# 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 parcellation config and stage UI classes."""
# General imports
import os
import subprocess
from traits.api import *
from traitsui.api import *
# Own imports
from cmp.stages.parcellation.parcellation import ParcellationConfig, ParcellationStage
[docs]class ParcellationConfigUI(ParcellationConfig):
"""Class that extends the :class:`ParcellationConfig` with graphical components.
Attributes
----------
custom_parcellation_view : traits.ui.View
VGroup that displays the different parts of a custom BIDS parcellation file
traits_view : traits.ui.View
TraitsUI view that displays the attributes of this class, e.g.
the parameters for the stage
See also
---------
cmp.stages.parcellation.parcellation.ParcellationConfig
"""
custom_parcellation_group = VGroup(
Item('object.custom_parcellation.toolbox_derivatives_dir', label="Derivatives directory"),
Item('object.custom_parcellation.atlas', label="atlas"),
Item('object.custom_parcellation.res', label="res"),
Item('object.custom_parcellation.suffix', label="suffix", style='readonly'),
label="Custom parcellation"
)
traits_view = View(
Item(
"parcellation_scheme", editor=EnumEditor(name="parcellation_scheme_editor")
),
Group(
Include('custom_parcellation_group'),
visible_when='parcellation_scheme=="Custom"',
),
Group(
"segment_hippocampal_subfields",
"segment_brainstem",
"include_thalamic_nuclei_parcellation",
Item(
"ants_precision_type",
label="ANTs precision type",
enabled_when="include_thalamic_nuclei_parcellation",
),
visible_when='parcellation_scheme=="Lausanne2018"',
),
)
[docs]class ParcellationStageUI(ParcellationStage):
"""Class that extends the :class:`ParcellationStage` with graphical components.
Attributes
----------
inspect_output_button : traits.ui.Button
Button that displays the selected output in an appropriate viewer
(present only in the window 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.parcellation.parcellation.ParcellationStage
"""
inspect_output_button = Button("View")
inspect_outputs_view = View(
Group(
Item("name", editor=TitleEditor(), show_label=False),
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=350,
width=600,
kind="livemodal",
title="Edit stage configuration",
buttons=["OK", "Cancel"],
)
def __init__(self, pipeline_mode, subject, session, bids_dir, output_dir):
"""Constructor of the ParcellationStageUI class.
Parameters
-----------
pipeline_mode : string
Pipeline mode that can be "Diffusion" or "fMRI"
bids_dir : path
BIDS root directory
output_dir : path
Output directory
See also
---------
cmp.stages.parcellation.parcellation.ParcellationStage.__init_
cmp.cmpbidsappmanager.stages.parcellation.parcellation.ParcellationStageUI
"""
ParcellationStage.__init__(self, pipeline_mode, subject, session, bids_dir, output_dir)
self.config = ParcellationConfigUI()
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])