Source code for cmp.bidsappmanager.stages.functional.functionalMRI

# 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 ModifFied BSD.

"""Definition of extra preprocessing of functional MRI (post-registration) config and stage UI classes."""

# General imports
import subprocess
from traits.api import *
from traitsui.api import *

# Own imports
from cmp.stages.functional.functionalMRI import FunctionalMRIConfig, FunctionalMRIStage


[docs]class FunctionalMRIConfigUI(FunctionalMRIConfig): """Class that extends the :class:`FunctionalMRIConfig` 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.functional.functionalMRI.FunctionalMRIConfig """ traits_view = View( # Item('smoothing'), # Item('discard_n_volumes'), HGroup( Item("detrending"), Item("detrending_mode", visible_when="detrending"), label="Detrending", show_border=True, ), HGroup( Item("global_nuisance", label="Global"), Item("csf"), Item("wm"), Item("motion"), label="Nuisance factors", show_border=True, ), HGroup( Item("bandpass_filtering", label="Perform bandpass filtering"), Item("lowpass_filter", label="Low cutoff (volumes)", visible_when="bandpass_filtering"), Item("highpass_filter", label="High cutoff (volumes)", visible_when="bandpass_filtering"), label="Bandpass filtering", show_border=True, ), )
[docs]class FunctionalMRIStageUI(FunctionalMRIStage): """Class that extends the :class:`FunctionalMRIStage` 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.functional.functionalMRI.FunctionalMRIStage """ 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=528, width=608, kind="livemodal", title="Edit stage configuration", buttons=["OK", "Cancel"], ) def __init__(self, bids_dir, output_dir): """Constructor of the FunctionalMRIStageUI class. Parameters ----------- bids_dir : path BIDS root directory output_dir : path Output directory See also --------- cmp.stages.functional.functionalMRI.FunctionalMRIStage.__init_ cmp.cmpbidsappmanager.stages.functional.functionalMRI.FunctionalMRIConfigUI """ FunctionalMRIStage.__init__(self, bids_dir, output_dir) self.config = FunctionalMRIConfigUI() 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])