pyreduce-astro 0.6.0__cp312-cp312-macosx_11_0_arm64.whl

pyreduce/instruments/instrument_schema.json

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+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "pyreduce.instrument_schema",
+    "title": "PyReduce Instrument Settings",
+    "description": "Keywords that need to be set for the PyReduce to sort files correctly and interpret the header",
+    "type": "object",
+    "properties": {
+        "__instrument__": {
+            "description": "Meta data, for which instrument this file is designed",
+            "type": "string"
+        },
+        "instrument": {
+            "description": "keyword for the instrument in the header",
+            "type": "string"
+        },
+        "id_instrument": {
+            "description": "Value of the instrument keyword, can be regex",
+            "type": "string"
+        },
+        "telescope": {
+            "description": "keyword for the telescope in the header",
+            "type": "string"
+        },
+        "target": {
+            "description": "keyword of the target in the header",
+            "type": "string"
+        },
+        "date": {
+            "description": "keyword of the datetime in the header",
+            "type": "string"
+        },
+        "date_format": {
+            "description": "format of the datetime in the header, e.g. fits (default), or mjd",
+            "type": "string"
+        },
+        "extension": {
+            "description": "the extension of the fits file to use to access the data",
+            "oneOf": [
+                {"type": "integer"},
+                {"type": "string"},
+                {
+                    "type": "array",
+                    "items": {
+                        "oneOf": [
+                            {"type": "integer"},
+                            {"type": "string"}
+                        ]
+                    }
+                }
+            ]
+        },
+        "orientation": {
+            "description": "the orientation of the input files, equal to the number of 90 degree flips necessary",
+            "oneOf": [
+                {"type": "integer"},
+                {
+                    "type": "array",
+                    "items": {"type": "integer"}
+                }
+            ]
+        },
+        "transpose": {
+            "description": "If true the image is transposed before rotation, thus flipping the image",
+            "type": "boolean"
+        },
+        "prescan_x": {
+            "description": "The horizontal prescan direction, before orientation, or the keyword that contains that value",
+            "oneOf": [
+                {"type": "integer"},
+                {"type": "string"}
+            ]
+        },
+        "overscan_x": {
+            "description": "The overscan in horizontal direction, before orientation, or the keyword that contains that value",
+            "oneOf": [
+                {"type": "integer"},
+                {"type": "string"}
+            ]
+        },
+        "prescan_y": {
+            "description": "The vertical prescan direction, before orientation, or the keyword that contains that value",
+            "oneOf": [
+                {"type": "integer"},
+                {"type": "string"}
+            ]
+        },
+        "overscan_y": {
+            "description": "The overscan in vertical direction, before orientation, or the keyword that contains that value",
+            "oneOf": [
+                {"type": "integer"},
+                {"type": "string"}
+            ]
+        },
+        "naxis_x": {
+            "description": "The size of the horizontal axis",
+            "oneOf": [
+                {"type": "integer"},
+                {"type": "string"}
+            ]
+        },
+        "naxis_y": {
+            "description": "The size of the vertical axis",
+            "oneOf": [
+                {"type": "integer"},
+                {"type": "string"}
+            ]
+        },
+        "gain": {
+            "description": "The gain of the instrument",
+            "oneOf": [
+                {"type": "number"},
+                {"type": "string"}
+            ]
+        },
+        "readnoise": {
+            "description": "The readnoise of the instrument",
+            "oneOf": [
+                {"type": "number"},
+                {"type": "string"}
+            ]
+        },
+        "dark": {
+            "description": "The dark current of the instrument",
+            "oneOf": [
+                {"type": "number"},
+                {"type": "string"}
+            ]
+        },
+        "sky": {
+            "description": "The sky background of the instrument",
+            "oneOf": [
+                {"type": "number"},
+                {"type": "string"}
+            ]
+        },
+        "exposure_time": {
+            "description": "The keyword for the exposure time in seconds of the observation",
+            "type": "string"
+        },
+        "ra": {
+            "description": "The keyword for the right acension of the observation",
+            "type": "string"
+        },
+        "dec": {
+            "description": "The keyword for the declination of the observation",
+            "type": "string"
+        },
+        "longitude": {
+            "description": "The longitude of the telescope on earth",
+            "oneOf": [
+                {"type": "number"},
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "latitude": {
+            "description": "The latitude of the telescope on earth",
+            "oneOf": [
+                {"type": "number"},
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "altitude": {
+            "description": "The altitude of the telescope on earth",
+            "oneOf": [
+                {"type": "number"},
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_bias": {
+            "description": "The keyword that identifies the bias files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_flat": {
+            "description": "The keyword that identifies the flat files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_curvature": {
+            "description": "The keyword that identifies the curvature files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_scatter": {
+            "description": "The keyword that identifies the background scatter files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_orders": {
+            "description": "The keyword that identifies the order definition files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_wave": {
+            "description": "The keyword that identifies the wavecal files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_comb": {
+            "description": "The keyword that identifies the laser frequency comb / fabry perot interferometer files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "kw_spec": {
+            "description": "The keyword that identifies the science files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_bias": {
+            "description": "The value that identifies the bias files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_flat": {
+            "description": "The value that identifies the flat files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_curvature": {
+            "description": "The value that identifies the curvature files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_scatter": {
+            "description": "The value that identifies the background scatter files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_orders": {
+            "description": "The value that identifies the order definition files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_wave": {
+            "description": "The value that identifies the wavecal files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_comb": {
+            "description": "The value that identifies the laser frequency comb / fabry perot interferometer files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        },
+        "id_spec": {
+            "description": "The value that identifies the science files",
+            "oneOf": [
+                {"type": "string"},
+                {"type": "null"}
+            ]
+        }
+    },
+    "required": [
+        "instrument",
+        "id_instrument",
+        "telescope",
+        "target",
+        "date",
+        "extension",
+        "orientation",
+        "naxis_x",
+        "naxis_y",
+        "gain",
+        "readnoise",
+        "exposure_time",
+        "ra",
+        "dec",
+        "kw_bias",
+        "kw_flat",
+        "kw_curvature",
+        "kw_scatter",
+        "kw_orders",
+        "kw_wave",
+        "kw_comb",
+        "kw_spec",
+        "id_bias",
+        "id_flat",
+        "id_orders",
+        "id_curvature",
+        "id_scatter",
+        "id_wave",
+        "id_comb",
+        "id_spec"
+    ],
+    "additionalProperties": true
+}

pyreduce/instruments/jwst_miri.json

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+{
+    "__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",
+    "modes": [
+        "LRS_SLITLESS"
+    ],
+    "modes_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",
+
+    "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_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, 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)
+        self.load_info()
+        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 = "{instrument}_{mode}_2D.npz".format(instrument="harps", mode=mode)
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname

pyreduce/instruments/jwst_niriss.json

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+{
+    "__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__": "JWST_NIRISS",
+    "instrument": "INSTRUME",
+    "id_instrument": "NIRISS",
+    "telescope": "JWST",
+    "date": "DATE-OBS",
+    "date_format": "iso",
+    "instrument_mode": "PUPIL",
+    "modes": ["GR700XD"],
+    "modes_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",
+
+    "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/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, 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)
+        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, mode):
+        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, mode, allow_calibration_only=False):
+        files = super().sort_files(
+            input_dir,
+            target,
+            night,
+            mode,
+            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, mode)
+            files[i][1]["science"] = files_split
+        return files
+
+    def get_wavecal_filename(self, header, mode, **kwargs):
+        """Get the filename of the wavelength calibration config file"""
+        cwd = os.path.dirname(__file__)
+        fname = "{instrument}_{mode}_2D.npz".format(instrument="harps", mode=mode)
+        fname = os.path.join(cwd, "..", "wavecal", fname)
+        return fname

pyreduce/instruments/lick_apf.json

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+{
+    "__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__": "LICK_APF",
+    "instrument": "version",
+    "id_instrument": "apf",
+    "telescope": "Lick",
+    "date": "DATE",
+    "date_format": "fits",
+    "modes": [""],
+    "modes_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",
+
+    "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/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, 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)
+        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, mode, **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