def plot_blob(cluster_labels, faces_verts, is_inflated=None, use_abs=None):
if use_abs is None:
use_abs = bpy.context.scene.coloring_use_abs
is_inflated = _addon().is_inflated() if is_inflated is None else is_inflated
fMRIPanel.dont_show_clusters_info = False
_addon().init_activity_map_coloring('FMRI')#, subcorticals=False)
blob_vertices = cluster_labels['vertices']
hemi = cluster_labels['hemi']
real_hemi = hemi
if is_inflated:
hemi = 'inflated_{}'.format(hemi)
# fMRIPanel.blobs_plotted = True
fMRIPanel.colors_in_hemis[hemi] = True
activity = fMRIPanel.constrast[real_hemi]
blob_activity = np.ones(activity.shape)
blob_activity[blob_vertices] = activity[blob_vertices]
if fMRIPanel.blobs_activity is None:
fMRIPanel.blobs_activity, _ = calc_blobs_activity(
fMRIPanel.constrast, fMRIPanel.clusters_labels_filtered, fMRIPanel.colors_in_hemis)
data_min, colors_ratio = calc_colors_ratio(fMRIPanel.blobs_activity)
threshold = bpy.context.scene.fmri_clustering_threshold
cur_obj = bpy.data.objects[hemi]
_addon().activity_map_obj_coloring(
cur_obj, blob_activity, faces_verts[real_hemi], threshold, True,
data_min=data_min, colors_ratio=colors_ratio, use_abs=use_abs)
other_real_hemi = mu.other_hemi(real_hemi)
other_hemi = mu.other_hemi(hemi)
if other_hemi in fMRIPanel.colors_in_hemis and fMRIPanel.colors_in_hemis[other_hemi]:
_addon().clear_cortex([other_real_hemi])
fMRIPanel.colors_in_hemis[other_hemi] = False
def load_camera(camera_fname=''):
if camera_fname == '':
camera_fname = op.join(mu.get_user_fol(), 'camera',
'{}.pkl'.format(bpy.context.scene.camera_files))
if op.isfile(camera_fname):
camera_name = mu.namebase(camera_fname)
for hemi in mu.HEMIS:
if hemi in camera_name:
_addon().show_hide_hemi(False, hemi)
_addon().show_hide_hemi(True, mu.other_hemi(hemi))
X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(
camera_fname)
RenderFigure.update_camera = False
bpy.context.scene.X_rotation = X_rotation
bpy.context.scene.Y_rotation = Y_rotation
bpy.context.scene.Z_rotation = Z_rotation
bpy.context.scene.X_location = X_location
bpy.context.scene.Y_location = Y_location
bpy.context.scene.Z_location = Z_location
# print('Camera loaded: rotation: {},{},{} locatioin: {},{},{}'.format(
# X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location))
# print('Camera loaded: {}'.format(camera_fname))
RenderFigure.update_camera = True
update_camera()
else:
pass
def 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 plot_blob(cluster_labels, faces_verts):
_addon().init_activity_map_coloring('FMRI', subcorticals=False)
blob_vertices = cluster_labels['vertices']
hemi = cluster_labels['hemi']
real_hemi = hemi
if _addon().is_inflated():
hemi = 'inflated_{}'.format(hemi)
fMRIPanel.colors_in_hemis[hemi] = True
activity = _addon().get_fMRI_activity(real_hemi)
blob_activity = np.ones((len(activity), 4))
blob_activity[blob_vertices] = activity[blob_vertices]
cur_obj = bpy.data.objects[hemi]
_addon().activity_map_obj_coloring(cur_obj, blob_activity, faces_verts[real_hemi],
bpy.context.scene.fmri_cluster_val_threshold, True)
other_real_hemi = mu.other_hemi(real_hemi)
other_hemi = mu.other_hemi(hemi)
if fMRIPanel.colors_in_hemis[other_hemi]:
_addon().clear_cortex([other_real_hemi])
fMRIPanel.colors_in_hemis[other_hemi] = False
def render_all_images():
camera_files = glob.glob(op.join(bpy.path.abspath(bpy.context.scene.output_path), 'camera_*.pkl'))
for camera_file in camera_files:
load_camera(camera_file)
camera_name = mu.namebase(camera_file)
for hemi in mu.HEMIS:
if hemi in camera_name:
RenderingMakerPanel.addon.show_hide_hemi(False, hemi)
RenderingMakerPanel.addon.show_hide_hemi(True, mu.other_hemi(hemi))
render_image('{}_fig'.format(camera_name[len('camera') + 1:]))
def render_all_images():
camera_files = glob.glob(
op.join(bpy.path.abspath(bpy.context.scene.output_path),
'camera_*.pkl'))
for camera_file in camera_files:
load_camera(camera_file)
camera_name = mu.namebase(camera_file)
for hemi in mu.HEMIS:
if hemi in camera_name:
RenderingMakerPanel.addon.show_hide_hemi(False, hemi)
RenderingMakerPanel.addon.show_hide_hemi(
True, mu.other_hemi(hemi))
render_image('{}_fig'.format(camera_name[len('camera') + 1:]))
def plot_blob(cluster_labels, faces_verts):
fMRIPanel.addon.init_activity_map_coloring('FMRI', subcorticals=False)
blob_vertices = cluster_labels['vertices']
hemi = cluster_labels['hemi']
fMRIPanel.colors_in_hemis[hemi] = True
activity = fMRIPanel.addon.get_fMRI_activity(hemi)
blob_activity = np.zeros((len(activity), 4))
blob_activity[blob_vertices] = activity[blob_vertices]
cur_obj = bpy.data.objects[hemi]
fMRIPanel.addon.activity_map_obj_coloring(cur_obj, blob_activity, faces_verts[hemi], 0, True)
other_hemi = mu.other_hemi(hemi)
if fMRIPanel.colors_in_hemis[other_hemi]:
fMRIPanel.addon.clear_cortex([other_hemi])
fMRIPanel.colors_in_hemis[other_hemi] = False
def _save_image():
if not bpy.context.scene.save_split_views:
save_image(view_selected=bpy.context.scene.save_selected_view,
add_colorbar=bpy.context.scene.save_views_with_cb)
else:
images = {}
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[hemi] = save_image(view_selected=bpy.context.scene.save_selected_view, add_colorbar=False)
for hemi in mu.HEMIS:
mu.get_hemi_obj(hemi).hide = org_hide[hemi]
combine_two_images_and_add_colorbar(images['lh'], images['rh'], images['lh'])
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_camera(camera_fname=''):
if camera_fname == '':
camera_fname = op.join(mu.get_user_fol(), 'camera', '{}.pkl'.format(bpy.context.scene.camera_files))
if op.isfile(camera_fname):
camera_name = mu.namebase(camera_fname)
for hemi in mu.HEMIS:
if hemi in camera_name:
_addon().show_hide_hemi(False, hemi)
_addon().show_hide_hemi(True, mu.other_hemi(hemi))
X_rotation, Y_rotation, Z_rotation, X_location, Y_location, Z_location = mu.load(camera_fname)
RenderFigure.update_camera = False
bpy.context.scene.X_rotation = X_rotation
bpy.context.scene.Y_rotation = Y_rotation
bpy.context.scene.Z_rotation = Z_rotation
bpy.context.scene.X_location = X_location
bpy.context.scene.Y_location = Y_location
bpy.context.scene.Z_location = Z_location
RenderFigure.update_camera = True
update_camera()
else:
print('No camera file was found in {}!'.format(camera_fname))
def 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 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
