def core_helper(plate,
settings_dict,
imagecontainer,
position,
version,
redirect=True,
debug=False):
"""Embeds analysis of a positon in a single function"""
# see http://stackoverflow.com/questions/3288595/
# multiprocessing-using-pool-map-on-a-function-defined-in-a-class
logger = logging.getLogger(str(os.getpid()))
import numpy
reload(numpy.core._dotblas)
try:
settings = ConfigSettings()
settings.from_dict(settings_dict)
settings.set('General', 'constrain_positions', True)
settings.set('General', 'positions', position)
environ = CecogEnvironment(version, redirect=redirect, debug=debug)
if debug:
environ.pprint()
analyzer = AnalyzerCore(plate, settings, imagecontainer)
post_hdf5_link_list = analyzer.processPositions()
return plate, position, copy.deepcopy(post_hdf5_link_list)
except Exception as e:
errortxt = "plate: %s, position: %s\n" % (plate, position)
errortxt = "".join([errortxt] + \
traceback.format_exception(*sys.exc_info()))
logger.error(errortxt)
raise e.__class__(errortxt)
def __init__(self):
RawConfigParser.__init__(self, allow_no_value=True)
self.environ = CecogEnvironment(version)
self._registry = OrderedDict()
self._current_section = None
self._old_file_format = False
self._section_registry = SectionRegistry()
for section_name in self._section_registry.section_names():
self.add_section(section_name)
section = self._section_registry.get_section(section_name)
for trait_name in section.get_trait_names():
trait = section.get_trait(trait_name)
self.set(section_name, trait_name, trait.default_value)
def __init__(self, configfile, outdir, image1, image2=None, image3=None):
super(CmdTool, self).__init__()
self.environ = CecogEnvironment(version, redirect=False, debug=False)
self.mapper = SettingsMapper(configfile)
self.images = dict()
names = [cl.NAME for cl in self.mapper.CHANNEL_CLASSES]
for name, image in zip(names, (image1, image2, image3)):
if image is not None:
self.images[name] = image
self.classifiers = dict()
self.outdir = outdir
self._setupClassifier()
def core_helper(plate,
settings_dict,
imagecontainer,
position,
version,
mode="r+",
redirect=True):
"""Embedds analysis of a positon in a single function"""
# see http://stackoverflow.com/questions/3288595/
# multiprocessing-using-pool-map-on-a-function-defined-in-a-class
logger = logging.getLogger(str(os.getpid()))
try:
# FIXME numpy 1.11 does not have ._dotblas
import numpy.core._dotblas
reload(numpy.core._dotblas)
except ImportError as e:
pass
try:
settings = ConfigSettings()
settings.from_dict(settings_dict)
settings.set('General', 'constrain_positions', True)
settings.set('General', 'positions', position)
environ = CecogEnvironment(version, redirect=redirect)
analyzer = PlateAnalyzer(plate, settings, imagecontainer, mode=mode)
analyzer()
return plate, position
except Exception as e:
errortxt = "Plate: %s, Site: %s\n" % (plate, position)
errortxt = "".join([errortxt] + \
traceback.format_exception(*sys.exc_info()))
logger.error(errortxt)
raise type(e)(errortxt)
def __init__(self, appname, version, redirect, debug=False, *args, **kw):
super(CecogAnalyzer, self).__init__(*args, **kw)
self.setWindowTitle("%s-%s" %(appname, version) + '[*]')
self.setCentralWidget(QtGui.QFrame(self))
self.setObjectName(appname)
self.version = version
self.appname = appname
self.debug = debug
self.environ = CecogEnvironment(version, redirect=redirect, debug=debug)
if debug:
self.environ.pprint()
self._is_initialized = False
self._imagecontainer = None
self._meta_data = None
self._browser = None
action_quit = self.create_action('&Quit', slot=self.close)
action_pref = self.create_action('&Preferences',
slot=self.open_preferences)
action_open = self.create_action('&Open Settings...',
shortcut=QtGui.QKeySequence.Open,
slot=self._on_file_open)
action_save = self.create_action('&Save Settings',
shortcut=QtGui.QKeySequence.Save,
slot=self._on_file_save)
self.action_save = action_save
action_save_as = self.create_action('&Save Settings As...',
shortcut=QtGui.QKeySequence.SaveAs,
slot=self._on_file_save_as)
menu_file = self.menuBar().addMenu('&File')
self.add_actions(menu_file, (action_pref,
None, action_open,
None, action_save, action_save_as,
None, action_quit))
action_open = self.create_action('&Open Browser...',
shortcut=QtGui.QKeySequence('CTRL+B'),
slot=self._on_browser_open)
menu_browser = self.menuBar().addMenu('&Browser')
self.add_actions(menu_browser, (action_open, ))
action_log = self.create_action('&Show Log Window...',
shortcut=QtGui.QKeySequence(Qt.CTRL + Qt.Key_L),
slot=self._on_show_log_window)
menu_window = self.menuBar().addMenu('&Window')
self.add_actions(menu_window, (action_log,))
action_help_startup = self.create_action('&Startup Help...',
shortcut=QtGui.QKeySequence.HelpContents,
slot=self._on_help_startup)
action_about = self.create_action('&About', slot=self.on_about)
menu_help = self.menuBar().addMenu('&Help')
self.add_actions(menu_help, (action_help_startup, action_about))
qApp._main_window = self
qApp._statusbar = QtGui.QStatusBar(self)
self.setStatusBar(qApp._statusbar)
self._selection = QtGui.QListWidget(self.centralWidget())
self._selection.setViewMode(QtGui.QListView.IconMode)
self._selection.setIconSize(QtCore.QSize(35, 35))
self._selection.setGridSize(QtCore.QSize(140, 60))
self._selection.setMovement(QtGui.QListView.Static)
self._selection.setMaximumWidth(self._selection.gridSize().width() + 5)
self._selection.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self._selection.setSizePolicy(
QtGui.QSizePolicy(QtGui.QSizePolicy.Fixed,
QtGui.QSizePolicy.Expanding))
self._pages = QtGui.QStackedWidget(self.centralWidget())
self._pages.main_window = self
self._settings_filename = None
self._settings = GuiConfigSettings(self, SECTION_REGISTRY)
self._tab_lookup = OrderedDict()
self._tabs = [GeneralFrame(self._settings, self._pages),
ObjectDetectionFrame(self._settings, self._pages),
FeatureExtractionFrame(self._settings, self._pages),
ClassificationFrame(self._settings, self._pages),
TrackingFrame(self._settings, self._pages),
ErrorCorrectionFrame(self._settings, self._pages),
PostProcessingFrame(self._settings, self._pages),
OutputFrame(self._settings, self._pages),
ProcessingFrame(self._settings, self._pages)]
if self.environ.analyzer_config.get('Analyzer', 'cluster_support'):
self._tabs.append(ClusterFrame(self._settings, self._pages,
self._imagecontainer))
widths = []
for tab in self._tabs:
size = self._add_page(tab)
widths.append(size.width())
self.set_modules_active(state=False)
self._pages.setMinimumWidth(max(widths) + 45)
self._selection.currentItemChanged.connect(self._on_change_page)
self._selection.setCurrentRow(0)
w_logo = QtGui.QLabel(self.centralWidget())
w_logo.setPixmap(QtGui.QPixmap(':cecog_logo_w145'))
layout = QtGui.QGridLayout(self.centralWidget())
layout.addWidget(self._selection, 0, 0)
layout.addWidget(w_logo, 1, 0, Qt.AlignBottom | Qt.AlignHCenter)
layout.addWidget(self._pages, 0, 1, 2, 1)
layout.setContentsMargins(1, 1, 1, 1)
handler = GuiLogHandler(self)
handler.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s %(levelname)-8s %(message)s')
handler.setFormatter(formatter)
self.log_window = LogWindow(self, handler)
self.log_window.setGeometry(50, 50, 600, 300)
logger = logging.getLogger()
logger.setLevel(logging.INFO)
qApp._image_dialog = None
qApp._graphics = None
self.setGeometry(0, 0, 1200, 700)
self.setMinimumSize(QtCore.QSize(700, 600))
self._is_initialized = True
(options, args) = parser.parse_args()
logger = logging.getLogger()
handler = logging.StreamHandler(sys.stdout)
handler.setLevel(logging.INFO)
formatter = logging.Formatter('%(asctime)s %(levelname)-6s %(message)s')
handler.setFormatter(formatter)
logger.addHandler(handler)
logger.setLevel(logging.INFO)
logger.info("*************************************************" + '*'*len(version))
logger.info("*** CellCognition - Batch Analyzer - Version %s ***" %version)
logger.info("*************************************************" + '*'*len(version))
logger.info('argv: %s' % sys.argv)
environ = CecogEnvironment(version)
if options.settings is None:
parser.error('Settings filename required.')
environ = CecogEnvironment(version, redirect=False, debug=False)
filename_settings = os.path.abspath(options.settings)
# read the settings data from file
settings = ConfigSettings()
settings.read(filename_settings)
settings.set_section(SECTION_NAME_GENERAL)
index = options.cluster_index
def __init__(self,
appname,
version,
redirect,
settings=None,
debug=False,
*args,
**kw):
super(CecogAnalyzer, self).__init__(*args, **kw)
self.setWindowTitle("%s-%s" % (appname, version) + '[*]')
self.setAcceptDrops(True)
self.setCentralWidget(QtWidgets.QFrame(self))
self.setObjectName(appname)
self.version = version
self.appname = appname
self.debug = debug
self.environ = CecogEnvironment(version=version,
redirect=redirect,
debug=debug)
if debug:
self.environ.pprint()
self._is_initialized = False
self._imagecontainer = None
self._meta_data = None
self._browser = None
action_quit = self.create_action('&Quit', slot=self.close)
action_pref = self.create_action('&Preferences',
slot=self.open_preferences)
action_load = self.create_action('&Load Settings...',
shortcut=QtGui.QKeySequence.Open,
slot=self._on_file_open)
action_save = self.create_action('&Save Settings',
shortcut=QtGui.QKeySequence.Save,
slot=self._on_file_save)
self.action_save = action_save
action_save_as = self.create_action('&Save Settings As...',
shortcut=QtGui.QKeySequence.SaveAs,
slot=self._on_file_save_as)
menu_file = self.menuBar().addMenu('&File')
self.add_actions(menu_file,
(action_pref, None, action_load, None, action_save,
action_save_as, None, action_quit))
action_log = self.create_action('&Log window',
shortcut=QtGui.QKeySequence(Qt.CTRL +
Qt.Key_L),
slot=self._on_show_log_window)
action_open = self.create_action('&Browser',
shortcut=QtGui.QKeySequence('CTRL+B'),
slot=self._on_browser_open)
menu_view = self.menuBar().addMenu('&View')
self.add_actions(menu_view, (action_log, ))
self.add_actions(menu_view, (action_open, ))
action_assistant = self.create_action(
'&Help',
shortcut=QtGui.QKeySequence.HelpContents,
slot=self.show_assistant)
action_about = self.create_action('&About', slot=self.on_about)
action_aboutQt = self.create_action('&About Qt', slot=self.about_qt)
menu_help = self.menuBar().addMenu('&Help')
self.add_actions(menu_help,
(action_assistant, action_about, action_aboutQt))
self.setStatusBar(QtWidgets.QStatusBar(self))
self._selection = QtWidgets.QListWidget(self.centralWidget())
self._selection.setViewMode(QtWidgets.QListView.IconMode)
self._selection.setIconSize(QtCore.QSize(35, 35))
self._selection.setGridSize(QtCore.QSize(140, 60))
self._selection.setMovement(QtWidgets.QListView.Static)
self._selection.setMaximumWidth(self._selection.gridSize().width() + 5)
self._selection.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self._selection.setSizePolicy(
QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed,
QtWidgets.QSizePolicy.Expanding))
self._pages = FrameStack(self)
self._settings_filename = None
self._settings = GuiConfigSettings(self)
self._tab_lookup = OrderedDict()
self._tabs = [
GeneralFrame(self._settings, self._pages, SECTION_NAME_GENERAL),
ObjectDetectionFrame(self._settings, self._pages,
SECTION_NAME_OBJECTDETECTION),
FeatureExtractionFrame(self._settings, self._pages,
SECTION_NAME_FEATURE_EXTRACTION),
ClassificationFrame(self._settings, self._pages,
SECTION_NAME_CLASSIFICATION),
TrackingFrame(self._settings, self._pages, SECTION_NAME_TRACKING),
EventSelectionFrame(self._settings, self._pages,
SECTION_NAME_EVENT_SELECTION),
ErrorCorrectionFrame(self._settings, self._pages,
SECTION_NAME_ERRORCORRECTION),
OutputFrame(self._settings, self._pages, SECTION_NAME_OUTPUT),
ProcessingFrame(self._settings, self._pages,
SECTION_NAME_PROCESSING)
]
# connections for the section frames
self._tabs[3].connect_browser_btn(self._on_browser_open)
for frame in self._tabs:
frame.status_message.connect(self.statusBar().showMessage)
app = AppPreferences()
if app.cluster_support:
clusterframe = ClusterFrame(self._settings, self._pages,
SECTION_NAME_CLUSTER)
clusterframe.set_imagecontainer(self._imagecontainer)
self._tabs.append(clusterframe)
try:
self.updateStyleSheet(loadStyle(app.stylesheet))
except Exception as e:
# proceed with no stylesheet
traceback.print_exc()
widths = []
for tab in self._tabs:
size = self._add_page(tab)
widths.append(size.width())
self.set_modules_active(state=False)
self._pages.setMinimumWidth(max(widths) + 45)
self._selection.currentItemChanged.connect(self._on_change_page)
self._selection.setCurrentRow(0)
w_logo = QtWidgets.QLabel(self.centralWidget())
w_logo.setPixmap(QtGui.QPixmap(':cecog_logo_w145'))
layout = QtWidgets.QGridLayout(self.centralWidget())
layout.addWidget(self._selection, 0, 0)
layout.addWidget(w_logo, 1, 0, Qt.AlignBottom | Qt.AlignHCenter)
layout.addWidget(self._pages, 0, 1, 2, 1)
layout.setContentsMargins(1, 1, 1, 1)
self.setGeometry(0, 0, 1250, 800)
self.setMinimumSize(QtCore.QSize(700, 600))
self._is_initialized = True
self._restore_geometry()
self.show()
# finally load (demo) - settings
if settings is None:
self.load_settings(self.environ.demo_settings)
elif os.path.isfile(settings):
self.load_settings(settings)
else:
QMessageBox.warning(self, "Warning",
"File (%s) does not exist" % settings)
for idx, info in enumerate(import_iter):
pass
if len(imagecontainer.plates) > 0:
plate = imagecontainer.plates[0]
imagecontainer.set_plate(plate)
return imagecontainer
def load_settings(settings_file):
settings = GuiConfigSettings(None)
settings.read(settings_file)
return settings
if __name__ == "__main__":
import sys
from cecog.environment import CecogEnvironment
from cecog.version import version
environ = CecogEnvironment(version)
app = QApplication(sys.argv)
settings = load_settings((r'C:\Users\sommerc\data\cecog'
'\Settings\exp911_version_150.conf'))
imagecontainer = load_image_container_from_settings(settings)
browser = Browser(settings, imagecontainer)
browser.show()
app.exec_()
