def set_deconvolve_with_sphere_options (parser):
set_formatter(parser)
parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]')
parser.set_description('Deconvolve INPUT_PATH with sphere.')
parser.add_option ('--sphere-diameter', dest='diameter',
type = 'float',
default = 170,
help = 'Specify sphere diameter in nanometers.')
parser.add_option ('--input-path', '-i',
type = 'file', metavar='PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='PATH',
help = 'Specify output PATH of 3D images.'
)
parser.add_option ('--max-nof-iterations',
type = 'int', default=10,
help = 'Specify maximum number of iterations.')
parser.add_option('--convergence-epsilon',
type = 'float', default=0.05,
help = 'Specify small positive number that determines the window for convergence criteria.')
from ..ops.script_options import get_fft_options_group
from ..io.script_options import get_microscope_options_group
parser.add_option_group(get_fft_options_group (parser))
parser.add_option_group(get_rltv_options_group (parser))
parser.add_option_group(get_microscope_options_group (parser))
def set_clusters_options(parser):
set_formatter(parser)
parser.set_usage('%prog [options] [ -i INPUT_PATH ]')
parser.set_description('Find clusters in INPUT_PATH field.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='INPUT_PATH',
dest='input_path',
help='Specify INPUT_PATH.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='OUTPUT_PATH',
dest='output_path',
help='Specify OUTPUT_PATH.')
parser.add_option(
'--detail-size',
dest='detail_size',
type='float',
help='Specify typical size of a detail to be resolved, in micrometers.'
)
from iocbio.ops.script_options import get_regress_options_group
parser.add_option_group(get_regress_options_group(parser))
from iocbio.ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group(parser))
def set_deconvolve_options(parser):
set_formatter(parser)
parser.set_usage('%prog [options] [ [-k] PSF_PATH [-i] INPUT_PATH [ [-o] OUTPUT_PATH] ]')
parser.set_description('Deconvolve INPUT_PATH with PSF_PATH.')
add_psflib_options(parser)
parser.add_option('--psf-path','-k', dest = 'psf_path',
type = 'file', metavar='PATH',
help = 'Specify PATH to PSF 3D images.'
)
parser.add_option ('--input-path', '-i',
type = 'file', metavar='PATH',
help = 'Specify input PATH of 3D images.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='PATH',
help = 'Specify output PATH of 3D images.'
)
parser.add_option ('--max-nof-iterations',
type = 'int', default=10,
help = 'Specify maximum number of iterations.')
parser.add_option('--convergence-epsilon',
type = 'float', default=0.05,
help = 'Specify small positive number that determines the window for convergence criteria.')
parser.add_option('--degrade-input', action='store_true',
help = 'Degrade input: apply noise to convolved input.')
parser.add_option('--no-degrade-input', action='store_false', dest='degrade_input',
help = 'See ``--degrade-input``.')
parser.add_option('--degrade-input-snr',
type = 'float', default=0.0,
help = 'Specify the signal-to-noise ratio when using --degrade-input.'\
'If set to 0, then snr will be estimated as sqrt(max(input image)).')
parser.add_option ('--first-estimate',
choices = ['input image',
'convolved input image',
'2x convolved input image',
'last result'
],
help = 'Specify first estimate for iteration.')
parser.add_option('--save-intermediate-results',
action = 'store_true',
help = 'Save intermediate results.')
parser.add_option('--no-save-intermediate-results',
dest = 'save_intermediate_results',
action = 'store_false',
help = 'See ``--save-intermediate-results`` option.')
from ..ops.script_options import get_apply_window_options_group
parser.add_option_group(get_apply_window_options_group (parser))
parser.add_option_group(get_rltv_options_group (parser))
from ..ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group (parser))
from ..script_options import get_runner_options_group
parser.add_option_group(get_runner_options_group (parser))
from ..io.script_options import get_io_options_group, get_microscope_options_group
parser.add_option_group(get_microscope_options_group (parser))
def set_clusters_options (parser):
set_formatter(parser)
parser.set_usage ('%prog [options] [ -i INPUT_PATH ]')
parser.set_description('Find clusters in INPUT_PATH field.')
parser.add_option ('--input-path','-i',
type = 'file', metavar='INPUT_PATH', dest='input_path',
help = 'Specify INPUT_PATH.'
)
parser.add_option ('--output-path','-o',
type = 'file', metavar='OUTPUT_PATH', dest='output_path',
help = 'Specify OUTPUT_PATH.'
)
parser.add_option ('--detail-size', dest='detail_size',type = 'float',
help = 'Specify typical size of a detail to be resolved, in micrometers.')
from iocbio.ops.script_options import get_regress_options_group
parser.add_option_group(get_regress_options_group (parser))
from iocbio.ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group (parser))
def set_deconvolve_with_sphere_options(parser):
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]')
parser.set_description('Deconvolve INPUT_PATH with sphere.')
parser.add_option('--sphere-diameter',
dest='diameter',
type='float',
default=170,
help='Specify sphere diameter in nanometers.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
parser.add_option('--max-nof-iterations',
type='int',
default=10,
help='Specify maximum number of iterations.')
parser.add_option(
'--convergence-epsilon',
type='float',
default=0.05,
help=
'Specify small positive number that determines the window for convergence criteria.'
)
from ..ops.script_options import get_fft_options_group
from ..io.script_options import get_microscope_options_group
parser.add_option_group(get_fft_options_group(parser))
parser.add_option_group(get_rltv_options_group(parser))
parser.add_option_group(get_microscope_options_group(parser))
def set_deconvolve_options(parser):
set_formatter(parser)
parser.set_usage(
'%prog [options] [ [-k] PSF_PATH [-i] INPUT_PATH [ [-o] OUTPUT_PATH] ]'
)
parser.set_description('Deconvolve INPUT_PATH with PSF_PATH.')
add_psflib_options(parser)
parser.add_option('--psf-path',
'-k',
dest='psf_path',
type='file',
metavar='PATH',
help='Specify PATH to PSF 3D images.')
parser.add_option('--input-path',
'-i',
type='file',
metavar='PATH',
help='Specify input PATH of 3D images.')
parser.add_option('--output-path',
'-o',
type='file',
metavar='PATH',
help='Specify output PATH of 3D images.')
parser.add_option('--max-nof-iterations',
type='int',
default=10,
help='Specify maximum number of iterations.')
parser.add_option(
'--convergence-epsilon',
type='float',
default=0.05,
help=
'Specify small positive number that determines the window for convergence criteria.'
)
parser.add_option('--degrade-input',
action='store_true',
help='Degrade input: apply noise to convolved input.')
parser.add_option('--no-degrade-input',
action='store_false',
dest='degrade_input',
help='See ``--degrade-input``.')
parser.add_option('--degrade-input-snr',
type = 'float', default=0.0,
help = 'Specify the signal-to-noise ratio when using --degrade-input.'\
'If set to 0, then snr will be estimated as sqrt(max(input image)).')
parser.add_option('--first-estimate',
choices=[
'input image', 'convolved input image',
'2x convolved input image', 'last result'
],
help='Specify first estimate for iteration.')
parser.add_option('--save-intermediate-results',
action='store_true',
help='Save intermediate results.')
parser.add_option('--no-save-intermediate-results',
dest='save_intermediate_results',
action='store_false',
help='See ``--save-intermediate-results`` option.')
from ..ops.script_options import get_apply_window_options_group
parser.add_option_group(get_apply_window_options_group(parser))
parser.add_option_group(get_rltv_options_group(parser))
from ..ops.script_options import get_fft_options_group
parser.add_option_group(get_fft_options_group(parser))
from ..script_options import get_runner_options_group
parser.add_option_group(get_runner_options_group(parser))
from ..io.script_options import get_io_options_group, get_microscope_options_group
parser.add_option_group(get_microscope_options_group(parser))
