def apply(self, experiment = None):
if not self.tubes or len(self.tubes) == 0:
raise CytoflowOpError("Must specify some tubes!")
# make sure each tube has the same conditions
tube0_conditions = set(self.tubes[0].conditions)
for tube in self.tubes:
tube_conditions = set(tube.conditions)
if len(tube0_conditions ^ tube_conditions) > 0:
raise CytoflowOpError("Tube {0} didn't have the same "
"conditions as tube {1}"
.format(tube.file, self.tubes[0].file))
# make sure experimental conditions are unique
for idx, i in enumerate(self.tubes[0:-1]):
for j in self.tubes[idx+1:]:
if i.conditions_equal(j):
raise CytoflowOpError("The same conditions specified for "
"tube {0} and tube {1}"
.format(i.file, j.file))
experiment = Experiment()
for condition, dtype in self.conditions.items():
is_log = False
if dtype == "log":
is_log = True
dtype = "float"
experiment.add_conditions({condition : dtype})
if is_log:
experiment.metadata[condition]["repr"] = "log"
for tube in self.tubes:
tube_fc = fcsparser.parse(tube.file, reformat_meta = True)
if self.coarse:
tube_meta, tube_data = tube_fc
tube_data = tube_data.loc[np.random.choice(tube_data.index,
self.coarse_events,
replace = False)]
tube_fc = (tube_meta, tube_data)
experiment.add_tube(tube_fc, tube.conditions, ignore_v = self.ignore_v)
return experiment
self.value = new
class SubsetEditor(BasicEditorFactory):
# the editor to be created
klass = _SubsetEditor
# the name of the trait containing the cytoflow.Experiment to build the UI
experiment = Str
if __name__ == '__main__':
import fcsparser
ex = Experiment()
ex.add_conditions({"Dox" : "bool"})
tube1 = fcsparser.parse('../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs',
reformat_meta = True,
channel_naming = "$PnN")
tube2 = fcsparser.parse('../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs',
reformat_meta = True,
channel_naming = "$PnN")
ex.add_tube(tube1, {"Dox" : True})
ex.add_tube(tube2, {"Dox" : False})
class C(HasTraits):
val = Str()
class SubsetEditor(BasicEditorFactory):
# the editor to be created
klass = _SubsetEditor
# the name of the trait containing the cytoflow.Experiment to build the UI
experiment = Str
if __name__ == '__main__':
import fcsparser
ex = Experiment()
ex.add_conditions({"Dox": "bool"})
tube1 = fcsparser.parse('../cytoflow/tests/data/Plate01/RFP_Well_A3.fcs',
reformat_meta=True,
channel_naming="$PnN")
tube2 = fcsparser.parse('../cytoflow/tests/data/Plate01/CFP_Well_A4.fcs',
reformat_meta=True,
channel_naming="$PnN")
ex.add_tube(tube1, {"Dox": True})
ex.add_tube(tube2, {"Dox": False})
class C(HasTraits):
val = Str()
