def combine_images(fol, movie_name, frame_rate=10, start_number=-1, images_prefix='', images_format='',
images_type='', ffmpeg_cmd='ffmpeg', **kwargs):
if images_type == '':
images_types = set([utils.file_type(image) for image in glob.glob(op.join(fol, '{}*.*'.format(images_prefix)))])
for opt_type in ['png', 'jpg', 'bmp', 'gif']:
if opt_type in images_types:
images_type = opt_type
print('Images type is {}'.format(images_type))
break
if images_type == '':
raise Exception("Can't find the images type!")
images = glob.glob(op.join(fol, '{}*.{}'.format(images_prefix, images_type)))
image_nb = utils.namebase(images[0])
number = utils.read_numbers_rx(image_nb)[0]
if images_prefix == '':
images_prefix = image_nb[:-len(number)]
if images_format == '':
images_format = '%0{}d'.format(len(number))
if start_number == -1:
start_number = min([int(utils.namebase(image)[len(images_prefix):]) for image in images])
images_prefix = op.join(fol, images_prefix)
movie_name = op.join(fol, movie_name)
combine_images_cmd = '{ffmpeg_cmd} -framerate {frame_rate} '
if start_number > 1:
# You might want to use a static ffmpeg if your ffmepg version doesn't support the start_number flag, like:
# ffmpeg_cmd = '~/space1/Downloads/ffmpeg-git-static/ffmpeg'
combine_images_cmd += '-start_number {start_number} '
combine_images_cmd += '-i {images_prefix}{images_format}.{images_type} '
# http://stackoverflow.com/questions/20847674/ffmpeg-libx264-height-not-divisible-by-2
combine_images_cmd += '-vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" '
combine_images_cmd += '-c:v libx264 -r 30 -pix_fmt yuv420p {movie_name}.mp4'
rs = utils.partial_run_script(locals())
rs(combine_images_cmd)
def init_clusters(subject, contrast_name, input_fol):
input_fname = op.join(input_fol,
'fmri_{}_{}.npy'.format(contrast_name, '{hemi}'))
contrast_per_hemi, verts_per_hemi = {}, {}
for hemi in utils.HEMIS:
fmri_fname = input_fname.format(hemi=hemi)
if utils.file_type(input_fname) == 'npy':
x = np.load(fmri_fname)
contrast_per_hemi[hemi] = x[:, 0]
else:
# try nibabel
x = nib.load(fmri_fname)
contrast_per_hemi[hemi] = x.get_data().ravel()
pial_npz_fname = op.join(BLENDER_ROOT_DIR, subject,
'{}.pial.npz'.format(hemi))
if not op.isfile(pial_npz_fname):
print('No pial npz file (), creating one'.format(pial_npz_fname))
verts, faces = utils.read_ply_file(
op.join(BLENDER_ROOT_DIR, subject, '{}.pial.ply'.format(hemi)))
np.savez(pial_npz_fname[:-4], verts=verts, faces=faces)
d = np.load(pial_npz_fname)
verts_per_hemi[hemi] = d['verts']
connectivity_fname = op.join(BLENDER_ROOT_DIR, subject,
'spatial_connectivity.pkl')
if not op.isfile(connectivity_fname):
from src.preproc import anatomy_preproc
anatomy_preproc.create_spatial_connectivity(subject)
connectivity_per_hemi = utils.load(connectivity_fname)
return contrast_per_hemi, connectivity_per_hemi, verts_per_hemi
def init_clusters(subject, contrast_name, input_fol):
input_fname = op.join(input_fol, 'fmri_{}_{}.npy'.format(contrast_name, '{hemi}'))
contrast_per_hemi, verts_per_hemi = {}, {}
for hemi in utils.HEMIS:
fmri_fname = input_fname.format(hemi=hemi)
if utils.file_type(input_fname) == 'npy':
x = np.load(fmri_fname)
contrast_per_hemi[hemi] = x[:, 0]
else:
# try nibabel
x = nib.load(fmri_fname)
contrast_per_hemi[hemi] = x.get_data().ravel()
pial_npz_fname = op.join(BLENDER_ROOT_DIR, subject, '{}.pial.npz'.format(hemi))
if not op.isfile(pial_npz_fname):
print('No pial npz file (), creating one'.format(pial_npz_fname))
verts, faces = utils.read_ply_file(op.join(BLENDER_ROOT_DIR, subject, '{}.pial.ply'.format(hemi)))
np.savez(pial_npz_fname[:-4], verts=verts, faces=faces)
d = np.load(pial_npz_fname)
verts_per_hemi[hemi] = d['verts']
connectivity_fname = op.join(BLENDER_ROOT_DIR, subject, 'spatial_connectivity.pkl')
if not op.isfile(connectivity_fname):
from src.preproc import anatomy_preproc
anatomy_preproc.create_spatial_connectivity(subject)
connectivity_per_hemi = utils.load(connectivity_fname)
return contrast_per_hemi, connectivity_per_hemi, verts_per_hemi
def project_and_calc_clusters(args):
if not op.isdir(args.root_fol):
print('You should first set args.root_fol!')
return False
img_files = [
f for f in glob.glob(op.join(args.root_fol, '*.img')) if op.isfile(f)
]
for img_fname in img_files:
mgz_fname = fu.mri_convert_to(img_fname, 'mgz', overwrite=False)
if ' ' in utils.namebase(mgz_fname):
mgz_new_fname = op.join(
utils.get_parent_fol(mgz_fname),
utils.namebase_with_ext(mgz_fname).replace(' ', '_').replace(
',', '').lower())
os.rename(mgz_fname, mgz_new_fname)
nii_files = [
f for f in glob.glob(op.join(args.root_fol, '*'))
if op.isfile(f) and utils.file_type(f) in ('nii', 'nii.gz', 'mgz')
]
for fname in nii_files:
fmri_args = fmri.read_cmd_args(
dict(subject=args.subject,
function='project_volume_to_surface,find_clusters',
fmri_file_template=fname,
threshold=args.cluster_threshold))
pu.run_on_subjects(fmri_args, fmri.main)
def find_images_props(fol,
start_number=-1,
images_prefix='',
images_format='',
images_type=''):
if images_type == '':
images_types = set([
utils.file_type(image)
for image in glob.glob(op.join(fol, '{}*.*'.format(images_prefix)))
])
for opt_type in ['png', 'jpg', 'jpeg', 'bmp', 'gif']:
if opt_type in images_types:
images_type = opt_type
print('Images type is {}'.format(images_type))
break
if images_type == '':
raise Exception("Can't find the images type!")
images = glob.glob(
op.join(fol, '{}*.{}'.format(images_prefix, images_type)))
image_nb = utils.namebase(images[0])
number = utils.read_numbers_rx(image_nb)[0]
if images_prefix == '':
images_prefix = image_nb[:-len(number)]
if images_format == '':
images_format = '%0{}d'.format(len(number))
if start_number == -1:
start_number = min([
int(utils.namebase(image)[len(images_prefix):]) for image in images
])
return images_type, images_prefix, images_format, len(number), start_number
def create_dup_frames_links(subject, dup_frames, fol):
fol = op.join(MMVT_DIR, subject, 'figures', fol)
utils.delete_folder_files(fol)
utils.make_dir(fol)
for ind, frame in enumerate(dup_frames):
utils.make_link(
frame, op.join(fol, 'dup_{}.{}'.format(ind,
utils.file_type(frame))))
return fol
def project_and_calc_clusters(args):
if not op.isdir(args.root_fol):
print('You should first set args.root_fol!')
return False
nii_files = [
f for f in glob.glob(op.join(args.root_fol, '*'))
if op.isfile(f) and utils.file_type(f) in ('nii', 'nii.gz', 'mgz')
]
for fname in nii_files:
args = fmri.read_cmd_args(
dict(subject=args.subject,
function='project_volume_to_surface,find_clusters',
fmri_file_template=fname))
pu.run_on_subjects(args, fmri.main)
def isotropization(subject,
ct_fname,
ct_fol,
new_image_fname='',
isotropization_type=1,
iso_vector_override=None):
if not op.isdir(ct_fol):
ct_fol = utils.make_dir(op.join(MMVT_DIR, subject, 'ct'))
if new_image_fname == '':
new_image_fname = 'iso_ct.{}'.format(utils.file_type(ct_fname))
ct_fname = op.join(ct_fol, ct_fname)
iso_img = ctu.isotropization(ct_fname,
isotropization_type=isotropization_type,
iso_vector_override=iso_vector_override)
nib.save(iso_img, op.join(ct_fol, new_image_fname))
def combine_two_figures_with_cb(fname1, fname2, data_max, data_min, cb_cm, cb_ticks=[], crop_figures=True,
background='black', cb_ticks_font_size=10):
if crop_figures:
crop_image(fname1, fname1, dx=150, dy=0, dw=50, dh=70)
crop_image(fname2, fname2, dx=150 + 50, dy=0, dw=0, dh=70)
new_image_fname = op.join(utils.get_parent_fol(fname1), '{}_{}.{}'.format(
utils.namebase(fname1), utils.namebase(fname2), utils.file_type(fname1)))
combine_two_images(fname1, fname2, new_image_fname, facecolor=background, dpi=400, w_fac=1, h_fac=1)
if len(cb_ticks) == 0:
cb_ticks = [data_min, data_max]
fol = utils.get_parent_fol(fname1)
plot_color_bar(data_max, data_min, cb_cm, do_save=True, cb_ticks=cb_ticks, fol=fol, background_color=background,
cb_ticks_font_size=cb_ticks_font_size)
cb_fname = op.join(fol, '{}_colorbar.jpg'.format(cb_cm))
cb_img = Image.open(cb_fname)
return combine_brain_with_color_bar(new_image_fname, cb_img, overwrite=True)
def combine_images(fol,
movie_name,
frame_rate=10,
start_number=-1,
images_prefix='',
images_format='',
images_type='',
ffmpeg_cmd='ffmpeg',
**kwargs):
if images_type == '':
images_types = set([
utils.file_type(image)
for image in glob.glob(op.join(fol, '{}*.*'.format(images_prefix)))
])
for opt_type in ['png', 'jpg', 'bmp', 'gif']:
if opt_type in images_types:
images_type = opt_type
print('Images type is {}'.format(images_type))
break
if images_type == '':
raise Exception("Can't find the images type!")
images = glob.glob(
op.join(fol, '{}*.{}'.format(images_prefix, images_type)))
image_nb = utils.namebase(images[0])
number = utils.read_numbers_rx(image_nb)[0]
if images_prefix == '':
images_prefix = image_nb[:-len(number)]
if images_format == '':
images_format = '%0{}d'.format(len(number))
if start_number == -1:
start_number = min([
int(utils.namebase(image)[len(images_prefix):]) for image in images
])
images_prefix = op.join(fol, images_prefix)
movie_name = op.join(fol, movie_name)
combine_images_cmd = '{ffmpeg_cmd} -framerate {frame_rate} '
if start_number > 1:
# You might want to use a static ffmpeg if your ffmepg version doesn't support the start_number flag, like:
# ffmpeg_cmd = '~/space1/Downloads/ffmpeg-git-static/ffmpeg'
combine_images_cmd += '-start_number {start_number} '
combine_images_cmd += '-i {images_prefix}{images_format}.{images_type} '
# http://stackoverflow.com/questions/20847674/ffmpeg-libx264-height-not-divisible-by-2
combine_images_cmd += '-vf "scale=trunc(iw/2)*2:trunc(ih/2)*2" '
combine_images_cmd += '-c:v libx264 -r 30 -pix_fmt yuv420p {movie_name}.mp4'
rs = utils.partial_run_script(locals())
rs(combine_images_cmd)
def save_subject_ct_trans(subject,
ct_name='ct_reg_to_mr.mgz',
overwrite=False):
fol = utils.make_dir(op.join(MMVT_DIR, subject, 'ct'))
output_fname = op.join(fol, 'ct_trans.npz')
if op.isfile(output_fname) and not overwrite:
return True
ct_fname, ct_exist = utils.locating_file(
ct_name, ['*.mgz', '*.nii', '*.nii.gz'], [
op.join(MMVT_DIR, subject, 'ct'),
op.join(SUBJECTS_DIR, subject, 'ct')
])
# ct_fname = op.join(MMVT_DIR, subject, 'ct', ct_name)
if not ct_exist: # op.isfile(ct_fname):
# subjects_ct_fname = op.join(SUBJECTS_DIR, subject, 'mri', ct_name)
ct_fname, ct_exist = utils.locating_file(
ct_name, ['*.mgz', '*.nii', '*.nii.gz'],
op.join(SUBJECTS_DIR, subject, 'mri'))
if ct_exist: #op.isfile(subjects_ct_fname):
utils.make_dir(op.join(MMVT_DIR, subject, 'ct'))
ct_fname = utils.copy(ct_fname, op.join(MMVT_DIR, subject, 'ct'))
else:
print("Can't find subject's CT! ({})".format(ct_fname))
return False
if utils.file_type(ct_fname) != 'mgz':
ct_fname = fu.mri_convert_to(ct_fname, 'mgz')
if ct_fname != op.join(MMVT_DIR, subject, 'ct', ct_name):
utils.make_link(ct_fname, op.join(MMVT_DIR, subject, 'ct', ct_name))
print('save_subject_ct_trans: loading {}'.format(ct_fname))
header = nib.load(ct_fname).header
ras_tkr2vox, vox2ras_tkr, vox2ras, ras2vox = anat.get_trans_functions(
header)
print('save_subject_ct_trans: Saving {}'.format(output_fname))
np.savez(output_fname,
ras_tkr2vox=ras_tkr2vox,
vox2ras_tkr=vox2ras_tkr,
vox2ras=vox2ras,
ras2vox=ras2vox)
return op.isfile(output_fname)
