# Path: freesas/autorg.py
# def auto_gpa(data, Rg_min=1.0, qRg_max=1.3, qRg_min=0.5):
#     def curate_data(data):
# def auto_guinier(data, Rg_min=1.0, qRg_max=1.3, relax=1.2):
#         I = data.T[1]
#         I = I[range0]
#         I0 = I[p1] * numpy.exp(q2[p1] * Rg ** 2 / 3.0)
#         I1 = I[range1]
# 
# Path: freesas/sas_argparser.py
# class GuinierParser:
#     """
#     Wrapper class for argparse ArgumentParser that provides predefined
#     arguments for auto_rg like programs.
#     """
# 
#     usage = ""
# 
#     def __init__(self, prog: str, description: str, epilog: str, **kwargs):
#         """
#         Create parser argparse ArgumentParser with argument
#         - standardized usage text
#         - standardized version text
#         - verbose and version args added by default
# 
#         :param prog:         name of the executable
#         :param description:  description param of argparse ArgumentParser
#         :param epilog:       epilog param of argparse ArgumentParser
#         :param kwargs:       additional kwargs for argparse ArgumentParser
#         """
# 
#         file_help_text = "dat files of the scattering curves"
#         self.parser = SASParser(
#             prog=prog, description=description, epilog=epilog, **kwargs
#         )
#         self.parser.add_file_argument(help_text=file_help_text)
#         self.parser.add_output_filename_argument()
#         self.parser.add_output_data_format(
#             "native", "csv", "ssf", default="native"
#         )
#         self.parser.add_q_unit_argument()
#         self.usage = self.parser.usage
# 
#     def parse_args(self, *args, **kwargs):
#         """ Wrapper for SASParser parse_args() """
#         return self.parser.parse_args(*args, **kwargs)
# 
#     def add_argument(self, *args, **kwargs):
#         """ Wrapper for SASParser add_argument() """
#         self.parser.add_argument(*args, **kwargs)
# 
# Path: freesas/fitting.py
# def run_guinier_fit(
#     fit_function: Callable[[ndarray], RG_RESULT],
#     parser: GuinierParser,
#     logger: logging.Logger,
# ) -> None:
#     """
#     reads in the data, performs the guinier fit with a given algotithm and
#     creates the
#     :param fit_function : A Guinier fit function data -> RG_RESULT
#     :param parser: a function that returns the output of argparse.parse()
#     :param logger: a Logger
#     """
#     args = parser.parse_args()
#     set_logging_level(args.verbose)
#     files = collect_files(args.file)
#     logger.debug("%s input files", len(files))
# 
#     with get_output_destination(args.output) as output_destination:
#         linesep = get_linesep(output_destination)
# 
#         output_destination.write(
#             get_guinier_header(
#                 linesep,
#                 args.format,
#             )
#         )
# 
#         for afile in files:
#             logger.info("Processing %s", afile)
#             try:
#                 data = load_scattering_data(afile)
#             except OSError:
#                 logger.error("Unable to read file %s", afile)
#             except ValueError:
#                 logger.error("Unable to parse file %s", afile)
#             else:
#                 if args.unit == "Å":
#                     data = convert_inverse_angstrom_to_nanometer(data)
#                 try:
#                     rg_result = fit_function(data)
#                 except (
#                     InsufficientDataError,
#                     NoGuinierRegionError,
#                     ValueError,
#                     IndexError,
#                 ) as err:
#                     sys.stderr.write(
#                         f"{afile}, {err.__class__.__name__}: {err} {os_linesep}"
#                     )
#                 else:
#                     res = rg_result_to_output_line(
#                         rg_result,
#                         afile,
#                         linesep,
#                         args.format,
#                     )
#                     output_destination.write(res)
#                     output_destination.flush()


import sys
import logging
from freesas.autorg import autoRg
from freesas.sas_argparser import GuinierParser
from freesas.fitting import run_guinier_fit
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.

__author__ = ["Jérôme Kieffer", "Martha Brennich"]
__license__ = "MIT"
__copyright__ = "2021, ESRF"
__date__ = "19/03/2021"


logging.basicConfig(level=logging.WARNING)
logger = logging.getLogger("auto_gpa")

if sys.version_info < (3, 6):
    logger.error("This code uses F-strings and requires Python 3.6+")


def build_parser() -> GuinierParser:
    """Build parser for input and return list of files.
    :return: parser
    """
    description = (
        "Calculate the radius of gyration using Guinier law"
        " for a set of scattering curves"
    )
    epilog = """free_rg is an open-source implementation of
    the autorg algorithm originately part of the ATSAS suite.
    As this is reverse engineered, some constants and results may differ
    """

# Path: freesas/autorg.py
# def auto_gpa(data, Rg_min=1.0, qRg_max=1.3, qRg_min=0.5):
#     def curate_data(data):
# def auto_guinier(data, Rg_min=1.0, qRg_max=1.3, relax=1.2):
#         I = data.T[1]
#         I = I[range0]
#         I0 = I[p1] * numpy.exp(q2[p1] * Rg ** 2 / 3.0)
#         I1 = I[range1]
# 
# Path: freesas/sas_argparser.py
# class GuinierParser:
#     """
#     Wrapper class for argparse ArgumentParser that provides predefined
#     arguments for auto_rg like programs.
#     """
# 
#     usage = ""
# 
#     def __init__(self, prog: str, description: str, epilog: str, **kwargs):
#         """
#         Create parser argparse ArgumentParser with argument
#         - standardized usage text
#         - standardized version text
#         - verbose and version args added by default
# 
#         :param prog:         name of the executable
#         :param description:  description param of argparse ArgumentParser
#         :param epilog:       epilog param of argparse ArgumentParser
#         :param kwargs:       additional kwargs for argparse ArgumentParser
#         """
# 
#         file_help_text = "dat files of the scattering curves"
#         self.parser = SASParser(
#             prog=prog, description=description, epilog=epilog, **kwargs
#         )
#         self.parser.add_file_argument(help_text=file_help_text)
#         self.parser.add_output_filename_argument()
#         self.parser.add_output_data_format(
#             "native", "csv", "ssf", default="native"
#         )
#         self.parser.add_q_unit_argument()
#         self.usage = self.parser.usage
# 
#     def parse_args(self, *args, **kwargs):
#         """ Wrapper for SASParser parse_args() """
#         return self.parser.parse_args(*args, **kwargs)
# 
#     def add_argument(self, *args, **kwargs):
#         """ Wrapper for SASParser add_argument() """
#         self.parser.add_argument(*args, **kwargs)
# 
# Path: freesas/fitting.py
# def run_guinier_fit(
#     fit_function: Callable[[ndarray], RG_RESULT],
#     parser: GuinierParser,
#     logger: logging.Logger,
# ) -> None:
#     """
#     reads in the data, performs the guinier fit with a given algotithm and
#     creates the
#     :param fit_function : A Guinier fit function data -> RG_RESULT
#     :param parser: a function that returns the output of argparse.parse()
#     :param logger: a Logger
#     """
#     args = parser.parse_args()
#     set_logging_level(args.verbose)
#     files = collect_files(args.file)
#     logger.debug("%s input files", len(files))
# 
#     with get_output_destination(args.output) as output_destination:
#         linesep = get_linesep(output_destination)
# 
#         output_destination.write(
#             get_guinier_header(
#                 linesep,
#                 args.format,
#             )
#         )
# 
#         for afile in files:
#             logger.info("Processing %s", afile)
#             try:
#                 data = load_scattering_data(afile)
#             except OSError:
#                 logger.error("Unable to read file %s", afile)
#             except ValueError:
#                 logger.error("Unable to parse file %s", afile)
#             else:
#                 if args.unit == "Å":
#                     data = convert_inverse_angstrom_to_nanometer(data)
#                 try:
#                     rg_result = fit_function(data)
#                 except (
#                     InsufficientDataError,
#                     NoGuinierRegionError,
#                     ValueError,
#                     IndexError,
#                 ) as err:
#                     sys.stderr.write(
#                         f"{afile}, {err.__class__.__name__}: {err} {os_linesep}"
#                     )
#                 else:
#                     res = rg_result_to_output_line(
#                         rg_result,
#                         afile,
#                         linesep,
#                         args.format,
#                     )
#                     output_destination.write(res)
#                     output_destination.flush()


# Path: freesas/app/autorg.py
import sys
import logging
from freesas.autorg import autoRg
from freesas.sas_argparser import GuinierParser
from freesas.fitting import run_guinier_fit

# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.

__author__ = ["Jérôme Kieffer", "Martha Brennich"]
__license__ = "MIT"
__copyright__ = "2021, ESRF"
__date__ = "19/03/2021"


logging.basicConfig(level=logging.WARNING)
logger = logging.getLogger("auto_gpa")

if sys.version_info < (3, 6):
    logger.error("This code uses F-strings and requires Python 3.6+")


def build_parser() -> GuinierParser:
    """Build parser for input and return list of files.
    :return: parser
    """
    description = (
        "Calculate the radius of gyration using Guinier law"
        " for a set of scattering curves"
    )
    epilog = """free_rg is an open-source implementation of
    the autorg algorithm originately part of the ATSAS suite.
    As this is reverse engineered, some constants and results may differ
    """

    return GuinierParser(