def set_rowfile_plot_options(parser): import matplotlib set_formatter(parser) if os.name == 'posix' and 1: matplotlib.use('GTkAgg') parser.run_methods = ['subcommand'] parser.set_usage('%prog [options] [[-i] ROWFILE]') parser.set_description('Plot data in ROWFILE') parser.add_option('--input-path', '-i', type='file', metavar='ROWFILE', help='Specify path to ROWFILE.') parser.add_option('--print-keys', action='store_true', help='Print keys of the rowfile and exit.') parser.add_option('--x-keys', help='Specify keys for x-axis.') parser.add_option( '--y-keys', help='Specify keys for y-axis. When not specified then use all keys.') parser.add_option('--output-path', '-o', type='file', metavar='OUTPUT_PATH', help='Specify output PATH for saving figure.')
def set_regress_options(parser): from ..io.script_options import get_microscope_options_group, get_io_options_group set_formatter(parser) parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH]]') parser.set_description( 'Apply local regression methods to INPUT_PATH scalar field.') parser.add_option('--quiet', dest='verbose', action='store_false', help='Disable output messages.') 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( "--kernel-width", dest="kernel_width", type='float', help="Specify the width of kernel in minimal voxel size unit.") parser.add_option( '--link-function', choices=['identity'], default='identity', help= "Specify link function to transform data before regression analysis.") get_regress_options_group(parser, group=parser) parser.add_option_group(get_io_options_group(parser)) parser.add_option_group(get_microscope_options_group(parser))
def set_run_mirrors_options(parser): set_formatter(parser) parser.set_usage('%prog [options]') parser.set_description('Run scanning mirrors.') if os.name == 'posix': parser.run_methods = ['subcommand'] from iocbio.scanner.configuration import camera_area_width, camera_area_height parser.add_option('--roi-x0', type='int', default=1) parser.add_option('--roi-x1', type='int', default=camera_area_width) parser.add_option('--roi-y0', type='int', default=1) parser.add_option('--roi-y1', type='int', default=camera_area_height) parser.add_option('--orientation-angle', type='float', default=0) parser.add_option('--pixel-time-usec', type='float') parser.add_option('--scan-speed', type='float') parser.add_option('--image-width', type='int') parser.add_option('--pixel-size-um', type='float') parser.add_option('--image-height', type='int', default=2) parser.add_option('--flyback', type='float') parser.add_option('--flyback-range', type='string') parser.add_option_group(get_mirror_parameter_options_group(parser)) parser.add_option_group(get_runner_options_group(parser)) try: parser.add_option_group(get_nidaqmx_options_group(parser)) except ImportError, msg: print '%s' % (msg)
def set_sumstacks_options(parser): import numpy set_formatter(parser) parser.set_usage( '%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]') parser.set_description( 'Sum the stacks in INPUT_PATH and save the result with specified type and format.' ) parser.add_option('--input-path', '-i', type='file', metavar='INPUT_PATH', help='Specify input PATH of 3D images.') parser.add_option('--output-path', '-o', type='file', metavar='OUTPUT_PATH', help='Specify output PATH of 3D images.') numpy_types = ['<detect>'] + sorted( set([t.__name__ for t in numpy.typeDict.values()])) parser.add_option("--output-type", dest="output_type", choices=numpy_types, default=numpy_types[0], help="Specify output image stack type.") parser.add_option('--output-ext', dest='output_ext', choices=['tif', 'vtk', 'data'], default='tif', help="Specify output format extension.") parser.add_option_group(get_io_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_run_mirrors_options(parser): set_formatter(parser) parser.set_usage ('%prog [options]') parser.set_description('Run scanning mirrors.') if os.name == 'posix': parser.run_methods = ['subcommand'] from iocbio.scanner.configuration import camera_area_width, camera_area_height parser.add_option('--roi-x0', type='int', default=1) parser.add_option('--roi-x1', type='int', default=camera_area_width) parser.add_option('--roi-y0', type='int', default=1) parser.add_option('--roi-y1', type='int', default=camera_area_height) parser.add_option('--orientation-angle', type='float', default=0) parser.add_option ('--pixel-time-usec', type='float') parser.add_option ('--scan-speed', type='float') parser.add_option('--image-width', type='int') parser.add_option('--pixel-size-um', type='float') parser.add_option('--image-height', type='int', default=2) parser.add_option ('--flyback', type='float') parser.add_option ('--flyback-range', type='string') parser.add_option_group (get_mirror_parameter_options_group(parser)) parser.add_option_group (get_runner_options_group(parser)) try: parser.add_option_group (get_nidaqmx_options_group(parser)) except ImportError, msg: print '%s' % (msg)
def set_convert_options (parser): import numpy set_formatter(parser) parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]') parser.set_description('Convert INPUT_PATH to specified type and format.') parser.add_option ('--input-path','-i', type = 'file', metavar='INPUT_PATH', help = 'Specify input PATH of 3D images.' ) parser.add_option ('--output-path','-o', type = 'file', metavar='OUTPUT_PATH', help = 'Specify output PATH of 3D images.' ) numpy_types = ['<detect>'] + sorted(set([t.__name__ for t in numpy.typeDict.values()])) parser.add_option("--output-type", dest="output_type", choices = numpy_types, default = numpy_types[0], help="Specify output image stack type.") parser.add_option("--scale", action="store_true", dest="scale", help='Specify whether to scale stack to the limits of the output type.') parser.add_option("--no-scale", action="store_false", dest="scale", help='See ``--scale`` option.') parser.add_option('--normalize', choices = ['none', 'unit volume'], help = 'Specify normalization.' ) parser.add_option('--output-ext', dest='output_ext', choices = ['tif', 'vtk', 'data'], default = 'tif', help="Specify output format extension.") parser.add_option_group(get_tiff_options_group(parser))
def set_sumstacks_options (parser): import numpy set_formatter(parser) parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]') parser.set_description('Sum the stacks in INPUT_PATH and save the result with specified type and format.') parser.add_option ('--input-path','-i', type = 'file', metavar='INPUT_PATH', help = 'Specify input PATH of 3D images.' ) parser.add_option ('--output-path','-o', type = 'file', metavar='OUTPUT_PATH', help = 'Specify output PATH of 3D images.' ) numpy_types = ['<detect>'] + sorted(set([t.__name__ for t in numpy.typeDict.values()])) parser.add_option("--output-type", dest="output_type", choices = numpy_types, default = numpy_types[0], help="Specify output image stack type.") parser.add_option('--output-ext', dest='output_ext', choices = ['tif', 'vtk', 'data'], default = 'tif', help="Specify output format extension.") parser.add_option_group(get_io_options_group(parser))
def set_apply_noise_options(parser): parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH] ]') set_formatter(parser) parser.set_description('Apply noise to INPUT_PATH scalar field.') parser.add_option('--quiet', dest='verbose', action='store_false', default=True, help='Disable output messages.') 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( "--noise-type", dest='noise_type', choices=['poisson'], default='poisson', help='Specify noise type.', )
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_ome_options (parser): import numpy set_formatter(parser) parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]') parser.set_description('Convert INPUT_PATH to OME-TIFF file.') parser.add_option ('--input-path','-i', type = 'file', metavar='INPUT_PATH', help = 'Specify input PATH of 3D images.' )
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_ome_options(parser): import numpy set_formatter(parser) parser.set_usage( '%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]') parser.set_description('Convert INPUT_PATH to OME-TIFF file.') parser.add_option('--input-path', '-i', type='file', metavar='INPUT_PATH', help='Specify input PATH of 3D images.')
def set_strathkelvin929_rate_options(parser): set_formatter(parser) parser.set_usage('%prog [options] <channel-files>') parser.set_description('Re-calculates oxygen respiration rates. Rewrites the channel files unless --tryrun is used.') parser.add_option('--nof-regression-points', '-n', type = 'int', default=10, help = 'Specify the number of regression points. When 0 then use the number from channel files.') parser.add_option('--tryrun', action = 'store_true', help = 'Re-calculate rates but do not save rates to file.') parser.add_option('--no-tryrun', action = 'store_false', dest='tryrun', help = 'See --tryrun.')
def set_show_options(parser): set_formatter(parser) import matplotlib if os.name == 'posix': matplotlib.use('GTkAgg') parser.run_methods = ['subcommand'] parser.set_usage('%prog [options] [ [-i] INPUT_PATH ]') parser.set_description('Display INPUT_PATH as 3D image.') parser.add_option ('--input-path', '-i', type = 'file', metavar='INPUT_PATH', help = 'Specify input PATH of 3D images.' ) parser.add_option('--interpolation', default='nearest', choices = sorted(['bilinear', 'nearest','bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermit', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos']), help="Specify image interpolation method.") #parser.add_option('--roll-axis', choices=['0','1','2'], help='Roll given axis to 0.', default='0') parser.add_option('--projection', choices=['XY','XZ','YZ'], help='Project image stack to given plane.', default='XY') parser.add_option('--rgb', action='store_true', default=False, help="Display as RGB(A) color images.") parser.add_option('--dpi', type='int', default=96, help="Specify plot resolution.") import matplotlib.cm as cm colormap_names = [name for name in cm.datad if not name.endswith ('_r')] lcolormap_names = sorted([name for name in colormap_names if name[0].islower()]) ucolormap_names = sorted([name for name in colormap_names if name[0].isupper()]) colormap_names = lcolormap_names + ucolormap_names parser.add_option('--cmap', choices = colormap_names, default='gray', help='Specify `colormap <http://matplotlib.sourceforge.net/plot_directive/mpl_examples/pylab_examples/show_colormaps.hires.png>`_.') parser.add_option ('--invert-cmap', action='store_true', default=False, help='Invert specified colormap.') parser.add_option ('--histogram-bins', type='int', default=0, help = 'Specify the number of bins for histogram. 0 means no histogram.') parser.add_option ('--auto-scale', action='store_true', default=False, help = 'Automatically scale each frame.') parser.add_option ('--view-3d', type='string', default='', help = 'Specify z=const, y=const, x=const planes for viewing 3d stack.') parser.add_option ('--output-path', '-o', type = 'file', metavar='OUTPUT_PATH', help = 'Specify output PATH for saving figure.' ) parser.add_option_group(get_io_options_group(parser)) parser.add_option_group(get_microscope_options_group (parser))
def set_estimate_snr_options(parser): from ..io.script_options import get_microscope_options_group set_formatter(parser) parser.set_usage('%prog [options] [ -i INPUT_PATH ]') parser.set_description( 'Estimate signal to noise ratio from the INPUT_PATH images.') parser.add_option('--input-path', '-i', type='file', metavar='PATH', help='Specify input PATH of 3D images.') parser.add_option_group(get_regress_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_convert_options(parser): import numpy set_formatter(parser) parser.set_usage( '%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ]]') parser.set_description('Convert INPUT_PATH to specified type and format.') parser.add_option('--input-path', '-i', type='file', metavar='INPUT_PATH', help='Specify input PATH of 3D images.') parser.add_option('--output-path', '-o', type='file', metavar='OUTPUT_PATH', help='Specify output PATH of 3D images.') numpy_types = ['<detect>'] + sorted( set([t.__name__ for t in numpy.typeDict.values()])) parser.add_option("--output-type", dest="output_type", choices=numpy_types, default=numpy_types[0], help="Specify output image stack type.") parser.add_option( "--scale", action="store_true", dest="scale", help='Specify whether to scale stack to the limits of the output type.' ) parser.add_option("--no-scale", action="store_false", dest="scale", help='See ``--scale`` option.') parser.add_option('--normalize', choices=['none', 'unit volume'], help='Specify normalization.') parser.add_option('--output-ext', dest='output_ext', choices=['tif', 'vtk', 'data'], default='tif', help="Specify output format extension.") parser.add_option_group(get_tiff_options_group(parser))
def set_sarcomere_length_options (parser): from ..io.script_options import get_microscope_options_group, get_io_options_group set_formatter (parser) parser.set_usage('%prog [options] [ -i INPUT_PATH ]') parser.set_description('Estimate the length of sarcomere.') parser.add_option ('--input-path','-i', type = 'file', metavar='PATH', help = 'Specify input PATH of 3D images.' ) parser.add_option ('--roi-center-line', help = 'Specify the coordinates of ROI center line in pixels: x0,y0,x1,y1') parser.add_option ('--roi-width', type = 'int', help = 'Specify the width of ROI in pixels') parser.add_option ('--nof-points', type = 'int', default = 512, help = 'Specify the number of interpolation points.') parser.add_option_group(get_io_options_group(parser)) parser.add_option_group(get_microscope_options_group(parser))
def set_apply_window_options(parser): from ..io.script_options import get_microscope_options_group set_formatter(parser) parser.set_usage('%prog [options] [ INPUT_PATH [OUTPUT_PATH]]') parser.set_description('Apply smooth window to INPUT_PATH scalar field.') parser.add_option('--quiet', dest='verbose', action='store_false', default=True, help='Disable output messages.') 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.') get_apply_window_options_group(parser, group=parser) parser.add_option_group(get_microscope_options_group(parser))
def set_strathkelvin929_rate_options(parser): set_formatter(parser) parser.set_usage('%prog [options] <channel-files>') parser.set_description( 'Re-calculates oxygen respiration rates. Rewrites the channel files unless --tryrun is used.' ) parser.add_option( '--nof-regression-points', '-n', type='int', default=10, help= 'Specify the number of regression points. When 0 then use the number from channel files.' ) parser.add_option('--tryrun', action='store_true', help='Re-calculate rates but do not save rates to file.') parser.add_option('--no-tryrun', action='store_false', dest='tryrun', help='See --tryrun.')
def set_sarcomere_length_options(parser): from ..io.script_options import get_microscope_options_group, get_io_options_group set_formatter(parser) parser.set_usage('%prog [options] [ -i INPUT_PATH ]') parser.set_description('Estimate the length of sarcomere.') parser.add_option('--input-path', '-i', type='file', metavar='PATH', help='Specify input PATH of 3D images.') parser.add_option( '--roi-center-line', help='Specify the coordinates of ROI center line in pixels: x0,y0,x1,y1' ) parser.add_option('--roi-width', type='int', help='Specify the width of ROI in pixels') parser.add_option('--nof-points', type='int', default=512, help='Specify the number of interpolation points.') parser.add_option_group(get_io_options_group(parser)) parser.add_option_group(get_microscope_options_group(parser))
def set_convolve_options(parser): from ..microscope.script_options import add_psflib_options set_formatter(parser) parser.set_usage( '%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]') parser.set_description('Convolve INPUT_PATH with KERNEL_PATH.') add_psflib_options(parser) parser.add_option('--kernel-path', '-k', type='file', metavar='PATH', help='Specify PATH to 3D images to be used as a kernel.') 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_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_rowfile_plot_options (parser): import matplotlib set_formatter(parser) if os.name == 'posix' and 1: matplotlib.use('GTkAgg') parser.run_methods = ['subcommand'] parser.set_usage ('%prog [options] [[-i] ROWFILE]') parser.set_description('Plot data in ROWFILE') parser.add_option ('--input-path', '-i', type = 'file', metavar='ROWFILE', help = 'Specify path to ROWFILE.' ) parser.add_option('--print-keys', action='store_true', help = 'Print keys of the rowfile and exit.') parser.add_option('--x-keys', help = 'Specify keys for x-axis.') parser.add_option('--y-keys', help = 'Specify keys for y-axis. When not specified then use all keys.') parser.add_option ('--output-path', '-o', type = 'file', metavar='OUTPUT_PATH', help = 'Specify output PATH for saving figure.' )
if os.path.basename(root)=='scripts': for script in files: script_name = os.path.splitext(script)[0] package_name = '.'.join(root[len(os.path.dirname(parent_path))+1:].split(os.sep)[:-1]) try: exec 'import %s.script_options as script_options' % (package_name) except ImportError, msg: print msg continue try: set_options = getattr (script_options, 'set_%s_options' % (script_name)) except AttributeError, msg: print msg continue parser = OptionParser() set_formatter (parser) parser.add_option('--no-gui', action='store_false', default=True, help='Run script without opening GUI.') set_options (parser) parser.prog = 'fparser.%s' % (script_name) if parser.description is None: print 'Warning: %s does not have a description (use parser.set_description in %s.script_options.%s)' % (parser.prog, package_name,set_options.__name__) parser.description = 'PFI' descr = parser.get_description() descr_title = descr.lstrip().split('\n')[0] help = parser.format_help() help += ''' See also ======== :mod:`%s` ''' % (package_name)
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_strathkelvin929_options (parser): set_formatter(parser) parser.set_usage('%prog') parser.set_description('Wrapper of Strathkelvin 929 System software, the GUI program.')
def set_estimate_psf_options(parser): set_formatter(parser) parser.set_usage( '%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]') parser.set_description( '''Find PSF estimate from the measurments of microspheres. Intermediate results are saved to INPUT_PATH/iocbio.estimate_psf/ directory and estimated PSF is saved to OUTPUT_PATH ''') parser.add_option( "--measurement-path", '--input-path', '-i', type='file', metavar='INPUT_PATH', dest='input_path', help='''Specify PATH to microsphere measurments.\ To select directory PATH, find a file PATH/{PATHINFO.txt, configuration.txt, SCANINFO.txt} and select it.''', ) parser.add_option("--psf-path", '--output-path', '-o', '-k', type='file', metavar='OUTPUT_PATH', dest='output_path', help='''Specify PATH for saving estimated PSF.''') #parser.add_option('--photon-counter-offset', # type = 'float', # help = 'Specify photon counter offset.' # ) parser.add_option( '--subtract-background-field', dest='subtract_background_field', action='store_true', help= 'Specify that subtraction of a background field should be carried out.' ) parser.add_option('--no-subtract-background-field', dest='subtract_background_field', action='store_false', help='See ``--subtract-background-field option``.') parser.add_option("--cluster-background-level", dest='cluster_background_level', type='float', metavar='FLOAT', help="""\ Specify maximum background level for defining PSF clusters: smaller value means larger clusters (a good thing) and higher probability of overlapping clusters (a bad thing); default will be estimated. """) parser.add_option( "--psf-field-size", dest='psf_field_size', type='float', default=7, metavar='FLOAT', help='Specify PSF field size in lateral and axial resolution units.') parser.add_option( "--show-plots", dest='show_plots', action='store_true', help='Show estimated PSF during computation.', ) parser.add_option( "--no-show-plots", dest='show_plots', action='store_false', help='See ``--show-plot option``.', ) parser.add_option( "--save-intermediate-results", dest='save_intermediate_results', action='store_true', help='Save intermediate results of computation.', ) parser.add_option('--no-save-intermediate-results', dest='save_intermediate_results', action='store_false', help='See ``--save-intermediate-results`` option.') parser.add_option( '--select-candidates', help= 'Specify which canditates are selected for computing the PSF estimate.' ) from ..io.script_options import get_io_options_group, get_microscope_options_group parser.add_option_group(get_io_options_group(parser)) parser.add_option_group(get_microscope_options_group(parser))
def set_strathkelvin929_options(parser): set_formatter(parser) parser.set_usage('%prog') parser.set_description( 'Wrapper of Strathkelvin 929 System software, the GUI program.')
def set_estimate_psf_options (parser): set_formatter(parser) parser.set_usage('%prog [options] [ [-i] INPUT_PATH [ [-o] OUTPUT_PATH ] ]') parser.set_description('''Find PSF estimate from the measurments of microspheres. Intermediate results are saved to INPUT_PATH/iocbio.estimate_psf/ directory and estimated PSF is saved to OUTPUT_PATH ''') parser.add_option ("--measurement-path", '--input-path','-i', type = 'file', metavar='INPUT_PATH', dest='input_path', help = '''Specify PATH to microsphere measurments.\ To select directory PATH, find a file PATH/{PATHINFO.txt, configuration.txt, SCANINFO.txt} and select it.''', ) parser.add_option ("--psf-path", '--output-path','-o','-k', type = 'file', metavar='OUTPUT_PATH', dest='output_path', help = '''Specify PATH for saving estimated PSF.''' ) #parser.add_option('--photon-counter-offset', # type = 'float', # help = 'Specify photon counter offset.' # ) parser.add_option('--subtract-background-field', dest='subtract_background_field', action = 'store_true', help='Specify that subtraction of a background field should be carried out.') parser.add_option('--no-subtract-background-field', dest='subtract_background_field', action = 'store_false', help='See ``--subtract-background-field option``.') parser.add_option ("--cluster-background-level", dest = 'cluster_background_level', type = 'float', metavar='FLOAT', help = """\ Specify maximum background level for defining PSF clusters: smaller value means larger clusters (a good thing) and higher probability of overlapping clusters (a bad thing); default will be estimated. """) parser.add_option ("--psf-field-size", dest = 'psf_field_size', type = 'float', default=7, metavar='FLOAT', help = 'Specify PSF field size in lateral and axial resolution units.' ) parser.add_option ("--show-plots", dest = 'show_plots', action = 'store_true', help = 'Show estimated PSF during computation.', ) parser.add_option ("--no-show-plots", dest = 'show_plots', action = 'store_false', help = 'See ``--show-plot option``.', ) parser.add_option ("--save-intermediate-results", dest = 'save_intermediate_results', action = 'store_true', help = 'Save intermediate results of computation.', ) parser.add_option ('--no-save-intermediate-results', dest = 'save_intermediate_results', action = 'store_false', help = 'See ``--save-intermediate-results`` option.' ) parser.add_option ('--select-candidates', help = 'Specify which canditates are selected for computing the PSF estimate.') from ..io.script_options import get_io_options_group, get_microscope_options_group parser.add_option_group(get_io_options_group (parser)) parser.add_option_group(get_microscope_options_group (parser))
def set_show_options(parser): set_formatter(parser) import matplotlib if os.name == 'posix': matplotlib.use('GTkAgg') parser.run_methods = ['subcommand'] parser.set_usage('%prog [options] [ [-i] INPUT_PATH ]') parser.set_description('Display INPUT_PATH as 3D image.') parser.add_option('--input-path', '-i', type='file', metavar='INPUT_PATH', help='Specify input PATH of 3D images.') parser.add_option('--interpolation', default='nearest', choices=sorted([ 'bilinear', 'nearest', 'bicubic', 'spline16', 'spline36', 'hanning', 'hamming', 'hermit', 'kaiser', 'quadric', 'catrom', 'gaussian', 'bessel', 'mitchell', 'sinc', 'lanczos' ]), help="Specify image interpolation method.") #parser.add_option('--roll-axis', choices=['0','1','2'], help='Roll given axis to 0.', default='0') parser.add_option('--projection', choices=['XY', 'XZ', 'YZ'], help='Project image stack to given plane.', default='XY') parser.add_option('--rgb', action='store_true', default=False, help="Display as RGB(A) color images.") parser.add_option('--dpi', type='int', default=96, help="Specify plot resolution.") import matplotlib.cm as cm colormap_names = [name for name in cm.datad if not name.endswith('_r')] lcolormap_names = sorted( [name for name in colormap_names if name[0].islower()]) ucolormap_names = sorted( [name for name in colormap_names if name[0].isupper()]) colormap_names = lcolormap_names + ucolormap_names parser.add_option( '--cmap', choices=colormap_names, default='gray', help= 'Specify `colormap <http://matplotlib.sourceforge.net/plot_directive/mpl_examples/pylab_examples/show_colormaps.hires.png>`_.' ) parser.add_option('--invert-cmap', action='store_true', default=False, help='Invert specified colormap.') parser.add_option( '--histogram-bins', type='int', default=0, help='Specify the number of bins for histogram. 0 means no histogram.') parser.add_option('--auto-scale', action='store_true', default=False, help='Automatically scale each frame.') parser.add_option( '--view-3d', type='string', default='', help='Specify z=const, y=const, x=const planes for viewing 3d stack.') parser.add_option('--output-path', '-o', type='file', metavar='OUTPUT_PATH', help='Specify output PATH for saving figure.') parser.add_option_group(get_io_options_group(parser)) parser.add_option_group(get_microscope_options_group(parser))