pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/instruments/neid.yaml

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+# NEID 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__: NEID
+id_instrument: NEID
+instrument: INSTRUME
+telescope: TELESCOP
+
+date: DATE-OBS
+date_format: fits
+
+arms: [HR]
+arms_id: [HR]
+namps: NAMPS
+extension: "AMPLIFIER {amp}"
+orientation: 0
+transpose: false
+
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: CCDGAIN
+readnoise: CCDRN
+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: OBS-MODE
+observation_type: "TNG DPR TYPE"
+
+id_fiber_sci: "LAMP,DARK,TUN"
+id_fiber_cal: "DARK,LAMP,TUN"
+id_fiber_sky: "DARK,LAMP,TUN"
+
+# File classification keywords and patterns
+kw_bias: OBJECT
+kw_flat: OBJECT
+kw_curvature: OBJECT
+kw_scatter: OBJECT
+kw_orders: OBJECT
+kw_wave: OBJECT
+kw_comb: OBJECT
+kw_spec: OBJECT
+
+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,*"

pyreduce/instruments/nirspec.py

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+"""
+Handles instrument specific info for the UVES spectrograph
+
+Mostly reading data from the header
+"""
+
+import glob
+import logging
+import os.path
+from datetime import datetime
+
+import numpy as np
+from astropy.io import fits
+from dateutil import parser
+from tqdm import tqdm
+
+from .common import Instrument, observation_date_to_night
+
+logger = logging.getLogger(__name__)
+
+
+class NIRSPEC(Instrument):
+    @staticmethod
+    def get_arm(header):
+        # TODO figure out the parameters to use for this
+        try:
+            fil1pos = header["FIL1POS"]
+            fil2pos = header["FIL2POS"]
+            filter = header["FILNAME"]
+        except KeyError:
+            return ""
+
+        # TODO get other settings
+        if filter == "NIRSPEC-1":
+            raise ValueError
+        elif filter == "NIRSPEC-2":
+            raise ValueError
+        elif filter == "NIRSPEC-4":
+            raise ValueError
+        elif filter == "NIRSPEC-5":
+            raise ValueError
+        elif filter == "NIRSPEC-7":
+            if fil1pos == 11 and fil2pos == 18:
+                setting = "K2"
+            else:
+                raise ValueError
+        else:
+            raise ValueError
+
+        return setting
+
+    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_setting"] = NIRSPEC.get_arm(header)
+        header["EXPTIME"] = header.get("ITIME", 0) * header.get("COADDS", 0)
+        return header
+
+    def sort_files(self, input_dir, target, night, arm, calibration_dir, **kwargs):
+        """
+        Sort a set of fits files into different categories
+        types are: bias, flat, wavecal, orderdef, spec
+
+        Parameters
+        ----------
+        input_dir : str
+            input directory containing the files to sort
+        target : str
+            name of the target as in the fits headers
+        night : str
+            observation night, possibly with wildcards
+        arm : str
+            instrument arm
+        Returns
+        -------
+        files_per_night : list[dict{str:dict{str:list[str]}}]
+            a list of file sets, one entry per night, where each night consists of a dictionary with one entry per setting,
+            each fileset has five lists of filenames: "bias", "flat", "order", "wave", "spec", organised in another dict
+        nights_out : list[datetime]
+            a list of observation times, same order as files_per_night
+        """
+
+        # TODO allow several names for the target?
+
+        info = self.info
+        target = target.casefold()
+        instrument = self.__class__.__name__
+
+        # Try matching with nights
+        try:
+            night = parser.parse(night).date()
+            individual_nights = [night]
+        except ValueError:
+            # if the input night can't be parsed, use all nights
+            # Usually the case if wildcards are involved
+            individual_nights = "all"
+
+        # find all fits files in the input dir(s)
+        input_dir = input_dir.format(
+            instrument=instrument.upper(), target=target, arm=arm, night=night
+        )
+        files = glob.glob(input_dir + "/*.fits")
+        files += glob.glob(input_dir + "/*.fits.gz")
+        files = np.array(files)
+
+        # Initialize arrays
+        # observed object
+        ob = np.zeros(len(files), dtype="U20")
+        # observed night, parsed into a datetime object
+        ni = np.zeros(len(files), dtype=datetime)
+        # instrument, used for observation
+        it = np.zeros(len(files), dtype="U20")
+
+        for i, f in enumerate(files):
+            with fits.open(f) as hdu:
+                h = hdu[0].header
+                ob[i] = h.get(info["target"], "")
+                ni_tmp = h.get(info["date"], "")
+                it[i] = h.get(info["instrument"], "")
+
+            # Sanitize input
+            ni[i] = observation_date_to_night(ni_tmp)
+            ob[i] = ob[i].replace("-", "").replace(" ", "").casefold()
+
+        if isinstance(individual_nights, str) and individual_nights == "all":
+            individual_nights = np.unique(ni)
+            logger.info(
+                "Can't parse night %s, use all %i individual nights instead",
+                night,
+                len(individual_nights),
+            )
+
+        files_per_observation = []
+        cache = {}
+
+        for ind_night in tqdm(individual_nights):
+            # Select files for this night, this instrument, this instrument arm
+            selection = (ni == ind_night) & (it == instrument) & (ob == target)
+
+            for file in files[selection]:
+                # Read caliblist
+                caliblist = file[:-8] + ".caliblist"
+                caliblist = np.genfromtxt(
+                    caliblist, skip_header=8, dtype=str, delimiter=" ", usecols=(0)
+                )
+                caliblist = np.array(
+                    [
+                        os.path.join(input_dir, calibration_dir, c) + ".gz"
+                        for c in caliblist
+                    ]
+                )
+
+                tp = np.zeros(len(caliblist), dtype="U20")
+                for i, c in enumerate(caliblist):
+                    try:
+                        tp[i] = cache[c]
+                    except KeyError:
+                        h = fits.open(c)[0].header
+                        if h[info["id_flat"]] == 1:
+                            tp[i] = "flat"
+                        elif (
+                            h[info["id_neon"]] == 1
+                            or h[info["id_argon"]] == 1
+                            or h[info["id_krypton"]] == 1
+                            or h[info["id_xenon"]] == 1
+                        ):
+                            tp[i] = "wavecal"
+                        elif h[info["id_etalon"]] == 1:
+                            tp[i] = "freq_comb"
+                        else:
+                            tp[i] = "bias"
+                        cache[c] = tp[i]
+                files_this_observation = {
+                    "bias": caliblist[tp == "bias"],
+                    "flat": caliblist[tp == "flat"],
+                    "orders": caliblist[tp == "flat"],
+                    "wavecal_master": caliblist[tp == "wavecal"],
+                    "freq_comb_master": caliblist[tp == "freq_comb"],
+                    "science": [file],
+                }
+                files_this_observation["curvature"] = (
+                    files_this_observation["freq_comb_master"]
+                    if len(files_this_observation["freq_comb_master"]) != 0
+                    else files_this_observation["wavecal_master"]
+                )
+                files_this_observation["scatter"] = files_this_observation["orders"]
+
+                files_per_observation.append(
+                    ({"night": ind_night, "target": target}, files_this_observation)
+                )
+
+        return files_per_observation
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        info = self.info
+        if header[info["id_neon"]] == 1:
+            pass
+        elif header[info["id_argon"]] == 1:
+            pass
+        elif header[info["id_krypton"]] == 1:
+            pass
+        elif header[info["id_xenon"]] == 1:
+            pass
+        else:
+            raise ValueError("Wavelength calibration element not recognised")
+
+        echelle_setting = "K2"
+
+        cwd = os.path.dirname(__file__)
+        fname = f"nirspec_{echelle_setting}.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname

pyreduce/instruments/nirspec.yaml

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+# NIRSPEC (Keck) instrument configuration
+
+__instrument__: NIRSPEC
+instrument: CURRINST
+id_instrument: NIRSPEC
+telescope: Keck
+
+date: DATE-OBS
+date_format: fits
+
+arms: [NIRSPEC]
+extension: 0
+orientation: 0
+transpose: false
+
+prescan_x: 5
+overscan_x: 5
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: DETGAIN
+readnoise: DETRN
+bias: DETBIAS
+dark: 0
+sky: 0
+air: AIRMASS
+exposure_time: ITIME
+
+image_type: OBJECT
+ra: HA
+dec: DEC
+jd: MJD-OBS
+longitude: -155.4783333
+latitude: 19.8283333
+altitude: 4160
+target: OBJECT
+
+id_neon: NEON
+id_argon: ARGON
+id_krypton: KRYPTON
+id_xenon: XENON
+id_etalon: ETALON
+
+# File classification keywords and patterns
+kw_bias: null
+kw_flat: null
+kw_curvature: null
+kw_scatter: null
+kw_orders: null
+kw_wave: null
+kw_comb: null
+kw_spec: null
+
+id_bias: BIAS
+id_flat: FLAT
+id_orders: null
+id_curvature: null
+id_scatter: null
+id_wave: null
+id_comb: null
+id_spec: null

pyreduce/instruments/nte.py

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+"""
+Handles instrument specific info for the NTE spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class NTE(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_ra"] /= 15
+        if header["e_jd"] is not None:
+            header["e_jd"] += header["e_exptime"] / (7200 * 24) + 0.5
+
+        return header
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        info = self.info
+        specifier = int(header[info["wavecal_specifier"]])
+
+        cwd = os.path.dirname(__file__)
+        fname = "{instrument}_{arm}_{specifier}nm_2D.npz".format(
+            instrument="nte", arm=arm.lower(), specifier=specifier
+        )
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_wavelength_range(self, header, arm):
+        wave = 7 * [7000, 20_000]
+        return wave

pyreduce/instruments/nte.yaml

@@ -0,0 +1,55 @@
+# NTE instrument configuration
+
+__instrument__: NTE
+instrument: INSTRUME
+id_instrument: NTE
+telescope: NOT
+
+category: IMAGECAT
+target: OBJECT
+date: DATE-OBS
+date_format: fits
+
+arms: [VIS, NIR]
+extension: 0
+orientation: 0
+
+prescan_x: 0
+overscan_x: 0
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: GAIN
+readnoise: RDNOISE
+dark: DARK
+sky: 0
+exposure_time: EXPTIME
+
+ra: RA
+dec: DEC
+longitude: LONGITUD
+latitude: LATITUD
+altitude: ELEVAT
+
+# File classification keywords and patterns
+kw_bias: IMAGETYP
+kw_dark: IMAGETYP
+kw_flat: IMAGETYP
+kw_curvature: IMAGETYP
+kw_scatter: IMAGETYP
+kw_orders: IMAGETYP
+kw_wave: IMAGETYP
+kw_comb: IMAGETYP
+kw_spec: IMAGETYP
+
+id_bias: BIAS
+id_dark: DARK
+id_flat: "LAMP,FLAT"
+id_orders: "LAMP,ORDERDEF"
+id_curvature: "LAMP,FPE"
+id_scatter: "LAMP,FLAT"
+id_wave: "LAMP,WAVE"
+id_comb: "LAMP,FPE"
+id_spec: OBJECT

pyreduce/instruments/uves.py

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+"""
+Handles instrument specific info for the UVES spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class UVES(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_ra"] /= 15
+        if header["e_jd"] is not None:
+            header["e_jd"] += header["e_exptime"] / (7200 * 24) + 0.5
+
+        return header
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        info = self.info
+        specifier = int(header[info["wavecal_specifier"]])
+
+        cwd = os.path.dirname(__file__)
+        fname = "{instrument}_{arm}_{specifier}nm_2D.npz".format(
+            instrument="uves", arm=arm.lower(), specifier=specifier
+        )
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_mask_filename(self, arm, **kwargs):
+        i = self.name.lower()
+        a = arm.lower()
+        fname = f"mask_{i}_{a}.fits.gz"
+        cwd = os.path.dirname(__file__)
+        fname = os.path.join(cwd, "..", "masks", fname)
+        return fname

pyreduce/instruments/uves.yaml

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+# UVES instrument configuration
+# Same structure as JSON, just YAML format for readability
+
+__instrument__: UVES
+instrument: INSTRUME
+id_instrument: UVES
+telescope: VLT
+
+date: DATE-OBS
+date_format: fits
+
+arms: [BLUE, MIDDLE, RED]
+arms_id: [blue, red, red]
+extension: [0, 2, 1]
+id: [[1, 5], [1, 4], [1, 4]]
+orientation: [2, 1, 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
+
+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
+
+ra: RA
+dec: DEC
+longitude: "HIERARCH ESO TEL GEOLON"
+latitude: "HIERARCH ESO TEL GEOLAT"
+altitude: "HIERARCH ESO TEL GEOELEV"
+
+target: OBJECT
+wavecal_element: thar
+wavecal_specifier: "ESO INS GRAT2 WLEN"
+
+category: "HIERARCH ESO DPR CATG"
+image_type: OBJECT
+observation_type: "ESO DPR TYPE"
+instrument_mode: "ESO INS MODE"
+instrument_mode_alternative: "ESO TPL NAME"
+
+# File classification keywords and patterns
+kw_bias: "ESO DPR TYPE"
+kw_flat: "ESO DPR TYPE"
+kw_curvature: OBJECT
+kw_scatter: "ESO DPR TYPE"
+kw_orders: "ESO DPR TYPE"
+kw_wave: OBJECT
+kw_comb: null
+kw_spec: "ESO DPR TYPE"
+
+id_bias: BIAS
+id_flat: "LAMP,FLAT"
+id_orders: "LAMP,ORDERDEF"
+id_curvature: "LAMP,WAVE"
+id_scatter: "LAMP,ORDERDEF"
+id_wave: "LAMP,WAVE"
+id_comb: null
+id_spec: "OBJECT,POINT"

pyreduce/instruments/xshooter.py

@@ -0,0 +1,39 @@
+"""
+Handles instrument specific info for the UVES spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class XSHOOTER(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_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        self.load_info()
+
+        cwd = os.path.dirname(__file__)
+        fname = f"xshooter_{arm.lower()}.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname

pyreduce/instruments/xshooter.yaml

@@ -0,0 +1,63 @@
+# XSHOOTER instrument configuration
+
+__instrument__: XSHOOTER
+instrument: INSTRUME
+id_instrument: "SHOOT|XSHOOTER"
+telescope: VLT
+
+date: MJD-OBS
+date_format: mjd
+
+arms: [UVB, VIS, NIR]
+kw_arm: "ESO DET CHIP*NAME"
+id_arm: ["E2V CC44-82", "MIT/LL CCID-20", "Hawaii2RG"]
+extension: 0
+orientation: [1, 0, 0]
+transpose: false
+
+prescan_x: 0
+overscan_x: 0
+prescan_y: 0
+overscan_y: 0
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: "HIERARCH ESO DET OUT1 GAIN"
+readnoise: "HIERARCH ESO DET OUT1 RON"
+dark: 10
+exposure_time: EXPTIME
+
+ra: RA
+dec: DEC
+jd: MJD-OBS
+longitude: "HIERARCH ESO TEL GEOLON"
+latitude: "HIERARCH ESO TEL GEOLAT"
+altitude: "HIERARCH ESO TEL GEOELEV"
+instrument_mode: "HIERARCH ESO SEQ ARM"
+observation_type: "HIERARCH ESO DPR TYPE"
+observation_category: "HIERARCH ESO DPR CATG"
+target: "HIERARCH ESO OBS TARG NAME"
+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: "LAMP,ORDERDEF"
+id_curvature: "LAMP,WAVE"
+id_scatter: "LAMP,FLAT"
+id_wave: "LAMP,WAVE"
+id_comb: null
+id_spec: OBJECT