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error_msg='defaced mri')
self.orig_img = read_image(self.images_for_id[unit_id]['original'],
error_msg='T1 mri')
self.render_img_list = list()
for rimg_path in self.images_for_id[unit_id]['render']:
try:
self.render_img_list.append(imread(rimg_path))
except:
raise IOError('Unable to read the 3D rendered image @\n {}'
''.format(rimg_path))
# crop, trim, and rescale
self.defaced_img = rescale_without_outliers(
self.defaced_img, padding=self.padding,
trim_percentile=cfg.defacing_trim_percentile)
self.orig_img = rescale_without_outliers(
self.orig_img, padding=self.padding,
trim_percentile=cfg.defacing_trim_percentile)
self.currently_showing = None
skip_subject = False
if np.count_nonzero(self.defaced_img) == 0 or \
np.count_nonzero(self.orig_img) == 0:
skip_subject = True
print('Defaced or original MR image is empty!')
self.slice_picker = SlicePicker(self.orig_img,
view_set=self.collage.view_set,
num_slices=self.collage.num_slices,
sampler=cfg.defacing_slice_locations)
def add_histogram_panel(self):
"""Extra axis for histogram of cortical thickness!"""
if not self.vis_type in cfg.cortical_types:
return
self.ax_hist = plt.axes(cfg.position_histogram_freesurfer)
self.ax_hist.set(xticks=cfg.xticks_histogram_freesurfer,
xticklabels=cfg.xticks_histogram_freesurfer,
yticks=[], autoscaley_on=True)
self.ax_hist.set_prop_cycle('color', cfg.color_histogram_freesurfer)
self.ax_hist.set_title(cfg.title_histogram_freesurfer, fontsize='small')
def __init__(self,
fig,
axes,
issue_list=cfg.defacing_default_issue_list,
next_button_callback=None,
quit_button_callback=None,
processing_choice_callback=None,
map_key_to_callback=None):
"""Constructor"""
super().__init__(fig, axes, next_button_callback, quit_button_callback)
self.issue_list = issue_list
self.prev_axis = None
self.prev_ax_pos = None
self.zoomed_in = False
self.next_button_callback = next_button_callback
self.quit_button_callback = quit_button_callback
self.processing_choice_callback = processing_choice_callback
def add_histogram_panel(self):
"""Extra axis for histogram"""
self.ax_hist = plt.axes(cfg.position_histogram_t1_mri)
self.ax_hist.set_xticks(cfg.xticks_histogram_t1_mri)
self.ax_hist.set_yticks([])
self.ax_hist.set_autoscaley_on(True)
self.ax_hist.set_prop_cycle('color', cfg.color_histogram_t1_mri)
self.ax_hist.set_title(cfg.title_histogram_t1_mri, fontsize='small')
or 'both' (using both aseg and aparc stats).
Default: {}.
\n""".format(cfg.t1_mri_features_OLD))
help_text_disable_outlier_detection = textwrap.dedent("""
This flag disables outlier detection and alerts altogether.
\n""")
in_out = parser.add_argument_group('Inputs', ' various ways to provide input')
in_out.add_argument("-i", "--id_list", action="store", dest="id_list",
default=None, required=False, help=help_text_id_list)
in_out.add_argument("-u", "--user_dir", action="store", dest="user_dir",
default=cfg.default_user_dir,
required=False, help=help_text_user_dir)
in_out.add_argument("-m", "--mri_name", action="store", dest="mri_name",
default=cfg.default_mri_name_T1w_generic, required=False,
help=help_text_mri_name)
in_out.add_argument("-f", "--fs_dir", action="store", dest="fs_dir",
default=cfg.default_freesurfer_dir,
required=False, help=help_text_fs_dir)
in_out.add_argument("-b", "--bids_dir", action="store", dest="bids_dir",
default=None,
required=False, help=help_text_bids_dir)
out_spec = parser.add_argument_group('Outputs',
'options related to outputs')
def add_alpha_slider(self):
"""Controls the transparency level of overlay"""
# alpha slider
ax_slider = plt.axes(cfg.position_slider_seg_alpha,
facecolor=cfg.color_slider_axis)
self.slider = Slider(ax_slider, label='transparency',
valmin=0.0, valmax=1.0, valinit=0.7, valfmt='%1.2f')
self.slider.label.set_position((0.99, 1.5))
self.slider.on_changed(self.set_alpha_value)
sub001
sub002
cn_003
cn_004
\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.
nargs='+', metavar='label',
required=False, help=help_text_label)
vis_args = parser.add_argument_group('Overlay options', ' ')
vis_args.add_argument("-v", "--vis_type", action="store", dest="vis_type",
choices=cfg.visualization_combination_choices,
default=cfg.default_vis_type, required=False,
help=help_text_vis_type)
vis_args.add_argument("-c", "--contour_color", action="store", dest="contour_color",
default=cfg.default_contour_face_color, required=False,
help=help_text_contour_color)
vis_args.add_argument("-a", "--alpha_set", action="store", dest="alpha_set",
metavar='alpha', nargs=2,
default=cfg.default_alpha_set,
required=False, help=help_text_alphas)
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",