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feat(multipoint): add Prev and Set XY to the flexible multipoint tab #617

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81 changes: 81 additions & 0 deletions software/control/core/core.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1513,6 +1513,10 @@ def set_autolevel(self, enabled):
class NavigationViewer(QFrame):
signal_coordinates_clicked = Signal(float, float) # Will emit x_mm, y_mm when clicked

# Colors for the position number labels drawn over the scan grid
POSITION_LABEL_COLOR = (252, 174, 30) # matches the yellow scan grid rectangles
POSITION_CURRENT_COLOR = (0, 200, 255) # cyan - distinct from the red current-FOV box

def __init__(self, objectivestore, camera, sample="glass slide", invertX=False, *args, **kwargs):
super().__init__(*args, **kwargs)
self._log = squid.logging.get_logger(self.__class__.__name__)
Expand Down Expand Up @@ -1630,20 +1634,29 @@ def create_layers(self):
self.scan_overlay = np.zeros((self.image_height, self.image_width, 4), dtype=np.uint8)
self.fov_overlay = np.zeros((self.image_height, self.image_width, 4), dtype=np.uint8)
self.focus_point_overlay = np.zeros((self.image_height, self.image_width, 4), dtype=np.uint8)
self.position_highlight_overlay = np.zeros((self.image_height, self.image_width, 4), dtype=np.uint8)

self.scan_overlay_item = pg.ImageItem()
self.fov_overlay_item = pg.ImageItem()
self.focus_point_overlay_item = pg.ImageItem()

self.position_highlight_item = pg.ImageItem()

self.view.addItem(self.scan_overlay_item)
self.view.addItem(self.fov_overlay_item)
self.view.addItem(self.focus_point_overlay_item)
self.view.addItem(self.position_highlight_item)

self.background_item.setZValue(-1) # Background layer at the bottom
self.scan_overlay_item.setZValue(0) # Scan overlay in the middle
self.focus_point_overlay_item.setZValue(1) # # Focus points next
self.position_highlight_item.setZValue(1.5) # Selected position highlight
self.fov_overlay_item.setZValue(2) # FOV overlay on top

# pg.TextItems for the position number labels. load_background_image() calls
# view.clear(), which drops every item, so this list is rebuilt here each time.
self.position_label_items = []

def update_display_properties(self, sample):
if sample == "glass slide":
self.location_update_threshold_mm = 0.2
Expand Down Expand Up @@ -1842,6 +1855,73 @@ def register_focus_point(self, x_mm, y_mm):
cv2.circle(self.focus_point_overlay, (center_x, center_y), radius, color, -1) # -1 thickness means filled
self.focus_point_overlay_item.setImage(self.focus_point_overlay)

def set_position_labels(self, labels, current_index=None):
"""
Draw a number label at each listed position. Full rebuild - call when the list changes.

Args:
labels: list of (x_mm, y_mm, text) tuples
current_index: index into labels to highlight, or None
"""
self.clear_position_labels()
for x_mm, y_mm, text in labels:
current_FOV_top_left, current_FOV_bottom_right = self.get_FOV_pixel_coordinates(x_mm, y_mm)
center_x = (current_FOV_top_left[0] + current_FOV_bottom_right[0]) / 2
center_y = (current_FOV_top_left[1] + current_FOV_bottom_right[1]) / 2
# pg.TextItem draws in screen space, so labels stay upright and legible
# regardless of the ViewBox's invertX/invertY or the current zoom level.
item = pg.TextItem(text=text, anchor=(0.5, 0.5))
item.setZValue(3)
item.setPos(center_x, center_y)
self.view.addItem(item)
self.position_label_items.append(item)
self.set_current_position(current_index)

def set_current_position(self, index, fov_list=None):
"""
Recolor the existing labels and redraw the highlight box around the selected region.
Cheap compared to set_position_labels - use this on selection changes.

Args:
index: index of the current position, or None
fov_list: FOVs of the current region to outline, as (x_mm, y_mm[, z_mm]) tuples
or FovCenter objects. None clears the highlight box.
"""
for i, item in enumerate(self.position_label_items):
is_current = i == index
item.setColor(self.POSITION_CURRENT_COLOR if is_current else self.POSITION_LABEL_COLOR)
font = item.textItem.font()
font.setBold(is_current)
item.setFont(font)

self.position_highlight_overlay.fill(0)
color = (*self.POSITION_CURRENT_COLOR, 255)
for fov in fov_list or []:
# Handle tuple (2D or 3D) and FovCenter object formats
if isinstance(fov, tuple):
x_mm = fov[0]
y_mm = fov[1]
else:
x_mm = fov.x_mm
y_mm = fov.y_mm
current_FOV_top_left, current_FOV_bottom_right = self.get_FOV_pixel_coordinates(x_mm, y_mm)
cv2.rectangle(
self.position_highlight_overlay,
current_FOV_top_left,
current_FOV_bottom_right,
color,
self.box_line_thickness,
)
self.position_highlight_item.setImage(self.position_highlight_overlay)

def clear_position_labels(self):
"""Remove all position number labels and the selected-position highlight"""
for item in self.position_label_items:
self.view.removeItem(item)
self.position_label_items = []
self.position_highlight_overlay.fill(0)
self.position_highlight_item.setImage(self.position_highlight_overlay)

def clear_focus_points(self):
"""Clear just the focus point overlay"""
self.focus_point_overlay = np.zeros((self.image_height, self.image_width, 4), dtype=np.uint8)
Expand All @@ -1857,6 +1937,7 @@ def clear_overlay(self):
self.scan_overlay_item.setImage(self.scan_overlay)
self.focus_point_overlay.fill(0)
self.focus_point_overlay_item.setImage(self.focus_point_overlay)
self.clear_position_labels()

def handle_mouse_click(self, evt):
if not evt.double():
Expand Down
150 changes: 137 additions & 13 deletions software/control/widgets.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6085,7 +6085,7 @@ def add_components(self):
self.dropdown_location_list.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed)
self.btn_add = QPushButton("Add")
self.btn_remove = QPushButton("Remove")
self.btn_previous = QPushButton("Previous")
self.btn_previous = QPushButton("Prev")
self.btn_next = QPushButton("Next")
self.btn_clear = QPushButton("Clear")

Expand All @@ -6100,7 +6100,8 @@ def add_components(self):
self.table_location_list.setColumnCount(4)
header_labels = ["x", "y", "z", "ID"]
self.table_location_list.setHorizontalHeaderLabels(header_labels)
self.btn_update_z = QPushButton("Update Z")
self.btn_update_xy = QPushButton("Set XY")
self.btn_update_z = QPushButton("Set Z")

self.entry_deltaX = QDoubleSpinBox()
self.entry_deltaX.setMinimum(0)
Expand Down Expand Up @@ -6304,15 +6305,25 @@ def add_components(self):
temp3.addWidget(QLabel("Location List"))
temp3.addWidget(self.dropdown_location_list)
self.grid_location_list_line1.addLayout(temp3, 0, 0, 1, 6) # Span across all columns except the last
self.grid_location_list_line1.addWidget(self.btn_update_z, 0, 6, 1, 2) # Align with other buttons
# Set XY / Set Z split the width the single Update Z button used to occupy
self.grid_location_list_line1.addWidget(self.btn_update_xy, 0, 6, 1, 1)
self.grid_location_list_line1.addWidget(self.btn_update_z, 0, 7, 1, 1)

self.grid_location_list_line2 = QGridLayout()
# Make all buttons span 2 columns for consistent width
self.grid_location_list_line2.addWidget(self.btn_add, 1, 0, 1, 2)
self.grid_location_list_line2.addWidget(self.btn_remove, 1, 2, 1, 2)
self.grid_location_list_line2.addWidget(self.btn_next, 1, 4, 1, 2)
# Prev / Next split the width the single Next button used to occupy
self.grid_location_list_line2.addWidget(self.btn_previous, 1, 4, 1, 1)
self.grid_location_list_line2.addWidget(self.btn_next, 1, 5, 1, 1)
self.grid_location_list_line2.addWidget(self.btn_clear, 1, 6, 1, 2)

# Even column widths, so the split buttons are genuinely half-width instead of
# shrinking to fit their text
for i in range(8):
self.grid_location_list_line1.setColumnStretch(i, 1)
self.grid_location_list_line2.setColumnStretch(i, 1)

self.grid_location_list_line3 = QGridLayout()
self.grid_location_list_line3.addWidget(self.btn_import_locations, 2, 0, 1, 3)
self.grid_location_list_line3.addWidget(self.btn_export_locations, 2, 3, 1, 3)
Expand Down Expand Up @@ -6506,6 +6517,7 @@ def setup_connections(self):
self.table_location_list.cellClicked.connect(self.cell_was_clicked)
self.table_location_list.cellChanged.connect(self.cell_was_changed)
self.btn_show_table_location_list.clicked.connect(self.table_location_list.show)
self.btn_update_xy.clicked.connect(self.update_xy)
self.btn_update_z.clicked.connect(self.update_z)
self.dropdown_location_list.currentIndexChanged.connect(self.go_to)

Expand Down Expand Up @@ -6615,17 +6627,96 @@ def _reset_reflection_af_reference(self):
):
error_dialog("Failed to set reference for reflection autofocus. Is the laser autofocus initialized?")

@staticmethod
def _location_str(x_mm, y_mm, z_mm):
"""Single source of truth for the location list display string."""
return f"x:{round(x_mm,3)} mm y:{round(y_mm,3)} mm z:{round(z_mm * 1000,1)} μm"

def _selected_location_index(self):
"""Current location list index, or None when there is nothing selected."""
index = self.dropdown_location_list.currentIndex()
if index < 0 or index >= len(self.location_list):
return None
return index

def update_z(self):
index = self._selected_location_index()
if index is None:
self._log.error("Cannot update Z, because no location is selected")
return

z_mm = self.stage.get_pos().z_mm
index = self.dropdown_location_list.currentIndex()
region_id = self.location_ids[index]
self.location_list[index, 2] = z_mm
self.scanCoordinates.region_centers[self.location_ids[index]][2] = z_mm
self.scanCoordinates.region_fov_coordinates[self.location_ids[index]] = [
(coord[0], coord[1], z_mm)
for coord in self.scanCoordinates.region_fov_coordinates[self.location_ids[index]]
]
location_str = f"x:{round(self.location_list[index,0],3)} mm y:{round(self.location_list[index,1],3)} mm z:{round(z_mm * 1000.0,3)} μm"
self.dropdown_location_list.setItemText(index, location_str)

# Z does not change the grid footprint, so the FOVs only need their z rewritten
if region_id in self.scanCoordinates.region_centers:
self.scanCoordinates.region_centers[region_id][2] = z_mm
if region_id in self.scanCoordinates.region_fov_coordinates:
self.scanCoordinates.region_fov_coordinates[region_id] = [
(coord[0], coord[1], z_mm) for coord in self.scanCoordinates.region_fov_coordinates[region_id]
]

self.dropdown_location_list.setItemText(
index, self._location_str(self.location_list[index, 0], self.location_list[index, 1], z_mm)
)
# Keep the table in sync without re-entering cell_was_changed
self.table_location_list.blockSignals(True)
if self.table_location_list.rowCount() > index:
self.table_location_list.setItem(index, 2, QTableWidgetItem(str(round(z_mm * 1000, 1))))
self.table_location_list.blockSignals(False)

def update_xy(self):
index = self._selected_location_index()
if index is None:
self._log.error("Cannot update XY, because no location is selected")
return

pos = self.stage.get_pos()
x = pos.x_mm
y = pos.y_mm
z = self.location_list[index, 2] # Z is left alone, that is what Set Z is for
region_id = self.location_ids[index]

# Erase the old grid rectangles before the region is re-tiled at the new center
if region_id in self.scanCoordinates.region_fov_coordinates:
self.navigationViewer.deregister_fovs_from_image(self.scanCoordinates.region_fov_coordinates[region_id])

self.location_list[index, 0] = x
self.location_list[index, 1] = y

# Re-tile the region at the new center; this re-registers its FOVs on the viewer
if self.use_overlap:
self.scanCoordinates.add_flexible_region(
region_id,
x,
y,
z,
self.entry_NX.value(),
self.entry_NY.value(),
overlap_percent=self.entry_overlap.value(),
)
else:
self.scanCoordinates.add_flexible_region_with_step_size(
region_id,
x,
y,
z,
self.entry_NX.value(),
self.entry_NY.value(),
self.entry_deltaX.value(),
self.entry_deltaY.value(),
)

self.dropdown_location_list.setItemText(index, self._location_str(x, y, z))
# Keep the table in sync without re-entering cell_was_changed
self.table_location_list.blockSignals(True)
if self.table_location_list.rowCount() > index:
self.table_location_list.setItem(index, 0, QTableWidgetItem(str(round(x, 3))))
self.table_location_list.setItem(index, 1, QTableWidgetItem(str(round(y, 3))))
self.table_location_list.blockSignals(False)

self.refresh_position_labels()

def update_Nz(self):
z_min = self.entry_minZ.value()
Expand Down Expand Up @@ -6746,6 +6837,8 @@ def update_fov_positions(self):
self.entry_deltaY.value(),
)

self.refresh_position_labels()

def set_deltaZ(self, value):
if self.checkbox_usePiezo.isChecked():
deltaZ = value
Expand Down Expand Up @@ -6960,6 +7053,7 @@ def add_location(self):
# Re-enable signals
self.table_location_list.blockSignals(False)
self.dropdown_location_list.blockSignals(False)
self.refresh_position_labels()
print(f"Added Region: {region_id} - x={x}, y={y}, z={z}")
else:
print("Invalid Region: Duplicate Location")
Expand Down Expand Up @@ -7020,6 +7114,7 @@ def remove_location(self):
# Re-enable signals
self.table_location_list.blockSignals(False)
self.dropdown_location_list.blockSignals(False)
self.refresh_position_labels()

def next(self):
index = self.dropdown_location_list.currentIndex()
Expand All @@ -7040,8 +7135,15 @@ def next(self):
self.stage.move_z_to(z)

def previous(self):
num_regions = self.dropdown_location_list.count()
if num_regions <= 0:
self._log.error("Cannot move to previous location, because there are no locations in the list")
return

index = self.dropdown_location_list.currentIndex()
index = max(index - 1, 0)
# With nothing selected, stepping back should land on the last entry, not on
# (-1 - 1) % num_regions, which would silently skip to the second to last.
index = num_regions - 1 if index < 0 else (index - 1) % num_regions
self.dropdown_location_list.setCurrentIndex(index)
x = self.location_list[index, 0]
y = self.location_list[index, 1]
Expand All @@ -7058,13 +7160,15 @@ def clear(self):
self.table_location_list.setRowCount(0)
self.navigationViewer.clear_overlay()

self.refresh_position_labels()
self._log.info("Cleared all locations and overlays.")

def clear_only_location_list(self):
self.location_list = np.empty((0, 3), dtype=float)
self.location_ids = np.empty((0,), dtype="<U20")
self.dropdown_location_list.clear()
self.table_location_list.setRowCount(0)
self.refresh_position_labels()

def go_to(self, index):
if index != -1:
Expand All @@ -7076,6 +7180,22 @@ def go_to(self, index):
self.stage.move_y_to(y)
self.stage.move_z_to(z)
self.table_location_list.selectRow(index)
self.navigationViewer.set_current_position(index, self._current_region_fovs(index))

def _current_region_fovs(self, index):
"""FOV coordinates of the region at index, or None if there is no such region."""
if 0 <= index < len(self.location_ids):
return self.scanCoordinates.region_fov_coordinates.get(self.location_ids[index])
return None

def refresh_position_labels(self):
"""Redraw the position number labels on the scan grid. Call after the list changes."""
labels = [
(self.location_list[i, 0], self.location_list[i, 1], str(i + 1)) for i in range(len(self.location_list))
]
index = self.dropdown_location_list.currentIndex()
self.navigationViewer.set_position_labels(labels, current_index=index)
self.navigationViewer.set_current_position(index, self._current_region_fovs(index))

def cell_was_clicked(self, row, column):
self.dropdown_location_list.setCurrentIndex(row)
Expand Down Expand Up @@ -7137,6 +7257,7 @@ def cell_was_changed(self, row, column):
location_str = f"x:{round(self.location_list[row,0],3)} mm y:{round(self.location_list[row,1],3)} mm z:{round(1000*self.location_list[row,2],3)} μm"
self.dropdown_location_list.setItemText(row, location_str)
self.go_to(row)
self.refresh_position_labels()

def keyPressEvent(self, event):
if event.key() == Qt.Key_A and event.modifiers() == Qt.ControlModifier:
Expand Down Expand Up @@ -7251,6 +7372,7 @@ def import_location_list(self):
self._log.warning("Duplicate values not added based on x and y.")
self.table_location_list.blockSignals(False)
self.dropdown_location_list.blockSignals(False)
self.refresh_position_labels()
self._log.debug(self.location_list)

def on_snap_images(self):
Expand Down Expand Up @@ -7526,6 +7648,8 @@ def _load_positions(self, positions):
self.entry_deltaY.value(),
)

self.refresh_position_labels()


class WellplateMultiPointWidget(AcquisitionYAMLDropMixin, _ApplyChannelOffsetMixin, QFrame):

Expand Down
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