pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/instruments/harpn.yaml

@@ -0,0 +1,140 @@
+# HARPN instrument configuration
+# Note: red and middle are in the same fits file, with different extensions,
+# i.e. share the same mode identifier, but have different extensions
+
+__instrument__: HARPN
+id_instrument: HARPN
+instrument: INSTRUME
+telescope: TELESCOP
+
+date: DATE-OBS
+date_format: fits
+
+arms: [HARPN]
+arms_id: [harpn]
+extension: [1]
+id: [[1, 2]]
+orientation: 2
+transpose: true
+
+prescan_x: "HIERARCH TNG DET OUT{id[0]} PRSCX"
+overscan_x: "HIERARCH TNG DET OUT{id[0]} OVSCX"
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: "HIERARCH TNG DET OUT{id[0]} GAIN"
+readnoise: "HIERARCH TNG DET OUT{id[0]} RON"
+dark: "HIERARCH TNG INS DET{id[1]} OFFDRK"
+sky: "HIERARCH TNG INS DET{id[1]} OFFSKY"
+exposure_time: EXPTIME
+
+image_type: "HIERARCH TNG OBS TARG NAME"
+category: "HIERARCH TNG DPR CATG"
+ra: RA
+dec: DEC
+longitude: GEOLON
+latitude: GEOLAT
+altitude: GEOELEV
+target: OBJECT
+instrument_mode: "HIERARCH TNG INS MODE"
+instrument_mode_alternative: "TNG TPL NAME"
+observation_type: "TNG DPR TYPE"
+
+id_fiber_a: "LAMP,DARK,TUN"
+id_fiber_b: "DARK,LAMP,TUN"
+
+# File classification keywords and patterns
+kw_bias: "HIERARCH TNG DPR TYPE"
+kw_flat: "HIERARCH TNG DPR TYPE"
+kw_curvature: "HIERARCH TNG DPR TYPE"
+kw_scatter: "HIERARCH TNG DPR TYPE"
+kw_orders: "HIERARCH TNG DPR TYPE"
+kw_wave: "HIERARCH TNG DPR TYPE"
+kw_comb: "HIERARCH TNG DPR TYPE"
+kw_spec: "HIERARCH TNG 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:
+  # HARPN mode
+  - - [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 +1,312 @@
+"""
+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.config.instrument),
+            "night": NightFilter(self.config.date),
+            # "branch": Filter(, regex=True),
+            "mode": Filter(
+                self.config.instrument_mode, regex=True, flags=re.IGNORECASE
+            ),
+            "type": TypeFilter(self.config.observation_type),
+            "polarization": PolarizationFilter(),
+            "target": ObjectFilter(self.config.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, arm=None, mode=None, fiber=None, polarimetry=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
+        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, arm):
+        extension = super().get_extension(header, arm)
+
+        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, 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
+
+            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 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, polarimetry, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = dirname(__file__)
+        if polarimetry:
+            pol = "_pol"
+        else:
+            pol = ""
+        fname = f"harps_{arm.lower()}{pol}_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)
+        # 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/harps.yaml

@@ -0,0 +1,144 @@
+# HARPS instrument configuration
+# Note: 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
+
+arms: [BLUE, RED]
+arms_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"
+
+# File classification keywords and patterns
+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:
+  # BLUE mode
+  - - [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]
+  # RED mode
+  - - [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]