class SectionClassification(SectionCore):
SECTION_NAME = SECTION_NAME_CLASSIFICATION
OPTIONS = [('%s_classification' % x, [ ('%s_classification_envpath' % x, \
StringTrait('', 1000, label='Classifier folder',
widget_info=StringTrait.STRING_PATH)),
('%s_classification_regionname' % x,
SelectionTrait2(None, [], label='Region name')),
('%s_classification_annotationfileext' % x,
StringTrait('xml', 50, label='Annotation ext.')) ]) \
for x in (CH_PRIMARY+CH_OTHER)] + \
[('collectsamples', [ ('collectsamples', BooleanTrait(False)),
('collectsamples_prefix', StringTrait('',100))]),
('merged_channel', [ ('merge_primary', BooleanTrait(True, label='primary')),
('merge_secondary', BooleanTrait(True, label='secondary')),
('merge_tertiary', BooleanTrait(True, label='tertiary')) ])
] + \
[('%s_classification' %CH_VIRTUAL[0],
[ ('%s_classification_envpath' %CH_VIRTUAL[0], \
StringTrait('', 1000, label='Classifier folder',
widget_info=StringTrait.STRING_PATH)),
('%s_primary_region' %CH_VIRTUAL[0],
SelectionTrait2(None, [], label='')),
('%s_secondary_region' %CH_VIRTUAL[0],
SelectionTrait2(None, [], label='')),
('%s_tertiary_region' %CH_VIRTUAL[0],
SelectionTrait2(None, [], label='')),
('%s_classification_annotationfileext' %CH_VIRTUAL[0],
StringTrait('xml', 50, label='Annotation ext.')),
('%s_classification_regionname' %CH_VIRTUAL[0],
SelectionTrait2(None, [], label="Region name"))
])]
class SectionEventSelection(SectionCore):
SECTION_NAME = SECTION_NAME_EVENT_SELECTION
OPTIONS = [
('event_selection',
[('eventchannel',
SelectionTrait2(None, [], label='Channel')),
('event_selection',
BooleanTrait(True, label='Event Selection')),
('backwardrange',
FloatTrait(0, -1, 4000, label='Duration [pre]')),
('forwardrange',
FloatTrait(0, -1, 4000, label='Duration [post]')),
('duration_unit',
SelectionTrait2(TimeConverter.FRAMES,
TimeConverter.units,
label='Duration unit')),
('backwardrange_min', BooleanTrait(False, label='Min.')),
('forwardrange_min', BooleanTrait(False, label='Min.')),
('maxindegree', IntTrait(1, 0, 4000, label='Max in-degree')),
('maxoutdegree', IntTrait(2, 0, 4000, label='Max out-degree')),
]),
('supervised_event_selection',
[('supervised_event_selection',
BooleanTrait(True, label='Supervised',
widget_info=BooleanTrait.RADIOBUTTON)),
('labeltransitions',
StringTrait('', 200, label='Class transition motif(s)')),
('backwardlabels',
StringTrait('', 200, label='Class filter [pre]',
mask='(\d+,)*\d+')),
('forwardlabels',
StringTrait('', 200, label='Class filter [post]',
mask='(\d+,)*\d+')),
('backwardcheck',
FloatTrait(2, 0, 4000, label='Filter duration [pre]')),
('forwardcheck',
FloatTrait(2, 0, 4000, label='Filter duration [post]')),
]),
('unsupervised_event_selection',
[('unsupervised_event_selection',
BooleanTrait(False, label='Unsupervised',
widget_info=BooleanTrait.RADIOBUTTON)),
('min_event_duration',
IntTrait(3, 1, 100, label='Min. event duration')),
('num_clusters',
IntTrait(6, 2, 15, label='Number of clusters',)),
('min_cluster_size',
IntTrait(2, 1, 10, label='Min. cluster size',)),
])
]
class SectionTracking(SectionCore):
SECTION_NAME = SECTION_NAME_TRACKING
OPTIONS = [
('tracking', [
('region', SelectionTrait2(None, [], label='Region name')),
('tracking_maxobjectdistance',
IntTrait(0, 0, 4000, label='Max object x-y distance')),
('tracking_maxtrackinggap',
IntTrait(0, 0, 4000, label='Max time-point gap')),
('tracking_maxsplitobjects',
IntTrait(0, 0, 4000, label='Max split events')),
('tracking_exporttrackfeatures',
BooleanTrait(True, label='Export tracks')),
('tracking_compressiontrackfeatures',
SelectionTrait(COMPRESSION_FORMATS[0],
COMPRESSION_FORMATS,
label='Compression')),
]),
('visualization', [
('tracking_visualization',
BooleanTrait(False, label='Visualization')),
('tracking_visualize_track_length',
IntTrait(5, -1, 10000, label='Max. time-points')),
('tracking_centroid_radius',
IntTrait(3, -1, 50, label='Centroid radius')),
]),
]
class SectionTracking(SectionCore):
SECTION_NAME = SECTION_NAME_TRACKING
OPTIONS = [
('tracking', [
('region', SelectionTrait2(None, [], label='Region name')),
('tracking_maxobjectdistance',
IntTrait(0, 0, 4000, label='Max object x-y distance')),
('tracking_maxtrackinggap',
IntTrait(0, 0, 4000, label='Max time-point gap')),
('tracking_maxsplitobjects',
IntTrait(0, 0, 4000, label='Max split events')),
]),
]
def __init__(self,
plugin_cls,
plugin_name,
settings,
manager,
set_default=True):
self._settings = settings
self._section = manager.section
self._lookup = {}
self._lookup_reverse = {}
self._observer_traits = []
self._plugin_name = plugin_name
params = plugin_cls.PARAMS
trait_name_template = manager.get_trait_name_template(
plugin_cls.NAME, plugin_name)
# inject traits controlling plugin requirements dynamically
foreign_managers = dict([(mngr.name, mngr)
for mngr in PLUGIN_MANAGERS])
if not plugin_cls.REQUIRES is None:
for idx, require in enumerate(plugin_cls.REQUIRES):
# get the foreign manager that controls the requirement
foreign_manager = foreign_managers[require]
# get the names of plugin instances of the foreign manager
names = foreign_manager.get_plugin_names()
# define an update callback which is triggered every time the requirement (plugin instance) is changed
update_callback = lambda referee: lambda new, old: foreign_manager.handle_referee(
new, old, referee)
# define a new trait for the current requirement
trait = SelectionTrait2(None if len(names) < 1 else names[0],
names,
label=foreign_manager.display_name,
update_callback=update_callback(
(manager.name, plugin_name)))
# register this trait to the foreign manager which controls the dependency for change notifications
foreign_manager.register_observer(trait)
self._observer_traits.append((foreign_manager, trait))
params.append((plugin_cls._REQUIRE_STR % idx, trait))
for param_name, trait in params:
trait_name = trait_name_template % param_name
self._lookup[param_name] = trait_name
self._lookup_reverse[trait_name] = param_name
settings.register_trait(self._section, self.GROUP_NAME, trait_name,
trait)
if set_default or not settings.has_option(self._section,
trait_name):
settings.set(self._section, trait_name, trait.default_value)
class SectionObjectdetection(SectionCore):
SECTION_NAME = SECTION_NAME_OBJECTDETECTION
OPTIONS = [
('primary_image',
[('primary_channelid',
SelectionTrait2(None, [], label='Primary channel ID')),
('primary_normalizemin',
IntTrait(0, -2**16, 2**16, label='Min.')),
('primary_normalizemax',
IntTrait(255, -2**16, 2**16, label='Max.')),
('primary_zslice_selection',
BooleanTrait(True, label='Z-slice selection',
widget_info=BooleanTrait.RADIOBUTTON)),
('primary_flat_field_correction',
BooleanTrait(False, label='Z-slice flat field correction',
widget_info=BooleanTrait.CHECKBOX)),
('primary_flat_field_correction_image_dir',
StringTrait('', 1000, label='Correction image directory',
widget_info=StringTrait.STRING_PATH)),
('primary_zslice_selection_slice',
IntTrait(1, 0, 1000, label='Slice')),
('primary_zslice_projection',
BooleanTrait(False, label='Z-slice projection',
widget_info=BooleanTrait.RADIOBUTTON)),
('primary_zslice_projection_method',
SelectionTrait(ZSLICE_PROJECTION_METHODS[0],
ZSLICE_PROJECTION_METHODS, label='Method')),
('primary_zslice_projection_begin',
IntTrait(1, 0, 1000, label='Begin')),
('primary_zslice_projection_end',
IntTrait(1, 0, 1000, label='End')),
('primary_zslice_projection_step',
IntTrait(1, 1, 1000, label='Step')),
# these two options are nopes, just to have no
# special casing in channel classes
('primary_channelregistration_x',
IntTrait(0, -99999, 99999, label='Shift X')),
('primary_channelregistration_y',
IntTrait(0, -99999, 99999, label='Shift Y')),
]),
] + \
unlist(
[[('%s_image' % prefix,
[('%s_channelid' % prefix,
SelectionTrait2(None, [], label='%s channel ID' % name)),
('%s_normalizemin' % prefix,
IntTrait(0, -2**16, 2**16, label='Min.')),
('%s_normalizemax' % prefix,
IntTrait(255, -2**16, 2**16, label='Max.')),
('%s_zslice_selection' % prefix,
BooleanTrait(True, label='Z-slice selection',
widget_info=BooleanTrait.RADIOBUTTON)),
('%s_flat_field_correction' % prefix,
BooleanTrait(False, label='Z-slice flat field correction',
widget_info=BooleanTrait.CHECKBOX)),
('%s_flat_field_correction_image_dir' % prefix,
StringTrait('', 1000, label='Correction image directory',
widget_info=StringTrait.STRING_PATH)),
('%s_zslice_selection_slice' % prefix,
IntTrait(1, 0, 1000, label='Slice')),
('%s_zslice_projection' % prefix,
BooleanTrait(False, label='Z-slice projection',
widget_info=BooleanTrait.RADIOBUTTON)),
('%s_zslice_projection_method' % prefix,
SelectionTrait(ZSLICE_PROJECTION_METHODS[0],
ZSLICE_PROJECTION_METHODS, label='Method')),
('%s_zslice_projection_begin' % prefix,
IntTrait(1, 0, 1000, label='Begin')),
('%s_zslice_projection_end' % prefix,
IntTrait(1, 0, 1000, label='End')),
('%s_zslice_projection_step' % prefix,
IntTrait(1, 1, 1000, label='Step')),
]),
('%s_registration' % prefix,
[('%s_channelregistration_x' % prefix,
IntTrait(0, -99999, 99999, label='Shift X')),
('%s_channelregistration_y' % prefix,
IntTrait(0, -99999, 99999, label='Shift Y')),
]),
]
for name, prefix in [('Secondary', 'secondary'),
('Tertiary', 'tertiary'),
# moste merged channel options are nopes
# to avoid special casing
('Merged', 'merged')
]]
)
class SectionTracking(SectionCore):
SECTION_NAME = SECTION_NAME_TRACKING
OPTIONS = [
('tracking', [
('tracking_regionname',
SelectionTrait2(None, [], label='Region name')),
('tracking_maxobjectdistance',
IntTrait(0, 0, 4000, label='Max object x-y distance')),
('tracking_maxtrackinggap',
IntTrait(0, 0, 4000, label='Max time-point gap')),
('tracking_maxsplitobjects',
IntTrait(0, 0, 4000, label='Max split events')),
('tracking_maxindegree', IntTrait(1,
0,
4000,
label='Max in-degree')),
('tracking_maxoutdegree',
IntTrait(2, 0, 4000, label='Max out-degree')),
('tracking_exporttrackfeatures',
BooleanTrait(True, label='Export tracks')),
('tracking_compressiontrackfeatures',
SelectionTrait(COMPRESSION_FORMATS[0],
COMPRESSION_FORMATS,
label='Compression')),
]),
('event_selection', [
('tracking_labeltransitions',
StringTrait('',
200,
label='Class transition motif(s)',
mask='(\(\d+,\d+\),)*\(\d+,\d+\)')),
('tracking_backwardrange',
FloatTrait(0, -1, 4000, label='Duration [pre]')),
('tracking_forwardrange',
FloatTrait(0, -1, 4000, label='Duration [post]')),
('tracking_backwardlabels',
StringTrait('',
200,
label='Class filter [pre]',
mask='(\d+,)*\d+')),
('tracking_forwardlabels',
StringTrait('',
200,
label='Class filter [post]',
mask='(\d+,)*\d+')),
('tracking_backwardcheck',
FloatTrait(2, 0, 4000, label='Filter duration [pre]')),
('tracking_forwardcheck',
FloatTrait(2, 0, 4000, label='Filter duration [post]')),
('tracking_duration_unit',
SelectionTrait2(TRACKING_DURATION_UNITS_DEFAULT[0],
TRACKING_DURATION_UNITS_DEFAULT,
label='Duration unit')),
('tracking_backwardrange_min', BooleanTrait(False, label='Min.')),
('tracking_forwardrange_min', BooleanTrait(False, label='Min.')),
]),
('visualization', [
('tracking_visualization',
BooleanTrait(False, label='Visualization')),
('tracking_visualize_track_length',
IntTrait(5, -1, 10000, label='Max. time-points')),
('tracking_centroid_radius',
IntTrait(3, -1, 50, label='Centroid radius')),
]),
]