pyreduce-astro 0.6.0b1__py3-none-any.whl

pyreduce/instruments/mcdonald.py

@@ -0,0 +1,123 @@
+"""
+Handles instrument specific info for the HARPS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+import re
+
+from astropy.time import Time
+
+from .common import InstrumentWithModes, getter
+
+logger = logging.getLogger(__name__)
+
+
+class MCDONALD(InstrumentWithModes):
+    def __init__(self):
+        super().__init__()
+        # The date is a combination of the two values
+        kw = f"{{{self.info['date']}}}T{{{self.info['universal_time']}}}"
+        self.filters["night"].keyword = kw
+
+    def _convert_time_deg(self, v):
+        v = [float(s) for s in v.split(":")]
+        v = v[0] + v[1] / 60 + v[2] / 3600
+        return v
+
+    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, **kwargs)
+        info = self.load_info()
+        get = getter(header, info, mode)
+
+        header["e_orient"] = get("orientation", 0)
+        # As per IDL rotate if orient is 4 or larger and transpose is undefined
+        # the image is transposed
+        header["e_transpose"] = get("transpose", (header["e_orient"] % 8 >= 4))
+
+        trimsec = get("trimsec")
+
+        if trimsec is not None:
+            pattern = r"\[(\d*?):(\d*?),(\d*?):(\d*?)\]"
+            res = re.match(pattern, trimsec)
+            prescan_x = int(res[1]) + 1
+            overscan_x = int(res[2])
+            prescan_y = int(res[3])
+            overscan_y = int(res[4])
+        else:
+            prescan_x = 2
+            overscan_x = 2048
+            prescan_y = 2
+            overscan_y = 2047
+
+        header["e_xlo"] = prescan_x
+        header["e_xhi"] = overscan_x
+
+        header["e_ylo"] = prescan_y
+        header["e_yhi"] = overscan_y
+
+        amp = get("amplifier")
+        gain = info["gain"].format(amplifier=amp)
+        readnoise = info["readnoise"].format(amplifier=amp)
+
+        header["e_gain"] = get(gain, 1)
+        header["e_readn"] = get(readnoise, 0)
+        header["e_exptim"] = get("exposure_time", 0)
+
+        header["e_sky"] = get("sky", 0)
+        header["e_drk"] = get("dark", 0)
+        header["e_backg"] = header["e_gain"] * (header["e_drk"] + header["e_sky"])
+
+        header["e_imtype"] = get("observation_type")
+        header["e_ctg"] = get("observation_type")
+
+        obs_date = get("date")
+        ut = get("universal_time")
+        if obs_date is not None and ut is not None:
+            obs_date = f"{obs_date}T{ut}"
+
+        dark_time = get("dark_time")
+        ra = get("ra")
+        dec = get("dec")
+
+        if ra is not None:
+            ra = self._convert_time_deg(ra)
+        if dec is not None:
+            dec = self._convert_time_deg(dec)
+        if dark_time is not None:
+            tmid = dark_time / 2
+        else:
+            tmid = 0
+        if obs_date is not None:
+            jd = Time(obs_date).mjd + tmid + 0.5
+        else:
+            jd = 0
+
+        header["e_ra"] = ra
+        header["e_dec"] = dec
+        header["e_jd"] = jd
+
+        header["e_obslon"] = self._convert_time_deg(info["longitude"])
+        header["e_obslat"] = self._convert_time_deg(info["latitude"])
+        header["e_obsalt"] = info["altitude"]
+
+        return header
+
+    def get_wavecal_filename(self, header, mode, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = "mcdonald.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname
+
+    def get_mask_filename(self, mode, **kwargs):
+        fname = "mask_mcdonald.fits.gz"
+        cwd = os.path.dirname(__file__)
+        fname = os.path.join(cwd, "..", "masks", fname)
+        return fname

pyreduce/instruments/metis_ifu.json

@@ -0,0 +1,63 @@
+{
+    "__instrument__": "METIS_IFU",
+    "instrument": "INSTRUME",
+    "id_instrument": "METIS_IFU",
+    "telescope": "ELT",
+    "date": "MJD-OBS",
+    "date_format": "mjd",
+    "modes": [
+	"IFU_NOMINAL",
+	"IFU_EXTENDED"
+    ],
+    "kw_modes": "INSTMODE",
+    "id_modes": [
+	"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",
+    "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_ifu.py

@@ -0,0 +1,45 @@
+"""
+Handles instrument specific info for the METIS_IFU IFU spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import InstrumentWithModes
+
+logger = logging.getLogger(__name__)
+
+
+class METIS_IFU(InstrumentWithModes):
+    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)
+
+        # 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, mode):
+        extension = 1
+
+        return extension
+
+    def get_wavecal_filename(self, header, mode, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        # info = self.load_info()
+        cwd = os.path.dirname(__file__)
+        fname = f"metis_ifu_{mode.lower()}_2D.npz"
+        # fname = f"metis_ifu_IFU_L_2D.npz" ## f"micado_IJ_2D_det1.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+
+        return fname

pyreduce/instruments/metis_lss.json

@@ -0,0 +1,65 @@
+{
+    "__instrument__": "METIS_LSS",
+    "instrument": "INSTRUME",
+    "id_instrument": "METIS_LSS",
+    "telescope": "ELT",
+    "date": "MJD-OBS",
+    "date_format": "mjd",
+    "modes": [
+	"LSS_L",
+	"LSS_M",
+	"LSS_N"
+    ],
+    "kw_modes": "INSTMODE",
+    "id_modes": [
+	"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",
+    "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

@@ -0,0 +1,45 @@
+"""
+Handles instrument specific info for the METIS_LSS LSS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import InstrumentWithModes
+
+logger = logging.getLogger(__name__)
+
+
+class METIS_LSS(InstrumentWithModes):
+    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)
+
+        # 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, mode):
+        extension = 1
+
+        return extension
+
+    def get_wavecal_filename(self, header, mode, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        # info = self.load_info()
+        cwd = os.path.dirname(__file__)
+        fname = f"metis_lss_{mode.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/micado.json

@@ -0,0 +1,53 @@
+{
+    "__instrument__": "MICADO",
+    "instrument": "INSTRUME",
+    "id_instrument": "MICADO",
+    "telescope": "ELT",
+    "date": "MJD-OBS",
+    "date_format": "mjd",
+    "modes": ["NIR"],
+    "kw_modes": "ESO DET CHIP*NAME",
+    "id_modes": ["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",
+    "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/micado.py

@@ -0,0 +1,45 @@
+"""
+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, 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)
+
+        # 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, mode):
+        extension = 5
+
+        return extension
+
+    def get_wavecal_filename(self, header, mode, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        # info = self.load_info()
+        cwd = os.path.dirname(__file__)
+        # fname = f"xshooter_{mode.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/neid.json

@@ -0,0 +1,51 @@
+{
+    "__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__": "NEID",
+    "id_instrument": "NEID",
+    "instrument": "INSTRUME",
+    "telescope": "TELESCOP",
+    "date": "DATE-OBS",
+    "date_format": "fits",
+    "modes": ["HR"],
+    "modes_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",
+    "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/neid.py

@@ -0,0 +1,154 @@
+"""
+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.info["instrument"]),
+            "night": NightFilter(self.info["date"]),
+            # "branch": Filter(, regex=True),
+            "mode": Filter(
+                self.info["instrument_mode"], regex=True, flags=re.IGNORECASE
+            ),
+            "type": Filter(self.info["observation_type"]),
+            "target": ObjectFilter(self.info["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, mode, fiber):
+        """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, mode):
+        extension = super().get_extension(header, mode)
+
+        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
+
+        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, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = dirname(__file__)
+        fname = f"NEID_{mode.lower()}_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)
+        return wave_range