def _on_import(self):
"""
Import format: CSV, first column is filename, path relative to CSV.
others are conditions, type is autodetected. first row is header
with names.
"""
file_dialog = FileDialog()
file_dialog.wildcard = "CSV files (*.csv)|*.csv|"
file_dialog.action = 'open'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
csv = pandas.read_csv(file_dialog.path)
csv_folder = Path(file_dialog.path).parent
if self.model.tubes or self.model.tube_traits:
if confirm(
parent=None,
message="This will clear the current conditions and tubes! "
"Are you sure you want to continue?",
title="Clear tubes and conditions?") != YES:
return
for col in csv.columns[1:]:
self.model.tube_traits.append(
TubeTrait(model=self.model,
name=util.sanitize_identifier(col),
type='category'))
for _, row in csv.iterrows():
filename = csv_folder / row[0]
try:
metadata, _ = parse_tube(str(filename), metadata_only=True)
except Exception as e:
warning(
None,
"Had trouble loading file {}: {}".format(filename, str(e)))
continue
metadata['CF_File'] = Path(filename).stem
new_tube = Tube(file=str(filename),
parent=self.model,
metadata=sanitize_metadata(metadata))
self.model.tubes.append(new_tube)
for col in csv.columns[1:]:
new_tube.trait_set(**{util.sanitize_identifier(col): row[col]})
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
# TODO - adding a set of files, then a condition, then another
# set doesn't work.
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("$PnN")
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
tube = Tube()
for trait_name, trait in self.model.tube_traits.items():
# TODO - do we still need to check for transient?
tube.add_trait(trait_name, trait)
# this magic makes sure the trait is actually defined
# in tube.__dict__, so it shows up in trait_names etc.
tube.trait_set(**{trait_name : trait.default_value})
if trait.condition:
tube.on_trait_change(self._try_multiedit, trait_name)
tube.trait_set(Source = tube_meta['$SRC'],
_file = path,
_parent = self.model)
if 'TUBE NAME' in tube_meta:
tube.Tube = tube_meta['TUBE NAME']
elif '$SMNO' in tube_meta:
tube.Tube = tube_meta['$SMNO']
self.model.tubes.append(tube)
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
# TODO - adding a set of files, then a condition, then another
# set doesn't work.
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("$PnN")
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
tube = Tube()
for trait_name, trait in self.model.tube_traits.items():
# TODO - do we still need to check for transient?
tube.add_trait(trait_name, trait)
# this magic makes sure the trait is actually defined
# in tube.__dict__, so it shows up in trait_names etc.
tube.trait_set(**{trait_name: trait.default_value})
if trait.condition:
tube.on_trait_change(self._try_multiedit, trait_name)
tube.trait_set(Source=tube_meta['$SRC'],
_file=path,
_parent=self.model)
if 'TUBE NAME' in tube_meta:
tube.Tube = tube_meta['TUBE NAME']
elif '$SMNO' in tube_meta:
tube.Tube = tube_meta['$SMNO']
self.model.tubes.append(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 *.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 _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
# TODO - adding a set of files, then a condition, then another
# set doesn't work.
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:
fcs = FCMeasurement(ID='new tube', datafile = path)
tube = Tube()
for trait_name, trait in self.model.tube_traits.items():
# TODO - do we still need to check for transient?
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(Source = fcs.meta['$SRC'],
_file = path,
_parent = self.model)
if 'TUBE NAME' in fcs.meta:
tube.Tube = fcs.meta['TUBE NAME']
elif '$SMNO' in fcs.meta:
tube.Tube = fcs.meta['$SMNO']
self.model.tubes.append(tube)
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
file_dialog = FileDialog()
file_dialog.wildcard = "Flow cytometry files (*.fcs)|*.fcs|"
file_dialog.action = 'open files'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
for path in file_dialog.paths:
try:
tube_meta = fcsparser.parse(path,
meta_data_only = True,
reformat_meta = True)
#tube_channels = tube_meta["_channels_"].set_index("$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)
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
# TODO - adding a set of files, then a condition, then another
# set doesn't work.
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("$PnN")
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}".format(path, e.value))
# if we're the first tube loaded, create a dummy experiment
if not self.model.dummy_experiment:
self.model.dummy_experiment = ImportOp(tubes=[CytoflowTube(file=path)], coarse_events=1).apply()
# check the next tube against the dummy experiment
try:
check_tube(path, self.model.dummy_experiment)
except util.CytoflowError as e:
error(None, e.__str__(), "Error importing tube")
return
tube = Tube()
for trait_name, trait in self.model.tube_traits.items():
# TODO - do we still need to check for transient?
tube.add_trait(trait_name, trait)
# this magic makes sure the trait is actually defined
# in tube.__dict__, so it shows up in trait_names etc.
tube.trait_set(**{trait_name: trait.default_value})
if trait.condition:
tube.on_trait_change(self._try_multiedit, trait_name)
tube.trait_set(file=path, parent=self.model)
if "$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"]})
self.model.tubes.append(tube)
self.btn_add_cond.setEnabled(True)
