def import_rois(base_path):
anatomy_inputs = {'Cortex-rh': op.join(base_path, '{}.pial.rh'.format(bpy.context.scene.atlas)),
'Cortex-lh': op.join(base_path, '{}.pial.lh'.format(bpy.context.scene.atlas)),
'Cortex-inflated-rh': op.join(base_path, '{}.inflated.rh'.format(bpy.context.scene.atlas)),
'Cortex-inflated-lh': op.join(base_path, '{}.inflated.lh'.format(bpy.context.scene.atlas)),
'Subcortical_structures': op.join(base_path, 'subcortical'),
'Cerebellum': op.join(base_path, 'cerebellum')}
brain_layer = _addon().BRAIN_EMPTY_LAYER
bpy.context.scene.layers = [ind == brain_layer for ind in range(len(bpy.context.scene.layers))]
layers_array = bpy.context.scene.layers
emptys_names = ['Brain'] + list(anatomy_inputs.keys()) # ["Brain", "Subcortical_structures", "Cortex-lh", "Cortex-rh", 'Cortex-inflated-rh', 'Cortex-inflated-rh']
for name in emptys_names:
create_empty_if_doesnt_exists(name, brain_layer, layers_array)
bpy.context.scene.layers = [ind == DataMakerPanel.addon.ROIS_LAYER for ind in range(len(bpy.context.scene.layers))]
# todo: check each hemi
inflated_imported = False
for anatomy_name, anatomy_input_base_path in anatomy_inputs.items():
if not op.isdir(anatomy_input_base_path):
print('The anatomy folder {} does not exist'.format(anatomy_input_base_path))
continue
current_mat = bpy.data.materials['unselected_label_Mat_cortex']
if anatomy_name in ['Subcortical_structures', 'Cerebellum']:
current_mat = bpy.data.materials['unselected_label_Mat_subcortical']
print('importing from {}'.format(anatomy_input_base_path))
for ply_fname in glob.glob(op.join(anatomy_input_base_path, '*.ply')):
try:
new_obj_name = mu.namebase(ply_fname)
fol_name = anatomy_input_base_path.split(op.sep)[-1]
surf_name = 'pial' if fol_name == 'subcortical' or len(fol_name.split('.')) == 1 else fol_name.split('.')[-2]
if surf_name == 'inflated':
new_obj_name = '{}_{}'.format(surf_name, new_obj_name)
mu.change_layer(_addon().INFLATED_ROIS_LAYER)
elif surf_name == 'pial':
mu.change_layer(_addon().ROIS_LAYER)
if not bpy.data.objects.get(new_obj_name) is None:
# print('{} was already imported'.format(new_obj_name))
continue
if 'inflated' in new_obj_name:
inflated_imported = True
bpy.ops.object.select_all(action='DESELECT')
# print(ply_fname)
bpy.ops.import_mesh.ply(filepath=op.join(anatomy_input_base_path, ply_fname))
cur_obj = bpy.context.selected_objects[0]
cur_obj.select = True
bpy.ops.object.shade_smooth()
cur_obj.parent = bpy.data.objects[anatomy_name]
cur_obj.scale = [0.1] * 3
cur_obj.active_material = current_mat
cur_obj.hide = False
cur_obj.name = new_obj_name
except:
print('Error in importing {}'.format(ply_fname))
# cur_obj.location[0] += 5.5 if 'rh' in anatomy_name else -5.5
# time.sleep(0.3)
if inflated_imported:
bpy.data.objects['Cortex-inflated-rh'].location[0] += 5.5
bpy.data.objects['Cortex-inflated-lh'].location[0] -= 5.5
bpy.ops.object.select_all(action='DESELECT')
def import_plane():
# plane.dimensions[0] = 5.59
# plane.dimensions[1] = 4.19
skull_plane = bpy.data.objects.get('skull_plane', None)
if skull_plane is not None:
pass
# return skull_plane
# skull_plane.select = True
# bpy.ops.object.delete()
else:
mu.change_layer(_addon().SKULL_LAYER)
emptys_name = 'Skull'
bpy.ops.object.select_all(action='DESELECT')
bpy.ops.import_mesh.ply(
filepath=op.join(mu.get_mmvt_dir(), 'skull_plane.ply'))
if len(bpy.context.selected_objects) == 0:
return None
skull_plane = bpy.context.selected_objects[0]
skull_plane.select = True
bpy.ops.object.shade_smooth()
bpy.ops.mesh.uv_texture_add()
skull_plane.data.uv_textures['UVMap'].data[0].image = bpy.data.images[
'neuropace.jpg']
skull_plane.active_material = bpy.data.materials['Activity_map_mat']
skull_plane.name = 'skull_plane'
skull_plane.parent = bpy.data.objects[emptys_name]
skull_plane.hide_select = True
skull_plane.location[0] = skull_plane.location[1] = 0
skull_plane.location[2] = 10
skull_plane.rotation_mode = 'XYZ'
skull_plane.rotation_euler[0] = skull_plane.rotation_euler[1] = 0
skull_plane.rotation_euler[2] = -math.pi / 2
def create_eeg_mesh():
mu.change_layer(_addon().BRAIN_EMPTY_LAYER)
create_empty_if_doesnt_exists('Helmets', _addon().BRAIN_EMPTY_LAYER, bpy.context.scene.layers, 'Functional maps')
mu.change_layer(_addon().EEG_LAYER)
current_mat = bpy.data.materials['unselected_label_Mat_cortex']
bpy.ops.import_mesh.ply(filepath=op.join(mu.get_user_fol(), 'eeg', 'eeg_helmet.ply'))
mesh_obj = bpy.context.selected_objects[0]
mesh_obj.name = 'eeg_helmet'
mesh_obj.select = True
bpy.ops.object.shade_smooth()
mesh_obj.parent = bpy.data.objects['Helmets']
mesh_obj.scale = [0.1] * 3
mesh_obj.active_material = current_mat
mesh_obj.hide = False
return mesh_obj
def import_hemis_for_functional_maps(base_path):
mu.change_layer(_addon().BRAIN_EMPTY_LAYER)
layers_array = bpy.context.scene.layers
emptys_names = [
'Functional maps', 'Subcortical_meg_activity_map',
'Subcortical_fmri_activity_map'
]
for name in emptys_names:
create_empty_if_doesnt_exists(name,
_addon().BRAIN_EMPTY_LAYER, layers_array,
'Functional maps')
# for ii in range(len(bpy.context.scene.layers)):
# bpy.context.scene.layers[ii] = (ii == brain_layer)
print("importing Hemispheres")
# # for cur_val in bpy.context.scene.layers:
# # print(cur_val)
# print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
now = time.time()
ply_files = glob.glob(op.join(base_path, 'surf', '*.ply'))
N = len(ply_files)
for ind, ply_fname in enumerate(ply_files):
mu.time_to_go(now, ind, N, 10)
bpy.ops.object.select_all(action='DESELECT')
obj_name = mu.namebase(ply_fname).split(sep='.')[0]
surf_name = mu.namebase(ply_fname).split(sep='.')[1]
if surf_name == 'inflated':
obj_name = '{}_{}'.format(surf_name, obj_name)
mu.change_layer(_addon().INFLATED_ACTIVITY_LAYER)
elif surf_name == 'pial':
mu.change_layer(_addon().ACTIVITY_LAYER)
else:
raise Exception(
'The surface type {} is not supported!'.format(surf_name))
if bpy.data.objects.get(obj_name) is None:
bpy.ops.import_mesh.ply(
filepath=op.join(base_path, 'surf', ply_fname))
cur_obj = bpy.context.selected_objects[0]
cur_obj.select = True
bpy.ops.object.shade_smooth()
cur_obj.scale = [0.1] * 3
cur_obj.hide = False
cur_obj.name = obj_name
if surf_name == 'inflated':
cur_obj.active_material = bpy.data.materials[
'Inflated_Activity_map_mat']
cur_obj.location[
0] += 5.5 if obj_name == 'inflated_rh' else -5.5
else:
cur_obj.active_material = bpy.data.materials[
'Activity_map_mat']
cur_obj.parent = bpy.data.objects["Functional maps"]
cur_obj.hide_select = True
cur_obj.data.vertex_colors.new()
else:
print('{} already exists'.format(ply_fname))
_addon().create_inflated_curv_coloring()
bpy.ops.object.select_all(action='DESELECT')
def import_skull():
mu.change_layer(_addon().BRAIN_EMPTY_LAYER)
base_path = op.join(mu.get_user_fol(), 'skull')
emptys_name = 'Skull'
layers_array = bpy.context.scene.layers
_addon().create_empty_if_doesnt_exists(emptys_name,
_addon().BRAIN_EMPTY_LAYER,
layers_array)
for skull_type in ['inner_skull', 'outer_skull']:
bpy.ops.object.select_all(action='DESELECT')
bpy.ops.import_mesh.ply(
filepath=op.join(base_path, '{}.ply'.format(skull_type)))
cur_obj = bpy.context.selected_objects[0]
cur_obj.select = True
bpy.ops.object.shade_smooth()
cur_obj.scale = [0.1] * 3
cur_obj.hide = False
cur_obj.name = skull_type
cur_obj.active_material = bpy.data.materials['Activity_map_mat']
cur_obj.parent = bpy.data.objects[emptys_name]
cur_obj.hide_select = True
cur_obj.data.vertex_colors.new()
def import_hemis_for_functional_maps(base_path):
mu.change_layer(_addon().BRAIN_EMPTY_LAYER)
layers_array = bpy.context.scene.layers
emptys_names = ['Functional maps', 'Subcortical_meg_activity_map', 'Subcortical_fmri_activity_map']
for name in emptys_names:
create_empty_if_doesnt_exists(name, _addon().BRAIN_EMPTY_LAYER, layers_array, 'Functional maps')
# for ii in range(len(bpy.context.scene.layers)):
# bpy.context.scene.layers[ii] = (ii == brain_layer)
print("importing Hemispheres")
# # for cur_val in bpy.context.scene.layers:
# # print(cur_val)
# print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
now = time.time()
ply_files = glob.glob(op.join(base_path, 'surf', '*.ply'))
N = len(ply_files)
for ind, ply_fname in enumerate(ply_files):
try:
mu.time_to_go(now, ind, N, 10)
bpy.ops.object.select_all(action='DESELECT')
obj_name = mu.namebase(ply_fname).split(sep='.')[0]
surf_name = mu.namebase(ply_fname).split(sep='.')[1]
if surf_name == 'inflated':
obj_name = '{}_{}'.format(surf_name, obj_name)
mu.change_layer(_addon().INFLATED_ACTIVITY_LAYER)
elif surf_name == 'pial':
mu.change_layer(_addon().ACTIVITY_LAYER)
else:
raise Exception('The surface type {} is not supported!'.format(surf_name))
if bpy.data.objects.get(obj_name) is None:
bpy.ops.import_mesh.ply(filepath=op.join(base_path, 'surf', ply_fname))
cur_obj = bpy.context.selected_objects[0]
cur_obj.select = True
bpy.ops.object.shade_smooth()
cur_obj.scale = [0.1] * 3
cur_obj.hide = False
cur_obj.name = obj_name
if surf_name == 'inflated':
cur_obj.active_material = bpy.data.materials['Inflated_Activity_map_mat']
cur_obj.location[0] += 5.5 if obj_name == 'inflated_rh' else -5.5
else:
cur_obj.active_material = bpy.data.materials['Activity_map_mat']
cur_obj.parent = bpy.data.objects["Functional maps"]
cur_obj.hide_select = True
cur_obj.data.vertex_colors.new()
# else:
# print('{} already exists'.format(ply_fname))
except:
print('Error in importing {}'.format(ply_fname))
_addon().create_inflated_curv_coloring()
bpy.ops.object.select_all(action='DESELECT')
def import_rois(base_path):
anatomy_inputs = {
'Cortex-rh':
op.join(base_path, '{}.pial.rh'.format(bpy.context.scene.atlas)),
'Cortex-lh':
op.join(base_path, '{}.pial.lh'.format(bpy.context.scene.atlas)),
'Cortex-inflated-rh':
op.join(base_path, '{}.inflated.rh'.format(bpy.context.scene.atlas)),
'Cortex-inflated-lh':
op.join(base_path, '{}.inflated.lh'.format(bpy.context.scene.atlas)),
'Subcortical_structures':
op.join(base_path, 'subcortical')
}
brain_layer = DataMakerPanel.addon.BRAIN_EMPTY_LAYER
bpy.context.scene.layers = [
ind == brain_layer for ind in range(len(bpy.context.scene.layers))
]
layers_array = bpy.context.scene.layers
emptys_names = ['Brain'] + list(
anatomy_inputs.keys()
) # ["Brain", "Subcortical_structures", "Cortex-lh", "Cortex-rh", 'Cortex-inflated-rh', 'Cortex-inflated-rh']
for name in emptys_names:
create_empty_if_doesnt_exists(name, brain_layer, layers_array)
bpy.context.scene.layers = [
ind == DataMakerPanel.addon.ROIS_LAYER
for ind in range(len(bpy.context.scene.layers))
]
for anatomy_name, anatomy_input_base_path in anatomy_inputs.items():
if not op.isdir(anatomy_input_base_path):
print('The anatomy folder {} does not exist'.format(
anatomy_input_base_path))
continue
current_mat = bpy.data.materials['unselected_label_Mat_cortex']
if anatomy_name == 'Subcortical_structures':
current_mat = bpy.data.materials[
'unselected_label_Mat_subcortical']
print('importing from {}'.format(anatomy_input_base_path))
for ply_fname in glob.glob(op.join(anatomy_input_base_path, '*.ply')):
new_obj_name = mu.namebase(ply_fname)
fol_name = anatomy_input_base_path.split(op.sep)[-1]
surf_name = 'pial' if fol_name == 'subcortical' else fol_name.split(
'.')[1]
if surf_name == 'inflated':
new_obj_name = '{}_{}'.format(surf_name, new_obj_name)
mu.change_layer(_addon().INFLATED_ROIS_LAYER)
elif surf_name == 'pial':
mu.change_layer(_addon().ROIS_LAYER)
if not bpy.data.objects.get(new_obj_name) is None:
continue
bpy.ops.object.select_all(action='DESELECT')
# print(ply_fname)
bpy.ops.import_mesh.ply(
filepath=op.join(anatomy_input_base_path, ply_fname))
cur_obj = bpy.context.selected_objects[0]
cur_obj.select = True
bpy.ops.object.shade_smooth()
cur_obj.parent = bpy.data.objects[anatomy_name]
cur_obj.scale = [0.1] * 3
cur_obj.active_material = current_mat
cur_obj.hide = False
cur_obj.name = new_obj_name
# cur_obj.location[0] += 5.5 if 'rh' in anatomy_name else -5.5
# time.sleep(0.3)
bpy.data.objects['Cortex-inflated-rh'].location[0] += 5.5
bpy.data.objects['Cortex-inflated-lh'].location[0] -= 5.5
bpy.ops.object.select_all(action='DESELECT')
