class SegmentationPluginPropagate(_SegmentationPlugin):
LABEL = 'Propagate region from primary'
NAME = 'propagate'
COLOR = '#FFFF99'
DOC = ":additional_segmentation_plugins"
REQUIRES = ['primary_segmentation']
PARAMS = [('presegmentation_median_radius', IntTrait(1, 0, 100, label='Median radius')),
('presegmentation_alpha', FloatTrait(1.0, 0, 4000, label='Otsu factor', digits=2)),
('lambda', FloatTrait(0.05, 0, 4000, label='Lambda', digits=2)),
('delta_width', IntTrait(1, 1, 4, label='Delta width')),
]
@stopwatch()
def _run(self, meta_image, container):
image = meta_image.image
img_prefiltered = ccore.disc_median(image, self.params['presegmentation_median_radius'])
t = int(ccore.get_otsu_threshold(img_prefiltered) * self.params['presegmentation_alpha'])
img_bin = ccore.threshold_image(img_prefiltered, t)
img_labels = ccore.segmentation_propagate(img_prefiltered, img_bin,
container.img_labels,
self.params['lambda'],
self.params['delta_width'])
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
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 SectionErrorcorrection(SectionCore):
SECTION_NAME = SECTION_NAME_ERRORCORRECTION
OPTIONS = [
('error_correction',
[('primary', BooleanTrait(True, label='primary')),
('secondary', BooleanTrait(False, label='secondary')),
('tertiary', BooleanTrait(False, label='tertiary')),
('merged', BooleanTrait(False, label='merged')),
('constrain_graph',
BooleanTrait(True, label='Constrain graph')),
('primary_graph',
StringTrait('', 1000, label='Primary file',
widget_info=StringTrait.STRING_FILE)),
('secondary_graph',
StringTrait('', 1000, label='Secondary file',
widget_info=StringTrait.STRING_FILE)),
('tertiary_graph',
StringTrait('', 1000, label='Tertiary file',
widget_info=StringTrait.STRING_FILE)),
('merged_graph',
StringTrait('', 1000, label='Merged ch. file',
widget_info=StringTrait.STRING_FILE)),
('groupby_position',
BooleanTrait(True, label='Position',
widget_info=BooleanTrait.RADIOBUTTON)),
('groupby_sirna',
BooleanTrait(False, label='siRNA',
widget_info=BooleanTrait.RADIOBUTTON)),
('hmm_smoothing',
BooleanTrait(True, label='Smoothing Model',
widget_info=BooleanTrait.RADIOBUTTON)),
('hmm_baumwelch',
BooleanTrait(False, label='Baum-Welch',
widget_info=BooleanTrait.RADIOBUTTON)),
('groupby_genesymbol',
BooleanTrait(False, label='Gene Symbol',
widget_info=BooleanTrait.RADIOBUTTON)),
('overwrite_time_lapse',
BooleanTrait(False, label='Overwrite time-lapse')),
('timelapse',
FloatTrait(1, 0, 2000, digits=2,
label='Time-lapse [min]')),
('max_time',
FloatTrait(-1, -1, 2000, digits=2,
label='Max. time in plot [min]')),
('ignore_tracking_branches',
BooleanTrait(False, label='Ignore tracking branches')),
('enable_sorting',
BooleanTrait(False, label='Sort by phase duration')),
('sorting_sequence',
StringTrait('', 1000, label='Label sequence',
mask='(\w+,)*\w+')),
('primary_sort',
StringTrait('', 100)),
('secondary_sort',
StringTrait('', 100)),
('compose_galleries',
BooleanTrait(False, label='Compose gallery images')),
('compose_galleries_sample',
IntTrait(-1, -1, 10000, label='Max. number of random samples')),
('resampling_factor',
FloatTrait(0.4, 0.01, 1.0, label="Resampling factor")),
('size_gallery_image',
IntTrait(60, 1, 1000, label='Size of gallery images (px)'))
])
]
class SectionErrorcorrection(SectionCore):
SECTION_NAME = SECTION_NAME_ERRORCORRECTION
OPTIONS = [('error_correction', [
('filename_to_r',
StringTrait('',
1000,
label='R-project executable',
widget_info=StringTrait.STRING_FILE)),
('constrain_graph', BooleanTrait(True, label='Constrain graph')),
('primary_graph',
StringTrait('',
1000,
label='Primary file',
widget_info=StringTrait.STRING_FILE)),
('secondary_graph',
StringTrait('',
1000,
label='Secondary file',
widget_info=StringTrait.STRING_FILE)),
('skip_processed_plates',
BooleanTrait(False, label='Skip processed plates')),
('position_labels', BooleanTrait(False, label='Position labels')),
('mappingfile_path',
StringTrait('',
1000,
label='Path',
widget_info=StringTrait.STRING_PATH)),
('groupby_position',
BooleanTrait(True,
label='Position',
widget_info=BooleanTrait.RADIOBUTTON)),
('groupby_oligoid',
BooleanTrait(False,
label='Oligo ID',
widget_info=BooleanTrait.RADIOBUTTON)),
('groupby_genesymbol',
BooleanTrait(False,
label='Gene symbol',
widget_info=BooleanTrait.RADIOBUTTON)),
('overwrite_time_lapse',
BooleanTrait(False, label='Overwrite time-lapse')),
('timelapse', FloatTrait(1,
0,
2000,
digits=2,
label='Time-lapse [min]')),
('max_time',
FloatTrait(100, 1, 2000, digits=2, label='Max. time in plot [min]')),
('ignore_tracking_branches',
BooleanTrait(False, label='Ignore tracking branches')),
('show_html', BooleanTrait(True, label='Open in browser')),
('enable_sorting', BooleanTrait(False,
label='Sort by phase duration')),
('sorting_sequence',
StringTrait('', 1000, label='Label sequence', mask='(\w+,)*\w+')),
('primary_sort', StringTrait('', 100)),
('secondary_sort', StringTrait('', 100)),
('compose_galleries',
BooleanTrait(False, label='Compose gallery images')),
('compose_galleries_sample',
IntTrait(-1, -1, 10000, label='Max. number of random samples')),
])]
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')),
]),
]
class SectionPostProcessing(SectionCore):
SECTION_NAME = SECTION_NAME_POST_PROCESSING
OPTIONS = [('post_processing', [
('ibb_analysis', BooleanTrait(True, label='IBB analysis')),
('mappingfile_path',
StringTrait('',
1000,
label='Mapping file path',
widget_info=StringTrait.STRING_PATH)),
('single_plot', BooleanTrait(
True,
label='Export single event',
)),
('single_plot_max_plots', IntTrait(
1,
1,
2000,
label='Max. number',
)),
('ibb_ratio_signal_threshold',
FloatTrait(
1.2,
0.5,
5,
label='IBB minimum ratio signal threshold',
)),
('ibb_range_signal_threshold',
FloatTrait(
3,
0.5,
5,
label='IBB minimum range threshold',
)),
('ibb_onset_factor_threshold',
FloatTrait(
1.2,
1,
5,
label='IBB onset slope threshold',
)),
('nebd_onset_factor_threshold',
FloatTrait(
1.2,
1,
5,
label='NEBD onset slope threshold',
)),
('plot_ylim1_low', IntTrait(
0,
0,
2000,
label='Y-axis limit (low)',
)),
('plot_ylim1_high',
IntTrait(
100,
1,
4000,
label='Y-axis limit (high)',
)),
('single_plot_ylim_low',
FloatTrait(
1,
0,
10,
label='Y-axis ratio range (low)',
)),
('single_plot_ylim_high',
IntTrait(
5,
1,
30,
label='Y-axis ratio range (high)',
)),
('group_by_position',
BooleanTrait(True,
label='Position',
widget_info=BooleanTrait.RADIOBUTTON)),
('group_by_oligoid',
BooleanTrait(False,
label='Oligo ID',
widget_info=BooleanTrait.RADIOBUTTON)),
('group_by_genesymbol',
BooleanTrait(False,
label='Gene symbol',
widget_info=BooleanTrait.RADIOBUTTON)),
('group_by_group',
BooleanTrait(False,
label='Group',
widget_info=BooleanTrait.RADIOBUTTON)),
('color_sort_by_position',
BooleanTrait(False,
label='Position',
widget_info=BooleanTrait.RADIOBUTTON)),
('color_sort_by_oligoid',
BooleanTrait(True,
label='Oligo ID',
widget_info=BooleanTrait.RADIOBUTTON)),
('color_sort_by_genesymbol',
BooleanTrait(False,
label='Gene symbol',
widget_info=BooleanTrait.RADIOBUTTON)),
('color_sort_by_group',
BooleanTrait(False,
label='Group',
widget_info=BooleanTrait.RADIOBUTTON)),
('securin_analysis', BooleanTrait(True, label='Securin analysis')),
])]