def execute(self, namespace):
from PYME.IO.image import ImageBounds
inp = namespace[self.inputLocalizations]
if not isinstance(inp, tabular.ColourFilter):
cf = tabular.ColourFilter(inp, None)
print('Created colour filter with chans: %s' % cf.getColourChans())
cf.mdh = inp.mdh
else:
cf = inp
#default to taking min and max localizations as image bounds
imb = ImageBounds.estimateFromSource(inp)
if self.zBoundsMode == 'min-max':
self.zBounds[0], self.zBounds[1] = float(imb.z0), float(imb.z1)
if (self.xyBoundsMode == 'inherit'
) and not (getattr(inp, 'imageBounds', None) is None):
imb = inp.imageBounds
elif self.xyBoundsMode == 'metadata':
imb = ImageBounds.extractFromMetadata(inp.mdh)
elif self.xyBoundsMode == 'manual':
imb.x0, imb.y0, imb.x1, imb.y1 = self.manualXYBounds
cf.imageBounds = imb
renderer = renderers.RENDERERS[str(self.renderingModule)](None, cf)
namespace[self.outputImage] = renderer.Generate(self.trait_get())
def execute(self, namespace):
inp = namespace[self.inputName]
map = tabular.ColourFilter(inp, currentColour=self.channel)
if 'mdh' in dir(inp):
map.mdh = inp.mdh
namespace[self.outputName] = map
def RegenFilter(self):
if not self.selectedDataSource is None:
self.filter = inpFilt.ResultsFilter(self.selectedDataSource,
**self.filterKeys)
if self.mapping:
self.mapping.resultsSource = self.filter
else:
self.mapping = inpFilt.MappingFilter(self.filter)
if not self.colourFilter:
self.colourFilter = inpFilt.ColourFilter(self.mapping, self)
self.edb = None
self.objects = None
self.GeneratedMeasures = {}
def Rebuild(self, **kwargs):
"""
Rebuild the pipeline. Called when the selected data source is changed/modified and/or the filter is changed.
"""
for s in self.dataSources.values():
if 'setMapping' in dir(s):
#keep raw measurements available
s.setMapping('x_raw', 'x')
s.setMapping('y_raw', 'y')
if 'z' in s.keys():
s.setMapping('z_raw', 'z')
if not self.selectedDataSource is None:
if not self.mapping is None:
# copy any mapping we might have made across to the new mapping filter (should fix drift correction)
# TODO - make drift correction a recipe module so that we don't need this code. Long term we should be
# ditching the mapping filter here.
old_mapping = self.mapping
self.mapping = tabular.MappingFilter(self.selectedDataSource)
self.mapping.mappings.update(old_mapping.mappings)
else:
self.mapping = tabular.MappingFilter(self.selectedDataSource)
#the filter, however needs to be re-generated with new keys and or data source
self.filter = tabular.ResultsFilter(self.mapping,
**self.filterKeys)
#we can also recycle the colour filter
if self.colourFilter is None:
self.colourFilter = tabular.ColourFilter(self.filter)
else:
self.colourFilter.resultsSource = self.filter
#self._process_colour()
self.ready = True
self.ClearGenerated()
