class Browser(QMainWindow):
ZOOM_STEP = 1.05
show_objects_toggled = pyqtSignal('bool')
show_contours_toggled = pyqtSignal('bool')
coordinates_changed = pyqtSignal(Coordinate)
def __init__(self, settings, imagecontainer):
super(Browser, self).__init__()
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
self._show_objects = False
self._object_region = None
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
#splitter.setSizePolicy(QSizePolicy(QSizePolicy.Minimum,
# QSizePolicy.Expanding))
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
#splitter.setChildrenCollapsible(False)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t-1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewer = ImageViewer(frame, auto_resize=True)
layout.addWidget(self.image_viewer, 0, 0)
#self.image_viewer.image_mouse_dblclk.connect(self._on_dbl_clk)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = QSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
# self._t_slider.setMaximum(self.max_frame)
self._t_slider.setTickPosition(QSlider.TicksBelow)
self._t_slider.valueChanged.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action('Next Plate',
shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action('Previous Plate',
shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action('Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action('Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(view_menu, (act_resize, None,
act_zoom100, act_zoomfit,
act_zoomin, act_zoomout,
None,
act_prev_t, act_next_t,
act_prev_pos, act_next_pos,
act_prev_plate, act_next_plate,
None,
act_refresh,
act_fullscreen, None,
act_show_contours, None,
act_anti, act_smooth,
))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
# tool bar
toolbar = self.addToolBar('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
region_names = []
for prefix in ['primary', 'secondary', 'tertiary']:
region_names.extend(['%s - %s' % (prefix.capitalize(), name) \
for name in REGION_INFO.names[prefix]])
# FIXME: something went wrong with setting up the current region
self._object_region = region_names[0].split(' - ')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
DisplayModule(self._module_manager, self, self._imagecontainer, region_names)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
# process and display the first image
self._process_image()
def create_action(self, text, slot=None, shortcut=None, icon=None,
tooltip=None, checkable=None, signal='triggered()',
checked=False):
action = QAction(text, self)
if icon is not None:
action.setIcon(QIcon(':/%s.png' % icon))
if shortcut is not None:
action.setShortcut(shortcut)
if tooltip is not None:
action.setToolTip(tooltip)
action.setStatusTip(tooltip)
if slot is not None:
self.connect(action, SIGNAL(signal), slot, Qt.DirectConnection)
if checkable is not None:
action.setCheckable(True)
action.setChecked(checked)
return action
def add_actions(self, target, actions):
for action in actions:
if action is None:
target.addSeparator()
else:
target.addAction(action)
def set_coords(self, coords):
self.image_viewer.remove_objects()
self.image_viewer.set_objects_by_crackcoords(coords)
widget = self._module_manager.get_widget(AnnotationModule.NAME)
widget.set_coords()
def show_image(self, image_dict):
widget = self._module_manager.get_widget(DisplayModule.NAME)
widget.set_image_dict(image_dict)
self.update_statusbar()
def update_statusbar(self):
meta_data = self._imagecontainer.get_meta_data()
if meta_data.has_timelapse:
timestamp = meta_data.get_timestamp_relative(self.coordinate)
time_info = ' | Frame: %d' % self.coordinate.time
if not numpy.isnan(timestamp):
time_info += ' (%.1f min)' % (timestamp / 60)
else:
time_info = ''
msg = 'Plate: %s | Position: %s%s || Zoom: %.1f%%' % \
(self.coordinate.plate, self.coordinate.position, time_info,
self.image_viewer.scale_factor*100)
self._statusbar.showMessage(msg)
def get_coordinate(self):
return self.coordinate.copy()
def on_coordinate_changed(self, coordinate):
"""
All coordinate changes are handled via the Navigator. The change event
from the Navigator is processed here and further propagated via
a new Browser event (the Modules are not supposed to know each other).
"""
self.coordinate = coordinate.copy()
self._t_slider.blockSignals(True)
self._imagecontainer.set_plate(coordinate.plate)
# the slider is always working with frames.
# reason: it is difficult to forbid slider values between allowed values.
frame = int(round(self.max_frame * (coordinate.time - self.min_time) /
max(float(self.max_time - self.min_time), 1)))
self._t_slider.setValue(frame)
self._t_slider.blockSignals(False)
self._process_image()
# propagate the signal further to other modules
self.coordinates_changed.emit(coordinate)
def set_coordinate(self, coordinate):
"""
Changes the Navigator to a fixed coordinate
"""
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_coordinate(coordinate)
def _process_image(self):
settings = _ProcessorMixin.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('redofailedonly', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('ObjectDetection')
prim_id = PrimaryChannel.NAME
#sec_id = SecondaryChannel.NAME
#sec_regions = settings.get2('secondary_regions')
settings.set_section('Processing')
settings.set2('primary_classification', False)
settings.set2('secondary_classification', False)
settings.set2('tertiary_classification', False)
settings.set2('merged_classification', False)
settings.set2('primary_featureextraction', False)
settings.set2('secondary_featureextraction', False)
settings.set2('objectdetection', self._show_objects)
settings.set2('tracking', False)
settings.set_section('Output')
settings.set2('rendering_contours_discwrite', False)
settings.set2('rendering_class_discwrite', False)
settings.set2('export_object_counts', False)
settings.set2('export_object_details', False)
settings.set2('export_track_data', False)
settings.set2('hdf5_create_file', False)
settings.set_section('Classification')
settings.set2('collectsamples', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
settings.set('Output', 'events_export_gallery_images', False)
# turn of output:
settings.set('Output', 'export_object_counts', False)
settings.set('Output', 'export_object_details', False)
settings.set('Output', 'export_file_names', False)
settings.set('Output', 'events_export_gallery_images', False)
settings.set('Output', 'export_track_data', False)
settings.set('Output', 'export_tracking_as_dot', False)
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the
# same color
if nchannels == 2:
settings.set('Processing', 'secondary_processChannel', True)
elif nchannels == 3:
settings.set('Processing', 'secondary_processChannel', True)
settings.set('Processing', 'tertiary_processChannel', True)
# need turn of virtual channels
settings.set('Processing', 'merged_processChannel', False)
settings.set('General', 'rendering', {})
analyzer = AnalyzerCore(self.coordinate.plate, settings,
self._imagecontainer)
# as long the GIL is not released, if GIL is released
# just use self.setCursor
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
analyzer.processPositions(myhack=self)
except Exception, e:
import traceback
traceback.print_exc()
raise(e)
finally:
def __init__(self, settings, imagecontainer):
super(Browser, self).__init__()
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
self._show_objects = False
self._object_region = None
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
#splitter.setSizePolicy(QSizePolicy(QSizePolicy.Minimum,
# QSizePolicy.Expanding))
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
#splitter.setChildrenCollapsible(False)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t-1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewer = ImageViewer(frame, auto_resize=True)
layout.addWidget(self.image_viewer, 0, 0)
#self.image_viewer.image_mouse_dblclk.connect(self._on_dbl_clk)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = QSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
# self._t_slider.setMaximum(self.max_frame)
self._t_slider.setTickPosition(QSlider.TicksBelow)
self._t_slider.valueChanged.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action('Next Plate',
shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action('Previous Plate',
shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action('Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action('Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(view_menu, (act_resize, None,
act_zoom100, act_zoomfit,
act_zoomin, act_zoomout,
None,
act_prev_t, act_next_t,
act_prev_pos, act_next_pos,
act_prev_plate, act_next_plate,
None,
act_refresh,
act_fullscreen, None,
act_show_contours, None,
act_anti, act_smooth,
))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
# tool bar
toolbar = self.addToolBar('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
region_names = []
for prefix in ['primary', 'secondary', 'tertiary']:
region_names.extend(['%s - %s' % (prefix.capitalize(), name) \
for name in REGION_INFO.names[prefix]])
# FIXME: something went wrong with setting up the current region
self._object_region = region_names[0].split(' - ')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
DisplayModule(self._module_manager, self, self._imagecontainer, region_names)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
# process and display the first image
self._process_image()
class Browser(QMainWindow):
ZOOM_STEP = 1.05
show_objects_toggled = pyqtSignal('bool')
show_contours_toggled = pyqtSignal('bool')
#coordinates_changed = pyqtSignal(Coordinate)
update_regions = pyqtSignal(dict)
def __init__(self, settings, imagecontainer, parent=None):
super(Browser, self).__init__(parent)
self.setWindowTitle('Annotation Browser')
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
# These params are used by process_image and contour visualization
self._detect_objects = False
self._show_objects_by = 'color'
self._object_region = None
self._contour_color = '#000000'
self._show_objects = True
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t-1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewers = {
'image' : ImageViewer(frame, auto_resize=True),
'gallery' : GalleryViewer(frame)
}
self.image_viewer = self.image_viewers['image']
layout.addWidget(self.image_viewer , 0, 0)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = TSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
self._t_slider.setTickPosition(QSlider.NoTicks)
self._t_slider.newValue.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
self._t_slider.valueChanged.connect(self.timeToolTip)
self._imagecontainer.check_dimensions()
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_close = self.create_action('Close',
shortcut=QKeySequence('CTRL+C'),
slot=self.close)
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action(
'Next Plate', shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action(
'Previous Plate', shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action(
'Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False
)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action(
'Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours
)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(view_menu, (act_resize, None,
act_zoom100, act_zoomfit,
act_zoomin, act_zoomout,
None,
act_prev_t, act_next_t,
act_prev_pos, act_next_pos,
act_prev_plate, act_next_plate,
None,
act_refresh,
act_fullscreen, None,
act_show_contours, None,
act_anti, act_smooth,
None, act_close))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
toolbar = self.addToolBar('Toolbar')
toolbar.setObjectName('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
# fallback if no Segmentation plugins have been specified
rdict = self._region_names()
if len(rdict) > 0:
self._object_region = rdict.keys()[0].split(' - ')
else:
self._object_region = ('Primary', 'primary')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
defautl_display_module = DisplayModule(
self._module_manager, self, self._imagecontainer, rdict)
self.set_display_module(defautl_display_module)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
try:
CellH5EventModule(self._module_manager,
self, self._settings, self._imagecontainer)
except Exception as e:
warning(self, str(e))
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
self.layout = layout
# process and display the first image
self._restore_geometry()
self._process_image()
def closeEvent(self, event):
self._save_geometry()
def _save_geometry(self):
settings = QSettings(version.organisation, version.appname)
settings.beginGroup('AnnotationBrowser')
settings.setValue('state', self.saveState())
settings.setValue('geometry', self.saveGeometry())
settings.endGroup()
def _restore_geometry(self):
settings = QSettings(version.organisation, version.appname)
settings.beginGroup('AnnotationBrowser')
if settings.contains('geometry'):
self.restoreGeometry(settings.value('geometry'))
if settings.contains('state'):
self.restoreState(settings.value('state'))
settings.endGroup()
def _region_names(self):
rdict = OrderedDict()
reginfo = MetaPluginManager().region_info
for channel, regions in reginfo.names.iteritems():
for region in regions:
rdict['%s - %s' % (channel.capitalize(), region)] = \
(channel.capitalize(), region)
return rdict
def set_image_viewer(self, viewer_type):
self.image_viewer.hide()
self.layout.removeWidget(self.image_viewer)
self.image_viewer = self.image_viewers[viewer_type]
self.layout.addWidget(self.image_viewer, 0, 0)
self.image_viewer.show()
def create_action(self, text, slot=None, shortcut=None, icon=None,
tooltip=None, checkable=None, signal='triggered()',
checked=False):
action = QAction(text, self)
if icon is not None:
action.setIcon(QIcon(':/%s.png' % icon))
if shortcut is not None:
action.setShortcut(shortcut)
if tooltip is not None:
action.setToolTip(tooltip)
action.setStatusTip(tooltip)
if slot is not None:
if signal == "triggered()":
action.triggered.connect(slot, Qt.DirectConnection)
else:
action.triggered[bool].connect(slot, Qt.DirectConnection)
if checkable is not None:
action.setCheckable(True)
action.setChecked(checked)
return action
def add_actions(self, target, actions):
for action in actions:
if action is None:
target.addSeparator()
else:
target.addAction(action)
def set_coords(self, coords):
self.image_viewer.set_objects_by_crackcoords(coords)
widget = self._module_manager.get_widget(AnnotationModule.NAME)
widget.set_coords()
def set_classified_crack_contours(self, coords):
self.image_viewer.set_objects_by_crackcoords_with_colors(coords)
widget = self._module_manager.get_widget(AnnotationModule.NAME)
widget.set_coords()
def show_image(self, image_dict):
widget = self.get_display_module()
widget.set_image_dict(image_dict)
self.update_statusbar()
def set_display_module(self, display_module ):
self.display_module = display_module
def get_display_module(self):
return self.display_module
def update_statusbar(self):
meta_data = self._imagecontainer.get_meta_data()
if meta_data.has_timelapse:
timestamp = meta_data.get_timestamp_relative(self.coordinate)
time_info = ' | Frame: %d' % self.coordinate.time
if not numpy.isnan(timestamp):
time_info += ' (%.1f min)' % (timestamp / 60)
else:
time_info = ''
msg = 'Plate: %s | Position: %s%s || Zoom: %.1f%%' % \
(self.coordinate.plate, self.coordinate.position, time_info,
self.image_viewer.scalefactor*100)
self._statusbar.showMessage(msg)
def get_coordinate(self):
return self.coordinate.copy()
def on_coordinate_changed(self, coordinate):
"""
All coordinate changes are handled via the Navigator. The change event
from the Navigator is processed here and further propagated via
a new Browser event (the Modules are not supposed to know each other).
"""
self.coordinate = coordinate.copy()
self._t_slider.blockSignals(True)
self._imagecontainer.set_plate(coordinate.plate)
self._t_slider.setValue(coordinate.time)
self._t_slider.blockSignals(False)
self._process_image()
# propagate the signal further to other modules
#self.coordinates_changed.emit(coordinate)
def set_coordinate(self, coordinate):
"""
Changes the Navigator to a fixed coordinate
"""
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_coordinate(coordinate)
def _process_image(self, ):
self.image_viewer.remove_objects()
settings = BaseProcessorFrame.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('redofailedonly', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('Processing')
_classify_objects = self._show_objects_by == 'classification'
settings.set2('primary_classification', _classify_objects )
settings.set2('secondary_classification', _classify_objects)
settings.set2('tertiary_classification', _classify_objects)
settings.set2('merged_classification', _classify_objects)
settings.set2('primary_featureextraction', _classify_objects)
settings.set2('secondary_featureextraction', _classify_objects)
settings.set2('objectdetection', self._detect_objects)
settings.set2('tracking', False)
settings.set_section('Output')
settings.set2('rendering_contours_discwrite', False)
settings.set2('rendering_class_discwrite', False)
settings.set2('export_object_counts', False)
settings.set2('export_object_details', False)
settings.set2('export_track_data', False)
settings.set2('hdf5_create_file', False)
settings.set_section('Classification')
settings.set2('collectsamples', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
settings.set('Output', 'events_export_gallery_images', False)
# turn of output:
settings.set('Output', 'export_object_counts', False)
settings.set('Output', 'export_object_details', False)
settings.set('Output', 'export_file_names', False)
settings.set('Output', 'events_export_gallery_images', False)
settings.set('Output', 'export_track_data', False)
settings.set('Output', 'export_tracking_as_dot', False)
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the same color
if nchannels == 2:
settings.set('General', 'process_secondary', True)
elif nchannels >= 3:
settings.set('General', 'process_secondary', True)
settings.set('General', 'process_tertiary', True)
settings.set('General', 'rendering', {})
analyzer = AnalyzerBrowser(self.coordinate.plate,
settings,
self._imagecontainer)
res = None
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
res = analyzer.processPositions()
self.render_browser(res)
except Exception, e:
import traceback
from cecog.gui.util import exception
traceback.print_exc()
exception(self, str(e))
raise
finally:
def __init__(self, settings, imagecontainer, parent=None):
super(Browser, self).__init__(parent)
self.setWindowTitle('Annotation Browser')
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
# These params are used by process_image and contour visualization
self._detect_objects = False
self._show_objects_by = 'color'
self._object_region = None
self._contour_color = '#000000'
self._show_objects = True
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t-1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewers = {
'image' : ImageViewer(frame, auto_resize=True),
'gallery' : GalleryViewer(frame)
}
self.image_viewer = self.image_viewers['image']
layout.addWidget(self.image_viewer , 0, 0)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = TSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
self._t_slider.setTickPosition(QSlider.NoTicks)
self._t_slider.newValue.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
self._t_slider.valueChanged.connect(self.timeToolTip)
self._imagecontainer.check_dimensions()
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_close = self.create_action('Close',
shortcut=QKeySequence('CTRL+C'),
slot=self.close)
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action(
'Next Plate', shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action(
'Previous Plate', shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action(
'Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False
)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action(
'Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours
)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(view_menu, (act_resize, None,
act_zoom100, act_zoomfit,
act_zoomin, act_zoomout,
None,
act_prev_t, act_next_t,
act_prev_pos, act_next_pos,
act_prev_plate, act_next_plate,
None,
act_refresh,
act_fullscreen, None,
act_show_contours, None,
act_anti, act_smooth,
None, act_close))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
toolbar = self.addToolBar('Toolbar')
toolbar.setObjectName('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
# fallback if no Segmentation plugins have been specified
rdict = self._region_names()
if len(rdict) > 0:
self._object_region = rdict.keys()[0].split(' - ')
else:
self._object_region = ('Primary', 'primary')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
defautl_display_module = DisplayModule(
self._module_manager, self, self._imagecontainer, rdict)
self.set_display_module(defautl_display_module)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
try:
CellH5EventModule(self._module_manager,
self, self._settings, self._imagecontainer)
except Exception as e:
warning(self, str(e))
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
self.layout = layout
# process and display the first image
self._restore_geometry()
self._process_image()
def __init__(self, settings, imagecontainer):
super(Browser, self).__init__()
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
self._show_objects = False
self._object_region = None
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
#splitter.setSizePolicy(QSizePolicy(QSizePolicy.Minimum,
# QSizePolicy.Expanding))
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
#splitter.setChildrenCollapsible(False)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t - 1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewer = ImageViewer(frame, auto_resize=True)
layout.addWidget(self.image_viewer, 0, 0)
#self.image_viewer.image_mouse_dblclk.connect(self._on_dbl_clk)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = QSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
# self._t_slider.setMaximum(self.max_frame)
self._t_slider.setTickPosition(QSlider.TicksBelow)
self._t_slider.valueChanged.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action(
'Next Plate',
shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action(
'Previous Plate',
shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action('Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action(
'Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(view_menu, (
act_resize,
None,
act_zoom100,
act_zoomfit,
act_zoomin,
act_zoomout,
None,
act_prev_t,
act_next_t,
act_prev_pos,
act_next_pos,
act_prev_plate,
act_next_plate,
None,
act_refresh,
act_fullscreen,
None,
act_show_contours,
None,
act_anti,
act_smooth,
))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
# tool bar
toolbar = self.addToolBar('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
region_names = []
for prefix in ['primary', 'secondary', 'tertiary']:
region_names.extend(['%s - %s' % (prefix.capitalize(), name) \
for name in REGION_INFO.names[prefix]])
# FIXME: something went wrong with setting up the current region
self._object_region = region_names[0].split(' - ')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
DisplayModule(self._module_manager, self, self._imagecontainer,
region_names)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
# process and display the first image
self._process_image()
class Browser(QMainWindow):
ZOOM_STEP = 1.05
show_objects_toggled = pyqtSignal('bool')
show_contours_toggled = pyqtSignal('bool')
coordinates_changed = pyqtSignal(Coordinate)
def __init__(self, settings, imagecontainer):
super(Browser, self).__init__()
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
self._show_objects = False
self._object_region = None
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
#splitter.setSizePolicy(QSizePolicy(QSizePolicy.Minimum,
# QSizePolicy.Expanding))
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
#splitter.setChildrenCollapsible(False)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t - 1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewer = ImageViewer(frame, auto_resize=True)
layout.addWidget(self.image_viewer, 0, 0)
#self.image_viewer.image_mouse_dblclk.connect(self._on_dbl_clk)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = QSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
# self._t_slider.setMaximum(self.max_frame)
self._t_slider.setTickPosition(QSlider.TicksBelow)
self._t_slider.valueChanged.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action(
'Next Plate',
shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action(
'Previous Plate',
shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action('Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action(
'Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(view_menu, (
act_resize,
None,
act_zoom100,
act_zoomfit,
act_zoomin,
act_zoomout,
None,
act_prev_t,
act_next_t,
act_prev_pos,
act_next_pos,
act_prev_plate,
act_next_plate,
None,
act_refresh,
act_fullscreen,
None,
act_show_contours,
None,
act_anti,
act_smooth,
))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
# tool bar
toolbar = self.addToolBar('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
region_names = []
for prefix in ['primary', 'secondary', 'tertiary']:
region_names.extend(['%s - %s' % (prefix.capitalize(), name) \
for name in REGION_INFO.names[prefix]])
# FIXME: something went wrong with setting up the current region
self._object_region = region_names[0].split(' - ')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
DisplayModule(self._module_manager, self, self._imagecontainer,
region_names)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
# process and display the first image
self._process_image()
def create_action(self,
text,
slot=None,
shortcut=None,
icon=None,
tooltip=None,
checkable=None,
signal='triggered()',
checked=False):
action = QAction(text, self)
if icon is not None:
action.setIcon(QIcon(':/%s.png' % icon))
if shortcut is not None:
action.setShortcut(shortcut)
if tooltip is not None:
action.setToolTip(tooltip)
action.setStatusTip(tooltip)
if slot is not None:
self.connect(action, SIGNAL(signal), slot, Qt.DirectConnection)
if checkable is not None:
action.setCheckable(True)
action.setChecked(checked)
return action
def add_actions(self, target, actions):
for action in actions:
if action is None:
target.addSeparator()
else:
target.addAction(action)
def set_coords(self, coords):
self.image_viewer.remove_objects()
self.image_viewer.set_objects_by_crackcoords(coords)
widget = self._module_manager.get_widget(AnnotationModule.NAME)
widget.set_coords()
def show_image(self, image_dict):
widget = self._module_manager.get_widget(DisplayModule.NAME)
widget.set_image_dict(image_dict)
self.update_statusbar()
def update_statusbar(self):
meta_data = self._imagecontainer.get_meta_data()
if meta_data.has_timelapse:
timestamp = meta_data.get_timestamp_relative(self.coordinate)
time_info = ' | Frame: %d' % self.coordinate.time
if not numpy.isnan(timestamp):
time_info += ' (%.1f min)' % (timestamp / 60)
else:
time_info = ''
msg = 'Plate: %s | Position: %s%s || Zoom: %.1f%%' % \
(self.coordinate.plate, self.coordinate.position, time_info,
self.image_viewer.scale_factor*100)
self._statusbar.showMessage(msg)
def get_coordinate(self):
return self.coordinate.copy()
def on_coordinate_changed(self, coordinate):
"""
All coordinate changes are handled via the Navigator. The change event
from the Navigator is processed here and further propagated via
a new Browser event (the Modules are not supposed to know each other).
"""
self.coordinate = coordinate.copy()
self._t_slider.blockSignals(True)
self._imagecontainer.set_plate(coordinate.plate)
# the slider is always working with frames.
# reason: it is difficult to forbid slider values between allowed values.
frame = int(
round(self.max_frame * (coordinate.time - self.min_time) /
max(float(self.max_time - self.min_time), 1)))
self._t_slider.setValue(frame)
self._t_slider.blockSignals(False)
self._process_image()
# propagate the signal further to other modules
self.coordinates_changed.emit(coordinate)
def set_coordinate(self, coordinate):
"""
Changes the Navigator to a fixed coordinate
"""
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_coordinate(coordinate)
def _process_image(self):
settings = _ProcessorMixin.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('redofailedonly', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('ObjectDetection')
prim_id = PrimaryChannel.NAME
#sec_id = SecondaryChannel.NAME
#sec_regions = settings.get2('secondary_regions')
settings.set_section('Processing')
settings.set2('primary_classification', False)
settings.set2('secondary_classification', False)
settings.set2('tertiary_classification', False)
settings.set2('merged_classification', False)
settings.set2('primary_featureextraction', False)
settings.set2('secondary_featureextraction', False)
settings.set2('objectdetection', self._show_objects)
settings.set2('tracking', False)
settings.set_section('Output')
settings.set2('rendering_contours_discwrite', False)
settings.set2('rendering_class_discwrite', False)
settings.set2('export_object_counts', False)
settings.set2('export_object_details', False)
settings.set2('export_track_data', False)
settings.set2('hdf5_create_file', False)
settings.set_section('Classification')
settings.set2('collectsamples', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
settings.set('Output', 'events_export_gallery_images', False)
# turn of output:
settings.set('Output', 'export_object_counts', False)
settings.set('Output', 'export_object_details', False)
settings.set('Output', 'export_file_names', False)
settings.set('Output', 'events_export_gallery_images', False)
settings.set('Output', 'export_track_data', False)
settings.set('Output', 'export_tracking_as_dot', False)
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the
# same color
if nchannels == 2:
settings.set('Processing', 'secondary_processChannel', True)
elif nchannels == 3:
settings.set('Processing', 'secondary_processChannel', True)
settings.set('Processing', 'tertiary_processChannel', True)
# need turn of virtual channels
settings.set('Processing', 'merged_processChannel', False)
settings.set('General', 'rendering', {})
analyzer = AnalyzerCore(self.coordinate.plate, settings,
self._imagecontainer)
# as long the GIL is not released, if GIL is released
# just use self.setCursor
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
analyzer.processPositions(myhack=self)
except Exception, e:
import traceback
traceback.print_exc()
raise (e)
finally:
def __init__(self, settings, imagecontainer, parent=None):
super(Browser, self).__init__(parent)
self.setWindowTitle('Annotation Browser')
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
# These params are used by process_image and contour visualization
self._detect_objects = False
self._show_objects_by = 'color'
self._object_region = None
self._contour_color = '#000000'
self._show_objects = True
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t - 1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewers = {
'image': ImageViewer(frame, auto_resize=True),
'gallery': GalleryViewer(frame)
}
self.image_viewer = self.image_viewers['image']
layout.addWidget(self.image_viewer, 0, 0)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = TSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
self._t_slider.setTickPosition(QSlider.NoTicks)
self._t_slider.newValue.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
self._t_slider.valueChanged.connect(self.timeToolTip)
self._imagecontainer.check_dimensions()
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_close = self.create_action('Close',
shortcut=QKeySequence('CTRL+C'),
slot=self.close)
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action(
'Next Plate',
shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action(
'Previous Plate',
shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action('Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action(
'Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(
view_menu,
(act_resize, None, act_zoom100, act_zoomfit, act_zoomin,
act_zoomout, None, act_prev_t, act_next_t, act_prev_pos,
act_next_pos, act_prev_plate, act_next_plate, None, act_refresh,
act_fullscreen, None, act_show_contours, None, act_anti,
act_smooth, None, act_close))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
toolbar = self.addToolBar('Toolbar')
toolbar.setObjectName('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
# fallback if no Segmentation plugins have been specified
rdict = self._region_names()
if len(rdict) > 0:
self._object_region = rdict.keys()[0].split(' - ')
else:
self._object_region = ('Primary', 'primary')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
defautl_display_module = DisplayModule(self._module_manager, self,
self._imagecontainer, rdict)
self.set_display_module(defautl_display_module)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
try:
CellH5EventModule(self._module_manager, self, self._settings,
self._imagecontainer)
except Exception as e:
QMessageBox.warning(self, "Warning", str(e))
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
self.layout = layout
# process and display the first image
self._restore_geometry()
self._process_image()
class Browser(QMainWindow):
ZOOM_STEP = 1.05
show_objects_toggled = pyqtSignal('bool')
show_contours_toggled = pyqtSignal('bool')
update_regions = pyqtSignal(dict)
def __init__(self, settings, imagecontainer, parent=None):
super(Browser, self).__init__(parent)
self.setWindowTitle('Annotation Browser')
frame = QFrame(self)
self.setCentralWidget(frame)
self._settings = settings
self._imagecontainer = imagecontainer
# These params are used by process_image and contour visualization
self._detect_objects = False
self._show_objects_by = 'color'
self._object_region = None
self._contour_color = '#000000'
self._show_objects = True
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet("QStatusBar { border-top: 1px solid gray; }")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
self.max_time = meta_data.times[-1]
self.min_time = meta_data.times[0]
self.max_frame = meta_data.dim_t - 1
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewers = {
'image': ImageViewer(frame, auto_resize=True),
'gallery': GalleryViewer(frame)
}
self.image_viewer = self.image_viewers['image']
layout.addWidget(self.image_viewer, 0, 0)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = TSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(self.min_time)
self._t_slider.setMaximum(self.max_time)
self._t_slider.setTickPosition(QSlider.NoTicks)
self._t_slider.newValue.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
self._t_slider.valueChanged.connect(self.timeToolTip)
self._imagecontainer.check_dimensions()
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_close = self.create_action('Close',
shortcut=QKeySequence('CTRL+C'),
slot=self.close)
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action(
'Next Plate',
shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action(
'Previous Plate',
shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_refresh = self.create_action('Refresh',
shortcut=QKeySequence('F5'),
slot=self.on_refresh)
act_fullscreen = self.create_action('Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action(
'Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(
view_menu,
(act_resize, None, act_zoom100, act_zoomfit, act_zoomin,
act_zoomout, None, act_prev_t, act_next_t, act_prev_pos,
act_next_pos, act_prev_plate, act_next_plate, None, act_refresh,
act_fullscreen, None, act_show_contours, None, act_anti,
act_smooth, None, act_close))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
toolbar = self.addToolBar('Toolbar')
toolbar.setObjectName('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
# fallback if no Segmentation plugins have been specified
rdict = self._region_names()
if len(rdict) > 0:
self._object_region = rdict.keys()[0].split(' - ')
else:
self._object_region = ('Primary', 'primary')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
defautl_display_module = DisplayModule(self._module_manager, self,
self._imagecontainer, rdict)
self.set_display_module(defautl_display_module)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
try:
CellH5EventModule(self._module_manager, self, self._settings,
self._imagecontainer)
except Exception as e:
QMessageBox.warning(self, "Warning", str(e))
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
self.layout = layout
# process and display the first image
self._restore_geometry()
self._process_image()
def closeEvent(self, event):
self._save_geometry()
def _save_geometry(self):
settings = QSettings(version.organisation, version.appname)
settings.beginGroup('AnnotationBrowser')
settings.setValue('state', self.saveState())
settings.setValue('geometry', self.saveGeometry())
settings.endGroup()
def _restore_geometry(self):
settings = QSettings(version.organisation, version.appname)
settings.beginGroup('AnnotationBrowser')
if settings.contains('geometry'):
self.restoreGeometry(settings.value('geometry'))
if settings.contains('state'):
self.restoreState(settings.value('state'))
settings.endGroup()
def _region_names(self):
rdict = OrderedDict()
reginfo = MetaPluginManager().region_info
for channel, regions in reginfo.names.iteritems():
for region in regions:
rdict['%s - %s' % (channel.capitalize(), region)] = \
(channel.capitalize(), region)
return rdict
def set_image_viewer(self, viewer_type):
self.image_viewer.hide()
self.layout.removeWidget(self.image_viewer)
self.image_viewer = self.image_viewers[viewer_type]
self.layout.addWidget(self.image_viewer, 0, 0)
self.image_viewer.show()
def create_action(self,
text,
slot=None,
shortcut=None,
icon=None,
tooltip=None,
checkable=None,
signal='triggered()',
checked=False):
action = QAction(text, self)
if icon is not None:
action.setIcon(QIcon(':/%s.png' % icon))
if shortcut is not None:
action.setShortcut(shortcut)
if tooltip is not None:
action.setToolTip(tooltip)
action.setStatusTip(tooltip)
if slot is not None:
if signal == "triggered()":
action.triggered.connect(slot, Qt.DirectConnection)
else:
action.triggered[bool].connect(slot, Qt.DirectConnection)
if checkable is not None:
action.setCheckable(True)
action.setChecked(checked)
return action
def add_actions(self, target, actions):
for action in actions:
if action is None:
target.addSeparator()
else:
target.addAction(action)
def set_coords(self, coords):
self.image_viewer.set_objects_by_crackcoords(coords)
widget = self._module_manager.get_widget(AnnotationModule.NAME)
widget.set_coords()
def set_classified_crack_contours(self, coords):
self.image_viewer.set_objects_by_crackcoords_with_colors(coords)
widget = self._module_manager.get_widget(AnnotationModule.NAME)
widget.set_coords()
def show_image(self, image_dict):
widget = self.get_display_module()
widget.set_image_dict(image_dict)
self.update_statusbar()
def set_display_module(self, display_module):
self.display_module = display_module
def get_display_module(self):
return self.display_module
def update_statusbar(self):
meta_data = self._imagecontainer.get_meta_data()
if meta_data.has_timelapse:
timestamp = meta_data.get_timestamp_relative(self.coordinate)
time_info = ' | Frame: %d' % self.coordinate.time
if not numpy.isnan(timestamp):
time_info += ' (%.1f min)' % (timestamp / 60)
else:
time_info = ''
msg = 'Plate: %s | Position: %s%s || Zoom: %.1f%%' % \
(self.coordinate.plate, self.coordinate.position, time_info,
self.image_viewer.scalefactor*100)
self._statusbar.showMessage(msg)
def get_coordinate(self):
return self.coordinate.copy()
def on_coordinate_changed(self, coordinate):
"""
All coordinate changes are handled via the Navigator. The change event
from the Navigator is processed here and further propagated via
a new Browser event (the Modules are not supposed to know each other).
"""
self.coordinate = coordinate.copy()
self._t_slider.blockSignals(True)
self._imagecontainer.set_plate(coordinate.plate)
self._t_slider.setValue(coordinate.time)
self._t_slider.blockSignals(False)
self._process_image()
# propagate the signal further to other modules
#self.coordinates_changed.emit(coordinate)
def set_coordinate(self, coordinate):
"""
Changes the Navigator to a fixed coordinate
"""
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_coordinate(coordinate)
def _process_image(self, ):
self.image_viewer.remove_objects()
settings = BaseProcessorFrame.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('skip_finished', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('Processing')
_classify_objects = self._show_objects_by == 'classification'
settings.set2('primary_classification', _classify_objects)
settings.set2('secondary_classification', _classify_objects)
settings.set2('tertiary_classification', _classify_objects)
settings.set2('merged_classification', _classify_objects)
settings.set2('primary_featureextraction', _classify_objects)
settings.set2('secondary_featureextraction', _classify_objects)
settings.set2('objectdetection', self._detect_objects)
settings.set2('tracking', False)
settings.set('Output', 'hdf5_create_file', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
nchannels = len(self._imagecontainer.channels)
# XXX channel mapping unclear
# processing channel <--> color channel
# i.e problems if 2 processing channels have the same color
if nchannels == 2:
settings.set('General', 'process_secondary', True)
elif nchannels >= 3:
settings.set('General', 'process_secondary', True)
settings.set('General', 'process_tertiary', True)
settings.set('General', 'rendering', {})
analyzer = AnalyzerBrowser(self.coordinate.plate, settings,
self._imagecontainer)
res = None
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
res = analyzer()
self.render_browser(res)
except Exception, e:
import traceback
traceback.print_exc()
QMessageBox.critical(self, "Error", str(e))
raise
finally:
class Browser(QMainWindow):
ZOOM_STEP = 1.05
show_objects_toggled = pyqtSignal('bool')
show_contours_toggled = pyqtSignal('bool')
coordinates_changed = pyqtSignal(Coordinate)
def __init__(self, settings, imagecontainer):
QMainWindow.__init__(self)
frame = QFrame(self)
self.setCentralWidget(frame)
self._stopwatch = StopWatch()
self._settings = settings
self._imagecontainer = imagecontainer
self._show_objects = False
self._object_region = None
self.coordinate = Coordinate()
self.grabGesture(Qt.SwipeGesture)
self.setStyleSheet(
"""
QStatusBar { border-top: 1px solid gray; }
""")
layout = QVBoxLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
splitter = QSplitter(Qt.Horizontal, frame)
#splitter.setSizePolicy(QSizePolicy(QSizePolicy.Minimum,
# QSizePolicy.Expanding))
layout.addWidget(splitter)
frame = QFrame(self)
frame_side = QStackedWidget(splitter)
#splitter.setChildrenCollapsible(False)
splitter.addWidget(frame)
splitter.addWidget(frame_side)
splitter.setStretchFactor(0, 1)
splitter.setStretchFactor(1, 0)
splitter.setSizes([-1, 80])
self.coordinate.plate = self._imagecontainer.plates[0]
self._imagecontainer.set_plate(self.coordinate.plate)
self.coordinate.channel = self._imagecontainer.channels[0]
meta_data = self._imagecontainer.get_meta_data()
layout = QGridLayout(frame)
layout.setContentsMargins(0, 0, 0, 0)
self.image_viewer = ImageViewer(frame, auto_resize=True)
layout.addWidget(self.image_viewer, 0, 0)
#self.image_viewer.image_mouse_dblclk.connect(self._on_dbl_clk)
self.image_viewer.zoom_info_updated.connect(self.on_zoom_info_updated)
self._t_slider = QSlider(Qt.Horizontal, frame)
self._t_slider.setMinimum(meta_data.times[0])
self._t_slider.setMaximum(meta_data.times[-1])
self._t_slider.setTickPosition(QSlider.TicksBelow)
self._t_slider.valueChanged.connect(self.on_time_changed_by_slider,
Qt.DirectConnection)
if self._imagecontainer.has_timelapse:
self._t_slider.show()
else:
self._t_slider.hide()
layout.addWidget(self._t_slider, 1, 0)
self.coordinate.position = meta_data.positions[0]
self.coordinate.time = self._t_slider.minimum()
# menus
act_next_t = self.create_action('Next Time-point',
shortcut=QKeySequence('Right'),
slot=self.on_act_next_t)
act_prev_t = self.create_action('Previous Time-point',
shortcut=QKeySequence('Left'),
slot=self.on_act_prev_t)
act_next_pos = self.create_action('Next Position',
shortcut=QKeySequence('Shift+Down'),
slot=self.on_act_next_pos)
act_prev_pos = self.create_action('Previous Position',
shortcut=QKeySequence('Shift+Up'),
slot=self.on_act_prev_pos)
act_next_plate = self.create_action('Next Plate',
shortcut=QKeySequence('Shift+Alt+Down'),
slot=self.on_act_next_plate)
act_prev_plate = self.create_action('Previous Plate',
shortcut=QKeySequence('Shift+Alt+Up'),
slot=self.on_act_prev_plate)
act_resize = self.create_action('Automatically Resize',
shortcut=QKeySequence('SHIFT+CTRL+R'),
slot=self.on_act_autoresize,
signal='triggered(bool)',
checkable=True,
checked=True)
self._act_resize = act_resize
act_zoomfit = self.create_action('Zoom to Fit',
shortcut=QKeySequence('CTRL+0'),
slot=self.on_act_zoomfit)
act_zoom100 = self.create_action('Actual Size',
shortcut=QKeySequence('CTRL+1'),
slot=self.on_act_zoom100)
act_zoomin = self.create_action('Zoom In',
shortcut=QKeySequence('CTRL++'),
slot=self.on_act_zoomin)
act_zoomout = self.create_action('Zoom Out',
shortcut=QKeySequence('CTRL+-'),
slot=self.on_act_zoomout)
act_fullscreen = self.create_action('Full Screen',
shortcut=QKeySequence('CTRL+F'),
slot=self.on_act_fullscreen,
signal='triggered(bool)',
checkable=True,
checked=False)
self._act_fullscreen = act_fullscreen
act_show_contours = self.create_action('Show Object Contours',
shortcut=QKeySequence('ALT+C'),
slot=self.on_act_show_contours,
signal='triggered(bool)',
checkable=True,
checked=self.image_viewer.show_contours)
self._act_show_contours = act_show_contours
act_anti = self.create_action('Antialiasing',
shortcut=QKeySequence('CTRL+ALT+A'),
slot=self.on_act_antialiasing,
signal='triggered(bool)',
checkable=True,
checked=True)
act_smooth = self.create_action('Smooth Transform',
shortcut=QKeySequence('CTRL+ALT+S'),
slot=self.on_act_smoothtransform,
signal='triggered(bool)',
checkable=True,
checked=True)
view_menu = self.menuBar().addMenu('&View')
self.add_actions(view_menu, (act_resize, None,
act_zoom100, act_zoomfit,
act_zoomin, act_zoomout,
None,
act_prev_t, act_next_t,
act_prev_pos, act_next_pos,
act_prev_plate, act_next_plate,
None,
act_fullscreen, None,
act_show_contours, None,
act_anti, act_smooth,
))
self._statusbar = QStatusBar(self)
self.setStatusBar(self._statusbar)
# tool bar
toolbar = self.addToolBar('Toolbar')
toolbar.setMovable(False)
toolbar.setFloatable(False)
region_names = ['Primary - primary']
self._settings.set_section('ObjectDetection')
for prefix in ['secondary', 'tertiary']:
if self._settings.get('Processing', '%s_processchannel' % prefix):
for name in REGION_NAMES_SECONDARY:
if self._settings.get2('%s_regions_%s' % (prefix, name)):
region_names.append('%s - %s' % (prefix.capitalize(), name))
# FIXME: something went wrong with setting up the current region
self._object_region = region_names[0].split(' - ')
# create a new ModuleManager with a QToolbar and QStackedFrame
self._module_manager = ModuleManager(toolbar, frame_side)
NavigationModule(self._module_manager, self, self._imagecontainer)
DisplayModule(self._module_manager, self, self._imagecontainer,
region_names)
AnnotationModule(self._module_manager, self, self._settings,
self._imagecontainer)
# set the Navigation module activated
self._module_manager.activate_tab(NavigationModule.NAME)
# process and display the first image
self._process_image()
def create_action(self, text, slot=None, shortcut=None, icon=None,
tooltip=None, checkable=None, signal='triggered()',
checked=False):
action = QAction(text, self)
if icon is not None:
action.setIcon(QIcon(':/%s.png' % icon))
if shortcut is not None:
action.setShortcut(shortcut)
if tooltip is not None:
action.setToolTip(tooltip)
action.setStatusTip(tooltip)
if slot is not None:
self.connect(action, SIGNAL(signal), slot, Qt.DirectConnection)
if checkable is not None:
action.setCheckable(True)
action.setChecked(checked)
return action
def add_actions(self, target, actions):
for action in actions:
if action is None:
target.addSeparator()
else:
target.addAction(action)
def set_coords(self, coords):
self.image_viewer.remove_objects()
self.image_viewer.set_objects_by_crackcoords(coords)
widget = self._module_manager.get_widget(AnnotationModule.NAME)
widget.set_coords()
def set_image(self, image_dict):
widget = self._module_manager.get_widget(DisplayModule.NAME)
widget.set_image_dict(image_dict)
self.update_statusbar()
def update_statusbar(self):
meta_data = self._imagecontainer.get_meta_data()
if meta_data.has_timelapse:
timestamp = meta_data.get_timestamp_relative(self.coordinate)
time_info = ' | Frame: %d' % self.coordinate.time
if not numpy.isnan(timestamp):
time_info += ' (%.1f min)' % (timestamp / 60)
else:
time_info = ''
msg = 'Plate: %s | Position: %s%s || Zoom: %.1f%%' % \
(self.coordinate.plate, self.coordinate.position, time_info,
self.image_viewer.scale_factor*100)
self._statusbar.showMessage(msg)
def get_coordinate(self):
return self.coordinate.copy()
def on_coordinate_changed(self, coordinate):
"""
All coordinate changes are handled via the Navigator. The change event
from the Navigator is processed here and further propagated via
a new Browser event (the Modules are not supposed to know each other).
"""
self.coordinate = coordinate.copy()
self._t_slider.blockSignals(True)
self._imagecontainer.set_plate(coordinate.plate)
meta_data = self._imagecontainer.get_meta_data()
self._t_slider.setMaximum(meta_data.dim_t)
self._t_slider.setValue(coordinate.time)
self._t_slider.blockSignals(False)
self._process_image()
# propagate the signal further to other modules
self.coordinates_changed.emit(coordinate)
def set_coordinate(self, coordinate):
"""
Changes the Navigator to a fixed coordinate
"""
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_coordinate(coordinate)
def _process_image(self):
print 'process image'
self._stopwatch.reset()
s = StopWatch()
settings = _ProcessorMixin.get_special_settings(self._settings)
settings.set_section('General')
settings.set2('constrain_positions', True)
settings.set2('positions', self.coordinate.position)
settings.set2('redofailedonly', False)
settings.set2('framerange', True)
settings.set2('framerange_begin', self.coordinate.time)
settings.set2('framerange_end', self.coordinate.time)
settings.set_section('ObjectDetection')
prim_id = PrimaryChannel.NAME
#sec_id = SecondaryChannel.NAME
#sec_regions = settings.get2('secondary_regions')
settings.set_section('Processing')
settings.set2('primary_classification', False)
settings.set2('secondary_classification', False)
settings.set2('primary_featureextraction', False)
settings.set2('secondary_featureextraction', False)
settings.set2('objectdetection', self._show_objects)
settings.set2('tracking', False)
settings.set_section('Output')
settings.set2('rendering_contours_discwrite', False)
settings.set2('rendering_class_discwrite', False)
settings.set2('export_object_counts', False)
settings.set2('export_object_details', False)
settings.set2('export_track_data', False)
settings.set_section('Classification')
settings.set2('collectsamples', False)
settings.set('General', 'rendering', {})
settings.set('General', 'rendering_class', {})
if len(self._imagecontainer.channels) > 1:
settings.set('Processing', 'secondary_processChannel', True)
settings.set('General', 'rendering', {})
print settings
analyzer = AnalyzerCore(self.coordinate.plate, settings,
self._imagecontainer)
analyzer.processPositions(myhack=self)
print('PROCESS IMAGE: %s' % s)
# slots
def on_zoom_info_updated(self, info):
self.update_statusbar()
def on_time_changed_by_slider(self, time):
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_time(time)
def on_object_region_changed(self, channel, region):
self._object_region = channel, region
self._process_image()
def on_act_prev_t(self):
self._t_slider.setValue(self._t_slider.value()-1)
def on_act_next_t(self):
self._t_slider.setValue(self._t_slider.value()+1)
def on_act_prev_pos(self):
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_prev_position()
def on_act_next_pos(self):
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_next_position()
def on_act_prev_plate(self):
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_prev_plate()
def on_act_next_plate(self):
nav = self._module_manager.get_widget(NavigationModule.NAME)
nav.nav_to_next_plate()
def on_act_fullscreen(self, checked):
if checked:
self.showFullScreen()
else:
self.showNormal()
self.raise_()
def on_act_show_contours(self, checked):
self._act_show_contours.blockSignals(True)
self._act_show_contours.setChecked(checked)
self._act_show_contours.blockSignals(False)
self.image_viewer.set_show_contours(checked)
self.show_contours_toggled.emit(checked)
def on_act_antialiasing(self, checked):
self.image_viewer.setRenderHint(QPainter.Antialiasing, checked)
self.image_viewer.update()
def on_act_smoothtransform(self, checked):
self.image_viewer.setRenderHint(QPainter.SmoothPixmapTransform,
checked)
self.image_viewer.update()
def on_act_autoresize(self, state):
self.image_viewer.set_auto_resize(state)
if state:
self.image_viewer.scale_to_fit()
def on_act_zoom100(self):
self.image_viewer.set_auto_resize(False)
self._act_resize.setChecked(False)
self.image_viewer.scale_reset()
def on_act_zoomfit(self):
self.image_viewer.set_auto_resize(False)
self._act_resize.setChecked(False)
self.image_viewer.scale_to_fit()
def on_act_zoomin(self):
self.image_viewer.set_auto_resize(False)
self._act_resize.setChecked(False)
self.image_viewer.scale_relative(self.ZOOM_STEP, ensure_fit=False)
def on_act_zoomout(self):
self.image_viewer.set_auto_resize(False)
self._act_resize.setChecked(False)
self.image_viewer.scale_relative(1/self.ZOOM_STEP, ensure_fit=True)
def on_act_transform(self, checked):
if checked:
self.image_viewer.set_scale_transform(Qt.FastTransformation)
else:
self.image_viewer.set_scale_transform(Qt.SmoothTransformation)
self._process_image()
def on_act_class_selected(self, class_label):
items = self._find_items_in_class_table(str(class_label),
self.COLUMN_CLASS_LABEL)
if len(items) == 1:
self._class_table.setCurrentItem(items[0])
def on_show_objects(self, state):
self._show_objects = state
self.image_viewer.remove_objects()
self._process_image()
self.show_objects_toggled.emit(state)
# Qt method overwrites
def keyPressEvent(self, ev):
QMainWindow.keyPressEvent(self, ev)
# allow to return from fullscreen via the Escape key
if self.isFullScreen() and ev.key() == Qt.Key_Escape:
self.showNormal()
self._act_fullscreen.setChecked(False)
self.raise_()
def gestureEvent(self, ev):
# determine whether a swipe gesture was detected
if not ev.gesture(Qt.SwipeGesture) is None:
gesture = ev.gesture(Qt.SwipeGesture)
if gesture.state() == Qt.GestureFinished:
if gesture.horizontalDirection() == QSwipeGesture.Left:
self._on_act_left()
elif gesture.horizontalDirection() == QSwipeGesture.Right:
self._on_act_right()
elif gesture.horizontalDirection() == QSwipeGesture.Up:
self._on_act_up()
elif gesture.horizontalDirection() == QSwipeGesture.Down:
self._on_act_down()
return True
def event(self, ev):
if ev.type() == QEvent.Gesture:
return self.gestureEvent(ev)
return QWidget.event(self, ev)
