def init(addon):
AppearanceMakerPanel.addon = addon
register()
AppearanceMakerPanel.init = True
bpy.context.scene.subcortical_layer = 'fmri'
change_to_solid_brain()
# show_rois()
loc_val = 0 #5
AppearanceMakerPanel.flat_map_exists = True
bpy.context.scene.show_appearance_settings = False
if bpy.data.objects.get('Cortex-inflated-rh') and bpy.data.objects.get(
'inflated_rh'):
AppearanceMakerPanel.cortex_inflated_rh = bpy.data.objects['Cortex-inflated-rh'].location[0] = \
bpy.data.objects['inflated_rh'].location[0] = loc_val
AppearanceMakerPanel.cortex_inflated_lh = bpy.data.objects['Cortex-inflated-lh'].location[0] = \
bpy.data.objects['inflated_lh'].location[0] = -1*loc_val
try:
bpy.data.shape_keys['Key'].key_blocks["flat"].value = 0
bpy.data.shape_keys['Key.001'].key_blocks["flat"].value = 0
except:
print('No flat mapping.')
AppearanceMakerPanel.flat_map_exists = False
try:
bpy.data.shape_keys['Key'].key_blocks["inflated"].value = 1
bpy.data.shape_keys['Key.001'].key_blocks["inflated"].value = 1
except:
AppearanceMakerPanel.flat_map_exists = False
print('No inflated mapping.')
for hemi in ['lh', 'rh']:
try:
mu.get_hemi_obj(
hemi).modifiers['mask_bad_vertices'].show_viewport = True
mu.get_hemi_obj(
hemi).modifiers['mask_bad_vertices'].show_render = True
except:
pass
if bpy.data.objects.get('Cortex-rh') and bpy.data.objects.get('lh'):
AppearanceMakerPanel.cortex_rh = bpy.data.objects['Cortex-rh'].location[0] = \
bpy.data.objects['rh'].location[0] = 0
AppearanceMakerPanel.cortex_lh = bpy.data.objects['Cortex-lh'].location[0] = \
bpy.data.objects['rh'].location[0] = 0
bpy.context.scene.hemis_distance = 0
bpy.context.scene.hemis_inf_distance = 0 #-5
bpy.context.scene.cursor_is_snapped = True
# set_inflated_ratio(0)
appearance_show_rois_activity_update()
AppearanceMakerPanel.showing_meg_sensors = showing_meg_sensors()
AppearanceMakerPanel.showing_eeg_sensors = showing_eeg()
AppearanceMakerPanel.showing_electrodes = showing_electordes()
# AppearanceMakerPanel.mesh = {hemi:mu.get_hemi_obj(hemi).to_mesh(bpy.context.scene, True, 'PREVIEW')
# for hemi in mu.HEMIS}
# show_inflated()
bpy.context.scene.panels_background_color = [0, 0, 0]
snap_cursor(True)
AppearanceMakerPanel.init = True
def _save_image():
if not bpy.context.scene.save_split_views:
save_image(view_selected=bpy.context.scene.save_selected_view,
add_colorbar=bpy.context.scene.save_views_with_cb)
else:
images = {}
org_hide = {hemi: mu.get_hemi_obj(hemi).hide for hemi in mu.HEMIS}
for hemi in mu.HEMIS:
mu.get_hemi_obj(hemi).hide = False
mu.get_hemi_obj(mu.other_hemi(hemi)).hide = True
images[hemi] = save_image(view_selected=bpy.context.scene.save_selected_view, add_colorbar=False)
for hemi in mu.HEMIS:
mu.get_hemi_obj(hemi).hide = org_hide[hemi]
combine_two_images_and_add_colorbar(images['lh'], images['rh'], images['lh'])
def save_all_views(views=None, inflated_ratio_in_file_name=False, rot_lh_axial=None, render_images=False, quality=0,
img_name_prefix='', add_colorbar=None, cb_ticks_num=None, cb_ticks_font_size=None, overwrite=True):
if not render_images:
_addon().change_to_solid_brain()
if add_colorbar is None:
add_colorbar = bpy.context.scene.save_views_with_cb
if cb_ticks_num is None:
cb_ticks_num = bpy.context.scene.cb_ticks_num
if cb_ticks_font_size is None:
cb_ticks_font_size = bpy.context.scene.cb_ticks_font_size
_addon().show_hemis()
if not bpy.context.scene.save_split_views:
rot_lh_axial = False if rot_lh_axial is None else rot_lh_axial
_save_all_views(views, inflated_ratio_in_file_name, rot_lh_axial, render_images, quality, img_name_prefix,
add_colorbar, cb_ticks_num, cb_ticks_font_size, overwrite)
else:
if views is None:
views = list(set(_addon().ANGLES_DICT.keys()) - set([_addon().ROT_MEDIAL_LEFT, _addon().ROT_MEDIAL_RIGHT]))
images_names = []
rot_lh_axial = True if rot_lh_axial is None else rot_lh_axial
org_hide = {hemi: mu.get_hemi_obj(hemi).hide for hemi in mu.HEMIS}
for hemi in mu.HEMIS:
mu.get_hemi_obj(hemi).hide = False
mu.get_hemi_obj(mu.other_hemi(hemi)).hide = True
images_names.extend(_save_all_views(
views, inflated_ratio_in_file_name, rot_lh_axial, render_images, quality, img_name_prefix, False,
overwrite=overwrite))
for hemi in mu.HEMIS:
mu.get_hemi_obj(hemi).hide = org_hide[hemi]
images_hemi_inv_list = set(
[mu.namebase(fname)[3:] for fname in images_names if mu.namebase(fname)[:2] in ['rh', 'lh']])
files = [[fname for fname in images_names if mu.namebase(fname)[3:] == img_hemi_inv] for img_hemi_inv in
images_hemi_inv_list]
fol = mu.get_fname_folder(files[0][0])
for files_coup in files:
hemi = 'rh' if mu.namebase(files_coup[0]).startswith('rh') else 'lh'
coup_template = files_coup[0].replace(hemi, '{hemi}')
coup = {hemi: coup_template.format(hemi=hemi) for hemi in mu.HEMIS}
new_image_fname = op.join(fol, mu.namebase_with_ext(files_coup[0])[3:])
combine_two_images_and_add_colorbar(
coup['lh'], coup['rh'], new_image_fname, cb_ticks_num, cb_ticks_font_size)
_addon().show_hemis()
def clear_contours():
# todo: there is a better way to do it
labels_contours = LabelsPanel.labels_contours
for hemi in mu.HEMIS:
contours = labels_contours[hemi]['contours']
selected_contours = np.zeros(contours.shape)
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, override_current_mat=True,
coloring_layer='contours', check_valid_verts=False)
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 view_name(view):
if mu.get_hemi_obj('rh').hide and not mu.get_hemi_obj('lh').hide:
hemi = 'lh'
elif not mu.get_hemi_obj('rh').hide and mu.get_hemi_obj('lh').hide:
hemi = 'rh'
elif not mu.get_hemi_obj('rh').hide and not mu.get_hemi_obj('lh').hide:
hemi = 'both'
if (hemi == 'rh' and view == ROT_SAGITTAL_LEFT) or (hemi == 'lh' and view == ROT_SAGITTAL_RIGHT):
view_name = 'medial'
elif (hemi == 'lh' and view == ROT_SAGITTAL_LEFT) or (hemi == 'rh' and view == ROT_SAGITTAL_RIGHT):
view_name = 'lateral'
else:
view_name = ANGLES_NAMES_DICT[view]
return view_name
def _inflating_update():
try:
if bpy.data.objects.get('rh', None) is None:
return
if bpy.context.scene.inflating > 0: #flattening
# _addon().show_coronal(True)
# _addon().view_all()
if AppearanceMakerPanel.flat_map_exists:
bpy.data.shape_keys['Key'].key_blocks[
"flat"].value = bpy.context.scene.inflating
bpy.data.shape_keys['Key.001'].key_blocks[
"flat"].value = bpy.context.scene.inflating
bpy.data.shape_keys['Key'].key_blocks["inflated"].value = 1
bpy.data.shape_keys['Key.001'].key_blocks["inflated"].value = 1
bpy.data.objects['inflated_rh'].location[
0] = 10 * bpy.context.scene.inflating
bpy.data.objects['inflated_lh'].location[
0] = -10 * bpy.context.scene.inflating
# bpy.data.objects['inflated_rh'].location[0] = bpy.context.scene.inflating
# bpy.data.objects['inflated_lh'].location[0] = bpy.context.scene.inflating
use_masking = True
else: #deflating
bpy.data.shape_keys['Key'].key_blocks[
"inflated"].value = bpy.context.scene.inflating + 1
bpy.data.shape_keys['Key.001'].key_blocks[
"inflated"].value = bpy.context.scene.inflating + 1
if AppearanceMakerPanel.flat_map_exists:
bpy.data.shape_keys['Key'].key_blocks["flat"].value = 0
bpy.data.shape_keys['Key.001'].key_blocks["flat"].value = 0
bpy.data.objects['inflated_rh'].location[0] = 0
bpy.data.objects['inflated_lh'].location[0] = 0
use_masking = False
# mu.set_zoom_level(bpy.context.scene.surface_type, abs(bpy.context.scene.inflating))
bpy.context.scene.layers[_addon().ACTIVITY_LAYER] = False
bpy.context.scene.layers[_addon().ELECTRODES_LAYER] = False
AppearanceMakerPanel.no_surface_type_update = True
infl = bpy.context.scene.inflating
if 0 < infl <= 1.0:
bpy.context.scene.surface_type = 'flat'
_addon().show_coronal(True)
elif -1.0 < infl <= 0.0:
bpy.context.scene.surface_type = 'inflated'
elif infl == -1.0:
bpy.context.scene.surface_type = 'pial'
bpy.context.scene.layers[_addon().ACTIVITY_LAYER] = True
if bpy.context.scene.show_hide_electrodes:
bpy.context.scene.layers[_addon().ELECTRODES_LAYER] = True
AppearanceMakerPanel.no_surface_type_update = False
if AppearanceMakerPanel.flat_map_exists:
for hemi in ['rh', 'lh']:
mu.get_hemi_obj(hemi).modifiers[
'mask_bad_vertices'].show_viewport = use_masking
mu.get_hemi_obj(hemi).modifiers[
'mask_bad_vertices'].show_render = use_masking
# print(use_masking)
# bpy.context.scene.hemis_inf_distance = - (1 - bpy.context.scene.inflating) * 5
if bpy.context.scene.cursor_is_snapped:
vert, obj_name = get_closest_vertex_and_mesh_to_cursor()
if obj_name != '':
if 'inflated' not in obj_name:
obj_name = 'inflated_{}'.format(obj_name)
obj = bpy.data.objects[obj_name]
move_cursor_according_to_vert(vert, obj)
except:
print('Error in inflating update!')
print(traceback.format_exc())
def _save_all_views(views=None,
inflated_ratio_in_file_name=False,
rot_lh_axial=True,
render_images=False,
quality=0,
img_name_prefix='',
add_colorbar=False,
cb_ticks_num=None,
cb_ticks_font_size=None,
overwrite=True):
def get_image_name(view_name):
return '{}{}{}_{}'.format(
'{}_'.format(hemi) if hemi != '' else '',
'{}_'.format(img_name_prefix) if img_name_prefix != '' else '',
surf_name, view_name)
def should_save_image(img_name):
return overwrite or not op.isfile(get_full_output_fname(img_name))
def save_medial_views():
if _addon().ROT_MEDIAL_LEFT in views:
image_name = '{}_left_medial'.format(surf_name)
if should_save_image(image_name):
_addon().hide_hemi('rh')
_addon().show_hemi('lh')
_addon().rotate_view(_addon().ROT_SAGITTAL_RIGHT)
image_fname = save_render_image(image_name, quality,
render_images, add_colorbar,
cb_ticks_num,
cb_ticks_font_size)
images_names.append(image_fname)
if _addon().ROT_MEDIAL_RIGHT in views:
image_name = '{}_right_medial'.format(surf_name)
if should_save_image(image_name):
_addon().show_hemi('rh')
_addon().hide_hemi('lh')
_addon().rotate_view(_addon().ROT_SAGITTAL_LEFT)
image_fname = save_render_image(
'{}_right_medial'.format(surf_name), quality,
render_images, add_colorbar, cb_ticks_num,
cb_ticks_font_size)
images_names.append(image_fname)
_addon().show_hemi('rh')
_addon().show_hemi('lh')
if views is None:
views = list(_addon().ANGLES_DICT.keys(
)) # + [_addon().ROT_MEDIAL_LEFT, _addon().ROT_MEDIAL_RIGHT]
else:
views = list(map(int, views))
inf_r = bpy.context.scene.inflating
if inflated_ratio_in_file_name:
surf_name_dict = {-1: 'pial', 0: 'inflated', 1: 'flat'}
surf_name = surf_name_dict.get(inf_r, '')
if surf_name == '':
if -1 < inf_r < 0:
surf_name = '{:.1f}_inflated'.format(1 - inf_r)
else:
surf_name = '{:.1f}_flat'.format(inf_r)
else:
surf_name = 'pial' if inf_r == -1 else 'inflated' if -1 < inf_r <= 0 else 'flat'
if mu.get_hemi_obj('rh').hide and not mu.get_hemi_obj('lh').hide:
hemi = 'lh'
elif not mu.get_hemi_obj('rh').hide and mu.get_hemi_obj('lh').hide:
hemi = 'rh'
elif not mu.get_hemi_obj('rh').hide and not mu.get_hemi_obj('lh').hide:
hemi = ''
else:
mu.write_to_stderr('You need to show at least one hemi')
org_view_ang = tuple(mu.get_view3d_region().view_rotation)
images_names = []
for view in views:
view_name = _addon().view_name(view)
img_name = get_image_name(view_name)
if not should_save_image(img_name):
continue
_addon().rotate_view(view)
if hemi == 'lh' and rot_lh_axial and view in (
_addon().ROT_AXIAL_SUPERIOR, _addon().ROT_AXIAL_INFERIOR):
_addon().rotate_brain(dz=180)
mu.center_view()
image_fname = save_render_image(img_name, quality, render_images,
add_colorbar, cb_ticks_num,
cb_ticks_font_size)
print(image_fname, view, hemi)
images_names.append(image_fname)
# if not mu.get_hemi_obj('rh').hide and not mu.get_hemi_obj('lh').hide:
if views is None:
save_medial_views()
# todo: doesn't work
mu.rotate_view3d(org_view_ang)
mu.center_view()
return images_names
def slice_brain(cut_pos=None, save_image=False):
coordinate = bpy.context.scene.cursor_location
cut_type = bpy.context.scene.slicer_cut_type
create_joint_brain_obj()
# coordinate = list(D.screens['Default'].areas[3].spaces[0].cursor_location)
optional_cut_types = ['sagital', 'coronal', 'axial']
optional_rots = [[1.5708, 0, 1.5708], [1.5708, 0, 3.14], [0, 3.14, 0]]
option_ind = optional_cut_types.index(cut_type)
bpy.context.scene.is_sliced_ind = option_ind
bpy.context.scene.last_cursor_location = coordinate
if cut_pos is None:
cut_pos = [0.0, 0.0, 0.0]
cut_pos[option_ind] = coordinate[option_ind]
print('slice_brain: cut pos {}'.format(cut_pos))
# print('rot={}'.format(optional_rots[option_ind]))
if bpy.data.objects.get('{}_plane'.format(cut_type)) is None:
bpy.ops.mesh.primitive_plane_add(radius=25.7 / 2.0, location=tuple(cut_pos))
bpy.context.object.name = '{}_plane'.format(cut_type)
bpy.context.object.rotation_euler = optional_rots[option_ind]
bpy.ops.mesh.uv_texture_add()
else:
bpy.data.objects['{}_plane'.format(cut_type)].hide = False
bpy.data.objects['{}_plane'.format(cut_type)].hide_render = False
optional_cut_types.remove(cut_type)
for cut in optional_cut_types:
if bpy.data.objects.get('{}_plane'.format(cut)):
bpy.data.objects['{}_plane'.format(cut)].hide = True
bpy.data.objects['{}_plane'.format(cut)].hide_render = True
cur_plane_obj = bpy.data.objects['{}_plane'.format(cut_type)]
cur_plane_obj.location = tuple(cut_pos)
# images_path = '{}_{}.png'.format(bpy.context.scene.slices_modality, cut_type)
images_path = '{}.{}'.format(cut_type, _addon().get_figure_format())
# slice_image_path = glob.glob('{}*{}*'.format(images_path, cut_type))
try:
slice_image = bpy.data.images[images_path]
print(slice_image)
cur_plane_obj.data.uv_textures['UVMap'].data[0].image = slice_image
except:
pass
if bpy.data.objects.get('masking_cube') is None:
bpy.ops.mesh.primitive_cube_add(radius=10)
bpy.context.object.name = 'masking_cube'
cube_location = [0, 0, 0]
if cut_pos[option_ind] > 0 or cut_type == 'axial':
cube_location[option_ind] = cut_pos[option_ind] + 9.99
elif cut_pos[option_ind] < 0:
cube_location[option_ind] = cut_pos[option_ind] - 9.99
bpy.data.objects['masking_cube'].location = tuple(cube_location)
bpy.data.objects['masking_cube'].hide = True
bpy.data.objects['masking_cube'].hide_render = True
for hemi in ['lh', 'rh']:
inflated_object = mu.get_hemi_obj(hemi)
if inflated_object.modifiers.get('mask_for_slice') is None:
inflated_object.modifiers.new('mask_for_slice', type='BOOLEAN')
inflated_object.modifiers['mask_for_slice'].object = bpy.data.objects['masking_cube']
inflated_object.modifiers['mask_for_slice'].operation = 'DIFFERENCE'
inflated_object.modifiers['mask_for_slice'].double_threshold = 0
bpy.context.scene.objects.active = cur_plane_obj
if cur_plane_obj.modifiers.get('Boolean') is None:
cur_plane_obj.modifiers.new('Boolean', type='BOOLEAN')
cur_plane_obj.modifiers['Boolean'].object = bpy.data.objects['joint_brain']
cur_plane_obj.modifiers['Boolean'].operation = 'INTERSECT'
cur_plane_obj.hide_select = True
if save_image:
_addon().save_image('slicing', bpy.context.scene.save_selected_view)
def slice_brain(cut_pos=None, save_image=False, render_image=False):
coordinate = bpy.context.scene.cursor_location
cut_type = bpy.context.scene.slicer_cut_type
create_joint_brain_obj()
# coordinate = list(D.screens['Default'].areas[3].spaces[0].cursor_location)
optional_cut_types = ['sagital', 'coronal', 'axial']
optional_rots = [[1.5708, 0, 1.5708], [1.5708, 0, 3.14], [0, 3.14, 0]]
option_ind = optional_cut_types.index(cut_type)
bpy.context.scene.is_sliced_ind = option_ind
bpy.context.scene.last_cursor_location = coordinate
if cut_pos is None:
cut_pos = [0.0, 0.0, 0.0]
cut_pos[option_ind] = coordinate[option_ind]
print('slice_brain: cut pos {}'.format(cut_pos))
# print('rot={}'.format(optional_rots[option_ind]))
if bpy.data.objects.get('{}_plane'.format(cut_type)) is None:
bpy.ops.mesh.primitive_plane_add(radius=25.7 / 2.0,
location=tuple(cut_pos))
bpy.context.object.name = '{}_plane'.format(cut_type)
bpy.context.object.rotation_euler = optional_rots[option_ind]
# if cut_type == 'axial':import
# bpy.ops.object.mode_set(mode='EDIT')
# bpy.ops.mesh.flip_normals()
# bpy.ops.object.mode_set(mode='OBJECT')
bpy.ops.mesh.uv_texture_add()
try:
bpy.context.object.active_material = bpy.data.materials[
'{}_plane_mat'.format(cut_type)]
except:
print('can\'t show slice on rendering mode')
else:
bpy.data.objects['{}_plane'.format(cut_type)].hide = False
bpy.data.objects['{}_plane'.format(cut_type)].hide_render = False
optional_cut_types.remove(cut_type)
for cut in optional_cut_types:
if bpy.data.objects.get('{}_plane'.format(cut)):
bpy.data.objects['{}_plane'.format(cut)].hide = True
bpy.data.objects['{}_plane'.format(cut)].hide_render = True
cur_plane_obj = bpy.data.objects['{}_plane'.format(cut_type)]
cur_plane_obj.location = tuple(cut_pos)
# images_path = '{}_{}.png'.format(bpy.context.scene.slices_modality, cut_type)
images_path = '{}.{}'.format(cut_type,
_addon().get_figure_format().upper())
# slice_image_path = glob.glob('{}*{}*'.format(images_path, cut_type))
try:
slice_image = bpy.data.images[images_path]
print(slice_image)
cur_plane_obj.data.uv_textures['UVMap'].data[0].image = slice_image
bpy.data.materials['{}_plane_mat'.format(cut_type)].node_tree.nodes[
'Image Texture'].image = bpy.data.images['{}.JPEG'.format(
cut_type)]
except:
print(traceback.format_exc())
print('can\'t show slice on rendering mode')
if bpy.data.objects.get('masking_cube') is None:
bpy.ops.mesh.primitive_cube_add(radius=10)
bpy.context.object.name = 'masking_cube'
cube_location = [0, 0, 0]
# if cut_pos[option_ind] > 0 or cut_type in ['axial','coronal']:
if bpy.context.scene.what_to_cut == '1':
cube_location[option_ind] = cut_pos[option_ind] + 9.98
is_coordinate_positive = True
# elif cut_pos[option_ind] < 0:
elif bpy.context.scene.what_to_cut == '2':
cube_location[option_ind] = cut_pos[option_ind] - 9.98
is_coordinate_positive = False
bpy.data.objects['masking_cube'].location = tuple(cube_location)
bpy.data.objects['masking_cube'].hide = True
bpy.data.objects['masking_cube'].hide_render = True
for hemi in ['lh', 'rh']:
inflated_object = mu.get_hemi_obj(hemi)
# if inflated_object.modifiers.get('mask_for_slice') is None:
# inflated_object.modifiers.new('mask_for_slice', type='BOOLEAN')
# inflated_object.modifiers['mask_for_slice'].object = bpy.data.objects['masking_cube']
# inflated_object.modifiers['mask_for_slice'].operation = 'DIFFERENCE'
# inflated_object.modifiers['mask_for_slice'].double_threshold = 0
mask_object_with_cube(inflated_object)
try:
# TODO Noam this is where I slice the head object.
if bpy.context.scene.slice_seghead:
# if we need to slice the head :
mask_object_with_cube(bpy.data.objects['seghead'])
else:
# else, make sure we don't show the slicing
bpy.data.objects['seghead'].modifiers[
'mask_for_slice'].show_viewport = False
bpy.data.objects['seghead'].modifiers[
'mask_for_slice'].show_render = False
except:
print('outer skin object does not exist.')
bpy.context.scene.objects.active = cur_plane_obj
if cur_plane_obj.modifiers.get('Boolean') is None:
cur_plane_obj.modifiers.new('Boolean', type='BOOLEAN')
cur_plane_obj.modifiers['Boolean'].object = bpy.data.objects[
'joint_brain']
cur_plane_obj.modifiers['Boolean'].operation = 'INTERSECT'
flip_slice_plane_if_needed(is_coordinate_positive)
cur_plane_obj.hide_select = True
if save_image:
_addon().save_image('slicing', bpy.context.scene.save_selected_view)
if render_image:
_addon().render_image(set_to_camera_mode=True)
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)