def __init__(
self,
strChannelId,
# either number of zsclice or projection type
oZSliceOrProjection=1,
channelRegistration=None,
registration_start=None,
new_image_size=None,
strImageOutCompression="80",
strPathOutDebug=None,
lstFeatureCategories=None,
dctFeatureParameters=None,
lstFeatureNames=None,
bFlatfieldCorrection=False,
strBackgroundImagePath="",
fBackgroundCorrection="",
fNormalizeMin="",
fNormalizeMax="",
fNormalizeRatio="",
fNormalizeOffset="",
check_for_plugins=True):
super(ChannelCore, self).__init__()
# remove all the hungarian bullshit as soon as possible!
self.strChannelId = strChannelId
# either number of zsclice or projection type
self.oZSliceOrProjection = oZSliceOrProjection
self.channelRegistration = channelRegistration
self.registration_start = registration_start
self.new_image_size = new_image_size
self.strImageOutCompression = strImageOutCompression
self.strPathOutDebug = strPathOutDebug
self.lstFeatureCategories = lstFeatureCategories
self.dctFeatureParameters = dctFeatureParameters
self.lstFeatureNames = lstFeatureNames
self.bFlatfieldCorrection = bFlatfieldCorrection
self.strBackgroundImagePath = strBackgroundImagePath
self.fBackgroundCorrection = fBackgroundCorrection
self.fNormalizeMin = fNormalizeMin
self.fNormalizeMax = fNormalizeMax
self.fNormalizeRatio = fNormalizeRatio
self.fNormalizeOffset = fNormalizeOffset
self._zslices = []
self.containers = {}
self._regions = {}
self.meta_image = None
self._features_calculated = False
try:
self.plugin_mgr = MetaPluginManager()[self.NAME.lower()]
if self.plugin_mgr.number_loaded_plugins() < 1:
if check_for_plugins:
raise RuntimeError(
("You need to load at least one segmentation"
" plugin for channel '%s'" % self.NAME))
except KeyError:
self.plugin_mgr = None
def readfp(self, fp):
for plugin_manager in MetaPluginManager():
plugin_manager.clear()
for section in self.sections():
self.remove_section(section)
result = RawConfigParser.readfp(self, fp)
self._old_file_format = False
if not self.has_option('General', 'version') or \
self.get('General', 'version') < version:
self._old_file_format = True
for section_name in self.sections():
if section_name in self._section_registry.section_names():
section = self._section_registry.get_section(section_name)
for option_name in self.options(section_name):
if option_name in section.get_trait_names():
# convert values according to traits
value = self.get_value(section_name, option_name)
self.set(section_name, option_name, value)
elif option_name.startswith('plugin'):
# plugins are okay, because they do not
# obey the old trait concept
pass
else:
try:
self._update_option_to_version(
section_name, option_name)
except NoOptionError as e:
pass
print("Warning: option '%s' in section '%s' is not "
"defined and will be deleted" %\
(option_name, section_name))
self.remove_option(section_name, option_name)
else:
print(
"Warning: section '%s' is not defined and will be "
"deleted" % section_name)
self.remove_section(section_name)
self._merge_registry()
for plugin_manager in MetaPluginManager():
plugin_manager.init_from_settings(self)
return result
def merge_regions(self, regions):
"""Set channels and regions to concatenate."""
reginfo = MetaPluginManager().region_info
reginfo.names[self.NAME.lower()] = [regions.values()]
self._merge_regions.update(regions)
def __init__(self, settings, parent, name):
super(BaseFrame, self).__init__(settings, parent, name)
self.plugin_mgr = MetaPluginManager()
self.name = name
self._is_active = False
self._intervals = list()
self._tab_name = None
self.process_control = ProcessControl(self)
layout = QVBoxLayout(self)
layout.setContentsMargins(0, 0, 0, 0)
self._tab = TabControl(self)
tabs = [self._tab_name] if self.TABS is None else self.TABS
for name in tabs:
frame = QFrame(self._tab)
frame._input_cnt = 0
layout2 = QGridLayout(frame)
layout2.setContentsMargins(20, 20, 20, 20)
self._tab.add_tab(name, frame)
self._tab.set_active_index(0)
self._tab.currentChanged.connect(self.on_tab_changed)
layout.addWidget(self._tab)
layout.addWidget(self.process_control)
def define_exp_features(self):
features = {}
for name in self.processing_channels:
region_features = {}
for region in MetaPluginManager().region_info.names[name.lower()]:
if name is self.MERGED_CHANNEL:
continue
# export all features extracted per regions
if self.settings.get('Output', 'events_export_all_features') or \
self.settings.get('Output', 'export_track_data'):
# None means all features
region_features[region] = None
# export selected features from settings
else:
region_features[region] = \
self.settings.get('General',
'%s_featureextraction_exportfeaturenames'
% name.lower())
features[name] = region_features
# special case for merged channel
if name is self.MERGED_CHANNEL:
mftrs = list()
for channel, region in self._channel_regions(name).iteritems():
if features[channel][region] is None:
mftrs = None
else:
for feature in features[channel][region]:
mftrs.append("_".join((channel, region, feature)))
region_features[self._all_channel_regions[name].values()] = mftrs
features[name] = region_features
return features
def __init__(self,
strChannelId,
# either number of zsclice or projection type
oZSliceOrProjection=1,
channelRegistration=None,
registration_start=None,
new_image_size=None,
strImageOutCompression="80",
strPathOutDebug=None,
lstFeatureCategories=None,
dctFeatureParameters=None,
lstFeatureNames=None,
bFlatfieldCorrection=False,
strBackgroundImagePath="",
fBackgroundCorrection="",
fNormalizeMin="",
fNormalizeMax="",
fNormalizeRatio="",
fNormalizeOffset="",
check_for_plugins=True):
super(ChannelCore, self).__init__()
# remove all the hungarian bullshit as soon as possible!
self.strChannelId = strChannelId
# either number of zsclice or projection type
self.oZSliceOrProjection = oZSliceOrProjection
self.channelRegistration = channelRegistration
self.registration_start = registration_start
self.new_image_size = new_image_size
self.strImageOutCompression = strImageOutCompression
self.strPathOutDebug = strPathOutDebug
self.lstFeatureCategories = lstFeatureCategories
self.dctFeatureParameters = dctFeatureParameters
self.lstFeatureNames = lstFeatureNames
self.bFlatfieldCorrection = bFlatfieldCorrection
self.strBackgroundImagePath = strBackgroundImagePath
self.fBackgroundCorrection = fBackgroundCorrection
self.fNormalizeMin = fNormalizeMin
self.fNormalizeMax = fNormalizeMax
self.fNormalizeRatio = fNormalizeRatio
self.fNormalizeOffset = fNormalizeOffset
self._zslices = []
self.containers = {}
self._regions = {}
self.meta_image = None
self._features_calculated = False
try:
self.plugin_mgr = MetaPluginManager()[self.NAME.lower()]
if self.plugin_mgr.number_loaded_plugins() < 1:
if check_for_plugins:
raise RuntimeError(
("You need to load at least one segmentation"
" plugin for channel '%s'" %self.NAME))
except KeyError:
self.plugin_mgr = None
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 from_dict(self, settings):
for section, group in settings.iteritems():
for option, value in group.iteritems():
RawConfigParser.set(self, section, option, value)
# # update the plugins
for plugin_manager in MetaPluginManager():
plugin_manager.clear()
plugin_manager.init_from_settings(self)
class ChannelCore(LoggerObject):
NAME = None
_rank = None
_is_virtual = False
def __init__(self,
strChannelId,
# either number of zsclice or projection type
oZSliceOrProjection=1,
channelRegistration=None,
registration_start=None,
new_image_size=None,
strImageOutCompression="80",
strPathOutDebug=None,
lstFeatureCategories=None,
dctFeatureParameters=None,
lstFeatureNames=None,
bFlatfieldCorrection=False,
strBackgroundImagePath="",
fBackgroundCorrection="",
fNormalizeMin="",
fNormalizeMax="",
fNormalizeRatio="",
fNormalizeOffset="",
check_for_plugins=True):
super(ChannelCore, self).__init__()
# remove all the hungarian bullshit as soon as possible!
self.strChannelId = strChannelId
# either number of zsclice or projection type
self.oZSliceOrProjection = oZSliceOrProjection
self.channelRegistration = channelRegistration
self.registration_start = registration_start
self.new_image_size = new_image_size
self.strImageOutCompression = strImageOutCompression
self.strPathOutDebug = strPathOutDebug
self.lstFeatureCategories = lstFeatureCategories
self.dctFeatureParameters = dctFeatureParameters
self.lstFeatureNames = lstFeatureNames
self.bFlatfieldCorrection = bFlatfieldCorrection
self.strBackgroundImagePath = strBackgroundImagePath
self.fBackgroundCorrection = fBackgroundCorrection
self.fNormalizeMin = fNormalizeMin
self.fNormalizeMax = fNormalizeMax
self.fNormalizeRatio = fNormalizeRatio
self.fNormalizeOffset = fNormalizeOffset
self._zslices = []
self.containers = {}
self._regions = {}
self.meta_image = None
self._features_calculated = False
try:
self.plugin_mgr = MetaPluginManager()[self.NAME.lower()]
if self.plugin_mgr.number_loaded_plugins() < 1:
if check_for_plugins:
raise RuntimeError(
("You need to load at least one segmentation"
" plugin for channel '%s'" %self.NAME))
except KeyError:
self.plugin_mgr = None
def __cmp__(self, channel):
return cmp(self._rank, channel._rank)
@classmethod
def is_virtual(cls):
return cls._is_virtual
def region_names(self):
return self._regions.keys()
def get_region(self, name):
return self._regions[name]
def has_region(self, name):
return self._regions.has_key(name)
def get_container(self, name):
return self.containers[name]
def append_zslice(self, meta_image):
self._zslices.append(meta_image)
def clear(self):
self._zslices = []
self._regions = {}
self.meta_image = None
self.containers = {}
class ChannelCore(LoggerObject):
NAME = None
_rank = None
_is_virtual = False
def __init__(
self,
strChannelId,
# either number of zsclice or projection type
oZSliceOrProjection=1,
channelRegistration=None,
registration_start=None,
new_image_size=None,
strImageOutCompression="80",
strPathOutDebug=None,
feature_groups=None,
lstFeatureNames=None,
bFlatfieldCorrection=False,
strBackgroundImagePath="",
fBackgroundCorrection="",
fNormalizeMin="",
fNormalizeMax="",
fNormalizeRatio="",
fNormalizeOffset="",
check_for_plugins=True):
super(ChannelCore, self).__init__()
# remove all the hungarian bullshit as soon as possible!
self.strChannelId = strChannelId
# either number of zsclice or projection type
self.oZSliceOrProjection = oZSliceOrProjection
self.channelRegistration = channelRegistration
self.registration_start = registration_start
self.new_image_size = new_image_size
self.strImageOutCompression = strImageOutCompression
self.strPathOutDebug = strPathOutDebug
self.feature_groups = feature_groups
self.lstFeatureNames = lstFeatureNames
self.bFlatfieldCorrection = bFlatfieldCorrection
self.strBackgroundImagePath = strBackgroundImagePath
self.fBackgroundCorrection = fBackgroundCorrection
self.fNormalizeMin = fNormalizeMin
self.fNormalizeMax = fNormalizeMax
self.fNormalizeRatio = fNormalizeRatio
self.fNormalizeOffset = fNormalizeOffset
self._zslices = []
self.containers = {}
self._regions = {}
self.meta_image = None
self._features_calculated = False
try:
self.plugin_mgr = MetaPluginManager()[self.NAME.lower()]
if self.plugin_mgr.number_loaded_plugins() < 1:
if check_for_plugins:
raise RuntimeError(
("You need to load at least one segmentation"
" plugin for channel '%s'" % self.NAME))
except KeyError:
self.plugin_mgr = None
def __cmp__(self, channel):
return cmp(self._rank, channel._rank)
@classmethod
def is_virtual(cls):
return cls._is_virtual
def region_names(self):
return self._regions.keys()
def get_region(self, name):
return self._regions[name]
def has_region(self, name):
return self._regions.has_key(name)
def get_container(self, name):
return self.containers[name]
def append_zslice(self, meta_image):
self._zslices.append(meta_image)
def clear(self):
self._zslices = []
self._regions = {}
self.meta_image = None
self.containers = {}