class projectModel(QObject):
"""
Model for storing and retrieving project data.
attributes
----------
fileManager: File manager for saving data to disk
fileModels: Individual file models. Type will depend on kind of file
fileWidgets: References to the UI widgets associated with the files
fileConfigs: Dictionary containing file types
"""
loadingComplete = pyqtSignal()
def __init__(self, name, global_config, file_manager):
super().__init__()
self.fileManager = file_manager
self.global_config = global_config
self.fileModels = {}
self.fileWidgets = {}
self.fileConfigs = {}
self.loaded = {}
self.active = None
self.getConfig()
self.widget = None
self.saveLocation = ""
self.name = name
def getConfig(self):
self.CONFIG_FILE = os.path.join(self.global_config['config_location'],
self.global_config['projectModel'])
self.config = toml.load(self.CONFIG_FILE)
def updateGlobalConfig(self, config):
self.global_config = config
for fmodel in self.fileModels.values():
fmodel.updateGlobalConfig(config)
def setFileManager(self, f):
"""
Used when loading a previously saved project
"""
self.fileManager = f
for model in self.fileModels.values():
model.setFileManager(f)
def __getstate__(self):
"""
Prepare project data for disk storage.
References to UI, and other things that are stateless are removed
"""
data = copy(self.__dict__)
del data['fileManager']
del data['widget']
del data['fileWidgets']
del data['config']
attributes = {}
for k, v in data['fileModels'].items():
att = v.attributes
attributes.update({k: att})
del data['fileModels']
data.update({'attributes': attributes})
return data
def __setstate__(self, state):
"""
Reads in the data as outputted by __getstate___
Automatically called when the project is opened
"""
super().__init__()
attributes = state.pop('attributes')
self.__dict__ = state
self.fileWidgets = {}
self.fileModels = {}
self.loaded = {}
self.widget = None
self.getConfig()
for fname, configtype in self.fileConfigs.items():
self.addFile(fname, configtype, attributes[fname])
def setVersion(self, vnumber):
self.version = vnumber
def addFile(self, fname, config_type, attributes={}):
"""
Adds a file to the project.
fname: absolute path to the file
config_type: one of the config types from
"""
if fname in self.fileModels.keys():
pass
else:
self.fileConfigs.update({fname: config_type})
loader = fileLoader(fname, config_type, self.global_config,
attributes)
loader.signals.result.connect(lambda x: self.updateFiles(x))
threadPool.start(loader)
def updateFiles(self, fileobj):
self.fileModels.update({fileobj.fname: fileobj})
fileobj.updateGlobalConfig(self.global_config)
self.loaded.update({fileobj.fname: True})
if self.widget is not None:
self.updateWidget()
if len(self.fileModels.keys()) > 0:
self.active = list(self.fileModels.keys())[-1]
if len(self.loaded) == len(self.fileConfigs.keys()):
self.loadingComplete.emit()
def removeFile(self, fname):
"""
Removes a file from the project
"""
for filename in self.fileModels.keys():
if fname in filename:
model = self.fileModels.pop(filename)
self.fileConfigs.pop(filename)
self.updateWidget(remove=filename)
del model
break
def getFileNames(self):
return self.fileConfigs.keys()
def getFileConfigs(self):
return self.fileConfigs
def getFileModel(self, fname):
if fname in self.fileModels.keys():
return self.fileModels[fname]
def getWidget(self):
"""
Gets a UI widget for a project.
Presently, this is just a stack of the widgets associated
with the various files
"""
self.widget = QStackedWidget()
for fname, model in self.fileModels.items():
widget = self.getFileWidget(fname)
self.fileWidgets.update({fname: widget})
self.widget.addWidget(widget)
return self.widget
def updateWidget(self, remove=None):
"""
Updates the widget. If no name is passed, checks
for new file models and adds their widget if found.
If a name is passed, removes that widget from the stack
"""
if remove:
widget = self.fileWidgets.pop(remove)
self.widget.removeWidget(widget)
if self.fileWidgets.keys():
self.setActive(list(self.fileWidgets.keys())[0])
del widget
for fname, model in self.fileModels.items():
if fname not in self.fileWidgets.keys():
widget = self.getFileWidget(fname)
self.fileWidgets.update({fname: widget})
self.widget.addWidget(widget)
self.widget.update()
def setActive(self, fname):
"""
Sets the active widget (i.e. top of the stack)
"""
for key, val in self.fileWidgets.items():
if fname in key:
self.widget.setCurrentWidget(self.fileWidgets[key])
self.active = fname
break
def getFileWidget(self, fname):
"""
Get UI widget for a particular file.
"""
config_type = self.fileConfigs[fname]
module = import_module(self.config['widgets'][config_type]['mod'])
obj = getattr(module, self.config['widgets'][config_type]['obj'])
return obj(self.fileModels[fname], self.fileConfigs[fname],
self.global_config)
def save(self):
"""
Sends itself to the file manager to be saved
"""
self.fileManager.saveProject(self)
def canHandle(self, target):
"""
Checks if this object can handle a signal aimed at a particular target
"""
if target in self.config['signals']['canHandle']:
return True
else:
return False
def handleSignal(self, signal):
if signal['target'] == 'fileModel':
self.fileModels[self.active].handleSignal(signal)
class ToolBar(QWidget):
mouseEntered = pyqtSignal()
mouseLeft = pyqtSignal()
toolChanged = pyqtSignal(str)
primaryInkChanged = pyqtSignal(str)
secondaryInkChanged = pyqtSignal(str)
def __init__(self):
super(ToolBar, self).__init__()
self.setAttribute(Qt.WA_StaticContents)
self.setAttribute(Qt.WA_NoSystemBackground)
self.setFont(ResourcesCache.get("BigFont"))
self._registeredTools = {}
self._registeredInks = {}
self._toolSlots = []
self._inkSlots = []
self._currentActiveToolSlot = None
self._previousActiveToolSlot = None
self._currentEditedInkSlot = None
self._previousEditedInkSlot = None
self._editMode = False
self._backgroundColor = QColor(40, 40, 40)
self._toolLabelColor = QColor(112, 231, 255)
self._layout = QVBoxLayout()
self._layout.setAlignment(Qt.AlignTop)
self._layout.setContentsMargins(4, 4, 4, 4)
top_layout = QHBoxLayout()
self._layout.addLayout(top_layout)
self._toolsLayout = QHBoxLayout()
self._inksLayout = QHBoxLayout()
self._toolsLayout.setContentsMargins(0, 0, 0, 0)
self._toolsLayout.setAlignment(Qt.AlignLeft)
self._inksLayout.setContentsMargins(0, 0, 0, 0)
self._inksLayout.setAlignment(Qt.AlignRight)
top_layout.addLayout(self._toolsLayout)
top_layout.addLayout(self._inksLayout)
self._toolsButtonGroup = QButtonGroup()
self._toolsButtonGroup.buttonClicked.connect(
self._on_tool_slot_triggered)
self._inksButtonGroup = QButtonGroup()
self._inksButtonGroup.setExclusive(False)
self._inksButtonGroup.buttonClicked.connect(
self._on_ink_slot_triggered)
self.setLayout(self._layout)
self._toolbarSubPanel = None
self._toolsListWidget = None
self._toolsOptionsPanel = None
self._init_edit_panel()
self._add_ink_slot(0)
self._add_ink_slot(1)
self.resize(0, 50)
# -------------------------------------------------------------------------
def get_tool_by_name(self, name):
return self._registeredTools[name]
def register_tool(self, tool, is_default=None):
if tool.name not in self._registeredTools:
self._registeredTools[tool.name] = tool
self._toolsListWidget.addItem(tool.name)
if is_default is True:
self._toolsListWidget.setCurrentRow(0)
self._build_tool_options_pane(tool)
if len(self._toolSlots) < 4:
slot_index = self._add_tool_slot(is_default)
self._assign_tool_to_slot(tool, slot_index)
def register_ink(self, ink, slot):
if not ink.name in self._registeredInks:
self._registeredInks[ink.name] = ink
self._inksListWidget.addItem(ink.name)
self._build_ink_options_pane(ink)
if self._inkSlots[slot]['id'] is None:
self._assign_ink_to_slot(ink, slot)
def switch_tool_slot(self, slot):
self._previousActiveToolSlot = self._currentActiveToolSlot
self._currentActiveToolSlot = slot
if self._currentActiveToolSlot == self._previousActiveToolSlot:
return
tool_name = self._toolSlots[slot]['id']
self._toolSlots[slot]['button'].setChecked(True)
self.toolChanged.emit(tool_name)
self._select_tool_on_list(tool_name)
# -------------------------------------------------------------------------
def _go_back_to_last_tool(self):
self.switch_tool_slot(self._previousActiveToolSlot)
def _add_tool_slot(self, selected=None):
slot_button = QPushButton()
slot_button.setCheckable(True)
index = len(self._toolSlots)
if selected is not None and selected is True:
slot_button.setChecked(True)
slot = {'id': None, 'button': slot_button}
if selected:
self._currentActiveToolSlot = index
self._toolSlots.append(slot)
self._toolsButtonGroup.addButton(slot_button, index)
self._toolsLayout.addWidget(slot_button)
return index
def _add_ink_slot(self, slot_number):
slot_button = QPushButton()
slot_button.setFont(self.font())
slot_button.setStyleSheet(
"border-color: rgb(56,56,56); background-color: rgb(17,17,"
"17); font-size: 12pt;")
index = len(self._inkSlots)
if slot_number == 0:
icon = QIcon()
icon.addPixmap(QPixmap(":/icons/ico_mouse_button1"), QIcon.Normal,
QIcon.Off)
slot_button.setIcon(icon)
slot_button.setIconSize(QSize(18, 23))
elif slot_number == 1:
icon = QIcon()
icon.addPixmap(QPixmap(":/icons/ico_mouse_button2"), QIcon.Normal,
QIcon.Off)
slot_button.setIcon(icon)
slot_button.setIconSize(QSize(18, 23))
slot = {'id': None, 'button': slot_button}
self._inkSlots.append(slot)
self._inksButtonGroup.addButton(slot_button)
self._inksButtonGroup.setId(slot_button, index)
self._inksLayout.addWidget(slot_button)
return index
def _assign_tool_to_slot(self, tool, slot):
if slot < 0 or slot > len(self._toolSlots) - 1:
raise Exception(
'[ToolBar] > _assignToolToSlot : invalid slot parameter')
self._toolSlots[slot]['id'] = tool.name
icon = tool.icon
if icon is not None:
tool_button = self._toolSlots[slot]['button']
tool_button.setIcon(tool.icon)
tool_button.setIconSize(QSize(24, 24))
def _assign_ink_to_slot(self, ink, slot):
if slot != 0 and slot != 1:
raise Exception(
'[ToolBar] > _assignInkToSlot : invalid slot parameter')
ink_name = ink.name
self._inkSlots[slot]['id'] = ink_name
self._inkSlots[slot]['button'].setText(ink_name)
if slot == 0:
self.primaryInkChanged.emit(ink_name)
elif slot == 1:
self.secondaryInkChanged.emit(ink_name)
def _init_edit_panel(self):
self._toolbarSubPanel = QStackedWidget()
# 1. Initialize Tools Control Panel -----------------------------------
self._toolsListWidget = QListWidget()
self._toolsListWidget.currentRowChanged.connect(
lambda v: self._toolsOptionsPanel.setCurrentIndex(v))
self._toolsListWidget.setMaximumSize(QSize(150, 200))
self._toolsListWidget.itemClicked.connect(
self._on_tool_list_item_clicked)
# Tools Subpanel ------------------------------------------------------
tools_control_panel = QWidget()
tools_control_panel_layout = QHBoxLayout()
tools_control_panel.setLayout(tools_control_panel_layout)
tools_control_panel_layout.setAlignment(Qt.AlignLeft)
# Tools List ----------------------------------------------------------
tools_list_sublayout = QVBoxLayout()
tools_list_sublayout.setAlignment(Qt.AlignTop)
tools_list_sublayout.setContentsMargins(0, 0, 0, 0)
tools_list_sublayout.addWidget(QLabel("Tools"))
tools_list_sublayout.addWidget(self._toolsListWidget)
tools_control_panel_layout.addLayout(tools_list_sublayout)
# Tools Options -------------------------------------------------------
tools_options_sublayout = QVBoxLayout()
tools_options_sublayout.setAlignment(Qt.AlignTop)
tools_control_panel_layout.addLayout(tools_options_sublayout)
self._toolsOptionsPanel = QStackedWidget()
tools_options_sublayout.addWidget(QLabel("Tools Options"))
tools_options_sublayout.addWidget(self._toolsOptionsPanel)
self._toolbarSubPanel.addWidget(tools_control_panel)
# 2. Initialize Inks Control Panel ------------------------------------
self._inksListWidget = QListWidget()
self._inksListWidget.currentRowChanged.connect(
lambda v: self._inksOptionsPanel.setCurrentIndex(v))
self._inksListWidget.setMaximumSize(QSize(150, 200))
self._inksListWidget.itemClicked.connect(
self._on_ink_list_item_clicked)
# Inks Subpanel -------------------------------------------------------
inks_control_panel = QWidget()
inks_control_panel_layout = QHBoxLayout()
inks_control_panel.setLayout(inks_control_panel_layout)
inks_control_panel_layout.setAlignment(Qt.AlignLeft)
# Inks List -----------------------------------------------------------
inks_list_sublayout = QVBoxLayout()
inks_list_sublayout.setAlignment(Qt.AlignTop)
inks_list_sublayout.setContentsMargins(0, 0, 0, 0)
inks_list_sublayout.addWidget(QLabel("Inks"))
inks_list_sublayout.addWidget(self._inksListWidget)
inks_control_panel_layout.addLayout(inks_list_sublayout)
# Inks Options --------------------------------------------------------
inks_options_sublayout = QVBoxLayout()
inks_options_sublayout.setAlignment(Qt.AlignTop)
inks_control_panel_layout.addLayout(inks_options_sublayout)
self._inksOptionsPanel = QStackedWidget()
inks_options_sublayout.addWidget(QLabel("Ink Options"))
inks_options_sublayout.addWidget(self._inksOptionsPanel)
self._toolbarSubPanel.addWidget(inks_control_panel)
# ---------------------------------------------------------------------
self._layout.addWidget(self._toolbarSubPanel)
self._toolbarSubPanel.setVisible(False)
def _build_tool_options_pane(self, tool):
pane = QWidget()
pane_layout = QVBoxLayout()
pane_layout.setAlignment(Qt.AlignTop)
pane.setLayout(pane_layout)
for prop in tool.properties.values():
field_layout = QHBoxLayout()
field_layout.addWidget(QLabel(prop.description))
prop_widget = prop.build_property_widget()
field_layout.addWidget(prop_widget)
pane_layout.addLayout(field_layout)
self._toolsOptionsPanel.addWidget(pane)
def _build_ink_options_pane(self, ink):
pane = QWidget()
pane_layout = QVBoxLayout()
pane_layout.setAlignment(Qt.AlignTop)
pane.setLayout(pane_layout)
for prop in ink.properties.values():
field_layout = QHBoxLayout()
field_layout.addWidget(QLabel(prop.description))
prop_widget = prop.build_property_widget()
field_layout.addWidget(prop_widget)
pane_layout.addLayout(field_layout)
self._inksOptionsPanel.addWidget(pane)
def _select_tool_on_list(self, tool_name):
tool_list_item = \
self._toolsListWidget.findItems(tool_name, Qt.MatchExactly)[0]
if tool_list_item is not None:
self._toolsListWidget.setCurrentItem(tool_list_item)
def _select_ink_on_list(self, ink_name):
ink_list_item = \
self._inksListWidget.findItems(ink_name, Qt.MatchExactly)[0]
if ink_list_item is not None:
self._inksListWidget.setCurrentItem(ink_list_item)
def _toggle_edit_mode(self):
if not self._editMode:
self._show_sub_panel()
else:
self._hide_sub_panel()
self.update()
def _show_sub_panel(self):
self._editMode = True
self.resize(self.width(), 300)
self._toolbarSubPanel.setVisible(True)
def _hide_sub_panel(self):
self._editMode = False
self.resize(self.width(), 50)
self._toolbarSubPanel.setVisible(False)
self._finish_ink_edit_mode()
def _finish_ink_edit_mode(self):
if self._currentEditedInkSlot is not None:
self._inksButtonGroup.button(self._currentEditedInkSlot). \
setStyleSheet("border-color: rgb(56,56,56);")
self._currentEditedInkSlot = None
self._previousEditedInkSlot = None
self._inksListWidget.setCurrentRow(0)
self._toolbarSubPanel.setCurrentIndex(0)
# -------------------------------------------------------------------------
def mousePressEvent(self, e):
self._toggle_edit_mode()
e.accept()
def wheelEvent(self, e):
e.accept()
def enterEvent(self, e):
self.mouseEntered.emit()
self.setCursor(Qt.PointingHandCursor)
def leaveEvent(self, e):
self.mouseLeft.emit()
def _on_tool_slot_triggered(self):
self._toolbarSubPanel.setCurrentIndex(0)
triggered_slot = self._toolsButtonGroup.checkedId()
if self._currentEditedInkSlot is not None:
self._finish_ink_edit_mode()
self.switch_tool_slot(triggered_slot)
self.update()
def _on_ink_slot_triggered(self, slot_button):
if not self._editMode:
self._show_sub_panel()
triggered_slot_id = self._inksButtonGroup.id(slot_button)
if triggered_slot_id != self._currentEditedInkSlot:
self._previousEditedInkSlot = self._currentEditedInkSlot
self._currentEditedInkSlot = triggered_slot_id
if self._previousEditedInkSlot is not None:
self._inksButtonGroup. \
button(self._previousEditedInkSlot). \
setStyleSheet("border-color: rgb(56,56,56);")
slot_button.setStyleSheet("border-color: rgb(255,0,0);")
self._toolbarSubPanel.setCurrentIndex(1)
ink_name = self._inkSlots[triggered_slot_id]['id']
self._select_ink_on_list(ink_name)
if triggered_slot_id == 0:
self.primaryInkChanged.emit(ink_name)
elif triggered_slot_id == 1:
self.secondaryInkChanged.emit(ink_name)
else:
self._hide_sub_panel()
def _on_tool_list_item_clicked(self, new_item):
new_item_name = new_item.text()
self._assign_tool_to_slot(self.get_tool_by_name(new_item_name),
self._currentActiveToolSlot)
self.toolChanged.emit(new_item_name)
self._toolbarSubPanel.update()
def _on_ink_list_item_clicked(self, item):
item_name = item.text()
ink = self._registeredInks[item_name]
if ink is not None:
self._assign_ink_to_slot(ink, self._currentEditedInkSlot)
class DAT_GUI(QtWidgets.QMainWindow):
def __init__(self, parent=None):
super().__init__(parent)
self.initUI()
def initUI(self):
screen = QApplication.desktop().screenNumber(
QApplication.desktop().cursor().pos())
centerPoint = QApplication.desktop().screenGeometry(screen).center()
# should fit in 1024x768 (old computer screens)
window_width = 900
window_height = 700
self.setGeometry(
QtCore.QRect(
centerPoint.x() - int(window_width / 2),
centerPoint.y() - int(window_height / 2), window_width,
window_height)) # should I rather center on the screen
# zoom parameters
self.scale = 1.0
self.min_scaling_factor = 0.1
self.max_scaling_factor = 20
self.zoom_increment = 0.05
self.setWindowTitle(__NAME__ + ' v' + str(__VERSION__))
self.paint = Createpaintwidget()
# initiate 2D image for 2D display
self.img = None
self.list = QListWidget(
self) # a list that contains files to read or play with
self.list.setSelectionMode(QAbstractItemView.ExtendedSelection)
self.list.selectionModel().selectionChanged.connect(
self.selectionChanged) # connect it to sel change
self.scrollArea = QScrollArea()
self.scrollArea.setBackgroundRole(QPalette.Dark)
self.scrollArea.setWidget(self.paint)
self.paint.scrollArea = self.scrollArea
self.table_widget = QWidget()
table_widget_layout = QVBoxLayout()
# Initialize tab screen
self.tabs = QTabWidget(self)
self.tab1 = QWidget()
self.tab2 = QWidget()
self.tab3 = QWidget()
# Add tabs
self.tabs.addTab(self.tab1, "Mask neuron")
self.tabs.addTab(self.tab2, "Mask cell body")
self.tabs.addTab(self.tab3, "Segment dendrites")
# listen to tab changes
self.tabs.currentChanged.connect(self._onTabChange)
# Create first tab
self.tab1.layout = QGridLayout()
self.tab1.layout.setAlignment(Qt.AlignTop)
self.tab1.layout.setHorizontalSpacing(3)
self.tab1.layout.setVerticalSpacing(3)
self.tab1.layout.setContentsMargins(0, 0, 0, 0)
label1_tab1 = QLabel('Step 1:')
self.tab1.layout.addWidget(label1_tab1, 0, 0)
self.local_threshold = QPushButton("Local threshold")
self.local_threshold.clicked.connect(self.run_threshold_neuron)
self.tab1.layout.addWidget(self.local_threshold, 0, 1)
self.global_threshold = QPushButton("Global threshold")
self.global_threshold.clicked.connect(self.run_threshold_neuron)
self.tab1.layout.addWidget(self.global_threshold, 0, 2)
self.local_n_global_threshold = QPushButton(
"Local AND Global threshold")
self.local_n_global_threshold.clicked.connect(
self.run_threshold_neuron)
self.tab1.layout.addWidget(self.local_n_global_threshold, 0, 3)
self.extra_value_for_threshold = QSpinBox()
self.extra_value_for_threshold.setSingleStep(1)
self.extra_value_for_threshold.setRange(0, 1_000_000)
self.extra_value_for_threshold.setValue(6)
self.tab1.layout.addWidget(self.extra_value_for_threshold, 0, 4)
self.threshold_method = QComboBox()
self.threshold_method.addItem('Mean')
self.threshold_method.addItem('Median')
self.tab1.layout.addWidget(self.threshold_method, 0, 5)
label2_tab1 = QLabel('Step 2 (optional):')
self.tab1.layout.addWidget(label2_tab1, 1, 0)
self.remove_pixel_blobs_smaller_or_equal = QPushButton(
"Remove pixel blobs smaller or equal to")
self.remove_pixel_blobs_smaller_or_equal.clicked.connect(
self.remove_blobs)
self.tab1.layout.addWidget(self.remove_pixel_blobs_smaller_or_equal, 1,
1)
self.remove_blobs_size = QSpinBox()
self.remove_blobs_size.setSingleStep(1)
self.remove_blobs_size.setRange(0, 1_000_000)
self.remove_blobs_size.setValue(1)
self.tab1.layout.addWidget(self.remove_blobs_size, 1, 2)
label3_tab1 = QLabel('Step 3: Save')
self.tab1.layout.addWidget(label3_tab1, 2, 0)
self.tab1.setLayout(self.tab1.layout)
self.tab2.layout = QGridLayout()
self.tab2.layout.setAlignment(Qt.AlignTop)
self.tab2.layout.setHorizontalSpacing(3)
self.tab2.layout.setVerticalSpacing(3)
self.tab2.layout.setContentsMargins(0, 0, 0, 0)
label1_tab2 = QLabel('Step 1:')
self.tab2.layout.addWidget(label1_tab2, 0, 0)
self.detect_cell_body = QPushButton("Detect cell body")
self.detect_cell_body.clicked.connect(self.detect_neuronal_cell_body)
self.tab2.layout.addWidget(self.detect_cell_body, 0, 1)
self.extraCutOff_cell_body = QSpinBox()
self.extraCutOff_cell_body.setSingleStep(1)
self.extraCutOff_cell_body.setRange(0, 1_000_000)
self.extraCutOff_cell_body.setValue(5)
self.tab2.layout.addWidget(self.extraCutOff_cell_body, 0, 2)
erosion_label = QLabel('erosion rounds')
self.tab2.layout.addWidget(erosion_label, 0, 3)
self.nb_erosion_cellbody = QSpinBox()
self.nb_erosion_cellbody.setSingleStep(1)
self.nb_erosion_cellbody.setRange(0, 1_000_000)
self.nb_erosion_cellbody.setValue(2)
self.tab2.layout.addWidget(self.nb_erosion_cellbody, 0, 4)
min_object_size_label = QLabel('minimum object size')
self.tab2.layout.addWidget(min_object_size_label, 0, 5)
self.min_obj_size_px = QSpinBox()
self.min_obj_size_px.setSingleStep(1)
self.min_obj_size_px.setRange(0, 1_000_000)
self.min_obj_size_px.setValue(600)
self.tab2.layout.addWidget(self.min_obj_size_px, 0, 6)
fill_label = QLabel('fill up to')
self.tab2.layout.addWidget(fill_label, 0, 7)
self.fill_holes_up_to = QSpinBox()
self.fill_holes_up_to.setSingleStep(1)
self.fill_holes_up_to.setRange(0, 1_000_000)
self.fill_holes_up_to.setValue(600)
self.tab2.layout.addWidget(self.fill_holes_up_to, 0, 8)
nb_dilation_cell_body_label = QLabel('nb dilation cell body')
self.tab2.layout.addWidget(nb_dilation_cell_body_label, 0, 9)
self.nb_dilation_cellbody = QSpinBox()
self.nb_dilation_cellbody.setSingleStep(1)
self.nb_dilation_cellbody.setRange(0, 1_000_000)
self.nb_dilation_cellbody.setValue(2)
self.tab2.layout.addWidget(self.nb_dilation_cellbody, 0, 10)
label2_tab2 = QLabel('Step 2: Save')
self.tab2.layout.addWidget(label2_tab2, 6, 0)
self.tab2.setLayout(self.tab2.layout)
self.tab3.layout = QGridLayout()
self.tab3.layout.setAlignment(Qt.AlignTop)
self.tab3.layout.setHorizontalSpacing(3)
self.tab3.layout.setVerticalSpacing(3)
self.tab3.layout.setContentsMargins(0, 0, 0, 0)
label1_tab3 = QLabel('Step 1:')
self.tab3.layout.addWidget(label1_tab3, 0, 0)
self.wshed = QPushButton("Watershed")
self.wshed.clicked.connect(self.watershed_segment_the_neuron)
self.tab3.layout.addWidget(self.wshed, 0, 1)
self.whsed_big_blur = QDoubleSpinBox()
self.whsed_big_blur.setSingleStep(0.1)
self.whsed_big_blur.setRange(0, 100)
self.whsed_big_blur.setValue(2.1)
self.tab3.layout.addWidget(self.whsed_big_blur, 0, 2)
self.whsed_small_blur = QDoubleSpinBox()
self.whsed_small_blur.setSingleStep(0.1)
self.whsed_small_blur.setRange(0, 100)
self.whsed_small_blur.setValue(1.4)
self.tab3.layout.addWidget(self.whsed_small_blur, 0, 3)
self.wshed_rm_small_cells = QSpinBox()
self.wshed_rm_small_cells.setSingleStep(1)
self.wshed_rm_small_cells.setRange(0, 1_000_000)
self.wshed_rm_small_cells.setValue(10)
self.tab3.layout.addWidget(self.wshed_rm_small_cells, 0, 4)
self.jSpinner11 = QSpinBox()
self.jSpinner11.setSingleStep(1)
self.jSpinner11.setRange(0, 1_000_000)
self.jSpinner11.setValue(10)
self.tab3.layout.addWidget(self.jSpinner11, 0, 5)
label1_bis_tab3 = QLabel('Alternative Step 1:')
self.tab3.layout.addWidget(label1_bis_tab3, 1, 0)
self.skel = QPushButton("Skeletonize")
self.skel.clicked.connect(self.skeletonize_mask)
self.tab3.layout.addWidget(self.skel, 1, 1)
label2_tab3 = QLabel('Step 2:')
self.tab3.layout.addWidget(label2_tab3, 2, 0)
self.apply_cell_body = QPushButton("Apply cell body")
self.apply_cell_body.clicked.connect(
self.apply_cell_body_to_skeletonized_mask)
self.tab3.layout.addWidget(self.apply_cell_body, 2, 1)
label3_tab3 = QLabel('Step 3 (Optional):')
self.tab3.layout.addWidget(label3_tab3, 3, 0)
self.prune = QPushButton("Prune")
self.prune.clicked.connect(self.prune_dendrites)
self.tab3.layout.addWidget(self.prune, 3, 1)
self.prune_length = QSpinBox()
self.prune_length.setSingleStep(1)
self.prune_length.setRange(0, 1_000_000)
self.prune_length.setValue(3)
self.tab3.layout.addWidget(self.prune_length, 3, 2)
label4_tab3 = QLabel('Step 4 (Optional):')
self.tab3.layout.addWidget(label4_tab3, 4, 0)
self.find_neurons = QPushButton("Find neurons")
self.find_neurons.clicked.connect(self.find_neurons_in_mask)
self.tab3.layout.addWidget(self.find_neurons, 4, 1)
self.find_neurons_min_size = QSpinBox()
self.find_neurons_min_size.setSingleStep(1)
self.find_neurons_min_size.setRange(0, 1_000_000)
self.find_neurons_min_size.setValue(45)
self.tab3.layout.addWidget(self.find_neurons_min_size, 4, 2)
self.prune_unconnected_segments = QPushButton(
"Prune unconnected segments (run 'Find neurons' first)")
self.prune_unconnected_segments.clicked.connect(
self.prune_neuron_unconnected_segments)
self.tab3.layout.addWidget(self.prune_unconnected_segments, 4, 3)
label6_tab3 = QLabel('Step 5: Save')
self.tab3.layout.addWidget(label6_tab3, 5, 0)
label5_tab3 = QLabel('Step 6:')
self.tab3.layout.addWidget(label5_tab3, 6, 0)
self.create_n_save_bonds = QPushButton("Segment dendrites")
self.create_n_save_bonds.clicked.connect(self.save_segmented_bonds)
self.tab3.layout.addWidget(self.create_n_save_bonds, 6, 1)
self.tab3.setLayout(self.tab3.layout)
# Add tabs to widget
table_widget_layout.addWidget(self.tabs)
self.table_widget.setLayout(table_widget_layout)
self.Stack = QStackedWidget(self)
self.Stack.addWidget(self.scrollArea)
# create a grid that will contain all the GUI interface
self.grid = QGridLayout()
self.grid.addWidget(self.Stack, 0, 0)
self.grid.addWidget(self.list, 0, 1)
# The first parameter of the rowStretch method is the row number, the second is the stretch factor. So you need two calls to rowStretch, like this: --> below the first row is occupying 80% and the second 20%
self.grid.setRowStretch(0, 75)
self.grid.setRowStretch(2, 25)
# first col 75% second col 25% of total width
self.grid.setColumnStretch(0, 75)
self.grid.setColumnStretch(1, 25)
# void QGridLayout::addLayout(QLayout * layout, int row, int column, int rowSpan, int columnSpan, Qt::Alignment alignment = 0)
self.grid.addWidget(self.table_widget, 2, 0, 1,
2) # spans over one row and 2 columns
# BEGIN TOOLBAR
# pen spin box and connect
self.penSize = QSpinBox()
self.penSize.setSingleStep(1)
self.penSize.setRange(1, 256)
self.penSize.setValue(3)
self.penSize.valueChanged.connect(self.penSizechange)
self.channels = QComboBox()
self.channels.addItem("merge")
self.channels.currentIndexChanged.connect(self.channelChange)
tb_drawing_pane = QToolBar()
save_button = QToolButton()
save_button.setText("Save")
save_button.clicked.connect(self.save_current_mask)
tb_drawing_pane.addWidget(save_button)
tb_drawing_pane.addWidget(QLabel("Channels"))
tb_drawing_pane.addWidget(self.channels)
# tb.addAction("Save")
#
tb_drawing_pane.addWidget(QLabel("Pen size"))
tb_drawing_pane.addWidget(self.penSize)
self.grid.addWidget(tb_drawing_pane, 1, 0)
# END toolbar
# toolbar for the list
tb_list = QToolBar()
del_button = QToolButton()
del_button.setText("Delete selection from list")
del_button.clicked.connect(self.delete_from_list)
tb_list.addWidget(del_button)
self.grid.addWidget(tb_list, 1, 1)
# self.setCentralWidget(self.scrollArea)
self.setCentralWidget(QFrame())
self.centralWidget().setLayout(self.grid)
# self.statusBar().showMessage('Ready')
statusBar = self.statusBar(
) # sets an empty status bar --> then can add messages in it
self.paint.statusBar = statusBar
# add progress bar to status bar
self.progress = QProgressBar(self)
self.progress.setGeometry(200, 80, 250, 20)
statusBar.addWidget(self.progress)
# Set up menu bar
self.mainMenu = self.menuBar()
self.zoomInAct = QAction(
"Zoom &In (25%)",
self, # shortcut="Ctrl++",
enabled=True,
triggered=self.zoomIn)
self.zoomOutAct = QAction(
"Zoom &Out (25%)",
self, # shortcut="Ctrl+-",
enabled=True,
triggered=self.zoomOut)
self.normalSizeAct = QAction(
"&Normal Size",
self, # shortcut="Ctrl+S",
enabled=True,
triggered=self.defaultSize)
self.viewMenu = QMenu("&View", self)
self.viewMenu.addAction(self.zoomInAct)
self.viewMenu.addAction(self.zoomOutAct)
self.viewMenu.addAction(self.normalSizeAct)
self.menuBar().addMenu(self.viewMenu)
self.setMenuBar(self.mainMenu)
# set drawing window fullscreen
fullScreenShortcut = QtWidgets.QShortcut(
QtGui.QKeySequence(QtCore.Qt.Key_F), self)
fullScreenShortcut.activated.connect(self.fullScreen)
fullScreenShortcut.setContext(QtCore.Qt.ApplicationShortcut)
escapeShortcut = QtWidgets.QShortcut(
QtGui.QKeySequence(QtCore.Qt.Key_Escape), self)
escapeShortcut.activated.connect(self.escape)
escapeShortcut.setContext(QtCore.Qt.ApplicationShortcut)
# Show/Hide the mask
escapeShortcut = QtWidgets.QShortcut(
QtGui.QKeySequence(QtCore.Qt.Key_H), self)
escapeShortcut.activated.connect(self.showHideMask)
escapeShortcut.setContext(QtCore.Qt.ApplicationShortcut)
zoomPlus = QtWidgets.QShortcut("Ctrl+Shift+=", self)
zoomPlus.activated.connect(self.zoomIn)
zoomPlus.setContext(QtCore.Qt.ApplicationShortcut)
zoomPlus2 = QtWidgets.QShortcut("Ctrl++", self)
zoomPlus2.activated.connect(self.zoomIn)
zoomPlus2.setContext(QtCore.Qt.ApplicationShortcut)
zoomMinus = QtWidgets.QShortcut("Ctrl+Shift+-", self)
zoomMinus.activated.connect(self.zoomOut)
zoomMinus.setContext(QtCore.Qt.ApplicationShortcut)
zoomMinus2 = QtWidgets.QShortcut("Ctrl+-", self)
zoomMinus2.activated.connect(self.zoomOut)
zoomMinus2.setContext(QtCore.Qt.ApplicationShortcut)
spaceShortcut = QtWidgets.QShortcut(
QtGui.QKeySequence(QtCore.Qt.Key_Space), self)
spaceShortcut.activated.connect(self.nextFrame)
spaceShortcut.setContext(QtCore.Qt.ApplicationShortcut)
backspaceShortcut = QtWidgets.QShortcut(
QtGui.QKeySequence(QtCore.Qt.Key_Backspace), self)
backspaceShortcut.activated.connect(self.prevFrame)
backspaceShortcut.setContext(QtCore.Qt.ApplicationShortcut)
# connect enter keys to edit dendrites
enterShortcut = QtWidgets.QShortcut(
QtGui.QKeySequence(QtCore.Qt.Key_Return), self)
enterShortcut.activated.connect(self.runSkel)
enterShortcut.setContext(QtCore.Qt.ApplicationShortcut)
enter2Shortcut = QtWidgets.QShortcut(
QtGui.QKeySequence(QtCore.Qt.Key_Enter), self)
enter2Shortcut.activated.connect(self.runSkel)
enter2Shortcut.setContext(QtCore.Qt.ApplicationShortcut)
#Qt.Key_Enter is the Enter located on the keypad:
#Qt::Key_Return 0x01000004
#Qt::Key_Enter 0x01000005 Typically located on the keypad.
self.setAcceptDrops(True) # KEEP IMPORTANT
def __get_mask_img_from_overlay(self):
if self.paint.imageDraw:
channels_count = 4
s = self.paint.imageDraw.bits().asstring(
self.img.shape[0] * self.img.shape[1] * channels_count)
arr = np.frombuffer(s, dtype=np.uint8).reshape(
(self.img.shape[0], self.img.shape[1], channels_count))
return Img(arr[..., 2].copy(), dimensions='hw')
else:
return None
def __get_output_folder(self):
selected_items = self.list.selectedItems()
if selected_items:
filename = selected_items[0].toolTip()
filename0_without_ext = os.path.splitext(filename)[0]
return filename0_without_ext
else:
return None
def delete_from_list(self):
list_items = self.list.selectedItems()
# empty list --> nothing to do
if not list_items:
return
for item in list_items:
self.list.takeItem(self.list.row(item))
def save_current_mask(self):
output_folder = self.__get_output_folder()
if output_folder is None:
logger.error('No image is selected --> nothing to save')
return
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to save')
return
if self.tabs.currentIndex() == 0:
print('saving', os.path.join(output_folder, 'mask.tif'))
mask.save(os.path.join(output_folder, 'mask.tif'))
elif self.tabs.currentIndex() == 1:
print('saving', os.path.join(output_folder, 'cellBodyMask.tif'))
mask.save(os.path.join(output_folder, 'cellBodyMask.tif'))
else:
print('saving', os.path.join(output_folder, 'handCorrection.tif'))
mask.save(os.path.join(output_folder, 'handCorrection.tif'))
def detect_neuronal_cell_body(self):
try:
# get image and detect cell body
mask = detect_cell_body(
self.img,
fillHoles=self.fill_holes_up_to.value(),
denoise=self.min_obj_size_px.value(),
nbOfErosions=self.nb_erosion_cellbody.value(),
nbOfDilatations=self.nb_dilation_cellbody.value(),
extraCutOff=self.extraCutOff_cell_body.value(),
channel=self.channels.currentText())
if mask is not None:
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
else:
logger.error('Cell body could not be detected')
except:
traceback.print_exc()
def __get_neuronal_mask(self, warn=True):
output_folder = self.__get_output_folder()
if output_folder is None:
if warn:
logger.error('No image selected --> nothing to do')
return None
if os.path.exists(os.path.join(output_folder, 'mask.tif')):
# NB should I check the nb of channels --> no I don't want to handle externally created files and want people to rely fully on my stuff that has
return Img(os.path.join(output_folder, 'mask.tif'))
else:
if warn:
logger.error(
'Neuronal mask not found --> Please create one in the "Mask neuron" tab first'
)
return None
def __get_corrected_mask(self, warn=True):
output_folder = self.__get_output_folder()
if output_folder is None:
if warn:
logger.error('No image selected --> nothing to do')
return None
if os.path.exists(os.path.join(output_folder, 'handCorrection.tif')):
return Img(os.path.join(output_folder, 'handCorrection.tif'))
elif os.path.exists(os.path.join(output_folder,
'mask.tif')) and not warn:
return Img(os.path.join(output_folder, 'mask.tif'))
return None
def __get_cellbody_mask(self, warn=True):
output_folder = self.__get_output_folder()
if output_folder is None:
if warn:
logger.error('No image selected --> nothing to do')
return None
if os.path.exists(os.path.join(output_folder, 'cellBodyMask.tif')):
# NB should I check the nb of channels --> no I don't want to handle externally created files and want people to rely fully on my stuff that has
return Img(os.path.join(output_folder, 'cellBodyMask.tif'))
else:
if warn:
logger.error(
'Cell body mask not found --> Please create one in the "Mask cell body" tab first'
)
return None
# seems ok for now
def watershed_segment_the_neuron(self):
try:
# get raw image and segment it using the watershed algorithm
# make it load the neuronal mask
neuronal_mask = self.__get_neuronal_mask()
if neuronal_mask is None:
return
# TODO should I add autoskel or not
mask = watershed_segment_neuron(
self.img,
neuronal_mask,
fillSize=self.jSpinner11.value(),
autoSkel=True,
first_blur=self.whsed_big_blur.value(),
second_blur=self.whsed_small_blur.value(),
min_size=self.wshed_rm_small_cells.value(),
channel=self.channels.currentText())
if mask is not None:
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
else:
logger.error(
'Something went wrong, the neuron could not be segmented, sorry...'
)
except:
traceback.print_exc()
def save_segmented_bonds(self):
output_folder = self.__get_output_folder()
if output_folder is None:
logger.error('No image is selected --> nothing to save')
return
# get mask the find neurons
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to do')
return
mask = detect_cell_bonds(mask)
if mask is None:
logger.error(
'Could not find dendrites, are you sure a mask is overlayed over the neuron'
)
return
# code for conversion of 24 bits numpy array to an RGB one --> keep and store in Img at some point cause useful
# convert 24 bits array to RGB
RGB_mask = np.zeros(shape=(*mask.shape, 3), dtype=np.uint8)
RGB_mask[..., 2] = mask & 255
RGB_mask[..., 1] = (mask >> 8) & 255
RGB_mask[..., 0] = (mask >> 16) & 255
Img(RGB_mask,
dimensions='hwc').save(os.path.join(output_folder, 'bonds.tif'))
def prune_neuron_unconnected_segments(self):
# get mask the find neurons
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to do')
return
mask = find_neurons(
mask,
neuron_minimum_size_threshold=self.find_neurons_min_size.value(),
return_unconnected=True)
if mask is None:
logger.error(
'Could not find neurons, are you sure a mask is overlayed over the neuron'
)
return
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
def apply_cell_body_to_skeletonized_mask(self):
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to do')
return
cell_body_mask = self.__get_cellbody_mask()
if cell_body_mask is None:
return
cell_body_outline = get_cell_body_outline(cell_body_mask, mask)
if cell_body_outline is None:
logger.error(
'Error could not add cell body outline to the neuronal mask...'
)
return
self.paint.imageDraw = Img(self.createRGBA(cell_body_outline),
dimensions='hwc').getQimage()
self.paint.update()
def find_neurons_in_mask(self):
# get mask the find neurons
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to do')
return
mask_copy = mask.copy()
mask = find_neurons(
mask,
neuron_minimum_size_threshold=self.find_neurons_min_size.value())
if mask is None:
logger.error(
'Could not find neurons, are you sure a mask is overlayed over the neuron'
)
return
# we set the red channel, the blue one, the alpha transparency (channel 4) and finally we only allow alpha channel in the two masks regions to keep the rest of the stuff
final_overlay = np.zeros(shape=(*mask_copy.shape, 4), dtype=np.uint8)
final_overlay[..., 0] = np.logical_xor(mask, mask_copy).astype(
np.uint8) * 255 # blue channel
final_overlay[mask == 0, 0] = 0
final_overlay[..., 1] = final_overlay[
...,
0] # green channel # copy the channel to make the stuff appear cyan
final_overlay[..., 2] = mask_copy # red channel
final_overlay[np.logical_or(mask, mask_copy) != 0,
3] = 255 # --> need set alpha transparency of the image
self.paint.imageDraw = Img(final_overlay, dimensions='hwc').getQimage()
self.paint.update()
def prune_dendrites(self):
prune_lgth = self.prune_length.value()
if prune_lgth <= 0:
logger.info('prune length is 0 --> nothing to do')
return
# get the mask from displayed image
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to do')
return
# see how to get the stuff ????
mask = prune_dendrites(mask, prune_below=prune_lgth)
if mask is None:
logger.error(
'Could not prune dendrites, are you sure there is a mask ovrlayed on the neuron'
)
return
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
def skeletonize_mask(self):
# get mask then skeletonize it then return it --> see exactly
try:
# get raw image and segment it using the skeletonize algorithm
# make it load the neuronal mask
neuronal_mask = self.__get_neuronal_mask()
if neuronal_mask is None:
return
mask = skel_segment_neuronal_mask(neuronal_mask)
if mask is not None:
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
else:
logger.error(
'Something went wrong, the neuron could not be sekeletonized, sorry...'
)
except:
traceback.print_exc()
def _onTabChange(self):
# if tab is changed --> do stuff
# load files or warn...
if self.tabs.currentIndex() == 0:
mask = self.__get_neuronal_mask(warn=False)
if mask is not None:
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
elif self.tabs.currentIndex() == 1:
mask = self.__get_cellbody_mask(warn=False)
if mask is not None:
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
elif self.tabs.currentIndex() == 2:
mask = self.__get_corrected_mask(warn=False)
if mask is not None:
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
def run_threshold_neuron(self):
try:
local_or_global = 'global'
if self.sender() == self.local_threshold:
local_or_global = 'local'
elif self.sender() == self.local_n_global_threshold:
local_or_global = 'local+global'
mask = threshold_neuron(
self.img,
mode=local_or_global,
blur_method=self.threshold_method.currentText(),
spin_value=self.extra_value_for_threshold.value(),
channel=self.channels.currentText())
if mask is not None:
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
except:
traceback.print_exc()
def channelChange(self, i):
if self.Stack.currentIndex() == 0:
if i == 0:
self.paint.setImage(self.img)
else:
channel_img = self.img.imCopy(c=i - 1)
self.paint.setImage(channel_img)
self.paint.update()
def penSizechange(self):
self.paint.brushSize = self.penSize.value()
def selectionChanged(self):
self.paint.maskVisible = True
selected_items = self.list.selectedItems()
if selected_items:
start = timer()
if self.img is not None:
# make sure we don't load the image twice
if selected_items[0].toolTip() != self.img.metadata['path']:
self.img = Img(selected_items[0].toolTip())
logger.debug("took " + str(timer() - start) +
" secs to load image")
else:
logger.debug("image already loaded --> ignoring")
else:
self.img = Img(selected_items[0].toolTip())
logger.debug("took " + str(timer() - start) +
" secs to load image")
if self.img is not None:
selection = self.channels.currentIndex()
self.channels.disconnect()
self.channels.clear()
comboData = ['merge']
if self.img.has_c():
for i in range(self.img.get_dimension('c')):
comboData.append(str(i))
logger.debug('channels found ' + str(comboData))
self.channels.addItems(comboData)
if selection != -1 and selection < self.channels.count():
self.channels.setCurrentIndex(selection)
else:
self.channels.setCurrentIndex(0)
self.channels.currentIndexChanged.connect(self.channelChange)
if selected_items:
self.statusBar().showMessage('Loading ' +
selected_items[0].toolTip())
selection = self.channels.currentIndex()
if selection == 0:
self.paint.setImage(self.img)
else:
self.paint.setImage(self.img.imCopy(c=selection - 1))
self.scaleImage(0)
self.update()
self.paint.update()
if self.list.currentItem() and self.list.currentItem().icon(
).isNull():
logger.debug('Updating icon')
icon = QIcon(QPixmap.fromImage(self.paint.image))
pixmap = icon.pixmap(24, 24)
icon = QIcon(pixmap)
self.list.currentItem().setIcon(icon)
else:
logger.debug("Empty selection")
self.paint.image = None
self.scaleImage(0)
self.update()
self.paint.update()
self.img = None
# try update also the masks if they are available
try:
self._onTabChange()
except:
pass
def clearlayout(self, layout):
for i in reversed(range(layout.count())):
layout.itemAt(i).widget().setParent(None)
def showHideMask(self):
self.paint.maskVisible = not self.paint.maskVisible
self.paint.update()
def escape(self):
if self.Stack.isFullScreen():
self.fullScreen()
def fullScreen(self):
if not self.Stack.isFullScreen():
self.Stack.setWindowFlags(
QtCore.Qt.Window | QtCore.Qt.CustomizeWindowHint |
# QtCore.Qt.WindowTitleHint |
# QtCore.Qt.WindowCloseButtonHint |
QtCore.Qt.WindowStaysOnTopHint)
self.Stack.showFullScreen()
else:
self.Stack.setWindowFlags(QtCore.Qt.Widget)
self.grid.addWidget(self.Stack, 0, 0)
# dirty hack to make it repaint properly --> obviously not all lines below are required but some are --> need test, the last line is key though
self.grid.update()
self.Stack.update()
self.Stack.show()
self.centralWidget().setLayout(self.grid)
self.centralWidget().update()
self.update()
self.show()
self.repaint()
self.Stack.update()
self.Stack.repaint()
self.centralWidget().repaint()
def nextFrame(self):
idx = self.list.model().index(self.list.currentRow() + 1, 0)
if idx.isValid():
self.list.selectionModel().setCurrentIndex(
idx, QItemSelectionModel.ClearAndSelect) # SelectCurrent
def remove_blobs(self):
blob_size = self.remove_blobs_size.value()
if blob_size <= 0:
logger.info('blob size is 0 --> nothing to do')
return
# get the mask from displayed image
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to save')
return
mask = remove_small_objects(mask.astype(np.bool),
min_size=blob_size,
connectivity=2,
in_place=False)
# then place back pixels in the mask
# now set the mask back
# plt.imshow(mask)
# plt.show()
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
def runSkel(self):
# only allow that for tab 3
if self.tabs.currentIndex() == 2:
mask = self.__get_mask_img_from_overlay()
if mask is None:
logger.error('No mask/overlay detected --> nothing to do')
return
# just skeletonize the image
mask = skel_segment_neuronal_mask(
mask, fill_holes=0) # should I put it to 0 or other things ???
if mask is None:
logger.error('Could not skeletonize user edited mask...')
return
self.paint.imageDraw = Img(self.createRGBA(mask),
dimensions='hwc').getQimage()
self.paint.update()
def createRGBA(self, handCorrection):
# use pen color to display the mask
# in fact I need to put the real color
RGBA = np.zeros((handCorrection.shape[0], handCorrection.shape[1], 4),
dtype=np.uint8)
red = self.paint.drawColor.red()
green = self.paint.drawColor.green()
blue = self.paint.drawColor.blue()
# bug somewhere --> fix it some day --> due to bgra instead of RGBA
RGBA[handCorrection != 0, 0] = blue # b
RGBA[handCorrection != 0, 1] = green # g
RGBA[handCorrection != 0, 2] = red # r
RGBA[..., 3] = 255 # alpha --> indeed alpha
RGBA[handCorrection == 0, 3] = 0 # very complex fix some day
return RGBA
def prevFrame(self):
idx = self.list.model().index(self.list.currentRow() - 1, 0)
if idx.isValid():
self.list.selectionModel().setCurrentIndex(
idx, QItemSelectionModel.ClearAndSelect)
def zoomIn(self):
self.statusBar().showMessage('Zooming in', msecs=200)
if self.Stack.currentIndex() == 0:
self.scaleImage(self.zoom_increment)
def zoomOut(self):
self.statusBar().showMessage('Zooming out', msecs=200)
if self.Stack.currentIndex() == 0:
self.scaleImage(-self.zoom_increment)
def defaultSize(self):
self.paint.adjustSize()
self.scale = 1.0
self.scaleImage(0)
def scaleImage(self, factor):
self.scale += factor
if self.paint.image is not None:
self.paint.resize(self.scale * self.paint.image.size())
else:
# no image set size to 0, 0 --> scroll pane will auto adjust
self.paint.resize(QSize(0, 0))
self.scale -= factor # reset zoom
self.paint.scale = self.scale
# self.paint.vdp.scale = self.scale
self.zoomInAct.setEnabled(self.scale < self.max_scaling_factor)
self.zoomOutAct.setEnabled(self.scale > self.min_scaling_factor)
# allow DND
def dragEnterEvent(self, event):
if event.mimeData().hasUrls:
event.accept()
else:
event.ignore()
def dragMoveEvent(self, event):
if event.mimeData().hasUrls:
event.setDropAction(QtCore.Qt.CopyAction)
event.accept()
else:
event.ignore()
# handle DND on drop
def dropEvent(self, event):
if event.mimeData().hasUrls:
event.setDropAction(QtCore.Qt.CopyAction)
event.accept()
urls = []
for url in event.mimeData().urls():
urls.append(url.toLocalFile())
for url in urls:
import os
item = QListWidgetItem(os.path.basename(url), self.list)
item.setToolTip(url)
self.list.addItem(item)
else:
event.ignore()
