new application free_dnn

pyproject.toml

@@ -49,7 +49,8 @@ requires = [
     "numpy; platform_machine != 'ppc64le'",
     'pyproject-metadata>=0.5.0',
     'tomli>=1.0.0',
-    'scipy'
+    'scipy',
+    'silx'
 ]
 
 [project.urls]
@@ -67,6 +68,7 @@ cormapy = 'freesas.app.cormap:main'
 supycomb = 'freesas.app.supycomb:main'
 free_bift = 'freesas.app.bift:main'
 extract_ascii = 'freesas.app.extract_ascii:main'
+free_dnn = 'freesas.app.dnn:main'
 
 [project.gui-scripts]
 freesas = 'freesas.app.plot_sas:main'

src/freesas/app/dnn.py

@@ -0,0 +1,74 @@
+#!/usr/bin/python3
+# coding: utf-8
+#
+#    Project: freesas
+#             https://github.com/kif/freesas
+#
+#    Copyright (C) 2020  European Synchrotron Radiation Facility, Grenoble, France
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# 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", "Mayank Yadav"]
+__license__ = "MIT"
+__copyright__ = "2024, ESRF"
+__date__ = "11/09/2024"
+
+import sys
+import logging
+from freesas.sas_argparser import SASParser
+from freesas.fitting import run_dnn
+
+logging.basicConfig(level=logging.WARNING)
+logger = logging.getLogger("free_dnn")
+
+if sys.version_info < (3, 6):
+    logger.error("This code uses F-strings and requires Python 3.6+")
+
+
+def build_parser() -> SASParser:
+    """Build parser for input and return list of files.
+    :return: parser
+    """
+    description = (
+        "Assess the radius of gyration (Rg) and the diameter of the particle (Dmax) using a Dense Neural-Network"
+        " for a set of scattering curves"
+    )
+    epilog = """free_dnn is an alternative implementation of
+    `gnnom` (https://doi.org/10.1016/j.str.2022.03.011).
+    As this tool used a different training set, some results are likely to differ.
+    """
+    parser = SASParser(prog="free_gpa", description=description, epilog=epilog)
+    file_help_text = "dat files of the scattering curves"
+    parser.add_file_argument(help_text=file_help_text)
+    parser.add_output_filename_argument()
+    parser.add_output_data_format("native", "csv", "ssf", default="native")
+    parser.add_q_unit_argument()
+
+    return parser
+
+
+
+def main() -> None:
+    """Entry point for free_gpa app"""
+    parser = build_parser()
+    run_dnn(parser=parser, logger=logger)
+
+
+if __name__ == "__main__":
+    main()

src/freesas/app/meson.build

@@ -7,7 +7,8 @@ py.install_sources([
     'cormap.py',
     'extract_ascii.py',
     'plot_sas.py',
-    'supycomb.py'
+    'supycomb.py',
+    'dnn.py'
 ],
   pure: false,    # Will be installed next to binaries
   subdir: 'freesas/app'  # Folder relative to site-packages to install to

src/freesas/fitting.py

@@ -5,7 +5,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "29/11/2023"
+__date__ = "11/09/2024"
 __status__ = "development"
 __docformat__ = "restructuredtext"
 
@@ -26,7 +26,7 @@
     load_scattering_data,
     convert_inverse_angstrom_to_nanometer,
 )
-from .sas_argparser import GuinierParser
+from .sas_argparser import GuinierParser, SASParser
 
 
 def set_logging_level(verbose_flag: int) -> None:
@@ -110,6 +110,28 @@ def get_guinier_header(
     else:
         return ""
 
+def get_dnn_header(
+    linesep: str, output_format: Optional[str] = None
+) -> str:
+    """Return appropriate header line for selected output format
+    :param output_format: output format from string parser
+    :param linesep: correct linesep for chosen destination
+    :return: a one-line string"""
+    # pylint: disable=R1705
+    if output_format == "csv":
+        return (
+            ",".join(
+                (
+                    "File",
+                    "Rg",
+                    "Dmax",
+                )
+            )
+            + linesep
+        )
+    else:
+        return ""
+
 
 def rg_result_to_output_line(
     rg_result: RG_RESULT,
@@ -161,6 +183,44 @@ def rg_result_to_output_line(
     else:
         return f"{afile} {rg_result}{linesep}"
 
+def dnn_result_to_output_line(
+    dnn_result: tuple,
+    afile: Path,
+    linesep: str,
+    output_format: Optional[str] = None,
+) -> str:
+    """Return result line formatted according to selected output format
+    :param dnn_result: Result of an dnn inference, 2 tuple
+    :param afile: The name of the file that was processed
+    :param output_format: The chosen output format
+    :param linesep: correct linesep for chosen destination
+    :return: a one-line string including linesep"""
+    # pylint: disable=R1705
+    if output_format == "csv":
+        return (
+            ",".join(
+                [
+                    f"{afile}",
+                    f"{dnn_result[0]:6.4f}",
+                    f"{dnn_result[1]:6.4f}",
+                ]
+            )
+            + linesep
+        )
+    elif output_format == "ssv":
+        return (
+            " ".join(
+                [
+                    f"{dnn_result[0]:6.4f}",
+                    f"{dnn_result[1]:6.4f}",
+                    f"{afile}",
+                ]
+            )
+            + linesep
+        )
+    else:
+        return f"{afile} {dnn_result[0]} {dnn_result[1]}{linesep}"
+
 
 def run_guinier_fit(
     fit_function: Callable[[ndarray], RG_RESULT],
@@ -220,3 +280,61 @@ def run_guinier_fit(
                     )
                     output_destination.write(res)
                     output_destination.flush()
+def run_dnn(
+    parser: SASParser,
+    logger: logging.Logger,
+) -> None:
+    """
+    reads in the data, infer the DNN and creates the result
+    :param parser: a function that returns the output of argparse.parse()
+    :param logger: a Logger
+    """
+    from .dnn import Rg_Dmax # heavy import
+
+    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_dnn_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)
+                q, I = data.T[:2]
+                try:
+                    dnn_result = Rg_Dmax(q, I)
+                except (
+                    InsufficientDataError,
+                    NoGuinierRegionError,
+                    ValueError,
+                    IndexError,
+                ) as err:
+                    sys.stderr.write(
+                        f"{afile}, {err.__class__.__name__}: {err} {os.linesep}"
+                    )
+                else:
+                    res = dnn_result_to_output_line(
+                        dnn_result,
+                        afile,
+                        linesep,
+                        args.format,
+                    )
+                    output_destination.write(res)
+                    output_destination.flush()

version.py

@@ -52,7 +52,7 @@
 __authors__ = ["Jérôme Kieffer"]
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "04/12/2023"
+__date__ = "11/09/2024"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 __all__ = ["date", "version_info", "strictversion", "hexversion", "debianversion",
@@ -68,11 +68,11 @@
                               "alpha": "a",
                               "beta": "b",
                               "candidate": "rc"}
-MAJOR = 0
+MAJOR = 2024
 MINOR = 9
-MICRO = 9
+MICRO = 0
 RELEV = "dev"  # <16
-SERIAL = 1  # <16
+SERIAL = 0  # <16
 
 date = __date__