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typos and pylance

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This commit is contained in:
tyler
2026-08-23 00:12:22 -07:00
parent e37275a1bb
commit d9d5b6d940
18 changed files with 115 additions and 114 deletions
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src/window/terminal.py
+2 -2
View File
@@ -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
+63 -68
View File
@@ -10,12 +10,9 @@ License: GPL-3.0
import os
import json
from enum import Enum, auto
from datetime import datetime
from typing import Optional
from typing import Any, List, Optional, cast
# 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"]
if not isinstance(observations, dict):
raise TypeError("'observations' must be a dictionary.")
observations = cast(dict[str, Any], data["observations"])
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 = {}
ch_positions = {}
# fiducials = {}
# ch_positions = {}
# Read the lines from the optode file
with open(file_b, 'r') as f:
for line in f:
if line.strip():
# Split by the semicolon and convert to meters
ch_name, coords_str = line.split(":")
coords = np.array(list(map(float, coords_str.strip().split()))) * 0.001
# # Read the lines from the optode file
# with open(file_b, 'r') as f:
# for line in f:
# if line.strip():
# # Split by the semicolon and convert to meters
# ch_name, coords_str = line.split(":")
# coords = np.array(list(map(float, coords_str.strip().split()))) * 0.001
# The key we have is a fiducial
if ch_name.lower() in ['lpa', 'nz', 'rpa']:
fiducials[ch_name.lower()] = coords
# # The key we have is a fiducial
# if ch_name.lower() in ['lpa', 'nz', 'rpa']:
# fiducials[ch_name.lower()] = coords
# The key we have is a source or detector
else:
ch_positions[ch_name.upper()] = coords
# # The key we have is a source or detector
# else:
# ch_positions[ch_name.upper()] = coords
# 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
# # 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
# 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
raw = read_raw_snirf(file_a, preload=True)
raw.set_montage(initial_montage)
write_raw_snirf(raw, save_path)
# # 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
# raw = read_raw_snirf(file_a, preload=True)
# raw.set_montage(initial_montage)
# write_raw_snirf(raw, save_path)
def _apply_events_to_snirf(self, raw, new_annotations, save_path):
raw.set_annotations(new_annotations)
write_raw_snirf(raw, save_path)
# def _apply_events_to_snirf(self, raw, new_annotations, save_path):
# raw.set_annotations(new_annotations)
# write_raw_snirf(raw, save_path)
def _write_event_mapping_json(
self,
file_a,
file_b,
selected_obs,
snirf_anchor,
boris_anchor,
time_shift,
mapped_events,
save_path
):
# def _write_event_mapping_json(
# self,
# file_a,
# file_b,
# selected_obs,
# snirf_anchor,
# boris_anchor,
# time_shift,
# mapped_events,
# save_path
# ):
payload = {
"source": {
"called_from": self.caller,
"snirf_file": os.path.basename(file_a),
"boris_file": os.path.basename(file_b),
"observation": selected_obs
},
"alignment": {
"snirf_anchor": snirf_anchor,
"boris_anchor": boris_anchor,
"time_shift_seconds": time_shift
},
"events": mapped_events,
"created_at": datetime.utcnow().isoformat() + "Z"
}
# payload = {
# "source": {
# "called_from": self.caller,
# "snirf_file": os.path.basename(file_a),
# "boris_file": os.path.basename(file_b),
# "observation": selected_obs
# },
# "alignment": {
# "snirf_anchor": snirf_anchor,
# "boris_anchor": boris_anchor,
# "time_shift_seconds": time_shift
# },
# "events": mapped_events,
# "created_at": datetime.utcnow().isoformat() + "Z"
# }
with open(save_path, "w", encoding="utf-8") as f:
json.dump(payload, f, indent=2)
# with open(save_path, "w", encoding="utf-8") as f:
# 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
+1 -2
View File
@@ -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],