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 SectionGeneral(SectionCore):
SECTION_NAME = SECTION_NAME_GENERAL
OPTIONS = [('general', [
('pathin',
StringTrait('',
label='Image Directory',
widget_info=StringTrait.STRING_PATH)),
('has_multiple_plates', BooleanTrait(False, label='Multiple Plates')),
('pathout',
StringTrait('',
label='Output Directory',
widget_info=StringTrait.STRING_PATH)),
('plate_layout',
StringTrait('',
label='Plate Layout',
widget_info=StringTrait.STRING_PATH)),
('namingscheme',
SelectionTrait(CecogEnvironment.naming_schema.sections()[0],
CecogEnvironment.naming_schema.sections(),
label='Image Naming Scheme')),
('framerange', BooleanTrait(False, label='Timelapse')),
('framerange_begin', IntTrait(1, 0, 10000, label='first')),
('framerange_end', IntTrait(1, 0, 1000, label='last')),
('frameincrement', IntTrait(1, 1, 100, label='increment')),
('skip_finished', BooleanTrait(False,
label='Skip finished positions')),
('constrain_positions', BooleanTrait(False, label='Positions')),
('positions', StringTrait('', 1000, label="", mask='(\w+,)*\w+')),
('process_primary', BooleanTrait(True, label='primary')),
('process_secondary', BooleanTrait(False, label='secondary')),
('process_tertiary', BooleanTrait(False, label='tertiary')),
('process_merged', BooleanTrait(False, label='merged')),
('crop_image', BooleanTrait(False, label='Image cropping')),
('crop_image_x0', IntTrait(-1, -1, 4000, label='upper left x:')),
('crop_image_y0', IntTrait(-1, -1, 4000, label='upper left y')),
('crop_image_x1', IntTrait(-1, -1, 4000, label='lower right x')),
('crop_image_y1', IntTrait(-1, -1, 4000, label='lower right y')),
('crop_image', BooleanTrait(False, label='Image cropping')),
('rendering', DictTrait({}, label='Rendering')),
('version',
StringTrait('',
6,
label='Cecog %s, file version:' % version,
widget_info=StringTrait.STRING_GRAYED)),
('rendering_class', DictTrait({}, label='Rendering class')),
('primary_featureextraction_exportfeaturenames',
ListTrait(['n2_avg', 'n2_stddev', 'roisize'],
label='Primary channel')),
('secondary_featureextraction_exportfeaturenames',
ListTrait(['n2_avg', 'n2_stddev', 'roisize'],
label='Secondary channel')),
('tertiary_featureextraction_exportfeaturenames',
ListTrait(['n2_avg', 'n2_stddev', 'roisize'],
label='Tertiary channel')),
])]
class SectionGeneral(SectionCore):
SECTION_NAME = SECTION_NAME_GENERAL
OPTIONS = [('general', [
('pathin',
StringTrait('',
1000,
label='Image folder',
widget_info=StringTrait.STRING_PATH)),
('has_multiple_plates', BooleanTrait(False, label='Multiple plates')),
('pathout',
StringTrait('',
1000,
label='Analysis folder',
widget_info=StringTrait.STRING_PATH)),
('image_import_namingschema',
BooleanTrait(True,
label='Import via naming schema',
widget_info=BooleanTrait.RADIOBUTTON)),
('image_import_structurefile',
BooleanTrait(False,
label='Import via coordinate file',
widget_info=BooleanTrait.RADIOBUTTON)),
('namingscheme',
SelectionTrait(CecogEnvironment.naming_schema.sections()[0],
CecogEnvironment.naming_schema.sections(),
label='Naming scheme')),
('structure_filename',
StringTrait('',
1000,
label='Coordinate filename',
widget_info=StringTrait.STRING_FILE)),
('structure_file_pathin',
BooleanTrait(True,
label='Image folder',
widget_info=BooleanTrait.RADIOBUTTON)),
('structure_file_pathout',
BooleanTrait(False,
label='Analysis folder',
widget_info=BooleanTrait.RADIOBUTTON)),
('structure_file_extra_path',
BooleanTrait(False,
label='Different location',
widget_info=BooleanTrait.RADIOBUTTON)),
('structure_file_extra_path_name',
StringTrait('',
1000,
label='Path',
widget_info=StringTrait.STRING_PATH)),
('constrain_positions', BooleanTrait(False,
label='Constrain positions')),
('positions',
StringTrait('', 1000, label='Positions', mask='(\w+,)*\w+')),
('crop_image', BooleanTrait(False, label='Crop image')),
('crop_image_x0', IntTrait(-1, -1, 4000, label='Upper left X')),
('crop_image_y0', IntTrait(-1, -1, 4000, label='Upper left Y')),
('crop_image_x1', IntTrait(-1, -1, 4000, label='Lower right X')),
('crop_image_y1', IntTrait(-1, -1, 4000, label='Lower right Y')),
('crop_image', BooleanTrait(False, label='Crop image')),
('redofailedonly', BooleanTrait(True,
label='Skip processed positions')),
('framerange', BooleanTrait(False, label='Constrain timepoints')),
('framerange_begin', IntTrait(1, 0, 10000, label='Begin')),
('framerange_end', IntTrait(1, 0, 1000, label='End')),
('frameincrement', IntTrait(1, 1, 100, label='Timepoint increment')),
('rendering', DictTrait({}, label='Rendering')),
('version',
StringTrait('',
6,
label='Cecog %s, file version:' % VERSION,
widget_info=StringTrait.STRING_GRAYED)),
('rendering_class', DictTrait({}, label='Rendering class')),
('primary_featureextraction_exportfeaturenames',
ListTrait(['n2_avg', 'n2_stddev', 'roisize'],
label='Primary channel')),
('secondary_featureextraction_exportfeaturenames',
ListTrait(['n2_avg', 'n2_stddev', 'roisize'],
label='Secondary channel')),
('tertiary_featureextraction_exportfeaturenames',
ListTrait(['n2_avg', 'n2_stddev', 'roisize'],
label='Tertiary channel')),
])]
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')),
]),
]