def main():
try:
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[util.parent_parser()],
)
parser.add_argument(
"-o", "--output", required=False, default=".bitunflip.cub"
)
parser.add_argument("cube", help="ISIS Cube file.")
args = parser.parse_args()
util.set_logger(args.verbose, args.logfile, args.log)
out_p = util.path_w_suffix(args.output, args.cube)
unflip(Path(args.cube), out_p, keep=args.keep)
except subprocess.CalledProcessError as err:
print("Had an ISIS error:", file=sys.stderr)
print(" ".join(err.cmd), file=sys.stderr)
print(err.stdout, file=sys.stderr)
print(err.stderr, file=sys.stderr)
def arg_parser():
parser = argparse.ArgumentParser(description=__doc__,
parents=[util.parent_parser()])
parser.add_argument("-c",
"--color",
action="store_true",
help="Perform Color processing.")
parser.add_argument(
"-p",
"--precision",
action="store_true",
help="Perform HiPrecision processing to result "
"in NOPROJ.cub that might be processed through "
"HiJACK.",
)
parser.add_argument(
"-j",
"--jack",
action="store_true",
help="Do not test if HiJACK is needed, but force HiJACK to run.",
)
parser.add_argument(
"img",
metavar="some.img-file",
nargs="+",
help="More than one can be listed here.",
)
parser.add_argument(
"--conf_dir",
required=False,
type=Path,
default=Path(pkg_resources.resource_filename(__name__, 'data/')),
)
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument(
"-o", "--output",
required=False,
default=".EDR_Stats.cub",
help="Output filename. Optionally, if it starts with a '.' it is "
"considered a suffix and will be swapped with the input"
"file's suffix to determine the file to write. "
"Default: %(default)s"
)
parser.add_argument(
"--db",
required=False,
default=".HiCat.json",
help="The .json file to output. Optionally, if it "
"starts with a '.' it is considered a suffix and "
"will be swapped with the input file's suffix to "
"determine the file to write. Default: %(default)s",
)
parser.add_argument(
"--histmin",
required=False,
default=0.01,
help="The minimum percentage above which DN are counted. This only "
"affects the value of STD_DN_LEVELS in the output .json file. "
"If it is lower, more DN will be counted. Default: %(default)s"
)
parser.add_argument(
"--histmax",
required=False,
default=99.99,
help="The minimum percentage below which DN are counted. See --histmin "
"for more information. Default: %(default)s"
)
parser.add_argument(
"-g",
"--gains",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(
__name__,
'data/EDR_Stats_gains_config.pvl'
),
help="Path to the gains config PVL file. Defaults to "
"EDR_Stats_gains_config.pvl distributed with the library.",
)
parser.add_argument(
"img",
metavar="some.img-file",
nargs="+",
help="More than one can be listed here.",
)
return parser
def arg_parser():
parser = argparse.ArgumentParser(description=__doc__,
parents=[util.parent_parser()])
parser.add_argument("-p",
"--plot",
action="store_true",
help="Display plots")
parser.add_argument("slithertxts", metavar="slither.txt files", nargs="+")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
conflict_handler="resolve",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"--db",
required=False,
default=".HiCat.json",
help="The .json file to use. Optionally, if it "
"starts with a '.' it is considered an extension and "
"will be swapped with the input file's extension to "
"find the .json file to use. Default: %(default)s",
)
parser.add_argument(
"--db2",
required=False,
default=".HiCat.json",
help="The second .json file to use. Optionally, if "
"it starts with a '.' it is considered a suffix "
"and will be swapped with the second input file's "
"suffix to find the .json file to use. Default: %(default)s",
)
parser.add_argument(
"--dbout",
required=False,
default=".HiCat.json",
help="The name of the output .json file to write. Optionally, if "
"it starts with a '.' it is considered a suffix "
"and will be added to the CCD ID of the observation of the "
"input files. Default: %(default)s",
)
parser.add_argument(
"-o",
"--output",
required=False,
default=".HiStitch.cub",
help="The name of the output .cub file to write. Optionally, if "
"it starts with a '.' it is considered a suffix"
"and will be added to the CCD ID of the observation of the "
"input files. Default: %(default)s",
)
parser.add_argument("-c",
"--conf",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(
__name__, 'data/HiStitch.conf'),
help="Path to the HiStitch config file. Defaults to "
"HiStitch.conf distributed with the library.")
parser.add_argument("cube0", metavar="cube0.cub-file")
parser.add_argument("cube1", metavar="cube1.cub-file", nargs="?")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[util.parent_parser()],
)
parser.add_argument("-o",
"--output",
required=False,
default=".lisfix.cub")
parser.add_argument("file", help="ISIS Cube file.")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"cubes",
metavar="RED balance.cub and color balance.precolor.cub files",
nargs="+",
help=r"Either one or both sets of RED .balance.cub and IR/BG "
r".balance.precolor.cub files. However, that's tedious to type,"
r"so you could just type in *.balance*cub here, and the program "
r"will sort out what it needs.")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
conflict_handler="resolve",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"-o_irb",
"--output_irb",
required=False,
default="_IRB.cub",
help="The filename to be used for the output IRB cube. If it "
"begins with an underscore ('_') it will be assumed to be a "
"suffix that will be appended to a name derived from the "
"observation. Default: %(default)s")
parser.add_argument(
"-o_rgb",
"--output_rgb",
required=False,
default="_RGB.cub",
help="The filename to be used for the output RGB cube. If it "
"begins with an underscore ('_') it will be assumed to be a "
"suffix that will be appended to a name derived from the "
"observation. Default: %(default)s")
parser.add_argument(
"-c",
"--conf",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(
__name__,
'data/HiBeautify.conf',
),
help="Path to the HiBeautify config file. Defaults to "
"HiBeautify.conf distributed with the library.")
# parser.add_argument('-f', '--frost', action='store_true',
# help='Use the frost/ice color stretch, and disable '
# 'auto-detection of frost/ice.')
# parser.add_argument('--nofrost', action='store_true',
# help='Do not use the frost/ice color stretch, and disable '
# 'auto-detection of frost/ice.')
parser.add_argument(
"cubes",
type=Path,
nargs=2,
metavar="HiColorNorm-cube",
help="The COLOR4.HiColorNorm.cub and COLOR5.HiColorNorm.cub files.")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__, parents=[util.parent_parser()]
)
parser.add_argument(
"-c", "--color", action="store_true", help="Perform Color processing."
)
parser.add_argument(
"-p",
"--precision",
action="store_true",
help="Perform HiPrecision processing to result "
"in NOPROJ.cub that might be processed through "
"HiJACK.",
)
parser.add_argument(
"-j",
"--jack",
action="store_true",
help="Do not test if HiJACK is needed, but force HiJACK to run.",
)
parser.add_argument(
"--max_workers",
default=None,
type=int,
help="This program uses multiprocessing to parallelize some of the "
"work. This multiprocessing will default to use the number of "
"processors on the host machine. If you want to throttle this "
"to use less resources on your machine, indicate the number of "
"processors you want to use."
)
parser.add_argument(
"img",
metavar="some.img-file",
nargs="+",
help="More than one can be listed here.",
)
parser.add_argument(
"--conf_dir",
required=False,
type=Path,
default=Path(pkg_resources.resource_filename(__name__, "data/")),
help="Directory where configuration files for each of the hiproc "
"algorithms are. Defaults to the configuration files "
"distributed with the library."
)
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument(
"-o", "--out_dir",
required=False,
default="./HiJACK",
help="The directory where HiJACK output will be placed. If it "
"doesn't already exist, it will be created. Default: %(default)s"
)
parser.add_argument(
"-c",
"--conf_dir",
required=False,
type=Path,
default=Path(pkg_resources.resource_filename(__name__, 'data/')),
help="Directory where ResolveJitter.conf and HiJACK.conf can be "
"found. Defaults to the directory distributed with the library.",
)
parser.add_argument(
"-n",
"--noplot",
action="store_false",
dest="plot",
help="Will stop the display of before and after jitter plots.",
)
parser.add_argument(
"-b", "--base_ccd_number",
required=False,
default=5,
help="The CCD number that will be used in a variety of ways to set "
"parameters for the resulting image. Default: %(default)s"
)
parser.add_argument(
"cubes",
metavar="balance.cub-files",
nargs="+",
help="All of the .balance.cub files created by HiccdStitch."
)
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"-c",
"--conf",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(__name__,
'data/HiPrecisionInit.conf'),
help="Path to the HiPrecisionInit config file. Defaults to "
"HiPrecisionInit.conf distributed with the library.")
parser.add_argument("slither_text",
metavar="slither.txt-files",
nargs="+",
help="The text files created by HiSlither.")
return parser
def arg_parser():
parser = argparse.ArgumentParser(description=__doc__,
parents=[util.parent_parser()])
parser.add_argument("-c",
"--conf",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(
__name__, 'data/HiJitReg.conf'),
help="Path to the HiJitReg config file. Defaults to "
"HiJitReg.conf distributed with the library.")
parser.add_argument(
"cubes",
metavar="balance.precolor.cub files",
nargs="+",
help="Either one or both sets of RED .balance.cub and IR/BG "
".balance.precolor.cub files. However, that's tedious to type,"
"so you could just type in *.balance*cub here, and the program "
"will sort out what it needs.")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"-o",
"--output_suffix",
required=False,
default=".precolor.cub",
help="The input color (BG & IR) color cubes will have their final "
"suffix removed, and this suffix added. Default: %(default)s")
parser.add_argument(
"cubes",
metavar="balance.cub-files",
nargs="+",
help="Either one or both sets of RED/IR/BG .balance.cub files. "
"However, that's tedious to type, so you could just type in "
"*.balance.cub here, and the program will sort out what it needs.")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
conflict_handler="resolve",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"-o",
"--output",
required=False,
default="_COLOR.cub",
help="The filename to be used for the output color cube. If it "
"begins with an underscore ('_') it will be assumed to be a "
"suffix that will be appended to a name derived from the "
"observation. Default: %(default)s")
parser.add_argument(
"-c",
"--conf",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(__name__,
'data/HiColorNorm.conf'),
help="Path to the HiColorNorm config file. Defaults to "
"HiColorNorm.conf distributed with the library.")
parser.add_argument(
"-n",
"--nounfiltered",
action="store_false",
dest="Make_Unfiltered",
help="Stops creation of an unfiltered cube.",
)
parser.add_argument("cubes",
type=Path,
nargs=2,
metavar="COLOR-cube",
help="The COLOR4.cub and COLOR5.cub files")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"-o",
"--output",
required=False,
default="_RED.NOPROJ.cub",
help="The filename to be used for the output noproj cube. If it "
"begins with an underscore ('_') it will be assumed to be a "
"suffix that will be appended to a name derived from the "
"observation. Default: %(default)s")
parser.add_argument("-c",
"--conf",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(
__name__, 'data/HiNoProj.conf'),
help="Path to the HiNoProj config file. Defaults to "
"HiNoProj.conf distributed with the library.")
parser.add_argument(
"-b",
"--base_ccd_number",
required=False,
default=5,
help="The CCD number that will be given to the MATCH parameter of "
"ISIS noproj. Default: %(default)s")
parser.add_argument(
"cubes",
type=Path,
metavar="balance.cub-files",
nargs="+",
help="The RED .balance.cub files created by HiccdStitch.")
return parser
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__,
parents=[util.parent_parser()],
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
"-o",
"--output",
required=False,
default=".HiccdStitch.cub",
help="The name of the output .cub file to write. Optionally, if "
"it starts with a '.' it is considered a suffix"
"and will be added to the Observation ID of the "
"input files. Default: %(default)s",
)
parser.add_argument(
"-c",
"--conf",
required=False,
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(
__name__,
'data/HiccdStitch.conf',
),
help="Path to the HiccdStitch config file. Defaults to "
"HiccdStitch.conf distributed with the library.")
parser.add_argument(
"--db",
required=False,
default=".HiCat.json",
help="The .json file to output. Optionally, if it "
"starts with a '.' it is considered an extension "
"and will be swapped with the output file's extension "
"to determine the .json filename to use. Default: %(default)s",
)
parser.add_argument(
"--sline",
required=False,
default=None,
type=int,
help="If given, will be used as the starting line to crop the image "
"at in order to create a training area to use for cubenorm "
"processing.")
parser.add_argument(
"--eline",
required=False,
default=None,
type=int,
help="If given, will be used as the ending line for cubenorm cropping, "
"see --sline for more information.")
parser.add_argument(
"--cubenorm",
required=False,
nargs="+",
type=bool,
help="To engage cubenorm processing a list of true or false values "
"(could be 0 or 1) that must match the number of input cubes"
"must be given to indicate which of the input cubes should "
"have cubenorm processing applied. If you only had four input"
"cubes, then ``--cubenorm 0 0 1 1`` would not run cubenorm "
"processing on the first two cubes, but would run it on the last"
"two, etc. The default is not to run this processing on any.")
parser.add_argument(
"cubes",
metavar="cub-file",
nargs="+",
help="Cubes to assemble, which are presumably the output of HiStitch. "
"They must all be from the same detectors, so either all RED, "
"all IR, or all BG cubes.")
return parser
def test_parent_parser(self):
self.assertIsInstance(util.parent_parser(), argparse.ArgumentParser)
def arg_parser():
parser = argparse.ArgumentParser(
description=__doc__, parents=[util.parent_parser()]
)
parser.add_argument(
"-c",
"--conf",
type=argparse.FileType('r'),
default=pkg_resources.resource_stream(
__name__,
'data/ResolveJitter.conf'
),
help="Path to a ResolveJitter.conf file, only needed if "
"--lineinterval isn't given.",
)
parser.add_argument(
"--csv",
action="store_true",
help="This program writes out a fixed-width data file with extra "
"information for plotting. This also writes out a "
"comma-separated version.",
)
parser.add_argument(
"--lineinterval",
type=float,
help="The number of lines to use to set the number of Fourier "
"transform intervals, defaults to Control_Lines in the "
"ResolveJitter.conf file.",
)
parser.add_argument(
"--outdir",
type=Path,
help="Output directory. Defaults to the directory of the first "
"input file.",
)
parser.add_argument(
"--outprefix",
help="Prefix string for output files. If not given, will default "
"to the Observation ID of the images.",
)
parser.add_argument(
"-p", "--plot", action="store_true", help="Displays interactive plot.",
)
parser.add_argument(
"--saveplot",
nargs="?",
default=False,
const=True,
help="Saves plot to a default filename in the output directory. "
"If a filename is provided it will be used to save the plot.",
)
parser.add_argument(
"--whichmatch1",
action="store_false",
dest="which1",
help="If specified, the sense of the offsets for the first "
"file will be relative to the MATCH cube, rather than the FROM "
"cube.",
)
parser.add_argument(
"--whichmatch2",
action="store_false",
dest="which2",
help="If specified, the sense of the offsets for the second "
"file will be relative to the MATCH cube, rather than the FROM "
"cube.",
)
parser.add_argument(
"--whichmatch3",
action="store_false",
dest="which3",
help="If specified, the sense of the offsets for the third "
"file will be relative to the MATCH cube, rather than the FROM "
"cube.",
)
parser.add_argument(
"files",
nargs="*",
help="Three flat.txt files that are the output of ISIS hijitreg.",
)
return parser
def main():
# Set the numpy type for elements in the main data area of the .dat file.
float_type = np.float32
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[util.parent_parser()],
)
parser.add_argument("-o",
"--output",
required=False,
default=".bitflip.dat")
parser.add_argument(
"-w",
"--width",
required=False,
default=5,
help="The number of medstd widths for bit-flip "
"cleaning.",
)
parser.add_argument(
"-r",
"--replacement",
required=False,
default=float_type(0),
type=float_type,
help="By default, the program will replace "
"identified pixels with an appropriate NULL data "
"value, but if provided this value will be used "
"instead.",
)
parser.add_argument(
"-p",
"--plot",
required=False,
action="store_true",
help="Displays plot for each area.",
)
parser.add_argument(
"-n",
"--dryrun",
required=False,
action="store_true",
help="Does not produce a cleaned output file.",
)
parser.add_argument("file", help="A .dat file to clean.")
args = parser.parse_args()
util.set_logger(args.verbose, args.logfile, args.log)
out_p = util.path_w_suffix(args.output, args.file)
clean(
args.file,
out_p,
args.replacement,
width=args.width,
plot=args.plot,
dryrun=args.dryrun,
)
sys.exit(0)
