def create_movie():
output_file = op.join(bpy.context.scene.output_path,
'combine_images_cmd.txt')
if op.isfile(output_file):
os.remove(output_file)
flags = '--fol {} --copy_files 1 --frame_rate {}'.format(
bpy.context.scene.output_path, bpy.context.scene.frames_num)
mu.run_mmvt_func('src.utils.movies_utils', 'combine_images', flags=flags)
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 grow_a_label():
closest_mesh_name, vertex_ind, _ = \
_addon().find_closest_vertex_index_and_mesh(use_shape_keys=True)
hemi = closest_mesh_name[len('infalted_'):] if _addon().is_inflated() else closest_mesh_name
subject, atlas = mu.get_user(), bpy.context.scene.subject_annot_files
label_name, label_r = bpy.context.scene.new_label_name, bpy.context.scene.new_label_r
flags = '-a {} --vertice_indice {} --hemi {} --label_name {} --label_r {}'.format(
atlas, vertex_ind, hemi, label_name, label_r)
mu.run_mmvt_func('src.preproc.anatomy', 'grow_label', flags=flags)
def invoke(self, context, event=None):
electrodes_pos_fname = op.join(
mu.get_user_fol(), 'electrodes',
'electrodes{}_positions.npz'.format(
'_bipolar' if bpy.context.scene.bipolar else ''))
flags = '-a {} -b {} --electrodes_pos_fname {} --ignore_missing 1'.format(
bpy.context.scene.atlas, bpy.context.scene.bipolar,
electrodes_pos_fname)
mu.run_mmvt_func('src.preproc.freeview', flags=flags)
bpy.context.scene.freeview_messages = 'Preparing...'
return {"FINISHED"}
def init(modality, modality_data=None, colormap=None, subject='', mmvt_dir=''):
if subject == '':
subject = mu.get_user()
if mmvt_dir == '':
mmvt_dir = mu.file_fol()
if modality_data is None:
if modality == 'mri':
fname = op.join(mmvt_dir, subject, 'freeview', 'mri_data.npz')
elif modality == 't2':
fname = op.join(mmvt_dir, subject, 'freeview', 't2_data.npz')
elif modality == 'ct':
fname = op.join(mmvt_dir, subject, 'ct', 'ct_data.npz'.format(modality))
if op.isfile(fname):
modality_data = mu.Bag(np.load(fname))
else:
print('To see the slices the following command is being called:'.format(modality))
print('python -m src.preproc.anatomy -s {} -f save_images_data_and_header'.format(mu.get_user()))
mu.run_mmvt_func('src.preproc.anatom', 'save_subject_orig_trans,save_images_data_and_header')
# cmd = '{} -m src.preproc.anatomy -s {} -f save_subject_orig_trans,save_images_data_and_header --ignore_missing 1'.format(
# bpy.context.scene.python_cmd, mu.get_user())
# mu.run_command_in_new_thread(cmd, False, cwd=mu.get_mmvt_code_root())
return None
if colormap is None:
if op.isfile(op.join(mmvt_dir, 'color_maps', 'gray.npy')):
colormap_fname = op.join(mmvt_dir, 'color_maps', 'gray.npy')
print("Can't find The gray colormap!")
else:
colormap_fname = glob.glob(op.join(mmvt_dir, 'color_maps', '*.npy'))[0]
colormap = np.load(colormap_fname)
affine = np.array(modality_data.affine, float)
data = modality_data.data
clim = modality_data.precentiles
if IN_BLENDER:
bpy.context.scene.slices_x_min, bpy.context.scene.slices_x_max = clim
colors_ratio = modality_data.colors_ratio
codes = axcodes2ornt(aff2axcodes(affine))
order = np.argsort([c[0] for c in codes])
print(modality, order)
flips = np.array([c[1] < 0 for c in codes])[order]
flips[0] = not flips[0]
sizes = [data.shape[order] for order in order]
scalers = voxel_sizes(affine)
r = [scalers[order[2]] / scalers[order[1]],
scalers[order[2]] / scalers[order[0]],
scalers[order[1]] / scalers[order[0]]]
extras = [0] * 3
pial_vol_mask_fname = op.join(mmvt_dir, subject, 'freeview', 'pial_vol_mask.npy')
pial_vol_mask = np.load(pial_vol_mask_fname) if op.isfile(pial_vol_mask_fname) else None
self = mu.Bag(dict(
data=data, affine=affine, order=order, sizes=sizes, flips=flips, clim=clim, r=r, colors_ratio=colors_ratio,
colormap=colormap, coordinates=[], modality=modality, extras=extras, pial_vol_mask=pial_vol_mask))
return self
def add_colorbar_to_image(image_fname, cb_ticks_num=None, cb_ticks_font_size=None):
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
data_max, data_min = _addon().get_colorbar_max_min()
cb_ticks = ','.join(_addon().get_colorbar_ticks(cb_ticks_num))
cb_ticks = cb_ticks.replace('-', '*') # Bug in argparse. todo: change the , to space
flags = '--figure_fname "{}" --data_max "{}" --data_min "{}" --colors_map {} --background_color {} '.format(
image_fname, data_max, data_min, _addon().get_colormap(), get_background_rgb_string()) + \
'--cb_title "{}" --cb_ticks "{}" --cb_ticks_font_size {} --perc {}'.format(
_addon().get_colorbar_title(), cb_ticks, cb_ticks_font_size, _addon().get_colorbar_prec())
mu.run_mmvt_func('src.utils.figures_utils', 'add_colorbar_to_image', flags=flags)
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 combine_two_images_and_add_colorbar(lh_figure_fname, rh_figure_fname, new_image_fname, cb_ticks_num=None,
cb_ticks_font_size=None):
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
data_max, data_min = _addon().get_colorbar_max_min()
cb_ticks = ','.join(_addon().get_colorbar_ticks(cb_ticks_num))
cb_ticks = cb_ticks.replace('-', '*') # Bug in argparse
flags = '--lh_figure_fname "{}" --rh_figure_fname "{}" '.format(lh_figure_fname, rh_figure_fname) + \
'--new_image_fname "{}" --data_max "{}" --data_min "{}" '.format(new_image_fname, data_max, data_min) + \
'--colors_map {} --background_color {} '.format(_addon().get_colormap(), get_background_rgb_string()) + \
'--add_cb {} --cb_title "{}" --cb_ticks "{}" --cb_ticks_font_size {} '.format(
bpy.context.scene.save_views_with_cb, _addon().get_colorbar_title(), cb_ticks, cb_ticks_font_size) + \
'--crop_figures 1 --remove_original_figures 1'
print('Combining {} and {}'.format(lh_figure_fname, rh_figure_fname))
mu.run_mmvt_func(
'src.utils.figures_utils', 'combine_two_images_and_add_colorbar', flags=flags)
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
