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Merged
richardkoehler merged 2 commits into from
Apr 18, 2026
Merged

Add pyside6-stubs dependency and update logging and UI components for… #36

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205c268
Add pyside6-stubs dependency and update logging and UI components for…
richardkoehler Apr 18, 2026
839e8d7
Merge remote-tracking branch 'upstream' into feat/improve-typing
richardkoehler Apr 18, 2026
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3 changes: 1 addition & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,7 @@ dev = [
"pre-commit>=3.6",
"ty>=0.0.30",
"pandas-stubs>=3.0.0.260204",
"pyside6-stubs>=6.7.3.0",
]
build = [
"pyinstaller>=6.15.0",
Expand Down Expand Up @@ -124,5 +125,3 @@ strict_optional = true
module = "PySide6.*"
ignore_missing_imports = true

[tool.ty.rules]
unresolved-attribute = "ignore"
6 changes: 4 additions & 2 deletions src/dbs_annotator/logging_config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,8 +128,10 @@ def qt_handler(mode: QtMsgType, context: QMessageLogContext, message: str) -> No
else:
level = logging.CRITICAL
suffix = ""
if context.file:
suffix = f" ({context.file}:{context.line})"
ctx_file = getattr(context, "file", None)
ctx_line = getattr(context, "line", None)
if ctx_file:
suffix = f" ({ctx_file}:{ctx_line})"
logging.getLogger("qt").log(level, "%s%s", message, suffix)

qInstallMessageHandler(qt_handler)
Expand Down
68 changes: 40 additions & 28 deletions src/dbs_annotator/models/electrode_viewer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,9 @@ def __init__(self, parent=None):
self.setContentsMargins(2, 2, 2, 2)
self.setAutoFillBackground(False)
self.setMouseTracking(True)
self.setCursor(Qt.PointingHandCursor)
self.setCursor(Qt.CursorShape.PointingHandCursor)
self.export_mode = False
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)

def set_export_mode(self, enabled: bool) -> None:
"""Toggle export mode (tighter padding, larger scale for PNG output)."""
Expand Down Expand Up @@ -198,7 +198,7 @@ def set_ring_state(self, ring_idx, state):
@typing.override
def mousePressEvent(self, event):
"""Handle clicks on contacts, rings and case"""
if event.button() == Qt.LeftButton:
if event.button() == Qt.MouseButton.LeftButton:
# Check if a contact was clicked
contact_id = self.get_contact_at_pos(event.pos())
if contact_id:
Expand Down Expand Up @@ -277,8 +277,8 @@ def paintEvent(self, event):
return

painter = QPainter(self)
painter.setRenderHint(QPainter.Antialiasing)
painter.setRenderHint(QPainter.SmoothPixmapTransform)
painter.setRenderHint(QPainter.RenderHint.Antialiasing)
painter.setRenderHint(QPainter.RenderHint.SmoothPixmapTransform)

# Background
palette = self.palette()
Expand Down Expand Up @@ -330,17 +330,21 @@ def paintEvent(self, event):
case_x + 2, case_y + 1, case_width * 0.4, case_height * 0.3
)
painter.setBrush(QColor(255, 255, 255, 40))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawRoundedRect(highlight_rect, 3, 3)

# Case label - smaller font in export mode
painter.setPen(Qt.white if self.case_state != ContactState.OFF else Qt.black)
painter.setPen(
Qt.GlobalColor.white
if self.case_state != ContactState.OFF
else Qt.GlobalColor.black
)
case_font_size = (
max(7, int(scale * 0.35)) if self.export_mode else max(8, int(scale * 0.4))
)
font = QFont("Arial", case_font_size, QFont.Bold)
font = QFont("Arial", case_font_size, QFont.Weight.Bold)
painter.setFont(font)
painter.drawText(self.case_rect, Qt.AlignCenter, "CASE")
painter.drawText(self.case_rect, Qt.AlignmentFlag.AlignCenter, "CASE")

# Draw electrode body (lead)
lead_width = self.model.lead_diameter * scale * 1.8
Expand All @@ -367,14 +371,14 @@ def paintEvent(self, event):
center_x - lead_width / 2, start_y, center_x + lead_width / 2, start_y
)

base_color = palette.color(QPalette.Midlight)
base_color = palette.color(QPalette.ColorRole.Midlight)
lead_gradient.setColorAt(0, base_color.darker(120))
lead_gradient.setColorAt(0.3, base_color)
lead_gradient.setColorAt(0.7, base_color)
lead_gradient.setColorAt(1, base_color.darker(120))

painter.setBrush(QBrush(lead_gradient))
painter.setPen(QPen(palette.color(QPalette.Dark), 2))
painter.setPen(QPen(palette.color(QPalette.ColorRole.Dark), 2))

if getattr(self.model, "tip_contact", False):
# Boston Scientific: flat bottom so lead seamlessly meets the tip contact
Expand Down Expand Up @@ -417,7 +421,7 @@ def paintEvent(self, event):
shadow_left.setColorAt(0, QColor(0, 0, 0, 30))
shadow_left.setColorAt(1, QColor(0, 0, 0, 0))
painter.setBrush(QBrush(shadow_left))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawRect(
int(center_x - lead_width / 2),
int(start_y),
Expand Down Expand Up @@ -485,7 +489,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
shadow_poly = QPolygonF(poly)
shadow_poly.translate(1, 2)
painter.setBrush(QColor(0, 0, 0, 30))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawPolygon(shadow_poly)

# Draw main segment
Expand Down Expand Up @@ -514,7 +518,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
]
)
painter.setBrush(QColor(255, 255, 255, 40))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawPolygon(highlight_poly)

self.contact_rects[contact_id] = bounds
Expand All @@ -528,15 +532,19 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
).united(path)

# Label - smaller font in export mode
painter.setPen(Qt.white if state != ContactState.OFF else Qt.black)
painter.setPen(
Qt.GlobalColor.white
if state != ContactState.OFF
else Qt.GlobalColor.black
)
font_size = (
max(6, int(scale * 0.3))
if self.export_mode
else max(7, int(scale * 0.4))
)
font = QFont("Arial", font_size, QFont.Bold)
font = QFont("Arial", font_size, QFont.Weight.Bold)
painter.setFont(font)
painter.drawText(bounds, Qt.AlignCenter, label)
painter.drawText(bounds, Qt.AlignmentFlag.AlignCenter, label)

# Segment 'a' (left) - extends left
contact_id_a = (contact_idx, 0)
Expand Down Expand Up @@ -673,7 +681,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
shadow_path = QPainterPath(tip_path)
shadow_path.translate(0, 2)
painter.setBrush(QColor(0, 0, 0, 20))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawPath(shadow_path)

painter.setBrush(QBrush(contact_gradient_tip))
Expand All @@ -688,7 +696,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
contact_height_px * 0.4,
)
painter.setBrush(QColor(255, 255, 255, 50))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawRoundedRect(highlight_rect, 2, 2)

self.contact_rects[contact_id] = tip_bounds
Expand All @@ -702,7 +710,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
shadow_rect = QRectF(rect)
shadow_rect.translate(0, 2)
painter.setBrush(QColor(0, 0, 0, 20))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawRoundedRect(shadow_rect, 3, 3)

painter.setBrush(QBrush(contact_gradient))
Expand All @@ -717,7 +725,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
rect.height() * 0.4,
)
painter.setBrush(QColor(255, 255, 255, 50))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawRoundedRect(highlight_rect, 2, 2)

self.contact_rects[contact_id] = rect
Expand All @@ -730,13 +738,13 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
).united(path)

# Contact number on the left - smaller font in export mode
painter.setPen(palette.color(QPalette.Text))
painter.setPen(palette.color(QPalette.ColorRole.Text))
elabel_size = (
max(7, int(scale * 0.35))
if self.export_mode
else max(10, int(scale * 0.5))
)
font = QFont("Arial", elabel_size, QFont.Bold)
font = QFont("Arial", elabel_size, QFont.Weight.Bold)
painter.setFont(font)

label_extension = base_extension if is_directional_contact else 0
Expand All @@ -761,7 +769,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
int(current_y),
35,
int(contact_height_px),
Qt.AlignVCenter | Qt.AlignRight,
Qt.AlignmentFlag.AlignVCenter | Qt.AlignmentFlag.AlignRight,
contact_label,
)

Expand Down Expand Up @@ -802,7 +810,7 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
shadow_rect = QRectF(ring_cap_rect)
shadow_rect.translate(0, 1)
painter.setBrush(QColor(0, 0, 0, 25))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawRoundedRect(shadow_rect, 3, 3)

# Draw ring cap
Expand All @@ -819,19 +827,23 @@ def draw_3d_segment(poly, state, is_hovered, contact_id, label):
ring_cap_rect.height() * 0.4,
)
painter.setBrush(QColor(255, 255, 255, 50))
painter.setPen(Qt.NoPen)
painter.setPen(Qt.PenStyle.NoPen)
painter.drawRoundedRect(highlight, 2, 2)

# Ring label - smaller font in export mode
painter.setPen(Qt.white if ring_state != ContactState.OFF else Qt.black)
painter.setPen(
Qt.GlobalColor.white
if ring_state != ContactState.OFF
else Qt.GlobalColor.black
)
ring_font_size = (
max(6, int(scale * 0.3))
if self.export_mode
else max(7, int(scale * 0.3))
)
font = QFont("Arial", ring_font_size)
painter.setFont(font)
painter.drawText(ring_cap_rect, Qt.AlignCenter, "Ring")
painter.drawText(ring_cap_rect, Qt.AlignmentFlag.AlignCenter, "Ring")

@typing.override
def resizeEvent(self, event):
Expand Down
29 changes: 19 additions & 10 deletions src/dbs_annotator/models/session_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,9 @@ def write_clinical_scales(
stimulation: Stimulation parameters
notes: Additional notes for this entry
"""
if not self.tsv_writer:
writer = self.tsv_writer
tsv_file = self.tsv_file
if writer is None or tsv_file is None:
raise ValueError("TSV file not opened. Call open_file() first.")

tz = self._resolve_timezone()
Expand Down Expand Up @@ -227,7 +229,7 @@ def write_clinical_scales(
"notes": notes,
**stim_dict,
}
self.tsv_writer.writerow(row)
writer.writerow(row)
else:
# Write one row per scale
for scale in valid_scales:
Expand All @@ -245,9 +247,9 @@ def write_clinical_scales(
"notes": notes,
**stim_dict,
}
self.tsv_writer.writerow(row)
writer.writerow(row)

self.tsv_file.flush()
tsv_file.flush()
self.block_id += 1

def write_session_scales(
Expand All @@ -266,7 +268,9 @@ def write_session_scales(
stimulation: Stimulation parameters
notes: Additional notes for this entry
"""
if not self.tsv_writer:
writer = self.tsv_writer
tsv_file = self.tsv_file
if writer is None or tsv_file is None:
raise ValueError("TSV file not opened. Call open_file() first.")

tz = self._resolve_timezone()
Expand Down Expand Up @@ -295,7 +299,7 @@ def write_session_scales(
"notes": notes,
**stim_dict,
}
self.tsv_writer.writerow(row)
writer.writerow(row)
else:
# Write one row per scale
for scale in valid_scales:
Expand All @@ -313,9 +317,9 @@ def write_session_scales(
"notes": notes,
**stim_dict,
}
self.tsv_writer.writerow(row)
writer.writerow(row)

self.tsv_file.flush()
tsv_file.flush()
self.block_id += 1

def is_file_open(self) -> bool:
Expand Down Expand Up @@ -430,6 +434,11 @@ def write_simple_annotation(self, annotation: str) -> None:
if not self.is_file_open():
raise ValueError("No file is open. Call initialize_simple_file first.")

writer = self.tsv_writer
tsv_file = self.tsv_file
if writer is None or tsv_file is None:
raise ValueError("No file is open. Call initialize_simple_file first.")

# Get current time
from datetime import datetime

Expand All @@ -445,5 +454,5 @@ def write_simple_annotation(self, annotation: str) -> None:
"timezone": tz_str,
"annotation": annotation,
}
self.tsv_writer.writerow(row)
self.tsv_file.flush()
writer.writerow(row)
tsv_file.flush()
4 changes: 2 additions & 2 deletions src/dbs_annotator/ui/amplitude_split_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,7 @@ def _create_regular_row(self, lbl: str, index: int) -> None:
# Percentage edit
pct_edit = QLineEdit()
pct_edit.setMaximumWidth(55)
pct_edit.setAlignment(Qt.AlignRight)
pct_edit.setAlignment(Qt.AlignmentFlag.AlignRight)
pct_edit.setValidator(QDoubleValidator(0.0, 100.0, 1))
pct_edit.setText(f"{self._percentages.get(lbl, 0.0):g}")
row_layout.addWidget(pct_edit)
Expand Down Expand Up @@ -256,7 +256,7 @@ def _create_segment_rows_only(self, parent_lbl: str) -> None:
# Percentage edit (editable for segments)
pct_edit = QLineEdit()
pct_edit.setMaximumWidth(55)
pct_edit.setAlignment(Qt.AlignRight)
pct_edit.setAlignment(Qt.AlignmentFlag.AlignRight)
pct_edit.setValidator(QDoubleValidator(0.0, 100.0, 1))
pct_edit.setText(f"{segment_percentage:g}")
row_layout.addWidget(pct_edit)
Expand Down
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