gammasimtools 0.25.0__py3-none-any.whl → 0.27.0__py3-none-any.whl

simtools/applications/db_development_tools/write_array_elements_positions_to_repository.py

@@ -1,160 +0,0 @@
-#!/usr/bin/python3
-"""
-    Read array element positions from file and add them to model repository.
-
-    This is an application for experts and should not be used by the general user.
-    Reading of input is fine-tuned to the array element files as provided by CTAO.
-
-    Command line arguments
-
-    input : str
-        File containing a table of array element positions.
-    repository_path : str
-        Path of local copy of model parameter repository.
-    parameter_version : str
-        Parameter version.
-    site : str
-        Observatory site.
-    coordinate_system : str
-        Coordinate system of array element positions (ground or utm).
-
-    Examples
-    --------
-    Add array element positions to repository:
-
-    .. code-block:: console
-
-        simtools-write-array-element-positions-to-repository \
-            --input /path/to/positions.txt \
-            --repository_path /path/to/repository \
-            --parameter_version 0.1.0 \
-            --coordinate_system ground \
-            --site North
-
-"""
-
-from pathlib import Path
-
-import astropy.table
-
-from simtools.application_control import get_application_label, startup_application
-from simtools.configuration import configurator
-from simtools.data_model.model_data_writer import ModelDataWriter
-from simtools.io import ascii_handler
-from simtools.model.array_model import ArrayModel
-
-
-def _parse():
-    """Parse command line configuration."""
-    config = configurator.Configurator(
-        label=get_application_label(__file__),
-        description="Add array element positions to model parameter repository",
-    )
-    config.parser.add_argument(
-        "--input",
-        help="File containing a table of array element positions.",
-        required=False,
-    )
-    config.parser.add_argument(
-        "--repository_path",
-        help="Output path to model parameter repository.",
-        type=Path,
-        required=False,
-    )
-    config.parser.add_argument(
-        "--coordinate_system",
-        help="Coordinate system of array element positions (utm or ground).",
-        default="ground",
-        required=False,
-        type=str,
-        choices=["ground", "utm"],
-    )
-
-    return config.initialize(db_config=True, simulation_model=["site", "parameter_version"])
-
-
-def write_utm_array_elements_to_repository(args_dict, logger):
-    """
-    Write UTM position of array elements to model repository.
-
-    Read array element positions from file. The ecsv row definition might
-    include telescope_name or asset_code and sequence_number.
-
-    Parameters
-    ----------
-    args_dict : dict
-        Command line arguments.
-    app_context.logger : app_context.logger
-        app_context.logger object.
-
-    """
-    array_elements = astropy.table.Table.read(args_dict["input"])
-    for row in array_elements:
-        instrument = (
-            row["telescope_name"]
-            if "telescope_name" in array_elements.colnames
-            else f"{row['asset_code']}-{row['sequence_number']}"
-        )
-        output_path = Path(args_dict["repository_path"]) / f"{instrument}"
-        output_path.mkdir(parents=True, exist_ok=True)
-        logger.info(f"Writing array element positions (utm) to {output_path}")
-
-        ModelDataWriter.dump_model_parameter(
-            parameter_name="array_element_position_utm",
-            instrument=instrument,
-            value=f"{row['utm_east']} {row['utm_north']} {row['altitude']}",
-            parameter_version=args_dict["parameter_version"],
-            output_path=output_path,
-            output_file="array_element_position_utm.json",
-        )
-
-
-def write_ground_array_elements_to_repository(args_dict, db_config, logger):
-    """
-    Write ground position of array elements to model repository.
-
-    Parameters
-    ----------
-    args_dict : dict
-        Command line arguments.
-    db_config : dict
-        Database configuration.
-    logger : logger
-        logger object.
-
-    """
-    array_model = ArrayModel(
-        db_config=db_config,
-        model_version=None,
-        site=args_dict["site"],
-        array_elements=args_dict["input"],
-    )
-    for element_name, data in array_model.array_elements.items():
-        output_path = Path(args_dict["repository_path"]) / f"{element_name}"
-        output_path.mkdir(parents=True, exist_ok=True)
-        logger.info(f"Writing array element positions (ground) to {output_path}")
-        ascii_handler.write_data_to_file(
-            data=data,
-            output_file=output_path / "array_element_position_ground.json",
-            sort_keys=False,
-            numpy_types=True,
-        )
-
-
-def main():
-    """Application main."""
-    app_context = startup_application(_parse)
-
-    if app_context.args["coordinate_system"] == "utm":
-        write_utm_array_elements_to_repository(app_context.args, app_context.logger)
-    elif app_context.args["coordinate_system"] == "ground":
-        write_ground_array_elements_to_repository(
-            app_context.args, app_context.db_config, app_context.logger
-        )
-    else:
-        app_context.logger.error("Invalid coordinate system. Allowed are 'utm' and 'ground'.")
-        raise ValueError
-
-
-if __name__ == "__main__":
-    main()

simtools/applications/print_version.py

@@ -1,53 +0,0 @@
-#!/usr/bin/python3
-"""
-Print the versions of the simtools software.
-
-The versions of simtools, the DB, sim_telarray, and CORSIKA are printed.
-
-"""
-
-from simtools import dependencies, version
-from simtools.application_control import get_application_label, startup_application
-from simtools.configuration import configurator
-from simtools.io import ascii_handler
-
-
-def _parse():
-    """Parse command line configuration."""
-    config = configurator.Configurator(
-        label=get_application_label(__file__),
-        description="Print the versions of simtools, the DB, sim_telarray and CORSIKA.",
-        usage="simtools-print-version",
-    )
-    return config.initialize(db_config=True, output=True, require_command_line=False)
-
-
-def main():
-    """Print the versions of the simtools software."""
-    app_context = startup_application(_parse)
-
-    version_string = dependencies.get_version_string(app_context.db_config)
-    version_dict = {"simtools version": version.__version__}
-
-    print()
-    # The loop below is not necessary, there is only one entry, but it is cleaner
-    for key, value in version_dict.items():  #
-        print(f"{key}: {value}")
-    print(version_string)
-
-    version_list = version_string.strip().split("\n")
-    for version_entry in version_list:
-        key, value = version_entry.split(": ", 1)
-        version_dict[key] = value
-
-    if not app_context.args.get("output_file_from_default", False):
-        ascii_handler.write_data_to_file(
-            data=version_dict,
-            output_file=app_context.io_handler.get_output_file(
-                app_context.args.get("output_file", "simtools_version.json")
-            ),
-        )
-
-
-if __name__ == "__main__":
-    main()

simtools/io/hdf5_handler.py

@@ -1,139 +0,0 @@
-"""Helper module for reading and writing in hd5 format."""
-
-import logging
-from pathlib import PosixPath
-
-import astropy.units as u
-import tables
-from astropy.table import Table
-from ctapipe.io import read_table
-
-from simtools.utils.names import sanitize_name
-
-_logger = logging.getLogger(__name__)
-
-
-def fill_hdf5_table(hist, x_bin_edges, y_bin_edges, x_label, y_label, meta_data):
-    """
-    Create and fill an hdf5 table with the histogram information.
-
-    It works for both 1D and 2D distributions.
-
-    Parameters
-    ----------
-    hist: numpy.ndarray
-        The counts of the histograms.
-    x_bin_edges: numpy.array
-        The x bin edges of the histograms.
-    y_bin_edges: numpy.array
-        The y bin edges of the histograms.
-        Use None for 1D histograms.
-    x_label: str
-        X bin edges label.
-    y_label: str
-        Y bin edges label.
-        Use None for 1D histograms.
-    meta_data: dict
-        Dictionary with the histogram metadata.
-    """
-    validate_histogram(hist, y_bin_edges)
-
-    meta_data["x_bin_edges"] = x_bin_edges
-    meta_data["x_bin_edges_unit"] = (
-        x_bin_edges.unit if isinstance(x_bin_edges, u.Quantity) else u.dimensionless_unscaled
-    )
-    if y_bin_edges is not None:
-        meta_data["y_bin_edges"] = y_bin_edges
-        meta_data["y_bin_edges_unit"] = (
-            y_bin_edges.unit if isinstance(y_bin_edges, u.Quantity) else u.dimensionless_unscaled
-        )
-
-    if hist.ndim == 1:
-        if x_label is not None:
-            names = sanitize_name(x_label)
-        try:
-            names = meta_data["Title"]
-        except KeyError:
-            _logger.warning("Title not found in metadata.")
-
-        table = Table(
-            [
-                x_bin_edges[:-1],
-                hist,
-            ],
-            names=(names, sanitize_name("Values")),
-            meta=meta_data,
-        )
-    else:
-        if y_label is not None:
-            names = [
-                f"{sanitize_name(y_label).split('__')[0]}_{i}" for i in range(len(y_bin_edges[:-1]))
-            ]
-        try:
-            names = [
-                f"{(meta_data['Title']).split('__')[0]}_{sanitize_name(y_label)}_{i}"
-                for i in range(len(y_bin_edges[:-1]))
-            ]
-        except KeyError:
-            _logger.warning("Title not found in metadata.")
-            names = [
-                f"{sanitize_name(y_label).split('__')[0]}_{i}" for i in range(len(y_bin_edges[:-1]))
-            ]
-
-        table = Table(
-            [hist[i, :] for i in range(len(y_bin_edges[:-1]))],
-            names=names,
-            meta=meta_data,
-        )
-
-    return table
-
-
-def validate_histogram(hist, y_bin_edges):
-    """Validate histogram dimensions and y_bin_edges consistency.
-
-    Parameters
-    ----------
-    hist (np.ndarray): The histogram array, expected to be 1D or 2D.
-    y_bin_edges (array-like or None): Bin edges for the second dimension (if applicable).
-
-    Raises
-    ------
-    ValueError: If histogram dimensions are invalid or inconsistent with y_bin_edges.
-    """
-    if hist.ndim not in (1, 2):
-        raise ValueError("Histogram must be either 1D or 2D.")
-
-    if hist.ndim == 1 and y_bin_edges is not None:
-        raise ValueError("y_bin_edges should be None for 1D histograms.")
-
-    if hist.ndim == 2 and y_bin_edges is None:
-        raise ValueError("y_bin_edges should not be None for 2D histograms.")
-
-
-def read_hdf5(hdf5_file_name):
-    """
-    Read a hdf5 output file.
-
-    Parameters
-    ----------
-    hdf5_file_name: str or Path
-        Name or Path of the hdf5 file to read from.
-
-    Returns
-    -------
-    list
-        The list with the astropy.Table instances for the various 1D and 2D histograms saved
-        in the hdf5 file.
-    """
-    if isinstance(hdf5_file_name, PosixPath):
-        hdf5_file_name = hdf5_file_name.absolute().as_posix()
-
-    tables_list = []
-
-    with tables.open_file(hdf5_file_name, mode="r") as file:
-        for node in file.walk_nodes("/", "Table"):
-            table_path = node._v_pathname  # pylint: disable=protected-access
-            table = read_table(hdf5_file_name, table_path)
-            tables_list.append(table)
-    return tables_list