def find_closest_label(atlas=None, plot_contour=True):
subjects_dir = mu.get_link_dir(mu.get_links_dir(), 'subjects')
if bpy.context.scene.cursor_is_snapped:
vertex_ind, hemi = _addon().get_closest_vertex_and_mesh_to_cursor()
else:
closest_mesh_name, vertex_ind, _ = \
_addon().find_closest_vertex_index_and_mesh(use_shape_keys=True)
hemi = closest_mesh_name[len('infalted_'):] if _addon().is_inflated() else closest_mesh_name
if vertex_ind == -1:
print("find_closest_label: Can't find the closest vertex")
return
hemi = 'rh' if 'rh' in hemi else 'lh'
if atlas is None:
atlas = bpy.context.scene.subject_annot_files
annot_fname = op.join(subjects_dir, mu.get_user(), 'label', '{}.{}.annot'.format(hemi, atlas))
if not op.isfile(annot_fname):
annot_fname = op.join(mu.get_user_fol(), 'labels', '{}.{}.annot'.format(hemi, atlas))
if op.isfile(annot_fname):
labels = mu.read_labels_from_annot(annot_fname)
vert_labels = [l for l in labels if vertex_ind in l.vertices]
if len(vert_labels) > 0:
label = vert_labels[0]
bpy.context.scene.closest_label_output = label.name
if plot_contour:
plot_closest_label_contour(label, hemi)
return label.name
else:
print("Can't find the annotation file for atlas {}!".format(atlas))
def init(addon):
HNNPanel.addon = addon
hnn_folder = mu.get_link_dir(mu.get_links_dir(), 'hnn')
if op.isdir(hnn_folder):
bpy.context.scene.hnn_folder = hnn_folder
init_hnn_files()
register()
HNNPanel.init = True
def set_hnn_folder(self, context):
hnn_folder = op.abspath(bpy.path.abspath(bpy.context.scene.hnn_folder))
if not op.isdir(hnn_folder):
return
hnn_link = op.join(mu.get_links_dir(), 'hnn')
if op.islink(hnn_link):
os.remove(hnn_link)
try:
os.symlink(hnn_folder, hnn_link)
except:
print('set_hnn_folder: Error in creating hnn link!')
init_hnn_files()
def init(addon):
try:
trans_fname = op.join(mu.get_user_fol(), 'orig_trans.npz')
volumes = glob.glob(
op.join(mu.get_user_fol(), 'freeview', '*+aseg.npy'))
luts = glob.glob(
op.join(mu.get_user_fol(), 'freeview', '*ColorLUT.npz'))
if op.isfile(trans_fname):
WhereAmIPanel.subject_orig_trans = mu.Bag(np.load(trans_fname))
for atlas_vol_fname, atlas_vol_lut_fname in zip(volumes, luts):
atlas = mu.namebase(atlas_vol_fname)[:-len('+aseg')]
WhereAmIPanel.vol_atlas[atlas] = np.load(atlas_vol_fname)
WhereAmIPanel.vol_atlas_lut[atlas] = np.load(atlas_vol_lut_fname)
subjects_dir = mu.get_link_dir(mu.get_links_dir(), 'subjects')
annot_files = glob.glob(
op.join(subjects_dir, mu.get_user(), 'label', 'rh.*.annot'))
if len(annot_files) > 0:
files_names = [mu.namebase(fname)[3:] for fname in annot_files]
items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(
items=items)
bpy.context.scene.subject_annot_files = files_names[0]
else:
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(
items=[])
# bpy.context.scene.subject_annot_files = ''
bpy.context.scene.closest_label_output = ''
bpy.context.scene.new_label_r = 5
mri_data_fname = op.join(mu.get_user_fol(), 'freeview',
'{}_data.npz'.format('mri'))
if op.isfile(mri_data_fname):
WhereAmIPanel.mri_data = mu.Bag(np.load(mri_data_fname))
gray_colormap_fname = op.join(mu.file_fol(), 'color_maps', 'gray.npy')
if op.isfile(gray_colormap_fname):
WhereAmIPanel.gray_colormap = np.load(gray_colormap_fname)
WhereAmIPanel.addon = addon
WhereAmIPanel.init = True
WhereAmIPanel.run_slices_listener = False
init_slices()
if WhereAmIPanel.run_slices_listener:
start_slicer_server()
else:
WhereAmIPanel.slicer_state = slicer.init('mri')
create_slices('mri', bpy.context.scene.cursor_location)
save_slices_cursor_pos()
register()
except:
print("Can't init where-am-I panel!")
print(traceback.format_exc())
def find_closest_label():
subjects_dir = mu.get_link_dir(mu.get_links_dir(), 'subjects')
closest_mesh_name, vertex_ind, vertex_co, _ = \
_addon().find_vertex_index_and_mesh_closest_to_cursor(use_shape_keys=True)
hemi = closest_mesh_name[len('infalted_'):] if _addon().is_inflated(
) else closest_mesh_name
annot_fname = op.join(
subjects_dir, mu.get_user(), 'label',
'{}.{}.annot'.format(hemi, bpy.context.scene.subject_annot_files))
labels = mu.read_labels_from_annot(annot_fname)
vert_labels = [l for l in labels if vertex_ind in l.vertices]
if len(vert_labels) > 0:
label = vert_labels[0]
bpy.context.scene.closest_label_output = label.name
return label.name, hemi
else:
return 'unknown', hemi
def init(addon):
try:
t1_trans_fname = op.join(mu.get_user_fol(), 't1_trans.npz')
if not op.isfile(t1_trans_fname):
# backward compatibility
t1_trans_fname = op.join(mu.get_user_fol(), 'orig_trans.npz')
t2_trans_fname = op.join(mu.get_user_fol(), 't2_trans.npz')
ct_trans_fname = op.join(mu.get_user_fol(), 'ct', 'ct_trans.npz')
volumes = glob.glob(op.join(mu.get_user_fol(), 'freeview', '*+aseg.npy'))
luts = glob.glob(op.join(mu.get_user_fol(), 'freeview', '*ColorLUT.npz'))
if op.isfile(t1_trans_fname):
WhereAmIPanel.subject_t1_trans = mu.Bag(np.load(t1_trans_fname))
if op.isfile(t2_trans_fname):
WhereAmIPanel.subject_t2_trans = mu.Bag(np.load(t2_trans_fname))
if op.isfile(ct_trans_fname):
WhereAmIPanel.subject_ct_trans = mu.Bag(np.load(ct_trans_fname))
for atlas_vol_fname, atlas_vol_lut_fname in zip(volumes, luts):
atlas = mu.namebase(atlas_vol_fname)[:-len('+aseg')]
WhereAmIPanel.vol_atlas[atlas] = np.load(atlas_vol_fname)
WhereAmIPanel.vol_atlas_lut[atlas] = np.load(atlas_vol_lut_fname)
try:
subjects_dir = mu.get_link_dir(mu.get_links_dir(), 'subjects')
annot_files = [mu.namebase(fname)[3:] for fname in glob.glob(
op.join(subjects_dir, mu.get_user(), 'label', 'rh.*.annot'))]
annot_files += [mu.namebase(fname)[3:] for fname in glob.glob(
op.join(mu.get_user_fol(), 'labels', 'rh.*.annot'))]
WhereAmIPanel.annot_files = annot_files = list(set(annot_files))
if len(annot_files) > 0:
items = [(c, c, '', ind) for ind, c in enumerate(annot_files)]
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(
items=items, update=subject_annot_files_update, description='List of different atlases.\n\nCurrent atlas')
ind = mu.index_in_list(bpy.context.scene.atlas, annot_files, 0)
bpy.context.scene.subject_annot_files = annot_files[ind]
else:
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(items=[])
# bpy.context.scene.subject_annot_files = ''
except:
bpy.types.Scene.subject_annot_files = bpy.props.EnumProperty(items=[])
bpy.context.scene.closest_label_output = ''
bpy.context.scene.new_label_r = 5
bpy.context.scene.find_closest_label_on_click = False
bpy.context.scene.plot_closest_label_contour = False
mri_data_fname = op.join(mu.get_user_fol(), 'freeview', 'mri_data.npz')
if op.isfile(mri_data_fname):
WhereAmIPanel.mri_data = mu.Bag(np.load(mri_data_fname))
gray_colormap_fname = op.join(mu.file_fol(), 'color_maps', 'gray.npy')
if op.isfile(gray_colormap_fname):
WhereAmIPanel.gray_colormap = np.load(gray_colormap_fname)
WhereAmIPanel.addon = addon
WhereAmIPanel.init = True
WhereAmIPanel.run_slices_listener = False
init_slices()
if WhereAmIPanel.run_slices_listener:
start_slicer_server()
else:
WhereAmIPanel.slicer_state = mu.Bag({})
WhereAmIPanel.slicer_state['mri'] = slicer.init(_addon(), 'mri')
create_slices(None, bpy.context.scene.cursor_location)
save_slices_cursor_pos()
register()
except:
print("Can't init where-am-I panel!")
print(traceback.format_exc())