def create_conncection_for_both_conditions(d, layers_rods, indices, mask,
windows_num, norm_fac, T, radius):
N = len(indices)
parent_obj = bpy.data.objects[PARENT_OBJ]
print('Create connections for both conditions')
now = time.time()
for run, (ind, conn_name, (i, j)) in enumerate(
zip(indices, d.con_names[mask], d.con_indices[mask])):
mu.time_to_go(now, run, N, runs_num_to_print=10)
if d.con_colors.ndim == 3:
con_color = np.hstack((d.con_colors[ind, 0, :], [0.]))
else:
con_color = np.hstack((d.con_colors[ind, :], [0.]))
p1, p2 = d.locations[i, :] * 0.1, d.locations[j, :] * 0.1
mu.cylinder_between(p1, p2, radius, layers_rods)
# mu.create_material('{}_mat'.format(conn_name), (0, 0, 1, 1), 1)
mu.create_material('{}_mat'.format(conn_name), con_color, 1)
cur_obj = bpy.context.active_object
cur_obj.name = conn_name
cur_obj.parent = parent_obj
# cur_obj.animation_data_clear()
if windows_num == 1:
continue
for cond_id, cond in enumerate(d.conditions):
# insert_frame_keyframes(cur_obj, '{}-{}'.format(conn_name, cond), d.con_values[ind, -1, cond_id], T)
for t in range(windows_num):
extra_time_points = 0 if norm_fac == 1 else 2
timepoint = t * norm_fac + extra_time_points
mu.insert_keyframe_to_custom_prop(
cur_obj, '{}-{}'.format(conn_name, cond),
d.con_values[ind, t, cond_id], timepoint)
finalize_fcurves(cur_obj)
def create_conncection_for_both_conditions(d, layers_rods, indices, mask, windows_num, norm_fac, T, radius):
N = len(indices)
parent_obj = bpy.data.objects[PARENT_OBJ]
print('Create connections for both conditions')
now = time.time()
for run, (ind, conn_name, (i, j)) in enumerate(zip(indices, d.con_names[mask], d.con_indices[mask])):
mu.time_to_go(now, run, N, runs_num_to_print=10)
if d.con_colors.ndim == 3:
con_color = np.hstack((d.con_colors[ind, 0, :], [0.]))
else:
con_color = np.hstack((d.con_colors[ind, :], [0.]))
p1, p2 = d.locations[i, :] * 0.1, d.locations[j, :] * 0.1
mu.cylinder_between(p1, p2, radius, layers_rods)
# mu.create_material('{}_mat'.format(conn_name), (0, 0, 1, 1), 1)
mu.create_material('{}_mat'.format(conn_name), con_color, 1)
cur_obj = bpy.context.active_object
cur_obj.name = conn_name
cur_obj.parent = parent_obj
# cur_obj.animation_data_clear()
if windows_num == 1:
continue
for cond_id, cond in enumerate(d.conditions):
# insert_frame_keyframes(cur_obj, '{}-{}'.format(conn_name, cond), d.con_values[ind, -1, cond_id], T)
for t in range(windows_num):
extra_time_points = 0 if norm_fac ==1 else 2
timepoint = t * norm_fac + extra_time_points
mu.insert_keyframe_to_custom_prop(cur_obj, '{}-{}'.format(conn_name, cond),
d.con_values[ind, t, cond_id], timepoint)
finalize_fcurves(cur_obj)
def plot_connections(self,
context,
d,
plot_time,
connections_type,
condition,
threshold,
abs_threshold=True):
windows_num = d.con_values.shape[1]
# xs, ys = get_fcurve_values('RPT3-RAT5')
# cond_id = [i for i, cond in enumerate(d.conditions) if cond == condition][0]
t = int(plot_time / ConnectionsPanel.addon.get_max_time_steps() *
windows_num) if windows_num > 1 else 0
print('plotting connections for t:{}'.format(t))
if t >= d.con_colors.shape[1] and windows_num > 1:
mu.message(self, 'time out of bounds! {}'.format(plot_time))
else:
# for conn_name, conn_colors in colors.items():
# vals = []
selected_objects, selected_indices = get_all_selected_connections(d)
for ind, con_name in zip(selected_indices, selected_objects):
# print(con_name, d.con_values[ind, t, 0], d.con_values[ind, t, 1], np.diff(d.con_values[ind, t, :]))
cur_obj = bpy.data.objects.get(con_name)
color = d.con_colors[
ind, t, :] if d.con_colors.ndim == 3 else d.con_colors[ind, :]
con_color = np.hstack((color, [0.]))
bpy.context.scene.objects.active = cur_obj
mu.create_material('{}_mat'.format(con_name), con_color, 1, False)
# vals.append(np.diff(d.con_values[ind, t])[0])
bpy.data.objects[PARENT_OBJ].select = True
ConnectionsPanel.addon.show_hide_connections()
def create_conncection_per_condition(d, layers_rods, indices, mask, windows_num, norm_fac, T, radius):
N = len(indices)
parent_obj = bpy.data.objects[get_connections_parent_name()]
print('Create connections for both conditions')
con_color = (1, 1, 1, 1)
now = time.time()
for run, (ind, conn_name, (i, j)) in enumerate(zip(indices, d.con_names[mask], d.con_indices[mask])):
mu.time_to_go(now, run, N, runs_num_to_print=10)
p1, p2 = d.locations[i, :] * 0.1, d.locations[j, :] * 0.1
mu.cylinder_between(p1, p2, radius, layers_rods)
mu.create_material('{}_mat'.format(conn_name), con_color, 1)
cur_obj = bpy.context.active_object
cur_obj.name = conn_name
cur_obj.parent = parent_obj
# cur_obj.animation_data_clear()
if windows_num == 1:
continue
for cond_id, cond in enumerate(d.conditions):
# insert_frame_keyframes(cur_obj, '{}-{}'.format(conn_name, cond), d.con_values[ind, -1, cond_id], T)
for t in range(windows_num):
extra_time_points = 0 if norm_fac == 1 else 2
timepoint = t * norm_fac + extra_time_points
mu.insert_keyframe_to_custom_prop(cur_obj, '{}-{}'.format(conn_name, cond),
d.con_values[ind, t, cond_id], timepoint)
fcurve = cur_obj.animation_data.action.fcurves[cond_id]
fcurve.keyframe_points[0].co[1] = 0
fcurve.keyframe_points[-1].co[1] = 0
finalize_fcurves(cur_obj)
mu.change_fcurves_colors(parent_obj.children)
def plot_connections(d, plot_time, threshold=None):
_addon().show_hide_connections()
windows_num = d.con_values.shape[1] if d.con_values.ndim >= 2 else 1
t = int(plot_time / ConnectionsPanel.T * windows_num) if windows_num > 1 else 0
print('plotting connections for t:{}'.format(t))
if 1 < windows_num <= t:
print('time out of bounds! {}'.format(plot_time))
else:
# selected_objects, selected_indices = get_all_selected_connections(d)
selected_objects = ConnectionsPanel.selected_objects
selected_indices = ConnectionsPanel.selected_indices
if len(selected_objects) == 0:
selected_objects, selected_indices = get_all_selected_connections(d)
if _addon().colorbar_values_are_locked():
data_min = _addon().get_colorbar_min()
data_max = _addon().get_colorbar_max()
else:
# Should set the percentile in GUI
data_min, data_max = ConnectionsPanel.data_minmax
_addon().set_colorbar_max_min(data_max, data_min)
colors_ratio = 256 / (data_max - data_min)
stat_vals = [calc_stat_data(d.con_values[ind, t], STAT_DIFF) if d.con_values.ndim >= 2 else d.con_values[ind]
for ind in selected_indices]
colors = _addon().calc_colors(np.array(stat_vals).squeeze(), data_min, colors_ratio)
colors = np.concatenate((colors, np.zeros((len(colors), 1))), 1)
_addon().show_hide_connections()
if threshold is None:
threshold = bpy.context.scene.coloring_threshold
for ind, con_name in enumerate(selected_objects):
cur_obj = bpy.data.objects.get(con_name)
if bpy.context.scene.hide_connection_under_threshold:
if abs(stat_vals[ind]) < threshold:
cur_obj.hide = True
cur_obj.hide_render = True
bpy.context.scene.objects.active = cur_obj
mu.create_material('{}_mat'.format(con_name), colors[ind], 1, False)
if bpy.context.scene.hide_connection_under_threshold:
filter_nodes()
parent_obj_name = get_connections_parent_name()
bpy.data.objects[parent_obj_name].select = True
connectivity_method = d['connectivity_method'] if 'connectivity_method' in d else 'connectivity'
# if 'corr' in connectivity_method:
# _addon().set_colorbar_max_min(1, -1)
# else:
# data_max, data_min = np.max(d.con_values[selected_indices]), np.min(d.con_values[selected_indices])
modality_names = dict(electrodes='Electrodes', meg='MEG', fmri='fMRI')
colorbar_title = 'Electrodes {}'.format(connectivity_method) \
if 'electrodes' in bpy.context.scene.connectivity_files else \
'{} {}'.format(bpy.context.scene.connectivity_files, connectivity_method) # Cortical labels
_addon().set_colorbar_title(colorbar_title)
def create_vertices(d, mask, verts_color='pink'):
layers = [False] * 20
layers[_addon().CONNECTIONS_LAYER] = True
vert_color = np.hstack((cu.name_to_rgb(verts_color), [0.]))
parent_name = 'connections_vertices'
parent_obj = mu.create_empty_if_doesnt_exists(parent_name, _addon().BRAIN_EMPTY_LAYER, None, get_connections_parent_name())
for vertice in ConnectionsPanel.vertices:
# for ind in range(len(d.names[mask])):
# for indice in indices:
p1 = d.locations[vertice, :] * 0.1
vert_name = '{}_vertice'.format(d.labels[vertice])
mu.create_ico_sphere(p1, layers, vert_name)
mu.create_material('{}_mat'.format(vert_name), vert_color, 1)
cur_obj = bpy.context.active_object
cur_obj.name = vert_name
cur_obj.parent = parent_obj
def create_lead(p1, p2, lead_name, radius=0.03):
if bpy.data.objects.get(lead_name) is not None:
return bpy.data.objects.get(lead_name)
layers = [False] * 20
lead_layer = _addon().ELECTRODES_LAYER
layers[lead_layer] = True
parent_name = 'leads'
mu.create_empty_if_doesnt_exists(parent_name, _addon().BRAIN_EMPTY_LAYER, None, parent_name)
mu.cylinder_between(p1, p2, radius, layers)
color = tuple(np.concatenate((bpy.context.scene.electrodes_leads_color, [1])))
mu.create_material('{}_mat'.format(lead_name), color, 1)
cur_obj = bpy.context.active_object
cur_obj.name = lead_name
cur_obj.parent = bpy.data.objects[parent_name]
bpy.data.objects[lead_name].select = False
return bpy.data.objects[lead_name]
def create_vertices(d, mask, verts_color='pink'):
indices = set()
layers = [False] * 20
layers[_addon().CONNECTIONS_LAYER] = True
vert_color = np.hstack((cu.name_to_rgb(verts_color), [0.]))
parent_name = 'connections_vertices'
parent_obj = mu.create_empty_if_doesnt_exists(parent_name, _addon().BRAIN_EMPTY_LAYER, None, PARENT_OBJ)
for (i, j) in d.con_indices[mask]:
indices.add(i)
indices.add(j)
for indice in indices:
p1 = d.locations[indice, :] * 0.1
vert_name = 'connection_{}'.format(indice)
mu.create_ico_sphere(p1, layers, vert_name)
mu.create_material('{}_mat'.format(vert_name), vert_color, 1)
cur_obj = bpy.context.active_object
cur_obj.name = vert_name
cur_obj.parent = parent_obj
def plot_connections(self, context, d, plot_time, connections_type, condition, threshold, abs_threshold=True):
windows_num = d.con_values.shape[1]
# xs, ys = get_fcurve_values('RPT3-RAT5')
# cond_id = [i for i, cond in enumerate(d.conditions) if cond == condition][0]
t = int(plot_time / ConnectionsPanel.addon.get_max_time_steps() * windows_num) if windows_num > 1 else 0
print('plotting connections for t:{}'.format(t))
if t >= d.con_colors.shape[1] and windows_num > 1:
mu.message(self, 'time out of bounds! {}'.format(plot_time))
else:
# for conn_name, conn_colors in colors.items():
# vals = []
selected_objects, selected_indices = get_all_selected_connections(d)
for ind, con_name in zip(selected_indices, selected_objects):
# print(con_name, d.con_values[ind, t, 0], d.con_values[ind, t, 1], np.diff(d.con_values[ind, t, :]))
cur_obj = bpy.data.objects.get(con_name)
color = d.con_colors[ind, t, :] if d.con_colors.ndim == 3 else d.con_colors[ind, :]
con_color = np.hstack((color, [0.]))
bpy.context.scene.objects.active = cur_obj
mu.create_material('{}_mat'.format(con_name), con_color, 1, False)
# vals.append(np.diff(d.con_values[ind, t])[0])
bpy.data.objects[PARENT_OBJ].select = True
ConnectionsPanel.addon.show_connections()
