imap-processing 0.19.0__py3-none-any.whl → 0.19.2__py3-none-any.whl

imap_processing/glows/l1b/glows_l1b_data.py

@@ -681,7 +681,6 @@ class HistogramL1B:
     histogram: np.ndarray
     flight_software_version: str
     seq_count_in_pkts_file: int
-    # ancillary_data_files: np.ndarray TODO Add this
     first_spin_id: int
     last_spin_id: int
     flags_set_onboard: int  # TODO: this should be renamed in L1B
@@ -705,9 +704,7 @@ class HistogramL1B:
     imap_time_offset: np.double  # No conversion needed from l1a->l1b
     glows_start_time: np.double  # No conversion needed from l1a->l1b
     glows_time_offset: np.double  # No conversion needed from l1a->l1b
-    # unique_block_identifier: str = field(
-    #     init=False
-    # )  # Could be datetime TODO: Can't put a string in data
+    unique_block_identifier: str = field(init=False)
     imap_spin_angle_bin_cntr: np.ndarray = field(init=False)  # Same size as bins
     histogram_flag_array: np.ndarray = field(init=False)
     # These two are retrieved from spin data
@@ -724,10 +721,9 @@ class HistogramL1B:
     flags: np.ndarray = field(init=False)
     ancillary_exclusions: InitVar[AncillaryExclusions]
     ancillary_parameters: InitVar[AncillaryParameters]
+    pipeline_settings: InitVar[PipelineSettings]
     # TODO:
     # - Determine a good way to output flags as "human readable"
-    # - Add spice pieces
-    # - also unique identifiers
     # - Bad angle algorithm using SPICE locations
     # - Move ancillary file to AWS
 
@@ -739,6 +735,7 @@ class HistogramL1B:
         pulse_length_variance: np.double,
         ancillary_exclusions: AncillaryExclusions,
         ancillary_parameters: AncillaryParameters,
+        pipeline_settings: PipelineSettings,
     ) -> None:
         """
         Will process data.
@@ -759,6 +756,8 @@ class HistogramL1B:
             Ancillary exclusions data for bad-angle flag processing.
         ancillary_parameters : AncillaryParameters
             Ancillary parameters for decoding histogram data.
+        pipeline_settings : PipelineSettings
+            Pipeline settings for processing thresholds and flags.
         """
         # self.histogram_flag_array = np.zeros((2,))
         day = met_to_datetime64(self.imap_start_time)
@@ -804,9 +803,9 @@ class HistogramL1B:
         # is_inside_excluded_region, is_excluded_by_instr_team,
         # is_suspected_transient] x 3600 bins
         self.histogram_flag_array = self._compute_histogram_flag_array(day_exclusions)
-        # self.unique_block_identifier = np.datetime_as_string(
-        #     np.datetime64(int(self.imap_start_time), "ns"), "s"
-        # )
+        # Generate ISO datetime string using SPICE functions
+        datetime64_time = met_to_datetime64(self.imap_start_time)
+        self.unique_block_identifier = np.datetime_as_string(datetime64_time, "s")
         self.flags = np.ones((FLAG_LENGTH,), dtype=np.uint8)
 
     def update_spice_parameters(self) -> None:
@@ -852,7 +851,7 @@ class HistogramL1B:
             geometry.frame_transform(
                 time_range,
                 np.array([0, 0, 1]),
-                SpiceFrame.IMAP_DPS,
+                SpiceFrame.IMAP_SPACECRAFT,
                 SpiceFrame.ECLIPJ2000,
             )
         )
@@ -873,7 +872,7 @@ class HistogramL1B:
         )
         position = imap_state[:, :3]
         velocity = imap_state[:, 3:]
-        # averange and standard deviation over time (rows)
+        # average and standard deviation over time (rows)
         self.spacecraft_location_average = np.average(position, axis=0)
         self.spacecraft_location_std_dev = np.std(position, axis=0)
         self.spacecraft_velocity_average = np.average(velocity, axis=0)

imap_processing/hi/hi_l1c.py

@@ -19,7 +19,7 @@ from imap_processing.hi.hi_l1a import (
     HALF_CLOCK_TICK_S,
 )
 from imap_processing.hi.utils import (
-    CoincidenceBitmap,
+    CalibrationProductConfig,
     create_dataset_variables,
     full_dataarray,
     parse_sensor_number,
@@ -378,8 +378,9 @@ def pset_counts(
                 filtered_de_df["spin_phase"].to_numpy() * N_SPIN_BINS
             ).astype(int)
             # When iterating over rows of a dataframe, the names of the multi-index
-            # are not preserved. Below, `config_row.Index[0]` gets the cal_prod_num
-            # value from the namedtuple representing the dataframe row.
+            # are not preserved. Below, `config_row.Index[0]` gets the
+            # calibration_prod value from the namedtuple representing the
+            # dataframe row.
             np.add.at(
                 counts_var["counts"].data[0, i_esa, config_row.Index[0]],
                 spin_bin_indices,
@@ -684,109 +685,3 @@ def good_time_and_phase_mask(
     """
     # TODO: Implement this once we have Goodtimes data product defined.
     return np.full_like(tick_mets, True, dtype=bool)
-
-
-@pd.api.extensions.register_dataframe_accessor("cal_prod_config")
-class CalibrationProductConfig:
-    """
-    Register custom accessor for calibration product configuration DataFrames.
-
-    Parameters
-    ----------
-    pandas_obj : pandas.DataFrame
-        Object to run validation and use accessor functions on.
-    """
-
-    index_columns = (
-        "cal_prod_num",
-        "esa_energy_step",
-    )
-    tof_detector_pairs = ("ab", "ac1", "bc1", "c1c2")
-    required_columns = (
-        "coincidence_type_list",
-        *[
-            f"tof_{det_pair}_{limit}"
-            for det_pair in tof_detector_pairs
-            for limit in ["low", "high"]
-        ],
-    )
-
-    def __init__(self, pandas_obj: pd.DataFrame) -> None:
-        self._validate(pandas_obj)
-        self._obj = pandas_obj
-        self._add_coincidence_values_column()
-
-    def _validate(self, df: pd.DataFrame) -> None:
-        """
-        Validate the current configuration.
-
-        Parameters
-        ----------
-        df : pandas.DataFrame
-            Object to validate.
-
-        Raises
-        ------
-        AttributeError : If the dataframe does not pass validation.
-        """
-        for index_name in self.index_columns:
-            if index_name in df.index:
-                raise AttributeError(
-                    f"Required index {index_name} not present in dataframe."
-                )
-        # Verify that the Dataframe has all the required columns
-        for col in self.required_columns:
-            if col not in df.columns:
-                raise AttributeError(f"Required column {col} not present in dataframe.")
-        # TODO: Verify that the same ESA energy steps exist in all unique calibration
-        #   product numbers
-
-    def _add_coincidence_values_column(self) -> None:
-        """Generate and add the coincidence_type_values column to the dataframe."""
-        # Add a column that consists of the coincidence type strings converted
-        # to integer values
-        self._obj["coincidence_type_values"] = self._obj.apply(
-            lambda row: tuple(
-                CoincidenceBitmap.detector_hit_str_to_int(entry)
-                for entry in row["coincidence_type_list"]
-            ),
-            axis=1,
-        )
-
-    @classmethod
-    def from_csv(cls, path: Path) -> pd.DataFrame:
-        """
-        Read configuration CSV file into a pandas.DataFrame.
-
-        Parameters
-        ----------
-        path : pathlib.Path
-            Location of the Calibration Product configuration CSV file.
-
-        Returns
-        -------
-        dataframe : pandas.DataFrame
-            Validated calibration product configuration data frame.
-        """
-        df = pd.read_csv(
-            path,
-            index_col=cls.index_columns,
-            converters={"coincidence_type_list": lambda s: tuple(s.split("|"))},
-            comment="#",
-        )
-        # Force the _init_ method to run by using the namespace
-        _ = df.cal_prod_config.number_of_products
-        return df
-
-    @property
-    def number_of_products(self) -> int:
-        """
-        Get the number of calibration products in the current configuration.
-
-        Returns
-        -------
-        number_of_products : int
-            The maximum number of calibration products defined in the list of
-            calibration product definitions.
-        """
-        return len(self._obj.index.unique(level="cal_prod_num"))

imap_processing/hi/hi_l2.py

@@ -13,6 +13,7 @@ from imap_processing.ena_maps.ena_maps import (
     RectangularSkyMap,
 )
 from imap_processing.ena_maps.utils.naming import MapDescriptor
+from imap_processing.hi.utils import CalibrationProductConfig
 
 logger = logging.getLogger(__name__)
 
@@ -153,14 +154,25 @@ def generate_hi_map(
     output_map.data_1d["obs_date_range"] = xr.zeros_like(output_map.data_1d["obs_date"])
 
     # Rename and convert coordinate from esa_energy_step energy
-    esa_energies = esa_energy_lookup(
+    esa_df = esa_energy_df(
         esa_energies_path, output_map.data_1d["esa_energy_step"].data
     )
     output_map.data_1d = output_map.data_1d.rename({"esa_energy_step": "energy"})
-    output_map.data_1d = output_map.data_1d.assign_coords(energy=esa_energies)
-    # Set the energy_step_delta values
-    # TODO: get the correct energy delta values (they are set to NaN) in
-    #    output_map.build_cdf_dataset()
+    output_map.data_1d = output_map.data_1d.assign_coords(
+        energy=esa_df["nominal_central_energy"].values
+    )
+    # Set the energy_step_delta values to the energy bandpass half-width-half-max
+    energy_delta = esa_df["bandpass_fwhm"].values / 2
+    output_map.data_1d["energy_delta_minus"] = xr.DataArray(
+        energy_delta,
+        name="energy_delta_minus",
+        dims=["energy"],
+    )
+    output_map.data_1d["energy_delta_plus"] = xr.DataArray(
+        energy_delta,
+        name="energy_delta_plus",
+        dims=["energy"],
+    )
 
     output_map.data_1d = output_map.data_1d.drop("esa_energy_step_label")
 
@@ -223,25 +235,26 @@ def calculate_ena_intensity(
     geometric_factors_path : str or pathlib.Path
         Where to get the geometric factors from.
     esa_energies_path : str or pathlib.Path
-        Where to get the energies from.
+        Where to get the esa energies, energy deltas, and geometric factors.
 
     Returns
     -------
     intensity_vars : dict[str, xarray.DataArray]
         ENA Intensity with statistical and systematic uncertainties.
     """
-    # TODO: Implement geometric factor lookup
-    if geometric_factors_path:
-        raise NotImplementedError
-    geometric_factor = xr.DataArray(
-        np.ones((map_ds["esa_energy_step"].size, map_ds["calibration_prod"].size)),
-        coords=[map_ds["esa_energy_step"], map_ds["calibration_prod"]],
+    # read calibration product configuration file
+    cal_prod_df = CalibrationProductConfig.from_csv(geometric_factors_path)
+    # reindex_like removes esa_energy_steps and calibration products not in the
+    # map_ds esa_energy_step and calibration_product coordinates
+    geometric_factor = cal_prod_df.to_xarray().reindex_like(map_ds)["geometric_factor"]
+    geometric_factor = geometric_factor.transpose(
+        *[coord for coord in map_ds.coords if coord in geometric_factor.coords]
     )
-
-    esa_energy = esa_energy_lookup(esa_energies_path, map_ds["esa_energy_step"].data)
+    energy_df = esa_energy_df(esa_energies_path, map_ds["esa_energy_step"].data)
+    esa_energy = energy_df.to_xarray()["nominal_central_energy"]
 
     # Convert ENA Signal Rate to Flux
-    flux_conversion_divisor = geometric_factor * esa_energy[:, np.newaxis]
+    flux_conversion_divisor = geometric_factor * esa_energy
     intensity_vars = {
         "ena_intensity": map_ds["ena_signal_rates"] / flux_conversion_divisor,
         "ena_intensity_stat_unc": map_ds["ena_signal_rate_stat_unc"]
@@ -267,9 +280,9 @@ def calculate_ena_intensity(
     return intensity_vars
 
 
-def esa_energy_lookup(
+def esa_energy_df(
     esa_energies_path: str | Path, esa_energy_steps: np.ndarray
-) -> np.ndarray:
+) -> pd.DataFrame:
     """
     Lookup the nominal central energy values for given esa energy steps.
 
@@ -282,13 +295,11 @@ def esa_energy_lookup(
 
     Returns
     -------
-    esa_energies: numpy.ndarray
-        The nominal central energy for the given esa energy steps.
+    esa_energies_df: pandas.DataFrame
+        Full data frame from the csv file filtered to only include the
+        esa_energy_steps input.
     """
     esa_energies_lut = pd.read_csv(
         esa_energies_path, comment="#", index_col="esa_energy_step"
     )
-    esa_energies = esa_energies_lut.loc[esa_energy_steps][
-        "nominal_central_energy"
-    ].values
-    return esa_energies
+    return esa_energies_lut.loc[esa_energy_steps]

imap_processing/hi/utils.py

@@ -1,9 +1,12 @@
 """IMAP-Hi utils functions."""
 
+from __future__ import annotations
+
 import re
 from collections.abc import Iterable, Sequence
 from dataclasses import dataclass
 from enum import IntEnum
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -392,3 +395,109 @@ class EsaEnergyStepLookupTable:
             return results.astype(self._esa_energy_step_dtype)[0]
         else:
             return results.astype(self._esa_energy_step_dtype)
+
+
+@pd.api.extensions.register_dataframe_accessor("cal_prod_config")
+class CalibrationProductConfig:
+    """
+    Register custom accessor for calibration product configuration DataFrames.
+
+    Parameters
+    ----------
+    pandas_obj : pandas.DataFrame
+        Object to run validation and use accessor functions on.
+    """
+
+    index_columns = (
+        "calibration_prod",
+        "esa_energy_step",
+    )
+    tof_detector_pairs = ("ab", "ac1", "bc1", "c1c2")
+    required_columns = (
+        "coincidence_type_list",
+        *[
+            f"tof_{det_pair}_{limit}"
+            for det_pair in tof_detector_pairs
+            for limit in ["low", "high"]
+        ],
+    )
+
+    def __init__(self, pandas_obj: pd.DataFrame) -> None:
+        self._validate(pandas_obj)
+        self._obj = pandas_obj
+        self._add_coincidence_values_column()
+
+    def _validate(self, df: pd.DataFrame) -> None:
+        """
+        Validate the current configuration.
+
+        Parameters
+        ----------
+        df : pandas.DataFrame
+            Object to validate.
+
+        Raises
+        ------
+        AttributeError : If the dataframe does not pass validation.
+        """
+        for index_name in self.index_columns:
+            if index_name in df.index:
+                raise AttributeError(
+                    f"Required index {index_name} not present in dataframe."
+                )
+        # Verify that the Dataframe has all the required columns
+        for col in self.required_columns:
+            if col not in df.columns:
+                raise AttributeError(f"Required column {col} not present in dataframe.")
+        # TODO: Verify that the same ESA energy steps exist in all unique calibration
+        #   product numbers
+
+    def _add_coincidence_values_column(self) -> None:
+        """Generate and add the coincidence_type_values column to the dataframe."""
+        # Add a column that consists of the coincidence type strings converted
+        # to integer values
+        self._obj["coincidence_type_values"] = self._obj.apply(
+            lambda row: tuple(
+                CoincidenceBitmap.detector_hit_str_to_int(entry)
+                for entry in row["coincidence_type_list"]
+            ),
+            axis=1,
+        )
+
+    @classmethod
+    def from_csv(cls, path: str | Path) -> pd.DataFrame:
+        """
+        Read configuration CSV file into a pandas.DataFrame.
+
+        Parameters
+        ----------
+        path : str or pathlib.Path
+            Location of the Calibration Product configuration CSV file.
+
+        Returns
+        -------
+        dataframe : pandas.DataFrame
+            Validated calibration product configuration data frame.
+        """
+        df = pd.read_csv(
+            path,
+            index_col=cls.index_columns,
+            converters={"coincidence_type_list": lambda s: tuple(s.split("|"))},
+            comment="#",
+        )
+        # Force the _init_ method to run by using the namespace
+        _ = df.cal_prod_config.number_of_products
+        return df
+
+    @property
+    def number_of_products(self) -> int:
+        """
+        Get the number of calibration products in the current configuration.
+
+        Returns
+        -------
+        number_of_products : int
+            The maximum number of calibration products defined in the list of
+            calibration product definitions.
+        """
+        return len(self._obj.index.unique(level="calibration_prod"))

imap_processing/ialirt/l0/ialirt_spice.py

@@ -133,6 +133,7 @@ def transform_instrument_vectors_to_inertial(
     spin_phase: NDArray,
     sc_inertial_right: NDArray,
     sc_inertial_decline: NDArray,
+    # TODO: Use correct IMAP_MAG_I or IMAP_MAG_O frame here
     instrument_frame: SpiceFrame = SpiceFrame.IMAP_MAG,
     spacecraft_frame: SpiceFrame = SpiceFrame.IMAP_SPACECRAFT,
 ) -> NDArray:

imap_processing/ialirt/utils/create_xarray.py

@@ -144,7 +144,7 @@ def create_xarray_from_records(records: list[dict]) -> xr.Dataset:  # noqa: PLR0
     # Populate the dataset variables
     for i, record in enumerate(records):
         for key, val in record.items():
-            if key in ["apid", "met", "met_in_utc", "ttj2000ns"]:
+            if key in ["apid", "met", "met_in_utc", "ttj2000ns", "last_modified"]:
                 continue
             elif key in ["mag_B_GSE", "mag_B_GSM", "mag_B_RTN"]:
                 dataset[key].data[i, :] = val

imap_processing/lo/ancillary_data/imap_lo_hydrogen-geometric-factor_v001.csv

@@ -0,0 +1,75 @@
+incident_E-Step,Observed_E-Step,Cntr_E,Cntr_E_unc,GF_Dbl_all,GF_Dbl_all_unc,GF_Trpl_all,GF_Trpl_all_unc,GF_Dbl_H,GF_Dbl_H_unc,GF_Trpl_H,GF_Trpl_H_unc
+Hi_Res,,[keV],[keV],[cm^2sr keV/keV],[cm^2sr keV/keV],[cm^2sr keV/keV],[cm^2sr keV/keV],[cm^2sr keV/keV],[cm^2sr keV/keV],[cm^2sr keV/keV],[cm^2sr keV/keV]
+1,1,0.015,0.00135,5.35E-05,4.82E-06,2.20E-05,1.87E-06,5.32E-05,4.26E-06,2.19E-05,1.86E-06
+2,1,0.015,0.00135,3.10E-05,2.79E-06,1.25E-05,1.06E-06,3.09E-05,2.47E-06,1.27E-05,1.08E-06
+2,2,0.029,0.00261,1.04E-04,9.36E-06,4.27E-05,3.63E-06,1.03E-04,8.26E-06,4.24E-05,3.61E-06
+3,1,0.015,0.00135,4.13E-05,3.72E-06,1.68E-05,1.43E-06,4.16E-05,3.33E-06,1.71E-05,1.45E-06
+3,2,0.029,0.00261,1.28E-04,1.15E-05,5.02E-05,4.26E-06,1.30E-04,1.04E-05,5.35E-05,4.55E-06
+3,3,0.055,0.00495,1.59E-04,1.43E-05,6.54E-05,5.56E-06,1.59E-04,1.27E-05,6.51E-05,5.54E-06
+4,1,0.015,0.00135,9.85E-06,8.86E-07,3.73E-06,3.17E-07,7.97E-06,6.38E-07,3.28E-06,2.79E-07
+4,2,0.029,0.00261,1.71E-05,1.54E-06,6.54E-06,5.56E-07,1.68E-05,1.34E-06,6.89E-06,5.86E-07
+4,3,0.055,0.00495,6.72E-05,6.05E-06,2.58E-05,2.19E-06,6.92E-05,5.53E-06,2.84E-05,2.42E-06
+4,4,0.11,0.0099,1.79E-04,1.61E-05,7.36E-05,6.25E-06,1.78E-04,1.42E-05,7.30E-05,6.20E-06
+5,1,0.015,0.00135,1.62E-05,1.46E-06,5.05E-06,4.29E-07,7.86E-06,6.29E-07,3.23E-06,2.75E-07
+5,2,0.029,0.00261,1.57E-05,1.41E-06,5.16E-06,4.39E-07,9.72E-06,7.77E-07,3.99E-06,3.39E-07
+5,3,0.055,0.00495,1.45E-05,1.31E-06,4.98E-06,4.24E-07,1.49E-05,1.20E-06,6.14E-06,5.22E-07
+5,4,0.11,0.0099,5.81E-05,5.23E-06,2.15E-05,1.83E-06,6.00E-05,4.80E-06,2.47E-05,2.10E-06
+5,5,0.209,0.01881,1.77E-04,1.59E-05,7.26E-05,6.17E-06,1.76E-04,1.41E-05,7.22E-05,6.14E-06
+6,1,0.015,0.00135,1.34E-05,1.21E-06,4.33E-06,3.68E-07,9.40E-06,7.52E-07,3.86E-06,3.28E-07
+6,2,0.029,0.00261,1.61E-05,1.45E-06,4.64E-06,3.94E-07,1.11E-05,8.92E-07,4.58E-06,3.89E-07
+6,3,0.055,0.00495,1.74E-05,1.57E-06,5.02E-06,4.27E-07,1.42E-05,1.14E-06,5.84E-06,4.96E-07
+6,4,0.11,0.0099,1.45E-05,1.30E-06,4.28E-06,3.64E-07,1.56E-05,1.25E-06,6.40E-06,5.44E-07
+6,5,0.209,0.01881,5.81E-05,5.23E-06,2.06E-05,1.75E-06,6.01E-05,4.81E-06,2.47E-05,2.10E-06
+6,6,0.439,0.03951,2.06E-04,1.85E-05,8.46E-05,7.19E-06,2.06E-04,1.64E-05,8.45E-05,7.18E-06
+7,1,0.015,0.00135,5.32E-06,4.79E-07,1.51E-06,1.29E-07,5.05E-06,4.04E-07,2.08E-06,1.76E-07
+7,2,0.029,0.00261,1.61E-05,1.45E-06,5.15E-06,4.38E-07,1.39E-05,1.11E-06,5.70E-06,4.85E-07
+7,3,0.055,0.00495,1.96E-05,1.77E-06,6.10E-06,5.19E-07,1.42E-05,1.14E-06,5.84E-06,4.96E-07
+7,4,0.11,0.0099,2.08E-05,1.87E-06,6.43E-06,5.46E-07,1.65E-05,1.32E-06,6.78E-06,5.77E-07
+7,5,0.209,0.01881,2.52E-05,2.27E-06,8.69E-06,7.39E-07,2.61E-05,2.09E-06,1.07E-05,9.11E-07
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imap_processing/lo/ancillary_data/imap_lo_oxygen-geometric-factor_v001.csv

@@ -0,0 +1,75 @@
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