def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('input', type=str, help='Blender .obj input file name')
parser.add_argument('--n', type=int, help='Number of pixels')
parser.add_argument('--supersampling-projection', type=int, default=1,
help='Supersampling for mesh projections computation')
parser.add_argument('--dset', type=str,
help='Data set name, if not specified guessed from input')
parser.add_argument('--num-projections', type=int, help='Number of projections')
parser.add_argument('--out-directory', type=str, default='dataset',
help="Output directory, result goes to 'out-directory/dset/projections'"
"or 'out-directory/dset/truth', depending on the --make-gt switch")
parser.add_argument('--pixel-size', type=float, default=[750.], nargs='+',
help='Pixel size in nm')
parser.add_argument('--rotation-angle', type=float, default=180,
help='Total rotation angle in degrees')
parser.add_argument('--lamino-angle', type=float, default=[5], nargs='+',
help='Laminographic angle in degrees')
parser.add_argument('--rotation-axis', type=str, choices=['y', 'z'], default=['y'],
nargs='+', help='Rotation axis (y - up, z - beam direction)')
parser.add_argument('--num-devices', type=int, default=1,
help='Number of compute devices to use')
parser.add_argument('--supersampling', type=int, default=[1], nargs='+',
help='Supersampling computes with n-times more pixels than usual')
parser.add_argument('--double-precision', action='store_true', help='Use double precision')
# Ground truth related
parser.add_argument('--z-chunk', type=int, default=100,
help='Number of ground truth slices to compute during one pass')
parser.add_argument('--make-gt', action='store_true',
help='Create ground truth instead of projections')
return parser.parse_args()
def main():
"""Parse command line arguments and execute one of the experiments."""
parser = get_default_parser(__doc__)
subparsers = parser.add_subparsers(help='sub-command help')
motion = subparsers.add_parser('motion', help='An experiment with motion')
motion.add_argument('--output',
type=str,
help='Output directory for moving objects.')
motion.add_argument('--show',
action='store_true',
help='Show images as they are produced')
motion.add_argument('--show-flat',
action='store_true',
help='Show a flat field image')
motion.add_argument('--conduct',
action='store_true',
help='Conduct the experiment')
motion.add_argument('--num-images',
type=int,
help='Number of images to produce')
motion.set_defaults(_func=make_motion)
flat = subparsers.add_parser(
'flat', help='Quantitatively correct flat field computation')
flat.set_defaults(_func=make_topo_tomo_flat)
args = parser.parse_args()
args._func(args)
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--output',
type=str,
help='Output directory for projections.')
return parser.parse_args()
def main():
parser = get_default_parser(__doc__)
subparsers = parser.add_subparsers(help='sub-command help')
manual = subparsers.add_parser(
'manual', help='Manual positioning via simple transformations')
trajectory = subparsers.add_parser(
'trajectory', help='Automatic positioning via trajectories')
subtrajectories = subparsers.add_parser('subtrajectories',
help='Automatic positioning with '
'local sub-body trajectories')
manual.set_defaults(_func=make_manual_sequence)
trajectory.set_defaults(_func=make_trajectory_sequence)
subtrajectories.add_argument(
'--t',
type=float,
help='Time at which to compute the projection normalized to '
'[0, 1], if not specified, complete sequence is shown')
subtrajectories.set_defaults(_func=make_complex_trajectory_sequence)
args = parser.parse_args()
syris.init(device_index=0)
# Set constants
args.n = 512
args.shape = (args.n, args.n)
args.ps = 1 * q.um
args._func(args)
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--energy-center', type=float, default=10,
help='Energy at which the filter is centered [keV]')
parser.add_argument('--energy-resolution', type=float, default=1e-2,
help='Energy resolution (FWHM of the Gaussian filter) [dE/E]')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--propagation-distance',
type=float,
default=2,
help='Propagation distance [m]')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--input', default='grid', choices=['grid', 'lena'],
help='Input image')
parser.add_argument('--output', type=str, help='Output file name')
parser.add_argument('--n', type=int, default=512, help='Number of pixels in one dimension')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument(
'--supersampling',
type=int,
default=8,
help='Supersampling used to prevent propagation artefacts')
return parser.parse_args()
def parse_args():
"""Parse command line arguments."""
parser = get_default_parser(__doc__)
parser.add_argument('--input', type=str, help='Input .obj file')
parser.add_argument('--units',
type=str,
default='um',
help='Mesh physical units')
parser.add_argument('--n', type=int, default=256, help='Number of pixels')
parser.add_argument('--supersampling',
type=int,
default=1,
help='Supersampling for mesh computation')
parser.add_argument('--pixel-size', type=float, help='Pixel size in um')
parser.add_argument('--center',
type=str,
help='Mesh centering on creation')
parser.add_argument('--translate',
type=float,
nargs=2,
help='Translation as (x, y) in um')
parser.add_argument('--x-rotate',
type=float,
default=0.,
help='Rotation around x axis [deg]')
parser.add_argument('--y-rotate',
type=float,
default=0.,
help='Rotation around y axis [deg]')
parser.add_argument('--margin',
type=float,
default=1.,
help='Margin in factor of the full FOV')
parser.add_argument('--projection-filename',
type=str,
help='Save projection to this filename')
parser.add_argument('--compute-slice',
action='store_true',
help='Compute also one slice')
parser.add_argument('--slice-filename',
type=str,
help='Save slice to this filename')
parser.add_argument('--double-precision',
action='store_true',
help='Use double precision')
args = parser.parse_args()
if args.pixel_size is not None:
args.pixel_size = args.pixel_size * q.um
args.x_rotate = args.x_rotate * q.deg
args.y_rotate = args.y_rotate * q.deg
if args.translate is not None:
args.translate = args.translate * q.um
return args
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument(
'--supersampling',
type=int,
choices=[2, 4, 8, 16, 32],
default=32,
help='Supersampling used to prevent transmission function aliasing')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--supersampling', type=int, default=8,
help='Supersampling used to prevent propagation artefacts')
parser.add_argument('--noise', action='store_true',
help='Apply noise on the polychromatic image')
parser.add_argument('--exposure', type=float, default=1,
help='Camera exposure time [ms], defines the amount of ' +
'noise in the polychromatic image')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument(
'--t',
type=float,
default=0.5,
help='Time at which to compute the projection normalized to [0, 1]')
args = parser.parse_args()
if args.t < 0 or args.t > 1:
raise ValueError('--t must be in the range [0, 1]')
return args
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--n', type=int, default=[1024], nargs='+',
help='List of number of pixels in one dimension')
parser.add_argument('--num-devices', type=int, default=1,
help='Number of compute devices to use')
parser.add_argument('--pixel-size', type=float, default=1, help='Pixel size [um]')
parser.add_argument('--platform', type=str, help='Platform name substring')
parser.add_argument('--runs', type=int, default=1, help='Number of runs')
parser.add_argument('--output', type=str, help='Output file name')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--energy-center',
type=float,
default=10,
help='Energy at which the filter is centered [keV]')
parser.add_argument(
'--energy-resolution',
type=float,
default=1e-2,
help='Energy resolution (FWHM of the Gaussian filter) [dE/E]')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--input',
default='grid',
choices=['grid', 'lena'],
help='Input image')
parser.add_argument('--output', type=str, help='Output file name')
parser.add_argument('--n',
type=int,
default=512,
help='Number of pixels in one dimension')
return parser.parse_args()
def parse_args():
"""Parse command line arguments."""
parser = get_default_parser(__doc__)
parser.add_argument('--fn', type=float, default=4.0, help='Fresnel number')
parser.add_argument('--energy', type=float, default=1.0, help='Energy [keV]')
parser.add_argument('--aperture', type=float, default=100.0,
help='Half the aperture width [um]')
parser.add_argument('--supersampling', type=int, default=4, help='Supersampling')
parser.add_argument('--numerical-divisors', type=int, nargs='+', default=[1],
help='A list of divisors which will divide the aliasing-free number '
'of pixels to produce aliased results to show the importance of proper '
'sampling')
parser.add_argument('--txt-output', type=str, help='File name where to store the data as text')
return parser.parse_args()
def main():
"""Parse command line arguments and execute one of the experiments."""
parser = get_default_parser(__doc__)
subparsers = parser.add_subparsers(help='sub-command help')
motion = subparsers.add_parser('motion', help='An experiment with motion')
motion.add_argument('--output', type=str, help='Output directory for moving objects.')
motion.add_argument('--show', action='store_true', help='Show images as they are produced')
motion.add_argument('--show-flat', action='store_true', help='Show a flat field image')
motion.add_argument('--conduct', action='store_true', help='Conduct the experiment')
motion.add_argument('--num-images', type=int, help='Number of images to produce')
motion.set_defaults(_func=make_motion)
flat = subparsers.add_parser('flat', help='Quantitatively correct flat field computation')
flat.set_defaults(_func=make_topo_tomo_flat)
args = parser.parse_args()
args._func(args)
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--n',
type=int,
default=[1024],
nargs='+',
help='List of number of pixels in one dimension')
parser.add_argument('--num-devices',
type=int,
default=1,
help='Number of compute devices to use')
parser.add_argument('--pixel-size',
type=float,
default=1,
help='Pixel size [um]')
parser.add_argument('--platform', type=str, help='Platform name substring')
parser.add_argument('--runs', type=int, default=1, help='Number of runs')
parser.add_argument('--output', type=str, help='Output file name')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--n',
type=int,
default=512**2,
help='Number of pixels (default 512^2)')
parser.add_argument('--m',
type=int,
default=64,
help='Number of pixel operations (default 64)')
parser.add_argument(
'--k',
type=float,
default=[1],
nargs='*',
help='Time complexity, there are n x m^k operations in total '
'(default 1). The argument might have one (single run) or 3 numbers '
'(meaning start stop step) when a scan is performed.')
parser.add_argument('--runs',
type=int,
default=1,
help='Number of runs per one complexity. '
'The result speedup is the mean.')
parser.add_argument('--plot', action='store_true', help='Plot results')
parser.add_argument('--verbose',
action='store_true',
help='Print infomation from individual runs')
parser.add_argument(
'--output',
type=str,
help='Output individual speedups from all '
'runs as a numpy array in this filename k is the complexity. '
'It must conatin a formatting string which will hold the complexity, '
'e.g. speedups{:>04}.npy.')
args = parser.parse_args()
m = args.k
if not (len(m) == 1 or len(m) == 3):
raise ValueError('--k must contain either 1 or 3 numbers')
return args
def parse_args():
parser = get_default_parser('Metaballs example')
parser.add_argument('--n', type=int, default=512, help='Number of image pixels')
parser.add_argument('--method', choices=['random', 'fixed', 'file'], default='random',
help='Use random number of metaballs, fixed metaballs or file with '
'packed metaball structure')
parser.add_argument('--num', type=int, default=50, help='Number of random metaballs')
parser.add_argument('--distance', type=float,
help='Distance of the two fixed metaballs in pixels')
parser.add_argument('--min-radius', type=int, default=5,
help='Minimum radius of random metaballs in pixels')
parser.add_argument('--max-radius', type=int, default=25,
help='Maximum radius of random metaballs in pixels')
parser.add_argument('--input', type=str, help='Input file for packed metaballs')
parser.add_argument('--output', type=str,
help='Output file for created metaballs as a packed structure')
parser.add_argument('--output-thickness', type=str,
help='Output file for projected thickness')
parser.add_argument('--algorithm', choices=['naive', 'fast'], default='fast',
help='Used algorithm for intersections computation')
return parser.parse_args()
def main():
parser = get_default_parser(__doc__)
subparsers = parser.add_subparsers(help='sub-command help')
manual = subparsers.add_parser('manual', help='Manual positioning via simple transformations')
trajectory = subparsers.add_parser('trajectory', help='Automatic positioning via trajectories')
subtrajectories = subparsers.add_parser('subtrajectories', help='Automatic positioning with '
'local sub-body trajectories')
manual.set_defaults(_func=make_manual_sequence)
trajectory.set_defaults(_func=make_trajectory_sequence)
subtrajectories.add_argument('--t', type=float,
help='Time at which to compute the projection normalized to '
'[0, 1], if not specified, complete sequence is shown')
subtrajectories.set_defaults(_func=make_complex_trajectory_sequence)
args = parser.parse_args()
syris.init(device_index=0)
# Set constants
args.n = 512
args.shape = (args.n, args.n)
args.ps = 1 * q.um
args._func(args)
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--n', type=int, default=512 ** 2, help='Number of pixels (default 512^2)')
parser.add_argument('--m', type=int, default=64, help='Number of pixel operations (default 64)')
parser.add_argument('--k', type=float, default=[1], nargs='*',
help='Time complexity, there are n x m^k operations in total '
'(default 1). The argument might have one (single run) or 3 numbers '
'(meaning start stop step) when a scan is performed.')
parser.add_argument('--runs', type=int, default=1, help='Number of runs per one complexity. '
'The result speedup is the mean.')
parser.add_argument('--plot', action='store_true', help='Plot results')
parser.add_argument('--verbose', action='store_true',
help='Print infomation from individual runs')
parser.add_argument('--output', type=str, help='Output individual speedups from all '
'runs as a numpy array in this filename k is the complexity. '
'It must conatin a formatting string which will hold the complexity, '
'e.g. speedups{:>04}.npy.')
args = parser.parse_args()
m = args.k
if not (len(m) == 1 or len(m) == 3):
raise ValueError('--k must contain either 1 or 3 numbers')
return args
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--output', type=str, help='Output directory for projections.')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--supersampling', type=int, choices=[2, 4, 8, 16, 32], default=32,
help='Supersampling used to prevent transmission function aliasing')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('--propagation-distance', type=float, default=2,
help='Propagation distance [m]')
return parser.parse_args()
def parse_args():
"""Parse command line arguments."""
parser = get_default_parser(__doc__)
parser.add_argument('--output', type=str, help='Output directory for moving objects.')
return parser.parse_args()
def parse_args():
parser = get_default_parser(__doc__)
parser.add_argument('input', type=str, help='Blender .obj input file name')
parser.add_argument('--n', type=int, help='Number of pixels')
parser.add_argument('--supersampling-projection',
type=int,
default=1,
help='Supersampling for mesh projections computation')
parser.add_argument(
'--dset',
type=str,
help='Data set name, if not specified guessed from input')
parser.add_argument('--num-projections',
type=int,
help='Number of projections')
parser.add_argument(
'--out-directory',
type=str,
default='dataset',
help="Output directory, result goes to 'out-directory/dset/projections'"
"or 'out-directory/dset/truth', depending on the --make-gt switch")
parser.add_argument('--pixel-size',
type=float,
default=[750.],
nargs='+',
help='Pixel size in nm')
parser.add_argument('--rotation-angle',
type=float,
default=180,
help='Total rotation angle in degrees')
parser.add_argument('--lamino-angle',
type=float,
default=[5],
nargs='+',
help='Laminographic angle in degrees')
parser.add_argument('--rotation-axis',
type=str,
choices=['y', 'z'],
default=['y'],
nargs='+',
help='Rotation axis (y - up, z - beam direction)')
parser.add_argument('--num-devices',
type=int,
default=1,
help='Number of compute devices to use')
parser.add_argument(
'--supersampling',
type=int,
default=[1],
nargs='+',
help='Supersampling computes with n-times more pixels than usual')
parser.add_argument('--double-precision',
action='store_true',
help='Use double precision')
# Ground truth related
parser.add_argument(
'--z-chunk',
type=int,
default=100,
help='Number of ground truth slices to compute during one pass')
parser.add_argument('--make-gt',
action='store_true',
help='Create ground truth instead of projections')
return parser.parse_args()
