# 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 reconstruction and tracking config and stage UI classes."""
# General imports
import subprocess
from traits.api import *
from traitsui.api import *
# Own imports
from cmp.bidsappmanager.stages.diffusion.reconstruction import *
from cmp.bidsappmanager.stages.diffusion.tracking import *
from cmp.stages.diffusion.diffusion import DiffusionConfig, DiffusionStage
[docs]class DiffusionConfigUI(DiffusionConfig):
"""Class that extends the :class:`DiffusionConfig` with graphical components.
It includes the graphical components defining the configuration of the diffusion
reconstruction and tractography sub-stages.
Attributes
----------
traits_view : traits.ui.View
TraitsUI view that displays the Diffusion Stage Parameter Attributes
of this class
See also
---------
cmp.stages.diffusion.diffusion.DiffusionConfig
"""
traits_view = View(
Item('diffusion_imaging_model', style='readonly'),
HGroup(
Item('dilate_rois'),
Item('dilation_radius', visible_when='dilate_rois', label="radius")
),
Group(Item('recon_processing_tool', label='Reconstruction processing tool',
editor=EnumEditor(name='recon_processing_tool_editor')),
Item('dipy_recon_config', style='custom',
visible_when='recon_processing_tool=="Dipy"'),
Item('mrtrix_recon_config', style='custom',
visible_when='recon_processing_tool=="MRtrix"'),
label='Reconstruction', show_border=True, show_labels=False,
visible_when='tracking_processing_tool!=Custom'),
Group(Item('tracking_processing_tool', label='Tracking processing tool',
editor=EnumEditor(name='tracking_processing_tool_editor')),
Item('diffusion_model', editor=EnumEditor(name='diffusion_model_editor'),
visible_when='tracking_processing_tool!="Custom"'),
Item('dipy_tracking_config', style='custom',
visible_when='tracking_processing_tool=="Dipy"'),
Item('mrtrix_tracking_config', style='custom',
visible_when='tracking_processing_tool=="MRtrix"'),
label='Tracking', show_border=True, show_labels=False),
Group(
Item('custom_track_file', style='simple'),
visible_when='tracking_processing_tool=="Custom"'),
height=750,
width=500
)
def __init__(self):
"""Constructor of the DiffusionConfigUI class.
See also
---------
cmp.stages.diffusion.diffusion.DiffusionConfig.__init_
cmp.cmpbidsappmanager.stages.diffusion.reconstruction.Dipy_recon_configUI
cmp.cmpbidsappmanager.stages.diffusion.reconstruction.MRtrix_recon_configUI
cmp.cmpbidsappmanager.stages.diffusion.tracking.Dipy_tracking_configUI
cmp.cmpbidsappmanager.stages.diffusion.tracking.MRtrix_tracking_configUI
"""
DiffusionConfig.__init__(self)
self.dipy_recon_config = Dipy_recon_configUI(imaging_model=self.diffusion_imaging_model,
recon_mode=self.diffusion_model,
tracking_processing_tool=self.tracking_processing_tool)
self.mrtrix_recon_config = MRtrix_recon_configUI(imaging_model=self.diffusion_imaging_model,
recon_mode=self.diffusion_model)
self.dipy_tracking_config = Dipy_tracking_configUI(imaging_model=self.diffusion_imaging_model,
tracking_mode=self.diffusion_model,
SD=self.mrtrix_recon_config.local_model)
self.mrtrix_tracking_config = MRtrix_tracking_configUI(tracking_mode=self.diffusion_model,
SD=self.mrtrix_recon_config.local_model)
self.mrtrix_recon_config.on_trait_change(
self.update_mrtrix_tracking_SD, 'local_model')
self.dipy_recon_config.on_trait_change(
self.update_dipy_tracking_SD, 'local_model')
self.dipy_recon_config.on_trait_change(
self.update_dipy_tracking_sh_order, 'lmax_order')
[docs]class DiffusionStageUI(DiffusionStage):
"""Class that extends the :class:`DiffusionStage` 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.diffusion.diffusion.DiffusionStage
"""
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=900,
width=500,
kind='livemodal',
title='Edit stage configuration',
buttons=['OK', 'Cancel']
)
def __init__(self, bids_dir, output_dir):
"""Constructor of the DiffusionStageUI class.
Parameters
-----------
bids_dir : path
BIDS root directory
output_dir : path
Output directory
See also
---------
cmp.stages.diffusion.diffusion.DiffusionStage.__init_
cmp.cmpbidsappmanager.stages.diffusion.diffusion.DiffusionConfigUI
"""
DiffusionStage.__init__(self, bids_dir, output_dir)
self.config = DiffusionConfigUI()
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])