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

simtools/applications/generate_simtel_array_histograms.py

@@ -0,0 +1,192 @@
+#!/usr/bin/python3
+
+"""
+    Summary
+    -------
+    This application allows to write sim_telarray histograms into pdf and hdf5 files.
+    It accepts multiple lists of histograms files, a single list or a histogram file.
+    Each histogram is plotted in a page of the pdf file if the --pdf option is activated.
+
+
+    Command line arguments
+    ----------------------
+    hist_file_names (str, optional)
+        Name of the histogram files to be plotted.
+        It can be given as the histogram file names (more than one option allowed) or as a text
+        file with the names of the histogram files in it.
+    figure_name (str, required)
+        File name for the pdf output (without extension).
+    pdf (bool, optional)
+        If set, histograms are saved into pdf files.
+        One pdf file contains all the histograms found in the file.
+        The name of the file is controlled via `output_file_name`.
+    hdf5: bool
+        If true, histograms are saved into hdf5 files.
+        At least one of `pdf` and `hdf5` has to be activated.
+    output_file_name (str, optional)
+        The name of the output hdf5 (and/or pdf) files (without the path).
+        If not given, `output_file_name` takes the name from the (first) input file
+        (`hist_file_names`).
+        If the output `output_file_name.hdf5` file already exists and `hdf5` is set, the tables
+        associated to `hdf5` will be overwritten. The remaining tables, if any, will stay
+        untouched.
+    verbosity (str, optional)
+        Log level to print.
+
+    Raises
+    ------
+    TypeError:
+        if argument passed through `hist_file_names` is not a file.
+
+    Example
+    -------
+    .. code-block:: console
+
+        simtools-generate-simtel-array-histograms --hist_file_names tests/resources/
+            run2_gamma_za20deg_azm0deg-North-Prod5_test-production-5.hdata.zst
+            --output_file_name test_hist_hdata --hdf5 --pdf
+
+"""
+
+import logging
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+from matplotlib.backends.backend_pdf import PdfPages
+
+import simtools.utils.general as gen
+from simtools.configuration import configurator
+from simtools.io_operations import io_handler
+from simtools.simtel.simtel_histograms import SimtelHistograms
+
+
+def _parse(label, description):
+    """
+    Parse command line configuration
+
+    Parameters
+    ----------
+    label: str
+        Label describing the application.
+    description: str
+        Description of the application.
+
+    Returns
+    -------
+    CommandLineParser
+        Command line parser object
+
+    """
+    config = configurator.Configurator(label=label, description=description)
+
+    config.parser.add_argument(
+        "--hist_file_names",
+        help="Name of the histogram files to be plotted or the text file containing the list of "
+        "histogram files.",
+        nargs="+",
+        required=True,
+        type=str,
+    )
+
+    config.parser.add_argument(
+        "--hdf5", help="Save histograms into a hdf5 file.", action="store_true", required=False
+    )
+
+    config.parser.add_argument(
+        "--pdf", help="Save histograms into a pdf file.", action="store_true", required=False
+    )
+
+    config.parser.add_argument(
+        "--output_file_name",
+        help="Name of the hdf5 (and/or pdf) file where to save the histograms.",
+        type=str,
+        required=False,
+        default=None,
+    )
+
+    config_parser, _ = config.initialize(db_config=False, paths=True)
+    if not config_parser["pdf"]:
+        if not config_parser["hdf5"]:
+            config.parser.error("At least one argument is required: `--pdf` or `--hdf5`.")
+
+    return config_parser
+
+
+def main():
+    label = Path(__file__).stem
+    description = "Display the simtel_array histograms."
+    io_handler_instance = io_handler.IOHandler()
+    config_parser = _parse(label, description)
+    output_path = io_handler_instance.get_output_directory(label, sub_dir="application-plots")
+    logger = logging.getLogger()
+    logger.setLevel(gen.get_log_level_from_user(config_parser["log_level"]))
+    logger.info("Starting the application.")
+
+    # Building list of histograms from the input files
+    histogram_files = []
+    for one_file in config_parser["hist_file_names"]:
+        try:
+            if Path(one_file).suffix in [".zst", ".simtel", ".hdata"]:
+                histogram_files.append(one_file)
+            else:
+                # Collecting hist files
+                with open(one_file, encoding="utf-8") as file:
+                    for line in file:
+                        # Removing '\n' from filename, in case it is left there.
+                        histogram_files.append(line.replace("\n", ""))
+        except FileNotFoundError as exc:
+            msg = f"{one_file} is not a file."
+            logger.error(msg)
+            raise FileNotFoundError from exc
+
+    # If no output name is passed, the tool gets the name of the first histogram of the list
+    if config_parser["output_file_name"] is None:
+        config_parser["output_file_name"] = Path(histogram_files[0]).absolute().name
+    output_file_name = Path(output_path).joinpath(f"{config_parser['output_file_name']}")
+
+    # If the hdf5 output file already exists, it is overwritten
+    if (Path(f"{config_parser['output_file_name']}.hdf5").exists()) and (config_parser["hdf5"]):
+        msg = (
+            f"Output hdf5 file {config_parser['output_file_name']}.hdf5 already exists. "
+            f"Overwriting it."
+        )
+        logger.warning(msg)
+        overwrite = True
+    else:
+        overwrite = False
+
+    # Building SimtelHistograms
+    simtel_histograms = SimtelHistograms(histogram_files)
+
+    if config_parser["pdf"]:
+        logger.debug(f"Creating the pdf file {output_file_name}.pdf")
+        pdf_pages = PdfPages(f"{output_file_name}.pdf")
+
+        if config_parser["test"]:
+            number_of_histograms = 2
+        else:
+            number_of_histograms = simtel_histograms.number_of_histograms
+
+        for i_hist in range(number_of_histograms):
+            title = simtel_histograms.get_histogram_title(i_hist)
+
+            logger.debug(f"Processing: {title}")
+
+            fig, ax = plt.subplots(1, 1, figsize=(6, 6))
+            simtel_histograms.plot_one_histogram(i_hist, ax)
+
+            plt.tight_layout()
+            pdf_pages.savefig(fig)
+            plt.clf()
+
+        plt.close()
+        pdf_pages.close()
+        logger.info(f"Wrote histograms to the pdf file {output_file_name}.pdf")
+
+    if config_parser["hdf5"]:
+        logger.info(f"Wrote histograms to the hdf5 file {output_file_name}.hdf5")
+        simtel_histograms.export_histograms(f"{output_file_name}.hdf5", overwrite=overwrite)
+
+
+if __name__ == "__main__":
+    main()

simtools/applications/get_file_from_db.py

@@ -18,7 +18,7 @@
         Name of the local output directory where to save the files.
         Default it $CWD.
     verbosity (str, optional)
-        Log level to print (default=INFO).
+        Log level to print.
 
     Example
     -------

simtools/applications/get_parameter.py

@@ -6,7 +6,7 @@
     Get a parameter entry from DB for a specific telescope or a site.
     The application receives a parameter name, a site, a telescope (if applicable) and \
     optionally a version. It then prints out the parameter entry.
-    If no version is provided, the value of the current model is printed..
+    If no version is provided, the value of the released model is printed..
 
     Command line arguments
     ----------------------
@@ -20,7 +20,7 @@
         Telescope model name (e.g. LST-1, SST-D, ...)
 
     log_level (str, optional)
-        Log level to print (default=INFO).
+        Log level to print.
 
     Raises
     ------
@@ -64,7 +64,7 @@ def main():
             "Get a parameter entry from DB for a specific telescope or a site. "
             "The application receives a parameter name a site, a telescope (if applicable), "
             " and optionally a version. It then prints out the parameter entry. "
-            "If no version is provided, the value of the current model is printed. "
+            "If no version is provided, the value of the released model is printed. "
         )
     )
     config.parser.add_argument("--parameter", help="Parameter name", type=str, required=True)

simtools/applications/make_regular_arrays.py

@@ -12,8 +12,12 @@
 
     Command line arguments
     ----------------------
+    site (str, required)
+        observatory site (e.g., North or South).
+    model_version (str, optional)
+        Model version to use (e.g., prod6). If not provided, the latest version is used.
     verbosity (str, optional)
-        Log level to print (default=INFO).
+        Log level to print.
 
     Example
     -------
@@ -21,28 +25,22 @@
 
     .. code-block:: console
 
-        simtools-make-regular-arrays
+        simtools-make-regular-arrays --site=North
 
-    The output is saved in simtools-output/make_regular_arrays.
-
-    Expected final print-out message:
-
-    .. code-block:: console
-
-        INFO::layout_array(l608)::export_telescope_list::Exporting telescope list to /workdir/exter\
-        nal/simtools/simtools-output/make_regular_arrays/layout/telescope_positions-North-4LS\
-        T-corsika.ecsv
 """
 
 import logging
+import os
 from pathlib import Path
 
 import astropy.units as u
 
+import simtools.data_model.model_data_writer as writer
 import simtools.utils.general as gen
-from simtools import db_handler, io_handler
+from simtools import db_handler
 from simtools.configuration import configurator
-from simtools.layout.layout_array import LayoutArray
+from simtools.io_operations import io_handler
+from simtools.layout.array_layout import ArrayLayout
 
 
 def main():
@@ -55,7 +53,7 @@ def main():
             "The array layout files created should be available at the data/layout directory."
         ),
     )
-    args_dict, db_config = config.initialize(db_config=True)
+    args_dict, db_config = config.initialize(db_config=True, site_model=True, output=True)
 
     label = "make_regular_arrays"
 
@@ -64,100 +62,98 @@ def main():
 
     _io_handler = io_handler.IOHandler()
 
-    corsika_pars = gen.collect_data_from_yaml_or_dict(
+    corsika_pars = gen.collect_data_from_file_or_dict(
         _io_handler.get_input_data_file("parameters", "corsika_parameters.yml"), None
     )
 
     # Reading site parameters from DB
     db = db_handler.DatabaseHandler(mongo_db_config=db_config)
+    site_pars_db = db.get_site_parameters(
+        site=args_dict["site"], model_version=args_dict["model_version"]
+    )
 
-    site_pars_db = {}
     layout_center_data = {}
+    layout_center_data["center_lat"] = float(site_pars_db["ref_lat"]["Value"]) * u.deg
+    layout_center_data["center_lon"] = float(site_pars_db["ref_long"]["Value"]) * u.deg
+    layout_center_data["center_alt"] = float(site_pars_db["altitude"]["Value"]) * u.m
+    layout_center_data["EPSG"] = site_pars_db["EPSG"]["Value"]
     corsika_telescope_data = {}
-    for site in ["North", "South"]:
-        site_pars_db[site] = db.get_site_parameters(site=site, model_version="prod5")
-
-        layout_center_data[site] = {}
-        layout_center_data[site]["center_lat"] = (
-            float(site_pars_db[site]["ref_lat"]["Value"]) * u.deg
-        )
-        layout_center_data[site]["center_lon"] = (
-            float(site_pars_db[site]["ref_long"]["Value"]) * u.deg
-        )
-        layout_center_data[site]["center_alt"] = (
-            float(site_pars_db[site]["altitude"]["Value"]) * u.m
-        )
-        layout_center_data[site]["EPSG"] = site_pars_db[site]["EPSG"]["Value"]
-        corsika_telescope_data[site] = {}
-        corsika_telescope_data[site]["corsika_obs_level"] = layout_center_data[site]["center_alt"]
-        corsika_telescope_data[site]["corsika_sphere_center"] = corsika_pars[
-            "corsika_sphere_center"
-        ]
-        corsika_telescope_data[site]["corsika_sphere_radius"] = corsika_pars[
-            "corsika_sphere_radius"
-        ]
+    corsika_telescope_data["corsika_obs_level"] = layout_center_data["center_alt"]
+    corsika_telescope_data["corsika_sphere_center"] = corsika_pars["corsika_sphere_center"]
+    corsika_telescope_data["corsika_sphere_radius"] = corsika_pars["corsika_sphere_radius"]
 
     # Telescope distances for 4 tel square arrays
     # !HARDCODED
     telescope_distance = {"LST": 57.5 * u.m, "MST": 70 * u.m, "SST": 80 * u.m}
 
-    for site in ["South", "North"]:
-        for array_name in ["1SST", "4SST", "1MST", "4MST", "1LST", "4LST"]:
-            logger.info(f"Processing array {array_name}")
-            layout = LayoutArray(
-                site=site,
-                mongo_db_config=db_config,
-                label=label,
-                name=f"{site}-{array_name}",
-                layout_center_data=layout_center_data[site],
-                corsika_telescope_data=corsika_telescope_data[site],
+    for array_name in ["1SST", "4SST", "1MST", "4MST", "1LST", "4LST"]:
+        logger.info(f"Processing array {array_name}")
+        layout = ArrayLayout(
+            site=args_dict["site"],
+            mongo_db_config=db_config,
+            label=label,
+            name=f"{args_dict['site']}-{array_name}",
+            layout_center_data=layout_center_data,
+            corsika_telescope_data=corsika_telescope_data,
+        )
+
+        tel_size = array_name[1:4]
+
+        # Single telescope at the center
+        if array_name[0] == "1":
+            layout.add_telescope(
+                telescope_name=tel_size + "-01",
+                crs_name="ground",
+                xx=0 * u.m,
+                yy=0 * u.m,
+                tel_corsika_z=0 * u.m,
+            )
+        # 4 telescopes in a regular square grid
+        else:
+            layout.add_telescope(
+                telescope_name=tel_size + "-01",
+                crs_name="ground",
+                xx=telescope_distance[tel_size],
+                yy=telescope_distance[tel_size],
+                tel_corsika_z=0 * u.m,
+            )
+            layout.add_telescope(
+                telescope_name=tel_size + "-02",
+                crs_name="ground",
+                xx=-telescope_distance[tel_size],
+                yy=telescope_distance[tel_size],
+                tel_corsika_z=0 * u.m,
+            )
+            layout.add_telescope(
+                telescope_name=tel_size + "-03",
+                crs_name="ground",
+                xx=telescope_distance[tel_size],
+                yy=-telescope_distance[tel_size],
+                tel_corsika_z=0 * u.m,
+            )
+            layout.add_telescope(
+                telescope_name=tel_size + "-04",
+                crs_name="ground",
+                xx=-telescope_distance[tel_size],
+                yy=-telescope_distance[tel_size],
+                tel_corsika_z=0 * u.m,
             )
 
-            tel_size = array_name[1:4]
-
-            # Single telescope at the center
-            if array_name[0] == "1":
-                layout.add_telescope(
-                    telescope_name=tel_size + "-01",
-                    crs_name="corsika",
-                    xx=0 * u.m,
-                    yy=0 * u.m,
-                    tel_corsika_z=0 * u.m,
-                )
-            # 4 telescopes in a regular square grid
-            else:
-                layout.add_telescope(
-                    telescope_name=tel_size + "-01",
-                    crs_name="corsika",
-                    xx=telescope_distance[tel_size],
-                    yy=telescope_distance[tel_size],
-                    tel_corsika_z=0 * u.m,
-                )
-                layout.add_telescope(
-                    telescope_name=tel_size + "-02",
-                    crs_name="corsika",
-                    xx=-telescope_distance[tel_size],
-                    yy=telescope_distance[tel_size],
-                    tel_corsika_z=0 * u.m,
-                )
-                layout.add_telescope(
-                    telescope_name=tel_size + "-03",
-                    crs_name="corsika",
-                    xx=telescope_distance[tel_size],
-                    yy=-telescope_distance[tel_size],
-                    tel_corsika_z=0 * u.m,
-                )
-                layout.add_telescope(
-                    telescope_name=tel_size + "-04",
-                    crs_name="corsika",
-                    xx=-telescope_distance[tel_size],
-                    yy=-telescope_distance[tel_size],
-                    tel_corsika_z=0 * u.m,
-                )
-
-            layout.convert_coordinates()
-            layout.print_telescope_list()
-            layout.export_telescope_list(crs_name="corsika", corsika_z=None)
+        layout.convert_coordinates()
+        layout.print_telescope_list()
+        output_file = args_dict.get("output_file", None)
+        if output_file is not None:
+            base_name, file_extension = os.path.splitext(output_file)
+            output_file = f"{base_name}-{args_dict['site']}-{array_name}{file_extension}"
+        writer.ModelDataWriter.dump(
+            args_dict=args_dict,
+            output_file=output_file,
+            metadata=None,
+            product_data=layout.export_telescope_list_table(
+                crs_name="ground",
+                corsika_z=False,
+            ),
+        )
 
 
 if __name__ == "__main__":

simtools/applications/{plot_layout_array.py → plot_array_layout.py}

@@ -19,21 +19,21 @@
         File name for the pdf output.
     telescope_list (str, optional)
         The telescopes file (.ecsv) with the array information.
-    layout_array_name (str, optional)
+    array_layout_name (str, optional)
         Name of the layout array (e.g., North-TestLayout, South-TestLayout, North-4LST, etc.).
     rotate_angle (float, optional)
         Angle to rotate the array before plotting (in degrees).
     show_tel_label (bool, optional)
         Shows the telescope labels in the plot.
     verbosity (str, optional)
-        Log level to print (default=INFO).
+        Log level to print.
 
     Example
     -------
     .. code-block:: console
 
         simtools-plot-layout-array --figure_name northern_array_alpha \
-        --layout_array_name North-TestLayout
+        --array_layout_name North-TestLayout
 
 """
 
@@ -44,9 +44,10 @@ import matplotlib.pyplot as plt
 from astropy import units as u
 
 import simtools.utils.general as gen
-from simtools import io_handler
 from simtools.configuration import configurator
-from simtools.layout.layout_array import LayoutArray
+from simtools.data_model import data_reader
+from simtools.io_operations import io_handler
+from simtools.layout.array_layout import ArrayLayout
 from simtools.visualization.visualize import plot_array
 
 
@@ -103,8 +104,8 @@ def _parse(label, description, usage):
         default=None,
     )
     input_group.add_argument(
-        "--layout_array_name",
-        help="Name of the layout array.",
+        "--array_layout_name",
+        help="Name of the array layout.",
         nargs="+",
         type=str,
         required=False,
@@ -117,7 +118,7 @@ def _parse(label, description, usage):
 def main():
     label = Path(__file__).stem
     description = "Plots layout array."
-    usage = "python applications/plot_layout_array.py --layout_array_name test_layout"
+    usage = "python applications/plot_array_layout.py --array_layout_name test_layout"
     args_dict, _ = _parse(label, description, usage)
     io_handler_instance = io_handler.IOHandler()
 
@@ -135,13 +136,13 @@ def main():
         logger.info("Plotting array from telescope list file(s).")
         telescope_file = args_dict["telescope_list"]
 
-    elif args_dict["layout_array_name"] is not None:
+    elif args_dict["array_layout_name"] is not None:
         logger.info("Plotting array from layout array name(s).")
         telescope_file = [
             io_handler_instance.get_input_data_file(
                 "layout", f"telescope_positions-{one_array}.ecsv"
             )
-            for one_array in args_dict["layout_array_name"]
+            for one_array in args_dict["array_layout_name"]
         ]
 
     for one_file in telescope_file:
@@ -150,19 +151,19 @@ def main():
             logger.debug(f"Processing: {one_angle}.")
             if args_dict["figure_name"] is None:
                 plot_file_name = (
-                    f"plot_layout_array_{(Path(one_file).name).split('.')[0]}_"
+                    f"plot_array_layout_{(Path(one_file).name).split('.')[0]}_"
                     f"{str((round((one_angle.to(u.deg).value))))}deg"
                 )
             else:
                 plot_file_name = args_dict["figure_name"]
 
-            telescope_table = LayoutArray.read_telescope_list_file(one_file)
-            telescopes_dict = LayoutArray.include_radius_into_telescope_table(telescope_table)
+            telescope_table = data_reader.read_table_from_file(one_file)
+            telescopes_dict = ArrayLayout.include_radius_into_telescope_table(telescope_table)
             fig_out = plot_array(
                 telescopes_dict, rotate_angle=one_angle, show_tel_label=args_dict["show_tel_label"]
             )
             output_dir = io_handler_instance.get_output_directory(
-                label, dir_type="application-plots"
+                label, sub_dir="application-plots"
             )
             plot_file = output_dir.joinpath(plot_file_name)