def main():
"""Commandline interface."""
parser = argparse.ArgumentParser()
parser.add_argument('filename',
metavar='path',
nargs='+',
help="Path to image. Multiple paths can be provided.")
parser.add_argument(
'--mode',
type=str,
required=False,
metavar=cfg.mode,
default=cfg.mode,
help="Gif creation mode. Available options are: 'normal', \
'pseudocolor', 'depth', 'rgb'")
parser.add_argument('--fps',
type=int,
required=False,
metavar=cfg.fps,
default=cfg.fps,
help="Frames per second.")
parser.add_argument('--size',
type=float,
required=False,
metavar=cfg.size,
default=cfg.size,
help="Image resizing factor.")
parser.add_argument(
'--cmap',
type=str,
required=False,
metavar=cfg.cmap,
default=cfg.cmap,
help="Color map. Used only in combination with 'pseudocolor' mode.")
args = parser.parse_args()
cfg.mode = (args.mode).lower()
cfg.size = args.size
cfg.fps = args.fps
cfg.cmap = args.cmap
# Welcome message
welcome_str = '{} {}'.format('gif_your_nifti', __version__)
welcome_decor = '=' * len(welcome_str)
print('{}\n{}\n{}'.format(welcome_decor, welcome_str, welcome_decor))
print('Selections:')
print(' mode = {}'.format(cfg.mode))
print(' size = {}'.format(cfg.size))
print(' fps = {}'.format(cfg.fps))
# Determine gif creation mode
if cfg.mode in ['normal', 'pseudocolor', 'depth']:
for f in args.filename:
if cfg.mode == 'normal':
core.write_gif_normal(f, cfg.size, cfg.fps)
elif cfg.mode == 'pseudocolor':
print(' cmap = {}'.format(cfg.cmap))
core.write_gif_pseudocolor(f, cfg.size, cfg.fps, cfg.cmap)
elif cfg.mode == 'depth':
core.write_gif_depth(f, cfg.size, cfg.fps)
elif cfg.mode == 'rgb':
if len(args.filename) != 3:
raise ValueError('RGB mode requires 3 input files.')
else:
core.write_gif_rgb(args.filename[0], args.filename[1],
args.filename[2], cfg.size, cfg.fps)
else:
raise ValueError("Unrecognized mode.")
print('Finished.')
def main():
"""Commandline interface."""
parser = argparse.ArgumentParser()
parser.add_argument('filename',
metavar='path',
nargs='+',
help="Path to image. Multiple paths can be provided.")
parser.add_argument(
'--mode',
type=str,
required=False,
metavar=cfg.mode,
default=cfg.mode,
help="Gif creation mode. Available options are: 'normal', \
'pseudocolor', 'depth', 'rgb'")
parser.add_argument('--fps',
type=int,
required=False,
metavar=cfg.fps,
default=cfg.fps,
help="Frames per second.")
parser.add_argument('--size',
type=float,
required=False,
metavar=cfg.size,
default=cfg.size,
help="Image resizing factor.")
parser.add_argument(
'--cmap',
type=str,
required=False,
metavar=cfg.cmap,
default=cfg.cmap,
help="Color map. Used only in combination with 'pseudocolor' mode.")
parser.add_argument('--iso',
action='store_true',
required=False,
default=cfg.iso,
help="Resample image to appear isotropic.")
parser.add_argument(
'--time',
type=str,
required=False,
metavar='method',
default=cfg.time,
help=
"Gif along time axis using 'coronal', 'sagittal', or the 'horizontal' plane."
)
parser.add_argument('--cols',
type=int,
required=False,
metavar='columns',
default=cfg.cols,
help="Number of columns to use in 4D grid mode.")
args = parser.parse_args()
cfg.mode = (args.mode).lower()
cfg.size = args.size
cfg.fps = args.fps
cfg.cmap = args.cmap
cfg.iso = args.iso
cfg.time = args.time
cfg.cols = args.cols
if 'cols' in vars(args) and 'time' not in vars(args):
parser.error('Option --cols requires an option for --time')
# Welcome message
welcome_str = '{} {}'.format('gif_your_nifti', __version__)
welcome_decor = '=' * len(welcome_str)
print('{}\n{}\n{}'.format(welcome_decor, welcome_str, welcome_decor))
print('Selections:')
print(' mode = {}'.format(cfg.mode))
print(' size = {}'.format(cfg.size))
print(' fps = {}'.format(cfg.fps))
print(' iso = {}'.format(cfg.iso))
print(' time = {}'.format(cfg.time))
print(' cols = {}'.format(cfg.cols))
# Determine gif creation mode
if cfg.mode in ['normal', 'pseudocolor', 'depth']:
for f in args.filename:
if cfg.mode == 'normal':
core.write_gif_normal(f, cfg.size, cfg.fps, cfg.iso, cfg.time,
cfg.cols)
elif cfg.mode == 'pseudocolor':
print(' cmap = {}'.format(cfg.cmap))
core.write_gif_pseudocolor(f, cfg.size, cfg.fps, cfg.cmap)
elif cfg.mode == 'depth':
core.write_gif_depth(f, cfg.size, cfg.fps)
elif cfg.mode == 'rgb':
if len(args.filename) != 3:
raise ValueError('RGB mode requires 3 input files.')
else:
core.write_gif_rgb(args.filename[0], args.filename[1],
args.filename[2], cfg.size, cfg.fps)
else:
raise ValueError("Unrecognized mode.")
print('Finished.')
def gif_defaced(bids_dir, subject_label, session=None, t2w=None):
"""
Create a gif that loops through slices of the defaced image in
x,y,z direction.
Parameters
----------
bids_dir : str
Path to BIDS root directory.
subject_label : str
Label of subject to be plotted (without 'sub-').
session : str, optional
If multiple sessions exist, create one gif per session.
session : bool, optional
If T2w image exists, create a gif for defaced T2w.
"""
from bids import BIDSLayout
from glob import glob
from os.path import join as opj
from shutil import move
import gif_your_nifti.core as gif2nif
layout = BIDSLayout(bids_dir)
bidsonym_path = opj(bids_dir, 'sourcedata/bidsonym/sub-%s' % subject_label)
if session is not None:
defaced_t1w = layout.get(subject=subject_label,
extension='nii.gz',
suffix='T1w',
return_type='filename',
session=session)
if t2w is not None:
defaced_t2w = layout.get(subject=subject_label,
extension='nii.gz',
suffix='T2w',
return_type='filename',
session=session)
else:
defaced_t1w = layout.get(subject=subject_label,
extension='nii.gz',
suffix='T1w',
return_type='filename')
if t2w is not None:
defaced_t2w = layout.get(subject=subject_label,
extension='nii.gz',
suffix='T2w',
return_type='filename',
session=session)
for t1_image in defaced_t1w:
gif2nif.write_gif_normal(t1_image)
if t2w is not None:
for t2_image in defaced_t2w:
gif2nif.write_gif_normal(t2_image)
if session is not None:
list_gifs = glob(
opj(bids_dir, 'sub-%s/ses-%s/anat' % (subject_label, session),
'sub-%s*.gif' % subject_label))
else:
list_gifs = glob(
opj(bids_dir, 'sub-%s/anat' % subject_label,
'sub-%s*.gif' % subject_label))
for gif_nii in list_gifs:
move(gif_nii, opj(bids_dir, bidsonym_path))
def main():
"""Commandline interface."""
parser = argparse.ArgumentParser()
parser.add_argument('filename',
metavar='path',
nargs='+',
help="Path to image. Multiple paths can be provided.")
parser.add_argument(
'--mode',
type=str,
required=False,
metavar=cfg.mode,
default=cfg.mode,
help="Gif creation mode. Available options are: 'normal', \
'pseudocolor', 'depth', 'rgb'")
parser.add_argument('--fps',
type=int,
required=False,
metavar=cfg.fps,
default=cfg.fps,
help="Frames per second.")
parser.add_argument('--size',
type=float,
required=False,
metavar=cfg.size,
default=cfg.size,
help="Image resizing factor.")
parser.add_argument(
'--cmap',
type=str,
required=False,
metavar=cfg.cmap,
default=cfg.cmap,
help="Color map. Used only in combination with 'pseudocolor' mode.")
parser.add_argument('--sliceCor',
type=int,
required=False,
metavar=cfg.sliceCor,
default=cfg.sliceCor,
help="Slice index for Coronal view.")
parser.add_argument('--sliceSag',
type=int,
required=False,
metavar=cfg.sliceSag,
default=cfg.sliceSag,
help="Slice index for Sagital view.")
parser.add_argument('--sliceAx',
type=int,
required=False,
metavar=cfg.sliceAx,
default=cfg.sliceAx,
help="Slice index for Axial view.")
parser.add_argument(
'--slicesOrder',
type=str,
required=False,
metavar=cfg.slicesOrder,
default='csa',
help="Order of the three columns cortical, sagital, axial."
" Can be csa, cas, asc, acs, sac or sca.")
parser.add_argument('--out_filename',
type=str,
required=False,
default=None,
help="Output GIF filename with extension.")
args = parser.parse_args()
cfg.mode = (args.mode).lower()
cfg.size = args.size
cfg.fps = args.fps
cfg.cmap = args.cmap
cfg.slices = [args.sliceCor, args.sliceSag, args.sliceAx]
cfg.slicesOrder = args.slicesOrder
# Determine gif creation mode
if cfg.mode in ['normal', 'pseudocolor', 'depth']:
for f in args.filename:
if cfg.mode == 'normal':
core.write_gif_normal(f, cfg.size, cfg.fps, cfg.slices,
cfg.slicesOrder, args.out_filename)
elif cfg.mode == 'pseudocolor':
core.write_gif_pseudocolor(f, cfg.size, cfg.fps, cfg.cmap,
cfg.slices, cfg.slicesOrder,
args.out_filename)
elif cfg.mode == 'depth':
core.write_gif_depth(f, cfg.size, cfg.fps, args.out_filename)
elif cfg.mode == 'rgb':
if len(args.filename) != 3:
raise ValueError('RGB mode requires 3 input files.')
else:
core.write_gif_rgb(args.filename[0], args.filename[1],
args.filename[2], cfg.size, cfg.fps,
args.out_filename)
else:
raise ValueError("Unrecognized mode.")
"""Example usage of gif_your_nifti.""" import gif_your_nifti.core as gif2nif # filename = 'mni_icbm152_t1_tal_nlin_asym_09c.nii' filename = r'C:\\Data\\Folder\\Subfolder\\5639\\CT-MRI-5639_MR_norm.nii' # Create a normal grayscale gif. gif2nif.write_gif_normal(filename) # Create a pseudocolored gif. gif2nif.write_gif_pseudocolor(filename, colormap='plasma') # Create a depth gif. gif2nif.write_gif_depth(filename) # Change the size of gifs. gif2nif.write_gif_pseudocolor(filename, size=0.5, colormap='cubehelix') gif2nif.write_gif_pseudocolor(filename, size=0.5, colormap='inferno') gif2nif.write_gif_pseudocolor(filename, size=0.5, colormap='viridis') # Create an RGB gif, based on gray matter, white matter and cerebrospinal fluid # images from MNI template. filename1 = 'mni_icbm152_gm_tal_nlin_asym_09c.nii' filename2 = 'mni_icbm152_wm_tal_nlin_asym_09c.nii' filename3 = 'mni_icbm152_csf_tal_nlin_asym_09c.nii' gif2nif.write_gif_rgb(filename1, filename2, filename3)