def init(addon, first=True):
ScriptsPanel.addon = addon
user_fol = mu.get_user_fol()
scripts_files = glob.glob(op.join(mu.get_mmvt_code_root(), 'src', 'examples', 'scripts', '*.py'))
scripts_files_names = [mu.namebase(f) for f in scripts_files]
scripts_files += [f for f in glob.glob(op.join(mu.get_parent_fol(user_fol), 'scripts', '*.py'))
if mu.namebase(f) not in scripts_files_names]
if len(scripts_files) == 0:
return None
sys.path.append(op.join(mu.get_mmvt_code_root(), 'src', 'examples', 'scripts'))
sys.path.append(op.join(mu.get_parent_fol(user_fol), 'scripts'))
scripts_files = sorted([f for f in scripts_files if check_script(mu.namebase(f))])[::-1]
ScriptsPanel.scripts_names = files_names = [mu.namebase(fname).replace('_', ' ') for fname in scripts_files]
scripts_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.scripts_files = bpy.props.EnumProperty(
items=scripts_items, update=scripts_items_update,
description='List of script in the folder:\n..\mmvt_root\mmvtcode\src\examples\scripts\n\nCurrent script')
bpy.context.scene.scripts_files = files_names[0]
bpy.context.scene.scripts_overwrite = True
try:
bpy.context.scene.report_use_script = bpy.context.scene.reports_files in ScriptsPanel.scripts_names
except:
pass
# bpy.context.scene.scripts_threshold = 2
# bpy.context.scene.scripts_cb_min = 2
# bpy.context.scene.scripts_cb_max = 6
if first:
register()
ScriptsPanel.init = True
def 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 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(addon):
ReportsPanel.addon = addon
if not PDFKIT_EXIST:
print('reports_panel: no pdfkit')
return None
if not wkhtmltopdf_exist():
print('reports_panel: no wkhtmltopdf')
return None
user_fol = mu.get_user_fol()
reports_files = glob.glob(
op.join(mu.get_parent_fol(user_fol), 'reports', '*.html'))
if len(reports_files) == 0:
print('reports_panel: no reports')
return None
files_names = [
mu.namebase(fname).replace('_', ' ') for fname in reports_files
]
reports_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.reports_files = bpy.props.EnumProperty(
items=reports_items,
description="reports files",
update=reports_files_update)
bpy.context.scene.reports_files = files_names[0]
bpy.context.scene.report_use_script = files_names[0] in _addon(
).get_scripts_names()
register()
ReportsPanel.init = True
def import_evokes(evokes_fname):
import importlib
import mne
mu.add_mmvt_code_root_to_path()
from src.preproc import meg
importlib.reload(meg)
opt_trans_files = glob.glob(
op.join(mu.get_parent_fol(evokes_fname), '*.fif'))
trans_files = meg.filter_trans_files(opt_trans_files)
trans_file = mu.select_one_file(trans_files,
template='*.fif',
files_desc='MRI-Head transformation')
args = mu.get_remote_subject_info_args()
evokes = mne.read_evokeds(evokes_fname)
events_keys = [ev.comment for ev in evokes]
meg.read_sensors_layout(mu.get_user(),
args,
info=evokes[0].info,
trans_file=trans_file)
meg.save_evokes_to_mmvt(evokes, events_keys, mu.get_user())
_addon().import_meg_sensors()
_addon().add_data_to_meg_sensors()
# _addon().load_all_panels()
_addon().show_meg_sensors()
def init_electrodes_labeling(addon):
ela_code_fol = op.join(mu.get_parent_fol(mu.get_mmvt_code_root()),
'electrodes_rois')
ElecsPanel.ela_code_exist = op.isfile(
op.join(ela_code_fol, 'find_rois', 'find_rois.py'))
ElecsPanel.labling_files = labling_files = find_elecrode_labeling_files()
if len(labling_files) > 0:
files_names = [
mu.namebase(fname) for fname in labling_files if mu.load(fname)
]
labeling_items = [(c, c, '', ind) for ind, c in enumerate(files_names)]
bpy.types.Scene.electrodes_labeling_files = bpy.props.EnumProperty(
items=labeling_items,
description='Labeling files',
update=electrodes_labeling_files_update)
bpy.context.scene.electrodes_labeling_files = files_names[0]
# ElecsPanel.electrodes_locs = mu.load(labling_files[0])
# ElecsPanel.lookup = create_lookup_table(ElecsPanel.electrodes_locs, ElecsPanel.electrodes)
ElecsPanel.faces_verts = addon.get_faces_verts()
atlases = mu.get_annot_files()
if len(atlases) > 0:
ElecsPanel.atlases_exist = True
atlases_items = [(c, c, '', ind) for ind, c in enumerate(atlases)]
bpy.types.Scene.ela_atlas = bpy.props.EnumProperty(
items=atlases_items, description='atlases')
bpy.context.scene.ela_atlas = atlases[0]
bpy.context.scene.ela_bipolar = bpy.context.scene.bipolar
return len(labling_files) > 0
def init_logo():
import bpy.utils.previews
pcoll = bpy.utils.previews.new()
hnn_icons_dir = op.join(mu.get_parent_fol(mu.get_user_fol()), 'icons')
# load a preview thumbnail of a file and store in the previews collection
pcoll.load("hnn_icon", os.path.join(hnn_icons_dir, "hnn.png"), 'IMAGE')
preview_collections["main"] = pcoll
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 wkhtmltopdf_exist():
wkhtmltopdf_bin_path = op.join(mu.get_parent_fol(mu.get_user_fol()),
'reports')
wkhtmltopdf_bin_name = 'wkhtmltopdf.exe' if mu.is_windows(
) else 'wkhtmltopdf'
if not op.isfile(op.join(wkhtmltopdf_bin_path, wkhtmltopdf_bin_name)):
print("Reports panel: Can't find wkhtmltopdf!" + \
'Please download wkhtmltopdf ({}) and put it in {}'.format(
'https://github.com/JazzCore/python-pdfkit/wiki/Installing-wkhtmltopdf', wkhtmltopdf_bin_path))
return False
os.environ["PATH"] += os.pathsep + wkhtmltopdf_bin_path
if mu.is_windows():
wkhtmltopdf = subprocess.Popen(
['where', 'wkhtmltopdf'],
stdout=subprocess.PIPE).communicate()[0].strip()
else:
wkhtmltopdf = subprocess.Popen(
['which', 'wkhtmltopdf'],
stdout=subprocess.PIPE).communicate()[0].strip()
try:
with open(wkhtmltopdf) as f:
return True
except IOError:
print('Reports panel: No wkhtmltopdf executable found! ' + \
'(https://github.com/JazzCore/python-pdfkit/wiki/Installing-wkhtmltopdf)')
return False
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 read_report_html():
fol = op.join(mu.get_parent_fol(mu.get_user_fol()), 'reports')
report_fname = op.join(
fol,
'{}.html'.format(bpy.context.scene.reports_files.replace(' ', '_')))
with open(report_fname, 'r') as f:
report_text = f.read()
return report_text
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 execute(self, context):
_addon().clear_colors()
fmri_file_template = load_surf_files(self.filepath[:-2])
if fmri_file_template != '':
_addon().plot_fmri_file(fmri_file_template)
if mu.get_parent_fol(self.filepath) != op.join(
mu.get_user_fol(), 'fmri'):
clean_nii_temp_files(fmri_file_template)
return {'RUNNING_MODAL'}
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 modal(self, context, event):
if event.type == 'TIMER' and ChooseNiftiiFile.running:
if mu.both_hemi_files_exist(self.fmri_npy_template_fname):
_addon().plot_fmri_file(self.fmri_file_template)
if mu.get_parent_fol(self.filepath) != op.join(
mu.get_user_fol(), 'fmri'):
clean_nii_temp_files(self.fmri_file_template)
ChooseNiftiiFile.running = False
bpy.context.scene.nii_label_output = ''
self.cancel(context)
return {'PASS_THROUGH'}
def draw(self, context):
layout = self.layout
user_fol = mu.get_user_fol()
aparc_name = bpy.context.scene.atlas
faces_verts_exist = mu.hemi_files_exists(op.join(user_fol, 'faces_verts_{hemi}.npy'))
fmri_files = glob.glob(op.join(user_fol, 'fmri', '*_lh.npy')) # mu.hemi_files_exists(op.join(user_fol, 'fmri_{hemi}.npy'))
# fmri_clusters_files_exist = mu.hemi_files_exists(op.join(user_fol, 'fmri', 'fmri_clusters_{hemi}.npy'))
meg_files_exist = mu.hemi_files_exists(op.join(user_fol, 'activity_map_{hemi}', 't0.npy'))
meg_labels_files_exist = op.isfile(op.join(user_fol, 'labels_vertices_{}.pkl'.format(aparc_name))) and \
mu.hemi_files_exists(op.join(user_fol, 'meg_labels_coloring_{hemi}.npz'))
electrodes_files_exist = op.isfile(op.join(mu.get_user_fol(), 'electrodes', 'electrodes_data_{}.npz'.format(
'avg' if bpy.context.scene.selection_type == 'conds' else 'diff'))) or \
op.isfile(op.join(mu.get_user_fol(), 'electrodes', 'electrodes_data_{}_data.npy'.format(
'avg' if bpy.context.scene.selection_type == 'conds' else 'diff')))
electrodes_stim_files_exist = len(glob.glob(op.join(
mu.get_user_fol(), 'electrodes', 'stim_electrodes_*.npz'))) > 0
electrodes_labels_files_exist = len(glob.glob(op.join(
mu.get_user_fol(), 'electrodes', '*_labels_*.npz'))) > 0 and \
len(glob.glob(op.join(mu.get_user_fol(), 'electrodes', '*_subcortical_*.npz'))) > 0
manually_color_files_exist = len(glob.glob(op.join(user_fol, 'coloring', '*.csv'))) > 0
manually_groups_file_exist = op.isfile(op.join(mu.get_parent_fol(user_fol),
'{}_groups.csv'.format(bpy.context.scene.atlas)))
volumetric_coloring_files_exist = len(glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv')))
layout.prop(context.scene, 'coloring_threshold', text="Threshold")
layout.prop(context.scene, 'coloring_both_pial_and_inflated', text="Both pial & inflated")
if faces_verts_exist:
if meg_files_exist:
layout.operator(ColorMeg.bl_idname, text="Plot MEG ", icon='POTATO')
if op.isfile(op.join(mu.get_user_fol(), 'subcortical_meg_activity.npz')):
layout.prop(context.scene, 'coloring_meg_subcorticals', text="Plot also subcorticals")
# if meg_labels_files_exist:
# layout.operator(ColorMegLabels.bl_idname, text="Plot MEG Labels ", icon='POTATO')
if len(fmri_files) > 0:
layout.prop(context.scene, "fmri_files", text="")
layout.operator(ColorFmri.bl_idname, text="Plot fMRI ", icon='POTATO')
if manually_color_files_exist:
layout.prop(context.scene, "coloring_files", text="")
layout.operator(ColorManually.bl_idname, text="Color Manually", icon='POTATO')
if manually_groups_file_exist:
layout.prop(context.scene, 'labels_groups', text="")
layout.operator(ColorGroupsManually.bl_idname, text="Color Groups", icon='POTATO')
if volumetric_coloring_files_exist:
layout.prop(context.scene, "vol_coloring_files", text="")
layout.operator(ColorVol.bl_idname, text="Color Volumes", icon='POTATO')
if not bpy.data.objects.get('eeg_helmet', None) is None:
layout.operator(ColorEEGHelmet.bl_idname, text="Plot EEG Helmet", icon='POTATO')
if electrodes_files_exist:
layout.operator(ColorElectrodes.bl_idname, text="Plot Electrodes", icon='POTATO')
if electrodes_labels_files_exist:
layout.prop(context.scene, "electrodes_sources_files", text="")
layout.operator(ColorElectrodesLabels.bl_idname, text="Plot Electrodes Sources", icon='POTATO')
if electrodes_stim_files_exist:
layout.operator(ColorElectrodesStim.bl_idname, text="Plot Electrodes Stimulation", icon='POTATO')
layout.operator(ClearColors.bl_idname, text="Clear", icon='PANEL_CLOSE')
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 draw(self, context):
layout = self.layout
user_fol = mu.get_user_fol()
aparc_name = bpy.context.scene.atlas
faces_verts_exist = mu.hemi_files_exists(op.join(user_fol, 'faces_verts_{hemi}.npy'))
fmri_files = glob.glob(op.join(user_fol, 'fmri', '*_lh.npy')) # mu.hemi_files_exists(op.join(user_fol, 'fmri_{hemi}.npy'))
# fmri_clusters_files_exist = mu.hemi_files_exists(op.join(user_fol, 'fmri', 'fmri_clusters_{hemi}.npy'))
meg_files_exist = mu.hemi_files_exists(op.join(user_fol, 'activity_map_{hemi}', 't0.npy'))
meg_labels_files_exist = op.isfile(op.join(user_fol, 'labels_vertices_{}.pkl'.format(aparc_name))) and \
mu.hemi_files_exists(op.join(user_fol, 'meg_labels_coloring_{hemi}.npz'))
electrodes_files_exist = op.isfile(op.join(mu.get_user_fol(), 'electrodes', 'electrodes_data_{}.npz'.format(
'avg' if bpy.context.scene.selection_type == 'conds' else 'diff'))) or \
op.isfile(op.join(mu.get_user_fol(), 'electrodes', 'electrodes_data_{}_data.npy'.format(
'avg' if bpy.context.scene.selection_type == 'conds' else 'diff')))
electrodes_stim_files_exist = len(glob.glob(op.join(
mu.get_user_fol(), 'electrodes', 'stim_electrodes_*.npz'))) > 0
electrodes_labels_files_exist = len(glob.glob(op.join(
mu.get_user_fol(), 'electrodes', '*_labels_*.npz'))) > 0 and \
len(glob.glob(op.join(mu.get_user_fol(), 'electrodes', '*_subcortical_*.npz'))) > 0
manually_color_files_exist = len(glob.glob(op.join(user_fol, 'coloring', '*.csv'))) > 0
manually_groups_file_exist = op.isfile(op.join(mu.get_parent_fol(user_fol),
'{}_groups.csv'.format(bpy.context.scene.atlas)))
volumetric_coloring_files_exist = len(glob.glob(op.join(user_fol, 'coloring', 'volumetric', '*.csv')))
layout.prop(context.scene, 'coloring_threshold', text="Threshold")
if faces_verts_exist:
if meg_files_exist:
layout.operator(ColorMeg.bl_idname, text="Plot MEG ", icon='POTATO')
# if meg_labels_files_exist:
# layout.operator(ColorMegLabels.bl_idname, text="Plot MEG Labels ", icon='POTATO')
if len(fmri_files) > 0:
layout.prop(context.scene, "fmri_files", text="")
layout.operator(ColorFmri.bl_idname, text="Plot fMRI ", icon='POTATO')
if manually_color_files_exist:
layout.prop(context.scene, "coloring_files", text="")
layout.operator(ColorManually.bl_idname, text="Color Manually", icon='POTATO')
if manually_groups_file_exist:
layout.prop(context.scene, 'labels_groups', text="")
layout.operator(ColorGroupsManually.bl_idname, text="Color Groups", icon='POTATO')
if volumetric_coloring_files_exist:
layout.prop(context.scene, "vol_coloring_files", text="")
layout.operator(ColorVol.bl_idname, text="Color Volumes", icon='POTATO')
if electrodes_files_exist:
layout.operator(ColorElectrodes.bl_idname, text="Plot Electrodes", icon='POTATO')
if electrodes_labels_files_exist:
layout.prop(context.scene, "electrodes_sources_files", text="")
layout.operator(ColorElectrodesLabels.bl_idname, text="Plot Electrodes Sources", icon='POTATO')
if electrodes_stim_files_exist:
layout.operator(ColorElectrodesStim.bl_idname, text="Plot Electrodes Stimulation", icon='POTATO')
layout.operator(ClearColors.bl_idname, text="Clear", icon='PANEL_CLOSE')
def load_fmri_volume(nii_fname):
import importlib
mu.add_mmvt_code_root_to_path()
from src.preproc import fMRI
importlib.reload(fMRI)
fmri_file_template = mu.namebase(nii_fname)
subject = mu.get_user()
flag, fmri_contrast_file_template = fMRI.project_volume_to_surface(
subject, fmri_file_template, remote_fmri_dir=mu.get_parent_fol(nii_fname))
if not flag:
print('load_fmri_volume: Error in fMRI.project_volume_to_surface!')
return False
flag = fMRI.calc_fmri_min_max(subject, fmri_contrast_file_template)
if not flag:
print('load_fmri_volume: Error in fMRI.calc_fmri_min_max!')
return False
# _addon().coloring.init(_addon(), register=False)
fMRI_file_name = fmri_contrast_file_template.replace('fmri_', '')
_addon().coloring.plot_fmri_file(fMRI_file_name)
return True
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_template = op.join(mu.get_parent_fol(mu.get_user_fol()),
'color_maps', '*.npy')
# colorbar_files_template = op.join(mu.file_fol(), 'color_maps', '*.npy')
colorbar_files = glob.glob(colorbar_files_template)
if len(colorbar_files) == 0:
print("No colorbar files ({}), Can't load the colorbar panel".format(
colorbar_files_template))
return None
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,
description="colormaps files",
update=colormap_update)
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 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 execute(self, context):
_addon().clear_colors()
fmri_file_template = load_surf_files(self.filepath[:-2])
_addon().plot_fmri_file(fmri_file_template)
if mu.get_parent_fol(self.filepath) != op.join(
mu.get_user_fol(), 'fmri'):
clean_nii_temp_files(fmri_file_template)
# self.fmri_file_template, hemi, other_hemi = load_surf_files(self.filepath[:-2])
# if hemi == '':
# bpy.context.scene.nii_label_prompt = "Can't determine the hemi!"
# return {'RUNNING_MODAL'}
# self.fmri_npy_template_fname = op.join(mu.get_user_fol(), 'fmri', 'fmri_{}.npy'.format(
# mu.namebase(self.fmri_file_template)))
# print('Waiting for both hemi files to be created ({})'.format(self.fmri_npy_template_fname))
# if self.fmri_file_template != '':
# bpy.context.scene.nii_label_output = 'Loading nii file...'
# ChooseNiftiiFile.running = True
# context.window_manager.modal_handler_add(self)
# self._timer = context.window_manager.event_timer_add(0.1, context.window)
# else:
# bpy.context.scene.nii_label_prompt = 'Please select the nii file for the {} hemi'.format(
# 'right' if hemi == 'lh' else 'left')
return {'RUNNING_MODAL'}
