pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/instruments/instrument_info.py

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+"""
+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, arm, **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
+    arm : str
+        instrument arm (e.g. BLUE/RED 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, arm, **kwargs)
+
+
+def get_supported_arms(instrument):
+    instrument = load_instrument(instrument)
+    return instrument.get_supported_arms()
+
+
+def arminfo(header, instrument, arm, **kwargs):
+    """Add instrument specific information to a header/dict
+
+    Parameters
+    ----------
+    header : fits.header, dict
+        header to add information to
+    instrument : str
+        instrument name
+    arm : str
+        instrument arm (e.g. BLUE/RED for HARPS)
+
+    Returns
+    -------
+    header
+        header with added information
+    """
+
+    instrument = load_instrument(instrument)
+    header = instrument.add_header_info(header, arm, **kwargs)
+    return header
+
+
+def get_wavecal_filename(header, instrument, arm, **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
+    arm : str
+        instrument arm (e.g. BLUE/RED for HARPS)
+
+    Returns
+    -------
+    filename : str
+        wavelength solution file
+    """
+
+    instrument = load_instrument(instrument)
+    return instrument.get_wavecal_filename(header, arm, **kwargs)

pyreduce/instruments/jwst_miri.py

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+"""
+Handles instrument specific info for the HARPS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class JWST_MIRI(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)
+        self.load_info()
+        return header
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = "{instrument}_{arm}_2D.npz".format(instrument="harps", arm=arm)
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname

pyreduce/instruments/jwst_miri.yaml

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+# JWST MIRI instrument configuration
+
+__instrument__: JWST_MIRI
+instrument: INSTRUME
+id_instrument: MIRI
+telescope: JWST
+
+date: DATE-OBS
+date_format: fits
+time: TIME-OBS
+
+target: OBJECT
+instrument_mode: EXP_TYPE
+arms: [LRS_SLITLESS]
+arms_id: [MIR_LRS-SLITLESS]
+extension: [SCI]
+orientation: 3
+transpose: false
+
+overscan_x: 5
+prescan_x: 15
+prescan_y: 0
+overscan_y: 0
+naxis_x: SUBSIZE1
+naxis_y: SUBSIZE2
+nints: NINTS
+ngroups: NGROUPS
+
+gain: GAINCF
+readnoise: RDNOISE
+ra: RA_V1
+dec: DEC_V1
+pa: PA_V3
+exposure_time: EXPTIME
+
+# 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: FILETYPE
+
+id_bias: null
+id_flat: null
+id_orders: null
+id_curvature: null
+id_scatter: null
+id_wave: null
+id_comb: null
+id_spec: ILLUMINATION

pyreduce/instruments/jwst_niriss.py

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+"""
+Handles instrument specific info for the HARPS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from astropy import units as q
+from astropy.io import fits
+from astropy.time import Time
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class JWST_NIRISS(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)
+        self.load_info()
+
+        # TODO: this references some files, I dont know where they should be
+        header["e_gain"] = 1.61
+        header["e_readn"] = 18.32
+        header["e_dark"] = 0.0257
+
+        # total exposure time
+        header["exptime"] = header.get("TFRAME", 0)
+
+        return header
+
+    def split_observation(self, fname, arm):
+        hdu = fits.open(fname)
+        dirname = os.path.dirname(fname)
+        fname = os.path.basename(fname)
+
+        header = hdu[0].header
+        if "mjd-obs" not in header:
+            if len(header["DATE-OBS"]) <= 10:
+                time = header["DATE-OBS"] + "T" + header["TIME-OBS"]
+            else:
+                time = header["DATE-OBS"]
+            header["MJD-OBS"] = Time(time).mjd
+
+        header2 = fits.Header()
+        header2["EXTNAME"] = "SCI"
+        shape = hdu["SCI"].data.shape
+
+        nframes = shape[0]
+        ngroups = shape[1]
+
+        if nframes == 1 and ngroups == 1:
+            return [os.path.join(dirname, fname)]
+
+        data = hdu["SCI"].data.reshape((-1, *shape[-2:]))
+        bias = data[0]
+        primary = fits.PrimaryHDU(header=header)
+        files = []
+        os.makedirs(os.path.join(dirname, "split"), exist_ok=True)
+        for i in range(1, nframes * ngroups):
+            data[i] - bias
+            bias = data[i]
+            fname_this = os.path.join(dirname, "split", f"pyreduce_{i}_{fname}")
+
+            header["MJD-OBS"] += header["TFRAME"] * q.s.to(q.day)
+            secondary = fits.ImageHDU(data=data, header=header2)
+            hdu_this = fits.HDUList([primary, secondary])
+            hdu_this.writeto(fname_this, overwrite=True)
+            files.append(fname_this)
+        hdu.close()
+        return files
+
+    def sort_files(self, input_dir, target, night, arm, allow_calibration_only=False):
+        files = super().sort_files(
+            input_dir,
+            target,
+            night,
+            arm,
+            allow_calibration_only=allow_calibration_only,
+        )
+        for i, (_k, file) in enumerate(files):
+            files_split = []
+            for f in file["science"]:
+                files_split += self.split_observation(f, arm)
+            files[i][1]["science"] = files_split
+        return files
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = "{instrument}_{arm}_2D.npz".format(instrument="harps", arm=arm)
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname

pyreduce/instruments/jwst_niriss.yaml

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+# JWST NIRISS 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__: JWST_NIRISS
+instrument: INSTRUME
+id_instrument: NIRISS
+telescope: JWST
+
+date: DATE-OBS
+date_format: iso
+
+instrument_mode: PUPIL
+arms: [GR700XD]
+arms_id: [GR700XD]
+extension: [SCI]
+orientation: 0
+transpose: false
+
+prescan_y: 0
+overscan_y: 4
+prescan_x: 3
+overscan_x: 4
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: R_GAIN
+readnoise: R_READNO
+exposure_time: EXPTIME
+
+image_type: OBJECT
+ra: TARG_RA
+dec: TARG_DEC
+"position.x": JWST_X
+"position.y": JWST_Y
+"position.z": JWST_Z
+"position.vx": JWST_DX
+"position.vy": JWST_DY
+"position.vz": JWST_DZ
+target: TARGNAME
+observation_type: FILETYPE
+
+# File classification keywords and patterns
+kw_bias: null
+kw_flat: FILENAME
+kw_curvature: null
+kw_scatter: FILENAME
+kw_orders: FILENAME
+kw_wave: null
+kw_comb: null
+kw_spec: INSTRUME
+
+id_bias: null
+id_flat: flat.fits
+id_orders: flat.fits
+id_curvature: null
+id_scatter: flat.fits
+id_wave: null
+id_comb: null
+id_spec: NIRISS

pyreduce/instruments/lick_apf.py

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+"""
+Handles instrument specific info for the HARPS spectrograph
+
+Mostly reading data from the header
+"""
+
+import logging
+import os.path
+
+from .common import Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class LICK_APF(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)
+        self.load_info()
+
+        # pos = EarthLocation.of_site("Lick Observatory")
+        # header["e_obslon"] = pos.lon.to_value("deg")
+        # header["e_obslat"] = pos.lat.to_value("deg")
+        # header["e_obsalt"] = pos.height.to_value("m")
+
+        return header
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = "lick_apf_2D.npz"
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname

pyreduce/instruments/lick_apf.yaml

@@ -0,0 +1,60 @@
+# LICK_APF 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__: LICK_APF
+instrument: version
+id_instrument: apf
+telescope: Lick
+
+date: DATE
+date_format: fits
+
+arms: [""]
+arms_id: [""]
+extension: [0]
+orientation: 3
+transpose: false
+
+prescan_y: TCPR1
+overscan_y: TCPR2
+prescan_x: PPRERD
+overscan_x: PPRERD
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+
+gain: GAIN
+readnoise: 0
+dark: 0
+sky: 0
+exposure_time: EXPTIME
+
+category: ""
+ra: RA
+dec: DEC
+longitude: -121.63667
+latitude: 37.34334
+altitude: 1290
+target: OBJECT
+observation_type: OBSTYPE
+
+# File classification keywords and patterns
+kw_mode: null
+kw_bias: OBSTYPE
+kw_flat: OBJECT
+kw_curvature: OBJECT
+kw_scatter: OBJECT
+kw_orders: OBJECT
+kw_wave: OBJECT
+kw_comb: null
+kw_spec: OBSTYPE
+
+id_mode: null
+id_bias: DARK
+id_flat: WideFlat
+id_orders: NarrowFlat
+id_curvature: ThAr
+id_scatter: NarrowFlat
+id_wave: ThAr
+id_comb: null
+id_spec: OBJECT

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 Instrument, getter
+
+logger = logging.getLogger(__name__)
+
+
+class MCDONALD(Instrument):
+    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, 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, **kwargs)
+        info = self.info  # Use cached info dict
+        get = getter(header, info, arm)
+
+        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, arm, **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, arm, **kwargs):
+        fname = "mask_mcdonald.fits.gz"
+        cwd = os.path.dirname(__file__)
+        fname = os.path.join(cwd, "..", "masks", fname)
+        return fname

pyreduce/instruments/mcdonald.yaml

@@ -0,0 +1,56 @@
+# MCDONALD instrument configuration
+
+__instrument__: MCDONALD
+instrument: OBSERVAT
+id_instrument: MCDONALD
+telescope: OBSERVAT
+
+date: DATE-OBS
+
+arms: [CS21, CS23, TS21, TS23]
+id_arm: [cs21-e2, cs23-e2, ts21-e2, ts23-e2]
+extension: 0
+orientation: 0
+transpose: false
+
+trimsec: TRIMSEC
+naxis_x: NAXIS1
+naxis_y: NAXIS2
+amplifier: AMPLIFIE
+gain: "GAIN{amplifier}"
+readnoise: "RDNOISE{amplifier}"
+dark: 1
+sky: 0
+dark_time: DARKTIME
+exposure_time: EXPTIME
+
+observation_type: IMAGETYP
+category: IMAGETYP
+ra: RA
+dec: DEC
+universal_time: UT
+longitude: "104:1:18"
+latitude: "30:40:18"
+altitude: 2075
+target: OBJECT
+instrument_mode: INSTRUME
+
+# File classification keywords and patterns
+kw_arm: INSTRUME
+kw_bias: OBJECT
+kw_flat: IMAGETYP
+kw_curvature: OBJECT
+kw_scatter: IMAGETYP
+kw_orders: IMAGETYP
+kw_wave: OBJECT
+kw_comb: null
+kw_spec: IMAGETYP
+
+id_bias: bias
+id_flat: flat
+id_orders: flat
+id_curvature: ThAr
+id_scatter: flat
+id_wave: ThAr
+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 Instrument
+
+logger = logging.getLogger(__name__)
+
+
+class METIS_IFU(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_extension(self, header, arm):
+        extension = 1
+
+        return extension
+
+    def get_wavecal_filename(self, header, arm, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        # info = self.load_info()
+        cwd = os.path.dirname(__file__)
+        fname = f"metis_ifu_{arm.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