def test_clone_trait(self):
""" Method to test trait clone from string description.
"""
# Test first to build trait description from nipype traits and then
# to instanciate the trait
to_test_fields = {
"timing_units": "traits.Enum(('secs', 'scans'))",
"bases": ("traits.Dict(traits.Enum(('hrf', 'fourier', "
"'fourier_han', 'gamma', 'fir')), traits.Any())"),
"mask_image": "traits.File(Undefined)",
"microtime_onset": "traits.Float()",
"mask_threshold": ("traits.Either(traits.Enum(('-Inf',)), "
"traits.Float())")
}
i = spm.Level1Design()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
to_test_fields = {
"contrasts": (
"traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())), "
"traits.Tuple(traits.Str(), traits.Enum(('F',)), "
"traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())"
"))))))"),
"use_derivs": "traits.Bool()"
}
i = spm.EstimateContrast()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
# Test to clone some traits
trait_description = ["Float", "Int"]
handler = clone_trait(trait_description)
trait = handler.as_ctrait()
self.assertEqual(trait_description, trait_ids(trait))
def sync_process_output_traits(process_instance, name, value):
""" Event handler function to update the process instance outputs
This callback is only called when an input process instance trait is
modified.
Parameters
----------
process_instance: process instance (mandatory)
the process instance that contain the nipype interface we want
to update.
name: str (mandatory)
the name of the trait we want to update.
value: type (manndatory)
the old trait value
"""
# Get all the input traits
input_traits = process_instance.traits(output=False)
# Try to update all the output process instance traits values when
# a process instance input trait is modified.
if name in input_traits:
# Try to set all the process instance output traits values from
# the nipype autocompleted traits values
try:
nipype_outputs = (process_instance.
_nipype_interface._list_outputs())
# Synchronize traits: check file existance
for out_name, out_value in nipype_outputs.iteritems():
# Get trait type
trait_type = trait_ids(
process_instance._nipype_interface.output_spec().
trait(out_name))
# Set the output process trait value
# If we have a file check that the file exists before
# setting the new value
if (trait_type[0] is not "File" or
os.path.isfile(repr(out_value))):
process_instance.set_parameter(
"_" + out_name, out_value)
# If we can't update the output process instance traits values,
# print a logging debug message.
except Exception:
ex_type, ex, tb = sys.exc_info()
logger.debug(
"Something wrong in the nipype output trait "
"synchronization:\n\n\tError: {0} - {1}\n"
"\tTraceback:\n{2}".format(
ex_type, ex, "".join(traceback.format_tb(tb))))
def onCreateViewerClicked(self):
""" Event to create the viewer
"""
# Get the viewer node and process
viewer_node = self.pipeline.nodes[self.viewer_node_name]
viewer_process = viewer_node.process
# Propagate the parameters to the input viewer node
# And check if the viewer is active (ie dependencies
# are specified -> corresponding process have run)
is_viewer_active = True
for plug_name, plug in six.iteritems(viewer_node.plugs):
if plug_name in ["nodes_activation", "selection_changed"]:
continue
# Since it is a viewer node we normally have only inputs
for (source_node_name, source_plug_name, source_node, source_plug,
weak_link) in plug.links_from:
# Get the source plug value and source trait
source_plug_value = getattr(source_node.process,
source_plug_name)
source_trait = source_node.process.trait(source_plug_name)
# Check if the viewer is active:
# 1) the source_plug_value has been set
if source_plug_value == source_trait.handler.default_value:
is_viewer_active = False
break
# 2) if the plug is a file, the file exists
str_description = trait_ids(source_trait)
if (len(str_description) == 1 and str_description[0] == "File"
and not os.path.isfile(source_plug_value)):
is_viewer_active = False
break
# Update destination trait
setattr(viewer_process, plug_name, source_plug_value)
# Just stop the iterations if the status of the viewer
# is alreadu known
if not is_viewer_active:
break
# Execute the viewer process using the defined study configuration
if is_viewer_active:
soma.subprocess.Popen(viewer_process.get_commandline())
# self.study_config.run(viewer_process)
else:
logging.error("The viewer is not active yet, maybe "
"because the processings steps have not run or are "
"not finished.")
def sync_process_output_traits(process_instance, name, value):
""" Event handler function to update the process instance outputs
This callback is only called when an input process instance trait is
modified.
Parameters
----------
process_instance: process instance (mandatory)
the process instance that contain the nipype interface we want
to update.
name: str (mandatory)
the name of the trait we want to update.
value: type (manndatory)
the old trait value
"""
# Get all the input traits
input_traits = process_instance.traits(output=False)
# Try to update all the output process instance traits values when
# a process instance input trait is modified or when the dedicated
# 'synchronize' trait value is modified
if name in input_traits or name == "synchronize":
# Try to set all the process instance output traits values from
# the nipype autocompleted traits values
try:
nipype_outputs = (
process_instance._nipype_interface._list_outputs())
# Synchronize traits: check file existance
for out_name, out_value in six.iteritems(nipype_outputs):
# Get trait type
trait_type = trait_ids(
process_instance._nipype_interface.output_spec().trait(
out_name))
# Set the output process trait value
process_instance.set_parameter("_" + out_name, out_value)
# If we can't update the output process instance traits values,
# print a logging debug message.
except Exception:
ex_type, ex, tb = sys.exc_info()
logger.debug("Something wrong in the nipype output trait "
"synchronization:\n\n\tError: {0} - {1}\n"
"\tTraceback:\n{2}".format(
ex_type, ex,
"".join(traceback.format_tb(tb))))
def _list_outputs(self):
""" Method to list all the interface outputs.
Returns
-------
outputs: dict
all the interface outputs
"""
# Get the outputs from the nipype method
outputs = self._list_outputs_core()
# Modify the output paths
corrected_outputs = {}
for trait_name, trait_value in outputs.iteritems():
trait_desc = trait_ids(self.output_spec().trait(trait_name))
if len(trait_desc) != 1:
raise ValueError("Do not deal for the moment with Either "
"nipype output traits.")
corrected_outputs[trait_name] = self._modify_path(
trait_value, trait_desc[0].split("_"))
return corrected_outputs
def test_clone_trait(self):
""" Method to test trait clone from string description.
"""
# Test first to build trait description from nipype traits and then
# to instanciate the trait
to_test_fields = {
"timing_units":
"traits.Enum(('secs', 'scans'))",
"bases": ("traits.Dict(traits.Enum(('hrf', 'fourier', "
"'fourier_han', 'gamma', 'fir')), traits.Any())"),
"mask_image":
"traits.File(Undefined)",
"microtime_onset":
"traits.Float()",
"mask_threshold": ("traits.Either(traits.Enum(('-Inf',)), "
"traits.Float())")
}
i = spm.Level1Design()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
to_test_fields = {
"contrasts":
("traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())), "
"traits.Tuple(traits.Str(), traits.Enum(('F',)), "
"traits.List(traits.Either(traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float())), traits.Tuple(traits.Str(), "
"traits.Enum(('T',)), traits.List(traits.Str()), "
"traits.List(traits.Float()), traits.List(traits.Float())"
"))))))"),
"use_derivs":
"traits.Bool()"
}
i = spm.EstimateContrast()
for field, result in six.iteritems(to_test_fields):
# Test to build the trait expression
trait = i.inputs.trait(field)
expression = build_expression(trait)
self.assertEqual(expression, result)
# Try to clone the trait
trait = eval_trait(expression)()
self.assertEqual(build_expression(trait), result)
# Test to clone some traits
trait_description = ["Float", "Int"]
handler = clone_trait(trait_description)
trait = handler.as_ctrait()
self.assertEqual(trait_description, trait_ids(trait))
def create_widget(parent,
control_name,
control_value,
trait,
label_class=None,
user_data=None):
""" Create the widget.
Parameters
----------
parent: QWidget (mandatory)
the parent widget
control_name: str (mandatory)
the name of the control we want to create
control_value: str (mandatory)
the default control value, here the enum values
trait: Tait (mandatory)
the trait associated to the control
label_class: Qt widget class (optional, default: None)
the label widget will be an instance of this class. Its constructor
will be called using 2 arguments: the label string and the parent
widget.
Returns
-------
out: 2-uplet
a two element tuple of the form (control widget: QComboBox,
associated label: QLabel)
"""
# Create the widget that will be used to select a value
widget = Qt.QWidget(parent)
# we have a combobox for the trait type, and one of the control types
# implementations depending on it
layout = Qt.QVBoxLayout()
widget.setLayout(layout)
widget.type_combo = Qt.QComboBox()
hlayout = Qt.QHBoxLayout()
#layout.addLayout(hlayout)
lwidget = Qt.QWidget()
lwidget.setLayout(hlayout)
hlayout.addWidget(Qt.QLabel('Compound type:'))
hlayout.addWidget(widget.type_combo)
widget.header_widget = lwidget
widget.user_data = user_data
# get compound types
types = trait_ids(trait)
for t in types:
widget.type_combo.addItem(t)
widget.type_combo.setCurrentIndex(0)
widget.compound_widget = None
widget.trait = trait # we need to access it later
widget.trait_name = control_name
widget.compound_label = None
type_id = CompoundControlWidget.type_id_for(trait.handler.handlers,
control_value)
widget.current_type_id = type_id
widget.type_combo.setCurrentIndex(type_id)
CompoundControlWidget.create_compound_widget(widget)
widget.type_combo.currentIndexChanged.connect(
partial(CompoundControlWidget.change_type_index, widget))
# Add a parameter to tell us if the widget is optional
widget.optional = trait.optional
# Create the label associated with the enum widget
control_label = trait.label
if control_label is None:
control_label = control_name
if label_class is None:
label_class = Qt.QLabel
if control_label is not None:
label = (label_class(control_label, parent), lwidget)
else:
label = lwidget
return (widget, label)