How to use the visualqc.config.default_views function in VisualQC

dest="outlier_fraction",
                          default=cfg.default_outlier_fraction, required=False,
                          help=help_text_outlier_fraction)

    outliers.add_argument("-olt", "--outlier_feat_types", action="store",
                          dest="outlier_feat_types",
                          default=cfg.t1_mri_features_OLD, required=False,
                          help=help_text_outlier_feat_types)

    outliers.add_argument("-old", "--disable_outlier_detection", action="store_true",
                          dest="disable_outlier_detection",
                          required=False, help=help_text_disable_outlier_detection)

    layout = parser.add_argument_group('Layout options', ' ')
    layout.add_argument("-w", "--views", action="store", dest="views",
                        default=cfg.default_views, required=False, nargs='+',
                        help=help_text_views)

    layout.add_argument("-s", "--num_slices", action="store", dest="num_slices",
                        default=cfg.default_num_slices, required=False,
                        help=help_text_num_slices)

    layout.add_argument("-r", "--num_rows", action="store", dest="num_rows",
                        default=cfg.default_num_rows, required=False,
                        help=help_text_num_rows)

    wf_args = parser.add_argument_group('Workflow', 'Options related to workflow '
                                                    'e.g. to pre-compute resource-intensive features, '
                                                    'and pre-generate all the visualizations required')
    wf_args.add_argument("-p", "--prepare_first", action="store_true",
                         dest="prepare_first",
                         help=help_text_prepare)

Color can be specified in many ways as documented in https://matplotlib.org/users/colors.html
    Default: {}.
    \n""".format(cfg.default_contour_face_color))

    help_text_alphas = textwrap.dedent("""
    Alpha values to control the transparency of MRI and aseg. 
    This must be a set of two values (between 0 and 1.0) separated by a space e.g. --alphas 0.7 0.5. 

    Default: {} {}.  Play with these values to find something that works for you and the dataset.
    \n""".format(cfg.default_alpha_mri, cfg.default_alpha_seg))

    help_text_views = textwrap.dedent("""
    Specifies the set of views to display - could be just 1 view, or 2 or all 3.
    Example: --views 0 (typically sagittal) or --views 1 2 (axial and coronal)
    Default: {} {} {} (show all the views in the selected segmentation)
    \n""".format(cfg.default_views[0], cfg.default_views[1], cfg.default_views[2]))

    help_text_num_slices = textwrap.dedent("""
    Specifies the number of slices to display per each view. 
    This must be even to facilitate better division.
    Default: {}.
    \n""".format(cfg.default_num_slices))

    help_text_num_rows = textwrap.dedent("""
    Specifies the number of rows to display per each axis. 
    Default: {}.
    \n""".format(cfg.default_num_rows))

    help_text_no_surface_vis = textwrap.dedent("""
    This flag disables batch-generation of 3d surface visualizations, which are shown along with cross-sectional overlays. This is not recommended, but could be used in situations where you do not have Freesurfer installed or want to focus solely on cross-sectional views.

    Default: False (required visualizations are generated at the beginning, which can take 5-10 seconds for each subject).

default=None, required=False, help=help_text_id_list)

    in_out.add_argument("-o", "--out_dir", action="store", dest="out_dir",
                        default=None, required=False, help=help_text_out_dir)

    vis = parser.add_argument_group('Visualization',
                                    'Customize behaviour of comparisons')

    vis.add_argument("-dl", "--delay_in_animation", action="store",
                     dest="delay_in_animation",
                     default=cfg.delay_in_animation, required=False,
                     help=help_text_delay_in_animation)

    layout = parser.add_argument_group('Layout options', ' ')
    layout.add_argument("-w", "--views", action="store", dest="views",
                        default=cfg.default_views, required=False, nargs='+',
                        help=help_text_views)

    layout.add_argument("-s", "--num_slices", action="store", dest="num_slices",
                        default=cfg.default_num_slices, required=False,
                        help=help_text_num_slices)

    layout.add_argument("-r", "--num_rows", action="store", dest="num_rows",
                        default=cfg.default_num_rows, required=False,
                        help=help_text_num_rows)

    wf_args = parser.add_argument_group('Workflow', 'Options related to workflow '
                                                    'e.g. to pre-compute '
                                                    'resource-intensive features, '
                                                    'and pre-generate all the '
                                                    'visualizations required')
    wf_args.add_argument("-p", "--prepare_first", action="store_true",

images_for_id,
                 in_dir,
                 out_dir,
                 vis_type=cfg.default_vis_type,
                 label_set=cfg.default_label_set,
                 issue_list=cfg.default_rating_list,
                 mri_name=cfg.default_mri_name,
                 seg_name=cfg.default_seg_name,
                 alpha_set=cfg.default_alpha_set,
                 outlier_method=cfg.default_outlier_detection_method,
                 outlier_fraction=cfg.default_outlier_fraction,
                 outlier_feat_types=cfg.freesurfer_features_outlier_detection,
                 source_of_features=cfg.default_source_of_features_freesurfer,
                 disable_outlier_detection=False,
                 no_surface_vis=False,
                 views=cfg.default_views,
                 num_slices_per_view=cfg.default_num_slices,
                 num_rows_per_view=cfg.default_num_rows):
        """Constructor"""

        super().__init__(id_list, in_dir, out_dir,
                         outlier_method, outlier_fraction,
                         outlier_feat_types, disable_outlier_detection)

        self.issue_list = issue_list
        # in_dir_type must be freesurfer; vis_type must be freesurfer

        self.mri_name = mri_name
        self.seg_name = seg_name
        self.label_set = label_set
        self.vis_type = vis_type
        self.images_for_id = images_for_id

Default: a new folder called ``{}`` will be created inside the input dir.
    \n""".format(cfg.default_out_dir_name))

    help_text_apply_preproc = textwrap.dedent("""
    Whether to apply basic preprocessing steps (detrend, slice timing correction etc), before building the carpet image.

    If the images are already preprocessed elsewhere, use this flag ``--apply_preproc``

    Default is NOT to apply any preprocessing (detrending etc) before showing images for review.
    \n""")

    help_text_views = textwrap.dedent("""
    Specifies the set of views to display - could be just 1 view, or 2 or all 3.
    Example: --views 0 (typically sagittal) or --views 1 2 (axial and coronal)
    Default: {} {} {} (show all the views in the selected segmentation)
    \n""".format(cfg.default_views[0], cfg.default_views[1], cfg.default_views[2]))

    help_text_num_slices = textwrap.dedent("""
    Specifies the number of slices to display per each view.
    This must be even to facilitate better division.
    Default: {}.
    \n""".format(cfg.default_num_slices))

    help_text_num_rows = textwrap.dedent("""
    Specifies the number of rows to display per each axis.
    Default: {}.
    \n""".format(cfg.default_num_rows))

    help_text_prepare = textwrap.dedent("""
    This flag enables batch-generation of 3d surface visualizations, prior to starting any review and rating operations.

    This makes the switch from one subject to the next, even more seamless (saving few seconds :) ).

help_text_out_dir = textwrap.dedent("""
    Output folder to store the visualizations & ratings.
    Default: a new folder called ``{}`` will be created inside the ``fs_dir``
    \n""".format(cfg.default_out_dir_name))

    help_text_delay_in_animation = textwrap.dedent("""
    Specifies the delay in animation of the display of two images (like in a GIF).

    Default: {} (units in seconds).
    \n""".format(cfg.delay_in_animation))

    help_text_views = textwrap.dedent("""
    Specifies the set of views to display - could be just 1 view, or 2 or all 3.
    Example: --views 0 (typically sagittal) or --views 1 2 (axial and coronal)
    Default: {} {} {} (show all the views in the selected segmentation)
    \n""".format(cfg.default_views[0], cfg.default_views[1], cfg.default_views[2]))

    help_text_num_slices = textwrap.dedent("""
    Specifies the number of slices to display per each view. 
    This must be even to facilitate better division.
    Default: {}.
    \n""".format(cfg.default_num_slices))

    help_text_num_rows = textwrap.dedent("""
    Specifies the number of rows to display per each axis. 
    Default: {}.
    \n""".format(cfg.default_num_rows))

    help_text_prepare = textwrap.dedent("""
    This flag does the heavy preprocessing first, prior to starting any review and 
    rating operations.
    Heavy processing can include computation of registration quality metrics and 

Default: a new folder called ``{}`` will be created inside the ``fs_dir``
    \n""".format(cfg.default_out_dir_name))

    help_text_no_preproc = textwrap.dedent("""
    Whether to apply basic preprocessing steps (detrend, slice timing correction etc), before building the carpet image.

    If the images are already preprocessed elsewhere, use this flag ``--no_preproc``

    Default is to apply minimal preprocessing (detrending etc) before showing images for review.
    \n""")

    help_text_views = textwrap.dedent("""
    Specifies the set of views to display - could be just 1 view, or 2 or all 3.
    Example: --views 0 (typically sagittal) or --views 1 2 (axial and coronal)
    Default: {} {} {} (show all the views in the selected segmentation)
    \n""".format(cfg.default_views[0], cfg.default_views[1], cfg.default_views[2]))

    help_text_num_slices = textwrap.dedent("""
    Specifies the number of slices to display per each view.
    This must be even to facilitate better division.
    Default: {}.
    \n""".format(cfg.default_num_slices))

    help_text_num_rows = textwrap.dedent("""
    Specifies the number of rows to display per each axis.
    Default: {}.
    \n""".format(cfg.default_num_rows))

    help_text_prepare = textwrap.dedent("""
    This flag enables batch-generation of 3d surface visualizations, prior to starting any review and rating operations.

    This makes the switch from one subject to the next, even more seamless (saving few seconds :) ).

dest="outlier_fraction",
                          default=cfg.default_outlier_fraction, required=False,
                          help=help_text_outlier_fraction)

    outliers.add_argument("-olt", "--outlier_feat_types", action="store",
                          dest="outlier_feat_types",
                          default=cfg.freesurfer_features_outlier_detection,
                          required=False, help=help_text_outlier_feat_types)

    outliers.add_argument("-old", "--disable_outlier_detection", action="store_true",
                          dest="disable_outlier_detection",
                          required=False, help=help_text_disable_outlier_detection)

    layout = parser.add_argument_group('Layout options', ' ')
    layout.add_argument("-w", "--views", action="store", dest="views",
                        default=cfg.default_views, required=False, nargs='+',
                        help=help_text_views)

    layout.add_argument("-s", "--num_slices", action="store", dest="num_slices",
                        default=cfg.default_num_slices, required=False,
                        help=help_text_num_slices)

    layout.add_argument("-r", "--num_rows", action="store", dest="num_rows",
                        default=cfg.default_num_rows, required=False,
                        help=help_text_num_rows)

    wf_args = parser.add_argument_group('Workflow', 'Options related to workflow '
                                                    'e.g. to pre-compute resource-intensive features, '
                                                    'and pre-generate all the visualizations required')

    wf_args.add_argument("-ns", "--no_surface_vis", action="store_true",
                         dest="no_surface_vis", help=help_text_no_surface_vis)

def __init__(self,
                 id_list,
                 in_dir,
                 image_names,
                 out_dir,
                 in_dir_type='generic',
                 prepare_first=True,
                 delay_in_animation=cfg.delay_in_animation,
                 views=cfg.default_views,
                 num_slices_per_view=cfg.default_num_slices,
                 num_rows_per_view=cfg.default_num_rows,
                 ):
        """Constructor"""

        self.disable_outlier_detection = True
        super().__init__(id_list, in_dir, out_dir,
                         None, None, None,  # might add outlier detection later
                         disable_outlier_detection=self.disable_outlier_detection)

        self.current_cmap = 'gray'
        self.vis_type = 'Animate'
        self.delay_in_animation = delay_in_animation
        self.continue_animation = True

        self.image_names = image_names

dest="outlier_fraction",
                          default=cfg.default_outlier_fraction, required=False,
                          help=help_text_outlier_fraction)

    outliers.add_argument("-olt", "--outlier_feat_types", action="store",
                          dest="outlier_feat_types",
                          default=cfg.t1_mri_features_OLD, required=False,
                          help=help_text_outlier_feat_types)

    outliers.add_argument("-old", "--disable_outlier_detection", action="store_true",
                          dest="disable_outlier_detection",
                          required=False, help=help_text_disable_outlier_detection)

    layout = parser.add_argument_group('Layout options', ' ')
    layout.add_argument("-w", "--views", action="store", dest="views",
                        default=cfg.default_views, required=False, nargs='+',
                        help=help_text_views)

    layout.add_argument("-s", "--num_slices", action="store", dest="num_slices",
                        default=cfg.default_num_slices, required=False,
                        help=help_text_num_slices)

    layout.add_argument("-r", "--num_rows", action="store", dest="num_rows",
                        default=cfg.default_num_rows, required=False,
                        help=help_text_num_rows)

    wf_args = parser.add_argument_group('Workflow', 'Options related to workflow '
                                                    'e.g. to pre-compute resource-intensive features, '
                                                    'and pre-generate all the visualizations required')
    wf_args.add_argument("-p", "--prepare_first", action="store_true",
                         dest="prepare_first",
                         help=help_text_prepare)