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imptovements for blazes and fix fold again

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This commit is contained in:
tyler
2026-05-01 11:40:34 -07:00
parent d74be5cdec
commit 69f3df8921
2 changed files with 41 additions and 110 deletions
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flares.py
+1 -1
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@@ -1743,7 +1743,7 @@ def fold_channels(raw: BaseRaw) -> None:
# Locate the fOLD excel files
if getattr(sys, 'frozen', False):
set_config('MNE_NIRS_FOLD_PATH', resource_path("/mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
set_config('MNE_NIRS_FOLD_PATH', resource_path("./mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
else:
path = os.path.expanduser("~") + "/mne_data/fOLD/fOLD-public-master/Supplementary"
set_config('MNE_NIRS_FOLD_PATH', resource_path(path)) # type: ignore
main.py
+28 -97
View File
@@ -46,7 +46,7 @@ from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleVa
from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
CURRENT_VERSION = "1.4.1"
CURRENT_VERSION = "1.4.3"
APP_NAME = "flares"
API_URL = f"https://git.research.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"
API_URL_SECONDARY = f"https://git.research2.dezeeuw.ca/api/v1/repos/tyler/{APP_NAME}/releases"
@@ -1413,43 +1413,43 @@ class UpdateEventsBlazesWindow(QWidget):
self.combo_snirf_events.setEnabled(False)
def browse_file_b(self):
file_path, _ = QFileDialog.getOpenFileName(self, "Select BLAZES File", "", "BLAZES project Files (*.blaze)")
file_path, _ = QFileDialog.getOpenFileName(self, "Select JSON Timeline File", "", "JSON Files (*.json)")
if file_path:
self.line_edit_file_b.setText(file_path)
try:
with open(file_path, 'r', encoding='utf-8') as f:
data = json.load(f)
self.blazes_data = data
self.json_data = data
obs_keys = self.extract_blazes_observation_strings(data)
obs_keys = self.extract_json_observation_strings(data)
self.combo_events.clear()
if obs_keys:
self.combo_events.addItems(obs_keys)
self.combo_events.setEnabled(True)
else:
QMessageBox.information(self, "No Events", "No observation keys found in BLAZES file.")
QMessageBox.information(self, "No Events", "No events found in JSON file.")
self.combo_events.setEnabled(False)
except (json.JSONDecodeError, FileNotFoundError, KeyError, TypeError) as e:
QMessageBox.warning(self, "Error", f"Failed to parse BLAZES file:\n{e}")
QMessageBox.warning(self, "Error", f"Failed to parse JSON file:\n{e}")
self.combo_events.clear()
self.combo_events.setEnabled(False)
def extract_blazes_observation_strings(self, data):
if "obs" not in data:
raise KeyError("Missing 'obs' key in BLAZES file.")
def extract_json_observation_strings(self, data):
if "events" not in data:
raise KeyError("Missing 'events' key in JSON file.")
obs = data["obs"]
event_strings = []
for event_name, occurrences in obs.items():
# occurrences is a list of dicts: [{"start_frame": 642, "start_time_sec": 26.777, ...}]
for entry in occurrences:
onset = entry.get("start_time_sec", 0.0)
# The new format is a flat list chronologically ordered
for event in data["events"]:
track_name = event.get("track_name", "Unknown")
onset = event.get("start_sec", 0.0)
# Formatting to match your SNIRF style: "Event Name @ 0.000s"
display_str = f"{event_name} @ {onset:.3f}s"
display_str = f"{track_name} @ {onset:.3f}s"
event_strings.append(display_str)
return event_strings
@@ -1465,16 +1465,16 @@ class UpdateEventsBlazesWindow(QWidget):
file_b = self.line_edit_file_b.text()
suffix = APP_NAME
if not hasattr(self, "blazes_data") or self.combo_events.count() == 0 or self.combo_snirf_events.count() == 0:
QMessageBox.warning(self, "Missing data", "Please make sure a BLAZES and SNIRF event are selected.")
if not hasattr(self, "json_data") or self.combo_events.count() == 0 or self.combo_snirf_events.count() == 0:
QMessageBox.warning(self, "Missing data", "Please make sure a JSON and SNIRF event are selected.")
return
try:
blaze_text = self.combo_events.currentText()
_, blaze_time_str = blaze_text.split(" @ ")
blaze_anchor_time = float(blaze_time_str.replace("s", "").strip())
json_text = self.combo_events.currentText()
_, json_time_str = json_text.split(" @ ")
json_anchor_time = float(json_time_str.replace("s", "").strip())
except Exception as e:
QMessageBox.critical(self, "BLAZE Event Error", f"Could not parse BLAZE anchor:\n{e}")
QMessageBox.critical(self, "JSON Event Error", f"Could not parse JSON anchor:\n{e}")
return
try:
@@ -1485,20 +1485,20 @@ class UpdateEventsBlazesWindow(QWidget):
QMessageBox.critical(self, "SNIRF Event Error", f"Could not parse SNIRF anchor:\n{e}")
return
time_shift = snirf_anchor_time - blaze_anchor_time
time_shift = snirf_anchor_time - json_anchor_time
onsets, durations, descriptions = [], [], []
skipped_count = 0
try:
ai_data = self.blazes_data.get("ai_tracks", {})
events_list = self.json_data.get("events", [])
for track_name, events in ai_data.items():
for event in events_list:
track_name = event.get("track_name", "Unknown")
clean_name = track_name.replace("AI: ", "").strip()
for event in events:
original_start = event.get("start_time_sec", 0.0)
original_end = event.get("end_time_sec", original_start)
original_start = event.get("start_sec", 0.0)
original_end = event.get("end_sec", original_start)
duration = original_end - original_start
# FILTER: Minimum 0.1s duration
@@ -1538,7 +1538,7 @@ class UpdateEventsBlazesWindow(QWidget):
description=descriptions
)
# Replace existing annotations with the new aligned AI tracks
# Replace existing annotations with the new aligned JSON tracks
raw.set_annotations(new_annotations)
write_raw_snirf(raw, save_path)
@@ -1548,75 +1548,6 @@ class UpdateEventsBlazesWindow(QWidget):
QMessageBox.critical(self, "Error", f"Failed to update SNIRF file:\n{e}")
def update_optode_positions(self, file_a, file_b, save_path):
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
# 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
# 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)
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
):
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)
return save_path
class ProgressBubble(QWidget):
"""