driftlessmap 1.1.0__py3-none-any.whl

driftlessmap/toolbox.py

@@ -0,0 +1,569 @@
+from PyQt6.QtGui import *
+from PyQt6.QtCore import *
+from PyQt6.QtWidgets import *
+import pyqtgraph as pg
+import numpy as np
+from pyqtgraph.Qt import QtGui, QtCore
+from .resources import resource_path
+
+
+class ToolBox(QObject):
+
+    def __init__(self):
+
+        QObject.__init__(self)
+
+        self.pencil_mask = np.ones((3, 3), 'uint8')
+        self.is_closed = False
+        self.multi_shanks = False
+
+        self.remove_inside = True
+
+        self.merge_sites = False
+
+        # action version
+        self.add_atlas = QAction(QIcon(resource_path('icons/toolbar/atlas_icon.png')), 'Upload Previous Loaded Volume Atlas', self)
+        self.add_image_stack = QAction(QIcon(resource_path('icons/toolbar/image_icon.svg')), 'Upload Histological Image', self)
+
+        self.vis2 = QAction(QIcon(resource_path('icons/toolbar/two_window.png')), 'Show 2 Windows', self)
+        self.vis4 = QAction(QIcon(resource_path('icons/toolbar/window4.png')), 'Show 4 Windows', self)
+        self.vis3 = QAction(QIcon(resource_path('icons/toolbar/window3.png')), 'Show 3 Windows', self)
+
+        self.toa_btn_off_icon = QIcon(resource_path('icons/toolbar/toa.svg'))
+        self.toa_btn_on_icon = QIcon(resource_path('icons/toolbar/toa_delete.svg'))
+
+        self.toh_btn_off_icon = QIcon(resource_path('icons/toolbar/toh.svg'))
+        self.toh_btn_on_icon = QIcon(resource_path('icons/toolbar/toh_delete.svg'))
+
+        self.toa_btn = QAction(QIcon(resource_path('icons/toolbar/toa.svg')), 'Transform to Atlas Slice Window', self)
+        self.toh_btn = QAction(QIcon(resource_path('icons/toolbar/toh.svg')), 'Transform to Histologist Image Window', self)
+        self.check_btn = QAction(QIcon(resource_path('icons/toolbar/accept.svg')), 'Accept and Transfer', self)
+
+        lasso_btn = QAction(QIcon(resource_path('icons/toolbar/lasso.svg')), 'Polygon Lasso', self)
+        lasso_btn.setCheckable(True)
+
+        magic_wand_btn = QAction(QIcon(resource_path('icons/toolbar/magic-wand.svg')), 'Magic Wand', self)
+        magic_wand_btn.setCheckable(True)
+
+        pencil_btn = QAction(QIcon(resource_path('icons/toolbar/pencil.svg')), 'Pencil', self)
+        pencil_btn.setCheckable(True)
+
+        eraser_btn = QAction(QIcon(resource_path('icons/toolbar/eraser.svg')), 'Eraser', self)
+        eraser_btn.setCheckable(True)
+
+        mask_btn = QAction(QIcon(resource_path('icons/toolbar/mask.svg')), 'Mask Maker', self)
+        mask_btn.setCheckable(True)
+
+        probe_btn = QAction(QIcon(resource_path('icons/toolbar/probe.svg')), 'Probe Marker', self)
+        probe_btn.setCheckable(True)
+
+        triang_btn = QAction(QIcon(resource_path('icons/toolbar/triangulation.svg')), 'Triangulation', self)
+        triang_btn.setCheckable(True)
+
+        loc_btn = QAction(QIcon(resource_path('icons/toolbar/location.svg')), 'Cell Selector', self)
+        loc_btn.setCheckable(True)
+
+        ruler_btn = QAction(QIcon(resource_path('icons/toolbar/ruler.svg')), 'Ruler', self)
+        ruler_btn.setCheckable(True)
+
+        self.checkable_btn_dict = {'ruler_btn': ruler_btn,
+                                   'pencil_btn': pencil_btn,
+                                   'eraser_btn': eraser_btn,
+                                   'lasso_btn': lasso_btn,
+                                   'magic_wand_btn': magic_wand_btn,
+                                   'probe_btn': probe_btn,
+                                   'triang_btn': triang_btn,
+                                   'loc_btn': loc_btn}
+
+        self.toolbox_btn_keys = list(self.checkable_btn_dict.keys())
+
+        # for ruler_btn, ruler wrap
+        ruler_color_label = QLabel('Color:')
+        self.ruler_color_btn = pg.ColorButton(padding=0)
+        self.ruler_color_btn.setColor('yellow')
+        self.ruler_color_btn.setFixedSize(60, 15)
+        ruler_width_label = QLabel('Size:')
+        self.ruler_width_slider = QSlider(Qt.Orientation.Horizontal)
+        self.ruler_width_slider.setFixedWidth(100)
+        self.ruler_width_slider.setMinimum(1)
+        self.ruler_width_slider.setMaximum(5)
+        self.ruler_width_slider.setValue(3)
+        self.ruler_width_slider.sliderMoved.connect(self.change_ruler_slider)
+
+        self.ruler_size_valt = QLineEdit()
+        self.ruler_size_valt.setFixedSize(50, 24)
+        self.ruler_size_valt.setAlignment(Qt.AlignmentFlag.AlignLeft)
+        self.ruler_size_valt.setValidator(QIntValidator(1, 5))
+        self.ruler_size_valt.setText('3')
+
+        self.ruler_length_label = QLabel('Length: ')
+
+        self.ruler_wrap = QFrame()
+        ruler_layout = QHBoxLayout(self.ruler_wrap)
+        ruler_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        ruler_layout.setContentsMargins(0, 0, 0, 0)
+        ruler_layout.setSpacing(10)
+        ruler_layout.addWidget(ruler_color_label)
+        ruler_layout.addWidget(self.ruler_color_btn)
+        ruler_layout.addSpacing(15)
+        ruler_layout.addWidget(ruler_width_label)
+        ruler_layout.addWidget(self.ruler_width_slider)
+        ruler_layout.addWidget(self.ruler_size_valt)
+        ruler_layout.addSpacing(25)
+        ruler_layout.addWidget(self.ruler_length_label)
+        ruler_layout.addStretch(1)
+
+        # for magic wand, magic wand wrap
+        magic_color_label = QLabel('Color:')
+        self.magic_color_btn = pg.ColorButton(padding=0)
+        self.magic_color_btn.setFixedSize(60, 15)
+        self.magic_color_btn.setColor(QColor(255, 0, 255, 255))
+        magic_tol_label = QLabel('Tolerance:')
+        self.magic_tol_val = QLineEdit()
+        self.magic_tol_val.setFixedWidth(40)
+        # self.magic_tol_val.setAlignment(Qt.AlignmentFlag.AlignLeft)
+        self.magic_tol_val.setValidator(QIntValidator())
+        self.magic_tol_val.setText('0')
+
+        self.magic_wand_kernel = QComboBox()
+        self.magic_wand_kernel.setFixedSize(150, 20)
+        self.magic_wand_kernel.addItems(["Kernel", "Rectangular", "Elliptical", "Cross-shaped"])
+
+        magic_wand_ksize_label = QLabel('Size:')
+        self.magic_wand_ksize = QSpinBox()
+        self.magic_wand_ksize.setFixedSize(80, 20)
+        self.magic_wand_ksize.setValue(0)
+        self.magic_wand_ksize.setMinimum(0)
+
+        self.magic_wand_virus_register = QPushButton()
+        self.magic_wand_virus_register.setFocusPolicy(Qt.FocusPolicy.NoFocus)
+        self.magic_wand_virus_register.setIcon(QIcon(resource_path('icons/toolbar/virus_register.svg')))
+        self.magic_wand_virus_register.setIconSize(QSize(20, 20))
+        self.magic_wand_bnd_register = QPushButton()
+        self.magic_wand_bnd_register.setFocusPolicy(Qt.FocusPolicy.NoFocus)
+        self.magic_wand_bnd_register.setIcon(QIcon(resource_path('icons/toolbar/boundary_register.svg')))
+        self.magic_wand_bnd_register.setIconSize(QSize(20, 20))
+
+        self.magic_wand_wrap = QFrame()
+        # self.magic_wand_wrap.setFixedHeight(32)
+        magic_wand_layout = QHBoxLayout(self.magic_wand_wrap)
+        magic_wand_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        magic_wand_layout.setContentsMargins(0, 0, 0, 0)
+        magic_wand_layout.setSpacing(10)
+        magic_wand_layout.addWidget(magic_color_label)
+        magic_wand_layout.addWidget(self.magic_color_btn)
+        magic_wand_layout.addSpacing(10)
+        magic_wand_layout.addWidget(magic_tol_label)
+        magic_wand_layout.addWidget(self.magic_tol_val)
+        magic_wand_layout.addWidget(self.magic_wand_kernel)
+        magic_wand_layout.addWidget(magic_wand_ksize_label)
+        magic_wand_layout.addWidget(self.magic_wand_ksize)
+        magic_wand_layout.addWidget(self.magic_wand_virus_register)
+        magic_wand_layout.addWidget(self.magic_wand_bnd_register)
+        magic_wand_layout.addStretch(1)
+        # magic_wand_layout.insertStretch(1, -1)
+
+        # for pencil_btn, pencil wrap
+        pencil_size_label = QLabel('Size:')
+        self.pencil_size_slider = QSlider(Qt.Orientation.Horizontal)
+        self.pencil_size_slider.setFixedWidth(100)
+        self.pencil_size_slider.setMinimum(1)
+        self.pencil_size_slider.setMaximum(5)
+        self.pencil_size_slider.setValue(2)
+        self.pencil_size_slider.sliderMoved.connect(self.change_pencil_slider)
+
+        self.pencil_size_valt = QLineEdit()
+        self.pencil_size_valt.setFixedSize(50, 24)
+        self.pencil_size_valt.setAlignment(Qt.AlignmentFlag.AlignLeft)
+        self.pencil_size_valt.setValidator(QIntValidator(1, 5))
+        self.pencil_size_valt.setText('2')
+
+        pencil_color_label = QLabel('Color:')
+        self.pencil_color_btn = pg.ColorButton(padding=0)
+        self.pencil_color_btn.setFixedSize(60, 15)
+        self.pencil_color_btn.setColor(QColor(255, 102, 0))
+
+        pencil_path_label = QLabel('Path Type:')
+        self.pencil_path_btn = QPushButton()
+        self.pencil_path_btn.setCheckable(True)
+        da_icon = QIcon()
+        da_icon.addPixmap(QPixmap(resource_path("icons/toolbar/closed_path.svg")), QIcon.Mode.Normal, QIcon.State.On)
+        da_icon.addPixmap(QPixmap(resource_path("icons/toolbar/open_path.svg")), QIcon.Mode.Normal, QIcon.State.Off)
+        self.pencil_path_btn.setIcon(da_icon)
+        self.pencil_path_btn.setIconSize(QSize(20, 20))
+        self.pencil_path_btn.clicked.connect(self.pencil_path_btn_clicked)
+
+        self.pencil_wrap = QFrame()
+        pencil_layout = QHBoxLayout(self.pencil_wrap)
+        pencil_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        pencil_layout.setContentsMargins(0, 0, 0, 0)
+        pencil_layout.setSpacing(10)
+        pencil_layout.addWidget(pencil_color_label)
+        pencil_layout.addWidget(self.pencil_color_btn)
+        pencil_layout.addSpacing(15)
+        pencil_layout.addWidget(pencil_size_label)
+        pencil_layout.addWidget(self.pencil_size_slider)
+        pencil_layout.addWidget(self.pencil_size_valt)
+        pencil_layout.addSpacing(15)
+        pencil_layout.addWidget(pencil_path_label)
+        pencil_layout.addWidget(self.pencil_path_btn)
+        pencil_layout.addStretch(1)
+
+        # for eraser_btn, eraser wrap
+        eraser_color_label = QLabel('Color:')
+        self.eraser_color_btn = pg.ColorButton(padding=0)
+        self.eraser_color_btn.setColor('red')
+        self.eraser_color_btn.setFixedSize(60, 15)
+        eraser_size_label = QLabel('Size:')
+        self.eraser_size_slider = QSlider(Qt.Orientation.Horizontal)
+        self.eraser_size_slider.setFixedWidth(100)
+        self.eraser_size_slider.setMinimum(1)
+        self.eraser_size_slider.setMaximum(500)
+        self.eraser_size_slider.setValue(20)
+        self.eraser_size_slider.valueChanged.connect(self.change_eraser_slider)
+
+        self.eraser_size_valt = QLineEdit()
+        self.eraser_size_valt.setFixedSize(50, 24)
+        self.eraser_size_valt.setAlignment(Qt.AlignmentFlag.AlignLeft)
+        self.eraser_size_valt.setValidator(QIntValidator(1, 500))
+        self.eraser_size_valt.setText('20')
+        self.eraser_size_valt.textChanged.connect(self.change_eraser_val)
+
+        self.eraser_wrap = QFrame()
+        eraser_layout = QHBoxLayout(self.eraser_wrap)
+        eraser_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        eraser_layout.setContentsMargins(0, 0, 0, 0)
+        eraser_layout.setSpacing(10)
+        eraser_layout.addWidget(eraser_color_label)
+        eraser_layout.addWidget(self.eraser_color_btn)
+        eraser_layout.addSpacing(15)
+        eraser_layout.addWidget(eraser_size_label)
+        eraser_layout.addWidget(self.eraser_size_slider)
+        eraser_layout.addWidget(self.eraser_size_valt)
+        eraser_layout.addStretch(1)
+
+        # for lasso_btn, lasso wrap
+        lasso_color_label = QLabel('Color:')
+        self.lasso_color_btn = pg.ColorButton(padding=0)
+        self.lasso_color_btn.setFixedSize(60, 15)
+        self.lasso_color_btn.setColor(QColor(0, 255, 255))
+
+        self.lasso_type_btn = QPushButton()
+        self.lasso_type_btn.setCheckable(True)
+        lt_icon = QIcon()
+        lt_icon.addPixmap(QPixmap(resource_path('icons/toolbar/outpart.svg')), QIcon.Mode.Normal, QIcon.State.On)
+        lt_icon.addPixmap(QPixmap(resource_path('icons/toolbar/inpart.svg')), QIcon.Mode.Normal, QIcon.State.Off)
+        self.lasso_type_btn.setIcon(lt_icon)
+        self.lasso_type_btn.setIconSize(QSize(20, 20))
+        self.lasso_type_btn.clicked.connect(self.lasso_type_changed)
+
+        self.lasso_wrap = QFrame()
+        lasso_layout = QHBoxLayout(self.lasso_wrap)
+        lasso_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        lasso_layout.setContentsMargins(0, 0, 0, 0)
+        lasso_layout.setSpacing(10)
+        lasso_layout.addWidget(lasso_color_label)
+        lasso_layout.addWidget(self.lasso_color_btn)
+        lasso_layout.addSpacing(10)
+        lasso_layout.addWidget(self.lasso_type_btn)
+        lasso_layout.addStretch(1)
+
+        # mask wrap
+        kernel_size_label = QLabel('Kernel Size: ')
+        self.kernel_size_slider = QSlider(Qt.Orientation.Horizontal)
+        self.kernel_size_slider.setFixedWidth(100)
+        self.kernel_size_slider.setMinimum(1)
+        self.kernel_size_slider.setMaximum(50)
+        self.kernel_size_slider.setValue(10)
+
+        self.mask_wrap = QFrame()
+        mask_layout = QHBoxLayout(self.mask_wrap)
+        mask_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        mask_layout.setContentsMargins(0, 0, 0, 0)
+        mask_layout.setSpacing(10)
+        mask_layout.addWidget(kernel_size_label)
+        mask_layout.addWidget(self.kernel_size_slider)
+        mask_layout.addStretch(1)
+
+        # for probe_btn, probe wrap
+        self.multi_prb_btn = QPushButton()
+        self.multi_prb_btn.setCheckable(True)
+        mp_icon = QIcon()
+        mp_icon.addPixmap(QPixmap(resource_path("icons/toolbar/multi_pencil.svg")), QIcon.Mode.Normal, QIcon.State.On)
+        mp_icon.addPixmap(QPixmap(resource_path("icons/toolbar/single_pencil.svg")), QIcon.Mode.Normal, QIcon.State.Off)
+        self.multi_prb_btn.setIcon(mp_icon)
+        self.multi_prb_btn.setIconSize(QSize(20, 20))
+        self.multi_prb_btn.setToolTip('Multi-shanks Switch')
+
+        probe_color_label = QLabel('Color:')
+        probe_color_label.setToolTip('Probe Color')
+        self.probe_color_btn = pg.ColorButton(padding=0)
+        self.probe_color_btn.setColor(QColor(0, 0, 255))
+        self.probe_color_btn.setFixedSize(60, 15)
+        probe_type_label = QLabel('Type:')
+        probe_type_label.setToolTip('Probe type')
+        self.probe_type_combo = QComboBox()
+        self.probe_type_combo.setFixedSize(150, 20)
+        self.probe_type_combo.addItems(["Neuropixel 1.0", "Neuropixel 2.0", "Linear-silicon", "Tetrode"])
+        self.probe_type_combo.setCurrentText("Neuropixel 1.0")
+
+        self.merge_sites_btn = QPushButton()
+        self.merge_sites_btn.setCheckable(True)
+        ms_icon = QIcon()
+        ms_icon.addPixmap(QPixmap(resource_path("icons/toolbar/line_sites.svg")), QIcon.Mode.Normal, QIcon.State.On)
+        ms_icon.addPixmap(QPixmap(resource_path("icons/toolbar/separate_sites.svg")), QIcon.Mode.Normal, QIcon.State.Off)
+        self.merge_sites_btn.setIcon(ms_icon)
+        self.merge_sites_btn.setIconSize(QSize(20, 20))
+        self.merge_sites_btn.setToolTip('Merge sites')
+        self.merge_sites_btn.clicked.connect(self.merge_sites_btn_clicked)
+
+        site_face_label = QLabel('Site-face:')
+        site_face_label.setToolTip('Sites Face Direction')
+        self.pre_site_face_combo = QComboBox()
+        self.pre_site_face_combo.setFixedSize(100, 20)
+        self.pre_site_face_combo.addItems(["Out", "In", "Left", "Right"])
+
+        self.after_site_face_combo = QComboBox()
+        self.after_site_face_combo.setFixedSize(100, 20)
+        self.after_site_face_combo.addItems(["Up", "Down", "Left", "Right"])
+        self.after_site_face_combo.setVisible(False)
+
+        self.linear_silicon_list = QPushButton()
+        self.linear_silicon_list.setFocusPolicy(Qt.FocusPolicy.NoFocus)
+        self.linear_silicon_list.setIcon(QIcon(resource_path('icons/toolbar/list.svg')))
+        self.linear_silicon_list.setIconSize(QSize(20, 20))
+        self.linear_silicon_list.setVisible(False)
+        self.linear_silicon_list.setToolTip('Linear Silicon Designer')
+
+        self.probe_wrap = QFrame()
+        probe_layout = QHBoxLayout(self.probe_wrap)
+        probe_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        probe_layout.setContentsMargins(0, 0, 0, 0)
+        probe_layout.setSpacing(10)
+        probe_layout.addWidget(self.multi_prb_btn)
+        probe_layout.addSpacing(20)
+        probe_layout.addWidget(probe_color_label)
+        probe_layout.addWidget(self.probe_color_btn)
+        probe_layout.addSpacing(10)
+        probe_layout.addWidget(probe_type_label)
+        probe_layout.addWidget(self.probe_type_combo)
+        probe_layout.addSpacing(10)
+        probe_layout.addWidget(self.merge_sites_btn)
+        probe_layout.addWidget(site_face_label)
+        probe_layout.addWidget(self.pre_site_face_combo)
+        probe_layout.addWidget(self.after_site_face_combo)
+        probe_layout.addStretch(1)
+        probe_layout.addWidget(self.linear_silicon_list)
+        probe_layout.addSpacing(10)
+
+        # for triang_btn, triang wrap
+        triang_color_label = QLabel('Color:')
+        self.triang_color_btn = pg.ColorButton(padding=0)
+        self.triang_color_btn.setFixedSize(60, 15)
+        bound_pnts_num_label = QLabel('Points Number:')
+        self.bound_pnts_num = QLineEdit()
+        self.bound_pnts_num.setFixedSize(50, 24)
+        self.bound_pnts_num.setAlignment(Qt.AlignmentFlag.AlignLeft)
+        self.bound_pnts_num.setMaxLength(2)
+        self.bound_pnts_num.setValidator(QIntValidator())
+        self.bound_pnts_num.setText('2')
+        self.triang_vis_btn = QPushButton()
+        self.triang_vis_btn.setCheckable(True)
+        vis_icon = QIcon()
+        vis_icon.addPixmap(QPixmap(resource_path("icons/toolbar/eye.svg")), QIcon.Mode.Normal, QIcon.State.On)
+        vis_icon.addPixmap(QPixmap(resource_path("icons/toolbar/eye_closed.svg")), QIcon.Mode.Normal, QIcon.State.Off)
+        self.triang_vis_btn.setIcon(vis_icon)
+        self.triang_vis_btn.setIconSize(QSize(20, 20))
+        self.triang_match_bnd = QPushButton()
+        self.triang_match_bnd.setIcon(QIcon(resource_path('icons/toolbar/matchbnd.svg')))
+        self.triang_match_bnd.setIconSize(QSize(20, 20))
+        self.triang_quality_label = QLabel("Mesh: waiting for paired landmarks")
+        self.triang_quality_label.setToolTip(
+            "Registration mesh quality. Green is healthy, yellow needs review, "
+            "and red is invalid or severely distorted. Folded or collapsed "
+            "triangles block transfer."
+        )
+        self.triang_quality_label.setStyleSheet(
+            "QLabel { color: #9a9a9a; padding: 1px 6px; }"
+        )
+
+        self.triang_wrap = QFrame()
+        self.triang_wrap.setSizePolicy(QSizePolicy.Policy.Minimum, QSizePolicy.Policy.Minimum)
+        triang_layout = QHBoxLayout(self.triang_wrap)
+        triang_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        triang_layout.setContentsMargins(0, 0, 0, 0)
+        triang_layout.setSpacing(10)
+        triang_layout.addWidget(self.triang_vis_btn)
+        triang_layout.addSpacing(10)
+        triang_layout.addWidget(self.triang_match_bnd)
+        triang_layout.addSpacing(10)
+        triang_layout.addWidget(triang_color_label)
+        triang_layout.addWidget(self.triang_color_btn)
+        triang_layout.addSpacing(10)
+        triang_layout.addWidget(bound_pnts_num_label)
+        triang_layout.addWidget(self.bound_pnts_num)
+        triang_layout.addSpacing(10)
+        triang_layout.addWidget(self.triang_quality_label)
+
+        triang_layout.addStretch(1)
+
+        # cell count wrap
+        cell_color_label = QLabel('Color:')
+        self.cell_color_btn = pg.ColorButton(padding=0)
+        self.cell_color_btn.setColor(QColor(0, 255, 0))
+        self.cell_color_btn.setFixedSize(60, 15)
+
+        self.cell_count_label_list = [QLabel('Count: ')]
+        self.cell_count_val_list = [QLabel('0')]
+
+        for i in range(4):
+            self.cell_count_label_list.append(QLabel('Count {}: '.format(i+1)))
+            self.cell_count_val_list.append(QLabel('0'))
+
+        for i in range(5):
+            self.cell_count_label_list[i].setVisible(False)
+            self.cell_count_val_list[i].setVisible(False)
+
+        self.cell_selector_btn = QPushButton()
+        self.cell_selector_btn.setToolTip('select cells manually')
+        self.cell_selector_btn.setCheckable(True)
+        selector_icon = QIcon()
+        selector_icon.addPixmap(QPixmap(resource_path("icons/toolbar/cell_select_not.svg")), QIcon.Mode.Normal, QIcon.State.Off)
+        selector_icon.addPixmap(QPixmap(resource_path("icons/toolbar/cell_select.svg")), QIcon.Mode.Normal, QIcon.State.On)
+        self.cell_selector_btn.setIcon(selector_icon)
+        self.cell_selector_btn.setIconSize(QSize(20, 20))
+
+        self.cell_aim_btn = QPushButton()
+        self.cell_aim_btn.setToolTip('select single cell body area')
+        self.cell_aim_btn.setCheckable(True)
+        aim_icon = QIcon()
+        aim_icon.addPixmap(QPixmap(resource_path("icons/toolbar/aim_not.svg")), QIcon.Mode.Normal, QIcon.State.Off)
+        aim_icon.addPixmap(QPixmap(resource_path("icons/toolbar/aim.svg")), QIcon.Mode.Normal, QIcon.State.On)
+        self.cell_aim_btn.setIcon(aim_icon)
+        self.cell_aim_btn.setIconSize(QSize(20, 20))
+        self.cell_radar_btn = QPushButton()
+        self.cell_radar_btn.setToolTip('automatically search for similar cell bodies')
+        self.cell_radar_btn.setIcon(QIcon(resource_path('icons/toolbar/radar.svg')))
+        self.cell_radar_btn.setIconSize(QSize(20, 20))
+
+        self.cell_count_wrap = QFrame()
+        cell_layout = QHBoxLayout(self.cell_count_wrap)
+        cell_layout.setAlignment(Qt.AlignmentFlag.AlignVCenter)
+        cell_layout.setContentsMargins(0, 0, 0, 0)
+        cell_layout.setSpacing(10)
+        cell_layout.addWidget(cell_color_label)
+        cell_layout.addWidget(self.cell_color_btn)
+        cell_layout.addSpacing(15)
+        cell_layout.addWidget(self.cell_selector_btn)
+        cell_layout.addSpacing(10)
+        cell_layout.addWidget(self.cell_aim_btn)
+        cell_layout.addSpacing(10)
+        cell_layout.addWidget(self.cell_radar_btn)
+        cell_layout.addSpacing(10)
+        cell_layout.addWidget(self.cell_count_label_list[0])
+        cell_layout.addWidget(self.cell_count_val_list[0])
+        for i in range(1, 5):
+            cell_layout.addWidget(self.cell_count_label_list[i])
+            cell_layout.addWidget(self.cell_count_val_list[i])
+            cell_layout.addSpacing(10)
+        cell_layout.addStretch(1)
+
+        # separator
+        self.sep_label = QLabel()
+        self.sep_label.setPixmap(QPixmap(resource_path('icons/toolbar/handle.png')))
+
+        # circle
+        r = int(self.eraser_size_valt.text())
+        angle = np.deg2rad(np.arange(0, 360, 1))
+        x = np.cos(angle)
+        y = np.sin(angle)
+        self.original_circle = np.vstack([x, y]).T
+        self.circle = self.original_circle * r
+
+        # triangle style
+        self.tri_line_style = pg.mkPen(color=(128, 128, 128), width=0.5, style=Qt.PenStyle.DashLine)
+
+        # ---------------------------- define all cursor shape
+        # self.eraser_cursor = QCursor(QPixmap(resource_path('icons/eraser_cursor.png')), hotX=7, hotY=27)
+
+    def update_cell_count_label(self, cell_count_list):
+        for layer_index in range(5):
+            self.update_single_cell_count_label(cell_count_list, layer_index)
+
+    def update_single_cell_count_label(self, cell_count_list, layer_index):
+        self.cell_count_val_list[layer_index].setText(str(cell_count_list[layer_index]))
+
+    def lasso_type_changed(self):
+        if self.lasso_type_btn.isChecked():
+            self.remove_inside = False
+        else:
+            self.remove_inside = True
+
+    def pencil_path_btn_clicked(self):
+        if self.pencil_path_btn.isChecked():
+            self.is_closed = True
+        else:
+            self.is_closed = False
+
+    def merge_sites_btn_clicked(self):
+        if self.merge_sites_btn.isChecked():
+            self.merge_sites = True
+        else:
+            self.merge_sites = False
+
+    def change_pencil_slider(self):
+        val = self.pencil_size_slider.value()
+        self.pencil_size_valt.setText(str(val))
+
+    def change_eraser_slider(self):
+        val = self.eraser_size_slider.value()
+        self.eraser_size_valt.setText(str(val))
+        self.circle = self.original_circle * val
+
+    def change_eraser_val(self):
+        val = int(self.eraser_size_valt.text())
+        self.eraser_size_slider.setValue(val)
+
+    def change_ruler_slider(self):
+        val = self.ruler_width_slider.value()
+        self.ruler_size_valt.setText(str(val))
+
+    def get_tool_data(self):
+        data = {'pencil_color': self.pencil_color_btn.color().getRgb(),
+                'pencil_size': self.pencil_size_valt.text(),
+                'magic_wand_color': self.magic_color_btn.color().getRgb(),
+                'magic_wand_tol': self.magic_tol_val.text(),
+                'magic_wand_kernel': self.magic_wand_kernel.currentText(),
+                'magic_wand_ksize': self.magic_wand_ksize.value(),
+                'probe_color': self.probe_color_btn.color().getRgb(),
+                'cell_color': self.cell_color_btn.color().getRgb(),
+                'is_closed': self.is_closed}
+        return data
+
+    def set_tool_data(self, data):
+        self.pencil_color_btn.setColor(data['pencil_color'])
+        self.pencil_size_valt.setText(str(data['pencil_size']))
+        self.pencil_path_btn.setChecked(data['is_closed'])
+        self.magic_color_btn.setColor(data['magic_wand_color'])
+        self.magic_tol_val.setText(str(data['magic_wand_tol']))
+        self.magic_wand_ksize.setValue(data['magic_wand_ksize'])
+        self.magic_wand_kernel.setCurrentText(data['magic_wand_kernel'])
+        self.probe_color_btn.setColor(data['probe_color'])
+        self.cell_color_btn.setColor(data['cell_color'])
+
+
+    def multi_prb_status_changed(self):
+        if self.multi_prb_btn.isChecked():
+            self.multi_shanks = True
+        else:
+            self.multi_shanks = False
+
+
+
+
+
+
+
+
+
+