def get_objects_to_color(self, names, objects_indices):
curves_num = 0
for ind in range(min(self.topK, len(objects_indices))):
orig_name = names[objects_indices[ind]]
if 'unknown' not in orig_name:
obj = bpy.data.objects.get(orig_name)
if not obj is None and not obj.animation_data is None:
curves_num += len(obj.animation_data.action.fcurves)
colors = cu.get_distinct_colors(curves_num)
objects_names, objects_colors, objects_data = defaultdict(
list), defaultdict(list), defaultdict(list)
for ind in range(min(self.topK, len(objects_indices)) - 1, -1, -1):
if bpy.data.objects.get(names[objects_indices[ind]]):
orig_name = names[objects_indices[ind]]
obj_type = mu.check_obj_type(orig_name)
objects_names[obj_type].append(orig_name)
objects_colors[obj_type].append(cu.name_to_rgb('green'))
objects_data[obj_type].append(1.0)
if 'unknown' not in orig_name:
filter_roi_func(orig_name)
for fcurve in bpy.data.objects[
orig_name].animation_data.action.fcurves:
fcurve.color_mode = 'CUSTOM'
fcurve.color = tuple(next(colors))
else:
print("Can't find {}!".format(names[objects_indices[ind]]))
return objects_names, objects_colors, objects_data
def plot_labels_probs(elc):
_addon().init_activity_map_coloring('FMRI')
if bpy.context.scene.electrodes_what_to_color == 'probs':
if len(elc['cortical_rois']) > 0:
hemi = mu.get_obj_hemi(elc['cortical_rois'][0])
if not hemi is None:
labels_data = dict(data=elc['cortical_probs'],
names=elc['cortical_rois'])
if not _addon().colorbar_values_are_locked():
_addon().set_colorbar_title('Electrodes probabilities')
_addon().set_colormap('YlOrRd')
atlas = bpy.context.scene.electrodes_labeling_files.split(
'_')[1:-6][0]
_addon().labels_coloring_hemi(labels_data,
ElecsPanel.faces_verts,
hemi,
0,
colors_min=0,
colors_max=1,
atlas=atlas)
colors = mu.get_distinct_colors(len(elc['cortical_rois']))
if bpy.context.scene.electrodes_label_contours:
_addon().color_contours(elc['cortical_rois'],
specific_colors=colors)
else:
print("Can't get the rois hemi!")
else:
_addon().clear_cortex()
_addon().clear_subcortical_regions()
if len(elc['subcortical_rois']) > 0:
cm = _addon().get_cm()
colors = mu.calc_colors_from_cm(elc['subcortical_probs'], 0, 256,
cm)
for region, color in zip(elc['subcortical_rois'], colors):
_addon().color_subcortical_region(region, color)
elif bpy.context.scene.electrodes_what_to_color == 'verts':
if len(elc['cortical_indices']) > 0:
hemi = bpy.data.objects[elc['hemi']]
if not hemi is None:
_addon().init_activity_map_coloring('FMRI', subcorticals=True)
vertices_num = np.max(elc['cortical_indices']) + 1
activity = np.ones((vertices_num, 4))
activity[:, 0] = 0
activity[elc['cortical_indices'], 0] = 1
activity[elc['cortical_indices'],
1:] = np.tile(cu.name_to_rgb('blue'),
(len(elc['cortical_indices']), 1))
print('Plot {} vertices with blue'.format(
len(elc['cortical_indices'])))
_addon().activity_map_obj_coloring(
hemi, activity, ElecsPanel.faces_verts[elc['hemi']], 0,
True)
else:
print("Can't get the elec's hemi!")
else:
_addon().clear_cortex()
print('No cortical vertices for {}'.format(elc['name']))
def save_colorbar(min_val=None,
max_val=None,
color_map=None,
ticks_num=None,
ticks_font_size=None,
prec=None,
title=None,
background_color_name=None,
colorbar_name='',
fol=''):
org_colorbar_min, org_colorbar_max = (get_colorbar_min(),
get_colorbar_max())
org_background_color = _addon().get_panels_background_color()
if min_val is None:
min_val = get_colorbar_min()
if max_val is None:
max_val = get_colorbar_max()
if color_map is None:
color_map = get_colormap_name()
if ticks_num is None:
ticks_num = get_colorbar_ticks_num()
if ticks_font_size is None:
ticks_font_size = get_cb_ticks_font_size()
if prec is None:
prec = get_colorbar_prec()
if title is None:
title = get_colorbar_title()
if background_color_name is None:
background_color_rgb = _addon().get_background_rgb_string()
else:
background_color_rgb = ','.join(
[str(x) for x in cu.name_to_rgb(background_color_name)])
if colorbar_name == '':
colorbar_name = '{}_colorbar.jpg'.format(color_map)
else:
if not colorbar_name.endswith('.jpg'):
colorbar_name = '{}.jpg'.format(colorbar_name)
if fol == '' or not op.isdir(fol):
fol = _addon().get_output_path()
cb_ticks = ','.join(get_colorbar_ticks(ticks_num, prec, min_val, max_val))
cb_ticks = cb_ticks.replace(
'-', '*') # Bug in argparse. todo: change the , to space
flags = '--colorbar_name "{}" --data_max "{}" --data_min "{}" --colors_map {} --background_color {} '.format(
colorbar_name, max_val, min_val, color_map, background_color_rgb) + \
'--cb_title "{}" --cb_ticks "{}" --cb_ticks_font_size {} --fol "{}"'.format(
title, cb_ticks, ticks_font_size, fol)
mu.run_mmvt_func('src.utils.figures_utils', 'plot_color_bar', flags=flags)
set_colorbar_max_min(org_colorbar_max, org_colorbar_min, force_update=True)
_addon().set_panels_background_color(org_background_color)
def filter_electrode_func(elec_name):
elec_obj = bpy.data.objects[elec_name]
if bpy.context.scene.mark_filter_items:
FilteringMakerPanel.electrodes_colors[elec_name] = FilteringMakerPanel.addon.get_obj_color(elec_obj)
FilteringMakerPanel.addon.object_coloring(elec_obj, cu.name_to_rgb('green'))
else:
elec_obj.active_material.node_tree.nodes["Layer Weight"].inputs[0].default_value = 0.3
# todo: selecting the electrode will show both of their conditions time series
# We don't want it to happen if selection_type == 'conds'...
if bpy.context.scene.selection_type == 'conds' or bpy.context.scene.filter_items_one_by_one:
bpy.data.objects[elec_name].select = True
bpy.context.scene.objects.active = bpy.data.objects[elec_name]
bpy.types.Scene.filter_is_on = True
def filter_rois(self, current_file_to_upload):
print('filter_ROIs')
_addon().show_rois()
source_files = [
op.join(self.current_activity_path,
current_file_to_upload.format(hemi=hemi))
for hemi in mu.HEMIS
]
objects_indices, names, self.filter_values = self.get_object_to_filter(
source_files)
Filtering.objects_indices, Filtering.filter_objects = objects_indices, names
deselect_all_objects()
if bpy.context.scene.selection_type == 'diff':
filter_obj_names = [names[ind] for ind in objects_indices]
brain_obj = bpy.data.objects['Brain']
for fcurve in brain_obj.animation_data.action.fcurves:
con_name = mu.get_fcurve_name(fcurve)
fcurve.hide = con_name not in filter_obj_names
fcurve.select = not fcurve.hide
brain_obj.select = True
curves_num = 0
for ind in range(min(self.topK, len(objects_indices))):
orig_name = names[objects_indices[ind]]
if 'unknown' not in orig_name:
obj = bpy.data.objects.get(orig_name)
if not obj is None and not obj.animation_data is None:
curves_num += len(obj.animation_data.action.fcurves)
colors = cu.get_distinct_colors(curves_num)
objects_names, objects_colors, objects_data = defaultdict(
list), defaultdict(list), defaultdict(list)
for ind in range(min(self.topK, len(objects_indices)) - 1, -1, -1):
if bpy.data.objects.get(names[objects_indices[ind]]):
orig_name = names[objects_indices[ind]]
obj_type = mu.check_obj_type(orig_name)
objects_names[obj_type].append(orig_name)
objects_colors[obj_type].append(cu.name_to_rgb('green'))
objects_data[obj_type].append(1.0)
if 'unknown' not in orig_name:
filter_roi_func(orig_name)
for fcurve in bpy.data.objects[
orig_name].animation_data.action.fcurves:
fcurve.color_mode = 'CUSTOM'
fcurve.color = tuple(next(colors))
else:
print("Can't find {}!".format(names[objects_indices[ind]]))
_addon().color_objects(objects_names, objects_colors, objects_data)
def filter_electrode_func(elec_name):
elec_obj = bpy.data.objects[elec_name]
if bpy.context.scene.mark_filter_items:
FilteringMakerPanel.electrodes_colors[elec_name] = _addon(
).get_obj_color(elec_obj)
_addon().object_coloring(elec_obj, cu.name_to_rgb('green'))
else:
elec_obj.active_material.node_tree.nodes["Layer Weight"].inputs[
0].default_value = 0.3
# todo: selecting the electrode will show both of their conditions time series
# We don't want it to happen if selection_type == 'conds'...
if bpy.context.scene.selection_type == 'conds' or bpy.context.scene.filter_items_one_by_one:
bpy.data.objects[elec_name].select = True
bpy.context.scene.objects.active = bpy.data.objects[elec_name]
bpy.types.Scene.filter_is_on = True
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 plot_labels_probs(elc):
_addon().init_activity_map_coloring('FMRI')
if bpy.context.scene.electrodes_what_to_color == 'probs':
if len(elc['cortical_rois']) > 0:
hemi = mu.get_obj_hemi(elc['cortical_rois'][0])
if not hemi is None:
labels_data = dict(data=elc['cortical_probs'],
names=elc['cortical_rois'])
_addon().set_colorbar_title('Electrodes probabilities')
_addon().set_colormap('YlOrRd')
_addon().labels_coloring_hemi(labels_data,
ElecsPanel.faces_verts,
hemi,
0,
colors_min=0,
colors_max=1)
else:
print("Can't get the rois hemi!")
else:
_addon().clear_cortex()
_addon().clear_subcortical_regions()
if len(elc['subcortical_rois']) > 0:
for region, color in zip(elc['subcortical_rois'],
elc['subcortical_colors'][:, :3]):
_addon().color_subcortical_region(region, color)
elif bpy.context.scene.electrodes_what_to_color == 'verts':
if len(elc['cortical_indices']) > 0:
hemi = bpy.data.objects[elc['hemi']]
if not hemi is None:
_addon().init_activity_map_coloring('FMRI', subcorticals=True)
vertices_num = np.max(elc['cortical_indices']) + 1
activity = np.ones((vertices_num, 4))
activity[:, 0] = 0
activity[elc['cortical_indices'], 0] = 1
activity[elc['cortical_indices'],
1:] = np.tile(cu.name_to_rgb('blue'),
(len(elc['cortical_indices']), 1))
print('Plot {} vertices with blue'.format(
len(elc['cortical_indices'])))
_addon().activity_map_obj_coloring(
hemi, activity, ElecsPanel.faces_verts[elc['hemi']], 0,
True)
else:
print("Can't get the elec's hemi!")
else:
_addon().clear_cortex()
print('No cortical vertices for {}'.format(elc['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_labels_probs(elc):
ElecsPanel.addon.init_activity_map_coloring('FMRI')
if bpy.context.scene.electrodes_what_to_color == 'probs':
if len(elc['cortical_rois']) > 0:
hemi = mu.get_obj_hemi(elc['cortical_rois'][0])
if not hemi is None:
# if no matplotlib should calculate the colors offline :(
labels_data = dict(data=elc['cortical_probs'],
colors=elc['cortical_colors'][:, :3],
names=elc['cortical_rois'])
ElecsPanel.addon.meg_labels_coloring_hemi(
labels_data, ElecsPanel.faces_verts, hemi, 0)
else:
print("Can't get the rois hemi!")
else:
ElecsPanel.addon.clear_cortex()
ElecsPanel.addon.clear_subcortical_regions()
if len(elc['subcortical_rois']) > 0:
for region, color in zip(elc['subcortical_rois'],
elc['subcortical_colors'][:, :3]):
ElecsPanel.addon.color_subcortical_region(region, color)
elif bpy.context.scene.electrodes_what_to_color == 'verts':
if len(elc['cortical_indices']) > 0:
hemi = bpy.data.objects[elc['hemi']]
if not hemi is None:
ElecsPanel.addon.init_activity_map_coloring('FMRI',
subcorticals=True)
vertices_num = np.max(elc['cortical_indices']) + 1
activity = np.ones((vertices_num, 4))
activity[:, 0] = 0
activity[elc['cortical_indices'], 0] = 1
activity[elc['cortical_indices'],
1:] = np.tile(cu.name_to_rgb('blue'),
(len(elc['cortical_indices']), 1))
print('Plot {} vertices with blue'.format(
len(elc['cortical_indices'])))
ElecsPanel.addon.activity_map_obj_coloring(
hemi, activity, ElecsPanel.faces_verts[elc['hemi']], 0,
True)
else:
print("Can't get the elec's hemi!")
else:
ElecsPanel.addon.clear_cortex()
print('No cortical vertices for {}'.format(elc['name']))
def read_groups_labels(colors):
groups_fname = op.join(mu.get_parent_fol(mu.get_user_fol()), '{}_groups.csv'.format(bpy.context.scene.atlas))
if not op.isfile(groups_fname):
return {}
groups = defaultdict(list) # OrderedDict() # defaultdict(list)
color_ind = 0
for line in mu.csv_file_reader(groups_fname):
group_name = line[0]
group_color = line[1]
labels = line[2:]
if group_name[0] == '#':
continue
groups[group_name] = []
for label in labels:
# group_color = cu.name_to_rgb(colors[color_ind])
groups[group_name].append(dict(name=label, color=cu.name_to_rgb(group_color)))
color_ind += 1
order_groups = OrderedDict()
groups_names = sorted(list(groups.keys()))
for group_name in groups_names:
order_groups[group_name] = groups[group_name]
return order_groups
def read_groups_labels(colors):
groups_fname = op.join(mu.get_parent_fol(mu.get_user_fol()), '{}_groups.csv'.format(bpy.context.scene.atlas))
if not op.isfile(groups_fname):
return {}
groups = defaultdict(list) # OrderedDict() # defaultdict(list)
color_ind = 0
for line in mu.csv_file_reader(groups_fname):
group_name = line[0]
group_color = line[1]
labels = line[2:]
if group_name[0] == '#':
continue
groups[group_name] = []
for label in labels:
# group_color = cu.name_to_rgb(colors[color_ind])
groups[group_name].append(dict(name=label, color=cu.name_to_rgb(group_color)))
color_ind += 1
order_groups = OrderedDict()
groups_names = sorted(list(groups.keys()))
for group_name in groups_names:
order_groups[group_name] = groups[group_name]
return order_groups
def plot_labels_probs(elc):
ElecsPanel.addon.init_activity_map_coloring('FMRI')
if bpy.context.scene.electrodes_what_to_color == 'probs':
if len(elc['cortical_rois']) > 0:
hemi = mu.get_obj_hemi(elc['cortical_rois'][0])
if not hemi is None:
# if no matplotlib should calculate the colors offline :(
labels_data = dict(data=elc['cortical_probs'], colors=elc['cortical_colors'][:, :3],
names=elc['cortical_rois'])
ElecsPanel.addon.meg_labels_coloring_hemi(labels_data, ElecsPanel.faces_verts, hemi, 0)
else:
print("Can't get the rois hemi!")
else:
ElecsPanel.addon.clear_cortex()
ElecsPanel.addon.clear_subcortical_regions()
if len(elc['subcortical_rois']) > 0:
for region, color in zip(elc['subcortical_rois'], elc['subcortical_colors'][:, :3]):
ElecsPanel.addon.color_subcortical_region(region, color)
elif bpy.context.scene.electrodes_what_to_color == 'verts':
if len(elc['cortical_indices']) > 0:
hemi = bpy.data.objects[elc['hemi']]
if not hemi is None:
ElecsPanel.addon.init_activity_map_coloring('FMRI', subcorticals=True)
vertices_num = np.max(elc['cortical_indices']) + 1
activity = np.ones((vertices_num, 4))
activity[:, 0] = 0
activity[elc['cortical_indices'], 0] = 1
activity[elc['cortical_indices'], 1:] = np.tile(
cu.name_to_rgb('blue'), (len(elc['cortical_indices']), 1))
print('Plot {} vertices with blue'.format(len(elc['cortical_indices'])))
ElecsPanel.addon.activity_map_obj_coloring(hemi, activity, ElecsPanel.faces_verts[elc['hemi']], 0, True)
else:
print("Can't get the elec's hemi!")
else:
ElecsPanel.addon.clear_cortex()
print('No cortical vertices for {}'.format(elc['name']))
def color_manually():
ColoringMakerPanel.what_is_colored.add(WIC_MANUALLY)
init_activity_map_coloring('FMRI')
subject_fol = mu.get_user_fol()
objects_names, colors, data = defaultdict(list), defaultdict(list), defaultdict(list)
for line in mu.csv_file_reader(op.join(subject_fol, 'coloring', '{}.csv'.format(bpy.context.scene.coloring_files))):
obj_name, color_name = line[0], line[1:]
if obj_name[0] == '#':
continue
if isinstance(color_name, list) and len(color_name) == 1:
color_name = color_name[0]
obj_type = mu.check_obj_type(obj_name)
if isinstance(color_name, str) and color_name.startswith('mark'):
import filter_panel
filter_panel.filter_roi_func(obj_name, mark=color_name)
else:
if isinstance(color_name, str):
color_rgb = cu.name_to_rgb(color_name)
# Check if the color is already in RBG
elif len(color_name) == 3:
color_rgb = color_name
else:
print('Unrecognize color! ({})'.format(color_name))
continue
color_rgb = list(map(float, color_rgb))
if obj_type is not None:
objects_names[obj_type].append(obj_name)
colors[obj_type].append(color_rgb)
data[obj_type].append(1.)
color_objects(objects_names, colors, data)
if op.isfile(op.join(subject_fol, 'coloring', '{}_legend.jpg'.format(bpy.context.scene.coloring_files))):
cmd = '{} -m src.preproc.electrodes_preproc -s {} -a {} -f show_labeling_coloring'.format(
bpy.context.scene.python_cmd, mu.get_user(), bpy.context.scene.atlas)
print('Running {}'.format(cmd))
mu.run_command_in_new_thread(cmd, False)
def color_manually():
ColoringMakerPanel.what_is_colored.add(WIC_MANUALLY)
init_activity_map_coloring('FMRI')
subject_fol = mu.get_user_fol()
objects_names, colors, data = defaultdict(list), defaultdict(list), defaultdict(list)
for line in mu.csv_file_reader(op.join(subject_fol, 'coloring', '{}.csv'.format(bpy.context.scene.coloring_files))):
obj_name, color_name = line[0], line[1:]
if obj_name[0] == '#':
continue
if isinstance(color_name, list) and len(color_name) == 1:
color_name = color_name[0]
obj_type = mu.check_obj_type(obj_name)
if isinstance(color_name, str) and color_name.startswith('mark'):
import filter_panel
filter_panel.filter_roi_func(obj_name, mark=color_name)
else:
if isinstance(color_name, str):
color_rgb = cu.name_to_rgb(color_name)
# Check if the color is already in RBG
elif len(color_name) == 3:
color_rgb = color_name
else:
print('Unrecognize color! ({})'.format(color_name))
continue
color_rgb = list(map(float, color_rgb))
if obj_type is not None:
objects_names[obj_type].append(obj_name)
colors[obj_type].append(color_rgb)
data[obj_type].append(1.)
color_objects(objects_names, colors, data)
if op.isfile(op.join(subject_fol, 'coloring', '{}_legend.jpg'.format(bpy.context.scene.coloring_files))):
cmd = '{} -m src.preproc.electrodes_preproc -s {} -a {} -f show_labeling_coloring'.format(
bpy.context.scene.python_cmd, mu.get_user(), bpy.context.scene.atlas)
print('Running {}'.format(cmd))
mu.run_command_in_new_thread(cmd, False)
def set_colorbar_background_color(color_name):
color_rgb = cu.name_to_rgb(color_name)
_addon().set_panels_background_color(color_rgb)
