def build_local_fname(nii_fname, user_fol):
if mu.get_hemi_from_fname(mu.namebase_with_ext(nii_fname)) == '':
local_fname = mu.get_label_for_full_fname(nii_fname)
# local_fname = '{}.{}.{}'.format(mu.namebase(nii_fname), hemi, mu.file_type(nii_fname))
else:
local_fname = mu.namebase_with_ext(nii_fname)
return op.join(user_fol, 'fmri', local_fname)
def color_contours(specific_labels=[], specific_hemi='both', labels_contours=None, cumulate=False, change_colorbar=False,
specific_colors=None, atlas='', move_cursor=True):
if _addon() is None:
return
if isinstance(specific_labels, str):
specific_labels = [specific_labels]
if atlas != '' and atlas != bpy.context.scene.contours_coloring and atlas in LabelsPanel.existing_contoures:
bpy.context.scene.contours_coloring = atlas
if atlas == '' and bpy.context.scene.atlas in LabelsPanel.existing_contoures:
bpy.context.scene.contours_coloring = bpy.context.scene.atlas
if labels_contours is None:
labels_contours = LabelsPanel.labels_contours
contour_max = max([labels_contours[hemi]['max'] for hemi in mu.HEMIS])
if not _addon().colorbar_values_are_locked() and change_colorbar:
_addon().set_colormap('jet')
_addon().set_colorbar_title('{} labels contours'.format(bpy.context.scene.contours_coloring))
_addon().set_colorbar_max_min(contour_max, 1)
_addon().set_colorbar_prec(0)
_addon().show_activity()
specific_label_ind = 0
if specific_colors is not None:
specific_colors = np.tile(specific_colors, (len(specific_labels), 1))
for hemi in mu.HEMIS:
contours = labels_contours[hemi]['contours']
if specific_hemi != 'both' and hemi != specific_hemi:
selected_contours = np.zeros(contours.shape) if specific_colors is None else np.zeros((contours.shape[0], 4))
elif len(specific_labels) > 0:
selected_contours = np.zeros(contours.shape) if specific_colors is None else np.zeros((contours.shape[0], 4))
for specific_label in specific_labels:
if mu.get_hemi_from_fname(specific_label) != hemi:
continue
label_ind = np.where(np.array(labels_contours[hemi]['labels']) == specific_label)
if len(label_ind) > 0 and len(label_ind[0]) > 0:
label_ind = label_ind[0][0]
selected_contours[np.where(contours == label_ind + 1)] = \
label_ind + 1 if specific_colors is None else [1, *specific_colors[specific_label_ind]]
specific_label_ind += 1
if move_cursor and len(specific_labels) == 1 and 'centers' in labels_contours[hemi]:
vert = labels_contours[hemi]['centers'][label_ind]
_addon().move_cursor_according_to_vert(vert, 'inflated_{}'.format(hemi))
_addon().set_closest_vertex_and_mesh_to_cursor(vert, 'inflated_{}'.format(hemi))
_addon().create_slices()
else:
print("Can't find {} in the labels contours!".format(specific_label))
else:
selected_contours = labels_contours[hemi]['contours']
mesh = mu.get_hemi_obj(hemi).data
mesh.vertex_colors.active_index = mesh.vertex_colors.keys().index('contours')
mesh.vertex_colors['contours'].active_render = True
_addon().color_hemi_data(hemi, selected_contours, 0.1, 256 / contour_max, override_current_mat=not cumulate,
coloring_layer='contours', check_valid_verts=False)
_addon().what_is_colored().add(_addon().WIC_CONTOURS)
def color_contours(specific_labels=[], specific_hemi='both', labels_contours=None, cumulate=False, change_colorbar=False,
specific_colors=None, atlas='', move_cursor=True, filter=''):
if _addon() is None:
return
if filter != '':
bpy.context.scene.labels_contours_filter = filter
if isinstance(LabelsPanel.labels['rh'], np.ndarray):
specific_labels = LabelsPanel.labels['rh'].tolist() + LabelsPanel.labels['lh'].tolist()
else:
specific_labels = LabelsPanel.labels['rh'] + LabelsPanel.labels['lh']
elif isinstance(specific_labels, str):
specific_labels = [specific_labels]
if atlas != '' and atlas != bpy.context.scene.contours_coloring and atlas in LabelsPanel.existing_contoures:
bpy.context.scene.contours_coloring = atlas
if atlas == '' and bpy.context.scene.atlas in LabelsPanel.existing_contoures:
bpy.context.scene.contours_coloring = bpy.context.scene.atlas
if labels_contours is None:
labels_contours = LabelsPanel.labels_contours
contour_max = max([labels_contours[hemi]['max'] for hemi in mu.HEMIS])
if contour_max == 0:
print('No contours!')
return False
if not _addon().colorbar_values_are_locked() and change_colorbar:
_addon().set_colormap('jet')
_addon().set_colorbar_title('{} labels contours'.format(bpy.context.scene.contours_coloring))
_addon().set_colorbar_max_min(contour_max, 1)
_addon().set_colorbar_prec(0)
_addon().show_activity()
specific_label_ind = 0
if specific_colors is not None:
specific_colors = np.tile(specific_colors, (len(specific_labels), 1))
for hemi in mu.HEMIS:
contours = labels_contours[hemi]['contours']
if specific_hemi != 'both' and hemi != specific_hemi:
selected_contours = np.zeros(contours.shape) if specific_colors is None else np.zeros((contours.shape[0], 4))
elif len(specific_labels) > 0:
selected_contours = np.zeros(contours.shape) if specific_colors is None else np.zeros((contours.shape[0], 4))
for specific_label in specific_labels:
if mu.get_hemi_from_fname(specific_label) != hemi:
continue
label_ind = np.where(np.array(labels_contours[hemi]['labels']) == specific_label)
if len(label_ind) > 0 and len(label_ind[0]) > 0:
label_ind = label_ind[0][0]
selected_contours[np.where(contours == label_ind + 1)] = \
label_ind + 1 if specific_colors is None else [1, *specific_colors[specific_label_ind]]
specific_label_ind += 1
if move_cursor and len(specific_labels) == 1 and 'centers' in labels_contours[hemi]:
vert = labels_contours[hemi]['centers'][label_ind]
_addon().move_cursor_according_to_vert(vert, 'inflated_{}'.format(hemi))
_addon().set_closest_vertex_and_mesh_to_cursor(vert, 'inflated_{}'.format(hemi))
_addon().create_slices()
_addon().snap_cursor(True)
_addon().set_tkreg_ras(bpy.context.scene.cursor_location * 10, False)
else:
print("Can't find {} in the labels contours!".format(specific_label))
else:
selected_contours = labels_contours[hemi]['contours']
mesh = mu.get_hemi_obj(hemi).data
mesh.vertex_colors.active_index = mesh.vertex_colors.keys().index('contours')
mesh.vertex_colors['contours'].active_render = True
# Saving the labels names and RGB values
unique_values = np.unique(contours)
contours_colors = _addon().coloring.calc_colors(unique_values, 0, 256 / contour_max)
contours_labels_info = np.column_stack((labels_contours[hemi]['labels'], contours_colors[1:, :]))
output_fname = op.join(mu.get_user_fol(), 'labels', '{}_{}_{}_labels_names_and_colors.csv'.format(
bpy.context.scene.contours_coloring, hemi, _addon().colorbar.get_colormap_name()))
np.savetxt(output_fname, contours_labels_info, ('%s', '%s', '%s', '%s'), ',')
print('Saving labels names and RGB values to {}'.format(output_fname))
# Color the hemi surface
_addon().color_hemi_data(
hemi, selected_contours, 0.1, 256 / contour_max, override_current_mat=not cumulate,
coloring_layer='contours', check_valid_verts=False)
_addon().what_is_colored().add(_addon().WIC_CONTOURS)
