def OnPick(self, event):
# FIXME - open rule in respective editing tab
raise NotImplementedError
from PYME.IO import tabular
k = event.artist._data
if not (isinstance(k, six.string_types)):
self.configureModule(k)
else:
outp = self.recipes.activeRecipe.namespace[k]
if isinstance(outp, ImageStack):
if not 'dsviewer' in dir(self.recipes):
dv = ViewIm3D(outp, mode='lite')
else:
if self.recipes.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(outp,
mode=mode,
glCanvas=self.recipes.dsviewer.glCanvas)
elif isinstance(outp, tabular.TabularBase):
from PYME.ui import recArrayView
f = recArrayView.ArrayFrame(outp,
parent=self,
title='Data table - %s' % k)
f.Show()
def OnPick(self, event):
from PYME.IO import tabular
from PYME.recipes import graphing
k = event.artist._data
if not (isinstance(k, six.string_types)):
if not self._editing:
self._editing = True
self.configureModule(k)
self._editing = False
else:
outp = self.recipes.activeRecipe.namespace[k]
if isinstance(outp, ImageStack):
if not 'dsviewer' in dir(self.recipes):
dv = ViewIm3D(outp, mode='lite')
else:
if self.recipes.dsviewer.mode == 'visGUI':
mode = 'visGUI'
else:
mode = 'lite'
dv = ViewIm3D(outp, mode=mode, glCanvas=self.recipes.dsviewer.glCanvas)
elif isinstance(outp, tabular.TabularBase):
from PYME.ui import recArrayView
f = recArrayView.ArrayFrame(outp, parent=self, title='Data table - %s' % k)
f.Show()
elif isinstance(outp, graphing.Plot):
outp.plot()
def OnMeasure(self, event):
from PYME.Analysis.points import objectMeasure
pipeline = self.visFr.pipeline
chans = pipeline.colourFilter.getColourChans()
# If we're not using objectIDs from an image, look for other clustering labels
# TODO - rather than trying a few pre-set objectID alternatives, make this a dialog instead
# - look for objectID and carry on if present
# - if not present, display a dialog "No objectID found - did you segment objects? Either cancel,
# segment, and come back, or choose an alternative column to use as an ID.
keys = ['objectID', 'dbscanClumpID', 'clumpIndex']
key = 'objectID'
for k in keys:
try:
ids = set(pipeline.mapping[k].astype('i'))
key = k
break
except (KeyError):
continue
# ids = set(pipeline.mapping['objectID'].astype('i'))
pipeline.objectMeasures = {}
if len(chans) == 0:
pipeline.objectMeasures[
'Everything'] = objectMeasure.measureObjectsByID(
pipeline.colourFilter, 10, ids, key)
from PYME.ui import recArrayView
f = recArrayView.ArrayFrame(pipeline.objectMeasures['Everything'],
parent=self.visFr,
title='Object Measurements')
f.Show()
else:
curChan = pipeline.colourFilter.currentColour
chanNames = chans[:]
# if 'Sample.Labelling' in metadata.getEntryNames():
# lab = metadata.getEntry('Sample.Labelling')
#
# for i in range(len(lab)):
# if lab[i][0] in chanNames:
# chanNames[chanNames.index(lab[i][0])] = lab[i][1]
for ch, i in zip(chans, range(len(chans))):
pipeline.colourFilter.setColour(ch)
#fitDecayChan(colourFilter, metadata, chanNames[i], i)
pipeline.objectMeasures[
chanNames[i]] = objectMeasure.measureObjectsByID(
pipeline.colourFilter, 10, ids, key)
pipeline.colourFilter.setColour(curChan)
from PYME.ui import recArrayView
from PYME.IO import tabular
from PYME.recipes.tablefilters import AggregateMeasurements
om = {
k: tabular.RecArraySource(v)
for k, v in pipeline.objectMeasures.items()
}
args = {}
for i, name in enumerate(chanNames):
args['inputMeasurements%d' % (i + 1)] = name
args['suffix%d' % (i + 1)] = ('_' + name)
args['outputName'] = 'aggregated'
agg = AggregateMeasurements(**args)
agg.execute(om)
f = recArrayView.ArrayFrame(om['aggregated'],
parent=self.visFr,
title='Object Measurements')
f.Show()