def __init_parser(self):
self.parser = argparse.ArgumentParser()
# TODO System for monitoring and registering models automatically
# The available models are just hard coded at the moment
self._registered_models = pybiosas.models.models
self.parser.add_argument('command',
type=str,
choices=['fit', 'calc', 'calculate'],
help="""Fit a model or calculate data given
a set of parameters and a model""")
self.parser.add_argument('-dataset',
type=str,
help="The dataset to fit in SasXML format")
models = []
for model in self._registered_models.iterkeys():
models.append(model)
self.parser.add_argument('-model',
type=str,
choices=models,
help=("""The model to fitted or calculated.
Available models are""" + str(models)))
self.parser.add_argument('-parameters',
type=str,
help="""The paramaters, as either a json
file or a list of dictionaries with structure as defined
for the parinfo option of mpfit.""")
self.parser.add_argument('-q_vals',
'-q_values',
type=str,
help="""A list of q values for calculating
intensities from a model. Provide as a string
or file containing either the list of q values
[1st, 2nd...last] or [1st, last, step] where
step is optional""",
default="[0.0, 0.5, 0.0005]")
self.parser.add_argument('-outpath',
type=str,
help="""A path to a directory for the output
files. If it is desired to name the output file
then terminate the path with that filename.
Otherwise terminate the path with a '/'.
Default is to place output files in
same directory as the input parameter file. The
default output filename is 'outfile.json'. If
parameters are passed as a string on the
command line then outpath defaults to the
current working directory.""")
self.parser.add_argument('-xml',
action='store_true',
help="""Write output to CML file.""")
def __init_parser(self):
self.parser = argparse.ArgumentParser()
# TODO System for monitoring and registering models automatically
# The available models are just hard coded at the moment
self._registered_models = pybiosas.models.models
self.parser.add_argument('command', type = str,
choices = ['fit', 'calc', 'calculate'],
help = """Fit a model or calculate data given
a set of parameters and a model""")
self.parser.add_argument('-dataset', type = str,
help = "The dataset to fit in SasXML format")
models = []
for model in self._registered_models.iterkeys():
models.append(model)
self.parser.add_argument('-model', type=str,
choices = models,
help = ("""The model to fitted or calculated.
Available models are""" +
str(models)))
self.parser.add_argument('-parameters', type = str,
help = """The paramaters, as either a json
file or a list of dictionaries with structure as defined
for the parinfo option of mpfit.""")
self.parser.add_argument('-q_vals', '-q_values', type = str,
help = """A list of q values for calculating
intensities from a model. Provide as a string
or file containing either the list of q values
[1st, 2nd...last] or [1st, last, step] where
step is optional""",
default = "[0.0, 0.5, 0.0005]")
self.parser.add_argument('-outpath', type = str,
help = """A path to a directory for the output
files. If it is desired to name the output file
then terminate the path with that filename.
Otherwise terminate the path with a '/'.
Default is to place output files in
same directory as the input parameter file. The
default output filename is 'outfile.json'. If
parameters are passed as a string on the
command line then outpath defaults to the
current working directory.""")
self.parser.add_argument('-xml', action = 'store_true',
help = """Write output to CML file.""")
def __init_parser(self):
"""Command line parser for taking in optional arguments"""
self.parser = argparse.ArgumentParser()
self._registered_models = pybiosas.models.models
self.parser.add_argument('-command',
type=str,
choices=['fit', 'write'],
help="""Fit models or write out a bag of
tasks given a parameter space to sweep""")
self.parser.add_argument('-script',
type=str,
help="""Location of the python script to
run the model fit on this system""")
self.parser.add_argument('-dataset',
type=str,
help="The dataset to use in SasXML format")
models = []
for model in self._registered_models.iterkeys():
models.append(model)
self.parser.add_argument('-model',
type=str,
choices=models,
help=("""The model to be fitted.
Available models are""" + str(models)))
self.parser.add_argument('-parameters',
type=str,
help="""The paramaters, as either a json
file or a list of dictionaries with structure as defined
for the parinfo option of mpfit. Parameter sweeps should
be defined as lists, 3-tuples (lowest, highest, step)"""
)
self.parser.add_argument('-outpath',
type=str,
help="""A path to a directory for the output
files. If it is desired to name the output file
then terminate the path with that filename.
Otherwise terminate the path with a '/'.
Default is to place output files in
same directory as the input data file.""")
self.parser.add_argument('-xml',
action='store_true',
help="""Write output to CML file.""")
def __init_parser(self):
"""Command line parser for taking in optional arguments"""
self.parser = argparse.ArgumentParser()
self._registered_models = pybiosas.models.models
self.parser.add_argument('-command', type = str,
choices = ['fit', 'write'],
help = """Fit models or write out a bag of
tasks given a parameter space to sweep""")
self.parser.add_argument('-script', type = str,
help = """Location of the python script to
run the model fit on this system""")
self.parser.add_argument('-dataset', type = str,
help = "The dataset to use in SasXML format")
models = []
for model in self._registered_models.iterkeys():
models.append(model)
self.parser.add_argument('-model', type=str,
choices = models,
help = ("""The model to be fitted.
Available models are""" +
str(models)))
self.parser.add_argument('-parameters', type = str,
help = """The paramaters, as either a json
file or a list of dictionaries with structure as defined
for the parinfo option of mpfit. Parameter sweeps should
be defined as lists, 3-tuples (lowest, highest, step)""")
self.parser.add_argument('-outpath', type = str,
help = """A path to a directory for the output
files. If it is desired to name the output file
then terminate the path with that filename.
Otherwise terminate the path with a '/'.
Default is to place output files in
same directory as the input data file.""")
self.parser.add_argument('-xml', action = 'store_true',
help = """Write output to CML file.""")
