def init(addon, first=True):
ScriptsPanel.addon = addon
user_fol = mu.get_user_fol()
scripts_files = glob.glob(op.join(mu.get_mmvt_code_root(), 'src', 'examples', 'scripts', '*.py'))
scripts_files_names = [mu.namebase(f) for f in scripts_files]
scripts_files += [f for f in glob.glob(op.join(mu.get_parent_fol(user_fol), 'scripts', '*.py'))
if mu.namebase(f) not in scripts_files_names]
if len(scripts_files) == 0:
return None
sys.path.append(op.join(mu.get_mmvt_code_root(), 'src', 'examples', 'scripts'))
sys.path.append(op.join(mu.get_parent_fol(user_fol), 'scripts'))
scripts_files = sorted([f for f in scripts_files if check_script(mu.namebase(f))])[::-1]
ScriptsPanel.scripts_names = files_names = [mu.namebase(fname).replace('_', ' ') for fname in scripts_files]
scripts_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.scripts_files = bpy.props.EnumProperty(
items=scripts_items, update=scripts_items_update,
description='List of script in the folder:\n..\mmvt_root\mmvtcode\src\examples\scripts\n\nCurrent script')
bpy.context.scene.scripts_files = files_names[0]
bpy.context.scene.scripts_overwrite = True
try:
bpy.context.scene.report_use_script = bpy.context.scene.reports_files in ScriptsPanel.scripts_names
except:
pass
# bpy.context.scene.scripts_threshold = 2
# bpy.context.scene.scripts_cb_min = 2
# bpy.context.scene.scripts_cb_max = 6
if first:
register()
ScriptsPanel.init = True
def run_ela_alg():
mmvt_code_fol = mu.get_mmvt_code_root()
ela_code_fol = op.join(mu.get_parent_fol(mmvt_code_fol), 'electrodes_rois')
if not op.isdir(ela_code_fol) or not op.isfile(op.join(ela_code_fol, 'find_rois', 'find_rois.py')):
print("Can't find ELA folder!")
return
import importlib
import sys
if ela_code_fol not in sys.path:
sys.path.append(ela_code_fol)
from find_rois import find_rois
importlib.reload(find_rois)
args = find_rois.get_args(['-s', mu.get_user(), '-a', bpy.context.scene.ela_atlas,
'-b', str(bpy.context.scene.ela_bipolar)])
find_rois.run_for_all_subjects(args)
import shutil
ela_output_fname_template = op.join(
ela_code_fol, 'electrodes', '{}_{}_electrodes_cigar_r_*_l_*{}.pkl'.format(
mu.get_user(), bpy.context.scene.ela_atlas, '_bipolar' if bpy.context.scene.ela_bipolar else '' ))
ela_output_fnames = glob.glob(ela_output_fname_template)
if len(ela_output_fnames) > 0:
for ela_output_fname in ela_output_fnames:
shutil.copyfile(ela_output_fname, op.join(
mu.get_user_fol(), 'electrodes', mu.namebase_with_ext(ela_output_fname)))
else:
print('couldn\'t find any ELA output! ({})'.format(ela_output_fname_template))
init(_addon(), False)
def init_electrodes_labeling(addon):
ela_code_fol = op.join(mu.get_parent_fol(mu.get_mmvt_code_root()),
'electrodes_rois')
ElecsPanel.ela_code_exist = op.isfile(
op.join(ela_code_fol, 'find_rois', 'find_rois.py'))
ElecsPanel.labling_files = labling_files = find_elecrode_labeling_files()
if len(labling_files) > 0:
files_names = [
mu.namebase(fname) for fname in labling_files if mu.load(fname)
]
labeling_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.electrodes_labeling_files = bpy.props.EnumProperty(
items=labeling_items,
description='Labeling files',
update=electrodes_labeling_files_update)
bpy.context.scene.electrodes_labeling_files = files_names[0]
# ElecsPanel.electrodes_locs = mu.load(labling_files[0])
# ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.electrodes)
ElecsPanel.faces_verts = addon.get_faces_verts()
atlases = mu.get_annot_files()
if len(atlases) > 0:
ElecsPanel.atlases_exist = True
atlases_items = [(c, c, '', ind) for ind, c in enumerate(atlases)]
bpy.types.Scene.ela_atlas = bpy.props.EnumProperty(
items=atlases_items, description='atlases')
bpy.context.scene.ela_atlas = atlases[0]
bpy.context.scene.ela_bipolar = bpy.context.scene.bipolar
return len(labling_files) > 0
def init(addon):
SlicerPanel.addon = addon
bpy.context.scene.show_full_slice = False
create_joint_brain_obj()
# print('init slicer')
# bpy.context.scene.is_sliced_ind = -1
# bpy.context.scene.last_cursor_location = [0.0, 0.0, 0.0]
bpy.types.Scene.last_cursor_location = bpy.props.FloatVectorProperty(
default=(0.0, 0.0, 0.0), size=3)
bpy.types.Scene.is_sliced_ind = bpy.props.IntProperty(default=-1)
bpy.context.scene.last_cursor_location = (0.0, 0.0, 0.0)
bpy.context.scene.is_sliced_ind = -1
bpy.context.scene.slicer_cut_type = 'coronal'
ct_trans_fname = op.join(mu.get_user_fol(), 'ct', 'ct_trans.npz')
t2_trans_fname = op.join(mu.get_user_fol(), 't2_trans.npz')
if op.isfile(ct_trans_fname) or op.isfile(t2_trans_fname):
items_ind = 1
items = [('mri', 'MRI', '', items_ind)]
if op.isfile(t2_trans_fname):
SlicerPanel.t2_exist = True
items_ind += 1
items.append(('t2', 'T2', '', items_ind))
if op.isfile(ct_trans_fname):
items_ind += 1
SlicerPanel.ct_exist = True
items.append(('ct', 'CT', '', items_ind))
if op.isfile(op.join(mu.get_user_fol(), 'ct', 't1_ct.mgz')):
items_ind += 1
SlicerPanel.t1_ct_exist = True
items.append(('t1_ct', 'T1&CT', '', items_ind))
bpy.types.Scene.slices_modality = bpy.props.EnumProperty(
items=items, update=slices_modality_update)
pial_vol_mask_fname = op.join(mu.get_user_fol(), 'freeview',
'pial_vol_mask.npy')
dural_vol_mask_fname = op.join(mu.get_user_fol(), 'freeview',
'dural_vol_mask.npy')
bpy.context.scene.pial_vol_mask_exist = op.isfile(pial_vol_mask_fname)
bpy.context.scene.dural_vol_mask_exist = op.isfile(dural_vol_mask_fname)
bpy.context.scene.slices_show_pial = False
bpy.context.scene.slices_show_dural = False
bpy.context.scene.slices_modality_mix = 0
bpy.context.scene.slices_zoom = 1
bpy.context.scene.new_electrode_num = 1
bpy.context.scene.slices_zoom_around_voxel = False
bpy.context.scene.slices_zoom_voxels_num = 30
bpy.context.scene.slices_zoom_interpolate = False
bpy.context.scene.slices_plot_cross = True
bpy.context.scene.slices_mark_voxel = True
bpy.context.scene.slices_modality = 'mri'
empty_brain_path = op.join(mu.get_mmvt_code_root(), 'resources',
'empty_subject.blend', 'Material')
for slice_str in ['coronal', 'sagital', 'axial']:
cur_mat_name = '{}_plane_mat'.format(slice_str)
if bpy.data.materials.get(cur_mat_name) is None:
print('Importing {} from empty_brain file'.format(cur_mat_name))
bpy.ops.wm.append(filename=cur_mat_name,
directory=empty_brain_path)
# bpy.context.scene['slice_plane_flipped'] = {'coronal': False, 'axial': False, 'sagital': False}
SlicerPanel.init = True
register()