. "
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else:
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magic_str += f"No short channel was specified. Channels between the lengths of {all_params['SHORT_CHANNELS_THRESHOLD']} and {all_params['LONG_CHANNELS_THRESHOLD']} meters were used with all other channles being discarded. "
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if all_params['HEART_RATE']:
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magic_str += f"The heart rate of the participant was attempted to be calculated. {all_params['SECONDS_TO_STRIP_HR']} seconds were ignored from the start of the file to avoid motion artifacts. "
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magic_str += f"The heart rate had hard limits of {all_params['MAX_LOW_HR']} to {all_params['MAX_HIGH_HR']} and was smoothed across {all_params['SMOOTHING_WINDOW_HR']} samples. "
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else:
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magic_str += "The heart rate of the participants was not attempted to be calculated. "
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if all_params['SCI']:
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magic_str += f"The Scalp Coupling Index was calculated over {all_params['SCI_TIME_WINDOW']} second windows. The threshold value was {all_params['SCI_THRESHOLD']}. "
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else:
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magic_str += "Scalp Coupling Index was not used. "
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if all_params['SNR']:
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magic_str += f"The Signal to Noise Ratio was calculated. The threshold value was set to {all_params['SNR_THRESHOLD']}db. "
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else:
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magic_str += "The Signal to Noise Ratio was not used. "
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if all_params['PSP']:
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magic_str += f"Peak Spectral Power was calculated over {all_params['PSP_TIME_WINDOW']} second windows. The threshold value was {all_params['PSP_THRESHOLD']}. "
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else:
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magic_str += "Peak Spectral Power was not used. "
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if all_params['COEFF_VAR']:
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magic_str += f"The Coefficient of Variation was calculated. The threshold value was set to {all_params['COEFF_VAR_THRESHOLD']}. "
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else:
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magic_str += "The Coefficient of Variation was not used. "
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if all_params['MAD']:
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magic_str += f"Median Absolute Deviation was calculated. The threshold value was set to {all_params['MAD_THRESHOLD']}. "
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else:
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magic_str += "Median Absolute Deviation was not used. "
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if all_params['PSD_NOISE']:
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magic_str += f"Power Spectral Density Noise was calculated with a target frequency divisor of {all_params['TARGET_FREQ_DIV']} and a decibal limit of {all_params['DB_LIMIT']}. "
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else:
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magic_str += f"Power Spectral Density Noise was not used. "
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magic_str += "More coming soon."
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return magic_str
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