def display_message(self, msg, title=None, is_error=False):
"""
Display the specified message to the user.
"""
# Ensure we record any reasons this method doesn't work. Especially
# since it's critical in displaying errors to users!
try:
# Attempt to identify the current application window.
parent_window = None
workbench = self.application.get_service('envisage.'
'workbench.IWorkbench')
if workbench is not None:
parent_window = workbench.active_window.control
# Display the requested message
if is_error:
error(parent_window, msg, title=title)
else:
information(parent_window, msg, title=title)
except:
logger.exception('Unable to display pop-up message')
return
def delete ( self, path = None ):
""" Deletes the associated directory from the file system.
"""
if path is None:
path = self.path
not_deleted = 0
try:
for name in listdir( path ):
fn = join( path, name )
if isfile( fn ):
if self.include_file( fn ):
remove( fn )
else:
not_deleted += 1
elif isdir( fn ) and (not self.delete( fn )):
not_deleted += 1
if not_deleted == 0:
rmdir( path )
return True
except:
error( self.handler.parent, "Could not delete '%s'" % fn )
# Indicate that the directory was not deleted:
return False
def _show_open_dialog(self, parent):
"""
Show the dialog to open a project.
"""
# Determine the starting point for browsing. It is likely most
# projects will be stored in the default path used when creating new
# projects.
default_path = self.model_service.get_default_path()
project_class = self.model_service.factory.PROJECT_CLASS
if self.model_service.are_projects_files():
dialog = FileDialog(parent=parent, default_directory=default_path,
title='Open Project')
if dialog.open() == OK:
path = dialog.path
else:
path = None
else:
dialog = DirectoryDialog(parent=parent, default_path=default_path,
message='Open Project')
if dialog.open() == OK:
path = project_class.get_pickle_filename(dialog.path)
if File(path).exists:
path = dialog.path
else:
error(parent, 'Directory does not contain a recognized '
'project')
path = None
else:
path = None
return path
def read_file(self):
"""Read the file."""
if op.exists(self.file):
if self.file.endswith('.fif'):
bem = read_bem_surfaces(self.file, verbose=False)[0]
self.points = bem['rr']
self.norms = bem['nn']
self.tris = bem['tris']
else:
try:
points, tris = read_surface(self.file)
points /= 1e3
self.points = points
self.norms = []
self.tris = tris
except Exception:
error(message="Error loading surface from %s (see "
"Terminal for details).",
title="Error Loading Surface")
self.reset_traits(['file'])
raise
else:
self.points = np.empty((0, 3))
self.norms = np.empty((0, 3))
self.tris = np.empty((0, 3))
def _get_hsp_raw(self):
fname = self.hsp_file
if not fname:
return
try:
pts = read_hsp(fname)
n_pts = len(pts)
if n_pts > KIT.DIG_POINTS:
msg = ("The selected head shape contains {n_in} points, "
"which is more than the recommended maximum ({n_rec}). "
"The file will be automatically downsampled, which "
"might take a while. A better way to downsample is "
"using FastScan.")
msg = msg.format(n_in=n_pts, n_rec=KIT.DIG_POINTS)
information(None, msg, "Too Many Head Shape Points")
pts = _decimate_points(pts, 5)
except Exception as err:
error(None, str(err), "Error Reading Head Shape")
self.reset_traits(['hsp_file'])
raise
else:
return pts
def perform(self, event):
plot_component = self.container.component
filter = 'PNG file (*.png)|*.png|\nTIFF file (*.tiff)|*.tiff|'
dialog = FileDialog(action='save as', wildcard=filter)
if dialog.open() != OK:
return
# Remove the toolbar before saving the plot, so the output doesn't
# include the toolbar.
plot_component.remove_toolbar()
filename = dialog.path
width, height = plot_component.outer_bounds
gc = PlotGraphicsContext((width, height), dpi=72)
gc.render_component(plot_component)
try:
gc.save(filename)
except KeyError as e:
errmsg = ("The filename must have an extension that matches "
"a graphics format, such as '.png' or '.tiff'.")
if str(e.message) != '':
errmsg = ("Unknown filename extension: '%s'\n" %
str(e.message)) + errmsg
error(None, errmsg, title="Invalid Filename Extension")
# Restore the toolbar.
plot_component.add_toolbar()
def _update_points(self):
"""Update the location of the plotted points"""
if not hasattr(self.src, "data"):
return
trans = self.trans
if np.any(trans):
if trans.ndim == 0 or trans.shape == (3,) or trans.shape == (1, 3):
pts = self.points * trans
elif trans.shape == (3, 3):
pts = np.dot(self.points, trans.T)
elif trans.shape == (4, 4):
pts = apply_trans(trans, self.points)
else:
err = (
"trans must be a scalar, a length 3 sequence, or an "
"array of shape (1,3), (3, 3) or (4, 4). "
"Got %s" % str(trans)
)
error(None, err, "Display Error")
raise ValueError(err)
else:
pts = self.points
self.src.data.points = pts
def _save_as_fired(self):
# create raw
try:
raw = self.model.get_raw()
except Exception as err:
error(None, str(err), "Error Creating KIT Raw")
raise
# find default path
stem, _ = os.path.splitext(self.sqd_file)
if not stem.endswith('raw'):
stem += '-raw'
default_path = stem + '.fif'
# save as dialog
dlg = FileDialog(action="save as",
wildcard="fiff raw file (*.fif)|*.fif",
default_path=default_path)
dlg.open()
if dlg.return_code != OK:
return
fname = dlg.path
if not fname.endswith('.fif'):
fname += '.fif'
if os.path.exists(fname):
answer = confirm(None, "The file %r already exists. Should it "
"be replaced?", "Overwrite File?")
if answer != YES:
return
self.queue.put((raw, fname))
self.queue_len += 1
def _inner(self, info, *args, **kw):
if not self.object_valid(info):
mesg = 'Unable to save the data due to the following problem(s)\n'
mesg += self.object_messages(info)
error(info.ui.control, mesg)
return False
return func(self, info, *args, **kw)
def _get_misc_data(self):
if not self.raw:
return
if self.show_gui:
# progress dialog with indefinite progress bar
prog = ProgressDialog(title="Loading SQD data...",
message="Loading stim channel data from SQD "
"file ...")
prog.open()
prog.update(0)
else:
prog = None
try:
data, times = self.raw[self.misc_chs]
except Exception as err:
if self.show_gui:
error(None, "Error reading SQD data file: %s (Check the "
"terminal output for details)" % str(err),
"Error Reading SQD File")
raise
finally:
if self.show_gui:
prog.close()
return data
def edit_function_call(func_def):
if func_def.code is None:
msg = "Perhaps your python path is not set correctly or\n" \
"there is an error in the file (or one it imports).\n"
error(None, msg, "Error loading function")
return None
# If it is a user-defined function, one would want to edit it
# else it can remain un-editable.
path_dir = os.path.dirname(func_def.filename)
usr_path = os.path.join(ETSConfig.user_data, USER_MODULE_NAME)
if path_dir == usr_path:
# This is a user function
is_ok = edit_user_function(func_def)
if is_ok:
if func_def.dirty:
func_def.write(overwrite = True)
return func_def
else:
is_ok = edit_sys_function(func_def)
if is_ok:
if func_def.dirty:
func_def.write(overwrite = False)
return func_def
def convert_output(self,tmp):
a=tmp.split(" ")
if len(a)<3:
error(parent=None, title="error", message= "fehler: falscher string sollte Konvertiert werden: "+ str(a))
return(tmp)
print "Konvertiere:", a
return(float(a[2]))
def get_prepare_bem_model_job(self, subject_to):
subjects_dir = self.mri.subjects_dir
subject_from = self.mri.subject
bem_name = "inner_skull-bem"
bem_file = bem_fname.format(subjects_dir=subjects_dir, subject=subject_from, name=bem_name)
if not os.path.exists(bem_file):
pattern = bem_fname.format(subjects_dir=subjects_dir, subject=subject_to, name="(.+-bem)")
bem_dir, bem_file = os.path.split(pattern)
m = None
bem_file_pattern = re.compile(bem_file)
for name in os.listdir(bem_dir):
m = bem_file_pattern.match(name)
if m is not None:
break
if m is None:
pattern = bem_fname.format(subjects_dir=subjects_dir, subject=subject_to, name="*-bem")
err = "No bem file found; looking for files matching " "%s" % pattern
error(err)
bem_name = m.group(1)
bem_file = bem_fname.format(subjects_dir=subjects_dir, subject=subject_to, name=bem_name)
# job
desc = "mne_prepare_bem_model for %s" % subject_to
func = prepare_bem_model
args = (bem_file,)
kwargs = {}
return (desc, func, args, kwargs)
def _children_items_changed ( self, event ):
""" Handles changes to the 'children' trait.
"""
for child in event.added:
if not isinstance( child, DirectoryNode ):
continue
new_path = join( self.path, child.dir_name )
if isfile( new_path ):
error( self.handler.parent,
("Cannot create the directory '%s'.\nThere is already a "
"file with that name.") % child.dir_name )
return
if not isdir( new_path ):
try:
mkdir( new_path )
except:
error( self.handler.parent, ("An error occurred creating "
"the directory '%s'") % child.dir_name )
return
child.set( path = new_path, file_space = self.file_space )
self.initialized = False
def _subject_changed(self):
subject = self.subject
subjects_dir = self.subjects_dir
if not subjects_dir or not subject:
return
path = None
if self.use_high_res_head:
path = _find_high_res_head(subjects_dir=subjects_dir,
subject=subject)
if not path:
error(None, "No high resolution head model was found for "
"subject {0}, using standard head instead. In order to "
"generate a high resolution head model, run:\n\n"
" $ mne make_scalp_surfaces -s {0}"
"\n\n".format(subject), "No High Resolution Head")
if not path:
path = head_bem_fname.format(subjects_dir=subjects_dir,
subject=subject)
self.bem.file = path
# find fiducials file
fid_files = _find_fiducials_files(subject, subjects_dir)
if len(fid_files) == 0:
self.fid.reset_traits(['file'])
self.lock_fiducials = False
else:
self.fid_file = fid_files[0].format(subjects_dir=subjects_dir,
subject=subject)
self.lock_fiducials = True
# does not seem to happen by itself ... so hard code it:
self.reset_fiducials()
def _us_error(e):
"""Display a message to the user after a UserStorageError exception has
been raised. If the message is empty then we assume the user has
already been informed."""
msg = str(e)
if msg:
error(None, msg)
def select_plugin(self, plugin_obj):
# Set up image capturing
self.camera = plugin_obj()
try:
self.camera.open()
except CameraError:
error(None, 'No camera was detected. Did you forget to plug it in?')
sys.exit()
def delete ( self ):
""" Deletes the associated file from the file system.
"""
try:
remove( self.path )
except:
error( self.handler.parent, "Could not delete the file '%s'" %
basename( self.path )[0] )
def init_model(self, op):
dtype_to_trait = {"category" : Str,
"float" : Float,
"bool" : Bool,
"int" : Int}
for op_tube in op.tubes:
tube = Tube(file = op_tube.file,
parent = self)
# first load the tube's metadata and set special columns
try:
tube_meta = fcsparser.parse(op_tube.file,
meta_data_only = True,
reformat_meta = True)
#tube_channels = tube_meta["_channels_"].set_index("$PnN")
except Exception as e:
error(None, "FCS reader threw an error on tube {0}: {1}"\
.format(op_tube.file, e.value),
"Error reading FCS file")
return
# if we're the first tube loaded, create a dummy experiment
if not self.dummy_experiment:
self.dummy_experiment = ImportOp(tubes = [op_tube],
conditions = op.conditions,
coarse_events = 1).apply()
if '$SRC' in tube_meta:
self.tube_traits["$SRC"] = Str(condition = False)
tube.add_trait("$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))
self.tube_traits["TUBE NAME"] = Str(condition = False)
tube.add_trait("TUBE NAME", Str(condition = False))
tube.trait_set(**{"TUBE NAME" : tube_meta['TUBE NAME']})
if '$SMNO' in tube_meta:
#self._add_metadata("$SMNO", "$SMNO", Str(condition = False))
self.tube_traits["$SMNO"] = Str(condition = False)
tube.add_trait("$SMNO", Str(condition = False))
tube.trait_set(**{"$SMNO" : tube_meta['SMNO']})
# next set conditions
for condition in op_tube.conditions:
condition_dtype = op.conditions[condition]
condition_trait = \
dtype_to_trait[condition_dtype](condition = True)
tube.add_trait(condition, condition_trait)
if not condition in self.tube_traits:
self.tube_traits[condition] = condition_trait
tube.trait_set(**op_tube.conditions)
self.tubes.append(tube)
def _get__info(self):
if self.file:
info = None
fid, tree, _ = fiff_open(self.file)
fid.close()
if len(dir_tree_find(tree, FIFF.FIFFB_MEAS_INFO)) > 0:
info = read_info(self.file, verbose=False)
elif len(dir_tree_find(tree, FIFF.FIFFB_ISOTRAK)) > 0:
info = read_dig_montage(fif=self.file)
if isinstance(info, DigMontage):
info.transform_to_head()
digs = list()
_append_fiducials(digs, info.lpa, info.nasion, info.rpa)
for idx, pos in enumerate(info.hsp):
dig = {'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': idx,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': pos}
digs.append(dig)
info = _empty_info(1)
info['dig'] = digs
elif info is None or info['dig'] is None:
error(None, "The selected FIFF file does not contain "
"digitizer information. Please select a different "
"file.", "Error Reading FIFF File")
self.reset_traits(['file'])
return
else:
# check that all fiducial points are present
has_point = {FIFF.FIFFV_POINT_LPA: False,
FIFF.FIFFV_POINT_NASION: False,
FIFF.FIFFV_POINT_RPA: False}
for d in info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_CARDINAL:
has_point[d['ident']] = True
if not all(has_point.values()):
points = _fiducial_coords(info['dig'])
if len(points) == 3:
_append_fiducials(info['dig'], *points.T)
else:
missing = []
if not has_point[FIFF.FIFFV_POINT_LPA]:
missing.append('LPA')
if not has_point[FIFF.FIFFV_POINT_NASION]:
missing.append('Nasion')
if not has_point[FIFF.FIFFV_POINT_RPA]:
missing.append('RPA')
error(None, "The selected FIFF file does not contain "
"all cardinal points (missing: %s). Please "
"select a different file." % ', '.join(missing),
"Error Reading FIFF File")
self.reset_traits(['file'])
return
return info
def _on_add_condition(self):
"""
Add a new condition. Use TraitsUI to make a simple dialog box.
"""
class ValidPythonIdentifier(BaseCStr):
info_text = 'a valid python identifier'
def validate(self, obj, name, value):
value = super(ValidPythonIdentifier, self).validate(obj, name, value)
if util.sanitize_identifier(value) == value:
return value
self.error(obj, name, value)
class NewTrait(HasTraits):
condition_name = ValidPythonIdentifier()
condition_type = Enum(["Category", "Number", "True/False"])
view = View(Item(name = 'condition_name'),
Item(name = 'condition_type'),
buttons = OKCancelButtons,
title = "Add a condition",
close_result = False)
def _validate_condition_name(self, x):
return util.sanitize_identifier(x)
new_trait = NewTrait()
new_trait.edit_traits(kind = 'modal')
if not new_trait.condition_name:
return
name = new_trait.condition_name
if name in self.model.dummy_experiment.channels:
error(None,
"Condition \"{0}\" conflicts with a channel name.".format(name),
"Error adding condition")
return
if name in self.model.tube_traits:
error(None,
"The experiment already has a condition named \"{0}\".".format(name),
"Error adding condition")
return
if new_trait.condition_type == "Category":
self._add_metadata(name, name + " (Category)", Str(condition = True))
elif new_trait.condition_type == "Number":
self._add_metadata(name, name + " (Number)", Float(condition = True))
else:
self._add_metadata(name, name + " (T/F)", Bool(condition = True))
def _get_inst(self):
if self.file:
info = read_info(self.file)
if info['dig'] is None:
error(None, "The selected FIFF file does not contain "
"digitizer information. Please select a different "
"file.", "Error Reading FIFF File")
self.reset_traits(['file'])
else:
return info
def saveas_file(self, info):
file = get_save_file(self.path, self.wildcard)
if file is not None:
try:
self.save_object(info, file)
self.file = file
self.path = os.path.dirname(file)
except BaseException, e:
log.exception(e)
error(info.ui.control, str(e))
def _save_project_graphically(self, parent, project, dirname):
""" Saves the given project to a name **dirname**. Gives the user
graphical feedback.
"""
# FIXME: pop up a progress bar
try:
project.save(dirname)
except Exception, e:
pyface.error(parent=parent, message='Error while saving project:\n%s' % str(e))
raise
def open(self):
super(ExperimentDialog, self).open()
if self.return_code == OK and not self.model.valid:
error(None, "Invalid experiment setup.\n"
"Was each tube's metadata unique?",
"Invalid experiment!")
self.open()
return self.return_code
def on_cameras_response(self):
info = self.cameras_dialog.get_plugin_info()
try:
self.select_plugin(*info)
except ImportError:
error(None, 'Loading the {} camera plugin failed. '
'Taking you back to the previous one.'.format(info[0]))
self.cameras_dialog.select_fallback()
info = self.cameras_dialog.get_plugin_info()
self.select_plugin(*info)
def on_cameras_response(self):
plugin_obj = self.cameras_dialog.get_plugin_object()
try:
self.select_plugin(plugin_obj)
except ImportError:
# some module was not available, select the dummy
error(None, 'Loading the {} camera plugin failed. '
'Taking you back to the dummy plugin.'.format(plugin_obj['name']))
self.cameras_dialog.select_fallback()
info = self.cameras_dialog.get_plugin_info()
self.select_plugin(*info)
def init_model(self, op):
# I DON'T KNOW WHY THIS STICKS AROUND ACROSS DIALOG INVOCATIONS.
del self.tubes[:]
dtype_to_trait = {"category": Str, "float": Float, "log": LogFloat, "bool": Bool, "int": Int}
for op_tube in op.tubes:
tube = Tube(file=op_tube.file, parent=self)
# first load the tube's metadata and set special columns
try:
tube_meta = fcsparser.parse(op_tube.file, meta_data_only=True, reformat_meta=True)
# tube_channels = tube_meta["_channels_"].set_index("$PnN")
except Exception as e:
error(
None,
"FCS reader threw an error on tube {0}: {1}".format(op_tube.file, e.value),
"Error reading FCS file",
)
return
if "$SRC" in tube_meta:
self.tube_traits["$SRC"] = Str(condition=False)
tube.add_trait("$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))
self.tube_traits["TUBE NAME"] = Str(condition=False)
tube.add_trait("TUBE NAME", Str(condition=False))
tube.trait_set(**{"TUBE NAME": tube_meta["TUBE NAME"]})
if "$SMNO" in tube_meta:
# self._add_metadata("$SMNO", "$SMNO", Str(condition = False))
self.tube_traits["$SMNO"] = Str(condition=False)
tube.add_trait("$SMNO", Str(condition=False))
tube.trait_set(**{"$SMNO": tube_meta["SMNO"]})
# next set conditions
for condition in op_tube.conditions:
condition_dtype = op.conditions[condition]
condition_trait = dtype_to_trait[condition_dtype](condition=True)
tube.add_trait(condition, condition_trait)
if not condition in self.tube_traits:
self.tube_traits[condition] = condition_trait
tube.trait_set(**op_tube.conditions)
# if we're the first tube loaded, create a dummy experiment
# to validate voltage, etc for later tubes
if not self.dummy_experiment:
self.model.dummy_experiment = ImportOp(tubes=[CytoflowTube(file=op_tube.file)], coarse_events=1).apply()
self.tubes.append(tube)
def save_file(self, info):
if self.file is None:
self.saveas_file(info)
else:
try:
self.save_object(info, self.file)
except BaseException, e:
log.exception(e)
mesg = 'There was an error saving the file.\n'
mesg += str(e)
error(info.ui.control, mesg)
def role_assignment():
"""Implement the role assignment for the current policy manager."""
# Create a dictionary of roles keyed by the role name.
all_roles = {}
try:
roles = get_permissions_manager().policy_manager.policy_storage.all_roles()
except PolicyStorageError, e:
error(None, str(e))
return
def activate_function_call(func_def):
""" Given a function and its path (optionally), open a function-call.
If the function is a user-defined/edited/saved function then make it
editable. If the user edits the code of the user-function, overwrite the
function and prompt the user to add the function. If the user does not
edit the code of the function, just add it as other functions would be
added.
Parameters:
-----------
func_def: FunctionDefinition
Contains the function, and its python path.
Returns:
--------
edited_function: function_object
The function that is edited.
activated_function: function_object
The function that must be activated.
python_string: List[Str]
includes import and function call to be added to a script.
"""
if func_def.code is None:
msg = "Perhaps your python path is not set correctly or\n" \
"there is an error in the file (or one it imports).\n"
error(None, msg, "Error loading function")
return None
# If it is a user-defined function, one would want to edit it
# else it can remain un-editable.
path_dir = os.path.dirname(func_def.filename)
usr_path = os.path.join(ETSConfig.user_data, USER_MODULE_NAME)
if path_dir == usr_path:
# This is a user function
# We no longer edit the function before dropping it on the canvas
#is_ok = edit_user_function(func_def)
# Note: If the user edits the code, one should save the
# code and ask the user if (s)he wants to continue
# adding the function to the block.
# If the user does not edit the code, it should be
# the same as it is for a regular function, that is,
# the user automatically adds the code to the block.
if func_def.dirty:
func_def.write(overwrite=True)
# Ask for confirmation if the user has to add it to
# block now or quit without adding.
msg= 'The user function \'%s' % func_def.name+ \
'\' has been edited and overwritten at \n' + \
'%s \n\n'% func_def.filename + \
'Do you wish to add the function to the block?'
if confirm(None, msg) == YES:
return func_def
else:
return None
else:
return func_def
else:
# This is a sys function which we are trying to override as a new user func
# We no longer edit the function before dropping it on the canvas
#is_ok = edit_sys_function(func_def)
if func_def.dirty:
func_def.write(overwrite=False)
# Ask for confirmation if the user has to add it to
# block now or quit without adding.
msg= 'The user function \'%s' % func_def.name+ \
'\' has been written at \n' + \
'%s \n\n'% func_def.filename + \
'Do you wish to add the function to the block?'
if confirm(None, msg) == YES:
return func_def
else:
return None
else:
return func_def
return None
def Reload(self, info):
try:
self.saveObject.load()
except:
error(None, 'Error Loading file.', title='Error')
return
logger.debug("Exporting {} datasets exported to {}.".format(
len(log_dfs), target_file))
df = pd.concat(log_dfs, axis=1)
df.to_csv(target_file)
logger.debug("Data exported to {}.".format(target_file))
central_pane = task.central_pane
active_chrom_plot = central_pane.active_editor.obj
if not isinstance(active_chrom_plot, ChromatogramModel):
msg = "Active tab is not a plot. Please select the plot you want to " \
"export and run again."
logger.exception(msg)
error(None, msg)
else:
export_path = to_csv_file_requester()
if export_path is not None:
export_ext = splitext(export_path)[1]
if not export_ext:
export_path += ".csv"
abort = False
# Only confirm on windows, since on Mac, the FileDialog has this builtin.
if exists(export_path) and IS_WINDOWS:
result = confirm(None, "The file already exists: overwrite?")
if result == NO:
abort = True
if export_path and not abort:
def error(owner, msg):
print "Exception caught, message: %s" % (msg)
general.printException()
pyfaceapi.error(owner, msg)
def open_file(self, path):
f = open(path, 'r')
unpickler = pickle.Unpickler(f)
try:
version = unpickler.load()
except TraitError:
error(parent=None,
message="This doesn't look like a Cytoflow file. Or maybe "
"you tried to load a workflow older than version "
"0.5?")
return
if version != self.model.version:
ret = confirm(
parent=None,
message="This is Cytoflow {}, but you're trying "
"to load a workflow from version {}. This may or "
"may not work! Are you sure you want to proceed?".format(
self.model.version, version),
title="Load workflow?")
if ret != YES:
return
try:
new_workflow = unpickler.load()
except TraitError:
error(parent=None, message="Error trying to load the workflow.")
return
# a few things to take care of when reloading
for wi_idx, wi in enumerate(new_workflow):
# clear the wi status
wi.status = "invalid"
# re-link the linked list. i thought this would get taken care
# of in deserialization, but i guess not...
if wi_idx > 0:
wi.previous = new_workflow[wi_idx - 1]
# reload the subset lists. i don't know why this is necessary.
for view in wi.views:
subset_list = view.subset_list
view.subset_list = []
for s in subset_list:
view.subset_list.append(s)
subset_list = wi.operation.subset_list
wi.operation.subset_list = []
for s in subset_list:
wi.operation.subset_list.append(s)
# replace the current workflow with the one we just loaded
if False: # for debugging the loading of things
from event_tracer import record_events
with record_events() as container:
self.model.workflow = new_workflow
container.save_to_directory(os.getcwd())
else:
self.model.workflow = new_workflow
self.model.modified = False
def show_error(self, error_string):
error(
None,
"An exception has occurred. Please report a problem from the Help menu!\n\n"
"Afterwards, may need to restart Cytoflow to continue working.\n\n"
+ error_string)
def open_file(self, path):
try:
new_workflow = load_yaml(path)
# a few things to take care of when reloading.
# we do this in the try block to catch people who
# load valid YAML files that aren't from cytoflow.
for wi_idx, wi in enumerate(new_workflow):
# get wi lock
wi.lock.acquire()
# clear the wi status
wi.status = "loading"
# re-link the linked list.
if wi_idx > 0:
wi.previous_wi = new_workflow[wi_idx - 1]
if wi_idx < len(new_workflow) - 1:
wi.next_wi = new_workflow[wi_idx + 1]
except yaml.parser.ParserError as e:
error(None,
"Parser error loading {} -- is it a Cytoflow file?\n\n{}"
.format(path, str(e)))
return
except Exception as e:
error(None,
"{} loading {} -- is it a Cytoflow file?\n\n{}"
.format(e.__class__.__name__, path, str(e)))
return
# are we just running a smoke test?
if 'startup_test' in new_workflow[0].metadata:
def quit_app(app):
app.exit(force = True)
from pyface.timer.api import do_after
do_after(5*1000, quit_app, self.application)
return
# check that the FCS files are all there
wi = new_workflow[0]
assert(wi.operation.id == "edu.mit.synbio.cytoflow.operations.import")
missing_tubes = 0
for tube in wi.operation.tubes:
file = pathlib.Path(tube.file)
if not file.exists():
missing_tubes += 1
if missing_tubes == len(wi.operation.tubes):
warning(self.window.control,
"Cytoflow couldn't find any of the FCS files from that "
"workflow. If they've been moved, please open one FCS "
"file to show Cytoflow where they've been moved to.")
dialog = FileDialog(parent = self.window.control,
action = 'open',
wildcard = (FileDialog.create_wildcard("FCS files", "*.fcs *.lmd"))) # @UndefinedVariable
if dialog.open() == OK:
# find the "best" file match -- ie, the one with the longest
# tail match
fcs_path = pathlib.Path(dialog.path).parts
best_path_len = -1
for tube in wi.operation.tubes:
tube_path = pathlib.Path(tube.file).parts
for i in range(len(fcs_path)):
if list(reversed(fcs_path))[:i] == list(reversed(tube_path))[:i] and i > best_path_len:
best_path_len = i
if best_path_len >= 0:
for tube in wi.operation.tubes:
tube_path = pathlib.Path(tube.file).parts
new_path = fcs_path[:-1 * best_path_len] + tube_path[-1 * best_path_len :]
tube.file = str(pathlib.Path(*new_path))
elif missing_tubes > 0:
warning(self.window.control,
"Cytoflow couldn't find some of the FCS files from that "
"workflow. You'll need to re-load them from the Import "
"operation.")
# replace the current workflow with the one we just loaded
if False: # for debugging the loading of things
from cytoflowgui.utility.event_tracer import record_events
with record_events() as container:
self.model.workflow = new_workflow
container.save_to_directory(os.getcwd())
else:
self.model.workflow = new_workflow
self.model.modified = False
for wi in self.model.workflow:
wi.lock.release()
if self.model.debug:
self.model.run_all()
else:
ret = confirm(parent = None,
message = "Do you want to execute the workflow now?",
title = "Run workflow?")
if ret == YES:
self.model.run_all()
def _get__info(self):
if self.file:
info = None
_, tree, _ = fiff_open(self.file)
if len(dir_tree_find(tree, FIFF.FIFFB_MEAS_INFO)) > 0:
info = read_info(self.file, verbose=False)
elif len(dir_tree_find(tree, FIFF.FIFFB_ISOTRAK)) > 0:
info = read_dig_montage(fif=self.file)
if info is None:
error(None, "The selected FIFF file does not contain "
"digitizer information. Please select a different "
"file.", "Error Reading FIFF File")
self.reset_traits(['file'])
return
elif isinstance(info, DigMontage):
info.transform_to_head()
digs = list()
digs.append({'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_LPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': info.lpa})
digs.append({'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_NASION,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': info.nasion})
digs.append({'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': FIFF.FIFFV_POINT_RPA,
'kind': FIFF.FIFFV_POINT_CARDINAL,
'r': info.rpa})
for idx, pos in enumerate(info.hsp):
dig = {'coord_frame': FIFF.FIFFV_COORD_HEAD,
'ident': idx,
'kind': FIFF.FIFFV_POINT_EXTRA,
'r': pos}
digs.append(dig)
info = _empty_info(1)
info['dig'] = digs
else:
# check that all fiducial points are present
has_point = {FIFF.FIFFV_POINT_LPA: False,
FIFF.FIFFV_POINT_NASION: False,
FIFF.FIFFV_POINT_RPA: False}
for d in info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_CARDINAL:
has_point[d['ident']] = True
if not all(has_point.values()):
missing = []
if not has_point[FIFF.FIFFV_POINT_LPA]:
missing.append('LPA')
if not has_point[FIFF.FIFFV_POINT_NASION]:
missing.append('Nasion')
if not has_point[FIFF.FIFFV_POINT_RPA]:
missing.append('RPA')
error(None, "The selected FIFF file does not contain "
"all cardinal points (missing: %s). Please select a "
"different file." % ', '.join(missing),
"Error Reading FIFF File")
self.reset_traits(['file'])
return
return info
def perform(self, event=None):
""" Open a URL in a web browser. """
try:
webbrowser.open(self.url)
except webbrowser.Error as exc:
error(None, str(exc))
def init_model(self, op):
dtype_to_trait = {
"category": Str,
"float": Float,
"bool": Bool,
"int": Int
}
new_tubes = []
for op_tube in op.tubes:
tube = Tube(file=op_tube.file, parent=self)
# first load the tube's metadata and set special columns
try:
tube_meta = fcsparser.parse(op_tube.file,
meta_data_only=True,
reformat_meta=True)
#tube_channels = tube_meta["_channels_"].set_index("$PnN")
except Exception as e:
error(None, "FCS reader threw an error on tube {0}: {1}"\
.format(op_tube.file, e.value),
"Error reading FCS file")
return
# if we're the first tube loaded, create a dummy experiment
if not self.dummy_experiment:
self.dummy_experiment = ImportOp(tubes=[op_tube],
conditions=op.conditions,
coarse_events=1).apply()
if '$SRC' in tube_meta:
self.tube_traits["$SRC"] = Str(condition=False)
tube.add_trait("$SRC", Str(condition=False))
tube.trait_set(**{"$SRC": tube_meta['$SRC']})
if 'TUBE NAME' in tube_meta:
self.tube_traits["TUBE NAME"] = Str(condition=False)
tube.add_trait("TUBE NAME", Str(condition=False))
tube.trait_set(**{"TUBE NAME": tube_meta['TUBE NAME']})
if '$SMNO' in tube_meta:
self.tube_traits["$SMNO"] = Str(condition=False)
tube.add_trait("$SMNO", Str(condition=False))
tube.trait_set(**{"$SMNO": tube_meta['SMNO']})
if 'WELL ID' in tube_meta:
pos = tube_meta['WELL ID']
row = pos[0]
col = int(pos[1:3])
self.tube_traits["Row"] = Str(condition=False)
self.tube_traits["Col"] = Int(condition=False)
tube.add_trait("Row", Str(condition=False))
tube.add_trait("Col", Int(condition=False))
tube.trait_set(**{"Row": row, "Col": col})
# next set conditions
try:
conditions_list = op_tube.conditions_list
except:
conditions_list = list(op_tube.conditions.keys())
for condition in conditions_list:
condition_dtype = op.conditions[condition]
condition_trait = \
dtype_to_trait[condition_dtype](condition = True)
tube.add_trait(condition, condition_trait)
tube.conditions[condition] = op_tube.conditions[condition]
if not condition in self.tube_traits:
self.tube_traits[condition] = condition_trait
tube.trait_set(**op_tube.conditions)
new_tubes.append(tube)
self.tubes.extend(new_tubes)
def error(msg):
"""Display an error message to the user."""
error(None, msg)
# Private interface.
###########################################################################
def _select_user(self, name):
"""Select a user returning the data as a tuple of name and description.
"""
# Get all users that satisfy the criteria.
try:
users = self.user_storage.matching_users(name)
except UserStorageError, e:
self._us_error(e)
return '', ''
if len(users) == 0:
error(None, "There is no user that matches \"%s\"." % name)
return '', ''
return select_user(users)
@staticmethod
def _us_error(e):
"""Display a message to the user after a UserStorageError exception has
been raised. If the message is empty then we assume the user has
already been informed."""
msg = str(e)
if msg:
error(None, msg)
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
new_tubes = []
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("$PnN")
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
# if we're the first tube loaded, create a dummy experiment
if not self.model.dummy_experiment:
self.model.dummy_experiment = ImportOp(
tubes=[CytoflowTube(file=path)], coarse_events=1).apply()
# check the next tube against the dummy experiment
try:
check_tube(path, self.model.dummy_experiment)
except util.CytoflowError as e:
error(None, e.__str__(), "Error importing tube")
return
tube = Tube()
for trait_name, trait in list(self.model.tube_traits.items()):
tube.add_trait(trait_name, trait)
# this magic makes sure the trait is actually defined
# in tube.__dict__, so it shows up in trait_names etc.
tube.trait_set(**{trait_name: trait.default_value})
if trait.condition:
tube.on_trait_change(self._try_multiedit, trait_name)
tube.trait_set(file=path, parent=self.model)
if '$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})
new_tubes.append(tube)
self.model.tubes.extend(new_tubes)
def _ps_error(e):
"""Display a message to the user after a PolicyStorageError exception
has been raised."""
error(None, str(e))
def error(msg, parent=None):
"""Handle an error message.
"""
logger.error(msg)
if pyface is not None:
pyface.error(parent, msg)