gammasimtools 0.24.0__py3-none-any.whl → 0.26.0__py3-none-any.whl

simtools/visualization/plot_pixels.py

@@ -21,7 +21,7 @@ from simtools.visualization import visualize
 logger = logging.getLogger(__name__)
 
 
-def plot(config, output_file, db_config=None):
+def plot(config, output_file):
     """
     Plot pixel layout based on configuration.
 
@@ -36,15 +36,13 @@ def plot(config, output_file, db_config=None):
         - telescope : str, name of the telescope
     output_file : str
         Path where to save the plot
-    db_config : dict, optional
-        Database configuration.
 
     Returns
     -------
     None
         The function saves the plot to the specified output file.
     """
-    db = db_handler.DatabaseHandler(db_config=db_config)
+    db = db_handler.DatabaseHandler()
     db.export_model_file(
         parameter=config["parameter"],
         site=config["site"],

simtools/visualization/plot_psf.py

@@ -654,7 +654,6 @@ def create_psf_vs_offaxis_plot(tel_model, site_model, args_dict, best_pars, outp
     ray = RayTracing(
         telescope_model=tel_model,
         site_model=site_model,
-        simtel_path=args_dict["simtel_path"],
         zenith_angle=args_dict["zenith"] * u.deg,
         source_distance=args_dict["src_distance"] * u.km,
         off_axis_angle=off_axis_angles * u.deg,

simtools/visualization/plot_simtel_event_histograms.py

@@ -1,4 +1,4 @@
-"""Plot simtel event histograms filled with SimtelIOEventHistograms."""
+"""Plot simtel event histograms filled with EventDataHistograms."""
 
 import logging
 
@@ -6,7 +6,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 from matplotlib.colors import LogNorm
 
-from simtools.simtel.simtel_io_event_histograms import SimtelIOEventHistograms
+from simtools.sim_events.histograms import EventDataHistograms
 
 _logger = logging.getLogger(__name__)
 
@@ -17,7 +17,7 @@ def plot(histograms, output_path=None, limits=None, rebin_factor=2, array_name=N
 
     Parameters
     ----------
-    histograms: SimtelIOEventHistograms
+    histograms: EventDataHistograms
         Instance containing the histograms to plot.
     output_path: Path or str, optional
         Directory to save plots. If None, plots will be displayed.
@@ -230,7 +230,7 @@ def _create_rebinned_plot(plot_args, filename, output_path, rebin_factor):
     data = plot_args["data"]
     bins = plot_args["bins"]
 
-    rebinned_data, rebinned_x_bins, rebinned_y_bins = SimtelIOEventHistograms.rebin_2d_histogram(
+    rebinned_data, rebinned_x_bins, rebinned_y_bins = EventDataHistograms.rebin_2d_histogram(
         data, bins[0], bins[1], rebin_factor
     )
 

simtools/visualization/plot_simtel_events.py

@@ -13,8 +13,7 @@ from ctapipe.visualization import CameraDisplay
 from scipy import signal as _signal
 
 from simtools.data_model.metadata_collector import MetadataCollector
-from simtools.visualization.plot_corsika_histograms import save_figs_to_pdf
-from simtools.visualization.visualize import save_figure
+from simtools.visualization.visualize import save_figure, save_figures_to_single_document
 
 _logger = logging.getLogger(__name__)
 
@@ -665,24 +664,21 @@ def plot_simtel_peak_timing(
 
     fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(10, 4), dpi=300)
 
-    edges = _histogram_edges(n_samp, timing_bins)
-    et_name = getattr(getattr(event.trigger, "event_type", None), "name", "?")
     tel = source.subarray.tel[tel_id]
     tel_label = getattr(tel, "name", f"CT{tel_id}")
     _draw_peak_hist(
         ax1,
         peak_samples,
-        edges,
+        _histogram_edges(n_samp, timing_bins),
         mean_sample,
         std_sample,
         tel_label,
-        et_name,
+        getattr(getattr(event.trigger, "event_type", None), "name", "?"),
         pix_ids.size,
         found_count,
     )
 
-    readout = source.subarray.tel[tel_id].camera.readout
-    t = _time_axis_from_readout(readout, n_samp)
+    t = _time_axis_from_readout(source.subarray.tel[tel_id].camera.readout, n_samp)
 
     ex_ids = pix_ids[: max(1, int(examples))]
     for pid in ex_ids:
@@ -698,13 +694,12 @@ def plot_simtel_peak_timing(
     fig.tight_layout()
 
     if return_stats:
-        stats = {
+        return fig, {
             "considered": int(pix_ids.size),
             "found": int(found_count),
             "mean": float(mean_sample),
             "std": float(std_sample),
         }
-        return fig, stats
     return fig
 
 
@@ -991,7 +986,7 @@ def generate_and_save_plots(
             continue
 
         try:
-            save_figs_to_pdf(figures, pdf_path)
+            save_figures_to_single_document(figures, pdf_path)
             _logger.info("Saved PDF: %s", pdf_path)
         except Exception as ex:  # pylint:disable=broad-except
             _logger.error("Failed to save PDF %s: %s", pdf_path, ex)

simtools/visualization/plot_tables.py

@@ -16,7 +16,7 @@ from simtools.visualization import visualize
 _logger = logging.getLogger(__name__)
 
 
-def plot(config, output_file, db_config=None, data_path=None):
+def plot(config, output_file, data_path=None):
     """
     Plot tabular data from data or from model parameter files.
 
@@ -26,12 +26,10 @@ def plot(config, output_file, db_config=None, data_path=None):
         Configuration dictionary for plotting.
     output_file: str
         Output file.
-    db_config: dict, optional
-        Database configuration dictionary for accessing the model parameter database.
     data_path: Path or str, optional
         Path to the data files (optional). Expect all files to be in the same directory.
     """
-    data = read_table_data(config, db_config, data_path)
+    data = read_table_data(config, data_path)
 
     fig = visualize.plot_1d(
         data,
@@ -42,7 +40,7 @@ def plot(config, output_file, db_config=None, data_path=None):
     return output_file
 
 
-def read_table_data(config, db_config, data_path=None):
+def read_table_data(config, data_path=None):
     """
     Read table data from file or parameter database.
 
@@ -50,8 +48,6 @@ def read_table_data(config, db_config, data_path=None):
     ----------
     config: dict
         Configuration dictionary for plotting.
-    db_config: dict
-        Database configuration dictionary for accessing the model parameter database.
     data_path: Path or str, optional
         Path to the data files (optional). Expect all files to be in the same directory.
 
@@ -64,7 +60,7 @@ def read_table_data(config, db_config, data_path=None):
 
     for _config in config["tables"]:
         if "parameter" in _config:
-            table = _read_table_from_model_database(_config, db_config)
+            table = _read_table_from_model_database(_config)
         elif "file_name" in _config:
             file_name = (
                 _config["file_name"]
@@ -117,7 +113,7 @@ def _process_table_data(table, _config):
     )
 
 
-def _read_table_from_model_database(table_config, db_config):
+def _read_table_from_model_database(table_config):
     """
     Read table data from model parameter database.
 
@@ -131,7 +127,7 @@ def _read_table_from_model_database(table_config, db_config):
     Table
         Astropy table
     """
-    db = db_handler.DatabaseHandler(db_config=db_config)
+    db = db_handler.DatabaseHandler()
     return db.export_model_file(
         parameter=table_config["parameter"],
         site=table_config["site"],
@@ -170,15 +166,11 @@ def _validate_config_columns(config, valid_columns, logger):
 
 def _get_valid_columns(table):
     """Return columns that exist and have valid data (not all NaN)."""
-    valid_columns = []
-    for col in table.colnames:
-        if not all(np.isnan(table[col])):
-            valid_columns.append(col)
-    return valid_columns
+    return [col for col in table.colnames if not all(np.isnan(table[col]))]
 
 
 def generate_plot_configurations(
-    parameter, parameter_version, site, telescope, output_path, plot_type, db_config
+    parameter, parameter_version, site, telescope, output_path, plot_type
 ):
     """
     Generate plot configurations for a model parameter from schema files.
@@ -197,8 +189,6 @@ def generate_plot_configurations(
         Output path for the plots.
     plot_type: str
         Plot type or "all" for all plots.
-    db_config: dict
-        Database configuration.
 
     Returns
     -------
@@ -226,7 +216,6 @@ def generate_plot_configurations(
             "telescope": telescope,
             "parameter_version": parameter_version,
         },
-        db_config=db_config,
     )
     valid_columns = _get_valid_columns(table)
 

simtools/visualization/visualize.py

@@ -11,6 +11,7 @@ import matplotlib.pyplot as plt
 from astropy.table import QTable
 from cycler import cycler
 from matplotlib import gridspec
+from matplotlib.backends.backend_pdf import PdfPages
 
 COLORS = {}
 COLORS["classic"] = [
@@ -615,7 +616,7 @@ def plot_hist_2d(data, **kwargs):
     return fig
 
 
-def save_figure(fig, output_file, figure_format=None, log_title="", dpi="figure"):
+def save_figure(fig, output_file, figure_format=("pdf", "png"), log_title="", dpi="figure"):
     """
     Save figure to output file(s).
 
@@ -630,10 +631,29 @@ def save_figure(fig, output_file, figure_format=None, log_title="", dpi="figure"
     title: str
         Title of the figure to be added to the log message.
     """
-    figure_format = figure_format or ["pdf", "png"]
     for fmt in figure_format:
         _file = Path(output_file).with_suffix(f".{fmt}")
         fig.savefig(_file, format=fmt, bbox_inches="tight", dpi=dpi)
         logging.info(f"Saved plot {log_title} to {_file}")
 
     fig.clf()
+
+
+def save_figures_to_single_document(figs, output_file_name):
+    """
+    Save multiple figures to a single PDF document.
+
+    Parameters
+    ----------
+    figs: list
+        List of plt.figure instances to save.
+    output_file_name: Path, str
+        PDF file name
+    """
+    _logger.info(f"Saving {len(figs)} figures to {output_file_name}")
+    pdf_pages = PdfPages(Path(output_file_name).absolute().as_posix())
+    for fig in figs:
+        plt.tight_layout()
+        pdf_pages.savefig(fig)
+
+    pdf_pages.close()

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

simtools/simtel/simtel_io_file_info.py

@@ -1,62 +0,0 @@
-#!/usr/bin/python3
-"""Read file info and run headers from sim_telarray files."""
-
-from eventio import EventIOFile
-from eventio.simtel import MCRunHeader, MCShower, RunHeader
-
-
-def get_corsika_run_number(file):
-    """
-    Return the CORSIKA run number from a sim_telarray file.
-
-    Parameters
-    ----------
-    file: str
-        Path to the sim_telarray file.
-
-    Returns
-    -------
-    int, None
-        CORSIKA run number. Returns None if not found.
-    """
-    run_header = get_corsika_run_header(file)
-    return run_header.get("run") if run_header else None
-
-
-def get_corsika_run_header(file):
-    """
-    Return the CORSIKA run header information from a sim_telarray file.
-
-    Reads both RunHeader and MCRunHeader object from file and
-    returns a merged dictionary. Adds primary id from the first event.
-
-    Parameters
-    ----------
-    file: str
-        Path to the sim_telarray file.
-
-    Returns
-    -------
-    dict, None
-        CORSIKA run header. Returns None if not found.
-    """
-    run_header = None
-    mc_run_header = None
-    primary_id = None
-
-    with EventIOFile(file) as f:
-        for o in f:
-            if isinstance(o, RunHeader) and run_header is None:
-                run_header = o.parse()
-            elif isinstance(o, MCRunHeader) and mc_run_header is None:
-                mc_run_header = o.parse()
-            elif isinstance(o, MCShower):  # get primary_id from first MCShower
-                primary_id = o.parse().get("primary_id")
-            if run_header and mc_run_header and primary_id is not None:
-                break
-
-    run_header = run_header or {}
-    mc_run_header = mc_run_header or {}
-    if primary_id is not None:
-        mc_run_header["primary_id"] = primary_id
-    return run_header | mc_run_header or None