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

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github raamana / visualqc / visualqc / alignment.py View on Github external
help_text_image2 = textwrap.dedent("""
    Specifies the name of second 3d image to serve as the comparison image
    Order of the two images does not typically matter.
    \n""")

    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: {}.
github raamana / visualqc / visualqc / quantitative.py View on Github external
in_out.add_argument("-n", "--image_names", action="store",
                        dest="image_names", nargs='+',
                        required=True, help=help_text_image_names)

    in_out.add_argument("-l", "--id_list", action="store", dest="id_list",
                        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 '
github raamana / visualqc / visualqc / diffusion.py View on Github external
in_out.add_argument("-n", "--name_pattern", action="store", dest="name_pattern",
                        default=cfg.default_name_pattern, required=False,
                        help=help_text_name_pattern)

    preproc = parser.add_argument_group('Preprocessing',
                                        'options related to preprocessing before review')

    preproc.add_argument("-ap", "--apply_preproc", action="store_true",
                         dest="apply_preproc",
                         required=False, help=help_text_apply_preproc)

    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)

    outliers = parser.add_argument_group('Outlier detection',
                                         'options related to automatically detecting possible outliers')
    outliers.add_argument("-olm", "--outlier_method", action="store",
                          dest="outlier_method",
                          default=cfg.default_outlier_detection_method, required=False,
                          help=help_text_outlier_detection_method)

    outliers.add_argument("-olf", "--outlier_fraction", action="store",
                          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",
github raamana / visualqc / visualqc / alignment.py View on Github external
in_out.add_argument("-i2", "--image2", action="store", dest="image2",
                        required=True, help=help_text_image2)

    in_out.add_argument("-l", "--id_list", action="store", dest="id_list",
                        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)

    outliers = parser.add_argument_group('Outlier detection',
                                         'options related to automatically detecting possible outliers')
    outliers.add_argument("-olm", "--outlier_method", action="store",
                          dest="outlier_method",
                          default=cfg.default_outlier_detection_method, required=False,
                          help=help_text_outlier_detection_method)

    outliers.add_argument("-olf", "--outlier_fraction", action="store",
                          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",
github raamana / visualqc / visualqc / quantitative.py View on Github external
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
github raamana / visualqc / visualqc / quantitative.py View on Github external
\n""")

    help_text_image_names = textwrap.dedent("""
    Specifies the names of 3d images to be QCed.
    \n""")

    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: {}.
github raamana / visualqc / visualqc / alignment.py View on Github external
def __init__(self,
                 id_list,
                 in_dir,
                 image1_name,
                 image2_name,
                 out_dir,
                 issue_list=cfg.default_rating_list,
                 in_dir_type='generic',
                 prepare_first=True,
                 vis_type=cfg.alignment_default_vis_type,
                 delay_in_animation=cfg.delay_in_animation,
                 outlier_method=cfg.default_outlier_detection_method,
                 outlier_fraction=cfg.default_outlier_fraction,
                 outlier_feat_types=cfg.freesurfer_features_outlier_detection,
                 disable_outlier_detection=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.vis_type = vis_type
        self.current_cmap = cfg.alignment_cmap[self.vis_type]