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))