pyreduce-astro 0.6.0b5__cp311-cp311-win_amd64.whl

pyreduce/instruments/harps.json

@@ -0,0 +1,155 @@
+{
+    "__comment__": "red and middle are in the same fits file, with different extensions, i.e. share the same mode identifier, but have different extensions",
+    "__instrument__": "HARPS",
+    "id_instrument": "HARPS(pol)?",
+    "instrument": "INSTRUME",
+    "telescope": "TELESCOP",
+    "date": "DATE-OBS",
+    "date_format": "fits",
+    "modes": [
+        "BLUE",
+        "RED"
+    ],
+    "modes_id": [
+        "HARPS",
+        "HARPS"
+    ],
+    "modes_id_polarimetry": [
+        "HARPSpol",
+        "HARPSpol"
+    ],
+    "extension": [
+        1,
+        2
+    ],
+    "id": [
+        [
+            1,
+            1
+        ],
+        [
+            1,
+            2
+        ]
+    ],
+    "orientation": 1,
+    "transpose": false,
+    "prescan_x": "HIERARCH ESO DET OUT{id[0]} PRSCX",
+    "overscan_x": "HIERARCH ESO DET OUT{id[0]} OVSCX",
+    "prescan_y": 0,
+    "overscan_y": 0,
+    "naxis_x": "NAXIS1",
+    "naxis_y": "NAXIS2",
+    "polarization_linear": "eso ins ret50 pos",
+    "polarization_circular": "eso ins ret25 pos",
+    "gain": "HIERARCH ESO DET OUT{id[0]} CONAD",
+    "readnoise": "HIERARCH ESO DET OUT{id[0]} RON",
+    "dark": "HIERARCH ESO INS DET{id[1]} OFFDRK",
+    "sky": "HIERARCH ESO INS DET{id[1]} OFFSKY",
+    "exposure_time": "EXPTIME",
+    "image_type": "OBJECT",
+    "category": "HIERARCH ESO DPR CATG",
+    "ra": "RA",
+    "dec": "DEC",
+    "longitude": "HIERARCH ESO TEL GEOLON",
+    "latitude": "HIERARCH ESO TEL GEOLAT",
+    "altitude": "HIERARCH ESO TEL GEOELEV",
+    "target": "OBJECT",
+    "instrument_mode": "ESO INS MODE",
+    "instrument_mode_alternative": "ESO TPL NAME",
+    "observation_type": "ESO DPR TYPE",
+    "id_fiber_a": "LAMP,DARK,TUN",
+    "id_fiber_b": "DARK,LAMP,TUN",
+    "kw_bias": "ESO DPR TYPE",
+    "kw_flat": "ESO DPR TYPE",
+    "kw_curvature": "ESO DPR TYPE",
+    "kw_scatter": "ESO DPR TYPE",
+    "kw_orders": "ESO DPR TYPE",
+    "kw_wave": "ESO DPR TYPE",
+    "kw_comb": "ESO DPR TYPE",
+    "kw_spec": "ESO DPR TYPE",
+    "id_bias": "BIAS,BIAS",
+    "id_flat": "LAMP,LAMP,TUN",
+    "id_orders": "LAMP,LAMP,TUN",
+    "id_curvature": "WAVE,WAVE,THAR2",
+    "id_scatter": "LAMP,LAMP,TUN",
+    "id_wave": "WAVE,WAVE,THAR2",
+    "id_comb": "WAVE,WAVE,COMB",
+    "id_spec": "STAR,*,*",
+    "wavelength_range": [[
+        [5245.4, 	5304.3],
+        [5200.5, 	5259.0],
+        [5156.5, 	5214.4],
+        [5113.2, 	5170.6],
+        [5070.6, 	5127.6],
+        [5028.7, 	5085.2],
+        [4987.5, 	5043.5],
+        [4946.9, 	5002.5],
+        [4907.0, 	4962.2],
+        [4867.8, 	4922.5],
+        [4829.2, 	4883.4],
+        [4791.1, 	4845.0],
+        [4753.7, 	4807.1],
+        [4716.9, 	4769.9],
+        [4680.6, 	4733.2],
+        [4644.9, 	4697.1],
+        [4609.7, 	4661.5],
+        [4575.1, 	4626.5],
+        [4540.9, 	4591.9],
+        [4507.3, 	4557.9],
+        [4474.2, 	4524.4],
+        [4441.5, 	4491.4],
+        [4409.3, 	4458.9],
+        [4377.6, 	4426.8],
+        [4346.4, 	4395.2],
+        [4315.5, 	4364.0],
+        [4285.2, 	4333.3],
+        [4255.2, 	4303.0],
+        [4225.7, 	4273.1],
+        [4196.5, 	4243.6],
+        [4167.8, 	4214.6],
+        [4139.4, 	4185.9],
+        [4111.5, 	4157.6],
+        [4083.9, 	4129.7],
+        [4056.7, 	4102.2],
+        [4029.8, 	4075.0],
+        [4003.3, 	4048.2],
+        [3977.1, 	4021.8],
+        [3951.3, 	3995.7],
+        [3925.8, 	3969.9],
+        [3900.7, 	3944.5],
+        [3875.8, 	3919.3],
+        [3851.3, 	3894.5],
+        [3827.1, 	3870.0],
+        [3803.2, 	3845.9],
+        [3779.6, 	3822.0]
+        ],[
+        [6835.9, 6913.0],
+        [6760.0, 6836.2],
+        [6685.7, 6761.1],
+        [6613.1, 6687.6],
+        [6542.0, 6615.7],
+        [6472.4, 6545.4],
+        [6404.3, 6476.5],
+        [6337.7, 6409.1],
+        [6272.3, 6343.0],
+        [6208.4, 6278.3],
+        [6145.7, 6214.9],
+        [6084.2, 6152.8],
+        [6024.0, 6091.9],
+        [5965.0, 6032.1],
+        [5907.1, 5973.6],
+        [5850.3, 5916.2],
+        [5794.6, 5859.8],
+        [5739.9, 5804.6],
+        [5686.3, 5750.3],
+        [5633.7, 5697.1],
+        [5582.0, 5644.8],
+        [5531.3, 5593.5],
+        [5481.5, 5543.2],
+        [5432.5, 5493.7],
+        [5384.5, 5445.1],
+        [5337.3, 5397.3]
+        ]
+    ]
+}

pyreduce/instruments/harps.py

@@ -0,0 +1,310 @@
+"""
+Handles instrument specific info for the HARPS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import re
+from os.path import dirname, join
+
+import numpy as np
+
+from .common import Instrument
+from .filters import Filter, InstrumentFilter, NightFilter, ObjectFilter
+
+logger = logging.getLogger(__name__)
+
+
+class TypeFilter(Filter):
+    def __init__(self, keyword="ESO DPR TYPE"):
+        super().__init__(keyword, regex=True)
+
+    def classify(self, value):
+        if value is not None:
+            match = self.match(value)
+            data = np.asarray(self.data)
+            data = np.unique(data[match])
+            try:
+                regex = re.compile(value)
+                keys = [regex.match(f) for f in data]
+                keys = [[g for g in d.groups() if g is not None][0] for d in keys]
+                unique = np.unique(keys)
+                assign = {
+                    u: [d for k, d in zip(keys, data, strict=False) if k == u]
+                    for u in unique
+                }
+                data = [(u, self.match("|".join(a))) for u, a in assign.items()]
+            except IndexError:
+                data = np.asarray(self.data)
+                data = np.unique(data[match])
+                data = [(d, self.match(d)) for d in data]
+        else:
+            data = np.unique(self.data)
+            data = [(d, self.match(d)) for d in data]
+        return data
+
+
+class FiberFilter(Filter):
+    def __init__(self, keyword="ESO DPR TYPE"):
+        super().__init__(keyword, regex=True)
+        self.lamp_values = ["LAMP", "STAR", "CIRPOL", "LINPOL"]
+
+    def collect(self, header):
+        value = header.get(self.keyword)
+        if value is None:
+            value = ""
+        else:
+            value = value.split(",")
+            if value[0] in self.lamp_values and value[1] in self.lamp_values:
+                value = "AB"
+            elif value[1] in self.lamp_values:
+                value = "B"
+            elif value[0] in self.lamp_values:
+                value = "A"
+            else:
+                value = ""
+
+        self.data.append(value)
+        return value
+
+
+class PolarizationFilter(Filter):
+    def __init__(self, keyword="ESO INS RET?? POS"):
+        super().__init__(keyword, regex=True)
+
+    def collect(self, header):
+        dpr_type = header.get("ESO DPR TYPE", "")
+        match = re.match(r"^.*,(CIR|LIN)POL,.*$", dpr_type)
+        if match is None:
+            value = "none"
+        elif match.group(1) == "CIR":
+            value = "circular"
+        elif match.group(1) == "LIN":
+            value = "linear"
+        else:
+            raise ValueError("Polarization not recognised")
+        self.data.append(value)
+        return value
+
+
+class HARPS(Instrument):
+    def __init__(self):
+        super().__init__()
+        self.filters = {
+            "instrument": InstrumentFilter(self.info["instrument"]),
+            "night": NightFilter(self.info["date"]),
+            # "branch": Filter(, regex=True),
+            "mode": Filter(
+                self.info["instrument_mode"], regex=True, flags=re.IGNORECASE
+            ),
+            "type": TypeFilter(self.info["observation_type"]),
+            "polarization": PolarizationFilter(),
+            "target": ObjectFilter(self.info["target"], regex=True),
+            "fiber": FiberFilter(),
+        }
+        self.night = "night"
+        self.science = "science"
+        self.shared = ["instrument", "night", "mode", "polarization", "fiber"]
+        self.find_closest = [
+            "bias",
+            "flat",
+            "wavecal_master",
+            "freq_comb_master",
+            "orders",
+            "scatter",
+            "curvature",
+        ]
+
+    def get_expected_values(self, target, night, mode, fiber, polarimetry):
+        """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
+        fiber : "A", "B", "AB"
+            Which of the fibers should carry observation signal
+        polarimetry : "none", "linear", "circular", bool
+            Whether the instrument is used in HARPS or HARPSpol mode
+            and which polarization is observed. Set to true for both kinds
+            of polarisation.
+
+        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 = ".*"
+
+        if fiber == "AB":
+            template = r"({a},{a}),{c}"
+        elif fiber == "A":
+            template = r"({a},{b}),{c}"
+        elif fiber == "B":
+            template = r"({b},{a}),{c}"
+        elif fiber is None:
+            template = None
+            fiber = "(AB)|(A)|(B)"
+        else:
+            raise ValueError(
+                "fiber keyword not understood, possible values are 'AB', 'A', 'B'"
+            )
+
+        if polarimetry == "none" or not polarimetry:
+            mode = "HARPS"
+            if template is not None:
+                id_orddef = template.format(a="LAMP", b="DARK", c=".*?")
+                id_spec = template.format(a="STAR", b="(?!STAR).*?", c=".*?")
+            else:
+                id_spec = (
+                    r"^(STAR,(?!STAR).*),.*$|^((?!STAR).*?,STAR),.*$|^(STAR,STAR),.*$"
+                )
+                id_orddef = r"^(LAMP,DARK),.*$|^(DARK,LAMP),.*$|^(LAMP,LAMP),.*$"
+            polarimetry = "none"
+        else:
+            mode = "HARPSpol"
+            id_orddef = r"(LAMP,LAMP),.*"
+            if polarimetry == r"linear":
+                id_spec = r"(STAR,LINPOL),.*"
+            elif polarimetry == "circular":
+                id_spec = r"(STAR,CIRPOL),.*"
+            elif polarimetry:
+                id_spec = r"(STAR,(?:LIN|CIR)POL),.*"
+                polarimetry = r"(circular|linear)"
+            else:
+                raise ValueError(
+                    f"polarization parameter not recognized. Expected one of 'none', 'linear', 'circular', but got {polarimetry}"
+                )
+
+        expectations = {
+            "bias": {"instrument": "HARPS", "night": night, "type": r"BIAS,BIAS"},
+            "flat": {"instrument": "HARPS", "night": night, "type": r"(LAMP,LAMP),.*"},
+            "orders": {
+                "instrument": "HARPS",
+                "night": night,
+                "fiber": fiber,
+                "type": id_orddef,
+            },
+            "scatter": {
+                "instrument": "HARPS",
+                "night": night,
+                "type": id_orddef,  # Same as orders or same as flat?
+            },
+            "curvature": {
+                "instrument": "HARPS",
+                "night": night,
+                "type": [r"(WAVE,WAVE,COMB)", r"(WAVE,WAVE,THAR)\d?"],
+            },
+            "wavecal_master": {
+                "instrument": "HARPS",
+                "night": night,
+                "type": r"(WAVE,WAVE,THAR)\d?",
+            },
+            "freq_comb_master": {
+                "instrument": "HARPS",
+                "night": night,
+                "type": r"(WAVE,WAVE,COMB)",
+            },
+            "science": {
+                "instrument": "HARPS",
+                "night": night,
+                "mode": mode,
+                "type": id_spec,
+                "fiber": fiber,
+                "polarization": polarimetry,
+                "target": target,
+            },
+        }
+        return expectations
+
+    def get_extension(self, header, mode):
+        extension = super().get_extension(header, mode)
+
+        try:
+            if (
+                header["NAXIS"] == 2
+                and header["NAXIS1"] == 4296
+                and header["NAXIS2"] == 4096
+            ):
+                extension = 0
+        except KeyError:
+            pass
+
+        return extension
+
+    def add_header_info(self, header, mode, **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, mode)
+
+        try:
+            header["e_ra"] /= 15
+            header["e_jd"] += header["e_exptim"] / (7200 * 24) + 0.5
+
+            pol_angle = header.get("eso ins ret25 pos")
+            if pol_angle is None:
+                pol_angle = header.get("eso ins ret50 pos")
+                if pol_angle is None:
+                    pol_angle = "no polarimeter"
+                else:
+                    pol_angle = "lin %i" % pol_angle
+            else:
+                pol_angle = "cir %i" % pol_angle
+
+            header["e_pol"] = (pol_angle, "polarization angle")
+        except:
+            pass
+
+        try:
+            if (
+                header["NAXIS"] == 2
+                and header["NAXIS1"] == 4296
+                and header["NAXIS2"] == 4096
+            ):
+                # both modes are in the same image
+                prescan_x = 50
+                overscan_x = 50
+                naxis_x = 2148
+                if mode == "BLUE":
+                    header["e_xlo"] = prescan_x
+                    header["e_xhi"] = naxis_x - overscan_x
+                elif mode == "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, mode, polarimetry, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = dirname(__file__)
+        if polarimetry:
+            pol = "_pol"
+        else:
+            pol = ""
+        fname = f"harps_{mode.lower()}{pol}_2D.npz"
+        fname = join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_wavelength_range(self, header, mode, **kwargs):
+        wave_range = super().get_wavelength_range(header, mode, **kwargs)
+        # The wavelength orders are in inverse order in the .json file
+        # because I was to lazy to invert them in the file
+        wave_range = wave_range[::-1]
+        return wave_range

pyreduce/instruments/instrument_info.py

@@ -0,0 +1,140 @@
+"""
+Interface for all instrument specific information
+The actual info is contained in the instruments/{name}.py modules/classes, which are all subclasses of "common"
+"""
+
+import importlib
+
+from .common import Instrument
+
+
+def load_instrument(instrument) -> Instrument:
+    """Load an python instrument module
+
+    Parameters
+    ----------
+    instrument : str
+        name of the instrument
+
+    Returns
+    -------
+    instrument : Instrument
+        Instance of the {instrument} class
+    """
+
+    # TODO: Loading arbitrary modules is probably bad style
+    # from instruments import uves, harps
+    # instruments = {"uves": uves.UVES, "harps": harps.HARPS}
+    # instrument = instruments[instrument.lower()]
+    # instrument = instrument()
+    if instrument is None:
+        instrument = "common"
+
+    fname = f".instruments.{instrument.lower()}"
+    lib = importlib.import_module(fname, package="pyreduce")
+    instrument = getattr(lib, instrument.upper())
+    instrument = instrument()
+
+    return instrument
+
+
+def get_instrument_info(instrument):
+    """Load instrument specific information
+
+    Parameters
+    ----------
+    instrument : str
+        Name of the instrument
+
+    Returns
+    -------
+    dict{str:obj}
+        Dictionary with information
+    """
+
+    instrument = load_instrument(instrument)
+    return instrument.info
+
+
+def sort_files(input_dir, target, night, instrument, mode, **kwargs):
+    """Sort a list of files into different categories and discard files that are not used
+
+    Parameters
+    ----------
+    input_dir : str
+        directory containing all files (with tags for target, night, and instrument)
+    target : str
+        observation target name, as found in the files
+    night : str
+        observation night of interest, as found in the files
+    instrument : str
+        instrument name
+    mode : str
+        instrument mode, if applicable (e.g. red/blue for HARPS)
+
+    Returns
+    -------
+    biaslist : list(str)
+        list of bias files
+    flatlist : list(str)
+        list of flat field files
+    wavelist : list(str)
+        list of wavelength calibration files
+    orderlist : list(str)
+        list of order definition files (for order tracing)
+    speclist : list(str)
+        list of science files, i.e. observations
+    """
+
+    instrument = load_instrument(instrument)
+    return instrument.sort_files(input_dir, target, night, mode, **kwargs)
+
+
+def get_supported_modes(instrument):
+    instrument = load_instrument(instrument)
+    return instrument.get_supported_modes()
+
+
+def modeinfo(header, instrument, mode, **kwargs):
+    """Add instrument specific information to a header/dict
+
+    Parameters
+    ----------
+    header : fits.header, dict
+        header to add information to
+    instrument : str
+        instrument name
+    mode : str
+        instrument mode (e.g. red/blue for HARPS)
+
+    Returns
+    -------
+    header
+        header with added information
+    """
+
+    instrument = load_instrument(instrument)
+    header = instrument.add_header_info(header, mode, **kwargs)
+    return header
+
+
+def get_wavecal_filename(header, instrument, mode, **kwargs):
+    """Get the filename of the pre-existing wavelength solution for the current settings
+
+    Parameters
+    ----------
+    header : fits.header, dict
+        header of the wavelength calibration file
+    instrument : str
+        instrument name
+    mode : str
+        instrument mode (e.g. red/blue for HARPS)
+
+    Returns
+    -------
+    filename : str
+        wavelength solution file
+    """
+
+    instrument = load_instrument(instrument)
+    return instrument.get_wavecal_filename(header, mode, **kwargs)