# 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 diffusion preprocessing config and stage UI classes."""
import subprocess
from traits.api import *
from traitsui.api import *
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])