pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/instruments/common.yaml

@@ -0,0 +1,57 @@
+# COMMON instrument configuration
+# Default/base configuration used as fallback for custom instruments
+
+__instrument__: COMMON
+instrument: INSTRUME
+id_instrument: COMMON
+telescope: TELESCOP
+target: OBJECT
+
+date: DATE-OBS
+date_format: fits
+
+extension: 0
+orientation: 0
+transpose: false
+
+prescan_x: 0
+overscan_x: 0
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: 1
+readnoise: 0
+dark: 0
+sky: 0
+exposure_time: EXPTIME
+
+ra: RA
+dec: DEC
+longitude: null
+latitude: null
+altitude: null
+
+# File classification keywords and patterns
+# These define the keywords we look for, and the values they should have
+# in the fits header, to be sorted into that category
+kw_bias: ""
+kw_flat: ""
+kw_curvature: ""
+kw_scatter: ""
+kw_orders: ""
+kw_wave: ""
+kw_comb: ""
+kw_spec: ""
+
+id_bias: BIAS
+id_flat: FLAT
+id_orders: ORDER
+id_curvature: CURV
+id_scatter: SCATTER
+id_wave: WAVE
+id_comb: COMB
+id_spec: SPEC
+
+wavelength_range: null

pyreduce/instruments/crires_plus.py

@@ -0,0 +1,103 @@
+"""
+Handles instrument specific info for the HARPS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+import re
+from itertools import product
+
+import numpy as np
+
+from .common import Instrument
+from .filters import Filter
+
+logger = logging.getLogger(__name__)
+
+
+class CRIRES_PLUS(Instrument):
+    def __init__(self):
+        super().__init__()
+        self.filters["lamp"] = Filter(self.info["id_lamp"])
+        self.filters["band"] = Filter(self.info["id_band"])
+        self.filters["decker"] = Filter(self.info["id_decker"])
+        self.shared += ["band", "decker"]
+
+    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
+        band, decker, detector = self.parse_arm(arm)
+        header = super().add_header_info(header, band)
+        self.load_info()
+
+        return header
+
+    def get_supported_arms(self):
+        settings = self.info["settings"]
+        deckers = self.info["deckers"]
+        detectors = self.info["chips"]
+        arms = [
+            "_".join([s, d, c]) for s, d, c in product(settings, deckers, detectors)
+        ]
+        return arms
+
+    def parse_arm(self, arm):
+        pattern = r"([YJHKLM]\d{4})(_(Open|pos1|pos2))?_det(\d)"
+        match = re.match(pattern, arm, flags=re.IGNORECASE)
+        if not match:
+            logger.error("no arm match")
+        else:
+            band = match.group(1).upper()
+        if match.group(3) is not None:
+            decker = match.group(3).lower().capitalize()
+        else:
+            decker = "Open"
+        detector = match.group(4)
+        return band, decker, detector
+
+    def get_expected_values(self, target, night, arm):
+        expectations = super().get_expected_values(target, night)
+        band, decker, detector = self.parse_arm(arm)
+
+        for key in expectations.keys():
+            if key == "bias":
+                continue
+            expectations[key]["band"] = band
+            expectations[key]["decker"] = decker
+
+        return expectations
+
+    def get_extension(self, header, arm):
+        band, decker, detector = self.parse_arm(arm)
+        extension = int(detector)
+        return extension
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = f"{self.name}_{arm}.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_mask_filename(self, arm, **kwargs):
+        i = self.name.lower()
+        band, decker, detector = self.parse_arm(arm)
+
+        fname = f"mask_{i}_det{detector}.fits.gz"
+        cwd = os.path.dirname(__file__)
+        fname = os.path.join(cwd, "..", "masks", fname)
+        return fname
+
+    def get_wavelength_range(self, header, arm, **kwargs):
+        wmin = [header["ESO INS WLEN MIN%i" % i] for i in range(1, 11)]
+        wmax = [header["ESO INS WLEN MAX%i" % i] for i in range(1, 11)]
+
+        wavelength_range = np.array([wmin, wmax]).T
+        # Invert the order numbering
+        wavelength_range = wavelength_range[::-1]
+        # Convert from nm to Angstrom
+        wavelength_range *= 10
+        return wavelength_range

pyreduce/instruments/crires_plus.yaml

@@ -0,0 +1,101 @@
+# CRIRES+ instrument configuration
+# The upgraded CRIRES at ESO VLT, a cross-dispersed IR spectrograph for YJHKLM bands.
+
+__instrument__: CRIRES_PLUS
+instrument: INSTRUME
+id_instrument: CRIRES
+telescope: VLT
+
+date: DATE-OBS
+date_format: fits
+
+id_mode: "ESO INS MODE"
+id_band: "ESO INS WLEN ID"
+id_decker: "ESO INS OPTI8 ID"
+id_lamp: "ESO INS1 LAMP? ID"
+
+arms: [J1228]
+deckers: [OPEN, pos1, pos2]
+bands: [Y, J, H, K, L, M]
+settings:
+  - Y1029
+  - Y1028
+  - J1232
+  - J1228
+  - J1226
+  - H1582
+  - H1575
+  - H1567
+  - H1559
+  - K2217
+  - K2192
+  - K2166
+  - K2148
+  - L3426
+  - L3412
+  - L3377
+  - L3340
+  - L3302
+  - L3262
+  - L3244
+  - M4519
+  - M4504
+  - M4461
+  - M4416
+  - M4368
+  - M4318
+  - M4266
+  - M4211
+  - M4187
+chips: [det1, det2, det3]
+
+extension: CHIP1.INT1
+orientation: 0
+transpose: false
+
+prescan_x: 5
+overscan_x: 5
+prescan_y: 5
+overscan_y: 5
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: "HIERARCH ESO DET CHIP GAIN"
+readnoise: "HIERARCH ESO DET CHIP RON"
+dark: "HIERARCH ESO DET DIT"
+sky: 0
+exposure_time: EXPTIME
+
+image_type: OBJECT
+category: "HIERARCH ESO DPR CATG"
+ra: RA
+dec: DEC
+jd: MJD-OBS
+longitude: "HIERARCH ESO TEL GEOLON"
+latitude: "HIERARCH ESO TEL GEOLAT"
+altitude: "HIERARCH ESO TEL GEOELEV"
+target: OBJECT
+observation_type: "ESO DPR TYPE"
+
+id_detcheck: "FLAT,LAMP,DETCHECK"
+id_lamp_wavecal: UNe_HCL
+id_lamp_etalon: Etalon_Halogen
+
+# 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: DARK
+id_flat: FLAT
+id_orders: FLAT
+id_curvature: "WAVE,FPET"
+id_scatter: FLAT
+id_wave: "WAVE,UNE"
+id_comb: "WAVE,FPET"
+id_spec: "STAR,*,*"

pyreduce/instruments/filters.py

@@ -0,0 +1,195 @@
+import logging
+import re
+from datetime import datetime
+from fnmatch import fnmatch
+
+import numpy as np
+from astropy import units as u
+from astropy.time import Time
+from dateutil import parser
+
+logger = logging.getLogger(__name__)
+
+
+class Filter:
+    def __init__(
+        self,
+        keyword,
+        dtype="U20",
+        wildcards=False,
+        regex=False,
+        flags=0,
+        unique=True,
+        ignorecase=True,
+    ):
+        self.keyword = keyword
+        self.dtype = dtype
+        self.wildcards = wildcards
+        self.regex = regex
+        self.flags = flags
+        self.data = []
+        self.unique = unique
+        self.ignorecase = ignorecase
+
+        if self.ignorecase and not self.flags & re.IGNORECASE:
+            self.flags += re.IGNORECASE
+
+    def _collect_value(self, header):
+        if self.keyword is None:
+            value = ""
+        elif "{" in self.keyword:
+            kws = re.findall(r"{([^{}]+)}", self.keyword)
+            values = {kw: header.get(kw, "") for kw in kws}
+            value = self.keyword.format(**values)
+        else:
+            value = header.get(self.keyword)
+        if value.__class__ == header.__class__:
+            if len(value) > 0:
+                value = value[0]
+            else:
+                value = ""
+        return value
+
+    def collect(self, header):
+        value = self._collect_value(header)
+        self.data.append(value)
+        return value
+
+    def match(self, value):
+        if self.keyword is None:
+            result = np.full(len(self.data), False)
+        else:
+            try:
+                if self.regex:
+                    regex = re.compile(f"^(?:{value})$", flags=self.flags)
+                elif self.wildcards:
+                    regex = re.compile(fnmatch.translate(value), flags=self.flags)
+                else:
+                    regex = re.compile(value, flags=self.flags)
+
+                result = [
+                    regex.match(f) is not None if f is not None else False
+                    for f in self.data
+                ]
+            except TypeError:
+                result = [f == value for f in self.data]
+        result = np.asarray(result, dtype=bool)
+        return result
+
+    def classify(self, value):
+        if self.unique:
+            if value is not None and value != "":
+                match = self.match(value)
+                data = np.asarray(self.data)
+                data = np.unique(data[match])
+            else:
+                data = set(self.data)
+            data = [(d, self.match(d)) for d in data]
+        else:
+            if value is not None and value != "":
+                match = self.match(value)
+            else:
+                match = np.full(len(self.data), True)
+            data = [(value, match)]
+        return data
+
+    def clear(self):
+        self.data = []
+
+
+class InstrumentFilter(Filter):
+    def __init__(self, keyword="INSTRUME", **kwargs):
+        kwargs["dtype"] = "U20"
+        kwargs["unique"] = False
+        super().__init__(keyword, **kwargs)
+
+
+class ObjectFilter(Filter):
+    def __init__(self, keyword="OBJECT", **kwargs):
+        kwargs["dtype"] = "U20"
+        kwargs["unique"] = False
+        super().__init__(keyword, **kwargs)
+
+
+class NightFilter(Filter):
+    def __init__(
+        self,
+        keyword="DATE-OBS",
+        timeformat="fits",
+        timezone="utc",
+        timezone_local=None,
+        **kwargs,
+    ):
+        super().__init__(keyword, dtype=datetime, **kwargs)
+        self.timeformat = timeformat
+        self.timezone = timezone
+        self.timezone_local = timezone_local
+
+    @staticmethod
+    def observation_date_to_night(observation_date):
+        """Convert an observation timestamp into the date of the observation night
+        Nights start at 12am and end at 12 am the next day
+        """
+        if observation_date.to_datetime().hour < 12:
+            observation_date -= 1 * u.day
+        return observation_date.to_datetime().date()
+
+    def collect(self, header):
+        value = super()._collect_value(header)
+        if value is not None:
+            try:
+                value = Time(value, format=self.timeformat, scale=self.timezone)
+                value = self.observation_date_to_night(value)
+            except ValueError:
+                logger.warning(
+                    "Could not determine the observation date of %s, skipping it",
+                    header,
+                )
+        else:
+            logger.warning(
+                "Could not determine the observation date of %s, skipping it", header
+            )
+        self.data.append(value)
+        return value
+
+    def match(self, value):
+        try:
+            value = parser.parse(value).date()
+        except Exception:
+            pass
+        match = super().match(value)
+        return match
+
+
+class ArmFilter(Filter):
+    def __init__(
+        self,
+        keyword,
+        dtype="U20",
+        wildcards=False,
+        regex=False,
+        flags=0,
+        unique=True,
+        ignorecase=True,
+        replacement=None,
+    ):
+        if replacement is None:
+            replacement = {}
+        super().__init__(
+            keyword,
+            dtype=dtype,
+            wildcards=wildcards,
+            regex=regex,
+            flags=flags,
+            unique=unique,
+            ignorecase=ignorecase,
+        )
+        self.replacement = replacement
+
+    def classify(self, value):
+        data = super().classify(value)
+        data = [
+            (self.replacement[d] if d in self.replacement.keys() else d, m)
+            for d, m in data
+        ]
+        return data

pyreduce/instruments/harpn.py

@@ -0,0 +1,203 @@
+"""
+Handles instrument specific info for the HARPN 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="TNG 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 HARPN(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),
+            "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 = {
+            "bias": {"instrument": "HARPN", "night": night, "type": r"BIAS,BIAS"},
+            "flat": {"instrument": "HARPN", "night": night, "type": r"LAMP,LAMP,TUN"},
+            "orders": {
+                "instrument": "HARPN",
+                "night": night,
+                "type": id_orddef,
+            },
+            "scatter": {
+                "instrument": "HARPN",
+                "night": night,
+                "type": id_orddef,  # Same as orders or same as flat?
+            },
+            "wavecal_master": {
+                "instrument": "HARPN",
+                "night": night,
+                "type": r"WAVE,WAVE,THAR2",
+            },
+            "freq_comb_master": {
+                "instrument": "HARPN",
+                "night": night,
+                "type": r"WAVE,WAVE,COMB",
+            },
+            "science": {
+                "instrument": "HARPN",
+                "night": night,
+                "mode": mode,
+                "type": id_spec,
+                "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
+
+        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"harpn_{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)
+        # 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