def load_connections_file():
d, vertices, vertices_lookup = None, None, None
conn_file_name = bpy.context.scene.connectivity_files.replace(' ', '_')
connectivity_file = op.join(mu.get_user_fol(), 'connectivity', '{}.npz'.format(conn_file_name))
vertices_file = op.join(mu.get_user_fol(), 'connectivity', '{}_vertices.pkl'.format(
conn_file_name.replace('_static', '')))
if op.isfile(connectivity_file):
print('loading connectivity: {}'.format(connectivity_file))
d = mu.Bag(np.load(connectivity_file))
d.labels = [l.astype(str) for l in d.labels]
d.hemis = [l.astype(str) for l in d.hemis]
d.con_names = np.array([l.astype(str) for l in d.con_names], dtype=np.str)
d.conditions = [l.astype(str) for l in d.conditions]
if d.con_values.ndim == 2:
d.con_values = d.con_values[:, :, np.newaxis]
conditions_items = [(cond, cond, '', cond_ind) for cond_ind, cond in enumerate(d.conditions)]
if len(d.conditions) > 1:
diff_cond = '{}-{} difference'.format(d.conditions[0], d.conditions[1])
conditions_items.append((diff_cond, diff_cond, '', len(d.conditions)))
bpy.types.Scene.conditions = bpy.props.EnumProperty(items=conditions_items, description="Conditions")
# bpy.context.scene.connections_max, bpy.context.scene.connections_min = d['data_max'], d['data_min']
else:
print('No connections file! {}'.format(connectivity_file))
if op.isfile(vertices_file):
vertices, vertices_lookup = mu.load(vertices_file)
else:
name_parts = mu.namebase(vertices_file).split('_')
vertices_files = glob.glob(
op.join(mu.get_parent_fol(vertices_file), '{}*_{}.pkl'.format(name_parts[0], name_parts[-1])))
if len(vertices_files) == 1:
vertices, vertices_lookup = mu.load(vertices_files[0])
else:
print('No vertices file! ({})'.format(vertices_file))
ConnectionsPanel.d, ConnectionsPanel.vertices, ConnectionsPanel.vertices_lookup = d, vertices, vertices_lookup
def init_electrodes_labeling(addon):
#todo: this panel should work also without labeling file
labeling_fname = '{}_{}_electrodes_cigar_r_*_l_*{}*.pkl'.format(
mu.get_user(), bpy.context.scene.atlas,
'_bipolar' if bpy.context.scene.bipolar else '')
labling_files = glob.glob(
op.join(mu.get_user_fol(), 'electrodes', labeling_fname))
if not bpy.context.scene.bipolar:
labling_files = [
fname for fname in labling_files if 'bipolar' not in fname
]
if len(labling_files) == 0:
print("!!! Can't find any electrodes labeling file in {} !!!".format(
op.join(mu.get_user_fol(), 'electrodes', labeling_fname)))
else:
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()
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 load_camera(camera_fname=''):
if camera_fname == '':
camera_fname = op.join(mu.get_user_fol(), 'camera',
'{}.pkl'.format(bpy.context.scene.camera_files))
if op.isfile(camera_fname):
camera_name = mu.namebase(camera_fname)
for hemi in mu.HEMIS:
if hemi in camera_name:
_addon().show_hide_hemi(False, hemi)
_addon().show_hide_hemi(True, mu.other_hemi(hemi))
X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(
camera_fname)
RenderFigure.update_camera = False
bpy.context.scene.X_rotation = X_rotation
bpy.context.scene.Y_rotation = Y_rotation
bpy.context.scene.Z_rotation = Z_rotation
bpy.context.scene.X_location = X_location
bpy.context.scene.Y_location = Y_location
bpy.context.scene.Z_location = Z_location
# print('Camera loaded: rotation: {},{},{} locatioin: {},{},{}'.format(
# X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location))
# print('Camera loaded: {}'.format(camera_fname))
RenderFigure.update_camera = True
update_camera()
else:
pass
def _electrodes_labeling_files_update():
labeling_fname = op.join(
mu.get_user_fol(), 'electrodes',
'{}.pkl'.format(bpy.context.scene.electrodes_labeling_files))
ElecsPanel.electrodes_locs = mu.load(labeling_fname)
ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs,
ElecsPanel.all_electrodes)
def electrodes_labeling_files_update(self, context):
# if ElecsPanel.init:
# todo: How to get the other file names?
# list(bpy.types.Scene.electrodes_labeling_files[1].items())[3][1]
labeling_fname = op.join(mu.get_user_fol(), 'electrodes', '{}.pkl'.format(
bpy.context.scene.electrodes_labeling_files))
ElecsPanel.electrodes_locs = mu.load(labeling_fname)
ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.all_electrodes)
def load_clusters_file(clusters_name=''):
if clusters_name == '':
clusters_name = bpy.context.scene.meg_clusters_labels_files
fname = MEGPanel.clusters_labels_fnames[clusters_name]
c = mu.Bag(mu.load(fname))
for ind in range(len(c.values)):
c.values[ind] = mu.Bag(c.values[ind])
return c
def init(addon):
user_fol = mu.get_user_fol()
# clusters_labels_files = glob.glob(op.join(user_fol, 'fmri', 'clusters_labels_*.pkl'))
# old code was saving those files as npy instead of pkl
# clusters_labels_files.extend(glob.glob(op.join(user_fol, 'fmri', 'clusters_labels_*.npy')))
# fmri_blobs = glob.glob(op.join(user_fol, 'fmri', 'blobs_*_rh.npy'))
fMRIPanel.addon = addon
fMRIPanel.lookup, fMRIPanel.clusters_labels = {}, {}
fMRIPanel.cluster_labels = {}
files_names, clusters_labels_files, clusters_labels_items = get_clusters_files(
user_fol)
fMRIPanel.fMRI_clusters_files_exist = len(
files_names) > 0 # and len(fmri_blobs) > 0
if not fMRIPanel.fMRI_clusters_files_exist:
register()
fMRIPanel.init = True
return
# files_names = [mu.namebase(fname)[len('clusters_labels_'):] for fname in clusters_labels_files]
fMRIPanel.clusters_labels_file_names = files_names
bpy.types.Scene.fmri_clusters_labels_files = bpy.props.EnumProperty(
items=clusters_labels_items,
description="fMRI files",
update=fmri_clusters_labels_files_update)
bpy.context.scene.fmri_clusters_labels_files = files_names[0]
bpy.context.scene.plot_fmri_cluster_contours = False
for file_name, clusters_labels_file in zip(files_names,
clusters_labels_files):
# Check if the constrast files exist
if all(
[get_contrast_fname(file_name, hemi) != '' for hemi in mu.HEMIS]):
key = file_name
fMRIPanel.clusters_labels[key] = c = mu.Bag(
mu.load(clusters_labels_file))
for ind in range(len(c.values)):
c.values[ind] = mu.Bag(c.values[ind])
fMRIPanel.lookup[key] = create_lookup_table(
fMRIPanel.clusters_labels[key])
# bpy.context.scene.fmri_cluster_val_threshold = 2
# bpy.context.scene.fmri_cluster_size_threshold = 20
bpy.context.scene.search_closest_cluster_only_in_filtered = True
bpy.context.scene.fmri_what_to_plot = 'blob'
bpy.context.scene.fmri_how_to_sort = 'tval'
bpy.context.scene.plot_current_cluster = True
update_clusters()
fMRIPanel.blobs_activity, _ = calc_blobs_activity(
fMRIPanel.constrast, fMRIPanel.clusters_labels_filtered,
fMRIPanel.colors_in_hemis)
bpy.context.scene.plot_fmri_cluster_per_click = False
fMRIPanel.dont_show_clusters_info = True
# addon.clear_cortex()
register()
fMRIPanel.init = True
def init(addon):
import shutil
ElecsPanel.addon = addon
ElecsPanel.parent = bpy.data.objects.get('Deep_electrodes')
if ElecsPanel.parent is None or len(ElecsPanel.parent.children) == 0:
print("Can't register electrodes panel, no Deep_electrodes object")
return
mu.make_dir(op.join(mu.get_user_fol(), 'electrodes'))
sorted_groups_fname = op.join(mu.get_user_fol(), 'electrodes',
'sorted_groups.pkl')
if not op.isfile(sorted_groups_fname):
# Try to get the file from the subject's root folder
if op.isfile(op.join(mu.get_user_fol(), 'sorted_groups.pkl')):
shutil.move(op.join(mu.get_user_fol(), 'sorted_groups.pkl'),
sorted_groups_fname)
else:
print("Can't register electrodes panel, no sorted groups file")
return
# show_hide_electrodes(True)
ElecsPanel.sorted_groups = mu.load(sorted_groups_fname)
ElecsPanel.groups_hemi = create_groups_hemi_lookup(
ElecsPanel.sorted_groups)
ElecsPanel.all_electrodes = [el.name for el in ElecsPanel.parent.children]
ElecsPanel.groups = create_groups_lookup_table(ElecsPanel.all_electrodes)
ElecsPanel.groups_first_electrode = find_first_electrode_per_group(
ElecsPanel.all_electrodes)
ElecsPanel.groups_electrodes = create_groups_electrodes_lookup(
ElecsPanel.all_electrodes)
init_leads_list()
init_electrodes_list()
ret = init_electrodes_labeling(addon)
if not ret:
print('No electrodes labeling files.')
return
# addon.clear_colors_from_parent_childrens('Deep_electrodes')
# addon.clear_cortex()
bpy.context.scene.show_only_lead = False
bpy.context.scene.listen_to_keyboard = False
bpy.context.scene.listener_is_running = False
bpy.context.scene.show_lh_electrodes = True
bpy.context.scene.show_rh_electrodes = True
_electrodes_labeling_files_update()
if not ElecsPanel.electrodes_locs or not ElecsPanel.lookup:
if not ElecsPanel.electrodes_locs:
print(
"!!! Can't find electrodes labeling files in user/electrdes!")
if not ElecsPanel.lookup:
print('No electrodes lookup table!')
print("!!! Can't plot electrodes' probabilties !!!")
if not ElecsPanel.groups or not ElecsPanel.groups_first_electrode or not ElecsPanel.sorted_groups or \
not ElecsPanel.groups_hemi or not ElecsPanel.groups_electrodes:
print('Error in electrodes panel init!')
else:
register()
ElecsPanel.init = True
def init(addon):
from random import shuffle
ColoringMakerPanel.addon = addon
user_fol = mu.get_user_fol()
ColoringMakerPanel.faces_verts = None
labels_vertices_fname = op.join(user_fol, 'labels_vertices_{}.pkl'.format(bpy.context.scene.atlas))
if not op.isfile(labels_vertices_fname):
print("!!! Can't find {}!".format('labels_vertices_{}.pkl'.format(bpy.context.scene.atlas)))
return None
labels_names, labels_vertices = mu.load(labels_vertices_fname)
ColoringMakerPanel.labels_vertices = dict(labels_names=labels_names, labels_vertices=labels_vertices)
fmri_files = glob.glob(op.join(user_fol, 'fmri', 'fmri_*_lh.npy'))
if len(fmri_files) > 0:
files_names = [mu.namebase(fname)[5:-3] for fname in fmri_files]
clusters_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.fmri_files = bpy.props.EnumProperty(
items=clusters_items, description="fMRI files", update=fmri_files_update)
bpy.context.scene.fmri_files = files_names[0]
for hemi in mu.HEMIS:
ColoringMakerPanel.fMRI[hemi] = np.load('{}_{}.npy'.format(fmri_files[0][:-7], hemi))
electrodes_source_files = glob.glob(op.join(user_fol, 'electrodes', '*_labels_*-rh.npz'))
if len(electrodes_source_files) > 0:
files_names = [mu.namebase(fname)[:-len('-rh')] for fname in electrodes_source_files]
items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.electrodes_sources_files = bpy.props.EnumProperty(
items=items, description="electrodes sources", update=electrodes_sources_files_update)
bpy.context.scene.electrodes_sources_files = files_names[0]
mu.make_dir(op.join(user_fol, 'coloring'))
manually_color_files = glob.glob(op.join(user_fol, 'coloring', '*.csv'))
if len(manually_color_files) > 0:
files_names = [mu.namebase(fname) for fname in manually_color_files]
coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.coloring_files = bpy.props.EnumProperty(items=coloring_items, description="Coloring files")
bpy.context.scene.coloring_files = files_names[0]
vol_color_files = glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv'))
if len(vol_color_files) > 0:
files_names = [mu.namebase(fname) for fname in vol_color_files]
coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.vol_coloring_files = bpy.props.EnumProperty(
items=coloring_items, description="Volumetric Coloring files")
bpy.context.scene.vol_coloring_files = files_names[0]
ColoringMakerPanel.colors = list(set(list(cu.NAMES_TO_HEX.keys())) - set(['black']))
shuffle(ColoringMakerPanel.colors)
ColoringMakerPanel.labels_groups = read_groups_labels(ColoringMakerPanel.colors)
if len(ColoringMakerPanel.labels_groups) > 0:
groups_items = [(gr, gr, '', ind) for ind, gr in enumerate(list(ColoringMakerPanel.labels_groups.keys()))]
bpy.types.Scene.labels_groups = bpy.props.EnumProperty(
items=groups_items, description="Groups")
ColoringMakerPanel.faces_verts = load_faces_verts()
register()
def electrodes_labeling_files_update(self, context):
# if ElecsPanel.init:
# todo: How to get the other file names?
# list(bpy.types.Scene.electrodes_labeling_files[1].items())[3][1]
if ElecsPanel.init:
labeling_fname = op.join(
mu.get_user_fol(), 'electrodes',
'{}.pkl'.format(bpy.context.scene.electrodes_labeling_files))
ElecsPanel.electrodes_locs = mu.load(labeling_fname)
ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs,
ElecsPanel.all_electrodes)
def init_sorted_groups():
import shutil
sorted_groups_fname = op.join(mu.get_user_fol(), 'electrodes', 'sorted_groups.pkl')
if not op.isfile(sorted_groups_fname):
# Try to get the file from the subject's root folder
if op.isfile(op.join(mu.get_user_fol(), 'sorted_groups.pkl')):
shutil.move(op.join(mu.get_user_fol(), 'sorted_groups.pkl'), sorted_groups_fname)
else:
print("electrodes_panel: no sorted groups file")
# return
if op.isfile(sorted_groups_fname):
ElecsPanel.sorted_groups = mu.load(sorted_groups_fname)
def fmri_files_update(self, context):
#todo: there are two frmi files list (the other one in fMRI panel)
user_fol = mu.get_user_fol()
for hemi in mu.HEMIS:
fname = op.join(user_fol, 'fmri', 'fmri_{}_{}.npy'.format(bpy.context.scene.fmri_files, hemi))
ColoringMakerPanel.fMRI[hemi] = np.load(fname)
fmri_data_maxmin_fname = op.join(mu.get_user_fol(), 'fmri', 'fmri_activity_map_minmax_{}.pkl'.format(
bpy.context.scene.fmri_files))
if op.isfile(fmri_data_maxmin_fname):
data_min, data_max = mu.load(fmri_data_maxmin_fname)
ColoringMakerPanel.fmri_activity_colors_ratio = 256 / (data_max - data_min)
ColoringMakerPanel.fmri_activity_data_min = data_min
ColoringMakerPanel.fmri_activity_data_max = data_max
def plot_pathway(self, context, layers_dti, pathway_name, pathway_type):
if pathway_type == TRACULA:
pkl_fname = op.join(SUBJECT_DTI_FOL, TRACULA, '{}{}.pkl'.format(pathway_name, TRACULA_POSTFIX))
mu.create_empty_if_doesnt_exists(pathway_name, DTIPanel.addon.CONNECTIONS_LAYER, None, PARENT_OBJ)
parent_obj = bpy.data.objects[pathway_name]
tracks = mu.load(pkl_fname)
N = len(tracks)
now = time.time()
for ind, track in enumerate(tracks[:1000]):
mu.time_to_go(now, ind, N, 100)
track = track * 0.1
# pprint(track)
cur_obj = mu.create_spline(track, layers_dti, bevel_depth=0.01)
# cur_obj.scale = [0.1] * 3
cur_obj.name = '{}_{}'.format(pathway_name, ind)
cur_obj.parent = parent_obj
def load_camera(camera_fname=''):
if camera_fname == '':
camera_fname = op.join(bpy.path.abspath(bpy.context.scene.output_path), 'camera.pkl')
if op.isfile(camera_fname):
X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(camera_fname)
RenderFigure.update_camera = False
bpy.context.scene.X_rotation = X_rotation
bpy.context.scene.Y_rotation = Y_rotation
bpy.context.scene.Z_rotation = Z_rotation
bpy.context.scene.X_location = X_location
bpy.context.scene.Y_location = Y_location
bpy.context.scene.Z_location = Z_location
RenderFigure.update_camera = True
update_camera()
else:
print('No camera file was found in {}!'.format(camera_fname))
def init_electrodes_labeling(addon):
#todo: this panel should work also without labeling file
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()
return len(labling_files) > 0
def init(addon):
import shutil
ElecsPanel.addon = addon
ElecsPanel.parent = bpy.data.objects.get('Deep_electrodes')
if ElecsPanel.parent is None or len(ElecsPanel.parent.children) == 0:
print("!!!! Can't register electrodes panel, no Deep_electrodes object!!!!")
return
mu.make_dir(op.join(mu.get_user_fol(), 'electrodes'))
sorted_groups_fname = op.join(mu.get_user_fol(), 'electrodes', 'sorted_groups.pkl')
if not op.isfile(sorted_groups_fname):
# Try to get the file from the subject's root folder
if op.isfile(op.join(mu.get_user_fol(), 'sorted_groups.pkl')):
shutil.move(op.join(mu.get_user_fol(), 'sorted_groups.pkl'), sorted_groups_fname)
else:
print("!!!! Can't register electrodes panel, no sorted groups file!!!!")
return
ElecsPanel.sorted_groups = mu.load(sorted_groups_fname)
ElecsPanel.groups_hemi = create_groups_hemi_lookup(ElecsPanel.sorted_groups)
ElecsPanel.all_electrodes = [el.name for el in ElecsPanel.parent.children]
ElecsPanel.groups = create_groups_lookup_table(ElecsPanel.all_electrodes)
ElecsPanel.groups_first_electrode = find_first_electrode_per_group(ElecsPanel.all_electrodes)
ElecsPanel.groups_electrodes = create_groups_electrodes_lookup(ElecsPanel.all_electrodes)
init_leads_list()
init_electrodes_list()
init_electrodes_labeling(addon)
addon.clear_colors_from_parent_childrens('Deep_electrodes')
addon.clear_cortex()
bpy.context.scene.show_only_lead = False
bpy.context.scene.listen_to_keyboard = False
bpy.context.scene.listener_is_running = False
bpy.context.scene.show_lh_electrodes = True
bpy.context.scene.show_rh_electrodes = True
_electrodes_labeling_files_update()
if not ElecsPanel.electrodes_locs or not ElecsPanel.lookup:
if not ElecsPanel.electrodes_locs:
print("!!! Can't find electrodes labeling files in user/electrdes!")
if not ElecsPanel.lookup:
print('No electrodes lookup table!')
print("!!! Can't plot electrodes' probabilties !!!")
if not ElecsPanel.groups or not ElecsPanel.groups_first_electrode or not ElecsPanel.sorted_groups or \
not ElecsPanel.groups_hemi or not ElecsPanel.groups_electrodes:
print('Error in electrodes panel init!')
else:
register()
ElecsPanel.init = True
def load_camera(camera_fname=''):
if camera_fname == '':
camera_fname = op.join(bpy.path.abspath(bpy.context.scene.output_path),
'camera.pkl')
if op.isfile(camera_fname):
X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(
camera_fname)
RenderFigure.update_camera = False
bpy.context.scene.X_rotation = X_rotation
bpy.context.scene.Y_rotation = Y_rotation
bpy.context.scene.Z_rotation = Z_rotation
bpy.context.scene.X_location = X_location
bpy.context.scene.Y_location = Y_location
bpy.context.scene.Z_location = Z_location
RenderFigure.update_camera = True
update_camera()
else:
print('No camera file was found in {}!'.format(camera_fname))
def init_electrodes_labeling(addon):
#todo: this panel should work also without labeling file
labeling_fname = '{}_{}_electrodes_cigar_r_*_l_*{}*.pkl'.format(mu.get_user(), bpy.context.scene.atlas,
'_bipolar' if bpy.context.scene.bipolar else '')
labling_files = glob.glob(op.join(mu.get_user_fol(), 'electrodes', labeling_fname))
if not bpy.context.scene.bipolar:
labling_files = [fname for fname in labling_files if 'bipolar' not in fname]
if len(labling_files) == 0:
print("!!! Can't find any electrodes labeling file in {} !!!".format(
op.join(mu.get_user_fol(), 'electrodes', labeling_fname)))
else:
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()
def find_elecrode_labeling_files():
files = []
blender_electrodes_names = set([o.name for o in bpy.data.objects['Deep_electrodes'].children])
# labeling_template = '{}_{}_electrodes_cigar_r_*_l_*.pkl'.format(mu.get_user(), bpy.context.scene.atlas)
labeling_template = '{}_*_electrodes_cigar_r_*_l_*.pkl'.format(mu.get_user(), bpy.context.scene.atlas)
labling_files = glob.glob(op.join(mu.get_user_fol(), 'electrodes', labeling_template))
for labling_file in labling_files:
try:
d = mu.load(labling_file)
electrodes_names = set([e['name'] for e in d])
# todo: find what is the problem... (mg96)
# if len(electrodes_names - blender_electrodes_names) == 0:
files.append(labling_file)
except:
print('Error reading {}'.format(labling_file))
continue
if len(files) == 0:
print("Can't find any labeling file that match the electrodes names in{}!".format(
op.join(mu.get_user_fol(), 'electrodes')))
return files
def plot_tracks():
tracks_name = bpy.context.scene.dti_tracks
tracks_fname = op.join(SUBJECT_DTI_FOL, '{}_tracks.npy'.format(tracks_name))
tracks_header = op.join(SUBJECT_DTI_FOL, '{}_header.pkl'.format(tracks_name))
world_matrix = mu.get_matrix_world()
tracks = np.load(tracks_fname) * 0.1
header = mu.load(tracks_header)
layers_dti = [False] * 20
dti_layer = DTIPanel.addon.CONNECTIONS_LAYER
layers_dti[dti_layer] = True
mu.create_empty_if_doesnt_exists(tracks_name, DTIPanel.addon.CONNECTIONS_LAYER, None, PARENT_OBJ)
parent_obj = bpy.data.objects[tracks_name]
# N = len(tracks)
# now = time.time()
# for ind, track in enumerate(tracks):
# mu.time_to_go(now, ind, N, 100)
cur_obj = mu.create_spline(tracks, layers_dti, bevel_depth=0.01)
cur_obj.name = tracks_name
cur_obj.parent = parent_obj
def load_camera(camera_fname=''):
if camera_fname == '':
camera_fname = op.join(mu.get_user_fol(), 'camera', '{}.pkl'.format(bpy.context.scene.camera_files))
if op.isfile(camera_fname):
camera_name = mu.namebase(camera_fname)
for hemi in mu.HEMIS:
if hemi in camera_name:
_addon().show_hide_hemi(False, hemi)
_addon().show_hide_hemi(True, mu.other_hemi(hemi))
X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(camera_fname)
RenderFigure.update_camera = False
bpy.context.scene.X_rotation = X_rotation
bpy.context.scene.Y_rotation = Y_rotation
bpy.context.scene.Z_rotation = Z_rotation
bpy.context.scene.X_location = X_location
bpy.context.scene.Y_location = Y_location
bpy.context.scene.Z_location = Z_location
RenderFigure.update_camera = True
update_camera()
else:
print('No camera file was found in {}!'.format(camera_fname))
def find_point_thickness():
vertex_ind, closest_mesh_name = _addon().snap_cursor()
vertex_co = bpy.data.objects['inner_skull'].data.vertices[vertex_ind].co
distances = np.load(op.join(mu.get_user_fol(), 'skull', 'ray_casts.npy'))
rays_info = mu.load(
op.join(mu.get_user_fol(), 'skull', 'ray_casts_info.pkl'))
# closest_mesh_name, vertex_ind, vertex_co, _ = _addon().find_vertex_index_and_mesh_closest_to_cursor(
# objects_names=['inner_skull'])
# distance = np.linalg.norm(f.intersections[vertex_ind, 0] - f.intersections[vertex_ind, 1])
distance = distances[vertex_ind][0]
(hit, loc, norm, index) = rays_info[vertex_ind]
# bpy.context.scene.cursor_location = vertex_co
print(closest_mesh_name, vertex_ind, vertex_co, distance, loc)
SkullPanel.vertex_skull_thickness = distance
if not bpy.context.scene.thickness_arrows and bpy.context.scene.show_point_arrow:
if SkullPanel.prev_vertex_arrow is not None:
SkullPanel.prev_vertex_arrow.hide = True
vertex_arrow = bpy.data.objects.get('mt_{}'.format(vertex_ind), None)
if vertex_arrow is not None:
vertex_arrow.hide = False
SkullPanel.prev_vertex_arrow = vertex_arrow
def init(addon):
from random import shuffle
ColoringMakerPanel.addon = addon
user_fol = mu.get_user_fol()
ColoringMakerPanel.faces_verts = None
labels_vertices_fname = op.join(user_fol, 'labels_vertices_{}.pkl'.format(bpy.context.scene.atlas))
if not op.isfile(labels_vertices_fname):
print("!!! Can't find {}!".format('labels_vertices_{}.pkl'.format(bpy.context.scene.atlas)))
return None
labels_names, labels_vertices = mu.load(labels_vertices_fname)
ColoringMakerPanel.labels_vertices = dict(labels_names=labels_names, labels_vertices=labels_vertices)
ColoringMakerPanel.max_labels_vertices_num = {}
meg_files_exist = mu.hemi_files_exists(op.join(user_fol, 'activity_map_{hemi}', 't0.npy'))
meg_data_maxmin_fname = op.join(mu.get_user_fol(), 'meg_activity_map_minmax.pkl')
if meg_files_exist and op.isfile(meg_data_maxmin_fname):
data_min, data_max = mu.load(meg_data_maxmin_fname)
ColoringMakerPanel.meg_activity_colors_ratio = 256 / (data_max - data_min)
ColoringMakerPanel.meg_activity_data_min = data_min
ColoringMakerPanel.meg_activity_data_max = data_max
print('data meg: {}-{}'.format(data_min, data_max))
_addon().set_colorbar_max_min(data_max, data_min, True)
_addon().set_colorbar_title('MEG')
fmri_files = glob.glob(op.join(user_fol, 'fmri', 'fmri_*_lh.npy'))
if len(fmri_files) > 0:
files_names = [mu.namebase(fname)[5:-3] for fname in fmri_files]
clusters_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.fmri_files = bpy.props.EnumProperty(
items=clusters_items, description="fMRI files", update=fmri_files_update)
bpy.context.scene.fmri_files = files_names[0]
for hemi in mu.HEMIS:
ColoringMakerPanel.fMRI[hemi] = np.load('{}_{}.npy'.format(fmri_files[0][:-7], hemi))
# Check separately for each contrast
fmri_data_maxmin_fname = op.join(mu.get_user_fol(), 'fmri', 'fmri_activity_map_minmax.pkl')
if op.isfile(fmri_data_maxmin_fname):
data_min, data_max = mu.load(fmri_data_maxmin_fname)
ColoringMakerPanel.fmri_activity_colors_ratio = 256 / (data_max - data_min)
ColoringMakerPanel.fmri_activity_data_min = data_min
ColoringMakerPanel.fmri_activity_data_max = data_max
electrodes_source_files = glob.glob(op.join(user_fol, 'electrodes', '*_labels_*-rh.npz'))
if len(electrodes_source_files) > 0:
files_names = [mu.namebase(fname)[:-len('-rh')] for fname in electrodes_source_files]
items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.electrodes_sources_files = bpy.props.EnumProperty(
items=items, description="electrodes sources", update=electrodes_sources_files_update)
bpy.context.scene.electrodes_sources_files = files_names[0]
mu.make_dir(op.join(user_fol, 'coloring'))
manually_color_files = glob.glob(op.join(user_fol, 'coloring', '*.csv'))
if len(manually_color_files) > 0:
files_names = [mu.namebase(fname) for fname in manually_color_files]
coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.coloring_files = bpy.props.EnumProperty(items=coloring_items, description="Coloring files")
bpy.context.scene.coloring_files = files_names[0]
vol_color_files = glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv'))
if len(vol_color_files) > 0:
files_names = [mu.namebase(fname) for fname in vol_color_files]
coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.vol_coloring_files = bpy.props.EnumProperty(
items=coloring_items, description="Volumetric Coloring files")
bpy.context.scene.vol_coloring_files = files_names[0]
ColoringMakerPanel.colors = list(set(list(cu.NAMES_TO_HEX.keys())) - set(['black']))
shuffle(ColoringMakerPanel.colors)
ColoringMakerPanel.labels_groups = read_groups_labels(ColoringMakerPanel.colors)
if len(ColoringMakerPanel.labels_groups) > 0:
groups_items = [(gr, gr, '', ind) for ind, gr in enumerate(list(ColoringMakerPanel.labels_groups.keys()))]
bpy.types.Scene.labels_groups = bpy.props.EnumProperty(
items=groups_items, description="Groups")
ColoringMakerPanel.faces_verts = load_faces_verts()
bpy.context.scene.coloring_meg_subcorticals = False
# ColoringMakerPanel.cm = np.load(op.join(mu.file_fol(), 'color_maps', 'BuPu_YlOrRd.npy'))
register()
def init(addon):
from random import shuffle
ColoringMakerPanel.addon = addon
user_fol = mu.get_user_fol()
ColoringMakerPanel.faces_verts = None
labels_vertices_fname = op.join(user_fol, 'labels_vertices_{}.pkl'.format(bpy.context.scene.atlas))
if not op.isfile(labels_vertices_fname):
print("!!! Can't find {}!".format('labels_vertices_{}.pkl'.format(bpy.context.scene.atlas)))
return None
labels_names, labels_vertices = mu.load(labels_vertices_fname)
ColoringMakerPanel.labels_vertices = dict(labels_names=labels_names, labels_vertices=labels_vertices)
meg_files_exist = mu.hemi_files_exists(op.join(user_fol, 'activity_map_{hemi}', 't0.npy'))
if meg_files_exist:
data_min, data_max = mu.load(op.join(mu.get_user_fol(), 'meg_activity_map_minmax.pkl'))
ColoringMakerPanel.meg_activity_colors_ratio = 256 / (data_max - data_min)
ColoringMakerPanel.meg_activity_data_min = data_min
print('data meg: {}-{}'.format(data_min, data_max))
fmri_files = glob.glob(op.join(user_fol, 'fmri', 'fmri_*_lh.npy'))
if len(fmri_files) > 0:
files_names = [mu.namebase(fname)[5:-3] for fname in fmri_files]
clusters_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.fmri_files = bpy.props.EnumProperty(
items=clusters_items, description="fMRI files", update=fmri_files_update)
bpy.context.scene.fmri_files = files_names[0]
for hemi in mu.HEMIS:
ColoringMakerPanel.fMRI[hemi] = np.load('{}_{}.npy'.format(fmri_files[0][:-7], hemi))
electrodes_source_files = glob.glob(op.join(user_fol, 'electrodes', '*_labels_*-rh.npz'))
if len(electrodes_source_files) > 0:
files_names = [mu.namebase(fname)[:-len('-rh')] for fname in electrodes_source_files]
items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.electrodes_sources_files = bpy.props.EnumProperty(
items=items, description="electrodes sources", update=electrodes_sources_files_update)
bpy.context.scene.electrodes_sources_files = files_names[0]
mu.make_dir(op.join(user_fol, 'coloring'))
manually_color_files = glob.glob(op.join(user_fol, 'coloring', '*.csv'))
if len(manually_color_files) > 0:
files_names = [mu.namebase(fname) for fname in manually_color_files]
coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.coloring_files = bpy.props.EnumProperty(items=coloring_items, description="Coloring files")
bpy.context.scene.coloring_files = files_names[0]
vol_color_files = glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv'))
if len(vol_color_files) > 0:
files_names = [mu.namebase(fname) for fname in vol_color_files]
coloring_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.vol_coloring_files = bpy.props.EnumProperty(
items=coloring_items, description="Volumetric Coloring files")
bpy.context.scene.vol_coloring_files = files_names[0]
ColoringMakerPanel.colors = list(set(list(cu.NAMES_TO_HEX.keys())) - set(['black']))
shuffle(ColoringMakerPanel.colors)
ColoringMakerPanel.labels_groups = read_groups_labels(ColoringMakerPanel.colors)
if len(ColoringMakerPanel.labels_groups) > 0:
groups_items = [(gr, gr, '', ind) for ind, gr in enumerate(list(ColoringMakerPanel.labels_groups.keys()))]
bpy.types.Scene.labels_groups = bpy.props.EnumProperty(
items=groups_items, description="Groups")
ColoringMakerPanel.faces_verts = load_faces_verts()
ColoringMakerPanel.cm = np.load(op.join(mu.file_fol(), 'color_maps', 'BuPu_YlOrRd.npy'))
register()
def _electrodes_labeling_files_update():
labeling_fname = op.join(mu.get_user_fol(), 'electrodes', '{}.pkl'.format(
bpy.context.scene.electrodes_labeling_files))
ElecsPanel.electrodes_locs = mu.load(labeling_fname)
ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.all_electrodes)