Source code for cmp.bidsappmanager.stages.preprocessing.fmri_preprocessing

# 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 fMRI preprocessing config and stage UI classes."""

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

# Own imports
from cmp.stages.preprocessing.fmri_preprocessing import (
    PreprocessingConfig,
    PreprocessingStage,
)


[docs]class PreprocessingConfigUI(PreprocessingConfig): """Class that extends the (functional) :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.fmri_preprocessing.PreprocessingConfig """ traits_view = View( "discard_n_volumes", "despiking", "slice_timing", Item("repetition_time", visible_when='slice_timing!="none"'), "motion_correction", )
[docs]class PreprocessingStageUI(PreprocessingStage): """Class that extends the (functional) :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.fmri_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=280, width=350, kind="livemodal", title="Edit stage configuration", buttons=["OK", "Cancel"], ) # General and UI members def __init__(self, bids_dir, output_dir): """Constructor of the functional PreprocessingStageUI class. Parameters ----------- bids_dir : path BIDS root directory output_dir : path Output directory See also --------- cmp.stages.preprocessing.fmri_preprocessing.PreprocessingStage.__init_ cmp.cmpbidsappmanager.stages.preprocessing.fmri_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])