def save_cycle():
if bpy.context.scene.save_streaming:
streaming_fol = datetime.strftime(datetime.now(), '%Y-%m-%d')
output_fol = op.join(mu.get_user_fol(), 'electrodes', 'streaming', streaming_fol)
output_fname = 'streaming_data_{}.npy'.format(datetime.strftime(datetime.now(), '%H-%M-%S'))
mu.make_dir(output_fol)
np.save(op.join(output_fol, output_fname), StreamingPanel.cycle_data)
def init(addon):
LoadResultsPanel.addon = addon
mu.make_dir(op.join(mu.get_user_fol(), 'meg'))
bpy.context.scene.nii_label_prompt = ''
bpy.context.scene.nii_label_output = ''
register()
LoadResultsPanel.init = True
def init(addon):
RenderingMakerPanel.addon = addon
bpy.data.objects['Target'].rotation_euler.x = 0
bpy.data.objects['Target'].rotation_euler.y = 0
bpy.data.objects['Target'].rotation_euler.z = 0
bpy.data.objects['Target'].location.x = 0
bpy.data.objects['Target'].location.y = 0
bpy.data.objects['Target'].location.z = 0
mu.make_dir(op.join(mu.get_user_fol(), 'camera'))
grab_camera(overwrite=False)
update_camera_files()
bpy.context.scene.in_camera_view = False
bpy.context.scene.save_selected_view = False
bpy.context.scene.view_distance = 17.36
bpy.context.scene.render.resolution_percentage = 100
bpy.context.scene.render.image_settings.file_format = 'JPEG'
# bpy.context.scene.lighting = 1.0
RenderingMakerPanel.queue = PriorityQueue()
mu.make_dir(op.join(mu.get_user_fol(), 'logs'))
logging.basicConfig(
filename=op.join(mu.get_user_fol(), 'logs', 'reander_panel.log'),
level=logging.DEBUG,
format='%(asctime)-15s %(levelname)8s %(name)s %(message)s')
RenderingMakerPanel.init = True
register()
def run_faulthandler():
import faulthandler
logs = op.join(mmvt_utils.get_user_fol(), 'logs')
mmvt_utils.make_dir(logs)
fault_handler = open(
op.join(logs,
'faulthandler_{}.txt'.format(mmvt_utils.rand_letters(5))), 'w')
faulthandler.enable(fault_handler)
def load_surf_files(nii_fname, run_fmri_preproc=True, user_fol='', debug=True):
fmri_file_template = ''
if user_fol == '':
user_fol = mu.get_user_fol()
nii_fol = mu.get_fname_folder(nii_fname)
if debug:
print('load_surf_files: nii_fol: {}'.format(nii_fol))
hemi, fmri_hemis = mu.get_hemi_from_full_fname(nii_fname)
if debug:
print('load_surf_files: hemi, fmri_hemis: {}, {}'.format(
hemi, fmri_hemis))
if hemi == '':
hemi = mu.find_hemi_using_vertices_num(nii_fname)
if hemi == '':
return ''
# fmri_hemis = mu.get_both_hemis_files(nii_fname)
local_fname = build_local_fname(nii_fname, user_fol)
if debug:
print('load_surf_files: local_fname: {}'.format(local_fname))
mu.make_dir(op.join(user_fol, 'fmri'))
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(nii_fname, local_fname, True)
other_hemi = mu.other_hemi(hemi)
if debug:
print('load_surf_files: other_hemi: {}'.format(other_hemi))
other_hemi_fname = fmri_hemis[other_hemi]
if other_hemi_fname == '':
other_hemi_fname = local_fname.replace(hemi, other_hemi)
if debug:
print('load_surf_files: other_hemi_fname: {}'.format(other_hemi_fname))
# todo: if the other hemi file doens't exist, just create an empty one
output_fname_template = ''
if op.isfile(other_hemi_fname):
local_other_hemi_fname = build_local_fname(other_hemi_fname, user_fol)
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(other_hemi_fname, local_other_hemi_fname, True)
fmri_file_template = mu.get_template_hemi_label_name(
mu.namebase_with_ext(local_fname))
if run_fmri_preproc:
mu.add_mmvt_code_root_to_path()
from src.preproc import fMRI
importlib.reload(fMRI)
vertices_num = mu.get_vertices_num()
ret, npy_output_fname_template = fMRI.load_surf_files(
mu.get_user(), fmri_hemis, vertices_num=vertices_num)
output_fname_template = op.join(
mu.get_parent_fol(npy_output_fname_template),
mu.namebase_with_ext(npy_output_fname_template)[len('fmri_'):])
else:
mu.run_mmvt_func(
'src.preproc.fMRI',
'load_surf_files',
flags='--fmri_file_template "{}"'.format(fmri_file_template))
# todo: find what should be the output_fname_template
else:
print(
"Couldn't find the other hemi file! ({})".format(other_hemi_fname))
return output_fname_template #, hemi, other_hemi
def run_faulthandler():
try:
import faulthandler
logs = op.join(mmvt_utils.get_user_fol(), 'logs')
mmvt_utils.make_dir(logs)
fault_handler = open(op.join(logs, 'faulthandler_{}.txt'.format(mmvt_utils.rand_letters(5))), 'w')
faulthandler.enable(fault_handler)
except:
print('Cannot create faulthandler log!')
mmvt_utils.print_last_error_line()
def export_electrodes():
import csv
mu.make_dir(op.join(mu.get_user_fol(), 'electrodes'))
csv_fname = op.join(mu.get_user_fol(), 'electrodes', '{}_RAS.csv'.format(mu.get_user()))
electrodes = [e for e in bpy.data.objects[_addon().electrodes_panel_parent].children]
with open(csv_fname, 'w') as csv_file:
wr = csv.writer(csv_file, quoting=csv.QUOTE_ALL)
wr.writerow(['Electrode Name','R','A','S'])
for elc in electrodes:
wr.writerow([elc.name, *['{:.2f}'.format(loc * 10) for loc in elc.location]])
def init(addon, do_register=True):
ElecsPanel.init = False
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'))
init_sorted_groups()
# show_hide_electrodes(True)
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()
ret = init_electrodes_list()
# if not ret:
# return
ret = init_electrodes_labeling(addon)
if ret:
ElecsPanel.electrodes_labeling_file_exist = True
_electrodes_labeling_files_update()
else:
ElecsPanel.electrodes_labeling_file_exist = False
print('No electrodes labeling files.')
# 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
bpy.context.scene.show_ela = False
bpy.context.scene.electrode_rotate = False
bpy.context.scene.electrodes_more_settings = False
bpy.context.scene.electrodes_create_curved_leads = False
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:
if do_register:
register()
ElecsPanel.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 save_cursor_position(pos=None):
# _addon().create_slices(pos=pos) # Don't call here create_slices!!!
pos = mathutils.Vector(pos) if not pos is None else bpy.context.scene.cursor_location
root = mu.get_user_fol()
point = pos * 10.0
freeview_cmd = 'freeview --ras {} {} {} tkreg\n'.format(point[0], point[1], point[2]) # .encode()
if FreeviewPanel.freeview_in_queue:
FreeviewPanel.freeview_in_queue.put(freeview_cmd)
freeview_fol = op.join(root, 'freeview')
mu.make_dir(freeview_fol)
# print('Cursor was saved in {}'.format(op.join(freeview_fol, 'edit.dat')))
np.savetxt(op.join(freeview_fol, 'edit.dat'), point)
def save_cursor_position():
root = mu.get_user_fol()
point = bpy.context.scene.cursor_location * 10.0
freeview_cmd = 'freeview --ras {} {} {} tkreg\n'.format(point[0], point[1], point[2]) # .encode()
if FreeviewPanel.freeview_in_queue:
FreeviewPanel.freeview_in_queue.put(freeview_cmd)
freeview_fol = op.join(root, 'freeview')
mu.make_dir(freeview_fol)
np.savetxt(op.join(freeview_fol, 'edit.dat'), point)
cursor_position = np.array(bpy.context.scene.cursor_location) * 10
ret = mu.conn_to_listener.send_command(dict(cmd='slice_viewer_change_pos',data=dict(
position=cursor_position)))
def init(addon_prefs):
set_play_to(get_max_time_steps())
mmvt_utils.view_all_in_graph_editor(bpy.context)
bpy.context.window.screen = bpy.data.screens['Neuro']
bpy.context.scene.atlas = mmvt_utils.get_atlas()
bpy.context.scene.python_cmd = addon_prefs.python_cmd
# set default values
figures_fol = op.join(mmvt_utils.get_user_fol(), 'figures')
mmvt_utils.make_dir(figures_fol)
set_render_output_path(figures_fol)
set_render_quality(60)
mmvt_utils.set_show_textured_solid()
code_fol = mmvt_utils.get_parent_fol(mmvt_utils.get_parent_fol())
os.chdir(code_fol)
def save_cursor_position():
root = mu.get_user_fol()
point = bpy.context.scene.cursor_location * 10.0
freeview_cmd = 'freeview --ras {} {} {} tkreg\n'.format(
point[0], point[1], point[2]) # .encode()
if FreeviewPanel.freeview_in_queue:
FreeviewPanel.freeview_in_queue.put(freeview_cmd)
freeview_fol = op.join(root, 'freeview')
mu.make_dir(freeview_fol)
np.savetxt(op.join(freeview_fol, 'edit.dat'), point)
cursor_position = np.array(bpy.context.scene.cursor_location) * 10
ret = mu.conn_to_listener.send_command(
dict(cmd='slice_viewer_change_pos',
data=dict(position=cursor_position)))
def init(addon_prefs):
set_play_to(get_max_time_steps())
mmvt_utils.view_all_in_graph_editor(bpy.context)
bpy.context.window.screen = bpy.data.screens['Neuro']
bpy.context.scene.atlas = mmvt_utils.get_atlas()
bpy.context.scene.python_cmd = addon_prefs.python_cmd
# set default values
figures_fol = op.join(mmvt_utils.get_user_fol(), 'figures')
mmvt_utils.make_dir(figures_fol)
set_render_output_path(figures_fol)
set_render_quality(60)
mmvt_utils.set_show_textured_solid()
mmvt_utils.hide_relationship_lines()
code_fol = mmvt_utils.get_parent_fol(mmvt_utils.get_parent_fol())
os.chdir(code_fol)
def init_labels_data_files():
user_fol = mu.get_user_fol()
mu.make_dir(op.join(user_fol, 'labels', 'labels_data'))
LabelsPanel.labels_data_files = labels_data_files = \
glob.glob(op.join(user_fol, 'labels', 'labels_data', '*.npz')) + \
glob.glob(op.join(user_fol, 'labels', 'labels_data', '*.mat'))
if len(labels_data_files) > 0:
files_names = [
mu.namebase(fname).replace('_', ' ') for fname in labels_data_files
]
labels_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.labels_data_files = bpy.props.EnumProperty(
items=labels_items,
description="label files",
update=labels_data_files_update)
bpy.context.scene.labels_data_files = files_names[0]
def init_pizco(mmvt):
log_fname = op.join(mu.make_dir(op.join(mu.get_user_fol(), 'logs')),
'pizco.log')
if op.isfile(log_fname):
try:
os.remove(log_fname)
except:
print('Can\'t remove {}'.format(log_fname))
for k in range(10):
try:
bpy.context.scene.pizco_server_address = 'tcp://127.0.0.1:800{}'.format(
str(k))
MMVT_Server(mmvt, bpy.context.scene.pizco_server_address)
pizco_exist = True
try:
with open(log_fname, 'w') as log:
log.write(bpy.context.scene.pizco_server_address)
except:
print('Can\'t write to {}'.format(log_fname))
break
except:
# print('No pizco')
# print(traceback.format_exc())
pizco_exist = False
if not pizco_exist:
print('No pizco')
return pizco_exist
def init_labels_data_files():
user_fol = mu.get_user_fol()
mu.make_dir(op.join(user_fol, 'labels', 'labels_data'))
LabelsPanel.labels_data_files = labels_data_files = \
glob.glob(op.join(user_fol, 'labels', 'labels_data', '*.npz')) + \
glob.glob(op.join(user_fol, 'labels', 'labels_data', '*.mat'))
try:
if len(labels_data_files) > 0:
files_names = [mu.namebase(fname).replace('_', ' ') for fname in labels_data_files]
labels_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.labels_data_files = bpy.props.EnumProperty(
items=labels_items, update=labels_data_files_update,
description='Selects labels file from the subject’s labels folder:'
'\n../mmvt_root/mmvt_blend/colin27/labels/labels_data\n\nCurrent file')
bpy.context.scene.labels_data_files = files_names[0]
except:
print('init_labels_data_files: Error!')
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 init(addon):
RenderingMakerPanel.addon = addon
bpy.data.objects['Target'].rotation_euler.x = 0
bpy.data.objects['Target'].rotation_euler.y = 0
bpy.data.objects['Target'].rotation_euler.z = 0
bpy.data.objects['Target'].location.x = 0
bpy.data.objects['Target'].location.y = 0
bpy.data.objects['Target'].location.z = 0
mu.make_dir(op.join(mu.get_user_fol(), 'camera'))
grab_camera()
update_camera_files()
# bpy.context.scene.lighting = 1.0
RenderingMakerPanel.queue = PriorityQueue()
mu.make_dir(op.join(mu.get_user_fol(), 'logs'))
logging.basicConfig(
filename=op.join(mu.get_user_fol(), 'logs', 'reander_panel.log'),
level=logging.DEBUG, format='%(asctime)-15s %(levelname)8s %(name)s %(message)s')
register()
def main(addon_prefs=None):
show_electrodes(False)
show_connections(False)
mmvt_utils.view_all_in_graph_editor(bpy.context)
bpy.context.window.screen = bpy.data.screens['Neuro']
bpy.context.scene.atlas = mmvt_utils.get_atlas()
bpy.context.scene.python_cmd = addon_prefs.python_cmd
# set default values
figures_fol = op.join(mmvt_utils.get_user_fol(), 'figures')
mmvt_utils.make_dir(figures_fol)
set_render_output_path(figures_fol)
set_render_quality(60)
code_fol = mmvt_utils.get_parent_fol(mmvt_utils.get_parent_fol())
os.chdir(code_fol)
try:
# _listener_in_queue, _listener__out_queue = start_listener()
current_module = sys.modules[__name__]
appearance_panel.init(current_module)
show_hide_panel.init(current_module)
selection_panel.init(current_module)
coloring_panel.init(current_module)
electrodes_panel.init(current_module)
play_panel.init(current_module)
filter_panel.init(current_module)
freeview_panel.init(current_module, addon_prefs)
render_panel.init(current_module)
fMRI_panel.init(current_module)
search_panel.init(current_module)
transparency_panel.init(current_module)
where_am_i_panel.init(current_module)
data_panel.init(current_module)
stim_panel.init(current_module)
dti_panel.init(current_module)
connections_panel.init(current_module)
# listener_panel.init(current_module)
vertex_data_panel.init(current_module)
except:
print('The classes are already registered!')
print(traceback.format_exc())
show_activity()
def init(addon):
if not bpy.data.objects.get('full_colorbar', None):
print("No full_colorbar object, Can't load the colorbar panel")
return
ColorbarPanel.addon = addon
colorbar_files_fol = mu.make_dir(
op.join(mu.get_parent_fol(mu.get_user_fol()), 'color_maps'))
colorbar_files_code_fol = op.join(mu.get_resources_dir(), 'color_maps')
colorbar_files_template = op.join(colorbar_files_fol, '*.npy')
colorbar_files_code_template = op.join(colorbar_files_code_fol, '*.npy')
# colorbar_files_template = op.join(mu.file_fol(), 'color_maps', '*.npy')
colorbar_files = glob.glob(colorbar_files_template)
colorbar_code_files = glob.glob(colorbar_files_code_template)
extra_files = list(
set([mu.namebase_with_ext(f) for f in colorbar_code_files]) -
set([mu.namebase_with_ext(f) for f in colorbar_files]))
for extra_file in extra_files:
print('Coping missing cb file: {}'.format(
mu.namebase_with_ext(extra_file)))
shutil.copyfile(
op.join(colorbar_files_code_fol, extra_file),
op.join(colorbar_files_fol, mu.namebase_with_ext(extra_file)))
if len(colorbar_files) == 0:
print("No colorbar files ({}), Can't load the colorbar panel".format(
colorbar_files_template))
return None
colorbar_files = glob.glob(colorbar_files_template)
files_names = [mu.namebase(fname)
for fname in colorbar_files] # .replace('_', '-')
ColorbarPanel.maps_names = files_names
colorbar_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.colorbar_files = bpy.props.EnumProperty(
items=colorbar_items,
update=colormap_update,
description='Selects the colorbar color palette.\n\nCurrent palette')
if not colorbar_values_are_locked():
bpy.context.scene.colorbar_files = files_names[0]
else:
load_colormap()
for space in mu.get_3d_spaces():
if space.lock_object and space.lock_object.name == 'full_colorbar':
space.show_only_render = True
register()
ColorbarPanel.init = True
bpy.context.scene.show_cb_in_render = False
mu.select_hierarchy('colorbar_camera', False, False)
if not ColorbarPanel.colorbar_updated and not colorbar_values_are_locked():
ColorbarPanel.should_not_lock_values = True
# bpy.context.scene.colorbar_min = -1
# bpy.context.scene.colorbar_max = 1
# bpy.context.scene.colorbar_title = ' MEG'
bpy.context.scene.colorbar_y = 0.18
bpy.context.scene.colorbar_text_y = -1.53
bpy.context.scene.colorbar_prec = 2
ColorbarPanel.should_not_lock_values = False
def load_surf_files(nii_fname):
fmri_file_template = ''
user_fol = mu.get_user_fol()
nii_fol = mu.get_fname_folder(nii_fname)
fmri_hemis = mu.get_both_hemis_files(nii_fname)
hemi = mu.get_hemi_from_full_fname(nii_fname)
local_fname = build_local_fname(nii_fname, user_fol)
mu.make_dir(op.join(user_fol, 'fmri'))
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(nii_fname, local_fname, True)
other_hemi = mu.other_hemi(hemi)
other_hemi_fname = fmri_hemis[other_hemi]
if op.isfile(other_hemi_fname):
local_other_hemi_fname = build_local_fname(other_hemi_fname, user_fol)
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(other_hemi_fname, local_other_hemi_fname, True)
fmri_file_template = mu.get_template_hemi_label_name(mu.namesbase_with_ext(local_fname))
cmd = '{} -m src.preproc.fMRI -s {} -f load_surf_files --fmri_file_template "{}"'.format(
bpy.context.scene.python_cmd, mu.get_user(), fmri_file_template)
mu.run_command_in_new_thread(cmd, False)
return fmri_file_template, hemi
def init(addon_prefs):
global settings
run_faulthandler()
print('filepath: {}'.format(bpy.data.filepath))
set_play_to(get_max_time_steps())
mmvt_utils.view_all_in_graph_editor(bpy.context)
bpy.context.window.screen = bpy.data.screens['Neuro']
bpy.context.scene.atlas = mmvt_utils.get_atlas()
bpy.context.scene.python_cmd = addon_prefs.python_cmd
# bpy.data.screens['Neuro'].areas[1].spaces[0].region_3d.view_rotation = [1, 0, 0, 0]
make_all_fcurve_visible()
# set default values
figures_fol = op.join(mmvt_utils.get_user_fol(), 'figures')
mmvt_utils.make_dir(figures_fol)
set_render_output_path(figures_fol)
set_render_quality(60)
mmvt_utils.set_show_textured_solid()
mmvt_utils.hide_relationship_lines()
code_fol = mmvt_utils.get_parent_fol(mmvt_utils.get_parent_fol())
settings = mmvt_utils.read_config_ini()
os.chdir(code_fol)
bpy.context.scene.mmvt_initialized = True
def load_surf_files(nii_fname, run_fmri_preproc=True, user_fol=''):
fmri_file_template = ''
if user_fol == '':
user_fol = mu.get_user_fol()
nii_fol = mu.get_fname_folder(nii_fname)
# hemi = mu.get_hemi_from_fname(mu.namebase(nii_fname))
# if hemi == '':
hemi, fmri_hemis = mu.get_hemi_from_full_fname(nii_fname)
if hemi == '':
hemi = mu.find_hemi_using_vertices_num(nii_fname)
if hemi == '':
return '', ''
# fmri_hemis = mu.get_both_hemis_files(nii_fname)
local_fname = build_local_fname(nii_fname, user_fol)
mu.make_dir(op.join(user_fol, 'fmri'))
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(nii_fname, local_fname, True)
other_hemi = mu.other_hemi(hemi)
other_hemi_fname = fmri_hemis[other_hemi]
# todo: if the other hemi file doens't exist, just create an empty one
if op.isfile(other_hemi_fname):
local_other_hemi_fname = build_local_fname(other_hemi_fname, user_fol)
if nii_fol != op.join(user_fol, 'fmri'):
mu.make_link(other_hemi_fname, local_other_hemi_fname, True)
fmri_file_template = mu.get_template_hemi_label_name(
mu.namebase_with_ext(local_fname))
if run_fmri_preproc:
mu.run_mmvt_func(
'src.preproc.fMRI',
'load_surf_files',
flags='--fmri_file_template "{}"'.format(fmri_file_template))
# cmd = '{} -m -s {} -f --fmri_file_template "{}" --ignore_missing 1'.format(
# bpy.context.scene.python_cmd, mu.get_user(), fmri_file_template)
# mu.run_command_in_new_thread(cmd, False, cwd=mu.get_mmvt_code_root())
else:
print(
"Couldn't find the other hemi file! ({})".format(other_hemi_fname))
return fmri_file_template, hemi, other_hemi
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 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()
