def rotate_brain_via_lookup(elc_name, loc):
cortical_probs_max, subcortical_probs_max = 0, 0
cortical_probs_rois = \
[(p, r) for p, r in zip(loc['cortical_probs'], loc['cortical_rois']) if 'white' not in r.lower()]
subcortical_probs_rois = \
[(p, r) for p, r in zip(loc['subcortical_probs'], loc['subcortical_rois']) if 'white' not in r.lower()]
if len(cortical_probs_rois) > 0:
cortical_probs_ind = np.argmax(cortical_probs_rois, 0)[0]
cortical_probs_max = cortical_probs_rois[cortical_probs_ind][0]
if len(subcortical_probs_rois) > 0:
subcortical_probs_ind = np.argmax(subcortical_probs_rois, 0)[0]
subcortical_probs_max = subcortical_probs_rois[subcortical_probs_ind][0]
if cortical_probs_max > subcortical_probs_max:
max_roi = cortical_probs_rois[cortical_probs_ind][1]
max_roi_is_cortical = True
else:
max_roi = subcortical_probs_rois[subcortical_probs_ind][1]
max_roi_is_cortical = False
if max_roi_is_cortical:
atlas = bpy.context.scene.electrodes_labeling_files.split('_')[1]
hemi = mu.get_obj_hemi(max_roi)
annot_fname = mu.get_annot_fname(hemi, atlas)
max_roi_vertices_indices = mu.read_label_vertices_from_annot(annot_fname, max_roi)
if max_roi_vertices_indices is None:
print('Can\'t find {} vertices in {}!'.format(max_roi, annot_fname))
return
elc_pos = bpy.data.objects[elc_name].location
mesh = 'inflated_{}'.format(hemi)
vert_ind, vert_pos = _addon().vertex_data.find_closest_vertices(
elc_pos, max_roi_vertices_indices, mesh, False)
vert_pos *= 0.1
mu.rotate_view_to_vertice(vert_ind, mesh)
def _clusters_update():
if fMRIPanel.addon is None or not fMRIPanel.init:
return
clusters_labels_file = bpy.context.scene.fmri_clusters_labels_files
# key = '{}_{}'.format(clusters_labels_file, bpy.context.scene.fmri_clusters_labels_parcs)
key = clusters_labels_file
fMRIPanel.cluster_labels = cluster = fMRIPanel.lookup[key][bpy.context.scene.fmri_clusters]
cluster_centroid = np.mean(cluster['coordinates'], 0) / 10.0
_addon().clear_closet_vertex_and_mesh_to_cursor()
_addon().set_vertex_data(cluster['max'])
if 'max_vert' in cluster:
bpy.context.scene.cursor_location = mu.get_vert_co(cluster.max_vert, cluster.hemi)
_addon().set_closest_vertex_and_mesh_to_cursor(cluster.max_vert, 'inflated_{}'.format(cluster.hemi))
else:
if _addon().is_pial():
bpy.context.scene.cursor_location = cluster_centroid
closest_mesh_name, vertex_ind, vertex_co = _addon().find_vertex_index_and_mesh_closest_to_cursor(
cluster_centroid, mu.HEMIS, False)
_addon().set_closest_vertex_and_mesh_to_cursor(vertex_ind, closest_mesh_name)
else:
closest_mesh_name, vertex_ind, vertex_co = _addon().find_vertex_index_and_mesh_closest_to_cursor(
cluster_centroid, mu.HEMIS, False)
inflated_mesh = 'inflated_{}'.format(closest_mesh_name)
me = bpy.data.objects[inflated_mesh].to_mesh(bpy.context.scene, True, 'PREVIEW')
bpy.context.scene.cursor_location = me.vertices[vertex_ind].co / 10.0
bpy.data.meshes.remove(me)
_addon().set_closest_vertex_and_mesh_to_cursor(vertex_ind, closest_mesh_name)
tkreg_ras = _addon().calc_tkreg_ras_from_cursor()
if tkreg_ras is not None:
_addon().set_tkreg_ras(tkreg_ras, move_cursor=False)
if bpy.context.scene.plot_current_cluster and not fMRIPanel.blobs_plotted:
faces_verts = fMRIPanel.addon.get_faces_verts()
if bpy.context.scene.fmri_what_to_plot == 'blob':
plot_blob(cluster, faces_verts, True)
if bpy.context.scene.plot_fmri_cluster_contours:
inter_labels = [inter_label['name'] for inter_label in cluster['intersects']]
atlas = fMRIPanel.clusters_labels[bpy.context.scene.fmri_clusters_labels_files].atlas
_addon().color_contours(
inter_labels, cluster.hemi, None, False, False,
specific_colors=bpy.context.scene.fmri_cluster_contours_color, atlas=atlas)
_addon().save_cursor_position()
_addon().create_slices(pos=tkreg_ras)
find_electrodes_in_cluster()
if bpy.context.scene.fmri_rotate_view_to_vertice:
mu.rotate_view_to_vertice()
def invoke(self, context, event=None):
label_name = context.scene.labels_regex
SearchMark.marked_objects_select = {}
objects = mu.get_non_functional_objects()
SearchPanel.marked_objects = []
for obj in objects:
SearchFilter.marked_objects_select[obj.name] = obj.select
obj.select = label_name in obj.name
try:
import fnmatch
if fnmatch.fnmatch(obj.name, '*{}*'.format(label_name)):
SearchPanel.marked_objects.append(obj.name)
except:
if label_name in obj.name:
SearchPanel.marked_objects.append(obj.name)
if len(SearchPanel.marked_objects) == 0:
print('No objects found for "{}"'.format(
context.scene.labels_regex))
return
# todo: show rois only if the object is an ROI. Also, move the cursor
selected_obj = bpy.data.objects[SearchPanel.marked_objects[0]]
verts = np.array([vert.co for vert in selected_obj.data.vertices])
center = np.mean(verts, axis=0)
if any([mu.obj_is_cortex(o) for o in SearchPanel.marked_objects]):
selected_roi = [
o for o in SearchPanel.marked_objects if mu.obj_is_cortex(o)
][0]
hemi = mu.get_obj_hemi(selected_roi)
center = _addon().where_am_i.pos_to_current_inflation(center,
hemis=[hemi])
else:
center = mathutils.Vector(center) * mu.get_matrix_world()
# if bpy.context.scene.search_plot_contour:
# _addon().where_am_i.plot_closest_label_contour(selected_roi, hemi)
# bpy.context.scene.cursor_location = tuple(center)
_addon().where_am_i.set_cursor_location(center)
# _addon().set_cursor_pos()
# _addon().set_tkreg_ras(bpy.context.scene.cursor_location * 10, False)
if bpy.context.scene.slices_rotate_view_on_click:
mu.rotate_view_to_vertice()
# if any([mu.obj_is_cortex(o.name) for o in SearchPanel.marked_objects]):
# SearchPanel.addon.show_rois()
return {"FINISHED"}
def modal(self, context, event):
if self.left_clicked:
self.left_clicked = False
active_image, pos = click_inside_images_view(event)
if active_image is not None:
xyz = _addon().slices_were_clicked(active_image, pos)
bpy.context.scene.cursor_location = tuple(xyz)
set_cursor_pos()
if bpy.context.scene.cursor_is_snapped: # and is_view_3d():
_addon().set_tkreg_ras(
bpy.context.scene.cursor_location * 10, False)
snap_cursor(True)
if bpy.context.scene.slices_rotate_view_on_click:
mu.rotate_view_to_vertice()
# if bpy.context.scene.slices_zoom > 1:
# ohad(pos/bpy.context.scene.slices_zoom)
return {'PASS_THROUGH'}
if not click_inside_3d_view(event):
return {'PASS_THROUGH'}
if _addon().meg.change_cursor_on_selection():
cluster = _addon().select_meg_cluster(
event, context, bpy.context.scene.cursor_location)
if cluster is not None:
return {'PASS_THROUGH'}
cursor_moved = np.linalg.norm(
SelectionListener.cursor_pos -
bpy.context.scene.cursor_location) > 1e-3
if cursor_moved and bpy.data.objects.get('inner_skull',
None) is not None:
_addon().find_point_thickness()
return {'PASS_THROUGH'}
if bpy.context.scene.cursor_is_snapped: # and is_view_3d():
snap_cursor(True)
if _addon().fMRI_clusters_files_exist(
) and bpy.context.scene.plot_fmri_cluster_per_click:
_addon().find_closest_cluster(only_within=True)
tkreg_ras = _addon().calc_tkreg_ras_from_cursor()
if tkreg_ras is not None:
_addon().set_tkreg_ras(tkreg_ras, move_cursor=False)
# if _addon().is_pial():
# tkreg_ras = bpy.context.scene.cursor_location * 10
# _addon().set_tkreg_ras(tkreg_ras)
# elif bpy.context.scene.cursor_is_snapped:
# tkreg_ras = _addon().calc_tkreg_ras_from_snapped_cursor()
# _addon().set_tkreg_ras(tkreg_ras)
if cursor_moved:
set_cursor_pos()
# print('cursor position was changed by the user!')
_addon().create_slices(pos=tkreg_ras)
_addon().freeview.save_cursor_position()
clear_slice()
if bpy.context.scene.find_closest_label_on_click: # coloring_panel.WIC_CONTOURS in _addon().what_is_colored():
_addon().find_closest_label(
plot_contour=bpy.context.scene.plot_closest_label_contour)
if self.right_clicked:
self.right_clicked = False
if not click_inside_3d_view(event):
return {'PASS_THROUGH'}
# print(bpy.context.selected_objects)
# cluster = _addon().select_meg_cluster(event, context)
# if cluster is not None:
# return {'PASS_THROUGH'}
if len(bpy.context.selected_objects):
mu.unfilter_graph_editor()
if bpy.context.scene.fit_graph_on_selection:
mu.view_all_in_graph_editor()
selected_obj = bpy.context.active_object # bpy.context.selected_objects[-1]
selected_obj_name = selected_obj.name
selected_obj_type = mu.check_obj_type(selected_obj_name)
if selected_obj_type in [
mu.OBJ_TYPE_CORTEX_LH, mu.OBJ_TYPE_CORTEX_RH
]:
_addon().select_roi(selected_obj_name)
elif selected_obj_type in [
mu.OBJ_TYPE_CORTEX_INFLATED_LH,
mu.OBJ_TYPE_CORTEX_INFLATED_RH
]:
pial_obj_name = selected_obj_name[len('inflated_'):]
pial_obj = bpy.data.objects.get(pial_obj_name)
if not pial_obj is None:
# pial_obj.select = True
_addon().select_roi(pial_obj_name)
# mu.change_selected_fcurves_colors(pial_obj)
# mu.change_selected_fcurves_colors()
elif selected_obj_type == mu.OBJ_TYPE_CON:
_addon().select_connection(selected_obj_name)
elif selected_obj_type == mu.OBJ_TYPE_CON_VERTICE:
_addon().vertices_selected(selected_obj_name)
elif selected_obj_type == mu.OBJ_TYPE_ELECTRODE:
bpy.context.scene.cursor_is_snapped = False
_addon().electode_was_manually_selected(selected_obj_name)
try:
_addon().dell.dell_ct_electrode_was_selected(
selected_obj_name)
except:
pass
if bpy.context.scene.find_curves_sep_auto:
_addon().calc_best_curves_sep()
elif bpy.context.scene.curves_sep > 0:
_addon().curves_sep_update()
else:
_addon().clear_electrodes_selection()
#todo: should call to _addon().clear_rois_selection()
# if is_activity():
# bpy.context.scene.cursor_location = mouse_coo_to_3d_loc(event, context)
# snap_cursor(True)
# _addon().find_closest_label()
if time.time() - self.press_time > 1 and event.value == 'PRESS':
if event.type == 'RIGHTMOUSE':
self.press_time = time.time()
self.right_clicked = True
if event.type == 'LEFTMOUSE':
self.press_time = time.time()
self.left_clicked = True
if time.time() - self.press_time > 0.1:
if event.type == 'TIMER':
if bpy.context.scene.rotate_brain:
if _addon().render.is_camera_view():
_addon().render.camera_mode('ORTHO')
_addon().show_hide.rotate_brain()
_addon().render.camera_mode('CAMERA')
else:
_addon().show_hide.rotate_brain()
if _addon() and _addon().render_in_queue():
rendering_data = mu.queue_get(_addon().render_in_queue())
if not rendering_data is None:
try:
rendering_data = rendering_data.decode(
sys.getfilesystemencoding(), 'ignore')
if '*** finish rendering! ***' in rendering_data.lower():
print('Finish rendering!')
_addon().finish_rendering()
except:
print("Can't read the stdout from the rendering")
return {'PASS_THROUGH'}