pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/instruments/metis_ifu.yaml

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+# METIS IFU instrument configuration
+
+__instrument__: METIS_IFU
+instrument: INSTRUME
+id_instrument: METIS_IFU
+telescope: ELT
+
+date: MJD-OBS
+date_format: mjd
+
+arms: [IFU_NOMINAL, IFU_EXTENDED]
+kw_arm: INSTMODE
+id_arm: [ifu_nom, ifu_ext]
+extension: 0
+orientation: [1, 1, 1]
+
+prescan_x: 0
+overscan_x: 0
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: 1
+readnoise: 4
+dark: 10
+exposure_time: "HIERARCH OBS_EXPTIME"
+
+ra: RA
+dec: DEC
+jd: MJD-OBS
+longitude: -70
+latitude: -24
+altitude: 3060
+instrument_mode: "HIERARCH ESO INS MODE"
+observation_type: "HIERARCH ESO DPR TYPE"
+observation_category: "HIERARCH ESO DPR CATG"
+target: ""
+object: OBJECT
+
+id_dark: DARK
+id_format: "LAMP,FMTCHK"
+id_tell: "STD,TELLURIC"
+
+# File classification keywords and patterns
+kw_bias: "HIERARCH ESO DPR TYPE"
+kw_flat: "HIERARCH ESO DPR TYPE"
+kw_curvature: "HIERARCH ESO DPR TYPE"
+kw_scatter: "HIERARCH ESO DPR TYPE"
+kw_orders: "HIERARCH ESO DPR TYPE"
+kw_wave: "HIERARCH ESO DPR TYPE"
+kw_comb: null
+kw_spec: "HIERARCH ESO DPR TYPE"
+
+id_bias: DARK
+id_flat: "LAMP,FLAT"
+id_orders: "FLAT,PINHOLE"
+id_curvature: "SKY,WAVE"
+id_scatter: "LAMP,FLAT"
+id_wave: "SKY,WAVE"
+id_comb: null
+id_spec: OBJECT

pyreduce/instruments/metis_lss.py

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+"""
+Handles instrument specific info for the METIS_LSS LSS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class METIS_LSS(Instrument):
+    def add_header_info(self, header, arm, **kwargs):
+        """read data from header and add it as REDUCE keyword back to the header"""
+        # "Normal" stuff is handled by the general version, specific changes to values happen here
+        # alternatively you can implement all of it here, whatever works
+        header = super().add_header_info(header, arm)
+
+        # header["e_backg"] = (
+        #     header["e_readn"] + header["e_exptime"] * header["e_drk"] / 3600
+        # )
+        #
+        # header["e_ra"] /= 15
+        # if header["e_jd"] is not None:
+        #     header["e_jd"] += header["e_exptime"] / 2 / 3600 / 24 + 0.5
+
+        return header
+
+    def get_extension(self, header, arm):
+        extension = 1
+
+        return extension
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        # info = self.load_info()
+        cwd = os.path.dirname(__file__)
+        fname = f"metis_lss_{arm.lower()}_2D.npz"
+        # fname = f"metis_lss_LSS_L_2D.npz" ## f"micado_IJ_2D_det1.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+
+        return fname

pyreduce/instruments/metis_lss.yaml

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+# METIS LSS instrument configuration
+
+__instrument__: METIS_LSS
+instrument: INSTRUME
+id_instrument: METIS_LSS
+telescope: ELT
+
+date: MJD-OBS
+date_format: mjd
+
+arms: [LSS_L, LSS_M, LSS_N]
+kw_arm: INSTMODE
+id_arm: [lss_l, lss_m, lss_n]
+extension: 0
+orientation: [1, 1, 1]
+
+prescan_x: 0
+overscan_x: 0
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: 1
+readnoise: 4
+dark: 10
+exposure_time: "HIERARCH OBS_EXPTIME"
+
+ra: RA
+dec: DEC
+jd: MJD-OBS
+longitude: -70
+latitude: -24
+altitude: 3060
+instrument_mode: "HIERARCH ESO INS MODE"
+observation_type: "HIERARCH ESO DPR TYPE"
+observation_category: "HIERARCH ESO DPR CATG"
+target: ""
+object: OBJECT
+
+id_dark: DARK
+id_format: "LAMP,FMTCHK"
+id_tell: "STD,TELLURIC"
+
+# File classification keywords and patterns
+kw_bias: "HIERARCH ESO DPR TYPE"
+kw_flat: "HIERARCH ESO DPR TYPE"
+kw_curvature: "HIERARCH ESO DPR TYPE"
+kw_scatter: "HIERARCH ESO DPR TYPE"
+kw_orders: "HIERARCH ESO DPR TYPE"
+kw_wave: "HIERARCH ESO DPR TYPE"
+kw_comb: null
+kw_spec: "HIERARCH ESO DPR TYPE"
+
+id_bias: DARK
+id_flat: "LAMP,FLAT"
+id_orders: "FLAT,PINHOLE"
+id_curvature: "SKY,WAVE"
+id_scatter: "LAMP,FLAT"
+id_wave: "SKY,WAVE"
+id_comb: null
+id_spec: OBJECT

pyreduce/instruments/micado.py

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+"""
+Handles instrument specific info for the MICADO spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class MICADO(Instrument):
+    def add_header_info(self, header, arm, **kwargs):
+        """read data from header and add it as REDUCE keyword back to the header"""
+        # "Normal" stuff is handled by the general version, specific changes to values happen here
+        # alternatively you can implement all of it here, whatever works
+        header = super().add_header_info(header, arm)
+
+        # header["e_backg"] = (
+        #     header["e_readn"] + header["e_exptime"] * header["e_drk"] / 3600
+        # )
+        #
+        # header["e_ra"] /= 15
+        # if header["e_jd"] is not None:
+        #     header["e_jd"] += header["e_exptime"] / 2 / 3600 / 24 + 0.5
+
+        return header
+
+    def get_extension(self, header, arm):
+        extension = 5
+
+        return extension
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        # info = self.load_info()
+        cwd = os.path.dirname(__file__)
+        # fname = f"xshooter_{arm.lower()}.npz"
+        fname = "MICADO_HK_3arcsec_chip5.npz"  ## f"micado_IJ_2D_det1.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+
+        return fname

pyreduce/instruments/micado.yaml

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+# MICADO instrument configuration
+
+__instrument__: MICADO
+instrument: INSTRUME
+id_instrument: MICADO
+telescope: ELT
+
+date: MJD-OBS
+date_format: mjd
+
+arms: [NIR]
+kw_arm: "ESO DET CHIP*NAME"
+id_arm: [Hawaii4RG]
+extension: 0
+orientation: [1]
+
+prescan_x: 0
+overscan_x: 0
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: 1
+readnoise: 4
+dark: 10
+exposure_time: "HIERARCH OBS_EXPTIME"
+
+ra: RA
+dec: DEC
+jd: MJD-OBS
+longitude: -70
+latitude: -24
+altitude: 3060
+instrument_mode: "HIERARCH ESO SEQ ARM"
+observation_type: "HIERARCH ESO DPR TYPE"
+observation_category: "HIERARCH ESO DPR CATG"
+target: ""
+object: OBJECT
+
+id_dark: DARK
+id_format: WAVE_PINH
+id_tell: "STD,TELLURIC"
+
+# File classification keywords and patterns
+kw_bias: "HIERARCH ESO DPR TYPE"
+kw_flat: "HIERARCH ESO DPR TYPE"
+kw_curvature: "HIERARCH ESO DPR TYPE"
+kw_scatter: "HIERARCH ESO DPR TYPE"
+kw_orders: "HIERARCH ESO DPR TYPE"
+kw_wave: "HIERARCH ESO DPR TYPE"
+kw_comb: null
+kw_spec: "HIERARCH ESO DPR TYPE"
+
+id_bias: DARK
+id_flat: SFLATSLIT
+id_orders: SFLAT_PINH
+id_curvature: WAVE
+id_scatter: "LAMP,FLAT"
+id_wave: WAVE
+id_comb: null
+id_spec: OBJECT

pyreduce/instruments/models.py

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+"""Pydantic models for instrument configuration validation.
+
+These models provide type-safe validation for instrument configuration files.
+Currently validates the flat YAML structure; will evolve toward the nested
+structure described in REDESIGN.md.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from pydantic import BaseModel, ConfigDict, field_validator
+
+
+class HeaderRef(BaseModel):
+    """Reference to a FITS header keyword."""
+
+    key: str
+
+    model_config = ConfigDict(extra="forbid")
+
+
+# Type for values that can be either a literal or a header reference
+HeaderOrValue = float | int | str | HeaderRef | None
+
+
+class FileClassification(BaseModel):
+    """Keywords and patterns for file type classification."""
+
+    kw_bias: str | None = None
+    kw_flat: str | None = None
+    kw_curvature: str | None = None
+    kw_scatter: str | None = None
+    kw_orders: str | None = None
+    kw_wave: str | None = None
+    kw_comb: str | None = None
+    kw_spec: str | None = None
+
+    id_bias: str | None = None
+    id_flat: str | None = None
+    id_curvature: str | None = None
+    id_scatter: str | None = None
+    id_orders: str | None = None
+    id_wave: str | None = None
+    id_comb: str | None = None
+    id_spec: str | None = None
+
+    model_config = ConfigDict(extra="allow")
+
+
+class InstrumentConfig(BaseModel):
+    """Configuration for an astronomical instrument.
+
+    This model validates the flat YAML structure used by instrument configs.
+    It allows extra fields for instrument-specific parameters.
+    """
+
+    # Required identification
+    __instrument__: str | None = None  # Internal name (uses alias due to dunder)
+    instrument: str  # Header keyword for instrument name
+    id_instrument: str  # Value/pattern to match
+
+    # Telescope
+    telescope: str | None = None
+
+    # Date handling
+    date: str = "DATE-OBS"
+    date_format: str = "fits"
+
+    # Arm system (detectors/channels)
+    arms: list[str] | None = None
+    arms_id: list[str] | None = None
+    kw_arm: str | None = None
+    id_arm: list[str] | None = None
+    extension: int | str | list[int | str] = 0
+    orientation: int | list[int] = 0
+    transpose: bool = False
+
+    # Detector dimensions
+    naxis_x: str | int = "NAXIS1"
+    naxis_y: str | int = "NAXIS2"
+
+    # Overscan/prescan regions
+    prescan_x: int | str = 0
+    overscan_x: int | str = 0
+    prescan_y: int | str = 0
+    overscan_y: int | str = 0
+
+    # Calibration values (can be literals or header keywords)
+    gain: float | int | str = 1
+    readnoise: float | int | str = 0
+    dark: float | int | str = 0
+    sky: float | int | str = 0
+    exposure_time: str = "EXPTIME"
+
+    # Location (for barycentric correction)
+    ra: str | None = "RA"
+    dec: str | None = "DEC"
+    longitude: float | str | None = None
+    latitude: float | str | None = None
+    altitude: float | str | None = None
+
+    # Target identification
+    target: str = "OBJECT"
+    observation_type: str | None = None
+    category: str | None = None
+    image_type: str | None = None
+    instrument_mode: str | None = None
+
+    # File classification - header keywords
+    kw_bias: str | None = None
+    kw_flat: str | None = None
+    kw_curvature: str | None = None
+    kw_scatter: str | None = None
+    kw_orders: str | None = None
+    kw_wave: str | None = None
+    kw_comb: str | None = None
+    kw_spec: str | None = None
+
+    # File classification - identifier patterns
+    id_bias: str | None = None
+    id_flat: str | None = None
+    id_curvature: str | None = None
+    id_scatter: str | None = None
+    id_orders: str | None = None
+    id_wave: str | None = None
+    id_comb: str | None = None
+    id_spec: str | None = None
+
+    # Wavelength information
+    wavelength_range: list | None = None
+    wavecal_specifier: str | None = None
+
+    # Allow additional fields for instrument-specific parameters
+    model_config = ConfigDict(
+        extra="allow",
+        populate_by_name=True,
+    )
+
+    @field_validator("arms", "arms_id", "id_arm", mode="before")
+    @classmethod
+    def ensure_list(cls, v):
+        """Convert single values to lists."""
+        if v is None:
+            return None
+        if isinstance(v, str):
+            return [v]
+        return v
+
+    @field_validator("extension", "orientation", mode="before")
+    @classmethod
+    def normalize_list_or_scalar(cls, v):
+        """Keep as-is, validation handles both forms."""
+        return v
+
+
+# Future models for the nested structure (REDESIGN.md)
+# These will be used when migrating to the new architecture
+
+
+class AmplifierConfig(BaseModel):
+    """Configuration for a detector readout amplifier."""
+
+    id: str
+    gain: float | dict[str, str]  # literal or {key: "HEADER_KEY"}
+    readnoise: float | dict[str, str]
+    region: dict[str, list[int]] | None = None
+    linearity: dict | None = None
+    bad_pixel_mask: str | None = None
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class DetectorConfig(BaseModel):
+    """Configuration for a physical detector."""
+
+    name: str
+    naxis: tuple[int, int] | list[int]
+    orientation: int = 0
+    prescan: dict[str, list[int] | None] | None = None
+    overscan: dict[str, list[int] | None] | None = None
+    amplifiers: list[AmplifierConfig] = []
+    bad_pixel_mask: str | None = None
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class BeamArmConfig(BaseModel):
+    """Configuration for a beam-splitter arm."""
+
+    name: str
+    polarization: str | None = None
+    wavelength_shift: float = 0.0
+    trace_offset: float = 0.0
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class OpticalPathConfig(BaseModel):
+    """Configuration for an optical path (fiber, slit position)."""
+
+    name: str
+    beam_arms: list[BeamArmConfig] | None = None
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class DimensionConfig(BaseModel):
+    """Configuration for a varying dimension (mode, fiber, etc.)."""
+
+    values: list[str]
+    header_key: str | None = None
+    optional: bool = False
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class InstrumentConfigV2(BaseModel):
+    """Future nested instrument configuration structure.
+
+    This model represents the target architecture from REDESIGN.md.
+    Not yet used - will be activated when migrating instruments.
+    """
+
+    instrument: str
+    telescope: str | None = None
+    id_instrument: str
+
+    detectors: list[DetectorConfig] = []
+    optical_paths: list[OpticalPathConfig] = []
+    dimensions: dict[str, DimensionConfig] = {}
+
+    headers: dict[str, str] = {}
+    file_types: dict[str, dict[str, str]] = {}
+
+    model_config = ConfigDict(extra="allow")
+
+
+def validate_instrument_config(data: dict[str, Any]) -> InstrumentConfig:
+    """Validate instrument configuration data.
+
+    Parameters
+    ----------
+    data : dict
+        Raw configuration data (from YAML or JSON)
+
+    Returns
+    -------
+    InstrumentConfig
+        Validated configuration
+
+    Raises
+    ------
+    pydantic.ValidationError
+        If validation fails
+    """
+    return InstrumentConfig(**data)

pyreduce/instruments/neid.py

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+"""
+Handles instrument specific info for the NEID spectrograph
+"""
+
+import logging
+import re
+from os.path import dirname, join
+
+from .common import Instrument
+from .filters import Filter, InstrumentFilter, NightFilter, ObjectFilter
+
+logger = logging.getLogger(__name__)
+
+
+class NEID(Instrument):
+    def __init__(self):
+        super().__init__()
+        self.filters = {
+            "instrument": InstrumentFilter(self.config.instrument),
+            "night": NightFilter(self.config.date),
+            # "branch": Filter(, regex=True),
+            "mode": Filter(
+                self.config.instrument_mode, regex=True, flags=re.IGNORECASE
+            ),
+            "type": Filter(self.config.observation_type),
+            "target": ObjectFilter(self.config.target, regex=True),
+        }
+        self.night = "night"
+        self.science = "science"
+        self.shared = [
+            "instrument",
+            "night",
+            "mode",
+        ]
+        self.find_closest = [
+            "bias",
+            "flat",
+            "wavecal_master",
+            "freq_comb_master",
+            "orders",
+            "scatter",
+        ]
+
+    def get_expected_values(
+        self, target, night, arm=None, mode=None, fiber=None, **kwargs
+    ):
+        """Determine the default expected values in the headers for a given observation configuration
+
+        Any parameter may be None, to indicate that all values are allowed
+
+        Parameters
+        ----------
+        target : str
+            Name of the star / observation target
+        night : str
+            Observation night/nights
+        Returns
+        -------
+        expectations: dict
+            Dictionary of expected header values, with one entry per step.
+            The entries for each step refer to the filters defined in self.filters
+
+        Raises
+        ------
+        ValueError
+            Invalid combination of parameters
+        """
+        if target is not None:
+            target = target.replace(" ", r"(?:\s*|-)")
+        else:
+            target = ".*"
+
+        id_orddef = "LAMP,DARK,TUN"
+        id_spec = "STAR,WAVE"
+
+        expectations = {
+            "flat": {"instrument": "NEID", "night": night, "type": r"LAMP,LAMP,TUN"},
+            "orders": {
+                "instrument": "NEID",
+                "night": night,
+                "type": id_orddef,
+            },
+            "scatter": {
+                "instrument": "NEID",
+                "night": night,
+                "type": id_orddef,  # Same as orders or same as flat?
+            },
+            "wavecal_master": {
+                "instrument": "NEID",
+                "night": night,
+                "type": r"WAVE,WAVE,THAR2",
+            },
+            "freq_comb_master": {
+                "instrument": "NEID",
+                "night": night,
+                "type": r"WAVE,WAVE,COMB",
+            },
+            "science": {
+                "instrument": "NEID",
+                "night": night,
+                "mode": mode,
+                "type": id_spec,
+                "target": target,
+            },
+        }
+        return expectations
+
+    def get_extension(self, header, arm):
+        extension = super().get_extension(header, arm)
+
+        return extension
+
+    def add_header_info(self, header, arm, **kwargs):
+        """read data from header and add it as REDUCE keyword back to the header"""
+        # "Normal" stuff is handled by the general version, specific changes to values happen here
+        # alternatively you can implement all of it here, whatever works
+        header = super().add_header_info(header, arm)
+
+        try:
+            header["e_ra"] /= 15
+            header["e_jd"] += header["e_exptim"] / (7200 * 24) + 0.5
+
+        except:
+            pass
+
+        try:
+            if (
+                header["NAXIS"] == 2
+                and header["NAXIS1"] == 4296
+                and header["NAXIS2"] == 4096
+            ):
+                # both arms are in the same image
+                prescan_x = 50
+                overscan_x = 50
+                naxis_x = 2148
+                if arm == "BLUE":
+                    header["e_xlo"] = prescan_x
+                    header["e_xhi"] = naxis_x - overscan_x
+                elif arm == "RED":
+                    header["e_xlo"] = naxis_x + prescan_x
+                    header["e_xhi"] = 2 * naxis_x - overscan_x
+        except KeyError:
+            pass
+
+        return header
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = dirname(__file__)
+        fname = f"NEID_{arm.lower()}_2D.npz"
+        fname = join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_wavelength_range(self, header, arm, **kwargs):
+        wave_range = super().get_wavelength_range(header, arm, **kwargs)
+        return wave_range