def _add_img(self, source, name=None, header=None, view_min=None,
view_max=None, alpha=255, colormap='gray'):
"""
Add image.
"""
# If model is NULL, then re-initialize it.
if not self.model:
self._init_label_config_center()
self.model = VolumeListModel([], self._label_config_center)
self.model.set_scale_factor(self.default_grid_scale_factor, 'grid')
self.model.set_scale_factor(self.default_orth_scale_factor, 'orth')
self.painter_status = PainterStatus(ViewSettings())
# Save previous opened directory (except `standard` directory)
file_path = str(source)
temp_dir = os.path.dirname(file_path)
if sys.platform == 'win32':
if not os.stat(temp_dir) == os.stat(os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
else:
if not os.path.samefile(temp_dir, os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
if self.model.addItem(file_path, None, name, header, view_min,
view_max, alpha, colormap):
# Take different acions in different case.
# If only one data in VolumeList, then initialize views.
if self.model.rowCount() == 1:
# initialize views
self.list_view = LayerView(self._label_config_center)
self.list_view.setModel(self.model)
self._init_roi_dialog()
self.image_view = GridView(self.model, self.painter_status)
# initialize display layout
central_widget = QWidget()
layout = QHBoxLayout()
central_widget.setLayout(layout)
central_widget.layout().addWidget(self.list_view)
central_widget.layout().addWidget(self.image_view)
self.setCentralWidget(central_widget)
# add a toolbar
self._add_toolbar()
#self.setUnifiedTitleAndToolBarOnMac(True)
# change button status
self._actions['save_image'].setEnabled(True)
#self._actions['ld_lbl'].setEnabled(True)
#self._actions['ld_glbl'].setEnabled(True)
self._actions['new_image'].setEnabled(True)
self._actions['close'].setEnabled(True)
self._actions['orth_view'].setEnabled(True)
self._actions['cross_hover_view'].setEnabled(True)
self._actions['original_view'].setEnabled(True)
self._actions['undo'].setEnabled(False)
self._actions['redo'].setEnabled(False)
self._functional_module_set_enabled(True)
# connect signals with slots
self.list_view.current_changed.connect(self._update_undo)
self.list_view.current_changed.connect(self._update_redo)
self.model.rowsInserted.connect(self._update_remove_image)
self.model.undo_stack_changed.connect(self._update_undo)
self.model.redo_stack_changed.connect(self._update_redo)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
# set crosshair as the center of the data
self.model.set_cross_pos([self.model.getY()/2,
self.model.getX()/2,
self.model.getZ()/2])
## Enable cursor tracking
# self.list_view._list_view.selectionModel().currentChanged.connect(
# self._switch_cursor_status)
elif self.model.rowCount() > 1:
self._actions['remove_image'].setEnabled(True)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
self.is_save_configure = True
else:
QMessageBox.information(self,'FreeROI', 'Cannot load ' + "filename" + '.')
class BpMainWindow(QMainWindow):
"""Class BpMainWindow provides UI interface of FreeROI.
Example:
--------
>>> from PyQt4.QtGui import QApplication
>>> import main
>>> app = QApplication([])
>>> win = main.BpMainWindow()
......
>>> win.show()
>>> app.exec_()
"""
def __init__(self, parent=None):
"""
Initialize an instance of BpMainWindow.
"""
# Inherited from QMainWindow
if sys.platform == 'darwin':
# Workaround for Qt issue on OS X that causes QMainWindow to
# hide when adding QToolBar, see
# https://bugreports.qt-project.org/browse/QTBUG-4300
super(BpMainWindow, self).__init__(parent,
Qt.MacWindowToolBarButtonHint)
else:
super(BpMainWindow, self).__init__(parent)
# temporary variable
self._temp_dir = None
self.is_save_configure = False
# pre-define a model variable
self.model = None
def config_extra_settings(self, data_dir):
"""
Set data directory and update some configurations.
"""
# load data directory configuration
self.label_path = data_dir
self.label_config_dir = os.path.join(self.label_path, 'labelconfig')
self.label_config_suffix = 'lbl'
# set icon configuration
self._icon_dir = get_icon_dir()
# set window title
self.setWindowTitle('FreeROI')
#self.resize(1280, 1000)
self.center()
# set window icon
self.setWindowIcon(QIcon(os.path.join(self._icon_dir,'icon.png')))
self._init_configuration()
# create actions
self._create_actions()
# create menus
self._create_menus()
def center(self):
"""
Display main window in the center of screen
"""
qr = self.frameGeometry()
cp = QDesktopWidget().availableGeometry().center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def _init_configuration(self):
"""
Load configuration for GUI.
"""
config_file = os.path.expanduser('~/.pybp.conf')
if os.path.exists(config_file):
config = ConfigParser.RawConfigParser()
config.read(config_file)
self.window_width = config.getint('width', 'int')
self.window_height = config.getint('height', 'int')
self.orth_scale_factor = config.getint('orth_scale', 'int')
self.grid_scale_factor = config.getint('grid_scale', 'int')
self.window_xpos = config.getint('xpos', 'int')
self.window_ypos = config.getint('ypos', 'int')
self.resize(self.window_width, self.window_height)
self.move(self.window_xpos, self.window_ypos)
self.default_orth_scale_factor = float(self.orth_scale_factor) / 100
self.default_grid_scale_factor = float(self.grid_scale_factor) / 100
else:
self.setWindowState(Qt.WindowMaximized)
self.default_orth_scale_factor = 1.0
self.default_grid_scale_factor = 2.0
def _save_configuration(self):
"""
Save GUI configuration to a file.
"""
config_file = os.path.expanduser('~/.pybp.conf')
config = ConfigParser.RawConfigParser()
config.add_section('width')
config.add_section('height')
config.add_section('orth_scale')
config.add_section('grid_scale')
config.add_section('xpos')
config.add_section('ypos')
config.set('width', 'int', self.width())
config.set('height', 'int', self.height())
config.set('xpos', 'int', self.x())
config.set('ypos', 'int', self.y())
if hasattr(self, 'model') and isinstance(self.model, VolumeListModel):
config.set('orth_scale', 'int',
int(self.model.get_scale_factor('orth')*100))
config.set('grid_scale', 'int',
int(self.model.get_scale_factor('grid')*100))
else:
config.set('orth_scale', 'int',
int(self.default_orth_scale_factor * 100))
config.set('grid_scale', 'int',
int(self.default_grid_scale_factor * 100))
with open(config_file, 'wb') as conf:
config.write(conf)
def closeEvent(self, e):
if self.is_save_configure:
self._save_configuration()
e.accept()
def _create_actions(self):
"""
Create actions.
"""
# create a dictionary to store actions info
self._actions = {}
# Open template action
self._actions['add_template'] = QAction(QIcon(os.path.join(
self._icon_dir, 'open.png')),
self.tr("&Open standard volume"),
self)
self._actions['add_template'].setShortcut(self.tr("Ctrl+O"))
self._actions['add_template'].triggered.connect(self._add_template)
self._actions['add_template'].setEnabled(True)
# Add a new image action
self._actions['add_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'add.png')),
self.tr("&Add volume"),
self)
self._actions['add_image'].setShortcut(self.tr("Ctrl+A"))
self._actions['add_image'].triggered.connect(self._add_image)
self._actions['add_image'].setEnabled(True)
# Remove an image
self._actions['remove_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'remove.png')),
self.tr("&Remove volume"),
self)
self._actions['remove_image'].setShortcut(self.tr("Ctrl+R"))
self._actions['remove_image'].triggered.connect(self._remove_image)
self._actions['remove_image'].setEnabled(False)
# New image
self._actions['new_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'create.png')),
self.tr("&New volume"),
self)
self._actions['new_image'].setShortcut(self.tr("Ctrl+N"))
self._actions['new_image'].triggered.connect(self.__new_image)
self._actions['new_image'].setEnabled(False)
# Save image
self._actions['save_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'save.png')),
self.tr("&Save volume as..."),
self)
self._actions['save_image'].setShortcut(self.tr("Ctrl+S"))
self._actions['save_image'].triggered.connect(self._save_image)
self._actions['save_image'].setEnabled(False)
## Load Label Config
#self._actions['ld_lbl'] = QAction('Load Label', self)
#self._actions['ld_lbl'].triggered.connect(self._ld_lbl)
#self._actions['ld_lbl'].setEnabled(False)
## Load Global Label Config
#self._actions['ld_glbl'] = QAction('Load Global Label', self)
#self._actions['ld_glbl'].triggered.connect(self._ld_glbl)
#self._actions['ld_glbl'].setEnabled(False)
# Close display
self._actions['close'] = QAction(self.tr("Close"), self)
self._actions['close'].setShortcut(self.tr("Ctrl+W"))
self._actions['close'].triggered.connect(self._close_display)
self._actions['close'].setEnabled(False)
# Quit action
self._actions['quit'] = QAction(QIcon(os.path.join(
self._icon_dir, 'quit.png')),
self.tr("&Quit"),
self)
self._actions['quit'].setShortcut(self.tr("Ctrl+Q"))
self._actions['quit'].triggered.connect(self.close)
# Grid view action
self._actions['grid_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'gridview.png')),
self.tr("Lightbox"),
self)
self._actions['grid_view'].triggered.connect(self._grid_view)
self._actions['grid_view'].setEnabled(False)
# Orth view action
self._actions['orth_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'orthview.png')),
self.tr("Orthographic"),
self)
self._actions['orth_view'].triggered.connect(self._orth_view)
self._actions['orth_view'].setEnabled(False)
# return original size
self._actions['original_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'original_size.png')),
self.tr("Reset view"),
self)
self._actions['original_view'].triggered.connect(self._reset_view)
self._actions['original_view'].setEnabled(False)
# whether display the cross hover
self._actions['cross_hover_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'cross_hover_enable.png')),
self.tr("Disable cross hover"),
self)
self._actions['cross_hover_view'].triggered.connect(
self._display_cross_hover)
self._actions['cross_hover_view'].setEnabled(False)
# Binaryzation view action
self._actions['binarization'] = QAction(QIcon(os.path.join(
self._icon_dir, 'binarization.png')),
self.tr("Binarization"),
self)
self._actions['binarization'].triggered.connect(self._binarization)
self._actions['binarization'].setEnabled(False)
# Intersection action
self._actions['intersect'] = QAction(QIcon(os.path.join(
self._icon_dir, 'intersect.png')),
self.tr("Intersection"),
self)
self._actions['intersect'].triggered.connect(self._intersect)
self._actions['intersect'].setEnabled(False)
# Extract mean time course
self._actions['meants'] = QAction(QIcon(os.path.join(self._icon_dir,
'voxel_curve.png')),
self.tr("Extract Mean Time Course"),
self)
self._actions['meants'].triggered.connect(self._meants)
self._actions['meants'].setEnabled(False)
# Local Max action
self._actions['localmax'] = QAction(QIcon(os.path.join(
self._icon_dir, 'localmax.png')),
self.tr("Local Max"),
self)
self._actions['localmax'].triggered.connect(self._local_max)
self._actions['localmax'].setEnabled(False)
# Inversion action
self._actions['inverse'] = QAction(QIcon(os.path.join(
self._icon_dir, 'inverse.icon')),
self.tr("Inversion"),
self)
self._actions['inverse'].triggered.connect(self._inverse)
self._actions['inverse'].setEnabled(False)
# Smoothing action
self._actions['smoothing'] = QAction(QIcon(os.path.join(
self._icon_dir, 'smoothing.png')),
self.tr("Smoothing"),
self)
self._actions['smoothing'].triggered.connect(self._smooth)
self._actions['smoothing'].setEnabled(False)
# Region Growing action
self._actions['region_grow'] = QAction(QIcon(os.path.join(
self._icon_dir, 'grow.png')),
self.tr("Region Growing"),
self)
self._actions['region_grow'].triggered.connect(self._region_grow)
self._actions['region_grow'].setEnabled(False)
# Watershed action
self._actions['watershed'] = QAction(QIcon(os.path.join(
self._icon_dir, 'watershed.png')),
self.tr("Watershed"),
self)
self._actions['watershed'].triggered.connect(self._watershed)
self._actions['watershed'].setEnabled(False)
# Cluster action
self._actions['cluster'] = QAction(QIcon(os.path.join(
self._icon_dir, 'cluster.png')),
self.tr("Cluster"),
self)
self._actions['cluster'].triggered.connect(self._cluster)
self._actions['cluster'].setEnabled(False)
# Opening
self._actions['opening'] = QAction(self.tr("Opening"), self)
self._actions['opening'].triggered.connect(self._opening)
self._actions['opening'].setEnabled(False)
# Binary_erosion view action
self._actions['binaryerosion'] = QAction(self.tr("Binary Erosion"),
self)
self._actions['binaryerosion'].triggered.connect(self._binaryerosion)
self._actions['binaryerosion'].setEnabled(False)
# Binary_dilation view action
self._actions['binarydilation'] = QAction(self.tr("Binary Dilation"),
self)
self._actions['binarydilation'].triggered.connect(self._binarydilation)
self._actions['binarydilation'].setEnabled(False)
# grey_erosion view action
self._actions['greyerosion'] = QAction(self.tr("Grey Erosion"),
self)
self._actions['greyerosion'].triggered.connect(self._greyerosion)
self._actions['greyerosion'].setEnabled(False)
# grey_dilation view action
self._actions['greydilation'] = QAction(self.tr("Grey Dilation"),
self)
self._actions['greydilation'].triggered.connect(self._greydilation)
self._actions['greydilation'].setEnabled(False)
# About software
self._actions['about_pybp'] = QAction(self.tr("About FreeROI"), self)
self._actions['about_pybp'].triggered.connect(self._about_pybp)
# About Qt
self._actions['about_qt'] = QAction(QIcon(os.path.join(
self._icon_dir, 'qt.png')),
self.tr("About Qt"),
self)
self._actions['about_qt'].triggered.connect(qApp.aboutQt)
# Hand
self._actions['hand'] = QAction(QIcon(os.path.join(
self._icon_dir, 'hand.png')),
self.tr("Hand"),
self)
self._actions['hand'].triggered.connect(self._hand_enable)
self._actions['hand'].setCheckable(True)
self._actions['hand'].setChecked(False)
self._actions['hand'].setEnabled(False)
# Cursor
self._actions['cursor'] = QAction(QIcon(os.path.join(
self._icon_dir, 'cursor.png')),
self.tr("Cursor"),
self)
self._actions['cursor'].triggered.connect(self._cursor_enable)
self._actions['cursor'].setCheckable(True)
self._actions['cursor'].setChecked(True)
self._actions['cursor'].setEnabled(True)
# Edit
self._actions['edit'] = QAction(QIcon(os.path.join(
self._icon_dir, 'edit.png')),
self.tr("Edit"), self)
self._actions['edit'].triggered.connect(self._roidialog_enable)
self._actions['edit'].setCheckable(True)
self._actions['edit'].setChecked(False)
# Undo
self._actions['undo'] = QAction(QIcon(os.path.join(
self._icon_dir, 'undo.png')),
self.tr("Undo"),
self)
self._actions['undo'].triggered.connect(self._undo)
# Redo
self._actions['redo'] = QAction(QIcon(os.path.join(
self._icon_dir, 'redo.png')),
self.tr("Redo"),
self)
self._actions['redo'].triggered.connect(self._redo)
# sphere and cube roi
self._actions['regular_roi'] = QAction(QIcon(os.path.join(
self._icon_dir,
'sphere_and_cube.png')),
self.tr("Regular ROI"), self)
self._actions['regular_roi'].triggered.connect(self._regular_roi)
self._actions['regular_roi'].setEnabled(False)
# ROI to Interface
self._actions['r2i'] = QAction(QIcon(os.path.join(
self._icon_dir, 'r2i.png')),
self.tr("ROI2Interface"), self)
self._actions['r2i'].triggered.connect(self._r2i)
self._actions['r2i'].setEnabled(False)
# Edge detection for ROI
self._actions['edge_dete'] = QAction(QIcon(os.path.join(
self._icon_dir,
'edge_detection.png')),
self.tr("Edge Detection"), self)
self._actions['edge_dete'].triggered.connect(self._edge_detection)
self._actions['edge_dete'].setEnabled(False)
# ROI Merging
self._actions['roi_merge'] = QAction(QIcon(os.path.join(
self._icon_dir, 'merging.png')),
self.tr("ROI Merging"), self)
self._actions['roi_merge'].triggered.connect(self._roi_merge)
self._actions['roi_merge'].setEnabled(False)
def _add_toolbar(self):
"""
Add toolbar.
"""
# Initialize a spinbox for zoom-scale selection
self._spinbox = QSpinBox()
self._spinbox.setMaximum(500)
self._spinbox.setMinimum(50)
self._spinbox.setSuffix('%')
self._spinbox.setSingleStep(10)
self._spinbox.setValue(self.default_grid_scale_factor * 100)
self._spinbox.valueChanged.connect(self._set_scale_factor)
# Add a toolbar
self._toolbar = self.addToolBar("Tools")
#self._toolbar.setIconSize(QSize(38,38))
# Add file actions
self._toolbar.addAction(self._actions['add_image'])
self._toolbar.addAction(self._actions['remove_image'])
self._toolbar.addAction(self._actions['new_image'])
self._toolbar.addAction(self._actions['save_image'])
# Add view actions
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['grid_view'])
self._toolbar.addAction(self._actions['orth_view'])
self._toolbar.addAction(self._actions['original_view'])
self._toolbar.addAction(self._actions['cross_hover_view'])
# Add cursor status
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['hand'])
self._toolbar.addAction(self._actions['cursor'])
self._toolbar.addAction(self._actions['edit'])
# Add undo redo
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['undo'])
self._toolbar.addAction(self._actions['redo'])
self._toolbar.addSeparator()
self._toolbar.addWidget(self._spinbox)
def _set_scale_factor(self, value):
"""
Set scale factor.
"""
value = float(value) / 100
self.model.set_scale_factor(value, self.image_view.display_type())
def _add_template(self):
"""
Open a dialog window and select a template file.
"""
template_dir = os.path.join(self.label_path, 'standard',
'MNI152_T1_2mm_brain.nii.gz')
template_name = QFileDialog.getOpenFileName(
self,
'Open standard file',
template_dir,
'Nifti files (*.nii.gz *.nii)')
if not template_name.isEmpty():
template_path = str(template_name)
self._add_img(template_path)
def _add_image(self):
"""
Add new item.
"""
if self._temp_dir == None:
temp_dir = QDir.currentPath()
else:
temp_dir = self._temp_dir
file_name = QFileDialog.getOpenFileName(self,
'Add new file',
temp_dir,
'Nifti files (*.nii.gz *.nii)')
if not file_name.isEmpty():
file_path = str(file_name)
self._add_img(file_path)
def _add_img(self, source, name=None, header=None, view_min=None,
view_max=None, alpha=255, colormap='gray'):
"""
Add image.
"""
# If model is NULL, then re-initialize it.
if not self.model:
self._init_label_config_center()
self.model = VolumeListModel([], self._label_config_center)
self.model.set_scale_factor(self.default_grid_scale_factor, 'grid')
self.model.set_scale_factor(self.default_orth_scale_factor, 'orth')
self.painter_status = PainterStatus(ViewSettings())
# Save previous opened directory (except `standard` directory)
file_path = str(source)
temp_dir = os.path.dirname(file_path)
if sys.platform == 'win32':
if not os.stat(temp_dir) == os.stat(os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
else:
if not os.path.samefile(temp_dir, os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
if self.model.addItem(file_path, None, name, header, view_min,
view_max, alpha, colormap):
# Take different acions in different case.
# If only one data in VolumeList, then initialize views.
if self.model.rowCount() == 1:
# initialize views
self.list_view = LayerView(self._label_config_center)
self.list_view.setModel(self.model)
self._init_roi_dialog()
self.image_view = GridView(self.model, self.painter_status)
# initialize display layout
central_widget = QWidget()
layout = QHBoxLayout()
central_widget.setLayout(layout)
central_widget.layout().addWidget(self.list_view)
central_widget.layout().addWidget(self.image_view)
self.setCentralWidget(central_widget)
# add a toolbar
self._add_toolbar()
#self.setUnifiedTitleAndToolBarOnMac(True)
# change button status
self._actions['save_image'].setEnabled(True)
#self._actions['ld_lbl'].setEnabled(True)
#self._actions['ld_glbl'].setEnabled(True)
self._actions['new_image'].setEnabled(True)
self._actions['close'].setEnabled(True)
self._actions['orth_view'].setEnabled(True)
self._actions['cross_hover_view'].setEnabled(True)
self._actions['original_view'].setEnabled(True)
self._actions['undo'].setEnabled(False)
self._actions['redo'].setEnabled(False)
self._functional_module_set_enabled(True)
# connect signals with slots
self.list_view.current_changed.connect(self._update_undo)
self.list_view.current_changed.connect(self._update_redo)
self.model.rowsInserted.connect(self._update_remove_image)
self.model.undo_stack_changed.connect(self._update_undo)
self.model.redo_stack_changed.connect(self._update_redo)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
# set crosshair as the center of the data
self.model.set_cross_pos([self.model.getY()/2,
self.model.getX()/2,
self.model.getZ()/2])
## Enable cursor tracking
# self.list_view._list_view.selectionModel().currentChanged.connect(
# self._switch_cursor_status)
elif self.model.rowCount() > 1:
self._actions['remove_image'].setEnabled(True)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
self.is_save_configure = True
else:
QMessageBox.information(self,'FreeROI', 'Cannot load ' + "filename" + '.')
def __new_image(self):
self._new_image()
def _update_remove_image(self):
if self.model.rowCount() == 1:
self._actions['remove_image'].setEnabled(False)
else:
self._actions['remove_image'].setEnabled(True)
def _new_image(self, data=None, name=None, colormap=None):
"""
Create a new volume for brain parcellation.
"""
if colormap is None:
colormap = self._label_config_center.get_first_label_config()
self.model.new_image(data, name, None, colormap)
self.list_view.setCurrentIndex(self.model.index(0))
# change button status
self._actions['remove_image'].setEnabled(True)
def new_image_action(self):
self._actions['remove_image'].setEnabled(True)
def _remove_image(self):
"""
Remove current image.
"""
row = self.list_view.currentRow()
self.model.delItem(row)
if self.model.rowCount() == 1:
self._actions['remove_image'].setEnabled(False)
def _save_image(self):
"""
Save image as a nifti file.
"""
index = self.model.currentIndex()
if self._temp_dir == None:
temp_dir = str(QDir.currentPath())
else:
temp_dir = self._temp_dir
file_path = os.path.join(temp_dir,
str(self.model.data(index, Qt.DisplayRole))+'.nii.gz')
path = QFileDialog.getSaveFileName(
self,
'Save image as...',
file_path,
'Nifti files (*.nii.gz *.nii)')
if not path.isEmpty():
self._temp_dir = os.path.dirname(str(path))
self.model._data[index.row()].save2nifti(str(path))
def _close_display(self):
"""
Close current display.
"""
self.setCentralWidget(QWidget())
self._set_scale_factor(self.default_grid_scale_factor)
self.removeToolBar(self._toolbar)
self.model = None
self._actions['add_template'].setEnabled(True)
self._actions['add_image'].setEnabled(True)
self._actions['remove_image'].setEnabled(False)
self._actions['new_image'].setEnabled(False)
self._actions['save_image'].setEnabled(False)
#self._actions['ld_glbl'].setEnabled(False)
#self._actions['ld_lbl'].setEnabled(False)
self._actions['close'].setEnabled(False)
self._actions['grid_view'].setEnabled(False)
self._actions['orth_view'].setEnabled(False)
self._actions['cross_hover_view'].setEnabled(False)
self._actions['original_view'].setEnabled(False)
self._functional_module_set_enabled(False)
def _about_pybp(self):
"""
About software.
"""
QMessageBox.about(self, self.tr("About FreeROI"),
self.tr("<p><b>FreeROI</b> is a versatile image "
"processing software developed for "
"neuroimaging data.</p>"
"<p>Its goal is to provide a user-friendly "
"interface for neuroimaging researchers "
"to visualize and analyze their data, "
"especially in defining region of interest "
"(ROI) for ROI analysis.</p>"
"<p>Written by: Lijie Huang, Zetian Yang, "
"Guangfu Zhou, Zhaoguo Liu, Xiaobin Dang, "
"Xiangzhen Kong, Xu Wang, and Zonglei Zhen."
"</p>"
"<p><b>FreeROI</b> is under Revised BSD "
"License.</p>"
"<p>Version: " + __version__ + "</p>"
"<p>Copyright(c) 2012-2014 "
"Neuroinformatic Team in LiuLab "
"from Beijing Normal University</p>"
"<p></p>"
"<p>Please report bugs to:</p>"
"<p><b>[email protected]</b></p>"))
def _create_menus(self):
"""Create menus."""
self.file_menu = self.menuBar().addMenu(self.tr("File"))
self.file_menu.addAction(self._actions['add_image'])
self.file_menu.addAction(self._actions['add_template'])
self.file_menu.addAction(self._actions['save_image'])
#self.file_menu.addSeparator()
#self.file_menu.addAction(self._actions['ld_lbl'])
#self.file_menu.addAction(self._actions['ld_glbl'])
self.file_menu.addSeparator()
self.file_menu.addAction(self._actions['close'])
self.file_menu.addAction(self._actions['quit'])
self.volume_menu = self.menuBar().addMenu(self.tr("Volume"))
self.volume_menu.addAction(self._actions['new_image'])
self.volume_menu.addAction(self._actions['remove_image'])
self.view_menu = self.menuBar().addMenu(self.tr("View"))
self.view_menu.addAction(self._actions['grid_view'])
self.view_menu.addAction(self._actions['orth_view'])
self.view_menu.addAction(self._actions['original_view'])
self.view_menu.addAction(self._actions['cross_hover_view'])
self.tool_menu = self.menuBar().addMenu(self.tr("Tools"))
basic_tools = self.tool_menu.addMenu(self.tr("Basic Tools"))
basic_tools.addAction(self._actions['binarization'])
basic_tools.addAction(self._actions['intersect'])
basic_tools.addAction(self._actions['localmax'])
basic_tools.addAction(self._actions['inverse'])
basic_tools.addAction(self._actions['smoothing'])
basic_tools.addAction(self._actions['meants'])
segment_tools = self.tool_menu.addMenu(self.tr("Segmentation"))
segment_tools.addAction(self._actions['region_grow'])
segment_tools.addAction(self._actions['watershed'])
segment_tools.addAction(self._actions['cluster'])
roi_tools = self.tool_menu.addMenu(self.tr("ROI Tools"))
roi_tools.addAction(self._actions['edge_dete'])
roi_tools.addAction(self._actions['roi_merge'])
roi_tools.addAction(self._actions['regular_roi'])
roi_tools.addAction(self._actions['r2i'])
morphological_tools = self.tool_menu.addMenu(
self.tr("Morphological Processing"))
morphological_tools.addAction(self._actions['opening'])
morphological_tools.addAction(self._actions['binarydilation'])
morphological_tools.addAction(self._actions['binaryerosion'])
morphological_tools.addAction(self._actions['greydilation'])
morphological_tools.addAction(self._actions['greyerosion'])
self.help_menu = self.menuBar().addMenu(self.tr("Help"))
self.help_menu.addAction(self._actions['about_pybp'])
self.help_menu.addAction(self._actions['about_qt'])
def _cursor_enable(self):
"""
Cursor enabled.
"""
if self._actions['cursor'].isChecked():
self._actions['cursor'].setChecked(True)
if isinstance(self.image_view, OrthView):
self._actions['hand'].setChecked(False)
if self.roidialog.isVisible():
self._roidialog_disable()
self.painter_status.set_draw_settings(ViewSettings())
self.image_view.set_cursor(Qt.ArrowCursor)
self.image_view.set_label_mouse_tracking(True)
else:
self._actions['cursor'].setChecked(True)
def _voxel_edit_enable(self):
"""
Brush enabled.
"""
self._label_config_center.set_is_roi_edit(False)
self.painter_status.set_draw_settings(self._label_config_center)
self.image_view.set_cursor(Qt.CrossCursor)
self.image_view.set_label_mouse_tracking(False)
def _roi_edit_enable(self):
"""
ROI brush enabled.
"""
self._label_config_center.set_is_roi_edit(True)
self.painter_status.set_draw_settings(self._label_config_center)
self.image_view.set_cursor(Qt.CrossCursor)
self.image_view.set_label_mouse_tracking(False)
def _roidialog_enable(self):
if self._actions['edit'].isChecked():
self._actions['cursor'].setChecked(False)
if isinstance(self.image_view, OrthView):
self._actions['hand'].setChecked(False)
self._actions['edit'].setChecked(True)
self.roidialog._voxel_clicked()
self.roidialog.show()
else:
self._actions['edit'].setChecked(True)
def _roi_batch_enable(self):
self.image_view.set_label_mouse_tracking(False)
self._label_config_center.set_is_roi_edit(False)
self.painter_status.set_draw_settings(self.roidialog)
def _roidialog_disable(self):
self.roidialog.hide()
self._actions['edit'].setChecked(False)
def _hand_enable(self):
"""
Hand enabled.
"""
if self._actions['hand'].isChecked():
self._actions['cursor'].setChecked(False)
self._actions['hand'].setChecked(True)
if hasattr(self, 'roidialog'):
self._roidialog_disable()
self.painter_status.set_draw_settings(MoveSettings())
self.image_view.set_cursor(Qt.OpenHandCursor)
self.image_view.set_label_mouse_tracking(True)
else:
self._actions['hand'].setChecked(True)
def _switch_cursor_status(self):
self._actions['cursor'].setChecked(True)
self._cursor_enable()
def _update_undo(self):
if self.model.current_undo_available():
self._actions['undo'].setEnabled(True)
else:
self._actions['undo'].setEnabled(False)
def _update_redo(self):
if self.model.current_redo_available():
self._actions['redo'].setEnabled(True)
else:
self._actions['redo'].setEnabled(False)
def _init_roi_dialog(self):
"""
Initialize ROI Dialog
"""
self.roidialog = ROIDialog(self.model, self._label_config_center)
self.roidialog.voxel_edit_enabled.connect(self._voxel_edit_enable)
self.roidialog.roi_edit_enabled.connect(self._roi_edit_enable)
self.roidialog.roi_batch_enabled.connect(self._roi_batch_enable)
self.list_view._list_view.selectionModel().currentChanged.connect(
self.roidialog.clear_rois)
def _init_label_config_center(self):
"""
Initialize LabelConfigCenter
"""
lbl_path = os.path.join(self.label_config_dir,
'*.' + self.label_config_suffix)
label_configs = glob.glob(lbl_path)
self.label_configs = map(LabelConfig, label_configs)
self._label_config_center = LabelConfigCenter(self.label_configs)
def _get_label_config(self, file_path):
"""
Get label config file.
"""
# Get label config file
dir = os.path.dirname(file_path)
file = os.path.basename(file_path)
split_list = file.split('.')
nii_index = split_list.index('nii')
file = ''.join(split_list[:nii_index])
config_file = os.path.join(file, 'lbl')
if os.path.isfile(config_file):
label_config = LabelConfig(config_file, False)
else:
label_config = self.label_config
return label_config
def _undo(self):
self.model.undo_current_image()
def _redo(self):
self.model.redo_current_image()
def _regular_roi(self):
regular_roi_dialog = RegularROIDialog(self.model)
regular_roi_dialog.exec_()
def _edge_detection(self):
new_dialog = Edge_detectionDialog(self.model)
new_dialog.exec_()
def _roi_merge(self):
new_dialog = ROIMergeDialog(self.model)
new_dialog.exec_()
def _r2i(self):
new_dialog = Roi2gwmiDialog(self.model)
new_dialog.exec_()
def _opening(self):
new_dialog = OpenDialog(self.model)
new_dialog.exec_()
def _ld_lbl(self):
file_name = QFileDialog.getOpenFileName(self,
'Load Label File',
QDir.currentPath(),
"Label files (*.lbl)")
if file_name:
label_config = LabelConfig(str(file_name), False)
self.model.set_cur_label(label_config)
def _ld_glbl(self):
file_name = QFileDialog.getOpenFileName(self,
'Load Label File',
QDir.currentPath(),
"Label files (*.lbl)")
if file_name:
label_config = LabelConfig(str(file_name), True)
self.model.set_global_label(label_config)
def _grid_view(self):
"""
Grid view option.
"""
self._actions['grid_view'].setEnabled(False)
self._actions['orth_view'].setEnabled(True)
self._actions['hand'].setEnabled(False)
self._actions['cursor'].trigger()
self.centralWidget().layout().removeWidget(self.image_view)
self.image_view.set_display_type('grid')
self.model.scale_changed.disconnect()
self.model.repaint_slices.disconnect()
self.model.cross_pos_changed.disconnect(self.image_view.update_cross_pos)
self.image_view.deleteLater()
self._spinbox.setValue(100 * self.model.get_scale_factor('grid'))
self.image_view = GridView(self.model, self.painter_status,
self._gridview_vertical_scrollbar_position)
self.centralWidget().layout().addWidget(self.image_view)
def _orth_view(self):
"""
Orth view option.
"""
self._actions['orth_view'].setEnabled(False)
self._actions['grid_view'].setEnabled(True)
self._actions['hand'].setEnabled(True)
self._actions['cursor'].trigger()
self._gridview_vertical_scrollbar_position = \
self.image_view.get_vertical_srollbar_position()
self.centralWidget().layout().removeWidget(self.image_view)
self.image_view.set_display_type('orth')
self.model.scale_changed.disconnect()
self.model.repaint_slices.disconnect()
self.model.cross_pos_changed.disconnect(self.image_view.update_cross_pos)
self.image_view.deleteLater()
self._spinbox.setValue(100 * self.model.get_scale_factor('orth'))
self.image_view = OrthView(self.model, self.painter_status)
self.centralWidget().layout().addWidget(self.image_view)
def _display_cross_hover(self):
if self.model._display_cross:
self.model.set_cross_status(False)
self._actions['cross_hover_view'].setText('Enable cross hover')
self._actions['cross_hover_view'].setIcon(QIcon(os.path.join(self._icon_dir,'cross_hover_disable.png')))
else:
self.model.set_cross_status(True)
self._actions['cross_hover_view'].setText('Disable cross hover')
self._actions['cross_hover_view'].setIcon(QIcon(os.path.join(self._icon_dir,'cross_hover_enable.png')))
def _reset_view(self):
"""
Reset view parameters.
"""
if self.image_view.display_type() == 'orth':
if not self.model.get_scale_factor('orth') == \
self.default_orth_scale_factor:
self._spinbox.setValue(100 * self.default_orth_scale_factor)
self.image_view.reset_view()
elif self.image_view.display_type() == 'grid':
if not self.model.get_scale_factor('grid') == \
self.default_grid_scale_factor:
self._spinbox.setValue(100 * self.default_grid_scale_factor)
def _binarization(self):
binarization_dialog = BinarizationDialog(self.model)
binarization_dialog.exec_()
def _binaryerosion(self):
binaryerosion_dialog = BinaryerosionDialog(self.model)
binaryerosion_dialog.exec_()
def _binarydilation(self):
binarydilation_dialog = BinarydilationDialog(self.model)
binarydilation_dialog.exec_()
def _greyerosion(self):
greyerosiondialog = GreyerosionDialog(self.model)
greyerosiondialog.exec_()
def _greydilation(self):
greydilation_dialog = GreydilationDialog(self.model)
greydilation_dialog.exec_()
def _intersect(self):
intersect_dialog = IntersectDialog(self.model)
intersect_dialog.exec_()
def _meants(self):
new_dialog = MeanTSDialog(self.model)
new_dialog.exec_()
def _local_max(self):
new_dialog = LocalMaxDialog(self.model, self)
new_dialog.exec_()
def _inverse(self):
inverse_image(self.model)
def _smooth(self):
new_dialog = SmoothingDialog(self.model)
new_dialog.exec_()
def _region_grow(self):
new_dialog = GrowDialog(self.model, self)
new_dialog.exec_()
def _watershed(self):
new_dialog = WatershedDialog(self.model, self)
new_dialog.exec_()
def _cluster(self):
new_dialog = ClusterDialog(self.model)
new_dialog.exec_()
def _functional_module_set_enabled(self, status):
self._actions['binarization'].setEnabled(status)
self._actions['intersect'].setEnabled(status)
self._actions['meants'].setEnabled(status)
self._actions['localmax'].setEnabled(status)
self._actions['inverse'].setEnabled(status)
self._actions['smoothing'].setEnabled(status)
self._actions['region_grow'].setEnabled(status)
self._actions['watershed'].setEnabled(status)
self._actions['cluster'].setEnabled(status)
self._actions['opening'].setEnabled(status)
self._actions['binarydilation'].setEnabled(status)
self._actions['binaryerosion'].setEnabled(status)
self._actions['greydilation'].setEnabled(status)
self._actions['greyerosion'].setEnabled(status)
self._actions['regular_roi'].setEnabled(status)
self._actions['r2i'].setEnabled(status)
self._actions['edge_dete'].setEnabled(status)
self._actions['roi_merge'].setEnabled(status)
def _add_img(self, source, name=None, header=None, view_min=None,
view_max=None, alpha=255, colormap='gray'):
"""
Add image.
"""
# If model is NULL, then re-initialize it.
if not self.model:
self._init_label_config_center()
self.model = VolumeListModel([], self._label_config_center)
self.model.set_scale_factor(self.default_grid_scale_factor, 'grid')
self.model.set_scale_factor(self.default_orth_scale_factor, 'orth')
self.painter_status = PainterStatus(ViewSettings())
# Save previous opened directory (except `standard` directory)
file_path = source
if sys.platform == 'win32':
temp_dir = os.path.dirname(unicode(file_path, 'gb2312'))
if not os.stat(temp_dir) == os.stat(os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
else:
temp_dir = os.path.dirname(file_path)
if not os.path.samefile(temp_dir, os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
if self.model.addItem(file_path, None, name, header, view_min,
view_max, alpha, colormap):
# Take different acions in different case.
# If only one data in VolumeList, then initialize views.
if self.model.rowCount() == 1:
# initialize views
self.list_view = LayerView(self._label_config_center)
self.list_view.setModel(self.model)
self._init_roi_dialog()
self.image_view = GridView(self.model, self.painter_status)
# initialize display layout
central_widget = QWidget()
layout = QHBoxLayout()
central_widget.setLayout(layout)
central_widget.layout().addWidget(self.list_view)
central_widget.layout().addWidget(self.image_view)
self.setCentralWidget(central_widget)
# add a toolbar
self._add_toolbar()
#self.setUnifiedTitleAndToolBarOnMac(True)
# change button status
self._actions['save_image'].setEnabled(True)
#self._actions['ld_lbl'].setEnabled(True)
#self._actions['ld_glbl'].setEnabled(True)
self._actions['new_image'].setEnabled(True)
self._actions['close'].setEnabled(True)
self._actions['orth_view'].setEnabled(True)
self._actions['cross_hover_view'].setEnabled(True)
self._actions['original_view'].setEnabled(True)
self._actions['undo'].setEnabled(False)
self._actions['redo'].setEnabled(False)
self._functional_module_set_enabled(True)
# connect signals with slots
self.list_view.current_changed.connect(self._update_undo)
self.list_view.current_changed.connect(self._update_redo)
self.model.rowsInserted.connect(self._update_remove_image)
self.model.undo_stack_changed.connect(self._update_undo)
self.model.redo_stack_changed.connect(self._update_redo)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
# set crosshair as the center of the data
self.model.set_cross_pos([self.model.getY()/2,
self.model.getX()/2,
self.model.getZ()/2])
## Enable cursor tracking
# self.list_view._list_view.selectionModel().currentChanged.connect(
# self._switch_cursor_status)
elif self.model.rowCount() > 1:
self._actions['remove_image'].setEnabled(True)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
self.is_save_configure = True
else:
QMessageBox.information(self,'FreeROI', 'Cannot load ' + \
file_path + ': due to mismatch data size.')
class BpMainWindow(QMainWindow):
"""Class BpMainWindow provides UI interface of FreeROI.
Example:
--------
>>> from PyQt4.QtGui import QApplication
>>> import main
>>> app = QApplication([])
>>> win = main.BpMainWindow()
......
>>> win.show()
>>> app.exec_()
"""
def __init__(self, parent=None):
"""
Initialize an instance of BpMainWindow.
"""
# Inherited from QMainWindow
if sys.platform == 'darwin':
# Workaround for Qt issue on OS X that causes QMainWindow to
# hide when adding QToolBar, see
# https://bugreports.qt-project.org/browse/QTBUG-4300
super(BpMainWindow, self).__init__(parent, Qt.MacWindowToolBarButtonHint)
else:
super(BpMainWindow, self).__init__(parent)
# temporary variable
self._temp_dir = None
self.is_save_configure = False
# pre-define a model variable
self.model = None
def config_extra_settings(self, data_dir):
"""
Set data directory and update some configurations.
"""
# load data directory configuration
self.label_path = data_dir
self.label_config_dir = os.path.join(self.label_path, 'labelconfig')
self.label_config_suffix = 'lbl'
# set icon configuration
self._icon_dir=get_icon_dir()
# set window title
self.setWindowTitle('FreeROI')
#self.resize(1280, 1000)
self.center()
# set window icon
self.setWindowIcon(QIcon(os.path.join(self._icon_dir,'icon.png')))
self._init_configuration()
self._init_label_config_center()
# create actions
self._create_actions()
# create menus
self._create_menus()
def center(self):
qr = self.frameGeometry()
cp = QDesktopWidget().availableGeometry().center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def _init_configuration(self):
config_file = os.path.expanduser('~/.pybp.conf')
if os.path.exists(config_file):
config = ConfigParser.RawConfigParser()
config.read(config_file)
self.window_width = config.getint('width', 'int')
self.window_height = config.getint('height', 'int')
self.orth_scale_factor = config.getint('orth_scale', 'int')
self.grid_scale_factor = config.getint('grid_scale', 'int')
self.window_xpos = config.getint('xpos', 'int')
self.window_ypos = config.getint('ypos', 'int')
self.resize(self.window_width, self.window_height)
self.move(self.window_xpos, self.window_ypos)
self.default_orth_scale_factor = float(self.orth_scale_factor) / 100
self.default_grid_scale_factor = float(self.grid_scale_factor) / 100
else:
self.setWindowState(Qt.WindowMaximized)
self.default_orth_scale_factor = 1.0
self.default_grid_scale_factor = 2.0
def _save_configuration(self):
config_file = os.path.expanduser('~/.pybp.conf')
config = ConfigParser.RawConfigParser()
config.add_section('width')
config.add_section('height')
config.add_section('orth_scale')
config.add_section('grid_scale')
config.add_section('xpos')
config.add_section('ypos')
config.set('width', 'int', self.width())
config.set('height', 'int', self.height())
config.set('xpos', 'int', self.x())
config.set('ypos', 'int', self.y())
if hasattr(self, 'model'):
config.set('orth_scale', 'int', int(self.model.get_scale_factor('orth')*100))
config.set('grid_scale', 'int', int(self.model.get_scale_factor('grid')*100))
else:
config.set('orth_scale', 'int', int(self.default_orth_scale_factor * 100))
config.set('grid_scale', 'int', int(self.default_grid_scale_factor * 100))
with open(config_file, 'wb') as conf:
config.write(conf)
def closeEvent(self, e):
if self.is_save_configure:
self._save_configuration()
e.accept()
def _create_actions(self):
"""
Create actions.
"""
# create a dictionary to store actions info
self._actions = {}
# Open template action
self._actions['add_template'] = QAction(QIcon(os.path.join(
self._icon_dir, 'open.png')),
self.tr("&Open standard volume"),
self)
self._actions['add_template'].setShortcut(self.tr("Ctrl+O"))
self._actions['add_template'].triggered.connect(self._add_template)
self._actions['add_template'].setEnabled(True)
# Add a new image action
self._actions['add_image'] = QAction(QIcon(os.path.join(
self._icon_dir,'add.png')),
self.tr("&Add volume"), self)
self._actions['add_image'].setShortcut(self.tr("Ctrl+A"))
self._actions['add_image'].triggered.connect(self._add_image)
self._actions['add_image'].setEnabled(True)
# Remove an image
self._actions['remove_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'remove.png')),
self.tr("&Remove volume"),
self)
self._actions['remove_image'].setShortcut(self.tr("Ctrl+R"))
self._actions['remove_image'].triggered.connect(self._remove_image)
self._actions['remove_image'].setEnabled(False)
# New image
self._actions['new_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'create.png')),
self.tr("&New volume"), self)
self._actions['new_image'].setShortcut(self.tr("Ctrl+N"))
self._actions['new_image'].triggered.connect(self.__new_image)
self._actions['new_image'].setEnabled(False)
# Save image
self._actions['save_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'save.png')),
self.tr("&Save volume as..."),
self)
self._actions['save_image'].setShortcut(self.tr("Ctrl+S"))
self._actions['save_image'].triggered.connect(self._save_image)
self._actions['save_image'].setEnabled(False)
# Load Label Config
self._actions['ld_lbl'] = QAction('Load Label', self)
self._actions['ld_lbl'].triggered.connect(self._ld_lbl)
self._actions['ld_lbl'].setEnabled(False)
# Load Global Label Config
self._actions['ld_glbl'] = QAction('Load Global Label', self)
self._actions['ld_glbl'].triggered.connect(self._ld_glbl)
self._actions['ld_glbl'].setEnabled(False)
# Close display
self._actions['close'] = QAction(self.tr("Close"), self)
#self._actions['close'].setShortcut(self.tr("Ctrl+W"))
self._actions['close'].triggered.connect(self._close_display)
self._actions['close'].setEnabled(False)
# Quit action
self._actions['quit'] = QAction(QIcon(os.path.join(
self._icon_dir, 'quit.png')),
self.tr("&Quit"), self)
self._actions['quit'].setShortcut(self.tr("Ctrl+Q"))
self._actions['quit'].triggered.connect(self.close)
# Grid view action
self._actions['grid_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'gridview.png')),
self.tr("Lightbox"), self)
self._actions['grid_view'].triggered.connect(self._grid_view)
self._actions['grid_view'].setEnabled(False)
# Orth view action
self._actions['orth_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'orthview.png')),
self.tr("Orthographic"), self)
self._actions['orth_view'].triggered.connect(self._orth_view)
self._actions['orth_view'].setEnabled(False)
# return original size
self._actions['original_view'] = QAction(QIcon(os.path.join(
self._icon_dir,
'original_size.png')),
self.tr("Reset view"), self)
self._actions['original_view'].triggered.connect(self._reset_view)
self._actions['original_view'].setEnabled(False)
# dwhether display the cross hover
self._actions['cross_hover_view'] = QAction(QIcon(os.path.join(
self._icon_dir,
'cross_hover_enable.png')),
self.tr("Disable cross hover"), self)
self._actions['cross_hover_view'].triggered.connect(self._display_cross_hover)
self._actions['cross_hover_view'].setEnabled(False)
#-- generated by zgf
# Binaryzation view action
self._actions['binaryzation'] = QAction(QIcon(os.path.join(
self._icon_dir, 'binaryzation.png')),
self.tr("Binaryzation"), self)
self._actions['binaryzation'].triggered.connect(self._binaryzation)
self._actions['binaryzation'].setEnabled(False)
# Binary_erosion view action
self._actions['binaryerosion'] = QAction(QIcon(os.path.join(
self._icon_dir, 'binary_erosion.png')),
self.tr("Binaryerosion"), self)
self._actions['binaryerosion'].triggered.connect(self._binaryerosion)
self._actions['binaryerosion'].setEnabled(False)
# Binary_dilation view action
self._actions['binarydilation'] = QAction(QIcon(os.path.join(
self._icon_dir, 'binary_dilation.png')),
self.tr("Binarydilation"), self)
self._actions['binarydilation'].triggered.connect(self._binarydilation)
self._actions['binarydilation'].setEnabled(False)
# grey_erosion view action
self._actions['greyerosion'] = QAction(QIcon(os.path.join(
self._icon_dir, 'grey_erosion.png')),
self.tr("Greyerosion"), self)
self._actions['greyerosion'].triggered.connect(self._greyerosion)
self._actions['greyerosion'].setEnabled(False)
# grey_dilation view action
self._actions['greydilation'] = QAction(QIcon(os.path.join(
self._icon_dir, 'grey_dilation.png')),
self.tr("Greydilation"), self)
self._actions['greydilation'].triggered.connect(self._greydilation)
self._actions['greydilation'].setEnabled(False)
# voxel time point curve view action
self._actions['roiorvoxelcurve'] = QAction(QIcon(os.path.join(
self._icon_dir, 'voxel_time_point_curve.png')),
self.tr("Roiorvoxelcurve"), self)
self._actions['roiorvoxelcurve'].triggered.connect(self._roiorvoxelcurve)
self._actions['roiorvoxelcurve'].setEnabled(False)
# three demension intensity view action
self._actions['volumeintensity'] = QAction(QIcon(os.path.join(
self._icon_dir, 'volumeintensity.png')),
self.tr("Volume Intensity"), self)
self._actions['volumeintensity'].triggered.connect(self._volumeintensity)
self._actions['volumeintensity'].setEnabled(False)
#-- generated by zgf
# About software
self._actions['about_pybp'] = QAction(self.tr("About FreeROI"), self)
self._actions['about_pybp'].triggered.connect(self._about_pybp)
# About Qt
self._actions['about_qt'] = QAction(QIcon(os.path.join(
self._icon_dir, 'qt.png')),
self.tr("About Qt"), self)
self._actions['about_qt'].triggered.connect(qApp.aboutQt)
# Hand
self._actions['hand'] = QAction(QIcon(os.path.join(self._icon_dir,
'hand.png')),
self.tr("Hand"), self)
self._actions['hand'].triggered.connect(self._hand_enable)
self._actions['hand'].setCheckable(True)
self._actions['hand'].setChecked(False)
self._actions['hand'].setEnabled(False)
# Cursor
self._actions['cursor'] = QAction(QIcon(os.path.join(
self._icon_dir, 'cursor.png')),
self.tr("Cursor"), self)
self._actions['cursor'].triggered.connect(self._cursor_enable)
self._actions['cursor'].setCheckable(True)
self._actions['cursor'].setChecked(True)
self._actions['cursor'].setEnabled(True)
# Brush
self._actions['brush'] = QAction(QIcon(os.path.join(
self._icon_dir, 'brush.png')),
self.tr("Voxel Edit"), self)
self._actions['brush'].triggered.connect(self._brush_enable)
self._actions['brush'].setCheckable(True)
self._actions['brush'].setChecked(False)
# ROI Brush
self._actions['roibrush'] = QAction(QIcon(os.path.join(
self._icon_dir, 'roibrush.png')),
self.tr("ROI Edictor"), self)
self._actions['roibrush'].triggered.connect(self._roibrush_enable)
self._actions['roibrush'].setCheckable(True)
self._actions['roibrush'].setChecked(False)
self._update_brush()
self._actions['roidialog'] = QAction(QIcon(os.path.join(
self._icon_dir,'roitool.png')),
self.tr("ROI Toolset"), self)
self._actions['roidialog'].setCheckable(True)
self._actions['roidialog'].triggered.connect(self._roidialog_enable)
# Undo
self._actions['undo'] = QAction(QIcon(os.path.join(
self._icon_dir, 'undo.png')),
self.tr("Undo"), self)
self._actions['undo'].triggered.connect(self._undo)
# Redo
self._actions['redo'] = QAction(QIcon(os.path.join(
self._icon_dir, 'redo.png')),
self.tr("Redo"), self)
self._actions['redo'].triggered.connect(self._redo)
# sphere and cube roi
self._actions['regular_roi'] = QAction(QIcon(os.path.join(
self._icon_dir, 'sphere_and_cube.png')),
self.tr("Regular ROI"), self)
self._actions['regular_roi'].triggered.connect(self._regular_roi)
self._actions['regular_roi'].setEnabled(False)
# Intersect
self._actions['intersect'] = QAction(QIcon(os.path.join(
self._icon_dir, 'intersect.png')),
self.tr("Intersection"), self)
self._actions['intersect'].triggered.connect(self._intersect)
self._actions['intersect'].setEnabled(False)
# ROI to Interface
self._actions['r2i'] = QAction(QIcon(os.path.join(
self._icon_dir, 'r2i.png')),
self.tr("ROI2Interface"), self)
self._actions['r2i'].triggered.connect(self._r2i)
self._actions['r2i'].setEnabled(False)
# Auto Labeling
self._actions['auto_label'] = QAction(QIcon(os.path.join(
self._icon_dir, 'auto_labeling.png')),
self.tr("Auto Labeling"), self)
self._actions['auto_label'].triggered.connect(self._auto_label)
self._actions['auto_label'].setEnabled(False)
# Open
self._actions['open'] = QAction(QIcon(os.path.join(
self._icon_dir, 'opening.png')),
self.tr("Opening"), self)
self._actions['open'].setShortcut("Ctrl+P")
self._actions['open'].triggered.connect(self._open)
self._actions['open'].setEnabled(False)
def _add_toolbar(self):
"""
Add toolbar.
"""
# Initialize a spinbox for zoom-scale selection
self._spinbox = QSpinBox()
self._spinbox.setMaximum(500)
self._spinbox.setMinimum(50)
self._spinbox.setSuffix('%')
self._spinbox.setSingleStep(10)
self._spinbox.setValue(self.default_grid_scale_factor * 100)
self._spinbox.valueChanged.connect(self._set_scale_factor)
# Add a toolbar
#self._toolbar = QToolBar()
self._toolbar = self.addToolBar("Tools")
self._toolbar.setIconSize(QSize(38,38))
# Add file actions
self._toolbar.addAction(self._actions['add_image'])
self._toolbar.addAction(self._actions['remove_image'])
self._toolbar.addAction(self._actions['new_image'])
self._toolbar.addAction(self._actions['save_image'])
# Add view actions
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['grid_view'])
self._toolbar.addAction(self._actions['orth_view'])
self._toolbar.addAction(self._actions['original_view'])
self._toolbar.addAction(self._actions['cross_hover_view'])
# Add draw tools
# self._toolbar.addSeparator()
# self._toolbar.addAction(self._actions['hand'])
# self._toolbar.addAction(self._actions['cursor'])
# self._toolbar.addAction(self._actions['brush'])
# self._toolbar.addAction(self._actions['roibrush'])
# Add undo redo
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['undo'])
self._toolbar.addAction(self._actions['redo'])
# Add automatic tools
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['regular_roi'])
self._toolbar.addAction(self._actions['intersect'])
self._toolbar.addAction(self._actions['open'])
self._toolbar.addAction(self._actions['r2i'])
self._toolbar.addAction(self._actions['roidialog'])
self._toolbar.addSeparator()
self._toolbar.addWidget(self._spinbox)
#self.addToolBar(self._toolbar)
def _set_scale_factor(self, value):
"""
Set scale factor.
"""
value = float(value) / 100
self.model.set_scale_factor(value, self.image_view.display_type())
def _add_template(self):
"""
Open a dialog window and select a template file.
"""
template_dir = os.path.join(self.label_path, 'standard',
'MNI152_T1_2mm_brain.nii.gz')
template_name = QFileDialog.getOpenFileName(
self,
'Open standard file',
template_dir,
'Nifti files (*.nii.gz *.nii)')
if not template_name.isEmpty():
template_path = str(template_name)
self._add_img(template_path)
def _add_image(self):
"""
Add new item.
"""
if self._temp_dir == None:
temp_dir = QDir.currentPath()
else:
temp_dir = self._temp_dir
file_name = QFileDialog.getOpenFileName(self,
'Add new file',
temp_dir,
'Nifti files (*.nii.gz *.nii)')
if not file_name.isEmpty():
file_path = str(file_name)
self._add_img(file_path)
def _add_img(self, source, name=None, header=None, view_min=None,
view_max=None, alpha=255, colormap='gray'):
"""
Add image.
"""
# If model is NULL, then re-initialize it.
if not self.model:
self._init_label_config_center()
self.model = VolumeListModel([], self._label_config_center)
self.model.set_scale_factor(self.default_grid_scale_factor, 'grid')
self.model.set_scale_factor(self.default_orth_scale_factor, 'orth')
self.painter_status = PainterStatus(ViewSettings())
# Save previous opened directory (except `standard` directory)
file_path = str(source)
temp_dir = os.path.dirname(file_path)
if not os.path.samefile(temp_dir, os.path.join(self.label_path, 'standard')):
self._temp_dir = temp_dir
if self.model.addItem(file_path, None, name, header, view_min,
view_max, alpha, colormap):
# Take different acions in different case.
# If only one data in VolumeList, then initialize views.
if self.model.rowCount() == 1:
# initialize views
self.list_view = LayerView(self._label_config_center)
self.list_view.setModel(self.model)
self.image_view = GridView(self.model, self.painter_status)
# initialize display layout
central_widget = QWidget()
layout = QHBoxLayout()
central_widget.setLayout(layout)
central_widget.layout().addWidget(self.list_view)
central_widget.layout().addWidget(self.image_view)
self.setCentralWidget(central_widget)
# add a toolbar
self._add_toolbar()
#self.setUnifiedTitleAndToolBarOnMac(True)
# change button status
self._actions['save_image'].setEnabled(True)
self._actions['ld_lbl'].setEnabled(True)
self._actions['ld_glbl'].setEnabled(True)
self._actions['new_image'].setEnabled(True)
self._actions['close'].setEnabled(True)
self._actions['orth_view'].setEnabled(True)
self._actions['cross_hover_view'].setEnabled(True)
self._actions['original_view'].setEnabled(True)
self._actions['open'].setEnabled(True)
self._actions['regular_roi'].setEnabled(True)
self._actions['r2i'].setEnabled(True)
self._actions['binaryzation'].setEnabled(True)
self._actions['binarydilation'].setEnabled(True)
self._actions['binaryerosion'].setEnabled(True)
self._actions['greydilation'].setEnabled(True)
self._actions['greyerosion'].setEnabled(True)
self._actions['roiorvoxelcurve'].setEnabled(True);
self._actions['volumeintensity'].setEnabled(True);
self._actions['undo'].setEnabled(False)
self._actions['redo'].setEnabled(False)
# connect signals with slots
self.list_view.current_changed.connect(self._update_undo)
self.list_view.current_changed.connect(self._update_redo)
self.model.undo_stack_changed.connect(self._update_undo)
self.model.redo_stack_changed.connect(self._update_redo)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
# set crosshair as the center of the data
self.model.set_cross_pos([self.model.getY()/2,
self.model.getX()/2,
self.model.getZ()/2])
## Enable cursor tracking
# self.list_view._list_view.selectionModel().currentChanged.connect(
# self._switch_cursor_status)
elif self.model.rowCount() > 1:
self._actions['remove_image'].setEnabled(True)
self._actions['intersect'].setEnabled(True)
self._actions['auto_label'].setEnabled(True)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
self.is_save_configure = True
else:
QMessageBox.information(self,'FreeROI', 'Cannot load ' + "filename" + '.')
def __new_image(self):
self._new_image()
def _new_image(self, data=None, name=None, colormap=None):
"""
Create a new volume for brain parcellation.
"""
if colormap is None:
colormap = self._label_config_center.get_first_label_config()
self.model.new_image(data, name, None, colormap)
self.list_view.setCurrentIndex(self.model.index(0))
# change button status
self._actions['remove_image'].setEnabled(True)
self._actions['intersect'].setEnabled(True)
self._actions['regular_roi'].setEnabled(True)
self._actions['r2i'].setEnabled(True)
self._actions['auto_label'].setEnabled(True)
self._actions['open'].setEnabled(True)
def new_image_action(self):
self._actions['remove_image'].setEnabled(True)
self._actions['intersect'].setEnabled(True)
self._actions['r2i'].setEnabled(True)
self._actions['auto_label'].setEnabled(True)
self._actions['open'].setEnabled(True)
def _remove_image(self):
"""
Remove current image.
"""
row = self.list_view.currentRow()
self.model.delItem(row)
if self.model.rowCount() == 1:
self._actions['remove_image'].setEnabled(False)
self._actions['intersect'].setEnabled(False)
self._actions['regular_roi'].setEnabled(False)
self._actions['r2i'].setEnabled(False)
self._actions['auto_label'].setEnabled(False)
self._actions['open'].setEnabled(False)
def _save_image(self):
"""
Save image as a nifti file.
"""
index = self.model.currentIndex()
if self._temp_dir == None:
temp_dir = str(QDir.currentPath())
else:
temp_dir = self._temp_dir
file_path = os.path.join(temp_dir,
str(self.model.data(index, Qt.DisplayRole))+'.nii.gz')
path = QFileDialog.getSaveFileName(
self,
'Save image as...',
file_path,
'Nifti files (*.nii.gz *.nii)')
if not path.isEmpty():
self._temp_dir = os.path.dirname(str(path))
self.model._data[index.row()].save2nifti(str(path))
def _close_display(self):
"""
Close current display.
"""
self.setCentralWidget(QWidget())
self._set_scale_factor(self.default_grid_scale_factor)
self.removeToolBar(self._toolbar)
self.model = None
self._actions['add_template'].setEnabled(True)
self._actions['add_image'].setEnabled(True)
self._actions['remove_image'].setEnabled(False)
self._actions['new_image'].setEnabled(False)
self._actions['save_image'].setEnabled(False)
self._actions['ld_glbl'].setEnabled(False)
self._actions['ld_lbl'].setEnabled(False)
self._actions['close'].setEnabled(False)
self._actions['intersect'].setEnabled(False)
self._actions['regular_roi'].setEnabled(False)
self._actions['r2i'].setEnabled(False)
self._actions['auto_label'].setEnabled(False)
self._actions['open'].setEnabled(False)
self._actions['grid_view'].setEnabled(False)
self._actions['orth_view'].setEnabled(False)
self._actions['original_view'].setEnabled(False)
self._actions['binaryzation'].setEnabled(False)
self._actions['binarydilation'].setEnabled(False)
self._actions['binaryerosion'].setEnabled(False)
self._actions['greydilation'].setEnabled(False)
self._actions['greyerosion'].setEnabled(False)
self._actions['roiorvoxelcurve'].setEnabled(False)
self._actions['volumeintensity'].setEnabled(False)
def _about_pybp(self):
"""
About software.
"""
QMessageBox.about(self,
self.tr("About FreeROI"),
self.tr("<p>the <b>FreeROI</b> could make ROI manually"
"and automatically.</p>"
"<p>Version: " + __version__ + "</p>"))
def _create_menus(self):
"""Create menus."""
self.file_menu = self.menuBar().addMenu(self.tr("File"))
self.file_menu.addAction(self._actions['add_image'])
self.file_menu.addAction(self._actions['add_template'])
self.file_menu.addAction(self._actions['save_image'])
self.file_menu.addSeparator()
self.file_menu.addAction(self._actions['ld_lbl'])
self.file_menu.addAction(self._actions['ld_glbl'])
self.file_menu.addSeparator()
self.file_menu.addAction(self._actions['close'])
self.file_menu.addAction(self._actions['quit'])
self.volume_menu = self.menuBar().addMenu(self.tr("Volume"))
self.volume_menu.addAction(self._actions['new_image'])
self.volume_menu.addAction(self._actions['remove_image'])
self.view_menu = self.menuBar().addMenu(self.tr("View"))
self.view_menu.addAction(self._actions['grid_view'])
self.view_menu.addAction(self._actions['orth_view'])
self.view_menu.addAction(self._actions['original_view'])
self.view_menu.addAction(self._actions['cross_hover_view'])
self.tool_menu = self.menuBar().addMenu(self.tr("Tools"))
self.tool_menu.addAction(self._actions['regular_roi'])
self.tool_menu.addAction(self._actions['intersect'])
self.tool_menu.addAction(self._actions['r2i'])
self.tool_menu.addAction(self._actions['auto_label'])
self.tool_menu.addAction(self._actions['open'])
self.tool_menu.addAction(self._actions['binaryzation'])
self.tool_menu.addAction(self._actions['binarydilation'])
self.tool_menu.addAction(self._actions['binaryerosion'])
self.tool_menu.addAction(self._actions['greydilation'])
self.tool_menu.addAction(self._actions['greyerosion'])
self.tool_menu.addAction(self._actions['roiorvoxelcurve'])
self.tool_menu.addAction(self._actions['volumeintensity'])
self.help_menu = self.menuBar().addMenu(self.tr("Help"))
self.help_menu.addAction(self._actions['about_pybp'])
self.help_menu.addAction(self._actions['about_qt'])
def _cursor_enable(self):
"""
Cursor enabled.
"""
if self._actions['cursor'].isChecked():
self._actions['brush'].setChecked(False)
self._actions['roibrush'].setChecked(False)
self._actions['cursor'].setChecked(True)
if isinstance(self.image_view, OrthView):
self._actions['hand'].setChecked(False)
self.painter_status.set_draw_settings(ViewSettings())
if hasattr(self, 'roidialog'):
self._roidialog_disable()
self.image_view.set_label_mouse_tracking(True)
else:
self._actions['cursor'].setChecked(True)
def _brush_enable(self):
"""
Brush enabled.
"""
if self._actions['brush'].isChecked():
self._actions['cursor'].setChecked(False)
self._actions['roibrush'].setChecked(False)
self._actions['brush'].setChecked(True)
if isinstance(self.image_view, OrthView):
self._actions['hand'].setChecked(False)
if hasattr(self, 'roidialog'):
self._roidialog_disable()
self._label_config_center.set_is_roi_edit(False)
self.painter_status.set_draw_settings(self._label_config_center)
self.image_view.set_label_mouse_tracking(False)
else:
self._actions['brush'].setChecked(True)
def _roibrush_enable(self):
"""
ROI brush enabled.
"""
if self._actions['roibrush'].isChecked():
self._actions['cursor'].setChecked(False)
self._actions['brush'].setChecked(False)
self._actions['roibrush'].setChecked(True)
if hasattr(self, 'roidialog'):
self._roidialog_disable()
self._label_config_center.set_is_roi_edit(True)
self.painter_status.set_draw_settings(self._label_config_center)
self.image_view.set_label_mouse_tracking(False)
else:
self._actions['roibrush'].setChecked(True)
def _roidialog_enable(self):
if not hasattr(self, 'roidialog'):
self._actions['cursor'].setChecked(False)
self._actions['brush'].setChecked(False)
self._actions['roibrush'].setChecked(False)
self._actions['roidialog'].setChecked(True)
self.roidialog = ROIDialog(self.model)
self.list_view._list_view.selectionModel().currentChanged.connect(
self.roidialog.clear_rois)
self.painter_status.set_draw_settings(self.roidialog)
self.roidialog.finished.connect(self._roidialog_disable)
self.roidialog.show()
self._actions['roidialog'].setChecked(True)
def _roidialog_disable(self):
if hasattr(self, 'roidialog'):
del self.roidialog
self._actions['roidialog'].setChecked(False)
def _hand_enable(self):
"""
Hand enabled.
"""
if self._actions['hand'].isChecked():
self._actions['cursor'].setChecked(False)
self._actions['brush'].setChecked(False)
#self._actions['eraser'].setChecked(False)
self._actions['hand'].setChecked(True)
self.painter_status.set_draw_settings(MoveSettings())
if hasattr(self, 'label_dialog'):
self.label_dialog.done(0)
del self.label_dialog
if hasattr(self, 'eraser_dialog'):
self.eraser_dialog.done(0)
del self.eraser_dialog
if hasattr(self, 'roilabel_dialog'):
self.roilabel_dialog.done(0)
del self.roilabel_dialog
if hasattr(self, 'roieraser_dialog'):
self.roieraser_dialog.done(0)
del self.roieraser_dialog
self.image_view.set_label_mouse_tracking(True)
else:
self._actions['hand'].setChecked(True)
def _switch_cursor_status(self):
self._actions['cursor'].setChecked(True)
self._cursor_enable()
def _regular_roi(self):
regular_roi_dialog = RegularROIDialog(self.model, self)
regular_roi_dialog.exec_()
#def _repaint_slices(self):
# self.model.update_current_rgba()
#def _roieraser_enable(self):
# """
# ROI Eraser enabled.
# """
# if self._actions['roieraser'].isChecked():
# self._actions['cursor'].setChecked(False)
# self._actions['brush'].setChecked(False)
# self._actions['eraser'].setChecked(False)
# self._actions['roibrush'].setChecked(False)
# self._actions['roieraser'].setChecked(True)
# if hasattr(self, 'label_dialog'):
# self.label_dialog.done(0)
# del self.label_dialog
# if hasattr(self, 'eraser_dialog'):
# self.eraser_dialog.done(0)
# del self.eraser_dialog
# if hasattr(self, 'roilabel_dialog'):
# self.roilabel_dialog.done(0)
# del self.roilabel_dialog
# self.roieraser_dialog = ROIEraserDialog(self)
# self.roieraser_dialog.show()
# self.painter_status.set_draw_settings(self.roieraser_dialog)
# self.image_view.set_label_mouse_tracking(False)
# else:
# self._actions['roieraser'].setChecked(True)
def _update_undo(self):
if self.model.current_undo_available():
self._actions['undo'].setEnabled(True)
else:
self._actions['undo'].setEnabled(False)
def _update_redo(self):
if self.model.current_redo_available():
self._actions['redo'].setEnabled(True)
else:
self._actions['redo'].setEnabled(False)
#def _current_layer_xyzvl_changed(self):
# """
# modified by dxb, need rethink the code.
# """
# self.image_view.xyz_updated.connect(self._update_xyzvl)
# self.image_view.xyz_updated.emit([self.model.get_current_pos()[1],
# self.model.get_current_pos()[0],
# self.model.get_current_pos()[2]])
#def _update_xyzvl(self, xyz):
# xyzvl = dict(zip(['y', 'x', 'z'], map(str, xyz)))
# value = self.model.get_current_value(xyz)
# xyzvl['value'] = str(value)
# xyzvl['label'] = self.model.get_current_value_label(int(value))
# self.list_view.update_xyzvl(xyzvl)
def _init_label_config_center(self):
lbl_path = os.path.join(self.label_config_dir,
'*.' + self.label_config_suffix)
label_configs = glob.glob(lbl_path)
self.label_configs = map(LabelConfig, label_configs)
self._label_config_center = LabelConfigCenter(self.label_configs)
# Label Config Changed
self._label_config_center.label_config_changed_signal().connect(self._update_brush)
def _init_label_config(self):
label_path = os.path.join(self.label_path, self.config_file)
if os.path.isfile(label_path):
cwd_config = label_path
else:
cwd = os.getcwd()
cwd_config = os.path.join(cwd, self.config_file)
if not os.path.isfile(cwd_config):
os.mknod(cwd_config)
self.label_config = LabelConfig(cwd_config)
def _get_label_config(self, file_path):
"""
Get label config file.
"""
# Get label config file
dir = os.path.dirname(file_path)
file = os.path.basename(file_path)
split_list = file.split('.')
nii_index = split_list.index('nii')
file = ''.join(split_list[:nii_index])
config_file = os.path.join(file, 'lbl')
if os.path.isfile(config_file):
label_config = LabelConfig(config_file, False)
else:
label_config = self.label_config
return label_config
def _undo(self):
self.model.undo_current_image()
def _redo(self):
self.model.redo_current_image()
def _intersect(self):
"""
Make a intersection between two layers.
"""
new_dialog = IntersectDialog(self.model)
new_dialog.exec_()
def _r2i(self):
new_dialog = Roi2gwmiDialog(self.model)
new_dialog.exec_()
def _auto_label(self):
auto_dialog = AutoLabelDialog(self.model)
auto_dialog.exec_()
def _open(self):
new_dialog = OpenDialog(self.model)
new_dialog.exec_()
def _ld_lbl(self):
file_name = QFileDialog.getOpenFileName(self,
'Load Label File',
QDir.currentPath(),
"Label files (*.lbl)")
if file_name:
label_config = LabelConfig(str(file_name), False)
self.model.set_cur_label(label_config)
def _ld_glbl(self):
file_name = QFileDialog.getOpenFileName(self,
'Load Label File',
QDir.currentPath(),
"Label files (*.lbl)")
if file_name:
label_config = LabelConfig(str(file_name), True)
self.model.set_global_label(label_config)
def _grid_view(self):
"""
Grid view option.
"""
self._actions['grid_view'].setEnabled(False)
self._actions['orth_view'].setEnabled(True)
self._actions['hand'].setEnabled(False)
self._actions['cursor'].trigger()
self.centralWidget().layout().removeWidget(self.image_view)
self.image_view.set_display_type('grid')
self.model.scale_changed.disconnect()
self.model.repaint_slices.disconnect()
self.model.cross_pos_changed.disconnect(self.image_view.update_cross_pos)
self.image_view.deleteLater()
self._spinbox.setValue(100 * self.model.get_scale_factor('grid'))
self.image_view = GridView(self.model, self.painter_status,
self._gridview_vertical_scrollbar_position)
self.centralWidget().layout().addWidget(self.image_view)
def _orth_view(self):
"""
Orth view option.
"""
self._actions['orth_view'].setEnabled(False)
self._actions['grid_view'].setEnabled(True)
self._actions['hand'].setEnabled(True)
self._actions['cursor'].trigger()
self._gridview_vertical_scrollbar_position = \
self.image_view.get_vertical_srollbar_position()
self.centralWidget().layout().removeWidget(self.image_view)
self.image_view.set_display_type('orth')
self.model.scale_changed.disconnect()
self.model.repaint_slices.disconnect()
self.model.cross_pos_changed.disconnect(self.image_view.update_cross_pos)
self.image_view.deleteLater()
self._spinbox.setValue(100 * self.model.get_scale_factor('orth'))
self.image_view = OrthView(self.model, self.painter_status)
self.centralWidget().layout().addWidget(self.image_view)
def _display_cross_hover(self):
if self.model._display_cross:
self.model.set_cross_status(False)
self._actions['cross_hover_view'].setText('Enable cross hover')
self._actions['cross_hover_view'].setIcon(QIcon(os.path.join(self._icon_dir,'cross_hover_disable.png')))
else:
self.model.set_cross_status(True)
self._actions['cross_hover_view'].setText('Disable cross hover')
self._actions['cross_hover_view'].setIcon(QIcon(os.path.join(self._icon_dir,'cross_hover_enable.png')))
def _reset_view(self):
"""
Reset view parameters.
"""
if self.image_view.display_type() == 'orth':
if not self.model.get_scale_factor('orth') == \
self.default_orth_scale_factor:
self._spinbox.setValue(100 * self.default_orth_scale_factor)
self.image_view.reset_view()
elif self.image_view.display_type() == 'grid':
if not self.model.get_scale_factor('grid') == \
self.default_grid_scale_factor:
self._spinbox.setValue(100 * self.default_grid_scale_factor)
def _update_brush(self):
if self._label_config_center.is_drawing_valid():
self._actions['brush'].setEnabled(True)
self._actions['roibrush'].setEnabled(True)
else:
self._actions['brush'].setEnabled(False)
self._actions['roibrush'].setEnabled(False)
def _binaryzation(self):
binaryzation_dialog = BinaryzationDialog(self.model)
binaryzation_dialog.exec_()
def _binaryerosion(self):
binaryerosion_dialog = BinaryerosionDialog(self.model)
binaryerosion_dialog.exec_()
def _binarydilation(self):
binarydilation_dialog = BinarydilationDialog(self.model)
binarydilation_dialog.exec_()
def _greyerosion(self):
greyerosiondialog = GreyerosionDialog(self.model)
greyerosiondialog.exec_()
def _roiorvoxelcurve(self):
self.ROI_or_voxel_dialog = ROIOrVoxelCurveDialog(self.model)
self.list_view.current_changed.connect(self.ROI_or_voxel_dialog.listview_current_index_changed)
self.ROI_or_voxel_dialog.exec_()
def _volumeintensity(self):
self.volume_intensity = VolumeIntensityDialog(self.model)
self.list_view.current_changed.connect(self.volume_intensity._plot)
self.volume_intensity.setModal(False)
self.volume_intensity.setWindowFlags(Qt.WindowStaysOnTopHint)
self.volume_intensity.show()
def _greydilation(self):
greydilation_dialog = GreydilationDialog(self.model)
greydilation_dialog.exec_()
class BpMainWindow(QMainWindow):
"""Class BpMainWindow provides UI interface of FreeROI.
Example:
--------
>>> from PyQt4.QtGui import QApplication
>>> import main
>>> app = QApplication([])
>>> win = main.BpMainWindow()
......
>>> win.show()
>>> app.exec_()
"""
def __init__(self, parent=None):
"""
Initialize an instance of BpMainWindow.
"""
# Inherited from QMainWindow
if sys.platform == 'darwin':
# Workaround for Qt issue on OS X that causes QMainWindow to
# hide when adding QToolBar, see
# https://bugreports.qt-project.org/browse/QTBUG-4300
super(BpMainWindow, self).__init__(parent,
Qt.MacWindowToolBarButtonHint)
else:
super(BpMainWindow, self).__init__(parent)
# temporary variable
self._temp_dir = None
self.is_save_configure = False
# pre-define a model variable
self.model = None
def config_extra_settings(self, data_dir):
"""
Set data directory and update some configurations.
"""
# load data directory configuration
self.label_path = data_dir
self.label_config_dir = os.path.join(self.label_path, 'labelconfig')
self.label_config_suffix = 'lbl'
# set icon configuration
self._icon_dir = get_icon_dir()
# set window title
self.setWindowTitle('FreeROI')
#self.resize(1280, 1000)
self.center()
# set window icon
self.setWindowIcon(QIcon(os.path.join(self._icon_dir,
'logo.png')))
self._init_configuration()
# create actions
self._create_actions()
# create menus
self._create_menus()
def center(self):
"""
Display main window in the center of screen
"""
qr = self.frameGeometry()
cp = QDesktopWidget().availableGeometry().center()
qr.moveCenter(cp)
self.move(qr.topLeft())
def _init_configuration(self):
"""
Load configuration for GUI.
"""
config_file = os.path.expanduser('~/.pybp.conf')
if os.path.exists(config_file):
config = ConfigParser.RawConfigParser()
config.read(config_file)
self.window_width = config.getint('width', 'int')
self.window_height = config.getint('height', 'int')
self.orth_scale_factor = config.getint('orth_scale', 'int')
self.grid_scale_factor = config.getint('grid_scale', 'int')
self.window_xpos = config.getint('xpos', 'int')
self.window_ypos = config.getint('ypos', 'int')
self.resize(self.window_width, self.window_height)
self.move(self.window_xpos, self.window_ypos)
self.default_orth_scale_factor = float(self.orth_scale_factor) / 100
self.default_grid_scale_factor = float(self.grid_scale_factor) / 100
else:
self.setWindowState(Qt.WindowMaximized)
self.default_orth_scale_factor = 1.0
self.default_grid_scale_factor = 2.0
def _save_configuration(self):
"""
Save GUI configuration to a file.
"""
config_file = os.path.expanduser('~/.pybp.conf')
config = ConfigParser.RawConfigParser()
config.add_section('width')
config.add_section('height')
config.add_section('orth_scale')
config.add_section('grid_scale')
config.add_section('xpos')
config.add_section('ypos')
config.set('width', 'int', self.width())
config.set('height', 'int', self.height())
config.set('xpos', 'int', self.x())
config.set('ypos', 'int', self.y())
if hasattr(self, 'model') and isinstance(self.model, VolumeListModel):
config.set('orth_scale', 'int',
int(self.model.get_scale_factor('orth')*100))
config.set('grid_scale', 'int',
int(self.model.get_scale_factor('grid')*100))
else:
config.set('orth_scale', 'int',
int(self.default_orth_scale_factor * 100))
config.set('grid_scale', 'int',
int(self.default_grid_scale_factor * 100))
with open(config_file, 'wb') as conf:
config.write(conf)
def closeEvent(self, e):
if self.is_save_configure:
self._save_configuration()
e.accept()
def _create_actions(self):
"""
Create actions.
"""
# create a dictionary to store actions info
self._actions = {}
# Open template action
self._actions['add_template'] = QAction(QIcon(os.path.join(
self._icon_dir, 'open.png')),
self.tr("&Open standard volume"),
self)
self._actions['add_template'].setShortcut(self.tr("Ctrl+O"))
self._actions['add_template'].triggered.connect(self._add_template)
self._actions['add_template'].setEnabled(True)
# Add a new image action
self._actions['add_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'add.png')),
self.tr("&Add volume"),
self)
self._actions['add_image'].setShortcut(self.tr("Ctrl+A"))
self._actions['add_image'].triggered.connect(self._add_image)
self._actions['add_image'].setEnabled(True)
# Remove an image
self._actions['remove_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'remove.png')),
self.tr("&Remove volume"),
self)
self._actions['remove_image'].setShortcut(self.tr("Ctrl+R"))
self._actions['remove_image'].triggered.connect(self._remove_image)
self._actions['remove_image'].setEnabled(False)
# New image
self._actions['new_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'create.png')),
self.tr("&New volume"),
self)
self._actions['new_image'].setShortcut(self.tr("Ctrl+N"))
self._actions['new_image'].triggered.connect(self.__new_image)
self._actions['new_image'].setEnabled(False)
# Save image
self._actions['save_image'] = QAction(QIcon(os.path.join(
self._icon_dir, 'save.png')),
self.tr("&Save volume as..."),
self)
self._actions['save_image'].setShortcut(self.tr("Ctrl+S"))
self._actions['save_image'].triggered.connect(self._save_image)
self._actions['save_image'].setEnabled(False)
## Load Label Config
#self._actions['ld_lbl'] = QAction('Load Label', self)
#self._actions['ld_lbl'].triggered.connect(self._ld_lbl)
#self._actions['ld_lbl'].setEnabled(False)
## Load Global Label Config
#self._actions['ld_glbl'] = QAction('Load Global Label', self)
#self._actions['ld_glbl'].triggered.connect(self._ld_glbl)
#self._actions['ld_glbl'].setEnabled(False)
# Close display
self._actions['close'] = QAction(self.tr("Close"), self)
self._actions['close'].setShortcut(self.tr("Ctrl+W"))
self._actions['close'].triggered.connect(self._close_display)
self._actions['close'].setEnabled(False)
# Quit action
self._actions['quit'] = QAction(QIcon(os.path.join(
self._icon_dir, 'quit.png')),
self.tr("&Quit"),
self)
self._actions['quit'].setShortcut(self.tr("Ctrl+Q"))
self._actions['quit'].triggered.connect(self.close)
# Grid view action
self._actions['grid_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'gridview.png')),
self.tr("Lightbox"),
self)
self._actions['grid_view'].triggered.connect(self._grid_view)
self._actions['grid_view'].setEnabled(False)
# Orth view action
self._actions['orth_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'orthview.png')),
self.tr("Orthographic"),
self)
self._actions['orth_view'].triggered.connect(self._orth_view)
self._actions['orth_view'].setEnabled(False)
# return original size
self._actions['original_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'original_size.png')),
self.tr("Reset view"),
self)
self._actions['original_view'].triggered.connect(self._reset_view)
self._actions['original_view'].setEnabled(False)
# whether display the cross hover
self._actions['cross_hover_view'] = QAction(QIcon(os.path.join(
self._icon_dir, 'cross_hover_enable.png')),
self.tr("Disable cross hover"),
self)
self._actions['cross_hover_view'].triggered.connect(
self._display_cross_hover)
self._actions['cross_hover_view'].setEnabled(False)
# Binaryzation view action
self._actions['binarization'] = QAction(QIcon(os.path.join(
self._icon_dir, 'binarization.png')),
self.tr("Binarization"),
self)
self._actions['binarization'].triggered.connect(self._binarization)
self._actions['binarization'].setEnabled(False)
# Intersection action
self._actions['intersect'] = QAction(QIcon(os.path.join(
self._icon_dir, 'intersect.png')),
self.tr("Intersection"),
self)
self._actions['intersect'].triggered.connect(self._intersect)
self._actions['intersect'].setEnabled(False)
# Extract mean time course
self._actions['meants'] = QAction(QIcon(os.path.join(self._icon_dir,
'voxel_curve.png')),
self.tr("Extract Mean Time Course"),
self)
self._actions['meants'].triggered.connect(self._meants)
self._actions['meants'].setEnabled(False)
# Voxel Stats
self._actions['voxelstats'] = QAction(self.tr("Voxel number stats"),
self)
self._actions['voxelstats'].triggered.connect(self._voxelstats)
self._actions['voxelstats'].setEnabled(False)
# Local Max action
self._actions['localmax'] = QAction(QIcon(os.path.join(
self._icon_dir, 'localmax.png')),
self.tr("Local Max"),
self)
self._actions['localmax'].triggered.connect(self._local_max)
self._actions['localmax'].setEnabled(False)
# Inversion action
self._actions['inverse'] = QAction(QIcon(os.path.join(
self._icon_dir, 'inverse.icon')),
self.tr("Inversion"),
self)
self._actions['inverse'].triggered.connect(self._inverse)
self._actions['inverse'].setEnabled(False)
# Smoothing action
self._actions['smoothing'] = QAction(QIcon(os.path.join(
self._icon_dir, 'smoothing.png')),
self.tr("Smoothing"),
self)
self._actions['smoothing'].triggered.connect(self._smooth)
self._actions['smoothing'].setEnabled(False)
# Region Growing action
self._actions['region_grow'] = QAction(QIcon(os.path.join(
self._icon_dir, 'grow.png')),
self.tr("Region Growing"),
self)
self._actions['region_grow'].triggered.connect(self._region_grow)
self._actions['region_grow'].setEnabled(False)
# Watershed action
self._actions['watershed'] = QAction(QIcon(os.path.join(
self._icon_dir, 'watershed.png')),
self.tr("Watershed"),
self)
self._actions['watershed'].triggered.connect(self._watershed)
self._actions['watershed'].setEnabled(False)
# Cluster action
self._actions['cluster'] = QAction(QIcon(os.path.join(
self._icon_dir, 'cluster.png')),
self.tr("Cluster"),
self)
self._actions['cluster'].triggered.connect(self._cluster)
self._actions['cluster'].setEnabled(False)
# Opening
self._actions['opening'] = QAction(self.tr("Opening"), self)
self._actions['opening'].triggered.connect(self._opening)
self._actions['opening'].setEnabled(False)
# Binary_erosion view action
self._actions['binaryerosion'] = QAction(self.tr("Binary Erosion"),
self)
self._actions['binaryerosion'].triggered.connect(self._binaryerosion)
self._actions['binaryerosion'].setEnabled(False)
# Binary_dilation view action
self._actions['binarydilation'] = QAction(self.tr("Binary Dilation"),
self)
self._actions['binarydilation'].triggered.connect(self._binarydilation)
self._actions['binarydilation'].setEnabled(False)
# grey_erosion view action
self._actions['greyerosion'] = QAction(self.tr("Grey Erosion"),
self)
self._actions['greyerosion'].triggered.connect(self._greyerosion)
self._actions['greyerosion'].setEnabled(False)
# grey_dilation view action
self._actions['greydilation'] = QAction(self.tr("Grey Dilation"),
self)
self._actions['greydilation'].triggered.connect(self._greydilation)
self._actions['greydilation'].setEnabled(False)
# About software
self._actions['about_pybp'] = QAction(self.tr("About FreeROI"), self)
self._actions['about_pybp'].triggered.connect(self._about_pybp)
# About Qt
self._actions['about_qt'] = QAction(QIcon(os.path.join(
self._icon_dir, 'qt.png')),
self.tr("About Qt"),
self)
self._actions['about_qt'].triggered.connect(qApp.aboutQt)
# Hand
self._actions['hand'] = QAction(QIcon(os.path.join(
self._icon_dir, 'hand.png')),
self.tr("Hand"),
self)
self._actions['hand'].triggered.connect(self._hand_enable)
self._actions['hand'].setCheckable(True)
self._actions['hand'].setChecked(False)
self._actions['hand'].setEnabled(False)
# Cursor
self._actions['cursor'] = QAction(QIcon(os.path.join(
self._icon_dir, 'cursor.png')),
self.tr("Cursor"),
self)
self._actions['cursor'].triggered.connect(self._cursor_enable)
self._actions['cursor'].setCheckable(True)
self._actions['cursor'].setChecked(True)
self._actions['cursor'].setEnabled(True)
# Edit
self._actions['edit'] = QAction(QIcon(os.path.join(
self._icon_dir, 'edit.png')),
self.tr("Edit"), self)
self._actions['edit'].triggered.connect(self._roidialog_enable)
self._actions['edit'].setCheckable(True)
self._actions['edit'].setChecked(False)
# Undo
self._actions['undo'] = QAction(QIcon(os.path.join(
self._icon_dir, 'undo.png')),
self.tr("Undo"),
self)
self._actions['undo'].triggered.connect(self._undo)
# Redo
self._actions['redo'] = QAction(QIcon(os.path.join(
self._icon_dir, 'redo.png')),
self.tr("Redo"),
self)
self._actions['redo'].triggered.connect(self._redo)
# sphere and cube roi
self._actions['regular_roi'] = QAction(QIcon(os.path.join(
self._icon_dir,
'sphere_and_cube.png')),
self.tr("Regular ROI"), self)
self._actions['regular_roi'].triggered.connect(self._regular_roi)
self._actions['regular_roi'].setEnabled(False)
# ROI to Interface
self._actions['r2i'] = QAction(QIcon(os.path.join(
self._icon_dir, 'r2i.png')),
self.tr("ROI2Interface"), self)
self._actions['r2i'].triggered.connect(self._r2i)
self._actions['r2i'].setEnabled(False)
# Edge detection for ROI
self._actions['edge_dete'] = QAction(QIcon(os.path.join(
self._icon_dir,
'edge_detection.png')),
self.tr("Edge Detection"), self)
self._actions['edge_dete'].triggered.connect(self._edge_detection)
self._actions['edge_dete'].setEnabled(False)
# ROI Merging
self._actions['roi_merge'] = QAction(QIcon(os.path.join(
self._icon_dir, 'merging.png')),
self.tr("ROI Merging"), self)
self._actions['roi_merge'].triggered.connect(self._roi_merge)
self._actions['roi_merge'].setEnabled(False)
def _add_toolbar(self):
"""
Add toolbar.
"""
# Initialize a spinbox for zoom-scale selection
self._spinbox = QSpinBox()
self._spinbox.setMaximum(500)
self._spinbox.setMinimum(50)
self._spinbox.setSuffix('%')
self._spinbox.setSingleStep(10)
self._spinbox.setValue(self.default_grid_scale_factor * 100)
self._spinbox.valueChanged.connect(self._set_scale_factor)
# Add a toolbar
self._toolbar = self.addToolBar("Tools")
#self._toolbar.setIconSize(QSize(38,38))
# Add file actions
self._toolbar.addAction(self._actions['add_image'])
self._toolbar.addAction(self._actions['remove_image'])
self._toolbar.addAction(self._actions['new_image'])
self._toolbar.addAction(self._actions['save_image'])
# Add view actions
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['grid_view'])
self._toolbar.addAction(self._actions['orth_view'])
self._toolbar.addAction(self._actions['original_view'])
self._toolbar.addAction(self._actions['cross_hover_view'])
# Add cursor status
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['hand'])
self._toolbar.addAction(self._actions['cursor'])
self._toolbar.addAction(self._actions['edit'])
# Add undo redo
self._toolbar.addSeparator()
self._toolbar.addAction(self._actions['undo'])
self._toolbar.addAction(self._actions['redo'])
self._toolbar.addSeparator()
self._toolbar.addWidget(self._spinbox)
def _set_scale_factor(self, value):
"""
Set scale factor.
"""
value = float(value) / 100
self.model.set_scale_factor(value, self.image_view.display_type())
def _add_template(self):
"""
Open a dialog window and select a template file.
"""
template_dir = os.path.join(self.label_path, 'standard',
'MNI152_T1_2mm_brain.nii.gz')
template_name = QFileDialog.getOpenFileName(
self,
'Open standard file',
template_dir,
'Nifti files (*.nii.gz *.nii)')
if not template_name.isEmpty():
if sys.platform == 'win32':
template_path = unicode(template_name).encode('gb2312')
else:
template_path = str(template_name)
self._add_img(template_path)
def _add_image(self):
"""
Add new item.
"""
if self._temp_dir == None:
temp_dir = QDir.currentPath()
else:
temp_dir = self._temp_dir
file_name = QFileDialog.getOpenFileName(self,
'Add new file',
temp_dir,
"Nifti files (*.nii *.nii.gz)")
if not file_name.isEmpty():
if sys.platform == 'win32':
file_path = unicode(file_name).encode('gb2312')
else:
file_path = str(file_name)
self._add_img(file_path)
def _add_img(self, source, name=None, header=None, view_min=None,
view_max=None, alpha=255, colormap='gray'):
"""
Add image.
"""
# If model is NULL, then re-initialize it.
if not self.model:
self._init_label_config_center()
self.model = VolumeListModel([], self._label_config_center)
self.model.set_scale_factor(self.default_grid_scale_factor, 'grid')
self.model.set_scale_factor(self.default_orth_scale_factor, 'orth')
self.painter_status = PainterStatus(ViewSettings())
# Save previous opened directory (except `standard` directory)
file_path = source
if sys.platform == 'win32':
temp_dir = os.path.dirname(unicode(file_path, 'gb2312'))
if not os.stat(temp_dir) == os.stat(os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
else:
temp_dir = os.path.dirname(file_path)
if not os.path.samefile(temp_dir, os.path.join(self.label_path,
'standard')):
self._temp_dir = temp_dir
if self.model.addItem(file_path, None, name, header, view_min,
view_max, alpha, colormap):
# Take different acions in different case.
# If only one data in VolumeList, then initialize views.
if self.model.rowCount() == 1:
# initialize views
self.list_view = LayerView(self._label_config_center)
self.list_view.setModel(self.model)
self._init_roi_dialog()
self.image_view = GridView(self.model, self.painter_status)
# initialize display layout
central_widget = QWidget()
layout = QHBoxLayout()
central_widget.setLayout(layout)
central_widget.layout().addWidget(self.list_view)
central_widget.layout().addWidget(self.image_view)
self.setCentralWidget(central_widget)
# add a toolbar
self._add_toolbar()
#self.setUnifiedTitleAndToolBarOnMac(True)
# change button status
self._actions['save_image'].setEnabled(True)
#self._actions['ld_lbl'].setEnabled(True)
#self._actions['ld_glbl'].setEnabled(True)
self._actions['new_image'].setEnabled(True)
self._actions['close'].setEnabled(True)
self._actions['orth_view'].setEnabled(True)
self._actions['cross_hover_view'].setEnabled(True)
self._actions['original_view'].setEnabled(True)
self._actions['undo'].setEnabled(False)
self._actions['redo'].setEnabled(False)
self._functional_module_set_enabled(True)
# connect signals with slots
self.list_view.current_changed.connect(self._update_undo)
self.list_view.current_changed.connect(self._update_redo)
self.model.rowsInserted.connect(self._update_remove_image)
self.model.undo_stack_changed.connect(self._update_undo)
self.model.redo_stack_changed.connect(self._update_redo)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
# set crosshair as the center of the data
self.model.set_cross_pos([self.model.getY()/2,
self.model.getX()/2,
self.model.getZ()/2])
## Enable cursor tracking
# self.list_view._list_view.selectionModel().currentChanged.connect(
# self._switch_cursor_status)
elif self.model.rowCount() > 1:
self._actions['remove_image'].setEnabled(True)
# set current volume index
self.list_view.setCurrentIndex(self.model.index(0))
self.is_save_configure = True
else:
QMessageBox.information(self,'FreeROI', 'Cannot load ' + \
file_path + ': due to mismatch data size.')
def __new_image(self):
self._new_image()
def _update_remove_image(self):
if self.model.rowCount() == 1:
self._actions['remove_image'].setEnabled(False)
else:
self._actions['remove_image'].setEnabled(True)
def _new_image(self, data=None, name=None, colormap=None):
"""
Create a new volume for brain parcellation.
"""
if colormap is None:
colormap = self._label_config_center.get_first_label_config()
self.model.new_image(data, name, None, colormap)
self.list_view.setCurrentIndex(self.model.index(0))
# change button status
self._actions['remove_image'].setEnabled(True)
def new_image_action(self):
self._actions['remove_image'].setEnabled(True)
def _remove_image(self):
"""
Remove current image.
"""
row = self.list_view.currentRow()
self.model.delItem(row)
if self.model.rowCount() == 1:
self._actions['remove_image'].setEnabled(False)
def _save_image(self):
"""
Save image as a nifti file.
"""
index = self.model.currentIndex()
if self._temp_dir == None:
temp_dir = str(QDir.currentPath())
else:
temp_dir = self._temp_dir
file_path = os.path.join(temp_dir,
str(self.model.data(index, Qt.DisplayRole))+'.nii.gz')
path = QFileDialog.getSaveFileName(
self,
'Save image as...',
file_path,
'Nifti files (*.nii.gz *.nii)')
if not path.isEmpty():
if sys.platform == 'win32':
path = unicode(path).encode('gb2312')
self._temp_dir = os.path.dirname(unicode(path, 'gb2312'))
else:
path = str(path)
self._temp_dir = os.path.dirname(path)
self.model._data[index.row()].save2nifti(path)
def _close_display(self):
"""
Close current display.
"""
self.setCentralWidget(QWidget())
self._set_scale_factor(self.default_grid_scale_factor)
self.removeToolBar(self._toolbar)
self.model = None
self._actions['add_template'].setEnabled(True)
self._actions['add_image'].setEnabled(True)
self._actions['remove_image'].setEnabled(False)
self._actions['new_image'].setEnabled(False)
self._actions['save_image'].setEnabled(False)
#self._actions['ld_glbl'].setEnabled(False)
#self._actions['ld_lbl'].setEnabled(False)
self._actions['close'].setEnabled(False)
self._actions['grid_view'].setEnabled(False)
self._actions['orth_view'].setEnabled(False)
self._actions['cross_hover_view'].setEnabled(False)
self._actions['original_view'].setEnabled(False)
self._functional_module_set_enabled(False)
def _about_pybp(self):
"""
About software.
"""
QMessageBox.about(self, self.tr("About FreeROI"),
self.tr("<p><b>FreeROI</b> is a versatile image "
"processing software developed for "
"neuroimaging data.</p>"
"<p>Its goal is to provide a user-friendly "
"interface for neuroimaging researchers "
"to visualize and analyze their data, "
"especially in defining region of interest "
"(ROI) for ROI analysis.</p>"
"<p>Version: " + __version__ + "</p>"
"<p>Written by: Lijie Huang, Zetian Yang, "
"Guangfu Zhou, Zhaoguo Liu, Xiaobin Dang, "
"Xiangzhen Kong, Xu Wang, and Zonglei Zhen."
"</p>"
"<p><b>FreeROI</b> is under Revised BSD "
"License.</p>"
"<p>Copyright(c) 2012-2014 "
"Neuroinformatic Team in LiuLab "
"from Beijing Normal University</p>"
"<p></p>"
"<p>Please join and report bugs to:</p>"
"<p><b>[email protected]</b></p>"))
def _create_menus(self):
"""Create menus."""
self.file_menu = self.menuBar().addMenu(self.tr("File"))
self.file_menu.addAction(self._actions['add_image'])
self.file_menu.addAction(self._actions['add_template'])
self.file_menu.addAction(self._actions['save_image'])
#self.file_menu.addSeparator()
#self.file_menu.addAction(self._actions['ld_lbl'])
#self.file_menu.addAction(self._actions['ld_glbl'])
self.file_menu.addSeparator()
self.file_menu.addAction(self._actions['close'])
self.file_menu.addAction(self._actions['quit'])
self.volume_menu = self.menuBar().addMenu(self.tr("Volume"))
self.volume_menu.addAction(self._actions['new_image'])
self.volume_menu.addAction(self._actions['remove_image'])
self.view_menu = self.menuBar().addMenu(self.tr("View"))
self.view_menu.addAction(self._actions['grid_view'])
self.view_menu.addAction(self._actions['orth_view'])
self.view_menu.addAction(self._actions['original_view'])
self.view_menu.addAction(self._actions['cross_hover_view'])
self.tool_menu = self.menuBar().addMenu(self.tr("Tools"))
basic_tools = self.tool_menu.addMenu(self.tr("Basic Tools"))
basic_tools.addAction(self._actions['binarization'])
basic_tools.addAction(self._actions['intersect'])
basic_tools.addAction(self._actions['localmax'])
basic_tools.addAction(self._actions['inverse'])
basic_tools.addAction(self._actions['smoothing'])
basic_tools.addAction(self._actions['meants'])
basic_tools.addAction(self._actions['voxelstats'])
segment_tools = self.tool_menu.addMenu(self.tr("Segmentation"))
segment_tools.addAction(self._actions['region_grow'])
segment_tools.addAction(self._actions['watershed'])
segment_tools.addAction(self._actions['cluster'])
roi_tools = self.tool_menu.addMenu(self.tr("ROI Tools"))
roi_tools.addAction(self._actions['edge_dete'])
roi_tools.addAction(self._actions['roi_merge'])
roi_tools.addAction(self._actions['regular_roi'])
roi_tools.addAction(self._actions['r2i'])
morphological_tools = self.tool_menu.addMenu(
self.tr("Morphological Processing"))
morphological_tools.addAction(self._actions['opening'])
morphological_tools.addAction(self._actions['binarydilation'])
morphological_tools.addAction(self._actions['binaryerosion'])
morphological_tools.addAction(self._actions['greydilation'])
morphological_tools.addAction(self._actions['greyerosion'])
self.help_menu = self.menuBar().addMenu(self.tr("Help"))
self.help_menu.addAction(self._actions['about_pybp'])
self.help_menu.addAction(self._actions['about_qt'])
def _cursor_enable(self):
"""
Cursor enabled.
"""
if self._actions['cursor'].isChecked():
self._actions['cursor'].setChecked(True)
if isinstance(self.image_view, OrthView):
self._actions['hand'].setChecked(False)
if self.roidialog.isVisible():
self._roidialog_disable()
self.painter_status.set_draw_settings(ViewSettings())
self.image_view.set_cursor(Qt.ArrowCursor)
self.image_view.set_label_mouse_tracking(True)
else:
self._actions['cursor'].setChecked(True)
def _voxel_edit_enable(self):
"""
Brush enabled.
"""
self._label_config_center.set_is_roi_edit(False)
self.painter_status.set_draw_settings(self._label_config_center)
self.image_view.set_cursor(Qt.CrossCursor)
self.image_view.set_label_mouse_tracking(False)
def _roi_edit_enable(self):
"""
ROI brush enabled.
"""
self._label_config_center.set_is_roi_edit(True)
self.painter_status.set_draw_settings(self._label_config_center)
self.image_view.set_cursor(Qt.CrossCursor)
self.image_view.set_label_mouse_tracking(False)
def _roidialog_enable(self):
if self._actions['edit'].isChecked():
self._actions['cursor'].setChecked(False)
if isinstance(self.image_view, OrthView):
self._actions['hand'].setChecked(False)
self._actions['edit'].setChecked(True)
self.roidialog._voxel_clicked()
self.roidialog.show()
else:
self._actions['edit'].setChecked(True)
def _roi_batch_enable(self):
self.image_view.set_label_mouse_tracking(False)
self._label_config_center.set_is_roi_edit(False)
self.painter_status.set_draw_settings(self.roidialog)
def _roidialog_disable(self):
self.roidialog.hide()
self._actions['edit'].setChecked(False)
def _hand_enable(self):
"""
Hand enabled.
"""
if self._actions['hand'].isChecked():
self._actions['cursor'].setChecked(False)
self._actions['hand'].setChecked(True)
if hasattr(self, 'roidialog'):
self._roidialog_disable()
self.painter_status.set_draw_settings(MoveSettings())
self.image_view.set_cursor(Qt.OpenHandCursor)
self.image_view.set_label_mouse_tracking(True)
else:
self._actions['hand'].setChecked(True)
def _switch_cursor_status(self):
self._actions['cursor'].setChecked(True)
self._cursor_enable()
def _update_undo(self):
if self.model.current_undo_available():
self._actions['undo'].setEnabled(True)
else:
self._actions['undo'].setEnabled(False)
def _update_redo(self):
if self.model.current_redo_available():
self._actions['redo'].setEnabled(True)
else:
self._actions['redo'].setEnabled(False)
def _init_roi_dialog(self):
"""
Initialize ROI Dialog
"""
self.roidialog = ROIDialog(self.model, self._label_config_center, self)
self.roidialog.voxel_edit_enabled.connect(self._voxel_edit_enable)
self.roidialog.roi_edit_enabled.connect(self._roi_edit_enable)
self.roidialog.roi_batch_enabled.connect(self._roi_batch_enable)
self.list_view._list_view.selectionModel().currentChanged.connect(
self.roidialog.clear_rois)
def _init_label_config_center(self):
"""
Initialize LabelConfigCenter
"""
lbl_path = os.path.join(self.label_config_dir,
'*.' + self.label_config_suffix)
label_configs = glob.glob(lbl_path)
self.label_configs = map(LabelConfig, label_configs)
self._label_config_center = LabelConfigCenter(self.label_configs)
def _get_label_config(self, file_path):
"""
Get label config file.
"""
# Get label config file
dir = os.path.dirname(file_path)
file = os.path.basename(file_path)
split_list = file.split('.')
nii_index = split_list.index('nii')
file = ''.join(split_list[:nii_index])
config_file = os.path.join(file, 'lbl')
if os.path.isfile(config_file):
label_config = LabelConfig(config_file, False)
else:
label_config = self.label_config
return label_config
def _undo(self):
self.model.undo_current_image()
def _redo(self):
self.model.redo_current_image()
def _regular_roi(self):
regular_roi_dialog = RegularROIDialog(self.model)
regular_roi_dialog.exec_()
def _edge_detection(self):
edge_detection(self.model)
def _roi_merge(self):
new_dialog = ROIMergeDialog(self.model)
new_dialog.exec_()
def _r2i(self):
new_dialog = Roi2gwmiDialog(self.model)
new_dialog.exec_()
def _opening(self):
new_dialog = OpenDialog(self.model)
new_dialog.exec_()
def _voxelstats(self):
new_dialog = VoxelStatsDialog(self.model, self)
new_dialog.show()
def _ld_lbl(self):
file_name = QFileDialog.getOpenFileName(self,
'Load Label File',
QDir.currentPath(),
"Label files (*.lbl)")
if file_name:
label_config = LabelConfig(str(file_name), False)
self.model.set_cur_label(label_config)
def _ld_glbl(self):
file_name = QFileDialog.getOpenFileName(self,
'Load Label File',
QDir.currentPath(),
"Label files (*.lbl)")
if file_name:
label_config = LabelConfig(str(file_name), True)
self.model.set_global_label(label_config)
def _grid_view(self):
"""
Grid view option.
"""
self._actions['grid_view'].setEnabled(False)
self._actions['orth_view'].setEnabled(True)
self._actions['hand'].setEnabled(False)
self._actions['cursor'].trigger()
self.centralWidget().layout().removeWidget(self.image_view)
self.image_view.set_display_type('grid')
self.model.scale_changed.disconnect()
self.model.repaint_slices.disconnect()
self.model.cross_pos_changed.disconnect(self.image_view.update_cross_pos)
self.image_view.deleteLater()
self._spinbox.setValue(100 * self.model.get_scale_factor('grid'))
self.image_view = GridView(self.model, self.painter_status,
self._gridview_vertical_scrollbar_position)
self.centralWidget().layout().addWidget(self.image_view)
def _orth_view(self):
"""
Orth view option.
"""
self._actions['orth_view'].setEnabled(False)
self._actions['grid_view'].setEnabled(True)
self._actions['hand'].setEnabled(True)
self._actions['cursor'].trigger()
self._gridview_vertical_scrollbar_position = \
self.image_view.get_vertical_srollbar_position()
self.centralWidget().layout().removeWidget(self.image_view)
self.image_view.set_display_type('orth')
self.model.scale_changed.disconnect()
self.model.repaint_slices.disconnect()
self.model.cross_pos_changed.disconnect(self.image_view.update_cross_pos)
self.image_view.deleteLater()
self._spinbox.setValue(100 * self.model.get_scale_factor('orth'))
self.image_view = OrthView(self.model, self.painter_status)
self.centralWidget().layout().addWidget(self.image_view)
def _display_cross_hover(self):
if self.model._display_cross:
self.model.set_cross_status(False)
self._actions['cross_hover_view'].setText('Enable cross hover')
self._actions['cross_hover_view'].setIcon(QIcon(os.path.join(self._icon_dir,'cross_hover_disable.png')))
else:
self.model.set_cross_status(True)
self._actions['cross_hover_view'].setText('Disable cross hover')
self._actions['cross_hover_view'].setIcon(QIcon(os.path.join(self._icon_dir,'cross_hover_enable.png')))
def _reset_view(self):
"""
Reset view parameters.
"""
if self.image_view.display_type() == 'orth':
if not self.model.get_scale_factor('orth') == \
self.default_orth_scale_factor:
self._spinbox.setValue(100 * self.default_orth_scale_factor)
self.image_view.reset_view()
elif self.image_view.display_type() == 'grid':
if not self.model.get_scale_factor('grid') == \
self.default_grid_scale_factor:
self._spinbox.setValue(100 * self.default_grid_scale_factor)
def _binarization(self):
binarization_dialog = BinarizationDialog(self.model)
binarization_dialog.exec_()
def _binaryerosion(self):
binaryerosion_dialog = BinaryerosionDialog(self.model)
binaryerosion_dialog.exec_()
def _binarydilation(self):
binarydilation_dialog = BinarydilationDialog(self.model)
binarydilation_dialog.exec_()
def _greyerosion(self):
greyerosiondialog = GreyerosionDialog(self.model)
greyerosiondialog.exec_()
def _greydilation(self):
greydilation_dialog = GreydilationDialog(self.model)
greydilation_dialog.exec_()
def _intersect(self):
intersect_dialog = IntersectDialog(self.model)
intersect_dialog.exec_()
def _meants(self):
new_dialog = MeanTSDialog(self.model)
new_dialog.exec_()
def _local_max(self):
new_dialog = LocalMaxDialog(self.model, self)
new_dialog.exec_()
def _inverse(self):
inverse_image(self.model)
def _smooth(self):
new_dialog = SmoothingDialog(self.model)
new_dialog.exec_()
def _region_grow(self):
new_dialog = GrowDialog(self.model, self)
new_dialog.exec_()
def _watershed(self):
new_dialog = WatershedDialog(self.model, self)
new_dialog.exec_()
def _cluster(self):
new_dialog = ClusterDialog(self.model, self)
new_dialog.exec_()
def _functional_module_set_enabled(self, status):
self._actions['binarization'].setEnabled(status)
self._actions['intersect'].setEnabled(status)
self._actions['meants'].setEnabled(status)
self._actions['voxelstats'].setEnabled(status)
self._actions['localmax'].setEnabled(status)
self._actions['inverse'].setEnabled(status)
self._actions['smoothing'].setEnabled(status)
self._actions['region_grow'].setEnabled(status)
self._actions['watershed'].setEnabled(status)
self._actions['cluster'].setEnabled(status)
self._actions['opening'].setEnabled(status)
self._actions['binarydilation'].setEnabled(status)
self._actions['binaryerosion'].setEnabled(status)
self._actions['greydilation'].setEnabled(status)
self._actions['greyerosion'].setEnabled(status)
self._actions['regular_roi'].setEnabled(status)
self._actions['r2i'].setEnabled(status)
self._actions['edge_dete'].setEnabled(status)
self._actions['roi_merge'].setEnabled(status)