# Copyright (C) 2009-2022, Ecole Polytechnique Federale de Lausanne (EPFL) and
# Hospital Center and University of Lausanne (UNIL-CHUV), Switzerland, and CMP3 contributors
# All rights reserved.
#
# This software is distributed under the open-source license Modified BSD.
"""Definition of structural connectome config and stage UI classes."""
# Global imports
import subprocess
from traits.api import *
from traitsui.api import *
# Own imports
from cmp.stages.connectome.connectome import ConnectomeConfig, ConnectomeStage
[docs]class ConnectomeConfigUI(ConnectomeConfig):
"""Class that extends the :class:`ConnectomeConfig` with graphical components.
Attributes
----------
output_types : list of string
A list of ``output_types``. Valid ``output_types`` are
'gpickle', 'mat', 'cff', 'graphml'
connectivity_metrics : list of string
A list of connectivity metrics to stored. Valid ``connectivity_metrics`` are
'Fiber number', 'Fiber length', 'Fiber density', 'Fiber proportion',
'Normalized fiber density', 'ADC', 'gFA'
traits_view : traits.ui.View
TraitsUI view that displays the Attributes of this class
See also
---------
cmp.stages.connectome.connectome.ConnectomeConfig
"""
output_types = List(
["gpickle"],
editor=CheckListEditor(values=["gpickle", "mat", "cff", "graphml"], cols=4),
)
connectivity_metrics = List(
[
"Fiber number",
"Fiber length",
"Fiber density",
"Fiber proportion",
"Normalized fiber density",
"ADC",
"gFA",
],
editor=CheckListEditor(
values=[
"Fiber number",
"Fiber length",
"Fiber density",
"Fiber proportion",
"Normalized fiber density",
"ADC",
"gFA",
],
cols=4,
),
)
traits_view = View(
Item("output_types", style="custom"),
Group(
Item("connectivity_metrics", label="Metrics", style="custom"),
Item("compute_curvature"),
label="Connectivity matrix",
show_border=True,
),
)
[docs]class ConnectomeStageUI(ConnectomeStage):
"""Class that extends the :class:`ConnectomeStage` with graphical components.
Attributes
----------
log_visualization : traits.Bool
If True, display with a log transformation
circular_layout : traits.Bool
If True, display the connectivity matrix using a circular layout
inspect_output_button : traits.ui.Button
Button that displays the selected connectivity matrix
in the graphical component for quality inspection
inspect_outputs_view : traits.ui.View
TraitsUI view that displays the quality inspection window of this stage
config_view : traits.ui.View
TraitsUI view that displays the configuration window of this stage
See also
---------
cmp.stages.connectome.connectome.ConnectomeStage
"""
log_visualization = Bool(True)
circular_layout = Bool(False)
inspect_output_button = Button("View")
inspect_outputs_view = View(
Group(
Item("name", editor=TitleEditor(), show_label=False),
Group(
Item("log_visualization", label="Log scale"),
Item("circular_layout", label="Circular layout"),
label="Visualization",
show_border=True,
),
Group(
Item("inspect_outputs_enum", show_label=False),
Item(
"inspect_output_button",
enabled_when='inspect_outputs_enum!="Outputs not available"',
show_label=False,
),
label="View outputs",
show_border=True,
),
),
scrollable=True,
resizable=True,
kind="livemodal",
title="Inspect stage outputs",
buttons=["OK", "Cancel"],
)
config_view = View(
Group(
Item("name", editor=TitleEditor(), show_label=False),
Group(
Item("config", style="custom", show_label=False),
label="Configuration",
show_border=True,
),
),
scrollable=True,
resizable=True,
height=270,
width=670,
kind="livemodal",
title="Edit stage configuration",
buttons=["OK", "Cancel"],
)
def __init__(self, bids_dir, output_dir):
"""Constructor of the ConnectomeStageUI class.
Parameters
----------
bids_dir : traits.Directory
BIDS root directory
output_dir : traits.Directory
Output directory
See also
---------
cmp.stages.connectome.connectome.ConnectomeStage.__init__
"""
ConnectomeStage.__init__(self, bids_dir, output_dir)
self.config = ConnectomeConfigUI()
self.log_visualization = self.config.log_visualization
self.circular_layout = self.config.circular_layout
def _log_visualization_changed(self, new):
"""Update the value of log_visualization in the config.
Parameters
----------
new : traits.Bool
New value
"""
self.config.log_visualization = new
self.define_inspect_outputs()
def _circular_layout_changed(self, new):
"""Update the value of circular_layout in the config.
Parameters
----------
new : traits.Bool
New value
"""
self.config.circular_layout = new
self.define_inspect_outputs()
def _inspect_output_button_fired(self, info):
"""Display the selected output when ``inspect_output_button`` is clicked.
Parameters
----------
info : traits.ui.Button
Button object
"""
subprocess.Popen(self.inspect_outputs_dict[self.inspect_outputs_enum])