Example: 'imgs/Jan01_2015_abc'
""",
nargs="?",
type=Path,
metavar="<file>")
parser.add_argument("-e",
"--extension",
default='pdf',
help="Extension of image type to use for output images.")
parser.add_argument("--limits",
default=None,
metavar='UPPER_LEFT_LOWER_RIGHT',
help="""Limits for cropping, from the upper left corner.
Example: '--limit 192,224,320,288' for a box centered at (256,256) of
width 128 and height 64. Leave blank for no cropping.""",
type=to_list_func(4, int))
parser.add_argument(
'-t',
'--thresholds',
type=to_list_func(3, FloatOrPercent),
default=(FloatOrPercent('90%'), FloatOrPercent('80%'),
FloatOrPercent('90%')),
help="""Set three thresholds. Value should either be in pixel value, e.g.
'20', or a percentage value, e.g. '99.9%%'. Percentage values will be
applied to the histogram to extract a threshold. Use a comma to separate.
Example: -t 99%%,10%%,99%%""")
parser.add_argument('-u',
'--upperthresholds',
metavar='THRESHOLD',
type=to_list_func(3, FloatOrPercent),
default=(FloatOrPercent('99.99%'), FloatOrPercent('99%'),
Example: 'imgs/Jan01_2015_abc'
""",
nargs="?",
type=Path,
metavar="<file>")
parser.add_argument("-e",
"--extension",
default='pdf',
help="Extension of image type to use for output images.")
parser.add_argument("--limits",
default=None,
metavar='UPPER,LEFT,LOWER,RIGHT',
help="""Limits for cropping, from the upper left corner.
Example: '--limit 192,224,320,288' for a box centered at (256,256) of
width 128 and height 64. Leave blank for no cropping.""",
type=to_list_func(4, int))
parser.add_argument(
'-t',
'--threshold',
type=FloatOrPercent,
default=FloatOrPercent('99%'),
help="""Set threshold for cyan. Value should either be in pixel value, e.g.
'20', or a percentage value, e.g. '99.9%%'. Percentage values will be
applied to the histogram to extract a threshold.""")
# TODO: add yellow threshold
parser.add_argument('-u',
'--upperthreshold',
metavar='THRESHOLD',
type=FloatOrPercent,
default=FloatOrPercent('99.9%'),
help="""
type=Path, metavar="<nucleus_file>.tif")
parser.add_argument("inputmeasure",
help="Input measure file. Should be a tif.",
type=Path, metavar="<measure_file>.tif")
parser.add_argument("output", default=None,
help="""Output file basename (without extension). Defaults to match input.
Example: 'imgs/Jan01_2015_abc'
""", nargs="?",
type=Path, metavar="<file>")
parser.add_argument("-e", "--extension", default='pdf',
help="Extension of image type to use for output images.")
parser.add_argument("--limits", default=None, metavar='UPPER_LEFT_LOWER_RIGHT',
help="""Limits for cropping, from the upper left corner.
Example: '--limit 192,224,320,288' for a box centered at (256,256) of
width 128 and height 64. Leave blank for no cropping.""",
type=to_list_func(4, int))
parser.add_argument('-t', '--thresholds',
type=to_list_func(3, FloatOrPercent),
default=(FloatOrPercent('90%'), FloatOrPercent('80%'), FloatOrPercent('90%')),
help="""Set three thresholds. Value should either be in pixel value, e.g.
'20', or a percentage value, e.g. '99.9%%'. Percentage values will be
applied to the histogram to extract a threshold. Use a comma to separate.
Example: -t 99%%,10%%,99%%""")
parser.add_argument('-u', '--upperthresholds', metavar='THRESHOLD',
type=to_list_func(3, FloatOrPercent),
default=(FloatOrPercent('99.99%'), FloatOrPercent('99%'), FloatOrPercent('99.99%')),
help="""
Set upper thresholds for normalization, with the same format as '--threshold'.
""")
parser.add_argument('--loghistogram', action='store_true',
help="""Use a logarithmic scale for the histograms.""")
parser.add_argument("input",
help="Input file. Should be a tif with a sequence of embedded images.",
type=Path, metavar="<file>.tif")
parser.add_argument("output", default=None,
help="""Output file basename (without extension). Defaults to match input.
Example: 'imgs/Jan01_2015_abc'
""", nargs="?",
type=Path, metavar="<file>")
parser.add_argument("-e", "--extension", default='pdf',
help="Extension of image type to use for output images.")
parser.add_argument("--limits", default=None, metavar='UPPER,LEFT,LOWER,RIGHT',
help="""Limits for cropping, from the upper left corner.
Example: '--limit 192,224,320,288' for a box centered at (256,256) of
width 128 and height 64. Leave blank for no cropping.""",
type=to_list_func(4, int))
parser.add_argument('-t', '--threshold',
type=FloatOrPercent, default=FloatOrPercent('99%'),
help="""Set threshold for cyan. Value should either be in pixel value, e.g.
'20', or a percentage value, e.g. '99.9%%'. Percentage values will be
applied to the histogram to extract a threshold.""")
# TODO: add yellow threshold
parser.add_argument('-u', '--upperthreshold', metavar='THRESHOLD',
type=FloatOrPercent, default=FloatOrPercent('99.9%'),
help="""
Set upper threshold for normalization, with the same format as '--threshold'.
""")
# TODO: add yellow upper threshold
# parser.add_argument('-b', '--binarize', action='store_true',
# help="""
# Use a binary input for the cyan channel. That is, for all pixels
