# 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 diffusion preprocessing config and stage UI classes."""
from traits.api import *
from traitsui.api import *
import subprocess
# from cmp.bidsappmanager.stages.common import Stage
from cmp.stages.preprocessing.preprocessing import PreprocessingConfig, PreprocessingStage
[docs]class PreprocessingConfigUI(PreprocessingConfig):
"""Class that extends the (diffusion) :class:`PreprocessingConfig` 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.preprocessing.preprocessing.PreprocessingConfig
"""
traits_view = View(
VGroup(
VGroup(
HGroup(
Item('denoising'),
Item('denoising_algo', label='Tool:',
visible_when='denoising==True'),
Item('dipy_noise_model', label='Noise model (Dipy):',
visible_when='denoising_algo=="Dipy (NLM)"')),
HGroup(
Item('bias_field_correction'),
Item('bias_field_algo', label='Tool:',
visible_when='bias_field_correction==True')),
VGroup(
HGroup(
Item('eddy_current_and_motion_correction'),
Item('eddy_correction_algo',
visible_when='eddy_current_and_motion_correction==True')),
Item('eddy_correct_motion_correction',
label='Motion correction',
visible_when='eddy_current_and_motion_correction==True and eddy_correction_algo=="FSL eddy_correct"'),
Item('total_readout',
label='Total readout time (s):',
visible_when='eddy_current_and_motion_correction==True and eddy_correction_algo=="FSL eddy"')),
label='Preprocessing steps'),
VGroup(
VGroup(
Item('resampling', label='Voxel size (x,y,z)',
editor=TupleEditor(cols=3)),
'interpolation'),
label='Final resampling')),
width=0.5,
height=0.5)
[docs]class PreprocessingStageUI(PreprocessingStage):
"""Class that extends the (diffusion) :class:`PreprocessingStage` 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.preprocessing.preprocessing.PreprocessingStage
"""
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=650,
kind='livemodal',
title='Edit stage configuration',
buttons=['OK', 'Cancel'])
# General and UI members
def __init__(self, bids_dir, output_dir):
"""Constructor of the diffusion PreprocessingStageUI class.
Parameters
-----------
bids_dir : path
BIDS root directory
output_dir : path
Output directory
See also
---------
cmp.stages.preprocessing.preprocessing.PreprocessingStage.__init_
cmp.cmpbidsappmanager.stages.preprocessing.preprocessing.PreprocessingStageUI
"""
PreprocessingStage.__init__(self, bids_dir, output_dir)
self.config = PreprocessingConfigUI()
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])