def build_local_fname(nii_fname, user_fol):
if mu.get_hemi_from_fname(mu.namebase_with_ext(nii_fname)) == '':
local_fname = mu.get_label_for_full_fname(nii_fname)
# local_fname = '{}.{}.{}'.format(mu.namebase(nii_fname), hemi, mu.file_type(nii_fname))
else:
local_fname = mu.namebase_with_ext(nii_fname)
return op.join(user_fol, 'fmri', local_fname)
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 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 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 execute(self, context):
stc_fname = self.filepath
user_fol = mu.get_user_fol()
stc_fol = mu.get_fname_folder(stc_fname)
if stc_fol != op.join(user_fol, 'meg'):
other_hemi_stc_fname = op.join(
stc_fol, '{}.stc'.format(
mu.get_other_hemi_label_name(mu.namebase(stc_fname))))
shutil.copy(
stc_fname,
op.join(user_fol, 'meg', mu.namebase_with_ext(stc_fname)))
shutil.copy(
other_hemi_stc_fname,
op.join(user_fol, 'meg',
mu.namebase_with_ext(other_hemi_stc_fname)))
_addon().init_meg_activity_map()
_, _, label, hemi = mu.get_hemi_delim_and_pos(
mu.namebase(stc_fname))
bpy.context.scene.meg_files = label
return {'FINISHED'}
def save_all_views(views=None, inflated_ratio_in_file_name=False, rot_lh_axial=None, render_images=False, quality=0,
img_name_prefix='', add_colorbar=None, cb_ticks_num=None, cb_ticks_font_size=None, overwrite=True):
if not render_images:
_addon().change_to_solid_brain()
if add_colorbar is None:
add_colorbar = bpy.context.scene.save_views_with_cb
if cb_ticks_num is None:
cb_ticks_num = bpy.context.scene.cb_ticks_num
if cb_ticks_font_size is None:
cb_ticks_font_size = bpy.context.scene.cb_ticks_font_size
_addon().show_hemis()
if not bpy.context.scene.save_split_views:
rot_lh_axial = False if rot_lh_axial is None else rot_lh_axial
_save_all_views(views, inflated_ratio_in_file_name, rot_lh_axial, render_images, quality, img_name_prefix,
add_colorbar, cb_ticks_num, cb_ticks_font_size, overwrite)
else:
if views is None:
views = list(set(_addon().ANGLES_DICT.keys()) - set([_addon().ROT_MEDIAL_LEFT, _addon().ROT_MEDIAL_RIGHT]))
images_names = []
rot_lh_axial = True if rot_lh_axial is None else rot_lh_axial
org_hide = {hemi: mu.get_hemi_obj(hemi).hide for hemi in mu.HEMIS}
for hemi in mu.HEMIS:
mu.get_hemi_obj(hemi).hide = False
mu.get_hemi_obj(mu.other_hemi(hemi)).hide = True
images_names.extend(_save_all_views(
views, inflated_ratio_in_file_name, rot_lh_axial, render_images, quality, img_name_prefix, False,
overwrite=overwrite))
for hemi in mu.HEMIS:
mu.get_hemi_obj(hemi).hide = org_hide[hemi]
images_hemi_inv_list = set(
[mu.namebase(fname)[3:] for fname in images_names if mu.namebase(fname)[:2] in ['rh', 'lh']])
files = [[fname for fname in images_names if mu.namebase(fname)[3:] == img_hemi_inv] for img_hemi_inv in
images_hemi_inv_list]
fol = mu.get_fname_folder(files[0][0])
for files_coup in files:
hemi = 'rh' if mu.namebase(files_coup[0]).startswith('rh') else 'lh'
coup_template = files_coup[0].replace(hemi, '{hemi}')
coup = {hemi: coup_template.format(hemi=hemi) for hemi in mu.HEMIS}
new_image_fname = op.join(fol, mu.namebase_with_ext(files_coup[0])[3:])
combine_two_images_and_add_colorbar(
coup['lh'], coup['rh'], new_image_fname, cb_ticks_num, cb_ticks_font_size)
_addon().show_hemis()
def load_labels_data(labels_data_fname):
ret = _load_labels_data(labels_data_fname)
if isinstance(ret, bool):
return ret
d, labels, data, atlas, cb_title, labels_max, labels_min, cmap = ret
_addon().color_labels_data(labels, data, atlas, cb_title, labels_max, labels_min, cmap)
new_fname = op.join(mu.get_user_fol(), 'labels', 'labels_data', mu.namebase_with_ext(labels_data_fname))
if 'atlas' not in d:
npz_dict = dict(d)
npz_dict['atlas'] = atlas
np.savez(new_fname, **npz_dict)
else:
if new_fname != labels_data_fname:
shutil.copy(labels_data_fname, new_fname)
# init_labels_data_files()
if atlas in _addon().where_am_i.get_annot_files() and bpy.context.scene.subject_annot_files != atlas:
bpy.context.scene.subject_annot_files = atlas
bpy.context.scene.find_closest_label_on_click = True
_addon().find_closest_label(atlas=atlas, plot_contour=bpy.context.scene.plot_closest_label_contour)
return 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
