def _connect(self):
self._check_host_url()
success = False
msg = 'Error on connecting to cluster control service on %s' % self._host_url
try:
client = RemotingService(self._host_url)
self.dlg = ProgressDialog("connecting to cluster...", None, 0, 0, self)
func = lambda: client.getService('clustercontrol')
self.dlg.exec_(func)
self._service = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
try:
self.dlg.exec_(self._service.get_cecog_versions)
cluster_versions = self.dlg.getTargetResult()
except Exception as e:
exception(self, msg + '(%s)' %str(e))
else:
if not VERSION in set(cluster_versions):
warning(self, 'Cecog version %s not supported by the cluster' %
VERSION, 'Valid versions are: %s' \
% ', '.join(cluster_versions))
else:
success = True
return success
def _connect(self):
self._check_host_url()
success = False
msg = 'Error on connecting to cluster control service on %s' % self._host_url
try:
client = RemotingService(self._host_url)
self.dlg = waitingProgressDialog('Please wait for the cluster...', self)
self.dlg.setTarget(client.getService, 'clustercontrol')
self.dlg.exec_()
self._service = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
try:
self.dlg.setTarget(self._service.get_cecog_versions)
self.dlg.exec_()
cluster_versions = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
if not VERSION in set(cluster_versions):
warning(self, 'Cecog version %s not supported by the cluster' %
VERSION, 'Valid versions are: %s' \
% ', '.join(cluster_versions))
else:
success = True
return success
def _connect(self):
self._check_host_url()
success = False
msg = 'Error on connecting to cluster control service on %s' % self._host_url
try:
client = RemotingService(self._host_url)
self.dlg = waitingProgressDialog('Please wait for the cluster...',
self)
self.dlg.setTarget(client.getService, 'clustercontrol')
self.dlg.exec_()
self._service = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
try:
self.dlg.setTarget(self._service.get_cecog_versions)
self.dlg.exec_()
cluster_versions = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
if not VERSION in set(cluster_versions):
warning(self, 'Cecog version %s not supported by the cluster' %
VERSION, 'Valid versions are: %s' \
% ', '.join(cluster_versions))
else:
success = True
return success
def _connect(self):
self._check_host_url()
success = False
msg = 'Error on connecting to cluster control service on %s' % self._host_url
try:
client = RemotingService(self._host_url)
self.dlg = ProgressDialog("connecting to cluster...", None, 0, 0, self)
func = lambda: client.getService('clustercontrol')
self.dlg.exec_(func)
self._service = self.dlg.getTargetResult()
except:
exception(self, msg)
else:
try:
self.dlg.exec_(self._service.get_cecog_versions)
cluster_versions = self.dlg.getTargetResult()
except Exception as e:
exception(self, msg + '(%s)' %str(e))
else:
if not version in set(cluster_versions):
warning(self, 'Cecog version %s not supported by the cluster' %
version, 'Valid versions are: %s' \
% ', '.join(cluster_versions))
else:
success = True
return success
def _on_class_apply(self):
'''
Apply class changes
'''
learner = self._learner
class_name_new = str(self._class_text.text())
class_label_new = self._class_sbox.value()
class_name = self._current_class
if not class_name is None:
class_label = learner.class_labels[class_name]
class_labels = learner.class_labels.values()
class_labels.remove(class_label)
class_names = learner.class_names.values()
class_names.remove(class_name)
if len(class_name_new) == 0:
warning(self,
"Invalid class name",
info="The class name must not be empty!")
elif (not class_name_new in class_names
and not class_label_new in class_labels):
del learner.class_names[class_label]
del learner.class_labels[class_name]
del learner.hexcolors[class_name]
item = self._find_items_in_class_table(
class_name, self.COLUMN_CLASS_NAME)[0]
learner.class_names[class_label_new] = class_name_new
learner.class_labels[class_name_new] = class_label_new
class_color = self._class_color_btn.current_color
learner.hexcolors[class_name_new] = \
qcolor_to_hex(class_color)
item.setText(class_name_new)
item2 = self._class_table.item(item.row(),
self.COLUMN_CLASS_LABEL)
item2.setText(str(class_label_new))
item2 = self._class_table.item(item.row(),
self.COLUMN_CLASS_COLOR)
item2.setBackground(QBrush(class_color))
col = get_qcolor_hicontrast(class_color)
self._class_table.resizeRowsToContents()
self._class_table.resizeColumnsToContents()
self._class_table.scrollToItem(item)
self._annotations.rename_class(class_name, class_name_new)
self._current_class = class_name_new
self._activate_objects_for_image(False)
self._activate_objects_for_image(True)
else:
warning(self, "Class names and labels must be unique!",
info="Class name '%s' or label '%s' already used." %\
(class_name_new, class_label_new))
def _on_class_apply(self):
'''
Apply class changes
'''
learner = self._learner
class_name_new = str(self._class_text.text())
class_label_new = self._class_sbox.value()
class_name = self._current_class
if not class_name is None:
class_label = learner.class_labels[class_name]
class_labels = learner.class_labels.values()
class_labels.remove(class_label)
class_names = learner.class_names.values()
class_names.remove(class_name)
if len(class_name_new) == 0:
warning(self, "Invalid class name",
info="The class name must not be empty!")
elif (not class_name_new in class_names and
not class_label_new in class_labels):
del learner.class_names[class_label]
del learner.class_labels[class_name]
del learner.hexcolors[class_name]
item = self._find_items_in_class_table(class_name,
self.COLUMN_CLASS_NAME)[0]
learner.class_names[class_label_new] = class_name_new
learner.class_labels[class_name_new] = class_label_new
class_color = self._class_color_btn.current_color
learner.hexcolors[class_name_new] = \
qcolor_to_hex(class_color)
item.setText(class_name_new)
item2 = self._class_table.item(item.row(),
self.COLUMN_CLASS_LABEL)
item2.setText(str(class_label_new))
item2 = self._class_table.item(item.row(),
self.COLUMN_CLASS_COLOR)
item2.setBackground(QBrush(class_color))
col = get_qcolor_hicontrast(class_color)
self._class_table.resizeRowsToContents()
self._class_table.resizeColumnsToContents()
self._class_table.scrollToItem(item)
self._annotations.rename_class(class_name, class_name_new)
self._current_class = class_name_new
self._activate_objects_for_image(False)
self._activate_objects_for_image(True)
else:
warning(self, "Class names and labels must be unique!",
info="Class name '%s' or label '%s' already used." %\
(class_name_new, class_label_new))
def _on_class_add(self):
"""Add a new class to definition"""
learner = self._learner
class_name_new = str(self._class_text.text())
class_label_new = self._class_sbox.value()
class_labels = learner.class_labels.values()
class_names = learner.class_names.values()
if len(class_name_new) == 0:
warning(self,
"Invalid class name",
info="The class name must not be empty!")
elif (not class_name_new in class_names
and not class_label_new in class_labels):
self._current_class = class_name_new
learner.class_names[class_label_new] = class_name_new
learner.class_labels[class_name_new] = class_label_new
class_color = self._class_color_btn.current_color
learner.hexcolors[class_name_new] = \
qcolor_to_hex(class_color)
row = self._class_table.rowCount()
self._class_table.insertRow(row)
self._class_table.setItem(row, self.COLUMN_CLASS_NAME,
QTableWidgetItem(class_name_new))
self._class_table.setItem(row, self.COLUMN_CLASS_LABEL,
QTableWidgetItem(str(class_label_new)))
self._class_table.setItem(row, self.COLUMN_CLASS_COUNT,
QTableWidgetItem('0'))
item = QTableWidgetItem()
item.setBackground(QBrush(class_color))
self._class_table.setItem(row, self.COLUMN_CLASS_COLOR, item)
self._class_table.resizeRowsToContents()
self._class_table.resizeColumnsToContents()
self._class_table.setCurrentItem(item)
ncl = len(learner.class_names) + 1
self._class_text.setText('class%d' % ncl)
self._class_sbox.setValue(ncl)
self._class_color_btn.set_color(
QColor(AnnotationModule.DEFAULT_CLASS_COLS[(ncl - 1) % len(
AnnotationModule.DEFAULT_CLASS_COLS)]))
else:
warning(self, "Class names and labels must be unique!",
info="Class name '%s' or label '%s' already used." %\
(class_name_new, class_label_new))
def _on_class_add(self):
"""Add a new class to definition"""
learner = self._learner
class_name_new = str(self._class_text.text())
class_label_new = self._class_sbox.value()
class_labels = learner.class_labels.values()
class_names = learner.class_names.values()
if len(class_name_new) == 0:
warning(self, "Invalid class name",
info="The class name must not be empty!")
elif (not class_name_new in class_names and
not class_label_new in class_labels):
self._current_class = class_name_new
learner.class_names[class_label_new] = class_name_new
learner.class_labels[class_name_new] = class_label_new
class_color = self._class_color_btn.current_color
learner.hexcolors[class_name_new] = \
qcolor_to_hex(class_color)
row = self._class_table.rowCount()
self._class_table.insertRow(row)
self._class_table.setItem(row, self.COLUMN_CLASS_NAME,
QTableWidgetItem(class_name_new))
self._class_table.setItem(row, self.COLUMN_CLASS_LABEL,
QTableWidgetItem(str(class_label_new)))
self._class_table.setItem(row, self.COLUMN_CLASS_COUNT,
QTableWidgetItem('0'))
item = QTableWidgetItem()
item.setBackground(QBrush(class_color))
self._class_table.setItem(row, self.COLUMN_CLASS_COLOR, item)
self._class_table.resizeRowsToContents()
self._class_table.resizeColumnsToContents()
self._class_table.setCurrentItem(item)
ncl = len(learner.class_names)+1
self._class_text.setText('class%d' % ncl)
self._class_sbox.setValue(ncl)
self._class_color_btn.set_color(
QColor(AnnotationModule.DEFAULT_CLASS_COLS[(ncl -1) \
% len(AnnotationModule.DEFAULT_CLASS_COLS)]))
else:
warning(self, "Class names and labels must be unique!",
info="Class name '%s' or label '%s' already used." %\
(class_name_new, class_label_new))
def _on_browser_open(self):
if self._imagecontainer is None:
warning(self, 'Data structure not loaded',
'The input data structure was not loaded.\n'
'Please click "Load image data" in General.')
elif self._browser is None:
try:
browser = Browser(self._settings, self._imagecontainer)
browser.show()
browser.raise_()
browser.setFocus()
self._browser = browser
except:
exception(self, 'Problem opening the browser')
else:
self._browser.show()
self._browser.raise_()
def _on_class_add(self):
'''
Add a new class
'''
learner = self._learner
class_name_new = str(self._class_text.text())
class_label_new = self._class_sbox.value()
class_labels = set(learner.lstClassLabels)
class_names = set(learner.lstClassNames)
if len(class_name_new) == 0:
warning(self, "Invalid class name",
info="The class name must not be empty!")
elif (not class_name_new in class_names and
not class_label_new in class_labels):
self._current_class = class_name_new
learner.dctClassNames[class_label_new] = class_name_new
learner.dctClassLabels[class_name_new] = class_label_new
class_color = self._class_color_btn.current_color
learner.dctHexColors[class_name_new] = \
qcolor_to_hex(class_color)
row = self._class_table.rowCount()
self._class_table.insertRow(row)
self._class_table.setItem(row, self.COLUMN_CLASS_NAME,
QTableWidgetItem(class_name_new))
self._class_table.setItem(row, self.COLUMN_CLASS_LABEL,
QTableWidgetItem(str(class_label_new)))
self._class_table.setItem(row, self.COLUMN_CLASS_COUNT,
QTableWidgetItem('0'))
item = QTableWidgetItem()
item.setBackground(QBrush(class_color))
self._class_table.setItem(row, self.COLUMN_CLASS_COLOR, item)
self._class_table.resizeRowsToContents()
self._class_table.resizeColumnsToContents()
self._class_table.setCurrentItem(item)
else:
warning(self, "Class names and labels must be unique!",
info="Class name '%s' or label '%s' already used." %\
(class_name_new, class_label_new))
def load_settings(self, filename):
try:
self._settings.read(filename)
except Exception as e:
critical(self,
"Error loading settings file",
info="Could not load settings file '%s'." % filename,
detail_tb=True)
self.statusBar().showMessage('Settings not successfully loaded.')
else:
self._settings_filename = filename
title = self.windowTitle().split(' - ')[0]
self.setWindowTitle('%s - %s[*]' % (title, filename))
try:
# reset naming scheme to load config file completely
nst = self._settings.get_trait("General", "namingscheme")
namingscheme_file = self._settings("General", "namingscheme")
if not namingscheme_file in nst.list_data:
self._settings.set("General", "namingscheme", nst.default_value)
warning(self, "Unkown naming scheme",
("Your current installation can not use the "
"naming scheme '%s'. Resetting to default '%s'"
%(namingscheme_file, nst.default_value)))
for widget in self._tabs:
widget.update_input()
except Exception as e:
critical(self, "Problem loading settings file.",
info="Fix the problem in file '%s' and load the "\
"settings file again." % filename,
detail_tb=True)
else:
# set settings to not-changed (assume no changed since loaded from file)
self.settings_changed(False)
# notify tabs about new settings loaded
for tab in self._tabs:
tab.settings_loaded()
self.statusBar().showMessage('Settings successfully loaded.')
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, 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 update_event_table(self, coord):
pos = self.ch5file.get_position_from_coord(coord)
try:
events = pos.get_event_items()
except KeyError as ke:
exception(self, "No event data found in CellH5. Make sure tracking and event selection has been enabled! ('%s)'"% str(ke))
return
except Exception as e:
exception(self, "An error has occured ('%s)'"% str(e))
return
if len(events) == 0:
warning(self, "No event data found...")
return
self.event_table.setRowCount(0)
selected_track = []
start_ids = map(lambda x: x[1][0], events)
time_idxs = pos.get_time_indecies(start_ids)
self.tracks = []
cnt = 0
for (e_id, e), time_idx in zip(events, time_idxs):
QApplication.processEvents()
if self._cb_track.checkState():
track = e[:-1] + pos.track_first(e[-1])
else:
track = e
selected_track.append(e)
self.event_table.insertRow(cnt)
event_id_item = QTableWidgetItem()
event_id_item.setData(Qt.DisplayRole, e_id)
self.event_table.setItem(cnt, 0, event_id_item)
tmp_i = QTableWidgetItem()
tmp_j = QTableWidgetItem()
# to make sorting according to numbers
tmp_i.setData(Qt.DisplayRole, len(track))
tmp_j.setData(Qt.DisplayRole, int(time_idx))
self.event_table.setItem(cnt, 1, tmp_i)
self.event_table.setItem(cnt, 2, tmp_j)
if cnt == 0:
self.event_table.resizeRowsToContents()
self.event_table.resizeColumnsToContents()
cnt+=1
self.tracks.append(track)
self.event_table.resizeRowsToContents()
self.event_table.resizeColumnsToContents()
self.event_table.setSortingEnabled(True)
def update_event_table(self, coord):
pos = self.ch5file.get_position_from_coord(coord)
try:
events = pos.get_event_items()
except KeyError as ke:
exception(
self,
"No event data found in CellH5. Make sure tracking and event selection has been enabled! ('%s)'"
% str(ke))
return
except Exception as e:
exception(self, "An error has occured ('%s)'" % str(e))
return
if len(events) == 0:
warning(self, "No event data found...")
return
self.event_table.setRowCount(0)
selected_track = []
start_ids = map(lambda x: x[1][0], events)
time_idxs = pos.get_time_indecies(start_ids)
self.tracks = []
cnt = 0
for (e_id, e), time_idx in zip(events, time_idxs):
QApplication.processEvents()
if self._cb_track.checkState():
track = e[:-1] + pos.track_first(e[-1])
else:
track = e
selected_track.append(e)
self.event_table.insertRow(cnt)
event_id_item = QTableWidgetItem()
event_id_item.setData(Qt.DisplayRole, e_id)
self.event_table.setItem(cnt, 0, event_id_item)
tmp_i = QTableWidgetItem()
tmp_j = QTableWidgetItem()
# to make sorting according to numbers
tmp_i.setData(Qt.DisplayRole, len(track))
tmp_j.setData(Qt.DisplayRole, int(time_idx))
self.event_table.setItem(cnt, 1, tmp_i)
self.event_table.setItem(cnt, 2, tmp_j)
if cnt == 0:
self.event_table.resizeRowsToContents()
self.event_table.resizeColumnsToContents()
cnt += 1
self.tracks.append(track)
self.event_table.resizeRowsToContents()
self.event_table.resizeColumnsToContents()
self.event_table.setSortingEnabled(True)