gammasimtools 0.5.1__py3-none-any.whl → 0.6.1__py3-none-any.whl

simtools/applications/submit_data_from_external.py

@@ -5,7 +5,7 @@
     Submit model parameter (value, table) through the command line.
 
     Input data and metadata is validated, and if necessary enriched
-    and converted following a predescribed schema.
+    and converted following a pre-described schema.
 
     Command line arguments
     ----------------------
@@ -33,7 +33,7 @@
 
     .. code-block:: console
 
-        INFO::model_data_writer(l70)::write_data::Writing data to\
+        INFO::model_data_writer(l70)::write_data::Writing data to \
             /simtools/simtools-output/d-2023-07-31/TEST-submit_data_from_external.ecsv
 
 """
@@ -78,7 +78,7 @@ def _parse(label, description):
         "--input",
         help="input data file",
         type=str,
-        required=False,
+        required=True,
     )
     config.parser.add_argument(
         "--schema",
@@ -101,16 +101,14 @@ def main():
     _metadata = MetadataCollector(args_dict=args_dict)
 
     data_validator = validate_data.DataValidator(
-        schema_file=args_dict.get("schema", None),
+        schema_file=_metadata.get_data_model_schema_file_name(),
         data_file=args_dict["input"],
     )
 
-    file_writer = writer.ModelDataWriter(
-        product_data_file=args_dict["output_file"],
-        product_data_format=args_dict["output_file_format"],
-    )
-    file_writer.write(
-        metadata=_metadata.top_level_meta, product_data=data_validator.validate_and_transform()
+    writer.ModelDataWriter.dump(
+        args_dict=args_dict,
+        metadata=_metadata.top_level_meta,
+        product_data=data_validator.validate_and_transform(),
     )
 
 

simtools/applications/tune_psf.py

@@ -37,11 +37,11 @@
     telescope (str, required)
         Telescope model name (e.g. LST-1, SST-D, ...).
     model_version (str, optional)
-        Model version (default="Current").
+        Model version.
     src_distance (float, optional)
-        Source distance in km (default=10).
+        Source distance in km.
     zenith (float, optional)
-        Zenith angle in deg (default=20).
+        Zenith angle in deg.
     data (str, optional)
         Name of the data file with the measured cumulative PSF.
     plot_all (activation mode, optional)
@@ -51,7 +51,7 @@
     test (activation mode, optional)
         If activated, application will be faster by simulating fewer photons.
     verbosity (str, optional)
-        Log level to print (default=INFO).
+        Log level to print.
 
     Example
     -------
@@ -94,8 +94,8 @@ import numpy as np
 from matplotlib.backends.backend_pdf import PdfPages
 
 import simtools.utils.general as gen
-from simtools import io_handler
 from simtools.configuration import configurator
+from simtools.io_operations import io_handler
 from simtools.model.model_utils import split_simtel_parameter
 from simtools.model.telescope_model import TelescopeModel
 from simtools.ray_tracing import RayTracing
@@ -127,13 +127,11 @@ def main():
     )
     config.parser.add_argument(
         "--src_distance",
-        help="Source distance in km (default=10)",
+        help="Source distance in km",
         type=float,
         default=10,
     )
-    config.parser.add_argument(
-        "--zenith", help="Zenith angle in deg (default=20)", type=float, default=20
-    )
+    config.parser.add_argument("--zenith", help="Zenith angle in deg", type=float, default=20)
     config.parser.add_argument(
         "--data", help="Data file name with the measured PSF vs radius [cm]", type=str
     )
@@ -159,7 +157,7 @@ def main():
 
     # Output directory to save files related directly to this app
     _io_handler = io_handler.IOHandler()
-    output_dir = _io_handler.get_output_directory(label, dir_type="application-plots")
+    output_dir = _io_handler.get_output_directory(label, sub_dir="application-plots")
 
     tel_model = TelescopeModel(
         site=args_dict["site"],
@@ -211,11 +209,11 @@ def main():
     mar_0 = split_simtel_parameter(raw_par)[0]
 
     logger.debug(
-        "Previous parameter values: \n"
-        "MRRA = " + str(mrra_0) + "\n"
-        "MRF = " + str(mfr_0) + "\n"
-        "MRRA2 = " + str(mrra2_0) + "\n"
-        "MAR = " + str(mar_0) + "\n"
+        "Previous parameter values:\n"
+        f"MRRA = {str(mrra_0)}\n"
+        f"MRF = {str(mfr_0)}\n"
+        f"MRRA2 = {str(mrra2_0)}\n"
+        f"MAR = {str(mar_0)}\n"
     )
 
     if args_dict["fixed"]:
@@ -224,8 +222,8 @@ def main():
     # Drawing parameters randonly
     # Range around the previous values are hardcoded
     # Number of runs is hardcoded
-    N_RUNS = 50
-    for _ in range(N_RUNS):
+    n_runs = 50
+    for _ in range(n_runs):
         mrra_range = 0.004 if not args_dict["fixed"] else 0
         mrf_range = 0.1
         mrra2_range = 0.03
@@ -285,7 +283,7 @@ def main():
         )
 
         if plot:
-            fig = visualize.plot_1D(
+            fig = visualize.plot_1d(
                 data_to_plot,
                 plot_difference=True,
                 no_markers=True,

simtools/applications/validate_camera_efficiency.py

@@ -22,9 +22,21 @@
     telescope (str, required)
         Telescope model name (e.g. LST-1, SST-D, ...)
     model_version (str, optional)
-        Model version (default='Current')
+        Model version (default='Released')
+    zenith_angle (float, optional)
+        Zenith angle in degrees (between 0 and 180).
+    azimuth_angle (float, optional)
+        Telescope pointing direction in azimuth. It can be in degrees between 0 and 360 or
+        one of north, south, east or west (case insensitive). Note that North is 0 degrees
+        and the azimuth grows clockwise, so East is 90 degrees.
+    nsb_spectrum (str, optional)
+        File with NSB spectrum to use for the efficiency simulation.
+        The expected format is two columns with wavelength in nm and
+        NSB flux with the units: [1e9 * ph/m2/s/sr/nm].
+        If the file has more than two columns, the first and third are used,
+        and the second is ignored (native sim_telarray behaviour).
     verbosity (str, optional)
-        Log level to print (default=INFO).
+        Log level to print
 
     Example
     -------
@@ -35,6 +47,8 @@
     .. code-block:: console
 
         simtools-validate-camera-efficiency --site North \
+            --azimuth_angle 0 --zenith_angle 20 \
+            --nsb_spectrum average_nsb_spectrum_CTAO-N_ze20_az0.txt \
             --telescope MST-NectarCam-D --model_version prod5
 
     The output is saved in simtools-output/validate_camera_efficiency.
@@ -47,19 +61,16 @@
         simtools/simtools-output/validate_camera_efficiency/application-plots/validate_camera\
         _efficiency_MST-NectarCam-D_nsb
 
-    .. todo::
-
-        * Change default model to default (after this feature is implemented in db_handler)
-        * Fix the set_style. For some reason, sphinx cannot built docs with it on.
 """
 
 import logging
 from pathlib import Path
 
 import simtools.utils.general as gen
-from simtools import io_handler
 from simtools.camera_efficiency import CameraEfficiency
 from simtools.configuration import configurator
+from simtools.configuration.commandline_parser import CommandLineParser
+from simtools.io_operations import io_handler
 from simtools.model.telescope_model import TelescopeModel
 
 
@@ -75,7 +86,44 @@ def _parse(label):
             "Plot the camera efficiency vs wavelength for cherenkov and NSB light."
         ),
     )
-    return config.initialize(db_config=True, telescope_model=True)
+    config.parser.add_argument(
+        "--azimuth_angle",
+        help=(
+            "Telescope pointing direction in azimuth. "
+            "It can be in degrees between 0 and 360 or one of north, south, east or west "
+            "(case insensitive). Note that North is 0 degrees and "
+            "the azimuth grows clockwise, so East is 90 degrees."
+        ),
+        type=CommandLineParser.azimuth_angle,
+        default=0,
+        required=False,
+    )
+    config.parser.add_argument(
+        "--zenith_angle",
+        help="Zenith angle in degrees (between 0 and 180).",
+        type=CommandLineParser.zenith_angle,
+        default=20,
+        required=False,
+    )
+    config.parser.add_argument(
+        "--nsb_spectrum",
+        help=(
+            "File with NSB spectrum to use for the efficiency simulation."
+            "The expected format is two columns with wavelength in nm and "
+            "NSB flux with the units: [1e9 * ph/m2/s/sr/nm]."
+            "If the file has more than two columns, the first and third are used,"
+            "and the second is ignored (native sim_telarray behaviour)."
+        ),
+        type=str,
+        default=None,
+        required=False,
+    )
+    _args_dict, _db_config = config.initialize(db_config=True, telescope_model=True)
+    if _args_dict["site"] is None or _args_dict["telescope"] is None:
+        config.parser.print_help()
+        print("\n\nSite and telescope must be provided\n\n")
+        raise RuntimeError("Site and telescope must be provided")
+    return _args_dict, _db_config
 
 
 def main():
@@ -87,7 +135,7 @@ def main():
 
     # Output directory to save files related directly to this app
     _io_handler = io_handler.IOHandler()
-    output_dir = _io_handler.get_output_directory(label, dir_type="application-plots")
+    output_dir = _io_handler.get_output_directory(label, sub_dir="application-plots")
 
     tel_model = TelescopeModel(
         site=args_dict["site"],
@@ -105,6 +153,12 @@ def main():
     ce = CameraEfficiency(
         telescope_model=tel_model,
         simtel_source_path=args_dict["simtel_path"],
+        label=label,
+        config_data={
+            "zenith_angle": args_dict["zenith_angle"],
+            "azimuth_angle": args_dict["azimuth_angle"],
+            "nsb_spectrum": args_dict["nsb_spectrum"],
+        },
     )
     ce.simulate(force=True)
     ce.analyze(force=True)

simtools/applications/validate_camera_fov.py

@@ -20,16 +20,16 @@
     telescope (str, required)
         Telescope model name (e.g. LST-1, SST-D, ...)
     model_version (str, optional)
-        Model version (default='Current')
+        Model version
     camera_in_sky_coor (bool, optional)
         Plot the camera layout in sky coordinates akin to looking at it from behind for single \
-         mirror telescopes (default=False)
+         mirror telescopes
     print_pixels_id (bool, optional)
-        Up to which pixel ID to print (default=50). To suppress printing of pixel IDs, set to zero\
+        Up to which pixel ID to print. To suppress printing of pixel IDs, set to zero\
          (--print_pixels_id 0). To print all pixels, set to 'All'."
 
     verbosity (str, optional)
-        Log level to print (default=INFO).
+        Log level to print
 
     Example
     -------
@@ -49,18 +49,14 @@
         Saved camera plot in /workdir/external/simtools/simtools-output/validate_camera_fov\
         /application-plots/validate_camera_fov_LST-1_pixel_layout.png
 
-    .. todo::
-
-        * Change default model to default (after this feature is implemented in db_handler)
-        * Fix the set_style. For some reason, sphinx cannot built docs with it on.
 """
 
 import logging
 from pathlib import Path
 
 import simtools.utils.general as gen
-from simtools import io_handler
 from simtools.configuration import configurator
+from simtools.io_operations import io_handler
 from simtools.model.telescope_model import TelescopeModel
 
 
@@ -84,7 +80,7 @@ def main():
     config.parser.add_argument(
         "--print_pixels_id",
         help=(
-            "Up to which pixel ID to print (default: 50). "
+            "Up to which pixel ID to print. "
             "To suppress printing of pixel IDs, set to zero (--print_pixels_id 0). "
             "To print all pixels, set to 'All'."
         ),
@@ -99,7 +95,7 @@ def main():
 
     # Output directory to save files related directly to this app
     _io_handler = io_handler.IOHandler()
-    output_dir = _io_handler.get_output_directory(label, dir_type="application-plots")
+    output_dir = _io_handler.get_output_directory(label, sub_dir="application-plots")
 
     tel_model = TelescopeModel(
         site=args_dict["site"],
@@ -126,14 +122,14 @@ def main():
         pixel_ids_to_print = int(args_dict["print_pixels_id"])
         if pixel_ids_to_print == 0:
             pixel_ids_to_print = -1  # so not print the zero pixel
-    except ValueError:
+    except ValueError as exc:
         if args_dict["print_pixels_id"].lower() == "all":
             pixel_ids_to_print = camera.get_number_of_pixels()
         else:
             raise ValueError(
                 f"The value provided to --print_pixels_id ({args_dict['print_pixels_id']}) "
                 "should be an integer or All"
-            )
+            ) from exc
     fig = camera.plot_pixel_layout(args_dict["camera_in_sky_coor"], pixel_ids_to_print)
     plot_file_prefix = output_dir.joinpath(f"{label}_{tel_model.name}_pixel_layout")
     for suffix in ["pdf", "png"]:

simtools/applications/validate_file_using_schema.py

@@ -0,0 +1,127 @@
+#!/usr/bin/python3
+"""
+    Summary
+    -------
+    Validate yaml, json, or ecsv file using a json schema file.
+
+    Command line arguments
+    ----------------------
+    file_name (str)
+      input file to be validated
+    schema (str)
+      schema file (jsonschema format) used for validation
+
+    Raises
+    ------
+    FileNotFoundError
+      if file to be validated is not found
+
+    Example
+    -------
+
+    .. code-block:: console
+
+        simtools-validate-file-using-schema \
+         --file_name tests/resources/MLTdata-preproduction.meta.yml \
+         --schema simtools/schemas/metadata.metaschema.yml
+
+"""
+
+import logging
+from pathlib import Path
+
+import simtools.utils.general as gen
+from simtools.configuration import configurator
+from simtools.data_model import data_reader, metadata_collector, validate_data
+
+
+def _parse(label, description):
+    """
+    Parse command line configuration
+
+    Parameters
+    ----------
+    label (str)
+        application label
+    description (str)
+        application description
+
+    Returns
+    -------
+    config (Configurator)
+        application configuration
+
+    """
+
+    config = configurator.Configurator(label=label, description=description)
+    config.parser.add_argument("--file_name", help="file to be validated", required=True)
+    config.parser.add_argument("--schema", help="json schema file", required=False)
+    config.parser.add_argument(
+        "--validate_metadata",
+        help="validate metadata",
+        action="store_true",
+        default=False,
+    )
+    return config.initialize(paths=False)
+
+
+def _validate_yaml_or_json_file(args_dict, logger):
+    """
+    Validate a yaml or json file.
+    Schema is either given as command line argument, read from the meta_schema_url or from
+    the metadata section of the data dictionary.
+
+    """
+
+    data_reader.read_value_from_file(
+        file_name=args_dict["file_name"],
+        schema_file=args_dict["schema"],
+        validate=True,
+    )
+    logger.debug("Successful validation of json/yaml file")
+
+
+def _validate_ecsv_file(args_dict, logger):
+    """
+    Validate an ecsv file
+
+    """
+
+    data_validator = validate_data.DataValidator(
+        schema_file=args_dict["schema"],
+        data_file=args_dict["file_name"],
+    )
+    data_validator.validate_and_transform()
+    logger.debug("Successful validation of escv file")
+
+
+def _validate_metadata(args_dict, logger):
+    """
+    Validate metadata.
+
+    """
+
+    # metadata_collector runs the metadata validation by default, no need to do anything else
+    metadata_collector.MetadataCollector(None, metadata_file_name=args_dict["file_name"])
+    logger.debug("Successful validation of metadata")
+
+
+def main():
+    label = Path(__file__).stem
+    args_dict, _ = _parse(label, description="Validate yaml or ecsv file using a json schema file.")
+
+    logger = logging.getLogger()
+    logger.setLevel(gen.get_log_level_from_user(args_dict["log_level"]))
+
+    if args_dict["validate_metadata"]:
+        _validate_metadata(args_dict, logger)
+    elif any(args_dict["file_name"].endswith(ext) for ext in (".yml", ".yaml", ".json")):
+        _validate_yaml_or_json_file(args_dict, logger)
+    elif args_dict["file_name"].endswith(".ecsv"):
+        _validate_ecsv_file(args_dict, logger)
+    else:
+        logger.error(f"File extension not supported for {args_dict['file_name']}")
+
+
+if __name__ == "__main__":
+    main()

simtools/applications/validate_optics.py

@@ -32,21 +32,21 @@
     telescope (str, required)
         Telescope model name (e.g. LST-1, SST-D, ...).
     model_version (str, optional)
-        Model version (default='Current').
+        Model version.
     src_distance (float, optional)
-        Source distance in km (default=10).
+        Source distance in km.
     zenith (float, optional)
-        Zenith angle in deg (default=20).
+        Zenith angle in deg.
     max_offset (float, optional)
-        Maximum offset angle in deg (default=4).
+        Maximum offset angle in deg.
     offset_steps (float, optional)
-        Offset angle step size (default=0.25 deg)
+        Offset angle step size.
     plot_images (activation mode, optional)
         Produce a multiple pages pdf file with the image plots.
     test (activation mode, optional)
         If activated, application will be faster by simulating fewer photons.
     verbosity (str, optional)
-        Log level to print (default=INFO).
+        Log level to print.
 
     Example
     -------
@@ -55,7 +55,7 @@
     .. code-block:: console
 
         simtools-validate-optics --site North --telescope LST-1 --max_offset 1.0 \
-        --zenith 20 --src_distance 11 --test
+        --zenith 20 --src_distance 10 --test
 
     The output is saved in simtools-output/validate_optics
 
@@ -77,8 +77,8 @@ import numpy as np
 from matplotlib.backends.backend_pdf import PdfPages
 
 import simtools.utils.general as gen
-from simtools import io_handler
 from simtools.configuration import configurator
+from simtools.io_operations import io_handler
 from simtools.model.telescope_model import TelescopeModel
 from simtools.ray_tracing import RayTracing
 
@@ -99,22 +99,20 @@ def _parse(label):
 
     config.parser.add_argument(
         "--src_distance",
-        help="Source distance in km (default=10)",
+        help="Source distance in km",
         type=float,
         default=10,
     )
-    config.parser.add_argument(
-        "--zenith", help="Zenith angle in deg (default=20)", type=float, default=20
-    )
+    config.parser.add_argument("--zenith", help="Zenith angle in deg", type=float, default=20)
     config.parser.add_argument(
         "--max_offset",
-        help="Maximum offset angle in deg (default=4)",
+        help="Maximum offset angle in deg",
         type=float,
         default=4,
     )
     config.parser.add_argument(
         "--offset_steps",
-        help="Offset angle step size (default=0.25 deg)",
+        help="Offset angle step size",
         type=float,
         default=0.25,
     )
@@ -134,7 +132,7 @@ def main():
     logger.setLevel(gen.get_log_level_from_user(args_dict["log_level"]))
 
     _io_handler = io_handler.IOHandler()
-    output_dir = _io_handler.get_output_directory(label, dir_type="application-plots")
+    output_dir = _io_handler.get_output_directory(label, sub_dir="application-plots")
 
     tel_model = TelescopeModel(
         site=args_dict["site"],