def SpecFromMetadata(self):
labels = self.mdh.getEntry('Sample.Labelling')
for structure, dye in labels:
ratio = dyeRatios.getRatio(dye, self.mdh)
if not ratio is None:
self.fluorSpecies[structure] = ratio
self.fluorSpeciesDyes[structure] = dye
self.mapping.setMapping(
'p_%s' % structure,
'(1.0/(ColourNorm*2*numpy.pi*fitError_Ag*fitError_Ar))*exp(-(fitResults_Ag - %f*A)**2/(2*fitError_Ag**2) - (fitResults_Ar - %f*A)**2/(2*fitError_Ar**2))'
% (ratio, 1 - ratio))
def _get_dye_ratios_from_metadata(self):
warnings.warn(DeprecationWarning('This should not be called (colour now handled by the ProcessColour recipe module)'))
labels = self.mdh.getOrDefault('Sample.Labelling', [])
seen_structures = []
for structure, dye in labels:
if structure in seen_structures:
strucname = structure + '_1'
else:
strucname = structure
seen_structures.append(structure)
ratio = dyeRatios.getRatio(dye, self.mdh)
if not ratio is None:
self.fluorSpecies[strucname] = ratio
self.fluorSpeciesDyes[strucname] = dye
def _get_dye_ratios_from_metadata(self, mdh):
from PYME.LMVis import dyeRatios
labels = mdh.getOrDefault('Sample.Labelling', [])
seen_structures = []
for structure, dye in labels:
#info might be unicode - convert to a standard string to keep traits happy
structure = str(structure)
dye = str(dye)
if structure in seen_structures:
strucname = structure + '_1'
else:
strucname = structure
seen_structures.append(structure)
ratio = dyeRatios.getRatio(dye, mdh)
if not ratio is None:
self.species_ratios[strucname] = ratio
self.species_dyes[strucname] = dye
