def update_import_op(self, op):
trait_to_dtype = {
"Str": "category",
"Float": "float",
"Bool": "bool",
"Int": "int"
}
conditions = {}
for trait_name, trait in list(self.tube_traits.items()):
if not trait.condition:
continue
trait_type = trait.__class__.__name__
conditions[trait_name] = trait_to_dtype[trait_type]
tubes = []
for tube in self.tubes:
op_tube = CytoflowTube(file=tube.file,
conditions=tube.trait_get(condition=True),
conditions_list=[
x for x in list(self.tube_traits.keys())
if self.tube_traits[x].condition
])
tubes.append(op_tube)
op.conditions = conditions
op.tubes = tubes
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
file_dialog = FileDialog()
file_dialog.wildcard = "Flow cytometry files (*.fcs *.lmd)|*.fcs *.lmd|"
file_dialog.action = 'open files'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
for path in file_dialog.paths:
try:
metadata, _ = parse_tube(path, metadata_only=True)
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
# if we're the first tube loaded, create a dummy experiment
# and setup default metadata columns
if not self.model.dummy_experiment:
self.model.dummy_experiment = \
ImportOp(tubes = [CytoflowTube(file = path)]).apply(metadata_only = True)
# check the next tube against the dummy experiment
try:
check_tube(path, self.model.dummy_experiment)
except util.CytoflowError as e:
error(None, e.__str__(), "Error importing tube")
return
metadata['CF_File'] = Path(path).stem
tube = Tube(file=path,
parent=self.model,
metadata=sanitize_metadata(metadata))
self.model.tubes.append(tube)
for trait in self.model.tube_traits:
if trait.type != 'metadata' and trait.name:
tube.on_trait_change(self._try_multiedit, trait.name)
def update_import_op(self, import_op):
if not self.tubes:
return
assert self.dummy_experiment is not None
conditions = {
trait.name: trait.type
for trait in self.tube_traits if trait.type != 'metadata'
}
tubes = []
events = 0
for tube in self.tubes:
op_tube = CytoflowTube(file=tube.file,
conditions=tube.trait_get(
list(conditions.keys())))
tubes.append(op_tube)
events += tube.metadata['TOT']
import_op.ret_events = events
import_op.conditions = conditions
import_op.tubes = tubes
import_op.original_channels = channels = self.dummy_experiment.channels
all_present = len(import_op.channels_list) > 0
if len(import_op.channels_list) > 0:
for c in import_op.channels_list:
if c.name not in channels:
all_present = False
if not all_present:
warning(
None, "Some of the operation's channels weren't found in "
"these FCS files. Resetting all channel names.",
"Resetting channel names")
if not all_present:
import_op.reset_channels()
def update_import_op(self, op):
trait_to_dtype = {
"Str": "category",
"Float": "float",
"LogFloat": "log",
"Bool": "bool",
"Int": "int"
}
op.conditions.clear()
for trait_name, trait in self.tube_traits.items():
if not trait.condition:
continue
trait_type = trait.__class__.__name__
op.conditions[trait_name] = trait_to_dtype[trait_type]
for tube in self.tubes:
op_tube = CytoflowTube(source=tube.Source,
tube=tube.Tube,
file=tube._file)
if "Row" in tube.trait_names():
op_tube.row = tube.Row
if "Col" in tube.trait_names():
op_tube.col = tube.Col
op_tube.conditions = tube.trait_get(condition=True)
# AFAICT this is going to cause the op to reload THE ENTIRE
# SET each time a tube is added. >.>
# TODO - FIX THIS. need a general strategy for only updating
# if there's a "pause" in the action.
op.tubes.append(op_tube)
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
file_dialog = FileDialog()
file_dialog.wildcard = "Flow cytometry files (*.fcs)|*.fcs|"
file_dialog.action = 'open files'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
for path in file_dialog.paths:
try:
tube_meta = fcsparser.parse(path,
meta_data_only = True,
reformat_meta = True)
#tube_channels = tube_meta["_channels_"].set_index("$PnN")
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
# if we're the first tube loaded, create a dummy experiment
if not self.model.dummy_experiment:
self.model.dummy_experiment = ImportOp(tubes = [CytoflowTube(file = path)],
coarse_events = 1).apply()
# check the next tube against the dummy experiment
try:
check_tube(path, self.model.dummy_experiment)
except util.CytoflowError as e:
error(None, e.__str__(), "Error importing tube")
return
tube = Tube()
for trait_name, trait in self.model.tube_traits.items():
tube.add_trait(trait_name, trait)
# this magic makes sure the trait is actually defined
# in tube.__dict__, so it shows up in trait_names etc.
tube.trait_set(**{trait_name : trait.default_value})
if trait.condition:
tube.on_trait_change(self._try_multiedit, trait_name)
tube.trait_set(file = path, parent = self.model)
if '$SRC' in tube_meta:
self._add_metadata("$SRC", "$SRC", Str(condition = False))
tube.trait_set(**{"$SRC" : tube_meta['$SRC']})
if 'TUBE NAME' in tube_meta:
self._add_metadata("TUBE NAME", "TUBE NAME", Str(condition = False))
tube.trait_set(**{"TUBE NAME" : tube_meta['TUBE NAME']})
if '$SMNO' in tube_meta:
self._add_metadata("$SMNO", "$SMNO", Str(condition = False))
tube.trait_set(**{"$SMNO" : tube_meta['$SMNO']})
if 'WELL ID' in tube_meta:
self._add_metadata("Row", "Row", Str(condition = False))
self._add_metadata("Col", "Col", Int(condition = False))
pos = tube_meta['WELL ID']
row = pos[0]
col = int(pos[1:3])
tube.trait_set(**{"Row" : row, "Col" : col})
self.model.tubes.append(tube)