# pyfli/roi_maker/roi_maker.py
"""
ROI Maker — PySide6-based interactive region-of-interest editor.
Public API (unchanged):
maker = ROIMaker(intensity_2d, save_path="mask.npy")
multi_mask = maker.draw()
maker.save_masks()
maker.get_multi_cluster_mask()
maker.get_binary_mask()
"""
import os
import sys
from typing import Any
import cv2 # importing cv2 overwrites QT_QPA_PLATFORM_PLUGIN_PATH
import numpy as np
from PySide6.QtCore import QPointF, QRectF, Qt, Signal
from PySide6.QtGui import (
QBrush,
QColor,
QCursor,
QFont,
QImage,
QPainter,
QPen,
QPixmap,
QPolygonF,
)
from PySide6.QtWidgets import (
QAbstractItemView,
QApplication,
QButtonGroup,
QColorDialog,
QDialog,
QDialogButtonBox,
QFrame,
QHBoxLayout,
QHeaderView,
QLabel,
QMainWindow,
QPushButton,
QScrollArea,
QSizePolicy,
QSlider,
QSpacerItem,
QSpinBox,
QStatusBar,
QTableWidget,
QTableWidgetItem,
QVBoxLayout,
QWidget,
)
from pyfli import logging
try:
from .roi_style import STYLE as _STYLE # imported as package
except ImportError:
from roi_style import STYLE as _STYLE # run directly as script
# ─────────────────────────────────────────────────────────────────────────────
# ROI data model
# ─────────────────────────────────────────────────────────────────────────────
[docs]
class ROIObject:
"""
Run the roiobject routine.
vertex list and provides geometry operations used by the ROI GUI.
Parameters
----------
pts : np.ndarray
ROI polygon vertices.
roi_id : int
Identifier assigned to the ROI.
"""
def __init__(self, pts: np.ndarray, roi_id: int = 0) -> None:
self.pts = np.array(pts, dtype=np.int32)
self.roi_id = int(roi_id)
self.assigned = False # True once the user explicitly assigns an ID
self.center = np.mean(self.pts, axis=0)
[docs]
def move(self, dx: np.ndarray, dy: np.ndarray) -> None:
"""
Run the move routine.
Parameters
----------
dx : np.ndarray
Horizontal displacement applied to ROI vertices.
dy : np.ndarray
Vertical displacement applied to ROI vertices.
Returns
-------
None
No object is returned; the function perform move.
"""
self.pts += [int(dx), int(dy)]
self.center = np.mean(self.pts, axis=0)
[docs]
def rotate(self, angle_deg: Any) -> None:
"""
Run the rotate routine.
Parameters
----------
angle_deg : Any
Rotation angle in degrees.
Returns
-------
None
No object is returned; the function perform rotate.
"""
rad = np.radians(angle_deg)
c, s = np.cos(rad), np.sin(rad)
M = np.array([[c, -s], [s, c]])
self.pts = ((self.pts - self.center) @ M.T + self.center).astype(np.int32)
self.center = np.mean(self.pts, axis=0)
[docs]
def scale(self, factor: np.ndarray) -> None:
"""
Run the scale routine.
Parameters
----------
factor : np.ndarray
Scale factor applied to ROI geometry.
Returns
-------
None
No object is returned; the function perform scale.
"""
self.pts = ((self.pts - self.center) * factor + self.center).astype(np.int32)
self.center = np.mean(self.pts, axis=0)
# ─────────────────────────────────────────────────────────────────────────────
# Per-ROI colour palette
# ─────────────────────────────────────────────────────────────────────────────
_PALETTE = [
QColor(30, 102, 245),
QColor(64, 160, 43),
QColor(210, 15, 57),
QColor(136, 57, 239),
QColor(223, 142, 29),
QColor(254, 100, 11),
QColor(23, 146, 153),
QColor(156, 160, 176),
]
def _roi_color(roi_id: int) -> QColor:
"""
Run the ROI color routine.
Parameters
----------
roi_id : int
Identifier assigned to the ROI.
Returns
-------
QColor
Object produced by ROI color.
"""
return _PALETTE[(roi_id - 1) % len(_PALETTE)]
# ─────────────────────────────────────────────────────────────────────────────
# ID Assignment Dialog (shown before saving in multi / both mode)
# ─────────────────────────────────────────────────────────────────────────────
class IDAssignDialog(QDialog):
"""
Let users rename and reorder ROI IDs before masks are saved. The dialog keeps
interactive ROI editing separate from final label assignment.
Parameters
----------
rois : list
ROI objects or label definitions managed by the dialog.
parent : np.ndarray | None
Optional parent GUI widget.
"""
def __init__(self, rois: list, parent: np.ndarray | None = None) -> None:
super().__init__(parent)
self.setWindowTitle("Assign Region IDs")
self.setMinimumWidth(360)
self.setStyleSheet(_STYLE)
layout = QVBoxLayout(self)
layout.setSpacing(10)
layout.setContentsMargins(14, 14, 14, 14)
lbl = QLabel(
"Set the ID for each drawn region.\nIDs must be positive integers (duplicates are allowed)."
)
lbl.setStyleSheet("color: #a6adc8; font-size: 11px;")
lbl.setWordWrap(True)
layout.addWidget(lbl)
self._table = QTableWidget(len(rois), 3)
self._table.setHorizontalHeaderLabels(["Color", "Auto ID", "New ID"])
self._table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.ResizeMode.Fixed
)
self._table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.ResizeMode.Stretch
)
self._table.horizontalHeader().setSectionResizeMode(
2, QHeaderView.ResizeMode.Stretch
)
self._table.setColumnWidth(0, 28)
self._table.verticalHeader().setVisible(False)
self._table.setEditTriggers(QAbstractItemView.EditTrigger.NoEditTriggers)
self._table.setSelectionMode(QAbstractItemView.SelectionMode.NoSelection)
# Next sequential number for unassigned ROIs
_next = max((r.roi_id for r in rois if r.assigned), default=0) + 1
self._spinboxes = []
for row, roi in enumerate(rois):
# colour swatch — grey for unassigned, palette colour for assigned
c = _roi_color(roi.roi_id) if roi.assigned else QColor(120, 120, 130)
swatch = QWidget()
swatch.setStyleSheet(
f"background-color: rgb({c.red()},{c.green()},{c.blue()});"
"border-radius: 3px; margin: 4px;"
)
self._table.setCellWidget(row, 0, swatch)
# status column: shows current ID or "unassigned"
status_text = str(roi.roi_id) if roi.assigned else "unassigned"
id_item = QTableWidgetItem(status_text)
id_item.setTextAlignment(Qt.AlignmentFlag.AlignCenter)
id_item.setForeground(
QBrush(QColor("#585b70") if roi.assigned else QColor("#f38ba8"))
)
self._table.setItem(row, 1, id_item)
# editable new ID — pre-fill with assigned ID or next sequential
default_id = roi.roi_id if roi.assigned else _next
if not roi.assigned:
_next += 1
spin = QSpinBox()
spin.setRange(1, 9999)
spin.setValue(default_id)
spin.setAlignment(Qt.AlignmentFlag.AlignCenter)
self._table.setCellWidget(row, 2, spin)
self._spinboxes.append(spin)
layout.addWidget(self._table)
btns = QDialogButtonBox(
QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
)
btns.accepted.connect(self.accept)
btns.rejected.connect(self.reject)
layout.addWidget(btns)
def get_assignments(self) -> dict:
"""Return {row_index: new_id} so callers can update roi.roi_id."""
return {i: spin.value() for i, spin in enumerate(self._spinboxes)}
# ─────────────────────────────────────────────────────────────────────────────
# Drawing canvas
# ─────────────────────────────────────────────────────────────────────────────
_HANDLE_R = 6
_MIN_BOX = 6
class ImageCanvas(QWidget):
"""
Display images and handle interactive ROI drawing, editing, thresholding, and mask
previews. It is the central canvas widget used by the ROI application.
Parameters
----------
rm : Any
ROI maker or ROI application state object.
parent : np.ndarray | None
Optional parent GUI widget.
"""
roi_changed = Signal()
def __init__(self, rm: Any, parent: np.ndarray | None = None) -> None:
super().__init__(parent)
self.rm = rm
self.selected_idx = -1
self.mode = "rect"
# drawing state
self._drawing = False
self._start_i = None
self._free_i = []
# move state
self._moving = False
self._mv_start_mi = None
self._mv_start_pts = None
# handle-resize state
self._resizing = False
self._rz_handle = -1
self._rz_start_mw = None
self._rz_start_bbox = None
self._rz_start_pts = None
self._cur_mw = QPointF(0, 0)
# transform
self._scale = 1.0
self._offset_x = 0.0
self._offset_y = 0.0
# base image
arr = np.asarray(rm.display_base, dtype=np.uint8)
h, w = arr.shape
self._pixmap = QPixmap.fromImage(
QImage(arr.tobytes(), w, h, w, QImage.Format.Format_Grayscale8)
)
# intensity overlay: stored as a numpy RGBA array so paintEvent can
# wrap it in a fresh QImage each frame without a copy or GC hazard.
self._int_overlay = None # np.ndarray (H, W, 4) uint8 or None
self.setMouseTracking(True)
self.setFocusPolicy(Qt.FocusPolicy.StrongFocus)
self.setSizePolicy(QSizePolicy.Policy.Expanding, QSizePolicy.Policy.Expanding)
self.setMinimumSize(200, 200)
# ── transform ─────────────────────────────────────────────────────────────
def _recompute_transform(self) -> None:
"""
Run the recompute transform routine.
Returns
-------
None
No object is returned; the function perform recompute transform.
"""
cw, ch = self.width(), self.height()
iw, ih = self._pixmap.width(), self._pixmap.height()
self._scale = min(cw / iw, ch / ih)
self._offset_x = (cw - iw * self._scale) / 2
self._offset_y = (ch - ih * self._scale) / 2
def _w2i(self, wx: np.ndarray, wy: np.ndarray) -> tuple[Any, ...]:
"""
Run the w2i routine.
Parameters
----------
wx : np.ndarray
Widget-space x coordinate.
wy : np.ndarray
Widget-space y coordinate.
Returns
-------
tuple[Any, ...]
Tuple containing coordinates converted from world to image space.
"""
return (
(wx - self._offset_x) / self._scale,
(wy - self._offset_y) / self._scale,
)
def _i2w(self, ix: np.ndarray, iy: np.ndarray) -> tuple[Any, ...]:
"""
Run the i2w routine.
Parameters
----------
ix : np.ndarray
Image-space x coordinate.
iy : np.ndarray
Image-space y coordinate.
Returns
-------
tuple[Any, ...]
Tuple containing coordinates converted from image to world space.
"""
return (ix * self._scale + self._offset_x, iy * self._scale + self._offset_y)
def _qpt_w2i(self, q: Any) -> Any:
"""
Run the qpt w2i routine.
Parameters
----------
q : Any
Qt point converted between widget and image coordinates.
Returns
-------
Any
Object produced by qpt w2i.
"""
x, y = self._w2i(q.x(), q.y())
return QPointF(x, y)
def _pts_to_poly_w(self, pts: np.ndarray) -> Any:
"""
Run the pts to poly w routine.
Parameters
----------
pts : np.ndarray
ROI polygon vertices.
Returns
-------
Any
Object produced by pts to poly w.
"""
return QPolygonF([QPointF(*self._i2w(float(p[0]), float(p[1]))) for p in pts])
# ── intensity overlay ──────────────────────────────────────────────────────
def update_intensity_overlay(self) -> None:
"""Recompute the RGBA overlay array for out-of-range pixels.
We store the raw numpy array rather than a QPixmap so that paintEvent
can wrap it in a QImage each frame. This avoids the deferred-copy bug
that occurs when QPixmap.fromImage() is called on an inline QImage.
"""
if not self.rm.intensity_active:
self._int_overlay = None
return
lo, hi = self.rm.intensity_low, self.rm.intensity_high
arr = self.rm._raw_img # (H, W) float64 — original values
below = arr < lo
above = arr > hi
rgba = np.zeros((self.rm.H, self.rm.W, 4), dtype=np.uint8)
rb, gb, bb = self.rm.mask_below_color
rgba[below, 0] = rb
rgba[below, 1] = gb
rgba[below, 2] = bb
rgba[below, 3] = 190
ra, ga, ba = self.rm.mask_above_color
rgba[above, 0] = ra
rgba[above, 1] = ga
rgba[above, 2] = ba
rgba[above, 3] = 190
self._int_overlay = rgba # keep array alive for QImage wrapping
# ── bounding-box handles ───────────────────────────────────────────────────
@staticmethod
def _bbox(pts: np.ndarray) -> tuple[Any, ...]:
"""
Run the bbox routine.
Parameters
----------
pts : np.ndarray
ROI polygon vertices.
Returns
-------
tuple[Any, ...]
Tuple containing bounding-box coordinates.
"""
return (
float(pts[:, 0].min()),
float(pts[:, 1].min()),
float(pts[:, 0].max()),
float(pts[:, 1].max()),
)
def _handle_pos_i(self, pts: np.ndarray) -> list[Any]:
"""
Run the handle pos i routine.
Parameters
----------
pts : np.ndarray
ROI polygon vertices.
Returns
-------
list[Any]
List containing the values produced by handle pos i.
"""
x0, y0, x1, y1 = self._bbox(pts)
mx, my = (x0 + x1) / 2, (y0 + y1) / 2
return [
(x0, y0),
(mx, y0),
(x1, y0),
(x1, my),
(x1, y1),
(mx, y1),
(x0, y1),
(x0, my),
]
def _hit_handle(self, wpt: np.ndarray, roi: Any) -> Any:
"""
Run the hit handle routine.
Parameters
----------
wpt : np.ndarray
Widget-space point tested against ROI geometry.
roi : Any
ROI object or identifier being transformed, drawn, or updated.
Returns
-------
Any
Object produced by hit handle.
"""
thresh2 = (_HANDLE_R + 3) ** 2
for i, (ix, iy) in enumerate(self._handle_pos_i(roi.pts)):
wx, wy = self._i2w(ix, iy)
if (wpt.x() - wx) ** 2 + (wpt.y() - wy) ** 2 <= thresh2:
return i
return -1
def _hit_roi(self, wpt: np.ndarray) -> Any:
"""
Run the hit ROI routine.
Parameters
----------
wpt : np.ndarray
Widget-space point tested against ROI geometry.
Returns
-------
Any
Object produced by hit ROI.
"""
ix, iy = self._w2i(wpt.x(), wpt.y())
for i, roi in enumerate(self.rm.rois):
if (
cv2.pointPolygonTest(
roi.pts.astype(np.float32), (float(ix), float(iy)), False
)
>= 0
):
return i
return -1
# ── painting ───────────────────────────────────────────────────────────────
def paintEvent(self, _: Any) -> None:
"""
Handle paint event callbacks.
Parameters
----------
_ : Any
Callback value passed through to the ROI interaction handler.
Returns
-------
None
No object is returned; the function perform paintevent.
"""
self._recompute_transform()
p = QPainter(self)
p.setRenderHint(QPainter.RenderHint.Antialiasing)
p.setRenderHint(QPainter.RenderHint.SmoothPixmapTransform)
p.fillRect(self.rect(), QColor(18, 18, 30))
iw, ih = self._pixmap.width(), self._pixmap.height()
target = QRectF(
self._offset_x, self._offset_y, iw * self._scale, ih * self._scale
)
if self.rm.show_bg:
p.drawPixmap(target, self._pixmap, QRectF(self._pixmap.rect()))
# intensity mask overlay — wrap the live numpy array in a QImage each
# frame so there is no stale-pointer or deferred-copy issue.
if self.rm.intensity_active and self._int_overlay is not None:
h, w = self._int_overlay.shape[:2]
_img = QImage(
self._int_overlay.data, w, h, 4 * w, QImage.Format.Format_RGBA8888
)
self._int_img_ref = _img # prevent GC while QPainter holds it
p.drawImage(target, _img)
for i, roi in enumerate(self.rm.rois):
self._paint_roi(p, roi, selected=(i == self.selected_idx))
if self._drawing and self._start_i is not None:
self._paint_preview(p)
p.end()
def _paint_roi(self, p: Any, roi: Any, selected: np.ndarray) -> None:
"""
Run the paint ROI routine.
Parameters
----------
p : Any
Detector parameter object or fitted parameter vector.
roi : Any
ROI object or identifier being transformed, drawn, or updated.
selected : np.ndarray
Whether the ROI is currently selected.
Returns
-------
None
No object is returned; the function perform paint ROI.
"""
if not roi.assigned:
color = QColor(0, 220, 100) if selected else QColor(140, 140, 155)
line_style = Qt.PenStyle.DashLine
label_text = "?"
else:
color = QColor(0, 220, 100) if selected else _roi_color(roi.roi_id)
line_style = Qt.PenStyle.SolidLine
label_text = f"ID:{roi.roi_id}"
poly = self._pts_to_poly_w(roi.pts)
fill = QColor(
color.red(), color.green(), color.blue(), 40 if not roi.assigned else 55
)
p.setBrush(QBrush(fill))
pen = QPen(color, 2.5 if selected else 1.5, line_style)
pen.setJoinStyle(Qt.PenJoinStyle.RoundJoin)
p.setPen(pen)
p.drawPolygon(poly)
if roi.pts.shape[0]:
wx, wy = self._i2w(float(roi.pts[0, 0]), float(roi.pts[0, 1]))
p.setPen(QPen(Qt.GlobalColor.white))
p.setFont(QFont("Segoe UI", 9, QFont.Weight.Bold))
p.drawText(int(wx) + 4, int(wy) + 13, label_text)
if selected:
self._paint_handles(p, roi)
def _paint_handles(self, p: Any, roi: Any) -> None:
"""
Run the paint handles routine.
Parameters
----------
p : Any
Detector parameter object or fitted parameter vector.
roi : Any
ROI object or identifier being transformed, drawn, or updated.
Returns
-------
None
No object is returned; the function perform paint handles.
"""
for ix, iy in self._handle_pos_i(roi.pts):
wx, wy = self._i2w(ix, iy)
r = _HANDLE_R
p.setBrush(QBrush(QColor(255, 255, 255, 230)))
p.setPen(QPen(QColor(30, 100, 220), 1.5))
p.drawEllipse(QRectF(wx - r, wy - r, r * 2, r * 2))
def _paint_preview(self, p: Any) -> None:
"""
Run the paint preview routine.
Parameters
----------
p : Any
Detector parameter object or fitted parameter vector.
Returns
-------
None
No object is returned; the function perform paint preview.
"""
pts = self._preview_pts()
if len(pts) < 3:
return
poly = QPolygonF(
[QPointF(*self._i2w(float(pt[0]), float(pt[1]))) for pt in pts]
)
p.setBrush(QBrush(QColor(255, 255, 255, 25)))
p.setPen(QPen(QColor(255, 255, 255, 160), 1.2, Qt.PenStyle.DashLine))
p.drawPolygon(poly)
def _preview_pts(self) -> Any:
"""
Run the preview pts routine.
Returns
-------
Any
Object produced by preview pts.
"""
if self._start_i is None:
return []
ix, iy = self._start_i
mx, my = self._w2i(self._cur_mw.x(), self._cur_mw.y())
if self.mode == "rect":
return [[ix, iy], [mx, iy], [mx, my], [ix, my]]
if self.mode == "circle":
r = max(int(np.hypot(mx - ix, my - iy)), 3)
return cv2.ellipse2Poly((int(ix), int(iy)), (r, r), 0, 0, 360, 8).tolist()
return list(self._free_i)
# ── mouse ──────────────────────────────────────────────────────────────────
def mousePressEvent(self, e: Any) -> None:
"""
Handle mouse press event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform mousepressevent.
"""
if e.button() != Qt.MouseButton.LeftButton:
return
wpt = e.position()
# ── Assign mode: click a ROI to give it the next sequential ID ──────
if self.mode == "assign":
hit = self._hit_roi(wpt)
if hit != -1:
roi = self.rm.rois[hit]
if not roi.assigned:
roi.roi_id = self.rm.assign_counter
roi.assigned = True
self.rm.assign_counter += 1
self.selected_idx = hit
else:
self.selected_idx = -1
self.update()
self.roi_changed.emit()
return
# ────────────────────────────────────────────────────────────────────
if self.selected_idx != -1:
hi = self._hit_handle(wpt, self.rm.rois[self.selected_idx])
if hi != -1:
roi = self.rm.rois[self.selected_idx]
self._resizing = True
self._rz_handle = hi
self._rz_start_mw = wpt
self._rz_start_bbox = self._bbox(roi.pts)
self._rz_start_pts = roi.pts.copy().astype(float)
self.update()
return
hit = self._hit_roi(wpt)
if hit != -1:
self.selected_idx = hit
self._moving = True
self._mv_start_mi = self._qpt_w2i(wpt)
self._mv_start_pts = self.rm.rois[hit].pts.copy().astype(float)
self.update()
self.roi_changed.emit()
return
if self.mode != "select":
self.selected_idx = -1
self._drawing = True
ix, iy = self._w2i(wpt.x(), wpt.y())
self._start_i = (ix, iy)
self._free_i = [(ix, iy)]
else:
self.selected_idx = -1
self.update()
self.roi_changed.emit()
def mouseMoveEvent(self, e: Any) -> None:
"""
Handle mouse move event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform mousemoveevent.
"""
wpt = e.position()
self._cur_mw = wpt
if self._resizing and self.selected_idx != -1:
self._apply_resize(wpt)
elif self._moving and self.selected_idx != -1:
cur_i = self._qpt_w2i(wpt)
dx = cur_i.x() - self._mv_start_mi.x()
dy = cur_i.y() - self._mv_start_mi.y()
roi = self.rm.rois[self.selected_idx]
new_pts = self._mv_start_pts + np.array([dx, dy])
roi.pts = np.clip(new_pts, 0, None).astype(np.int32)
roi.center = np.mean(roi.pts, axis=0)
elif self._drawing and self.mode == "freehand" and self._start_i:
ix, iy = self._w2i(wpt.x(), wpt.y())
self._free_i.append((ix, iy))
# adaptive cursor
if self.selected_idx != -1 and not self._drawing:
hi = self._hit_handle(wpt, self.rm.rois[self.selected_idx])
cursors = {
0: Qt.CursorShape.SizeFDiagCursor,
4: Qt.CursorShape.SizeFDiagCursor,
2: Qt.CursorShape.SizeBDiagCursor,
6: Qt.CursorShape.SizeBDiagCursor,
1: Qt.CursorShape.SizeVerCursor,
5: Qt.CursorShape.SizeVerCursor,
3: Qt.CursorShape.SizeHorCursor,
7: Qt.CursorShape.SizeHorCursor,
}
if hi in cursors:
self.setCursor(cursors[hi])
elif self._hit_roi(wpt) != -1:
self.setCursor(Qt.CursorShape.SizeAllCursor)
else:
self.setCursor(
Qt.CursorShape.CrossCursor
if self.mode != "select"
else Qt.CursorShape.ArrowCursor
)
else:
self.setCursor(
Qt.CursorShape.CrossCursor
if self.mode not in ("select", None)
else Qt.CursorShape.ArrowCursor
)
self.update()
def mouseReleaseEvent(self, e: Any) -> None:
"""
Handle mouse release event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform mousereleaseevent.
"""
if e.button() != Qt.MouseButton.LeftButton:
return
if self._resizing:
self._resizing = False
self.roi_changed.emit()
if self._moving:
self._moving = False
self.roi_changed.emit()
if self._drawing:
self._drawing = False
wpt = e.position()
ix, iy = self._w2i(wpt.x(), wpt.y())
pts = self._finalise_pts(ix, iy)
if len(pts) >= 3:
roi = ROIObject(pts) # roi_id=0, assigned=False until user assigns
self.rm.rois.append(roi)
self.selected_idx = len(self.rm.rois) - 1
self._start_i = None
self._free_i = []
self.roi_changed.emit()
self.update()
def _finalise_pts(self, mx: np.ndarray, my: np.ndarray) -> Any:
"""
Run the finalise pts routine.
Parameters
----------
mx : np.ndarray
Mouse x coordinate used while finalizing ROI points.
my : np.ndarray
Mouse y coordinate used while finalizing ROI points.
Returns
-------
Any
Object produced by finalise pts.
"""
if self._start_i is None:
return []
ix, iy = self._start_i
if self.mode == "rect":
return np.array([[ix, iy], [mx, iy], [mx, my], [ix, my]])
if self.mode == "circle":
r = max(int(np.hypot(mx - ix, my - iy)), 3)
return cv2.ellipse2Poly((int(ix), int(iy)), (r, r), 0, 0, 360, 8)
pts = np.array(self._free_i)
return pts if len(pts) >= 3 else []
def _apply_resize(self, wpt: np.ndarray) -> None:
"""
Apply resize.
Parameters
----------
wpt : np.ndarray
Widget-space point tested against ROI geometry.
Returns
-------
None
No object is returned; the function apply resize.
"""
roi = self.rm.rois[self.selected_idx]
dix = (wpt.x() - self._rz_start_mw.x()) / self._scale
diy = (wpt.y() - self._rz_start_mw.y()) / self._scale
x0, y0, x1, y1 = self._rz_start_bbox
nx0, ny0, nx1, ny1 = x0, y0, x1, y1
hi = self._rz_handle
if hi in (0, 6, 7):
nx0 = x0 + dix
if hi in (2, 3, 4):
nx1 = x1 + dix
if hi in (0, 1, 2):
ny0 = y0 + diy
if hi in (4, 5, 6):
ny1 = y1 + diy
if nx1 - nx0 < _MIN_BOX:
nx1 = nx0 + _MIN_BOX
if ny1 - ny0 < _MIN_BOX:
ny1 = ny0 + _MIN_BOX
bw = max(x1 - x0, 1.0)
bh = max(y1 - y0, 1.0)
pts = self._rz_start_pts.copy()
pts[:, 0] = nx0 + (pts[:, 0] - x0) * (nx1 - nx0) / bw
pts[:, 1] = ny0 + (pts[:, 1] - y0) * (ny1 - ny0) / bh
roi.pts = np.clip(pts, 0, None).astype(np.int32)
roi.center = np.mean(roi.pts, axis=0)
def keyPressEvent(self, e: Any) -> None:
"""
Handle key press event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform keypressevent.
"""
if e.key() in (Qt.Key.Key_Delete, Qt.Key.Key_Backspace):
self._delete_selected()
def _delete_selected(self) -> None:
"""
Run the delete selected routine.
Returns
-------
None
No object is returned; the function perform delete selected.
"""
if 0 <= self.selected_idx < len(self.rm.rois):
self.rm.rois.pop(self.selected_idx)
self.selected_idx = -1
# Recalculate assign_counter so it stays above all existing IDs
assigned_ids = [r.roi_id for r in self.rm.rois if r.assigned]
self.rm.assign_counter = (max(assigned_ids) + 1) if assigned_ids else 1
self.roi_changed.emit()
self.update()
# ─────────────────────────────────────────────────────────────────────────────
# Main window
# ─────────────────────────────────────────────────────────────────────────────
class ROIApp(QMainWindow):
"""
Host the full interactive ROI maker interface. The widget wires image display,
threshold controls, ROI editing actions, ID assignment, and mask saving into one
application window.
Parameters
----------
rm : Any
ROI maker or ROI application state object.
"""
def __init__(self, rm: Any) -> None:
super().__init__()
self.rm = rm
self.setWindowTitle("ROI Maker")
self.setStyleSheet(_STYLE)
central = QWidget()
self.setCentralWidget(central)
root_layout = QHBoxLayout(central)
root_layout.setContentsMargins(0, 0, 0, 0)
root_layout.setSpacing(0)
# Canvas first so _build_sidebar signals can reference it safely
self.canvas = ImageCanvas(rm, self)
self.canvas.roi_changed.connect(self._refresh_status)
self.canvas.update_intensity_overlay()
sidebar = self._build_sidebar()
root_layout.addWidget(sidebar)
root_layout.addWidget(self.canvas, stretch=1)
self.setStatusBar(QStatusBar(self))
self._refresh_status()
# ── sidebar ───────────────────────────────────────────────────────────────
def _build_sidebar(self) -> Any:
"""
Build sidebar.
Returns
-------
Any
Object produced by build sidebar.
"""
scroll = QScrollArea()
scroll.setWidgetResizable(True)
scroll.setHorizontalScrollBarPolicy(Qt.ScrollBarPolicy.ScrollBarAlwaysOff)
scroll.setStyleSheet(
"QScrollArea { border: none; background: #181825; }"
"QScrollBar:vertical { width: 6px; background: #181825; }"
"QScrollBar::handle:vertical { background: #313244; border-radius: 3px; }"
)
scroll.setFixedWidth(185)
sb = QWidget()
sb.setObjectName("sidebar")
layout = QVBoxLayout(sb)
layout.setContentsMargins(10, 12, 10, 12)
layout.setSpacing(4)
scroll.setWidget(sb)
# Title
title = QLabel("⬡ ROI Maker")
title.setObjectName("title_lbl")
title.setAlignment(Qt.AlignmentFlag.AlignCenter)
layout.addWidget(title)
layout.addWidget(self._divider())
# ── TOOLS ──
layout.addWidget(self._section_label("TOOLS"))
self._tool_btns = {}
for key, icon, label, sc in [
("select", "↖", "Select / Move", "S"),
("rect", "▭", "Rectangle", "R"),
("circle", "◯", "Circle", "C"),
("freehand", "✏", "Freehand", "F"),
("assign", "⊕", "Assign IDs", "A"),
]:
btn = self._tool_button(icon, label, sc)
btn.toggled.connect(lambda on, k=key: self._on_tool_toggled(k, on))
self._tool_btns[key] = btn
layout.addWidget(btn)
reset_btn = self._action_button("↺", "Reset IDs", "")
reset_btn.setToolTip(
"Clear all ID assignments — ROIs return to unassigned state"
)
reset_btn.clicked.connect(self._reset_ids)
layout.addWidget(reset_btn)
auto_btn = self._action_button("⟳", "Auto-assign IDs", "")
auto_btn.setToolTip(
"Assign sequential IDs to all unassigned ROIs automatically"
)
auto_btn.clicked.connect(self._auto_assign_ids)
layout.addWidget(auto_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── OUTPUT TYPE ──
layout.addWidget(self._section_label("OUTPUT TYPE"))
self._mask_type_group = QButtonGroup(self)
self._mask_type_group.setExclusive(True)
for val, icon, label in [
("binary", "◻", "Binary"),
("multi", "◼", "Multi-ID"),
("both", "⊞", "Both"),
]:
btn = QPushButton(f"{icon} {label}")
btn.setObjectName("tool_btn")
btn.setCheckable(True)
btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
btn.setToolTip(f"Save as: {label}")
self._mask_type_group.addButton(btn)
layout.addWidget(btn)
if val == self.rm.mask_type:
btn.setChecked(True)
self._mask_type_group.buttonClicked.connect(self._on_mask_type_btn)
# store reference to buttons by order
self._mask_type_btns = {
v: self._mask_type_group.buttons()[i]
for i, v in enumerate(["binary", "multi", "both"])
}
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── EDIT ──
layout.addWidget(self._section_label("EDIT"))
self._bg_btn = self._action_button("◑", "Toggle Image", "B")
self._bg_btn.clicked.connect(self._toggle_bg)
layout.addWidget(self._bg_btn)
del_btn = self._action_button("✕", "Delete ROI", "Del")
del_btn.clicked.connect(self._delete_selected)
layout.addWidget(del_btn)
del_all_btn = self._action_button("⊘", "Delete All ROIs", "")
del_all_btn.setToolTip("Remove every ROI and start fresh")
del_all_btn.clicked.connect(self._delete_all)
layout.addWidget(del_all_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── INTENSITY FILTER ──
layout.addWidget(self._section_label("INTENSITY FILTER"))
self._int_btn = QPushButton("⚡ Enable Filter")
self._int_btn.setObjectName("action_btn")
self._int_btn.setCheckable(True)
self._int_btn.setChecked(self.rm.intensity_active)
self._int_btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
self._int_btn.toggled.connect(self._on_intensity_toggled)
layout.addWidget(self._int_btn)
# Low threshold
self._lo_lbl = QLabel("Low threshold")
self._lo_lbl.setStyleSheet("color: #a6adc8; font-size: 11px;")
layout.addWidget(self._lo_lbl)
_lo_row = QWidget()
_lo_rl = QHBoxLayout(_lo_row)
_lo_rl.setContentsMargins(0, 0, 0, 0)
_lo_rl.setSpacing(4)
self._lo_slider = QSlider(Qt.Orientation.Horizontal)
self._lo_slider.setRange(self.rm.img_min, self.rm.img_max)
self._lo_slider.setValue(self.rm.intensity_low)
self._lo_slider.valueChanged.connect(self._on_lo_changed)
_lo_rl.addWidget(self._lo_slider)
self._lo_spin = QSpinBox()
self._lo_spin.setRange(self.rm.img_min, self.rm.img_max)
self._lo_spin.setValue(self.rm.intensity_low)
self._lo_spin.setFixedWidth(58)
self._lo_spin.valueChanged.connect(self._on_lo_spin_changed)
_lo_rl.addWidget(self._lo_spin)
layout.addWidget(_lo_row)
# High threshold
self._hi_lbl = QLabel("High threshold")
self._hi_lbl.setStyleSheet("color: #a6adc8; font-size: 11px;")
layout.addWidget(self._hi_lbl)
_hi_row = QWidget()
_hi_rl = QHBoxLayout(_hi_row)
_hi_rl.setContentsMargins(0, 0, 0, 0)
_hi_rl.setSpacing(4)
self._hi_slider = QSlider(Qt.Orientation.Horizontal)
self._hi_slider.setRange(self.rm.img_min, self.rm.img_max)
self._hi_slider.setValue(self.rm.intensity_high)
self._hi_slider.valueChanged.connect(self._on_hi_changed)
_hi_rl.addWidget(self._hi_slider)
self._hi_spin = QSpinBox()
self._hi_spin.setRange(self.rm.img_min, self.rm.img_max)
self._hi_spin.setValue(self.rm.intensity_high)
self._hi_spin.setFixedWidth(58)
self._hi_spin.valueChanged.connect(self._on_hi_spin_changed)
_hi_rl.addWidget(self._hi_spin)
layout.addWidget(_hi_row)
# Mask-color pickers (separate for below/above)
self._below_color_btn = QPushButton("▼ Below color")
self._below_color_btn.setObjectName("action_btn")
self._below_color_btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
self._below_color_btn.setToolTip("Color for pixels below low threshold")
self._below_color_btn.clicked.connect(self._pick_below_color)
self._refresh_below_color_btn()
layout.addWidget(self._below_color_btn)
self._above_color_btn = QPushButton("▲ Above color")
self._above_color_btn.setObjectName("action_btn")
self._above_color_btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
self._above_color_btn.setToolTip("Color for pixels above high threshold")
self._above_color_btn.clicked.connect(self._pick_above_color)
self._refresh_above_color_btn()
layout.addWidget(self._above_color_btn)
thresh_btn = self._action_button("⊞", "Create Threshold ROI", "")
thresh_btn.setToolTip(
"Convert the current intensity threshold into ROI(s).\n"
"They are added as unassigned ROIs — assign IDs the same way as drawn ROIs."
)
thresh_btn.clicked.connect(self._create_threshold_rois)
layout.addWidget(thresh_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── FILE ──
layout.addWidget(self._section_label("FILE"))
save_btn = QPushButton("✓ Save && Close ↵")
save_btn.setObjectName("save_btn")
save_btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
save_btn.clicked.connect(self._save_close)
layout.addWidget(save_btn)
cancel_btn = QPushButton("✗ Cancel Esc")
cancel_btn.setObjectName("cancel_btn")
cancel_btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
cancel_btn.clicked.connect(self._cancel)
layout.addWidget(cancel_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# Status
self._status_lbl = QLabel()
self._status_lbl.setAlignment(
Qt.AlignmentFlag.AlignLeft | Qt.AlignmentFlag.AlignTop
)
self._status_lbl.setWordWrap(True)
self._status_lbl.setStyleSheet(
"color: #585b70; font-size: 11px; padding: 4px 2px;"
)
layout.addWidget(self._status_lbl)
layout.addItem(
QSpacerItem(0, 0, QSizePolicy.Policy.Minimum, QSizePolicy.Policy.Expanding)
)
# Activate default tool
self._tool_btns["rect"].setChecked(True)
return scroll
# ── widget helpers ────────────────────────────────────────────────────────
def _divider(self) -> Any:
"""
Run the divider routine.
Returns
-------
Any
Object produced by divider.
"""
line = QFrame()
line.setObjectName("divider")
line.setFrameShape(QFrame.Shape.HLine)
return line
def _section_label(self, text: np.ndarray) -> Any:
"""
Run the section label routine.
Parameters
----------
text : np.ndarray
Text rendered into a UI label or formatted table cell.
Returns
-------
Any
Object produced by section label.
"""
lbl = QLabel(text)
lbl.setObjectName("section_lbl")
lbl.setContentsMargins(2, 6, 2, 2)
return lbl
def _tool_button(self, icon: Any, label: str, shortcut: np.ndarray) -> np.ndarray:
"""
Run the tool button routine.
Parameters
----------
icon : Any
Icon text shown on a UI button.
label : str
Display label assigned to the data or plot element.
shortcut : np.ndarray
Keyboard shortcut assigned to the UI button.
Returns
-------
np.ndarray
Qt button configured for the requested tool.
"""
btn = QPushButton(f"{icon} {label}")
btn.setObjectName("tool_btn")
btn.setCheckable(True)
btn.setAutoExclusive(True)
btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
btn.setToolTip(f"{label} [{shortcut}]")
return btn
def _action_button(self, icon: Any, label: str, shortcut: np.ndarray) -> np.ndarray:
"""
Run the action button routine.
Parameters
----------
icon : Any
Icon text shown on a UI button.
label : str
Display label assigned to the data or plot element.
shortcut : np.ndarray
Keyboard shortcut assigned to the UI button.
Returns
-------
np.ndarray
Qt button configured for the requested action.
"""
btn = QPushButton(f"{icon} {label}")
btn.setObjectName("action_btn")
btn.setCursor(QCursor(Qt.CursorShape.PointingHandCursor))
btn.setToolTip(f"{label} [{shortcut}]")
return btn
def _refresh_below_color_btn(self) -> None:
"""
Run the refresh below color btn routine.
Returns
-------
None
No object is returned; the function perform refresh below color btn.
"""
r, g, b = self.rm.mask_below_color
luma = 0.299 * r + 0.587 * g + 0.114 * b
fg = "#000" if luma > 128 else "#fff"
self._below_color_btn.setStyleSheet(
f"QPushButton#action_btn {{ background-color: rgb({r},{g},{b}); "
f"color: {fg}; border: 1px solid #313244; border-radius: 8px; "
"padding: 8px 10px; text-align: left; }"
f"QPushButton#action_btn:hover {{ background-color: rgb({min(r + 20, 255)},{min(g + 20, 255)},{min(b + 20, 255)}); }}"
)
def _refresh_above_color_btn(self) -> None:
"""
Run the refresh above color btn routine.
Returns
-------
None
No object is returned; the function perform refresh above color btn.
"""
r, g, b = self.rm.mask_above_color
luma = 0.299 * r + 0.587 * g + 0.114 * b
fg = "#000" if luma > 128 else "#fff"
self._above_color_btn.setStyleSheet(
f"QPushButton#action_btn {{ background-color: rgb({r},{g},{b}); "
f"color: {fg}; border: 1px solid #313244; border-radius: 8px; "
"padding: 8px 10px; text-align: left; }"
f"QPushButton#action_btn:hover {{ background-color: rgb({min(r + 20, 255)},{min(g + 20, 255)},{min(b + 20, 255)}); }}"
)
# ── actions ───────────────────────────────────────────────────────────────
def _on_tool_toggled(self, key: str, on: Any) -> None:
"""
Run the on tool toggled routine.
Parameters
----------
key : str
Dictionary key or parameter-map name to extract.
on : Any
Toggle state emitted by the UI control.
Returns
-------
None
No object is returned; the function perform on tool toggled.
"""
if on:
self.canvas.mode = key
self.canvas.selected_idx = -1
self.canvas.update()
self._refresh_status()
def _on_mask_type_btn(self, btn: np.ndarray) -> None:
"""
Run the on mask type btn routine.
Parameters
----------
btn : np.ndarray
Button that triggered the UI callback.
Returns
-------
None
No object is returned; the function perform on mask type btn.
"""
labels = {"◻ Binary": "binary", "◼ Multi-ID": "multi", "⊞ Both": "both"}
self.rm.mask_type = labels.get(btn.text(), "multi")
self._refresh_status()
def _toggle_bg(self) -> None:
"""
Run the toggle bg routine.
Returns
-------
None
No object is returned; the function perform toggle bg.
"""
self.rm.show_bg = not self.rm.show_bg
self._bg_btn.setStyleSheet(
""
if self.rm.show_bg
else "QPushButton#action_btn { background-color: #1e66f5; color: #fff; "
"border: 1px solid #1d62e8; border-radius: 8px; padding: 8px 10px; }"
)
self.canvas.update()
def _delete_selected(self) -> None:
"""
Run the delete selected routine.
Returns
-------
None
No object is returned; the function perform delete selected.
"""
self.canvas._delete_selected()
def _on_intensity_toggled(self, active: np.ndarray) -> None:
"""
Run the on intensity toggled routine.
Parameters
----------
active : np.ndarray
Whether the UI control is active.
Returns
-------
None
No object is returned; the function perform on intensity toggled.
"""
self.rm.intensity_active = active
self.canvas.update_intensity_overlay()
self.canvas.update()
self._refresh_status()
def _on_lo_changed(self, val: np.ndarray) -> None:
"""
Run the on lo changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on lo changed.
"""
val = min(val, self.rm.intensity_high)
self._lo_slider.blockSignals(True)
self._lo_slider.setValue(val)
self._lo_slider.blockSignals(False)
self._lo_spin.blockSignals(True)
self._lo_spin.setValue(val)
self._lo_spin.blockSignals(False)
self.rm.intensity_low = val
self.canvas.update_intensity_overlay()
self.canvas.update()
def _on_lo_spin_changed(self, val: np.ndarray) -> None:
"""
Run the on lo spin changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on lo spin changed.
"""
self._lo_slider.setValue(val)
def _on_hi_changed(self, val: np.ndarray) -> None:
"""
Run the on hi changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on hi changed.
"""
val = max(val, self.rm.intensity_low)
self._hi_slider.blockSignals(True)
self._hi_slider.setValue(val)
self._hi_slider.blockSignals(False)
self._hi_spin.blockSignals(True)
self._hi_spin.setValue(val)
self._hi_spin.blockSignals(False)
self.rm.intensity_high = val
self.canvas.update_intensity_overlay()
self.canvas.update()
def _on_hi_spin_changed(self, val: np.ndarray) -> None:
"""
Run the on hi spin changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on hi spin changed.
"""
self._hi_slider.setValue(val)
def _pick_below_color(self) -> None:
"""
Run the pick below color routine.
Returns
-------
None
No object is returned; the function perform pick below color.
"""
r, g, b = self.rm.mask_below_color
chosen = QColorDialog.getColor(
QColor(r, g, b), self, "Pick color for below-threshold pixels"
)
if chosen.isValid():
self.rm.mask_below_color = (chosen.red(), chosen.green(), chosen.blue())
self._refresh_below_color_btn()
self.canvas.update_intensity_overlay()
self.canvas.update()
def _pick_above_color(self) -> None:
"""
Run the pick above color routine.
Returns
-------
None
No object is returned; the function perform pick above color.
"""
r, g, b = self.rm.mask_above_color
chosen = QColorDialog.getColor(
QColor(r, g, b), self, "Pick color for above-threshold pixels"
)
if chosen.isValid():
self.rm.mask_above_color = (chosen.red(), chosen.green(), chosen.blue())
self._refresh_above_color_btn()
self.canvas.update_intensity_overlay()
self.canvas.update()
def _create_threshold_rois(self) -> None:
"""Convert the current intensity threshold mask into ROIObject(s).
Each contiguous region in the threshold mask becomes an unassigned ROI,
identical in behaviour to any hand-drawn ROI. The user then assigns IDs
and saves them through the normal pipeline.
"""
if not self.rm.intensity_active:
self.statusBar().showMessage(" Enable the intensity filter first.", 3000)
return
n = self.rm.create_rois_from_threshold()
if n == 0:
self.statusBar().showMessage(
" No regions found in threshold mask (try wider range).", 3000
)
else:
self.statusBar().showMessage(
f" Added {n} threshold-based ROI(s). Assign IDs before saving.", 4000
)
self.canvas.update()
self._refresh_status()
def _save_threshold_mask(self) -> None:
"""Save a binary mask built purely from intensity thresholds (no ROI polygons)."""
if not self.rm.intensity_active:
self.statusBar().showMessage(" Enable the intensity filter first.", 3000)
return
path = self.rm.save_threshold_binary_mask()
self.statusBar().showMessage(f" Saved threshold binary mask → {path}", 5000)
def _reset_ids(self) -> None:
"""Clear all ID assignments — every ROI returns to unassigned state."""
for roi in self.rm.rois:
roi.roi_id = 0
roi.assigned = False
self.rm.assign_counter = 1
self.canvas.update()
self._refresh_status()
def _delete_all(self) -> None:
"""Remove every ROI and reset the assign counter."""
if not self.rm.rois:
self.statusBar().showMessage(" No ROIs to delete.", 2000)
return
n = len(self.rm.rois)
self.rm.rois.clear()
self.rm.assign_counter = 1
self.canvas.selected_idx = -1
self.canvas.update()
self._refresh_status()
self.statusBar().showMessage(f" Deleted {n} ROI(s).", 2000)
def _auto_assign_ids(self) -> None:
"""Assign sequential IDs to all unassigned ROIs without showing a dialog."""
pending = [r for r in self.rm.rois if not r.assigned]
if not pending:
self.statusBar().showMessage(" All ROIs already have IDs.", 2000)
return
for roi in pending:
roi.roi_id = self.rm.assign_counter
roi.assigned = True
self.rm.assign_counter += 1
self.canvas.update()
self._refresh_status()
self.statusBar().showMessage(
f" Auto-assigned IDs to {len(pending)} ROI(s).", 2000
)
def _show_id_dialog(self) -> bool:
"""Show ID-assignment dialog for remaining unassigned ROIs before save."""
dlg = IDAssignDialog(self.rm.rois, self)
if dlg.exec() == QDialog.DialogCode.Accepted:
for i, new_id in dlg.get_assignments().items():
self.rm.rois[i].roi_id = new_id
self.rm.rois[i].assigned = True
assigned = [r.roi_id for r in self.rm.rois if r.assigned]
self.rm.assign_counter = (max(assigned) + 1) if assigned else 1
self.canvas.update()
return True
return False
def _save_close(self) -> None:
"""
Save close.
Returns
-------
None
No object is returned; the function save close.
"""
if self.rm.mask_type in ("multi", "both") and self.rm.rois:
unassigned = [r for r in self.rm.rois if not r.assigned]
if unassigned:
# Only show dialog when some ROIs still lack IDs
if not self._show_id_dialog():
return
self.rm.save_masks()
self.close()
def _cancel(self) -> None:
"""
Run the cancel routine.
Returns
-------
None
No object is returned; the function perform cancel.
"""
self.close()
def _refresh_status(self) -> None:
"""
Run the refresh status routine.
Returns
-------
None
No object is returned; the function perform refresh status.
"""
n = len(self.rm.rois)
n_assigned = sum(1 for r in self.rm.rois if r.assigned)
n_pending = n - n_assigned
sel = self.canvas.selected_idx
sel_str = f"#{self.rm.rois[sel].roi_id}" if 0 <= sel < n else "—"
mode_map = {
"select": "Select/Move",
"rect": "Rectangle",
"circle": "Circle",
"freehand": "Freehand",
"assign": "Assign IDs",
}
type_map = {"binary": "Binary", "multi": "Multi-ID", "both": "Both"}
hint = (
"Click ROIs to number them"
if self.canvas.mode == "assign"
else "Drag handles to resize"
)
self._status_lbl.setText(
f"Mode: {mode_map.get(self.canvas.mode, '')}\n"
f"Output: {type_map.get(self.rm.mask_type, '')}\n"
f"Filter: {'ON' if self.rm.intensity_active else 'off'} "
f"[{self.rm.intensity_low}–{self.rm.intensity_high}]\n"
f"ROIs: {n} (✓{n_assigned} ?{n_pending})\n"
f"Sel: {sel_str}"
)
self.statusBar().showMessage(
f" {mode_map.get(self.canvas.mode, '')} │ "
f"Output: {type_map.get(self.rm.mask_type, '')} │ "
f"ROIs: {n} ✓{n_assigned} assigned ?{n_pending} pending │ "
f"{hint} · [R/C/F/S/A/B/Del/↵/Esc]"
)
# ── keyboard ──────────────────────────────────────────────────────────────
def keyPressEvent(self, e: Any) -> None:
"""
Handle key press event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform keypressevent.
"""
key_map = {
Qt.Key.Key_S: "select",
Qt.Key.Key_R: "rect",
Qt.Key.Key_C: "circle",
Qt.Key.Key_F: "freehand",
Qt.Key.Key_A: "assign",
}
if e.key() in key_map:
self._tool_btns[key_map[e.key()]].setChecked(True)
elif e.key() == Qt.Key.Key_B:
self._toggle_bg()
elif e.key() in (Qt.Key.Key_Delete, Qt.Key.Key_Backspace):
self._delete_selected()
elif e.key() in (Qt.Key.Key_Return, Qt.Key.Key_Enter):
self._save_close()
elif e.key() == Qt.Key.Key_Escape:
self._cancel()
else:
super().keyPressEvent(e)
# ─────────────────────────────────────────────────────────────────────────────
# Public ROIMaker
# ─────────────────────────────────────────────────────────────────────────────
# ─────────────────────────────────────────────────────────────────────────────
# Per-ROI colour palette
# ─────────────────────────────────────────────────────────────────────────────
_PALETTE = [
QColor(30, 102, 245),
QColor(64, 160, 43),
QColor(210, 15, 57),
QColor(136, 57, 239),
QColor(223, 142, 29),
QColor(254, 100, 11),
QColor(23, 146, 153),
QColor(156, 160, 176),
]
def _roi_color(roi_id: int) -> QColor:
"""
Run the ROI color routine.
Parameters
----------
roi_id : int
Identifier assigned to the ROI.
Returns
-------
QColor
Object produced by ROI color.
"""
return _PALETTE[(roi_id - 1) % len(_PALETTE)]
# ─────────────────────────────────────────────────────────────────────────────
# ID Assignment Dialog (shown before saving in multi / both mode)
# ─────────────────────────────────────────────────────────────────────────────
[docs]
class IDAssignDialog(QDialog): # noqa: F811
"""
Let users rename and reorder ROI IDs before masks are saved. The dialog keeps
interactive ROI editing separate from final label assignment.
Parameters
----------
rois : list
ROI objects or label definitions managed by the dialog.
parent : np.ndarray | None
Optional parent GUI widget.
"""
def __init__(self, rois: list, parent: np.ndarray | None = None) -> None:
super().__init__(parent)
self.setWindowTitle("Assign Region IDs")
self.setMinimumWidth(360)
self.setStyleSheet(_STYLE)
layout = QVBoxLayout(self)
layout.setSpacing(10)
layout.setContentsMargins(14, 14, 14, 14)
lbl = QLabel(
"Set the ID for each drawn region.\nIDs must be positive integers (duplicates are allowed)."
)
lbl.setStyleSheet("color: #a6adc8; font-size: 11px;")
lbl.setWordWrap(True)
layout.addWidget(lbl)
self._table = QTableWidget(len(rois), 3)
self._table.setHorizontalHeaderLabels(["Color", "Auto ID", "New ID"])
self._table.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
self._table.horizontalHeader().setSectionResizeMode(1, QHeaderView.Stretch)
self._table.horizontalHeader().setSectionResizeMode(2, QHeaderView.Stretch)
self._table.setColumnWidth(0, 28)
self._table.verticalHeader().setVisible(False)
self._table.setEditTriggers(QAbstractItemView.NoEditTriggers)
self._table.setSelectionMode(QAbstractItemView.NoSelection)
# Next sequential number for unassigned ROIs
_next = max((r.roi_id for r in rois if r.assigned), default=0) + 1
self._spinboxes = []
for row, roi in enumerate(rois):
# colour swatch — grey for unassigned, palette colour for assigned
c = _roi_color(roi.roi_id) if roi.assigned else QColor(120, 120, 130)
swatch = QWidget()
swatch.setStyleSheet(
f"background-color: rgb({c.red()},{c.green()},{c.blue()});"
"border-radius: 3px; margin: 4px;"
)
self._table.setCellWidget(row, 0, swatch)
# status column: shows current ID or "unassigned"
status_text = str(roi.roi_id) if roi.assigned else "unassigned"
id_item = QTableWidgetItem(status_text)
id_item.setTextAlignment(Qt.AlignCenter)
id_item.setForeground(
QColor("#585b70") if roi.assigned else QColor("#f38ba8")
)
self._table.setItem(row, 1, id_item)
# editable new ID — pre-fill with assigned ID or next sequential
default_id = roi.roi_id if roi.assigned else _next
if not roi.assigned:
_next += 1
spin = QSpinBox()
spin.setRange(1, 9999)
spin.setValue(default_id)
spin.setAlignment(Qt.AlignCenter)
self._table.setCellWidget(row, 2, spin)
self._spinboxes.append(spin)
layout.addWidget(self._table)
btns = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel)
btns.accepted.connect(self.accept)
btns.rejected.connect(self.reject)
layout.addWidget(btns)
[docs]
def get_assignments(self) -> dict:
"""Return {row_index: new_id} so callers can update roi.roi_id."""
return {i: spin.value() for i, spin in enumerate(self._spinboxes)}
# ─────────────────────────────────────────────────────────────────────────────
# Drawing canvas
# ─────────────────────────────────────────────────────────────────────────────
_HANDLE_R = 6
_MIN_BOX = 6
[docs]
class ImageCanvas(QWidget): # noqa: F811
"""
Display images and handle interactive ROI drawing, editing, thresholding, and mask
previews. It is the central canvas widget used by the ROI application.
Parameters
----------
rm : Any
ROI maker or ROI application state object.
parent : np.ndarray | None
Optional parent GUI widget.
"""
roi_changed = Signal()
def __init__(self, rm: Any, parent: np.ndarray | None = None) -> None:
super().__init__(parent)
self.rm = rm
self.selected_idx = -1
self.mode = "rect"
# drawing state
self._drawing = False
self._start_i = None
self._free_i = []
# move state
self._moving = False
self._mv_start_mi = None
self._mv_start_pts = None
# handle-resize state
self._resizing = False
self._rz_handle = -1
self._rz_start_mw = None
self._rz_start_bbox = None
self._rz_start_pts = None
self._cur_mw = QPointF(0, 0)
# transform
self._scale = 1.0
self._offset_x = 0.0
self._offset_y = 0.0
# zoom / pan
self._zoom = 1.0
self._pan_x = 0.0
self._pan_y = 0.0
self._fit_scale = 1.0
self._panning = False
self._pan_start_w = None
self._pan_start_ox = None
self._pan_start_oy = None
# base image
self._pixmap = None
self.refresh_base_pixmap()
# intensity overlay: stored as a numpy RGBA array so paintEvent can
# wrap it in a fresh QImage each frame without a copy or GC hazard.
self._int_overlay = None # np.ndarray (H, W, 4) uint8 or None
self.setMouseTracking(True)
self.setFocusPolicy(Qt.StrongFocus)
self.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
self.setMinimumSize(200, 200)
# ── transform ─────────────────────────────────────────────────────────────
def _recompute_transform(self) -> None:
"""
Run the recompute transform routine.
Returns
-------
None
No object is returned; the function perform recompute transform.
"""
cw, ch = self.width(), self.height()
iw, ih = self._pixmap.width(), self._pixmap.height()
self._fit_scale = min(cw / iw, ch / ih)
self._scale = self._fit_scale * self._zoom
self._offset_x = (cw - iw * self._scale) / 2 + self._pan_x
self._offset_y = (ch - ih * self._scale) / 2 + self._pan_y
[docs]
def wheelEvent(self, e: Any) -> None:
"""
Handle wheel event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform wheelevent.
"""
delta = e.angleDelta().y()
if delta == 0:
return
self._recompute_transform()
mx_w = e.position().x()
my_w = e.position().y()
# Image-space coords under the cursor before zooming
ix, iy = self._w2i(mx_w, my_w)
factor = 1.15 if delta > 0 else (1.0 / 1.15)
new_zoom = max(1.0, min(self._zoom * factor, 20.0))
if abs(new_zoom - self._zoom) < 1e-9:
return
self._zoom = new_zoom
# Recompute natural center offset at new scale, then shift pan so the
# image-space point under the cursor stays under the cursor.
new_scale = self._fit_scale * new_zoom
cw, ch = self.width(), self.height()
iw, ih = self._pixmap.width(), self._pixmap.height()
desired_ox = mx_w - ix * new_scale
desired_oy = my_w - iy * new_scale
self._pan_x = desired_ox - (cw - iw * new_scale) / 2
self._pan_y = desired_oy - (ch - ih * new_scale) / 2
self.update()
[docs]
def reset_zoom(self) -> None:
"""
Run the reset zoom routine.
Returns
-------
None
No object is returned; the function perform reset zoom.
"""
self._zoom = 1.0
self._pan_x = 0.0
self._pan_y = 0.0
self.update()
[docs]
def refresh_base_pixmap(self) -> None:
"""Rebuild the grayscale pixmap from ``rm.display_base``.
Called on construction and again whenever the histogram display-window
adjuster changes ``rm.display_low`` / ``rm.display_high``.
Returns
-------
None
No object is returned; the function refreshes ``self._pixmap``.
"""
arr = np.asarray(self.rm.display_base, dtype=np.uint8)
h, w = arr.shape
self._pixmap = QPixmap.fromImage(
QImage(arr.tobytes(), w, h, w, QImage.Format_Grayscale8)
)
def _w2i(self, wx: np.ndarray, wy: np.ndarray) -> tuple[Any, ...]:
"""
Run the w2i routine.
Parameters
----------
wx : np.ndarray
Widget-space x coordinate.
wy : np.ndarray
Widget-space y coordinate.
Returns
-------
tuple[Any, ...]
Tuple containing coordinates converted from world to image space.
"""
return (
(wx - self._offset_x) / self._scale,
(wy - self._offset_y) / self._scale,
)
def _i2w(self, ix: np.ndarray, iy: np.ndarray) -> tuple[Any, ...]:
"""
Run the i2w routine.
Parameters
----------
ix : np.ndarray
Image-space x coordinate.
iy : np.ndarray
Image-space y coordinate.
Returns
-------
tuple[Any, ...]
Tuple containing coordinates converted from image to world space.
"""
return (ix * self._scale + self._offset_x, iy * self._scale + self._offset_y)
def _qpt_w2i(self, q: Any) -> Any:
"""
Run the qpt w2i routine.
Parameters
----------
q : Any
Qt point converted between widget and image coordinates.
Returns
-------
Any
Object produced by qpt w2i.
"""
x, y = self._w2i(q.x(), q.y())
return QPointF(x, y)
def _pts_to_poly_w(self, pts: np.ndarray) -> Any:
"""
Run the pts to poly w routine.
Parameters
----------
pts : np.ndarray
ROI polygon vertices.
Returns
-------
Any
Object produced by pts to poly w.
"""
return QPolygonF([QPointF(*self._i2w(float(p[0]), float(p[1]))) for p in pts])
# ── intensity overlay ──────────────────────────────────────────────────────
[docs]
def update_intensity_overlay(self) -> None:
"""Recompute the RGBA overlay array for out-of-range pixels.
We store the raw numpy array rather than a QPixmap so that paintEvent
can wrap it in a QImage each frame. This avoids the deferred-copy bug
that occurs when QPixmap.fromImage() is called on an inline QImage.
"""
if not self.rm.intensity_active:
self._int_overlay = None
return
lo, hi = self.rm.intensity_low, self.rm.intensity_high
arr = self.rm._raw_img # (H, W) float64 — original values
below = arr < lo
above = arr > hi
rgba = np.zeros((self.rm.H, self.rm.W, 4), dtype=np.uint8)
rb, gb, bb = self.rm.mask_below_color
rgba[below, 0] = rb
rgba[below, 1] = gb
rgba[below, 2] = bb
rgba[below, 3] = 190
ra, ga, ba = self.rm.mask_above_color
rgba[above, 0] = ra
rgba[above, 1] = ga
rgba[above, 2] = ba
rgba[above, 3] = 190
self._int_overlay = rgba # keep array alive for QImage wrapping
# ── bounding-box handles ───────────────────────────────────────────────────
@staticmethod
def _bbox(pts: np.ndarray) -> tuple[Any, ...]:
"""
Run the bbox routine.
Parameters
----------
pts : np.ndarray
ROI polygon vertices.
Returns
-------
tuple[Any, ...]
Tuple containing bounding-box coordinates.
"""
return (
float(pts[:, 0].min()),
float(pts[:, 1].min()),
float(pts[:, 0].max()),
float(pts[:, 1].max()),
)
def _handle_pos_i(self, pts: np.ndarray) -> list[Any]:
"""
Run the handle pos i routine.
Parameters
----------
pts : np.ndarray
ROI polygon vertices.
Returns
-------
list[Any]
List containing the values produced by handle pos i.
"""
x0, y0, x1, y1 = self._bbox(pts)
mx, my = (x0 + x1) / 2, (y0 + y1) / 2
return [
(x0, y0),
(mx, y0),
(x1, y0),
(x1, my),
(x1, y1),
(mx, y1),
(x0, y1),
(x0, my),
]
def _hit_handle(self, wpt: np.ndarray, roi: Any) -> Any:
"""
Run the hit handle routine.
Parameters
----------
wpt : np.ndarray
Widget-space point tested against ROI geometry.
roi : Any
ROI object or identifier being transformed, drawn, or updated.
Returns
-------
Any
Object produced by hit handle.
"""
thresh2 = (_HANDLE_R + 3) ** 2
for i, (ix, iy) in enumerate(self._handle_pos_i(roi.pts)):
wx, wy = self._i2w(ix, iy)
if (wpt.x() - wx) ** 2 + (wpt.y() - wy) ** 2 <= thresh2:
return i
return -1
def _hit_roi(self, wpt: np.ndarray) -> Any:
"""
Run the hit ROI routine.
Parameters
----------
wpt : np.ndarray
Widget-space point tested against ROI geometry.
Returns
-------
Any
Object produced by hit ROI.
"""
ix, iy = self._w2i(wpt.x(), wpt.y())
for i, roi in enumerate(self.rm.rois):
if (
cv2.pointPolygonTest(
roi.pts.astype(np.float32), (float(ix), float(iy)), False
)
>= 0
):
return i
return -1
# ── painting ───────────────────────────────────────────────────────────────
[docs]
def paintEvent(self, _: Any) -> None:
"""
Handle paint event callbacks.
Parameters
----------
_ : Any
Callback value passed through to the ROI interaction handler.
Returns
-------
None
No object is returned; the function perform paintevent.
"""
self._recompute_transform()
p = QPainter(self)
p.setRenderHint(QPainter.Antialiasing)
p.setRenderHint(QPainter.SmoothPixmapTransform)
p.fillRect(self.rect(), QColor(18, 18, 30))
iw, ih = self._pixmap.width(), self._pixmap.height()
target = QRectF(
self._offset_x, self._offset_y, iw * self._scale, ih * self._scale
)
if self.rm.show_bg:
p.drawPixmap(target, self._pixmap, QRectF(self._pixmap.rect()))
# intensity mask overlay — wrap the live numpy array in a QImage each
# frame so there is no stale-pointer or deferred-copy issue.
if self.rm.intensity_active and self._int_overlay is not None:
h, w = self._int_overlay.shape[:2]
_img = QImage(self._int_overlay.data, w, h, 4 * w, QImage.Format_RGBA8888)
self._int_img_ref = _img # prevent GC while QPainter holds it
p.drawImage(target, _img)
for i, roi in enumerate(self.rm.rois):
self._paint_roi(p, roi, selected=(i == self.selected_idx))
if self._drawing and self._start_i is not None:
self._paint_preview(p)
p.end()
def _paint_roi(self, p: Any, roi: Any, selected: np.ndarray) -> None:
"""
Run the paint ROI routine.
Parameters
----------
p : Any
Detector parameter object or fitted parameter vector.
roi : Any
ROI object or identifier being transformed, drawn, or updated.
selected : np.ndarray
Whether the ROI is currently selected.
Returns
-------
None
No object is returned; the function perform paint ROI.
"""
if not roi.assigned:
color = QColor(0, 220, 100) if selected else QColor(140, 140, 155)
line_style = Qt.DashLine
label_text = "?"
else:
color = QColor(0, 220, 100) if selected else _roi_color(roi.roi_id)
line_style = Qt.SolidLine
label_text = f"ID:{roi.roi_id}"
poly = self._pts_to_poly_w(roi.pts)
fill = QColor(
color.red(), color.green(), color.blue(), 40 if not roi.assigned else 55
)
p.setBrush(QBrush(fill))
pen = QPen(color, 2.5 if selected else 1.5, line_style)
pen.setJoinStyle(Qt.RoundJoin)
p.setPen(pen)
p.drawPolygon(poly)
if roi.pts.shape[0]:
wx, wy = self._i2w(float(roi.pts[0, 0]), float(roi.pts[0, 1]))
p.setPen(QPen(Qt.white))
p.setFont(QFont("Segoe UI", 9, QFont.Bold))
p.drawText(int(wx) + 4, int(wy) + 13, label_text)
if selected:
self._paint_handles(p, roi)
def _paint_handles(self, p: Any, roi: Any) -> None:
"""
Run the paint handles routine.
Parameters
----------
p : Any
Detector parameter object or fitted parameter vector.
roi : Any
ROI object or identifier being transformed, drawn, or updated.
Returns
-------
None
No object is returned; the function perform paint handles.
"""
for ix, iy in self._handle_pos_i(roi.pts):
wx, wy = self._i2w(ix, iy)
r = _HANDLE_R
p.setBrush(QBrush(QColor(255, 255, 255, 230)))
p.setPen(QPen(QColor(30, 100, 220), 1.5))
p.drawEllipse(QRectF(wx - r, wy - r, r * 2, r * 2))
def _paint_preview(self, p: Any) -> None:
"""
Run the paint preview routine.
Parameters
----------
p : Any
Detector parameter object or fitted parameter vector.
Returns
-------
None
No object is returned; the function perform paint preview.
"""
pts = self._preview_pts()
if len(pts) < 3:
return
poly = QPolygonF(
[QPointF(*self._i2w(float(pt[0]), float(pt[1]))) for pt in pts]
)
p.setBrush(QBrush(QColor(255, 255, 255, 25)))
p.setPen(QPen(QColor(255, 255, 255, 160), 1.2, Qt.DashLine))
p.drawPolygon(poly)
def _preview_pts(self) -> Any:
"""
Run the preview pts routine.
Returns
-------
Any
Object produced by preview pts.
"""
if self._start_i is None:
return []
ix, iy = self._start_i
mx, my = self._w2i(self._cur_mw.x(), self._cur_mw.y())
if self.mode == "rect":
return [[ix, iy], [mx, iy], [mx, my], [ix, my]]
if self.mode == "circle":
r = max(int(np.hypot(mx - ix, my - iy)), 3)
return cv2.ellipse2Poly((int(ix), int(iy)), (r, r), 0, 0, 360, 8).tolist()
return list(self._free_i)
# ── mouse ──────────────────────────────────────────────────────────────────
[docs]
def mousePressEvent(self, e: Any) -> None:
"""
Handle mouse press event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform mousepressevent.
"""
if e.button() == Qt.MiddleButton:
self._recompute_transform()
self._panning = True
self._pan_start_w = QPointF(e.pos())
self._pan_start_ox = self._pan_x
self._pan_start_oy = self._pan_y
self.setCursor(Qt.ClosedHandCursor)
return
if e.button() != Qt.LeftButton:
return
wpt = QPointF(e.pos())
# ── Assign mode: click a ROI to give it the next sequential ID ──────
if self.mode == "assign":
hit = self._hit_roi(wpt)
if hit != -1:
roi = self.rm.rois[hit]
if not roi.assigned:
roi.roi_id = self.rm.assign_counter
roi.assigned = True
self.rm.assign_counter += 1
self.selected_idx = hit
else:
self.selected_idx = -1
self.update()
self.roi_changed.emit()
return
# ────────────────────────────────────────────────────────────────────
if self.selected_idx != -1:
hi = self._hit_handle(wpt, self.rm.rois[self.selected_idx])
if hi != -1:
roi = self.rm.rois[self.selected_idx]
self._resizing = True
self._rz_handle = hi
self._rz_start_mw = wpt
self._rz_start_bbox = self._bbox(roi.pts)
self._rz_start_pts = roi.pts.copy().astype(float)
self.update()
return
hit = self._hit_roi(wpt)
if hit != -1:
self.selected_idx = hit
self._moving = True
self._mv_start_mi = self._qpt_w2i(wpt)
self._mv_start_pts = self.rm.rois[hit].pts.copy().astype(float)
self.update()
self.roi_changed.emit()
return
if self.mode != "select":
self.selected_idx = -1
self._drawing = True
ix, iy = self._w2i(wpt.x(), wpt.y())
self._start_i = (ix, iy)
self._free_i = [(ix, iy)]
else:
self.selected_idx = -1
self.update()
self.roi_changed.emit()
[docs]
def mouseMoveEvent(self, e: Any) -> None:
"""
Handle mouse move event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform mousemoveevent.
"""
wpt = QPointF(e.pos())
self._cur_mw = wpt
if self._panning:
self._pan_x = self._pan_start_ox + wpt.x() - self._pan_start_w.x()
self._pan_y = self._pan_start_oy + wpt.y() - self._pan_start_w.y()
self.update()
return
if self._resizing and self.selected_idx != -1:
self._apply_resize(wpt)
elif self._moving and self.selected_idx != -1:
cur_i = self._qpt_w2i(wpt)
dx = cur_i.x() - self._mv_start_mi.x()
dy = cur_i.y() - self._mv_start_mi.y()
roi = self.rm.rois[self.selected_idx]
new_pts = self._mv_start_pts + np.array([dx, dy])
roi.pts = np.clip(new_pts, 0, None).astype(np.int32)
roi.center = np.mean(roi.pts, axis=0)
elif self._drawing and self.mode == "freehand" and self._start_i:
ix, iy = self._w2i(wpt.x(), wpt.y())
self._free_i.append((ix, iy))
# adaptive cursor
if self.selected_idx != -1 and not self._drawing:
hi = self._hit_handle(wpt, self.rm.rois[self.selected_idx])
cursors = {
0: Qt.SizeFDiagCursor,
4: Qt.SizeFDiagCursor,
2: Qt.SizeBDiagCursor,
6: Qt.SizeBDiagCursor,
1: Qt.SizeVerCursor,
5: Qt.SizeVerCursor,
3: Qt.SizeHorCursor,
7: Qt.SizeHorCursor,
}
if hi in cursors:
self.setCursor(cursors[hi])
elif self._hit_roi(wpt) != -1:
self.setCursor(Qt.SizeAllCursor)
else:
self.setCursor(
Qt.CrossCursor if self.mode != "select" else Qt.ArrowCursor
)
else:
self.setCursor(
Qt.CrossCursor if self.mode not in ("select", None) else Qt.ArrowCursor
)
self.update()
[docs]
def mouseReleaseEvent(self, e: Any) -> None:
"""
Handle mouse release event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform mousereleaseevent.
"""
if e.button() == Qt.MiddleButton:
self._panning = False
self.setCursor(Qt.ArrowCursor)
return
if e.button() != Qt.LeftButton:
return
if self._resizing:
self._resizing = False
self.roi_changed.emit()
if self._moving:
self._moving = False
self.roi_changed.emit()
if self._drawing:
self._drawing = False
wpt = QPointF(e.pos())
ix, iy = self._w2i(wpt.x(), wpt.y())
pts = self._finalise_pts(ix, iy)
if len(pts) >= 3:
roi = ROIObject(pts) # roi_id=0, assigned=False until user assigns
self.rm.rois.append(roi)
self.selected_idx = len(self.rm.rois) - 1
self._start_i = None
self._free_i = []
self.roi_changed.emit()
self.update()
def _finalise_pts(self, mx: np.ndarray, my: np.ndarray) -> Any:
"""
Run the finalise pts routine.
Parameters
----------
mx : np.ndarray
Mouse x coordinate used while finalizing ROI points.
my : np.ndarray
Mouse y coordinate used while finalizing ROI points.
Returns
-------
Any
Object produced by finalise pts.
"""
if self._start_i is None:
return []
ix, iy = self._start_i
if self.mode == "rect":
return np.array([[ix, iy], [mx, iy], [mx, my], [ix, my]])
if self.mode == "circle":
r = max(int(np.hypot(mx - ix, my - iy)), 3)
return cv2.ellipse2Poly((int(ix), int(iy)), (r, r), 0, 0, 360, 8)
pts = np.array(self._free_i)
return pts if len(pts) >= 3 else []
def _apply_resize(self, wpt: np.ndarray) -> None:
"""
Apply resize.
Parameters
----------
wpt : np.ndarray
Widget-space point tested against ROI geometry.
Returns
-------
None
No object is returned; the function apply resize.
"""
roi = self.rm.rois[self.selected_idx]
dix = (wpt.x() - self._rz_start_mw.x()) / self._scale
diy = (wpt.y() - self._rz_start_mw.y()) / self._scale
x0, y0, x1, y1 = self._rz_start_bbox
nx0, ny0, nx1, ny1 = x0, y0, x1, y1
hi = self._rz_handle
if hi in (0, 6, 7):
nx0 = x0 + dix
if hi in (2, 3, 4):
nx1 = x1 + dix
if hi in (0, 1, 2):
ny0 = y0 + diy
if hi in (4, 5, 6):
ny1 = y1 + diy
if nx1 - nx0 < _MIN_BOX:
nx1 = nx0 + _MIN_BOX
if ny1 - ny0 < _MIN_BOX:
ny1 = ny0 + _MIN_BOX
bw = max(x1 - x0, 1.0)
bh = max(y1 - y0, 1.0)
pts = self._rz_start_pts.copy()
pts[:, 0] = nx0 + (pts[:, 0] - x0) * (nx1 - nx0) / bw
pts[:, 1] = ny0 + (pts[:, 1] - y0) * (ny1 - ny0) / bh
roi.pts = np.clip(pts, 0, None).astype(np.int32)
roi.center = np.mean(roi.pts, axis=0)
[docs]
def keyPressEvent(self, e: Any) -> None:
"""
Handle key press event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform keypressevent.
"""
if e.key() in (Qt.Key_Delete, Qt.Key_Backspace):
self._delete_selected()
elif e.key() == Qt.Key_Home:
self.reset_zoom()
def _delete_selected(self) -> None:
"""
Run the delete selected routine.
Returns
-------
None
No object is returned; the function perform delete selected.
"""
if 0 <= self.selected_idx < len(self.rm.rois):
self.rm.rois.pop(self.selected_idx)
self.selected_idx = -1
# Recalculate assign_counter so it stays above all existing IDs
assigned_ids = [r.roi_id for r in self.rm.rois if r.assigned]
self.rm.assign_counter = (max(assigned_ids) + 1) if assigned_ids else 1
self.roi_changed.emit()
self.update()
# ─────────────────────────────────────────────────────────────────────────────
# Intensity histogram + display-window adjuster
# ─────────────────────────────────────────────────────────────────────────────
# ─────────────────────────────────────────────────────────────────────────────
# Main window
# ─────────────────────────────────────────────────────────────────────────────
[docs]
class ROIApp(QMainWindow): # noqa: F811
"""
Host the full interactive ROI maker interface. The widget wires image display,
threshold controls, ROI editing actions, ID assignment, and mask saving into one
application window.
Parameters
----------
rm : Any
ROI maker or ROI application state object.
"""
def __init__(self, rm: Any) -> None:
super().__init__()
self.rm = rm
self.setWindowTitle("ROI Maker")
self.setStyleSheet(_STYLE)
central = QWidget()
self.setCentralWidget(central)
root_layout = QHBoxLayout(central)
root_layout.setContentsMargins(0, 0, 0, 0)
root_layout.setSpacing(0)
# Canvas first so _build_sidebar signals can reference it safely
self.canvas = ImageCanvas(rm, self)
self.canvas.roi_changed.connect(self._refresh_status)
self.canvas.update_intensity_overlay()
self.histogram = HistogramWidget(rm, self)
self.histogram.window_changed.connect(self._on_display_window_changed)
sidebar = self._build_sidebar()
root_layout.addWidget(sidebar)
image_area = QWidget()
image_col = QVBoxLayout(image_area)
image_col.setContentsMargins(0, 0, 0, 0)
image_col.setSpacing(0)
image_col.addWidget(self.histogram)
image_col.addWidget(self.canvas, stretch=1)
root_layout.addWidget(image_area, stretch=1)
self.setStatusBar(QStatusBar(self))
self._refresh_status()
# ── sidebar ───────────────────────────────────────────────────────────────
def _build_sidebar(self) -> Any:
"""
Build sidebar.
Returns
-------
Any
Object produced by build sidebar.
"""
scroll = QScrollArea()
scroll.setWidgetResizable(True)
scroll.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
scroll.setStyleSheet(
"QScrollArea { border: none; background: #181825; }"
"QScrollBar:vertical { width: 6px; background: #181825; }"
"QScrollBar::handle:vertical { background: #313244; border-radius: 3px; }"
)
scroll.setFixedWidth(185)
sb = QWidget()
sb.setObjectName("sidebar")
layout = QVBoxLayout(sb)
layout.setContentsMargins(10, 12, 10, 12)
layout.setSpacing(4)
scroll.setWidget(sb)
# Title
title = QLabel("⬡ ROI Maker")
title.setObjectName("title_lbl")
title.setAlignment(Qt.AlignCenter)
layout.addWidget(title)
layout.addWidget(self._divider())
# ── TOOLS ──
layout.addWidget(self._section_label("TOOLS"))
self._tool_btns = {}
for key, icon, label, sc in [
("select", "↖", "Select / Move", "S"),
("rect", "▭", "Rectangle", "R"),
("circle", "◯", "Circle", "C"),
("freehand", "✏", "Freehand", "F"),
("assign", "⊕", "Assign IDs", "A"),
]:
btn = self._tool_button(icon, label, sc)
btn.toggled.connect(lambda on, k=key: self._on_tool_toggled(k, on))
self._tool_btns[key] = btn
layout.addWidget(btn)
reset_btn = self._action_button("↺", "Reset IDs", "")
reset_btn.setToolTip(
"Clear all ID assignments — ROIs return to unassigned state"
)
reset_btn.clicked.connect(self._reset_ids)
layout.addWidget(reset_btn)
auto_btn = self._action_button("⟳", "Auto-assign IDs", "")
auto_btn.setToolTip(
"Assign sequential IDs to all unassigned ROIs automatically"
)
auto_btn.clicked.connect(self._auto_assign_ids)
layout.addWidget(auto_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── OUTPUT TYPE ──
layout.addWidget(self._section_label("OUTPUT TYPE"))
self._mask_type_group = QButtonGroup(self)
self._mask_type_group.setExclusive(True)
for val, icon, label in [
("binary", "◻", "Binary"),
("multi", "◼", "Multi-ID"),
("both", "⊞", "Both"),
]:
btn = QPushButton(f"{icon} {label}")
btn.setObjectName("tool_btn")
btn.setCheckable(True)
btn.setCursor(QCursor(Qt.PointingHandCursor))
btn.setToolTip(f"Save as: {label}")
self._mask_type_group.addButton(btn)
layout.addWidget(btn)
if val == self.rm.mask_type:
btn.setChecked(True)
self._mask_type_group.buttonClicked.connect(self._on_mask_type_btn)
# store reference to buttons by order
self._mask_type_btns = {
v: self._mask_type_group.buttons()[i]
for i, v in enumerate(["binary", "multi", "both"])
}
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── EDIT ──
layout.addWidget(self._section_label("EDIT"))
self._bg_btn = self._action_button("◑", "Toggle Image", "B")
self._bg_btn.clicked.connect(self._toggle_bg)
layout.addWidget(self._bg_btn)
del_btn = self._action_button("✕", "Delete ROI", "Del")
del_btn.clicked.connect(self._delete_selected)
layout.addWidget(del_btn)
del_all_btn = self._action_button("⊘", "Delete All ROIs", "")
del_all_btn.setToolTip("Remove every ROI and start fresh")
del_all_btn.clicked.connect(self._delete_all)
layout.addWidget(del_all_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── INTENSITY FILTER ──
layout.addWidget(self._section_label("INTENSITY FILTER"))
self._int_btn = QPushButton("⚡ Enable Filter")
self._int_btn.setObjectName("action_btn")
self._int_btn.setCheckable(True)
self._int_btn.setChecked(self.rm.intensity_active)
self._int_btn.setCursor(QCursor(Qt.PointingHandCursor))
self._int_btn.toggled.connect(self._on_intensity_toggled)
layout.addWidget(self._int_btn)
# Low threshold
self._lo_lbl = QLabel("Low threshold")
self._lo_lbl.setStyleSheet("color: #a6adc8; font-size: 11px;")
layout.addWidget(self._lo_lbl)
_lo_row = QWidget()
_lo_rl = QHBoxLayout(_lo_row)
_lo_rl.setContentsMargins(0, 0, 0, 0)
_lo_rl.setSpacing(4)
self._lo_slider = QSlider(Qt.Horizontal)
self._lo_slider.setRange(self.rm.img_min, self.rm.img_max)
self._lo_slider.setValue(self.rm.intensity_low)
self._lo_slider.valueChanged.connect(self._on_lo_changed)
_lo_rl.addWidget(self._lo_slider)
self._lo_spin = QSpinBox()
self._lo_spin.setRange(self.rm.img_min, self.rm.img_max)
self._lo_spin.setValue(self.rm.intensity_low)
self._lo_spin.setFixedWidth(58)
self._lo_spin.valueChanged.connect(self._on_lo_spin_changed)
_lo_rl.addWidget(self._lo_spin)
layout.addWidget(_lo_row)
# High threshold
self._hi_lbl = QLabel("High threshold")
self._hi_lbl.setStyleSheet("color: #a6adc8; font-size: 11px;")
layout.addWidget(self._hi_lbl)
_hi_row = QWidget()
_hi_rl = QHBoxLayout(_hi_row)
_hi_rl.setContentsMargins(0, 0, 0, 0)
_hi_rl.setSpacing(4)
self._hi_slider = QSlider(Qt.Horizontal)
self._hi_slider.setRange(self.rm.img_min, self.rm.img_max)
self._hi_slider.setValue(self.rm.intensity_high)
self._hi_slider.valueChanged.connect(self._on_hi_changed)
_hi_rl.addWidget(self._hi_slider)
self._hi_spin = QSpinBox()
self._hi_spin.setRange(self.rm.img_min, self.rm.img_max)
self._hi_spin.setValue(self.rm.intensity_high)
self._hi_spin.setFixedWidth(58)
self._hi_spin.valueChanged.connect(self._on_hi_spin_changed)
_hi_rl.addWidget(self._hi_spin)
layout.addWidget(_hi_row)
# Mask-color pickers (separate for below/above)
self._below_color_btn = QPushButton("▼ Below color")
self._below_color_btn.setObjectName("action_btn")
self._below_color_btn.setCursor(QCursor(Qt.PointingHandCursor))
self._below_color_btn.setToolTip("Color for pixels below low threshold")
self._below_color_btn.clicked.connect(self._pick_below_color)
self._refresh_below_color_btn()
layout.addWidget(self._below_color_btn)
self._above_color_btn = QPushButton("▲ Above color")
self._above_color_btn.setObjectName("action_btn")
self._above_color_btn.setCursor(QCursor(Qt.PointingHandCursor))
self._above_color_btn.setToolTip("Color for pixels above high threshold")
self._above_color_btn.clicked.connect(self._pick_above_color)
self._refresh_above_color_btn()
layout.addWidget(self._above_color_btn)
thresh_btn = self._action_button("⊞", "Create Threshold ROI", "")
thresh_btn.setToolTip(
"Convert the current intensity threshold into ROI(s).\n"
"They are added as unassigned ROIs — assign IDs the same way as drawn ROIs."
)
thresh_btn.clicked.connect(self._create_threshold_rois)
layout.addWidget(thresh_btn)
save_thresh_btn = self._action_button("◈", "Save Threshold Mask", "")
save_thresh_btn.setToolTip(
"Save a binary mask directly from intensity thresholds.\n"
"Each pixel = 1 if inside [low, high], else 0.\n"
"No ROI polygons — hollow structures stay correct.\n"
"Saved as <name>_threshold_binary.npy"
)
save_thresh_btn.clicked.connect(self._save_threshold_mask)
layout.addWidget(save_thresh_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# ── FILE ──
layout.addWidget(self._section_label("FILE"))
save_btn = QPushButton("✓ Save && Close ↵")
save_btn.setObjectName("save_btn")
save_btn.setCursor(QCursor(Qt.PointingHandCursor))
save_btn.clicked.connect(self._save_close)
layout.addWidget(save_btn)
cancel_btn = QPushButton("✗ Cancel Esc")
cancel_btn.setObjectName("cancel_btn")
cancel_btn.setCursor(QCursor(Qt.PointingHandCursor))
cancel_btn.clicked.connect(self._cancel)
layout.addWidget(cancel_btn)
layout.addSpacing(4)
layout.addWidget(self._divider())
# Status
self._status_lbl = QLabel()
self._status_lbl.setAlignment(Qt.AlignLeft | Qt.AlignTop)
self._status_lbl.setWordWrap(True)
self._status_lbl.setStyleSheet(
"color: #585b70; font-size: 11px; padding: 4px 2px;"
)
layout.addWidget(self._status_lbl)
layout.addItem(QSpacerItem(0, 0, QSizePolicy.Minimum, QSizePolicy.Expanding))
# Activate default tool
self._tool_btns["rect"].setChecked(True)
return scroll
# ── widget helpers ────────────────────────────────────────────────────────
def _divider(self) -> Any:
"""
Run the divider routine.
Returns
-------
Any
Object produced by divider.
"""
line = QFrame()
line.setObjectName("divider")
line.setFrameShape(QFrame.HLine)
return line
def _section_label(self, text: np.ndarray) -> Any:
"""
Run the section label routine.
Parameters
----------
text : np.ndarray
Text rendered into a UI label or formatted table cell.
Returns
-------
Any
Object produced by section label.
"""
lbl = QLabel(text)
lbl.setObjectName("section_lbl")
lbl.setContentsMargins(2, 6, 2, 2)
return lbl
def _tool_button(self, icon: Any, label: str, shortcut: np.ndarray) -> np.ndarray:
"""
Run the tool button routine.
Parameters
----------
icon : Any
Icon text shown on a UI button.
label : str
Display label assigned to the data or plot element.
shortcut : np.ndarray
Keyboard shortcut assigned to the UI button.
Returns
-------
np.ndarray
Qt button configured for the requested tool.
"""
btn = QPushButton(f"{icon} {label}")
btn.setObjectName("tool_btn")
btn.setCheckable(True)
btn.setAutoExclusive(True)
btn.setCursor(QCursor(Qt.PointingHandCursor))
btn.setToolTip(f"{label} [{shortcut}]")
return btn
def _action_button(self, icon: Any, label: str, shortcut: np.ndarray) -> np.ndarray:
"""
Run the action button routine.
Parameters
----------
icon : Any
Icon text shown on a UI button.
label : str
Display label assigned to the data or plot element.
shortcut : np.ndarray
Keyboard shortcut assigned to the UI button.
Returns
-------
np.ndarray
Qt button configured for the requested action.
"""
btn = QPushButton(f"{icon} {label}")
btn.setObjectName("action_btn")
btn.setCursor(QCursor(Qt.PointingHandCursor))
btn.setToolTip(f"{label} [{shortcut}]")
return btn
def _refresh_below_color_btn(self) -> None:
"""
Run the refresh below color btn routine.
Returns
-------
None
No object is returned; the function perform refresh below color btn.
"""
r, g, b = self.rm.mask_below_color
luma = 0.299 * r + 0.587 * g + 0.114 * b
fg = "#000" if luma > 128 else "#fff"
self._below_color_btn.setStyleSheet(
f"QPushButton#action_btn {{ background-color: rgb({r},{g},{b}); "
f"color: {fg}; border: 1px solid #313244; border-radius: 8px; "
"padding: 8px 10px; text-align: left; }"
f"QPushButton#action_btn:hover {{ background-color: rgb({min(r + 20, 255)},{min(g + 20, 255)},{min(b + 20, 255)}); }}"
)
def _refresh_above_color_btn(self) -> None:
"""
Run the refresh above color btn routine.
Returns
-------
None
No object is returned; the function perform refresh above color btn.
"""
r, g, b = self.rm.mask_above_color
luma = 0.299 * r + 0.587 * g + 0.114 * b
fg = "#000" if luma > 128 else "#fff"
self._above_color_btn.setStyleSheet(
f"QPushButton#action_btn {{ background-color: rgb({r},{g},{b}); "
f"color: {fg}; border: 1px solid #313244; border-radius: 8px; "
"padding: 8px 10px; text-align: left; }"
f"QPushButton#action_btn:hover {{ background-color: rgb({min(r + 20, 255)},{min(g + 20, 255)},{min(b + 20, 255)}); }}"
)
# ── actions ───────────────────────────────────────────────────────────────
def _on_tool_toggled(self, key: str, on: Any) -> None:
"""
Run the on tool toggled routine.
Parameters
----------
key : str
Dictionary key or parameter-map name to extract.
on : Any
Toggle state emitted by the UI control.
Returns
-------
None
No object is returned; the function perform on tool toggled.
"""
if on:
self.canvas.mode = key
self.canvas.selected_idx = -1
self.canvas.update()
self._refresh_status()
def _on_mask_type_btn(self, btn: np.ndarray) -> None:
"""
Run the on mask type btn routine.
Parameters
----------
btn : np.ndarray
Button that triggered the UI callback.
Returns
-------
None
No object is returned; the function perform on mask type btn.
"""
labels = {"◻ Binary": "binary", "◼ Multi-ID": "multi", "⊞ Both": "both"}
self.rm.mask_type = labels.get(btn.text(), "multi")
self._refresh_status()
def _toggle_bg(self) -> None:
"""
Run the toggle bg routine.
Returns
-------
None
No object is returned; the function perform toggle bg.
"""
self.rm.show_bg = not self.rm.show_bg
self._bg_btn.setStyleSheet(
""
if self.rm.show_bg
else "QPushButton#action_btn { background-color: #1e66f5; color: #fff; "
"border: 1px solid #1d62e8; border-radius: 8px; padding: 8px 10px; }"
)
self.canvas.update()
def _delete_selected(self) -> None:
"""
Run the delete selected routine.
Returns
-------
None
No object is returned; the function perform delete selected.
"""
self.canvas._delete_selected()
def _on_intensity_toggled(self, active: np.ndarray) -> None:
"""
Run the on intensity toggled routine.
Parameters
----------
active : np.ndarray
Whether the UI control is active.
Returns
-------
None
No object is returned; the function perform on intensity toggled.
"""
self.rm.intensity_active = active
self.canvas.update_intensity_overlay()
self.canvas.update()
self._refresh_status()
def _on_lo_changed(self, val: np.ndarray) -> None:
"""
Run the on lo changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on lo changed.
"""
val = min(val, self.rm.intensity_high)
self._lo_slider.blockSignals(True)
self._lo_slider.setValue(val)
self._lo_slider.blockSignals(False)
self._lo_spin.blockSignals(True)
self._lo_spin.setValue(val)
self._lo_spin.blockSignals(False)
self.rm.intensity_low = val
self.canvas.update_intensity_overlay()
self.canvas.update()
def _on_lo_spin_changed(self, val: np.ndarray) -> None:
"""
Run the on lo spin changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on lo spin changed.
"""
self._lo_slider.setValue(val)
def _on_hi_changed(self, val: np.ndarray) -> None:
"""
Run the on hi changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on hi changed.
"""
val = max(val, self.rm.intensity_low)
self._hi_slider.blockSignals(True)
self._hi_slider.setValue(val)
self._hi_slider.blockSignals(False)
self._hi_spin.blockSignals(True)
self._hi_spin.setValue(val)
self._hi_spin.blockSignals(False)
self.rm.intensity_high = val
self.canvas.update_intensity_overlay()
self.canvas.update()
def _on_hi_spin_changed(self, val: np.ndarray) -> None:
"""
Run the on hi spin changed routine.
Parameters
----------
val : np.ndarray
Numeric value emitted by a slider or spin box.
Returns
-------
None
No object is returned; the function perform on hi spin changed.
"""
self._hi_slider.setValue(val)
def _pick_below_color(self) -> None:
"""
Run the pick below color routine.
Returns
-------
None
No object is returned; the function perform pick below color.
"""
r, g, b = self.rm.mask_below_color
chosen = QColorDialog.getColor(
QColor(r, g, b), self, "Pick color for below-threshold pixels"
)
if chosen.isValid():
self.rm.mask_below_color = (chosen.red(), chosen.green(), chosen.blue())
self._refresh_below_color_btn()
self.canvas.update_intensity_overlay()
self.canvas.update()
def _pick_above_color(self) -> None:
"""
Run the pick above color routine.
Returns
-------
None
No object is returned; the function perform pick above color.
"""
r, g, b = self.rm.mask_above_color
chosen = QColorDialog.getColor(
QColor(r, g, b), self, "Pick color for above-threshold pixels"
)
if chosen.isValid():
self.rm.mask_above_color = (chosen.red(), chosen.green(), chosen.blue())
self._refresh_above_color_btn()
self.canvas.update_intensity_overlay()
self.canvas.update()
def _create_threshold_rois(self) -> None:
"""Convert the current intensity threshold mask into ROIObject(s).
Each contiguous region in the threshold mask becomes an unassigned ROI,
identical in behaviour to any hand-drawn ROI. The user then assigns IDs
and saves them through the normal pipeline.
"""
if not self.rm.intensity_active:
self.statusBar().showMessage(" Enable the intensity filter first.", 3000)
return
n = self.rm.create_rois_from_threshold()
if n == 0:
self.statusBar().showMessage(
" No regions found in threshold mask (try wider range).", 3000
)
else:
self.statusBar().showMessage(
f" Added {n} threshold-based ROI(s). Assign IDs before saving.", 4000
)
self.canvas.update()
self._refresh_status()
def _save_threshold_mask(self) -> None:
"""Save a binary mask built purely from intensity thresholds (no ROI polygons)."""
if not self.rm.intensity_active:
self.statusBar().showMessage(" Enable the intensity filter first.", 3000)
return
path = self.rm.save_threshold_binary_mask()
self.statusBar().showMessage(f" Saved threshold binary mask → {path}", 5000)
def _reset_ids(self) -> None:
"""Clear all ID assignments — every ROI returns to unassigned state."""
for roi in self.rm.rois:
roi.roi_id = 0
roi.assigned = False
self.rm.assign_counter = 1
self.canvas.update()
self._refresh_status()
def _delete_all(self) -> None:
"""Remove every ROI and reset the assign counter."""
if not self.rm.rois:
self.statusBar().showMessage(" No ROIs to delete.", 2000)
return
n = len(self.rm.rois)
self.rm.rois.clear()
self.rm.assign_counter = 1
self.canvas.selected_idx = -1
self.canvas.update()
self._refresh_status()
self.statusBar().showMessage(f" Deleted {n} ROI(s).", 2000)
def _auto_assign_ids(self) -> None:
"""Assign sequential IDs to all unassigned ROIs without showing a dialog."""
pending = [r for r in self.rm.rois if not r.assigned]
if not pending:
self.statusBar().showMessage(" All ROIs already have IDs.", 2000)
return
for roi in pending:
roi.roi_id = self.rm.assign_counter
roi.assigned = True
self.rm.assign_counter += 1
self.canvas.update()
self._refresh_status()
self.statusBar().showMessage(
f" Auto-assigned IDs to {len(pending)} ROI(s).", 2000
)
def _show_id_dialog(self) -> bool:
"""Show ID-assignment dialog for remaining unassigned ROIs before save."""
dlg = IDAssignDialog(self.rm.rois, self)
if dlg.exec_() == QDialog.Accepted:
for i, new_id in dlg.get_assignments().items():
self.rm.rois[i].roi_id = new_id
self.rm.rois[i].assigned = True
assigned = [r.roi_id for r in self.rm.rois if r.assigned]
self.rm.assign_counter = (max(assigned) + 1) if assigned else 1
self.canvas.update()
return True
return False
def _save_close(self) -> None:
"""
Save close.
Returns
-------
None
No object is returned; the function save close.
"""
if self.rm.mask_type in ("multi", "both") and self.rm.rois:
unassigned = [r for r in self.rm.rois if not r.assigned]
if unassigned:
# Only show dialog when some ROIs still lack IDs
if not self._show_id_dialog():
return
self.rm.save_masks()
self.close()
def _cancel(self) -> None:
"""
Run the cancel routine.
Returns
-------
None
No object is returned; the function perform cancel.
"""
self.close()
def _refresh_status(self) -> None:
"""
Run the refresh status routine.
Returns
-------
None
No object is returned; the function perform refresh status.
"""
n = len(self.rm.rois)
n_assigned = sum(1 for r in self.rm.rois if r.assigned)
n_pending = n - n_assigned
sel = self.canvas.selected_idx
sel_str = f"#{self.rm.rois[sel].roi_id}" if 0 <= sel < n else "—"
mode_map = {
"select": "Select/Move",
"rect": "Rectangle",
"circle": "Circle",
"freehand": "Freehand",
"assign": "Assign IDs",
}
type_map = {"binary": "Binary", "multi": "Multi-ID", "both": "Both"}
hint = (
"Click ROIs to number them"
if self.canvas.mode == "assign"
else "Drag handles to resize"
)
self._status_lbl.setText(
f"Mode: {mode_map.get(self.canvas.mode, '')}\n"
f"Output: {type_map.get(self.rm.mask_type, '')}\n"
f"Filter: {'ON' if self.rm.intensity_active else 'off'} "
f"[{self.rm.intensity_low}–{self.rm.intensity_high}]\n"
f"ROIs: {n} (✓{n_assigned} ?{n_pending})\n"
f"Sel: {sel_str}"
)
self.statusBar().showMessage(
f" {mode_map.get(self.canvas.mode, '')} │ "
f"Output: {type_map.get(self.rm.mask_type, '')} │ "
f"ROIs: {n} ✓{n_assigned} assigned ?{n_pending} pending │ "
f"{hint} · [R/C/F/S/A/B/Del/↵/Esc]"
)
# ── keyboard ──────────────────────────────────────────────────────────────
[docs]
def keyPressEvent(self, e: Any) -> None:
"""
Handle key press event callbacks.
Parameters
----------
e : Any
GUI or plotting event object supplied by the framework.
Returns
-------
None
No object is returned; the function perform keypressevent.
"""
key_map = {
Qt.Key_S: "select",
Qt.Key_R: "rect",
Qt.Key_C: "circle",
Qt.Key_F: "freehand",
Qt.Key_A: "assign",
}
if e.key() in key_map:
self._tool_btns[key_map[e.key()]].setChecked(True)
elif e.key() == Qt.Key_B:
self._toggle_bg()
elif e.key() in (Qt.Key_Delete, Qt.Key_Backspace):
self._delete_selected()
elif e.key() in (Qt.Key_Return, Qt.Key_Enter):
self._save_close()
elif e.key() == Qt.Key_Escape:
self._cancel()
elif e.key() == Qt.Key_Home:
self.canvas.reset_zoom()
else:
super().keyPressEvent(e)
def _on_display_window_changed(self, low: float, high: float) -> None:
"""
Apply a new display window from the histogram adjuster.
Parameters
----------
low : float
Lower intensity bound of the display window.
high : float
Upper intensity bound of the display window.
Returns
-------
None
No object is returned; the function remaps the on-screen image.
"""
self.rm.set_display_window(low, high)
self.canvas.refresh_base_pixmap()
self.canvas.update()
# ─────────────────────────────────────────────────────────────────────────────
# Public ROIMaker
# ─────────────────────────────────────────────────────────────────────────────
[docs]
class ROIMaker:
"""
Provide a programmatic wrapper around the ROI application. It launches the
interactive editor, exposes generated masks, creates threshold-derived ROIs, and
saves mask outputs.
Parameters
----------
image_2d : np.ndarray
Two-dimensional image used as the ROI editing canvas.
save_path : str
Output path used when saving generated masks, figures, or data.
"""
def __init__(self, image_2d: np.ndarray, save_path: str = "masks/mask.npy") -> None:
arr = np.asarray(image_2d, dtype=np.float64)
self._raw_img = arr # original values for thresholding
self.img_min = int(np.floor(arr.min()))
self.img_max = int(np.ceil(arr.max()))
self.display_low = float(arr.min())
self.display_high = float(arr.max())
self.display_base = cv2.normalize(arr, None, 0, 255, cv2.NORM_MINMAX).astype(
np.uint8
)
self.H, self.W = arr.shape
self.save_path = save_path
self.rois = []
self.assign_counter = 1 # next ID to hand out in assign mode
self.show_bg = True
# output type: 'binary' | 'multi' | 'both'
self.mask_type = "multi"
# intensity filter — defaults span the full image range
self.intensity_active = False
self.intensity_low = self.img_min
self.intensity_high = self.img_max
self.mask_below_color = (0, 0, 139) # RGB — pixels below low threshold
self.mask_above_color = (139, 0, 0) # RGB — pixels above high threshold
if os.path.exists(self.save_path):
self.load_mask(self.save_path)
# ── display window ────────────────────────────────────────────────────────
[docs]
def set_display_window(self, low: float, high: float) -> None:
"""Remap the on-screen grayscale image to the intensity window [low, high].
Affects canvas visibility only — ``self._raw_img``, the saved masks and
the intensity filter are left untouched.
Parameters
----------
low : float
Lower intensity bound of the display window.
high : float
Upper intensity bound of the display window.
Returns
-------
None
No object is returned; the function updates ``display_base``.
"""
lo = float(min(low, high))
hi = float(max(low, high))
if hi - lo < 1e-9:
hi = lo + 1e-9
self.display_low = lo
self.display_high = hi
scaled = (self._raw_img - lo) / (hi - lo)
self.display_base = np.clip(scaled * 255.0, 0.0, 255.0).astype(np.uint8)
# ── mask generators ───────────────────────────────────────────────────────
[docs]
def get_intensity_mask(self) -> np.ndarray:
"""Binary (H,W) uint8: 1 where pixel intensity is inside [low, high].
Always independent of the ROI masks — saved as a separate file."""
lo, hi = self.intensity_low, self.intensity_high
return ((self._raw_img >= lo) & (self._raw_img <= hi)).astype(np.uint8)
[docs]
def create_rois_from_threshold(self, min_area: int = 10) -> int:
"""Convert the current intensity threshold mask into ROIObjects.
Each contiguous region in the threshold mask is added to ``self.rois``
as an unassigned ROI, indistinguishable from a hand-drawn one. The
caller is responsible for assigning IDs and saving via the normal flow.
Parameters
----------
min_area : minimum contour area in pixels (default 10).
Returns
-------
Number of ROIs added.
"""
mask = self.get_intensity_mask() # (H, W) uint8
cnts, _ = cv2.findContours(mask, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
added = 0
for cnt in cnts:
if cv2.contourArea(cnt) < min_area:
continue
roi = ROIObject(cnt.reshape(-1, 2)) # assigned=False, roi_id=0
self.rois.append(roi)
added += 1
return added
[docs]
def get_binary_mask(self) -> np.ndarray:
"""All drawn ROIs → 1, background → 0. Intensity filter NOT applied."""
mask = np.zeros((self.H, self.W), dtype=np.uint8)
for roi in self.rois:
cv2.fillPoly(mask, [roi.pts.astype(np.int32)], 1)
return mask
[docs]
def get_threshold_binary_mask(self) -> np.ndarray:
"""Binary (H,W) uint8 mask built purely from intensity thresholds.
Every pixel whose value is within [intensity_low, intensity_high] is 1;
everything else is 0. No polygon filling is involved, so pixels that
sit inside a closed/ring-shaped ROI boundary but fall outside the
intensity range are correctly excluded — the problem that arises when
fillPoly floods a hollow structure's interior.
"""
lo, hi = self.intensity_low, self.intensity_high
return ((self._raw_img >= lo) & (self._raw_img <= hi)).astype(np.uint8)
[docs]
def save_threshold_binary_mask(self) -> str:
"""Save a binary mask derived purely from intensity thresholds and return the path.
Each pixel is 1 if its value is within [intensity_low, intensity_high], 0 otherwise.
No ROI polygons or fillPoly are involved, so hollow/ring structures are handled
correctly — interior pixels that fall outside the range stay excluded.
Saved independently of the main ROI mask pipeline as <stem>_threshold_binary.npy.
"""
stem, _ = os.path.splitext(os.path.abspath(self.save_path))
os.makedirs(os.path.dirname(stem) or ".", exist_ok=True)
path = f"{stem}_threshold_binary.npy"
np.save(path, self.get_threshold_binary_mask())
return path
[docs]
def get_multi_cluster_mask(self) -> np.ndarray:
"""Each ROI → its roi_id; background → 0. Intensity filter NOT applied."""
mask = np.zeros((self.H, self.W), dtype=np.int32)
for roi in self.rois:
cv2.fillPoly(mask, [roi.pts.astype(np.int32)], int(roi.roi_id))
return mask
# ── load / save ───────────────────────────────────────────────────────────
[docs]
def load_mask(self, path: str) -> None:
"""
Load mask.
Parameters
----------
path : str
Filesystem path loaded or saved by the routine.
Returns
-------
None
No object is returned; the function load mask.
"""
try:
loaded = np.load(path)
for uid in np.unique(loaded):
if uid == 0:
continue
cnts, _ = cv2.findContours(
(loaded == uid).astype(np.uint8),
cv2.RETR_EXTERNAL,
cv2.CHAIN_APPROX_SIMPLE,
)
for cnt in cnts:
if cv2.contourArea(cnt) > 5:
roi = ROIObject(cnt.reshape(-1, 2), uid)
roi.assigned = True # loaded ROIs already have IDs
self.rois.append(roi)
if self.rois:
self.assign_counter = max(r.roi_id for r in self.rois) + 1
except Exception as exc:
logging.warning(f"Load mask failed: {exc}")
[docs]
def save_masks(self) -> None:
"""
Save masks.
Returns
-------
None
No object is returned; the function save masks.
"""
stem, _ = os.path.splitext(os.path.abspath(self.save_path))
os.makedirs(os.path.dirname(stem) or ".", exist_ok=True)
if self.mask_type == "binary":
np.save(self.save_path, self.get_binary_mask())
logging.info(f"Saved binary mask → {self.save_path}")
elif self.mask_type == "multi":
m = self.get_multi_cluster_mask()
np.save(self.save_path, m)
logging.info(
f"Saved multi-ID mask ({len(np.unique(m)) - 1} region(s)) → {self.save_path}"
)
elif self.mask_type == "both":
binary_path = f"{stem}_binary.npy"
multi_path = f"{stem}_multi.npy"
np.save(binary_path, self.get_binary_mask())
logging.info(f"Saved binary mask → {binary_path}")
m = self.get_multi_cluster_mask()
np.save(multi_path, m)
logging.info(
f"Saved multi-ID mask ({len(np.unique(m)) - 1} region(s)) → {multi_path}"
)
# Intensity mask is always its own separate file — never merged into ROI masks
if self.intensity_active:
path = f"{stem}_intensity.npy"
np.save(path, self.get_intensity_mask())
logging.info(f"Saved intensity mask → {path}")
# ── draw ──────────────────────────────────────────────────────────────────
[docs]
def draw(self) -> Any:
"""Open the editor window (blocks). Returns the chosen mask type."""
app = QApplication.instance() or QApplication(sys.argv)
win = ROIApp(self)
win.resize(min(self.W + 210, 1440), min(self.H + 160, 920))
win.show()
app.exec()
return self.get_multi_cluster_mask()
# ─────────────────────────────────────────────────────────────────────────────
if __name__ == "__main__":
from pyfli import DataOperations
_HERE = os.path.dirname(os.path.abspath(__file__))
loader = DataOperations(
data_path=os.path.normpath(
os.path.join(_HERE, "../../../../data/ICCD/mouseR_740bp")
),
irf_path=os.path.normpath(
os.path.join(_HERE, "../../../../data/ICCD/mouseR_IRF")
),
)
fli_cube = loader.load_data()
if fli_cube is None:
raise FileNotFoundError(
f"Data not found. Tried: {os.path.abspath(loader.data_path)}"
)
logging.info(f"FLI shape: {fli_cube.shape}")
irf_cube = loader.load_irf()
if irf_cube is None:
raise FileNotFoundError(
f"IRF not found. Tried: {os.path.abspath(loader.irf_path)}"
)
logging.info(f"IRF shape: {irf_cube.shape}")
intensity_proj = np.sum(fli_cube, axis=-1)
maker = ROIMaker(intensity_proj, save_path="mouseL_mask.npy")
multi = maker.draw()
import matplotlib.pyplot as plt
plt.imshow(multi)
plt.show()
