# Copyright (C) 2009-2021, 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 segmentation config and stage UI classes."""
# General imports
import subprocess
from traits.api import *
from traitsui.api import *
# Own imports
from cmp.stages.segmentation.segmentation import SegmentationConfig, SegmentationStage
[docs]class SegmentationConfigUI(SegmentationConfig):
"""Class that extends the :class:`SegmentationConfig` with graphical components.
Attributes
----------
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.segmentation.segmentation.SegmentationConfig
"""
traits_view = View(Item('seg_tool', label="Segmentation tool"),
Group(
HGroup('make_isotropic',
Item('isotropic_vox_size', label="Voxel size (mm)", visible_when='make_isotropic')),
Item('isotropic_interpolation', label='Interpolation',
visible_when='make_isotropic'),
Item('number_of_threads', label='Number of threads used for multithreading in Freesurfer and ANTs'),
'brain_mask_extraction_tool',
Item('ants_templatefile', label='Template',
visible_when='brain_mask_extraction_tool == "ANTs"'),
Item('ants_probmaskfile', label='Probability mask',
visible_when='brain_mask_extraction_tool == "ANTs"'),
Item('ants_regmaskfile', label='Extraction mask',
visible_when='brain_mask_extraction_tool == "ANTs"'),
Item('brain_mask_path', label='Brain mask path',
visible_when='brain_mask_extraction_tool == "Custom"'),
'freesurfer_args',
visible_when="seg_tool=='Freesurfer'"))
[docs]class SegmentationStageUI(SegmentationStage):
"""Class that extends the :class:`SegmentationStage` 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.segmentation.segmentation.SegmentationStage
"""
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=400, width=450,
kind='livemodal',
title='Edit stage configuration',
buttons=['OK', 'Cancel'])
# General and UI members
def __init__(self, bids_dir, output_dir):
"""Constructor of the SegmentationStageUI class.
Parameters
-----------
bids_dir : path
BIDS root directory
output_dir : path
Output directory
See also
---------
cmp.stages.segmentation.segmentation.SegmentationStage.__init_
cmp.cmpbidsappmanager.stages.segmentation.segmentation.SegmentationStageUI
"""
SegmentationStage.__init__(self, bids_dir, output_dir)
self.config = SegmentationConfigUI()
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])